- bump ome-metadata dependency

- add extract-ome cli subcommand

.github/workflows/pytest.yml

@@ -1,22 +0,0 @@
-name: PyTest
-
-on: [workflow_call, push, pull_request]
-
-jobs:
-  pytest:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.11", "3.12"]
-
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
-        run: |
-          pip install .[test]
-      - name: Test with pytest
-        run: pytest

.gitignore

@@ -1,12 +1,75 @@
-._*
-*.pyc
-/build/
-*.egg-info
-/venv/
-.idea
-/.pytest_cache/
-/ndbioimage/_version.py
-/ndbioimage/jars
+/target
+/Cargo.lock
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version
+
 /tests/files/*
-/poetry.lock
-/dist/

Cargo.toml

@@ -0,0 +1,70 @@
+[package]
+name = "ndbioimage"
+version = "2026.1.2"
+edition = "2024"
+rust-version = "1.85.1"
+authors = ["Wim Pomp <w.pomp@nki.nl>"]
+license = "MIT"
+description = "Read bio image formats using the bio-formats java package."
+homepage = "https://github.com/wimpomp/ndbioimage/tree/rs"
+repository = "https://github.com/wimpomp/ndbioimage/tree/rs"
+documentation = "https://docs.rs/ndbioimage"
+readme = "README.md"
+keywords = ["bioformats", "imread", "ndarray", "metadata"]
+categories = ["multimedia::images", "science"]
+exclude = ["/tests"]
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+[lib]
+name = "ndbioimage"
+crate-type = ["cdylib", "rlib"]
+
+[dependencies]
+clap = { version = "4", features = ["derive"] }
+ffmpeg-sidecar = { version = "2", optional = true }
+itertools = "0.14"
+indexmap = { version = "2", features = ["serde"] }
+indicatif = { version = "0.18", features = ["rayon"], optional = true }
+j4rs = "0.24"
+ndarray = { version = "0.17", features = ["serde"] }
+num = "0.4"
+numpy = { version = "0.27", optional = true }
+ordered-float = "5"
+rayon = { version = "1", optional = true }
+serde = { version = "1", features = ["rc"] }
+serde_json = { version = "1", optional = true }
+serde_with = "3"
+tiffwrite = { version = "2025.12.0", optional = true}
+thread_local = "1"
+ome-metadata = "0.4"
+lazy_static = "1"
+thiserror = "2"
+
+[dependencies.pyo3]
+version = "0.27"
+features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
+optional = true
+
+[dev-dependencies]
+downloader = "0.2"
+rayon = "1"
+regex = "1"
+reqwest = { version = "0.13", features = ["blocking"] }
+
+[build-dependencies]
+j4rs = "0.24"
+ffmpeg-sidecar = "2"
+retry = "2"
+
+[features]
+# Enables formats for which code in bioformats with a GPL license is needed
+gpl-formats = []
+# Enables python ffi using pyO3
+python = ["dep:pyo3", "dep:numpy", "dep:serde_json"]
+# Enables writing as tiff
+tiff = ["dep:tiffwrite", "dep:indicatif", "dep:rayon"]
+# Enables writing as mp4 using ffmpeg
+movie = ["dep:ffmpeg-sidecar"]
+
+[package.metadata.docs.rs]
+features = ["gpl-formats", "tiff", "movie"]

LICENSE

@@ -1,674 +1,19 @@
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-  12. No Surrender of Others' Freedom.
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-
-  13. Use with the GNU Affero General Public License.
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-                     END OF TERMS AND CONDITIONS
-
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-possible use to the public, the best way to achieve this is to make it
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-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
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-    Copyright (C) <year>  <name of author>
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-    it under the terms of the GNU General Public License as published by
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-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <https://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
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-    <program>  Copyright (C) <year>  <name of author>
-    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
-  You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<https://www.gnu.org/licenses/>.
-
-  The GNU General Public License does not permit incorporating your program
-into proprietary programs.  If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.  But first, please read
-<https://www.gnu.org/licenses/why-not-lgpl.html>.
+Copyright (c) 2025 Wim Pomp
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,6 +1,9 @@
+# ndbioimage
 [![Pytest](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
 
-# ndbioimage
+## Work in progress
+Rust rewrite of python version. Read bio image formats using the bio-formats java package.
+[https://www.openmicroscopy.org/bio-formats/](https://www.openmicroscopy.org/bio-formats/)
 
 Exposes (bio) images as a numpy ndarray-like object, but without loading the whole
 image into memory, reading from the file only when needed. Some metadata is read
@@ -65,30 +68,37 @@ with Imread('image_file.tif', axes='cztyx') as im:
     array = np.asarray(im[0, 0])
 ```
 
+### Rust
+```
+use ndarray::Array2;
+use ndbioimage::Reader;
+
+let path = "/path/to/file";
+let reader = Reader::new(&path, 0)?;
+println!("size: {}, {}", reader.size_y, reader.size_y);
+let frame = reader.get_frame(0, 0, 0).unwrap();
+if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
+    println!("{:?}", arr);
+} else {
+    println!("could not convert Frame to Array<i8>");
+}
+let xml = reader.get_ome_xml().unwrap();
+println!("{}", xml);
+```
+
+``` 
+use ndarray::Array2;
+use ndbioimage::Reader;
+
+let path = "/path/to/file";
+let reader = Reader::new(&path, 0)?;
+let view = reader.view();
+let view = view.max_proj(3)?;
+let array = view.as_array::<u16>()?
+```
+
 ### Command line
 ```ndbioimage --help```: show help  
 ```ndbioimage image```: show metadata about image  
 ```ndbioimage image -w {name}.tif -r```: copy image into image.tif (replacing {name} with image), while registering channels  
 ```ndbioimage image -w image.mp4 -C cyan lime red``` copy image into image.mp4 (z will be max projected), make channel colors cyan lime and red
-
-## Adding more formats
-Readers for image formats subclass AbstractReader. When an image reader is imported, Imread will
-automatically recognize it and use it to open the appropriate file format. Image readers
-are required to implement the following methods:
-
-- staticmethod _can_open(path): return True if path can be opened by this reader
-- \_\_frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file
-
-Optional methods:
-- get_ome: reads metadata from file and adds them to an OME object imported
-from the ome-types library 
-- open(self): maybe open some file handle
-- close(self): close any file handles
-
-Optional fields:
-- priority (int): Imread will try readers with a lower number first, default: 99
-- do_not_pickle (strings): any attributes that should not be included when the object is pickled,
-for example: any file handles
-
-# TODO
-- more image formats

build.rs

@@ -0,0 +1,131 @@
+#[cfg(not(feature = "python"))]
+use j4rs::{JvmBuilder, MavenArtifact, MavenArtifactRepo, MavenSettings, errors::J4RsError};
+#[cfg(not(feature = "python"))]
+use retry::{delay, delay::Exponential, retry};
+use std::error::Error;
+#[cfg(not(feature = "python"))]
+use std::fmt::Display;
+#[cfg(not(feature = "python"))]
+use std::fmt::Formatter;
+#[cfg(not(feature = "python"))]
+use std::path::PathBuf;
+#[cfg(not(feature = "python"))]
+use std::{env, fs};
+
+#[cfg(feature = "python")]
+use j4rs::Jvm;
+
+#[cfg(feature = "movie")]
+use ffmpeg_sidecar::download::auto_download;
+
+#[cfg(not(feature = "python"))]
+#[derive(Clone, Debug)]
+enum BuildError {
+    BioFormatsNotDownloaded,
+}
+
+#[cfg(not(feature = "python"))]
+impl Display for BuildError {
+    fn fmt(&self, fmt: &mut Formatter) -> Result<(), std::fmt::Error> {
+        write!(fmt, "Bioformats package not downloaded")
+    }
+}
+
+#[cfg(not(feature = "python"))]
+impl Error for BuildError {}
+
+fn main() -> Result<(), Box<dyn Error>> {
+    println!("cargo::rerun-if-changed=build.rs");
+
+    if std::env::var("DOCS_RS").is_err() {
+        #[cfg(feature = "movie")]
+        auto_download()?;
+
+        #[cfg(not(feature = "python"))]
+        {
+            retry(
+                Exponential::from_millis(1000).map(delay::jitter).take(4),
+                deploy_java_artifacts,
+            )?;
+            let path = default_jassets_path()?;
+            if !path.join("bioformats_package-8.3.0.jar").exists() {
+                Err(BuildError::BioFormatsNotDownloaded)?;
+            }
+        }
+
+        #[cfg(feature = "python")]
+        {
+            let py_src_path = std::env::current_dir()?.join("py").join("ndbioimage");
+            let py_jassets_path = py_src_path.join("jassets");
+            let py_deps_path = py_src_path.join("deps");
+            if py_jassets_path.exists() {
+                std::fs::remove_dir_all(&py_jassets_path)?;
+            }
+            if py_deps_path.exists() {
+                std::fs::remove_dir_all(&py_deps_path)?;
+            }
+
+            Jvm::copy_j4rs_libs_under(py_src_path.to_str().unwrap())?;
+
+            // rename else maturin will ignore them
+            for file in std::fs::read_dir(&py_deps_path)? {
+                let f = file?.path().to_str().unwrap().to_string();
+                if !f.ends_with("_") {
+                    std::fs::rename(&f, std::format!("{f}_"))?;
+                }
+            }
+
+            // remove so we don't include too much accidentally
+            for file in std::fs::read_dir(&py_jassets_path)? {
+                let f = file?.path();
+                if !f.file_name().unwrap().to_str().unwrap().starts_with("j4rs") {
+                    std::fs::remove_file(&f)?;
+                }
+            }
+        }
+    }
+
+    Ok(())
+}
+
+#[cfg(not(feature = "python"))]
+fn default_jassets_path() -> Result<PathBuf, J4RsError> {
+    let is_build_script = env::var("OUT_DIR").is_ok();
+
+    let mut start_path = if is_build_script {
+        PathBuf::from(env::var("OUT_DIR")?)
+    } else {
+        env::current_exe()?
+    };
+    start_path = fs::canonicalize(start_path)?;
+
+    while start_path.pop() {
+        for entry in std::fs::read_dir(&start_path)? {
+            let path = entry?.path();
+            if path.file_name().map(|x| x == "jassets").unwrap_or(false) {
+                return Ok(path);
+            }
+        }
+    }
+
+    Err(J4RsError::GeneralError(
+        "Can not find jassets directory".to_owned(),
+    ))
+}
+
+#[cfg(not(feature = "python"))]
+fn deploy_java_artifacts() -> Result<(), J4RsError> {
+    let jvm = JvmBuilder::new()
+        .skip_setting_native_lib()
+        .with_maven_settings(MavenSettings::new(vec![MavenArtifactRepo::from(
+            "openmicroscopy::https://artifacts.openmicroscopy.org/artifactory/ome.releases",
+        )]))
+        .build()?;
+
+    jvm.deploy_artifact(&MavenArtifact::from("ome:bioformats_package:8.3.0"))?;
+
+    #[cfg(feature = "gpl-formats")]
+    jvm.deploy_artifact(&MavenArtifact::from("ome:formats-gpl:8.3.0"))?;
+
+    Ok(())
+}

ndbioimage/jvm.py

@@ -1,77 +0,0 @@
-from pathlib import Path
-from urllib import request
-
-
-class JVMException(Exception):
-    pass
-
-
-try:
-    class JVM:
-        """ There can be only one java virtual machine per python process,
-            so this is a singleton class to manage the jvm.
-        """
-        _instance = None
-        vm_started = False
-        vm_killed = False
-        success = True
-
-        def __new__(cls, *args):
-            if cls._instance is None:
-                cls._instance = object.__new__(cls)
-            return cls._instance
-
-        def __init__(self, jars=None):
-            if not self.vm_started and not self.vm_killed:
-                try:
-                    jar_path = Path(__file__).parent / 'jars'
-                    if jars is None:
-                        jars = {}
-                    for jar, src in jars.items():
-                        if not (jar_path / jar).exists():
-                            JVM.download(src, jar_path / jar)
-                    classpath = [str(jar_path / jar) for jar in jars.keys()]
-
-                    import jpype
-                    jpype.startJVM(classpath=classpath)
-                except Exception:  # noqa
-                    self.vm_started = False
-                else:
-                    self.vm_started = True
-                try:
-                    import jpype.imports
-                    from loci.common import DebugTools  # noqa
-                    from loci.formats import ChannelSeparator  # noqa
-                    from loci.formats import FormatTools  # noqa
-                    from loci.formats import ImageReader  # noqa
-                    from loci.formats import MetadataTools  # noqa
-
-                    DebugTools.setRootLevel("ERROR")
-
-                    self.image_reader = ImageReader
-                    self.channel_separator = ChannelSeparator
-                    self.format_tools = FormatTools
-                    self.metadata_tools = MetadataTools
-                except Exception:  # noqa
-                    pass
-
-            if self.vm_killed:
-                raise Exception('The JVM was killed before, and cannot be restarted in this Python process.')
-
-        @staticmethod
-        def download(src, dest):
-            print(f'Downloading {dest.name} to {dest}.')
-            dest.parent.mkdir(exist_ok=True)
-            dest.write_bytes(request.urlopen(src).read())
-
-        @classmethod
-        def kill_vm(cls):
-            self = cls._instance
-            if self is not None and self.vm_started and not self.vm_killed:
-                import jpype
-                jpype.shutdownJVM()  # noqa
-            self.vm_started = False
-            self.vm_killed = True
-
-except ImportError:
-    JVM = None

ndbioimage/readers/__init__.py

@@ -1 +0,0 @@
-__all__ = 'bfread', 'cziread', 'fijiread', 'ndread', 'seqread', 'tifread', 'metaseriesread'

ndbioimage/readers/bfread.py

@@ -1,208 +0,0 @@
-import multiprocessing
-from abc import ABC
-from multiprocessing import queues
-from pathlib import Path
-from traceback import format_exc
-
-import numpy as np
-
-from .. import JVM, AbstractReader, JVMException
-
-jars = {'bioformats_package.jar': 'https://downloads.openmicroscopy.org/bio-formats/latest/artifacts/'
-                                  'bioformats_package.jar'}
-
-
-class JVMReader:
-    def __init__(self, path: Path, series: int) -> None:
-        mp = multiprocessing.get_context('spawn')
-        self.path = path
-        self.series = series
-        self.queue_in = mp.Queue()
-        self.queue_out = mp.Queue()
-        self.done = mp.Event()
-        self.process = mp.Process(target=self.run)
-        self.process.start()
-        status, message = self.queue_out.get()
-        if status == 'status' and message == 'started':
-            self.is_alive = True
-        else:
-            raise JVMException(message)
-
-    def close(self) -> None:
-        if self.is_alive:
-            self.done.set()
-            while not self.queue_in.empty():
-                self.queue_in.get()
-            self.queue_in.close()
-            self.queue_in.join_thread()
-            while not self.queue_out.empty():
-                print(self.queue_out.get())
-            self.queue_out.close()
-            self.process.join()
-            self.process.close()
-            self.is_alive = False
-
-    def frame(self, c: int, z: int, t: int) -> np.ndarray:
-        self.queue_in.put((c, z, t))
-        status, message = self.queue_out.get()
-        if status == 'frame':
-            return message
-        else:
-            raise JVMException(message)
-
-    def run(self) -> None:
-        """ Read planes from the image reader file.
-            adapted from python-bioformats/bioformats/formatreader.py
-        """
-        jvm = None
-        try:
-            jvm = JVM(jars)
-            reader = jvm.image_reader()
-            ome_meta = jvm.metadata_tools.createOMEXMLMetadata()
-            reader.setMetadataStore(ome_meta)
-            reader.setId(str(self.path))
-            reader.setSeries(self.series)
-
-            open_bytes_func = reader.openBytes
-            width, height = int(reader.getSizeX()), int(reader.getSizeY())
-
-            pixel_type = reader.getPixelType()
-            little_endian = reader.isLittleEndian()
-
-            if pixel_type == jvm.format_tools.INT8:
-                dtype = np.int8
-            elif pixel_type == jvm.format_tools.UINT8:
-                dtype = np.uint8
-            elif pixel_type == jvm.format_tools.UINT16:
-                dtype = '<u2' if little_endian else '>u2'
-            elif pixel_type == jvm.format_tools.INT16:
-                dtype = '<i2' if little_endian else '>i2'
-            elif pixel_type == jvm.format_tools.UINT32:
-                dtype = '<u4' if little_endian else '>u4'
-            elif pixel_type == jvm.format_tools.INT32:
-                dtype = '<i4' if little_endian else '>i4'
-            elif pixel_type == jvm.format_tools.FLOAT:
-                dtype = '<f4' if little_endian else '>f4'
-            elif pixel_type == jvm.format_tools.DOUBLE:
-                dtype = '<f8' if little_endian else '>f8'
-            else:
-                dtype = None
-            self.queue_out.put(('status', 'started'))
-
-            while not self.done.is_set():
-                try:
-                    c, z, t = self.queue_in.get(True, 0.02)
-                    if reader.isRGB() and reader.isInterleaved():
-                        index = reader.getIndex(z, 0, t)
-                        image = np.frombuffer(open_bytes_func(index), dtype)
-                        image.shape = (height, width, reader.getSizeC())
-                        if image.shape[2] > 3:
-                            image = image[:, :, :3]
-                    elif c is not None and reader.getRGBChannelCount() == 1:
-                        index = reader.getIndex(z, c, t)
-                        image = np.frombuffer(open_bytes_func(index), dtype)
-                        image.shape = (height, width)
-                    elif reader.getRGBChannelCount() > 1:
-                        n_planes = reader.getRGBChannelCount()
-                        rdr = jvm.channel_separator(reader)
-                        planes = [np.frombuffer(rdr.openBytes(rdr.getIndex(z, i, t)), dtype) for i in range(n_planes)]
-                        if len(planes) > 3:
-                            planes = planes[:3]
-                        elif len(planes) < 3:
-                            # > 1 and < 3 means must be 2
-                            # see issue #775
-                            planes.append(np.zeros(planes[0].shape, planes[0].dtype))
-                        image = np.dstack(planes)
-                        image.shape = (height, width, 3)
-                        del rdr
-                    elif reader.getSizeC() > 1:
-                        images = [np.frombuffer(open_bytes_func(reader.getIndex(z, i, t)), dtype)
-                                  for i in range(reader.getSizeC())]
-                        image = np.dstack(images)
-                        image.shape = (height, width, reader.getSizeC())
-                        # if not channel_names is None:
-                        #     metadata = MetadataRetrieve(self.metadata)
-                        #     for i in range(self.reader.getSizeC()):
-                        #         index = self.reader.getIndex(z, 0, t)
-                        #         channel_name = metadata.getChannelName(index, i)
-                        #         if channel_name is None:
-                        #             channel_name = metadata.getChannelID(index, i)
-                        #         channel_names.append(channel_name)
-                    elif reader.isIndexed():
-                        #
-                        # The image data is indexes into a color lookup-table
-                        # But sometimes the table is the identity table and just generates
-                        # a monochrome RGB image
-                        #
-                        index = reader.getIndex(z, 0, t)
-                        image = np.frombuffer(open_bytes_func(index), dtype)
-                        if pixel_type in (jvm.format_tools.INT16, jvm.format_tools.UINT16):
-                            lut = reader.get16BitLookupTable()
-                            if lut is not None:
-                                lut = np.array(lut)
-                                # lut = np.array(
-                                #     [env.get_short_array_elements(d)
-                                #      for d in env.get_object_array_elements(lut)]) \
-                                #     .transpose()
-                        else:
-                            lut = reader.get8BitLookupTable()
-                            if lut is not None:
-                                lut = np.array(lut)
-                                # lut = np.array(
-                                #     [env.get_byte_array_elements(d)
-                                #      for d in env.get_object_array_elements(lut)]) \
-                                #     .transpose()
-                        image.shape = (height, width)
-                        if (lut is not None) and not np.all(lut == np.arange(lut.shape[0])[:, np.newaxis]):
-                            image = lut[image, :]
-                    else:
-                        index = reader.getIndex(z, 0, t)
-                        image = np.frombuffer(open_bytes_func(index), dtype)
-                        image.shape = (height, width)
-
-                    if image.ndim == 3:
-                        self.queue_out.put(('frame', image[..., c]))
-                    else:
-                        self.queue_out.put(('frame', image))
-                except queues.Empty:  # noqa
-                    continue
-        except (Exception,):
-            self.queue_out.put(('error', format_exc()))
-        finally:
-            if jvm is not None:
-                jvm.kill_vm()
-
-
-def can_open(path: Path) -> bool:
-    try:
-        jvm = JVM(jars)
-        reader = jvm.image_reader()
-        reader.getFormat(str(path))
-        return True
-    except (Exception,):
-        return False
-    finally:
-        jvm.kill_vm()  # noqa
-
-
-class Reader(AbstractReader, ABC):
-    """ This class is used as a last resort, when we don't have another way to open the file. We don't like it
-        because it requires the java vm.
-    """
-    priority = 99  # panic and open with BioFormats
-    do_not_pickle = 'reader', 'key', 'jvm'
-
-    @staticmethod
-    def _can_open(path: Path) -> bool:
-        """ Use java BioFormats to make an ome metadata structure. """
-        with multiprocessing.get_context('spawn').Pool(1) as pool:
-            return pool.map(can_open, (path,))[0]
-
-    def open(self) -> None:
-        self.reader = JVMReader(self.path, self.series)
-
-    def __frame__(self, c: int, z: int, t: int) -> np.ndarray:
-        return self.reader.frame(c, z, t)
-
-    def close(self) -> None:
-        self.reader.close()

ndbioimage/readers/cziread.py

@@ -1,606 +0,0 @@
-import re
-import warnings
-from abc import ABC
-from functools import cached_property
-from io import BytesIO
-from itertools import product
-from pathlib import Path
-from typing import Any, Callable, Optional, TypeVar
-
-import czifile
-import imagecodecs
-import numpy as np
-from lxml import etree
-from ome_types import OME, model
-from tifffile import repeat_nd
-
-from .. import AbstractReader
-
-try:
-    # TODO: use zoom from imagecodecs implementation when available
-    from scipy.ndimage.interpolation import zoom
-except ImportError:
-    try:
-        from ndimage.interpolation import zoom
-    except ImportError:
-        zoom = None
-
-
-Element = TypeVar('Element')
-
-
-def zstd_decode(data: bytes) -> bytes:  # noqa
-    """ decode zstd bytes, copied from BioFormats ZeissCZIReader """
-    def read_var_int(stream: BytesIO) -> int:  # noqa
-        a = stream.read(1)[0]
-        if a & 128:
-            b = stream.read(1)[0]
-            if b & 128:
-                c = stream.read(1)[0]
-                return (c << 14) | ((b & 127) << 7) | (a & 127)
-            return (b << 7) | (a & 127)
-        return a & 255
-
-    try:
-        with BytesIO(data) as stream:
-            size_of_header = read_var_int(stream)
-            high_low_unpacking = False
-            while stream.tell() < size_of_header:
-                chunk_id = read_var_int(stream)
-                # only one chunk ID defined so far
-                if chunk_id == 1:
-                    high_low_unpacking = (stream.read(1)[0] & 1) == 1
-                else:
-                    raise ValueError(f'Invalid chunk id: {chunk_id}')
-            pointer = stream.tell()
-    except Exception:  # noqa
-        high_low_unpacking = False
-        pointer = 0
-
-    decoded = imagecodecs.zstd_decode(data[pointer:])
-    if high_low_unpacking:
-        second_half = len(decoded) // 2
-        return bytes([decoded[second_half + i // 2] if i % 2 else decoded[i // 2] for i in range(len(decoded))])
-    else:
-        return decoded
-
-
-def data(self, raw: bool = False, resize: bool = True, order: int = 0) -> np.ndarray:
-    """Read image data from file and return as numpy array."""
-    DECOMPRESS = czifile.czifile.DECOMPRESS  # noqa
-    DECOMPRESS[5] = imagecodecs.zstd_decode
-    DECOMPRESS[6] = zstd_decode
-
-    de = self.directory_entry
-    fh = self._fh
-    if raw:
-        with fh.lock:
-            fh.seek(self.data_offset)
-            data = fh.read(self.data_size)  # noqa
-        return data
-    if de.compression:
-        # if de.compression not in DECOMPRESS:
-        #     raise ValueError('compression unknown or not supported')
-        with fh.lock:
-            fh.seek(self.data_offset)
-            data = fh.read(self.data_size)  # noqa
-        data = DECOMPRESS[de.compression](data)  # noqa
-        if de.compression == 2:
-            # LZW
-            data = np.fromstring(data, de.dtype)  # noqa
-        elif de.compression in (5, 6):
-            # ZSTD
-            data = np.frombuffer(data, de.dtype)  # noqa
-    else:
-        dtype = np.dtype(de.dtype)
-        with fh.lock:
-            fh.seek(self.data_offset)
-            data = fh.read_array(dtype, self.data_size // dtype.itemsize)  # noqa
-
-    data = data.reshape(de.stored_shape)  # noqa
-    if de.compression != 4 and de.stored_shape[-1] in (3, 4):
-        if de.stored_shape[-1] == 3:
-            # BGR -> RGB
-            data = data[..., ::-1]  # noqa
-        else:
-            # BGRA -> RGBA
-            tmp = data[..., 0].copy()
-            data[..., 0] = data[..., 2]
-            data[..., 2] = tmp
-    if de.stored_shape == de.shape or not resize:
-        return data
-
-    # sub / supersampling
-    factors = [j / i for i, j in zip(de.stored_shape, de.shape)]
-    factors = [(int(round(f)) if abs(f - round(f)) < 0.0001 else f)
-               for f in factors]
-
-    # use repeat if possible
-    if order == 0 and all(isinstance(f, int) for f in factors):
-        data = repeat_nd(data, factors).copy()  # noqa
-        data.shape = de.shape
-        return data
-
-    # remove leading dimensions with size 1 for speed
-    shape = list(de.stored_shape)
-    i = 0
-    for s in shape:
-        if s != 1:
-            break
-        i += 1
-    shape = shape[i:]
-    factors = factors[i:]
-    data.shape = shape
-
-    # resize RGB components separately for speed
-    if zoom is None:
-        raise ImportError("cannot import 'zoom' from scipy or ndimage")
-    if shape[-1] in (3, 4) and factors[-1] == 1.0:
-        factors = factors[:-1]
-        old = data
-        data = np.empty(de.shape, de.dtype[-2:])  # noqa
-        for i in range(shape[-1]):
-            data[..., i] = zoom(old[..., i], zoom=factors, order=order)
-    else:
-        data = zoom(data, zoom=factors, order=order)  # noqa
-
-    data.shape = de.shape
-    return data
-
-
-# monkeypatch zstd into czifile
-czifile.czifile.SubBlockSegment.data = data
-
-
-class Reader(AbstractReader, ABC):
-    priority = 0
-    do_not_pickle = 'reader', 'filedict'
-
-    @staticmethod
-    def _can_open(path: Path) -> bool:
-        return isinstance(path, Path) and path.suffix == '.czi'
-
-    def open(self) -> None:
-        self.reader = czifile.CziFile(self.path)
-        filedict = {}
-        for directory_entry in self.reader.filtered_subblock_directory:
-            idx = self.get_index(directory_entry, self.reader.start)
-            if 'S' not in self.reader.axes or self.series in range(*idx[self.reader.axes.index('S')]):
-                for c in range(*idx[self.reader.axes.index('C')]):
-                    for z in range(*idx[self.reader.axes.index('Z')]):
-                        for t in range(*idx[self.reader.axes.index('T')]):
-                            if (c, z, t) in filedict:
-                                filedict[c, z, t].append(directory_entry)
-                            else:
-                                filedict[c, z, t] = [directory_entry]
-        if len(filedict) == 0:
-            raise FileNotFoundError(f'Series {self.series} not found in {self.path}.')
-        self.filedict = filedict  # noqa
-
-    def close(self) -> None:
-        self.reader.close()
-
-    def get_ome(self) -> OME:
-        return OmeParse.get_ome(self.reader, self.filedict)
-
-    def __frame__(self, c: int = 0, z: int = 0, t: int = 0) -> np.ndarray:
-        f = np.zeros(self.base_shape['yx'], self.dtype)
-        if (c, z, t) in self.filedict:
-            directory_entries = self.filedict[c, z, t]
-            x_min = min([f.start[f.axes.index('X')] for f in directory_entries])
-            y_min = min([f.start[f.axes.index('Y')] for f in directory_entries])
-            xy_min = {'X': x_min, 'Y': y_min}
-            for directory_entry in directory_entries:
-                subblock = directory_entry.data_segment()
-                tile = subblock.data(resize=True, order=0)
-                axes_min = [xy_min.get(ax, 0) for ax in directory_entry.axes]
-                index = [slice(i - j - m, i - j + k)
-                         for i, j, k, m in zip(directory_entry.start, self.reader.start, tile.shape, axes_min)]
-                index = tuple(index[self.reader.axes.index(i)] for i in 'YX')
-                f[index] = tile.squeeze()
-        return f
-
-    @staticmethod
-    def get_index(directory_entry: czifile.DirectoryEntryDV, start: tuple[int]) -> list[tuple[int, int]]:
-        return [(i - j, i - j + k) for i, j, k in zip(directory_entry.start, start, directory_entry.shape)]
-
-
-class OmeParse:
-    size_x: int
-    size_y: int
-    size_c: int
-    size_z: int
-    size_t: int
-
-    nm = model.UnitsLength.NANOMETER
-    um = model.UnitsLength.MICROMETER
-
-    @classmethod
-    def get_ome(cls, reader: czifile.CziFile, filedict: dict[tuple[int, int, int], Any]) -> OME:
-        new = cls(reader, filedict)
-        new.parse()
-        return new.ome
-
-    def __init__(self, reader: czifile.CziFile, filedict: dict[tuple[int, int, int], Any]) -> None:
-        self.reader = reader
-        self.filedict = filedict
-        xml = reader.metadata()
-        self.attachments = {i.attachment_entry.name: i.attachment_entry.data_segment()
-                            for i in reader.attachments()}
-        self.tree = etree.fromstring(xml)
-        self.metadata = self.tree.find('Metadata')
-        version = self.metadata.find('Version')
-        if version is not None:
-            self.version = version.text
-        else:
-            self.version = self.metadata.find('Experiment').attrib['Version']
-
-        self.ome = OME()
-        self.information = self.metadata.find('Information')
-        self.display_setting = self.metadata.find('DisplaySetting')
-        self.experiment = self.metadata.find('Experiment')
-        self.acquisition_block = self.experiment.find('ExperimentBlocks').find('AcquisitionBlock')
-        self.instrument = self.information.find('Instrument')
-        self.image = self.information.find('Image')
-
-        if self.version == '1.0':
-            self.experiment = self.metadata.find('Experiment')
-            self.acquisition_block = self.experiment.find('ExperimentBlocks').find('AcquisitionBlock')
-            self.multi_track_setup = self.acquisition_block.find('MultiTrackSetup')
-        else:
-            self.experiment = None
-            self.acquisition_block = None
-            self.multi_track_setup = None
-
-    def parse(self) -> None:
-        self.get_experimenters()
-        self.get_instruments()
-        self.get_detectors()
-        self.get_objectives()
-        self.get_tubelenses()
-        self.get_light_sources()
-        self.get_filters()
-        self.get_pixels()
-        self.get_channels()
-        self.get_planes()
-        self.get_annotations()
-
-    @staticmethod
-    def text(item: Optional[Element], default: str = "") -> str:
-        return default if item is None else item.text
-
-    @staticmethod
-    def def_list(item: Any) -> list[Any]:
-        return [] if item is None else item
-
-    @staticmethod
-    def try_default(fun: Callable[[Any, ...], Any] | type, default: Any = None, *args: Any, **kwargs: Any) -> Any:
-        try:
-            return fun(*args, **kwargs)
-        except Exception:  # noqa
-            return default
-
-    def get_experimenters(self) -> None:
-        if self.version == '1.0':
-            self.ome.experimenters = [
-                model.Experimenter(id='Experimenter:0',
-                                   user_name=self.information.find('User').find('DisplayName').text)]
-        elif self.version in ('1.1', '1.2'):
-            self.ome.experimenters = [
-                model.Experimenter(id='Experimenter:0',
-                                   user_name=self.information.find('Document').find('UserName').text)]
-
-    def get_instruments(self) -> None:
-        if self.version == '1.0':
-            self.ome.instruments.append(model.Instrument(id=self.instrument.attrib['Id']))
-        elif self.version in ('1.1', '1.2'):
-            for _ in self.instrument.find('Microscopes'):
-                self.ome.instruments.append(model.Instrument(id='Instrument:0'))
-
-    def get_detectors(self) -> None:
-        if self.version == '1.0':
-            for detector in self.instrument.find('Detectors'):
-                try:
-                    detector_type = model.Detector_Type(self.text(detector.find('Type')).upper() or "")
-                except ValueError:
-                    detector_type = model.Detector_Type.OTHER
-
-                self.ome.instruments[0].detectors.append(
-                    model.Detector(
-                        id=detector.attrib['Id'], model=self.text(detector.find('Manufacturer').find('Model')),
-                        amplification_gain=float(self.text(detector.find('AmplificationGain'))),
-                        gain=float(self.text(detector.find('Gain'))), zoom=float(self.text(detector.find('Zoom'))),
-                        type=detector_type
-                    ))
-        elif self.version in ('1.1', '1.2'):
-            for detector in self.instrument.find('Detectors'):
-                try:
-                    detector_type = model.Detector_Type(self.text(detector.find('Type')).upper() or "")
-                except ValueError:
-                    detector_type = model.Detector_Type.OTHER
-
-                self.ome.instruments[0].detectors.append(
-                    model.Detector(
-                        id=detector.attrib['Id'].replace(' ', ''),
-                        model=self.text(detector.find('Manufacturer').find('Model')),
-                        type=detector_type
-                    ))
-
-    def get_objectives(self) -> None:
-        for objective in self.instrument.find('Objectives'):
-            self.ome.instruments[0].objectives.append(
-                model.Objective(
-                    id=objective.attrib['Id'],
-                    model=self.text(objective.find('Manufacturer').find('Model')),
-                    immersion=self.text(objective.find('Immersion')),  # type: ignore
-                    lens_na=float(self.text(objective.find('LensNA'))),
-                    nominal_magnification=float(self.text(objective.find('NominalMagnification')))))
-
-    def get_tubelenses(self) -> None:
-        if self.version == '1.0':
-            for idx, tube_lens in enumerate({self.text(track_setup.find('TubeLensPosition'))
-                                             for track_setup in self.multi_track_setup}):
-                try:
-                    nominal_magnification = float(re.findall(r'\d+[,.]\d*', tube_lens)[0].replace(',', '.'))
-                except Exception:  # noqa
-                    nominal_magnification = 1.0
-
-                self.ome.instruments[0].objectives.append(
-                    model.Objective(id=f'Objective:Tubelens:{idx}', model=tube_lens,
-                                    nominal_magnification=nominal_magnification))
-        elif self.version in ('1.1', '1.2'):
-            for tubelens in self.def_list(self.instrument.find('TubeLenses')):
-                try:
-                    nominal_magnification = float(re.findall(r'\d+(?:[,.]\d*)?',
-                                                             tubelens.attrib['Name'])[0].replace(',', '.'))
-                except Exception:  # noqa
-                    nominal_magnification = 1.0
-
-                self.ome.instruments[0].objectives.append(
-                    model.Objective(
-                        id=f"Objective:{tubelens.attrib['Id']}",
-                        model=tubelens.attrib['Name'],
-                        nominal_magnification=nominal_magnification))
-
-    def get_light_sources(self) -> None:
-        if self.version == '1.0':
-            for light_source in self.def_list(self.instrument.find('LightSources')):
-                try:
-                    if light_source.find('LightSourceType').find('Laser') is not None:
-                        self.ome.instruments[0].lasers.append(
-                            model.Laser(
-                                id=light_source.attrib['Id'],
-                                model=self.text(light_source.find('Manufacturer').find('Model')),
-                                power=float(self.text(light_source.find('Power'))),
-                                wavelength=float(
-                                    self.text(light_source.find('LightSourceType').find('Laser').find('Wavelength')))))
-                except AttributeError:
-                    pass
-        elif self.version in ('1.1', '1.2'):
-            for light_source in self.def_list(self.instrument.find('LightSources')):
-                try:
-                    if light_source.find('LightSourceType').find('Laser') is not None:
-                        self.ome.instruments[0].lasers.append(
-                            model.Laser(
-                                id=f"LightSource:{light_source.attrib['Id']}",
-                                power=float(self.text(light_source.find('Power'))),
-                                wavelength=float(light_source.attrib['Id'][-3:])))  # TODO: follow Id reference
-                except (AttributeError, ValueError):
-                    pass
-
-    def get_filters(self) -> None:
-        if self.version == '1.0':
-            for idx, filter_ in enumerate({self.text(beam_splitter.find('Filter'))
-                                           for track_setup in self.multi_track_setup
-                                           for beam_splitter in track_setup.find('BeamSplitters')}):
-                self.ome.instruments[0].filter_sets.append(
-                    model.FilterSet(id=f'FilterSet:{idx}', model=filter_)
-                )
-
-    def get_pixels(self) -> None:
-        x_min = min([f.start[f.axes.index('X')] for f in self.filedict[0, 0, 0]])
-        y_min = min([f.start[f.axes.index('Y')] for f in self.filedict[0, 0, 0]])
-        x_max = max([f.start[f.axes.index('X')] + f.shape[f.axes.index('X')] for f in self.filedict[0, 0, 0]])
-        y_max = max([f.start[f.axes.index('Y')] + f.shape[f.axes.index('Y')] for f in self.filedict[0, 0, 0]])
-        self.size_x = x_max - x_min
-        self.size_y = y_max - y_min
-        self.size_c, self.size_z, self.size_t = (self.reader.shape[self.reader.axes.index(directory_entry)]
-                                                 for directory_entry in 'CZT')
-        image = self.information.find('Image')
-        pixel_type = self.text(image.find('PixelType'), 'Gray16')
-        if pixel_type.startswith('Gray'):
-            pixel_type = 'uint' + pixel_type[4:]
-        objective_settings = image.find('ObjectiveSettings')
-
-        self.ome.images.append(
-            model.Image(
-                id='Image:0',
-                name=f"{self.text(self.information.find('Document').find('Name'))} #1",
-                pixels=model.Pixels(
-                    id='Pixels:0', size_x=self.size_x, size_y=self.size_y,
-                    size_c=self.size_c, size_z=self.size_z, size_t=self.size_t,
-                    dimension_order='XYCZT', type=pixel_type,  # type: ignore
-                    significant_bits=int(self.text(image.find('ComponentBitCount'))),
-                    big_endian=False, interleaved=False, metadata_only=True),  # type: ignore
-                experimenter_ref=model.ExperimenterRef(id='Experimenter:0'),
-                instrument_ref=model.InstrumentRef(id='Instrument:0'),
-                objective_settings=model.ObjectiveSettings(
-                    id=objective_settings.find('ObjectiveRef').attrib['Id'],
-                    medium=self.text(objective_settings.find('Medium')),  # type: ignore
-                    refractive_index=float(self.text(objective_settings.find('RefractiveIndex')))),
-                stage_label=model.StageLabel(
-                    name=f'Scene position #0',
-                    x=self.positions[0], x_unit=self.um,
-                    y=self.positions[1], y_unit=self.um,
-                    z=self.positions[2], z_unit=self.um)))
-
-        for distance in self.metadata.find('Scaling').find('Items'):
-            if distance.attrib['Id'] == 'X':
-                self.ome.images[0].pixels.physical_size_x = float(self.text(distance.find('Value'))) * 1e6
-            elif distance.attrib['Id'] == 'Y':
-                self.ome.images[0].pixels.physical_size_y = float(self.text(distance.find('Value'))) * 1e6
-            elif self.size_z > 1 and distance.attrib['Id'] == 'Z':
-                self.ome.images[0].pixels.physical_size_z = float(self.text(distance.find('Value'))) * 1e6
-
-    @cached_property
-    def positions(self) -> tuple[float, float, Optional[float]]:
-        if self.version == '1.0':
-            scenes = self.image.find('Dimensions').find('S').find('Scenes')
-            positions = scenes[0].find('Positions')[0]
-            return float(positions.attrib['X']), float(positions.attrib['Y']), float(positions.attrib['Z'])
-        elif self.version in ('1.1', '1.2'):
-            try:  # TODO
-                scenes = self.image.find('Dimensions').find('S').find('Scenes')
-                center_position = [float(pos) for pos in self.text(scenes[0].find('CenterPosition')).split(',')]
-            except AttributeError:
-                center_position = [0, 0]
-            return center_position[0], center_position[1], None
-
-    @cached_property
-    def channels_im(self) -> dict:
-        return {channel.attrib['Id']: channel for channel in self.image.find('Dimensions').find('Channels')}
-
-    @cached_property
-    def channels_ds(self) -> dict:
-        return {channel.attrib['Id']: channel for channel in self.display_setting.find('Channels')}
-
-    @cached_property
-    def channels_ts(self) -> dict:
-        return {detector.attrib['Id']: track_setup
-                for track_setup in
-                self.experiment.find('ExperimentBlocks').find('AcquisitionBlock').find('MultiTrackSetup')
-                for detector in track_setup.find('Detectors')}
-
-    def get_channels(self) -> None:
-        if self.version == '1.0':
-            for idx, (key, channel) in enumerate(self.channels_im.items()):
-                detector_settings = channel.find('DetectorSettings')
-                laser_scan_info = channel.find('LaserScanInfo')
-                detector = detector_settings.find('Detector')
-                try:
-                    binning = model.Binning(self.text(detector_settings.find('Binning')))
-                except ValueError:
-                    binning = model.Binning.OTHER
-
-                filterset = self.text(self.channels_ts[key].find('BeamSplitters')[0].find('Filter'))
-                filterset_idx = [filterset.model for filterset in self.ome.instruments[0].filter_sets].index(filterset)
-
-                light_sources_settings = channel.find('LightSourcesSettings')
-                # no space in ome for multiple lightsources simultaneously
-                if len(light_sources_settings) > idx:
-                    light_source_settings = light_sources_settings[idx]
-                else:
-                    light_source_settings = light_sources_settings[0]
-                light_source_settings = model.LightSourceSettings(
-                    id=light_source_settings.find('LightSource').attrib['Id'],
-                    attenuation=float(self.text(light_source_settings.find('Attenuation'))),
-                    wavelength=float(self.text(light_source_settings.find('Wavelength'))),
-                    wavelength_unit=self.nm)
-
-                self.ome.images[0].pixels.channels.append(
-                    model.Channel(
-                        id=f'Channel:{idx}',
-                        name=channel.attrib['Name'],
-                        acquisition_mode=self.text(channel.find('AcquisitionMode')),  # type: ignore
-                        color=model.Color(self.text(self.channels_ds[channel.attrib['Id']].find('Color'), 'white')),
-                        detector_settings=model.DetectorSettings(id=detector.attrib['Id'], binning=binning),
-                        # emission_wavelength=text(channel.find('EmissionWavelength')),  # TODO: fix
-                        excitation_wavelength=light_source_settings.wavelength,
-                        filter_set_ref=model.FilterSetRef(id=self.ome.instruments[0].filter_sets[filterset_idx].id),
-                        illumination_type=self.text(channel.find('IlluminationType')),  # type: ignore
-                        light_source_settings=light_source_settings,
-                        samples_per_pixel=int(self.text(laser_scan_info.find('Averaging')))))
-        elif self.version in ('1.1', '1.2'):
-            for idx, (key, channel) in enumerate(self.channels_im.items()):
-                detector_settings = channel.find('DetectorSettings')
-                laser_scan_info = channel.find('LaserScanInfo')
-                detector = detector_settings.find('Detector')
-                try:
-                    color = model.Color(self.text(self.channels_ds[channel.attrib['Id']].find('Color'), 'white'))
-                except Exception:  # noqa
-                    color = None
-                try:
-                    if (i := self.text(channel.find('EmissionWavelength'))) != '0':
-                        emission_wavelength = float(i)
-                    else:
-                        emission_wavelength = None
-                except Exception:  # noqa
-                    emission_wavelength = None
-                if laser_scan_info is not None:
-                    samples_per_pixel = int(self.text(laser_scan_info.find('Averaging'), '1'))
-                else:
-                    samples_per_pixel = 1
-                try:
-                    binning = model.Binning(self.text(detector_settings.find('Binning')))
-                except ValueError:
-                    binning = model.Binning.OTHER
-
-                light_sources_settings = channel.find('LightSourcesSettings')
-                # no space in ome for multiple lightsources simultaneously
-                if light_sources_settings is not None:
-                    light_source_settings = light_sources_settings[0]
-                    light_source_settings = model.LightSourceSettings(
-                        id='LightSource:' + '_'.join([light_source_settings.find('LightSource').attrib['Id']
-                                                      for light_source_settings in light_sources_settings]),
-                        attenuation=self.try_default(float, None, self.text(light_source_settings.find('Attenuation'))),
-                        wavelength=self.try_default(float, None, self.text(light_source_settings.find('Wavelength'))),
-                        wavelength_unit=self.nm)
-                else:
-                    light_source_settings = None
-
-                self.ome.images[0].pixels.channels.append(
-                    model.Channel(
-                        id=f'Channel:{idx}',
-                        name=channel.attrib['Name'],
-                        acquisition_mode=self.text(channel.find('AcquisitionMode')).replace(  # type: ignore
-                            'SingleMoleculeLocalisation', 'SingleMoleculeImaging'),
-                        color=color,
-                        detector_settings=model.DetectorSettings(
-                            id=detector.attrib['Id'].replace(' ', ""),
-                            binning=binning),
-                        emission_wavelength=emission_wavelength,
-                        excitation_wavelength=self.try_default(float, None,
-                                                               self.text(channel.find('ExcitationWavelength'))),
-                        # filter_set_ref=model.FilterSetRef(id=ome.instruments[0].filter_sets[filterset_idx].id),
-                        illumination_type=self.text(channel.find('IlluminationType')),  # type: ignore
-                        light_source_settings=light_source_settings,
-                        samples_per_pixel=samples_per_pixel))
-
-    def get_planes(self) -> None:
-        try:
-            exposure_times = [float(self.text(channel.find('LaserScanInfo').find('FrameTime')))
-                              for channel in self.channels_im.values()]
-        except Exception:  # noqa
-            exposure_times = [None] * len(self.channels_im)
-        delta_ts = self.attachments['TimeStamps'].data()
-        dt = np.diff(delta_ts)
-        if len(dt) and np.std(dt) / np.mean(dt) > 0.02:
-            dt = np.median(dt[dt > 0])
-            delta_ts = dt * np.arange(len(delta_ts))
-            warnings.warn(f'delta_t is inconsistent, using median value: {dt}')
-
-        for t, z, c in product(range(self.size_t), range(self.size_z), range(self.size_c)):
-            self.ome.images[0].pixels.planes.append(
-                model.Plane(the_c=c, the_z=z, the_t=t, delta_t=delta_ts[t],
-                            exposure_time=exposure_times[c],
-                            position_x=self.positions[0], position_x_unit=self.um,
-                            position_y=self.positions[1], position_y_unit=self.um,
-                            position_z=self.positions[2], position_z_unit=self.um))
-
-    def get_annotations(self) -> None:
-        idx = 0
-        for layer in [] if (ml := self.metadata.find('Layers')) is None else ml:
-            rectangle = layer.find('Elements').find('Rectangle')
-            if rectangle is not None:
-                geometry = rectangle.find('Geometry')
-                roi = model.ROI(id=f'ROI:{idx}', description=self.text(layer.find('Usage')))
-                roi.union.append(
-                    model.Rectangle(
-                        id='Shape:0:0',
-                        height=float(self.text(geometry.find('Height'))),
-                        width=float(self.text(geometry.find('Width'))),
-                        x=float(self.text(geometry.find('Left'))),
-                        y=float(self.text(geometry.find('Top')))))
-                self.ome.rois.append(roi)
-                self.ome.images[0].roi_refs.append(model.ROIRef(id=f'ROI:{idx}'))
-                idx += 1

ndbioimage/readers/fijiread.py

@@ -1,59 +0,0 @@
-from abc import ABC
-from itertools import product
-from pathlib import Path
-from struct import unpack
-from warnings import warn
-
-import numpy as np
-from ome_types import model
-from tifffile import TiffFile
-
-from .. import AbstractReader
-
-
-class Reader(AbstractReader, ABC):
-    """ Can read some tif files written with Fiji which are broken because Fiji didn't finish writing. """
-    priority = 90
-    do_not_pickle = 'reader'
-
-    @staticmethod
-    def _can_open(path):
-        if isinstance(path, Path) and path.suffix in ('.tif', '.tiff'):
-            with TiffFile(path) as tif:
-                return tif.is_imagej and not tif.is_bigtiff
-        else:
-            return False
-
-    def __frame__(self, c, z, t):  # Override this, return the frame at c, z, t
-        self.reader.filehandle.seek(self.offset + t * self.count)
-        return np.reshape(unpack(self.fmt, self.reader.filehandle.read(self.count)), self.base_shape['yx'])
-
-    def open(self):
-        warn(f'File {self.path.name} is probably damaged, opening with fijiread.')
-        self.reader = TiffFile(self.path)
-        assert self.reader.pages[0].compression == 1, 'Can only read uncompressed tiff files.'
-        assert self.reader.pages[0].samplesperpixel == 1, 'Can only read 1 sample per pixel.'
-        self.offset = self.reader.pages[0].dataoffsets[0]  # noqa
-        self.count = self.reader.pages[0].databytecounts[0]  # noqa
-        self.bytes_per_sample = self.reader.pages[0].bitspersample // 8  # noqa
-        self.fmt = self.reader.byteorder + self.count // self.bytes_per_sample * 'BHILQ'[self.bytes_per_sample - 1]  # noqa
-
-    def close(self):
-        self.reader.close()
-
-    def get_ome(self):
-        size_y, size_x = self.reader.pages[0].shape
-        size_c, size_z = 1, 1
-        size_t = int(np.floor((self.reader.filehandle.size - self.reader.pages[0].dataoffsets[0]) / self.count))
-        pixel_type = model.PixelType(self.reader.pages[0].dtype.name)
-        ome = model.OME()
-        ome.instruments.append(model.Instrument())
-        ome.images.append(
-            model.Image(
-                pixels=model.Pixels(
-                    size_c=size_c, size_z=size_z, size_t=size_t, size_x=size_x, size_y=size_y,
-                    dimension_order='XYCZT', type=pixel_type),
-                objective_settings=model.ObjectiveSettings(id='Objective:0')))
-        for c, z, t in product(range(size_c), range(size_z), range(size_t)):
-            ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=0))
-        return ome

ndbioimage/readers/metaseriesread.py

@@ -1,80 +0,0 @@
-import re
-from abc import ABC
-from pathlib import Path
-from typing import Optional
-
-import tifffile
-from ome_types import model
-from ome_types.units import _quantity_property  # noqa
-
-from .. import AbstractReader
-
-
-class Reader(AbstractReader, ABC):
-    priority = 20
-    do_not_pickle = 'last_tif'
-
-    @staticmethod
-    def _can_open(path):
-        return isinstance(path, Path) and (path.is_dir() or
-                                           (path.parent.is_dir() and path.name.lower().startswith('pos')))
-
-    @staticmethod
-    def get_positions(path: str | Path) -> Optional[list[int]]:
-        pat = re.compile(rf's(\d)_t\d+\.(tif|TIF)$')
-        return sorted({int(m.group(1)) for file in Path(path).iterdir() if (m := pat.search(file.name))})
-
-    def get_ome(self):
-        ome = model.OME()
-        tif = self.get_tif(0)
-        metadata = tif.metaseries_metadata
-        size_z = len(tif.pages)
-        page = tif.pages[0]
-        shape = {axis.lower(): size for axis, size in zip(page.axes, page.shape)}
-        size_x, size_y = shape['x'], shape['y']
-
-        ome.instruments.append(model.Instrument())
-
-        size_c = 1
-        size_t = max(self.filedict.keys()) + 1
-        pixel_type = f"uint{metadata['PlaneInfo']['bits-per-pixel']}"
-        ome.images.append(
-            model.Image(
-                pixels=model.Pixels(
-                    size_c=size_c, size_z=size_z, size_t=size_t,
-                    size_x=size_x, size_y=size_y,
-                    dimension_order='XYCZT', type=pixel_type),
-                objective_settings=model.ObjectiveSettings(id='Objective:0')))
-        return ome
-
-    def open(self):
-        pat = re.compile(rf's{self.series}_t\d+\.(tif|TIF)$')
-        filelist = sorted([file for file in self.path.iterdir() if pat.search(file.name)])
-        pattern = re.compile(r't(\d+)$')
-        self.filedict = {int(pattern.search(file.stem).group(1)) - 1: file for file in filelist}
-        if len(self.filedict) == 0:
-            raise FileNotFoundError
-        self.last_tif = 0, tifffile.TiffFile(self.filedict[0])
-
-    def close(self) -> None:
-        self.last_tif[1].close()
-
-    def get_tif(self, t: int = None):
-        last_t, tif = self.last_tif
-        if (t is None or t == last_t) and not tif.filehandle.closed:
-            return tif
-        else:
-            tif.close()
-            tif = tifffile.TiffFile(self.filedict[t])
-            self.last_tif = t, tif
-            return tif
-
-    def __frame__(self, c=0, z=0, t=0):
-        tif = self.get_tif(t)
-        page = tif.pages[z]
-        if page.axes.upper() == 'YX':
-            return page.asarray()
-        elif page.axes.upper() == 'XY':
-            return page.asarray().T
-        else:
-            raise NotImplementedError(f'reading axes {page.axes} is not implemented')

ndbioimage/readers/ndread.py

@@ -1,53 +0,0 @@
-from abc import ABC
-from itertools import product
-
-import numpy as np
-from ome_types import model
-
-from .. import AbstractReader
-
-
-class Reader(AbstractReader, ABC):
-    priority = 20
-
-    @staticmethod
-    def _can_open(path):
-        return isinstance(path, np.ndarray) and 1 <= path.ndim <= 5
-
-    def get_ome(self):
-        def shape(size_x=1, size_y=1, size_c=1, size_z=1, size_t=1):  # noqa
-            return size_x, size_y, size_c, size_z, size_t
-        size_x, size_y, size_c, size_z, size_t = shape(*self.array.shape)
-        try:
-            pixel_type = model.PixelType(self.array.dtype.name)
-        except ValueError:
-            if self.array.dtype.name.startswith('int'):
-                pixel_type = model.PixelType('int32')
-            else:
-                pixel_type = model.PixelType('float')
-
-        ome = model.OME()
-        ome.instruments.append(model.Instrument())
-        ome.images.append(
-            model.Image(
-                pixels=model.Pixels(
-                    size_c=size_c, size_z=size_z, size_t=size_t, size_x=size_x, size_y=size_y,
-                    dimension_order='XYCZT', type=pixel_type),
-                objective_settings=model.ObjectiveSettings(id='Objective:0')))
-        for c, z, t in product(range(size_c), range(size_z), range(size_t)):
-            ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=0))
-        return ome
-
-    def open(self):
-        if isinstance(self.path, np.ndarray):
-            self.array = np.array(self.path)
-            while self.array.ndim < 5:
-                self.array = np.expand_dims(self.array, -1)  # noqa
-            self.path = 'numpy array'
-
-    def __frame__(self, c, z, t):
-        frame = self.array[:, :, c, z, t]
-        if self.axes.find('y') > self.axes.find('x'):
-            return frame.T
-        else:
-            return frame

ndbioimage/readers/seqread.py

@@ -1,146 +0,0 @@
-import re
-from abc import ABC
-from datetime import datetime
-from itertools import product
-from pathlib import Path
-
-import tifffile
-import yaml
-from ome_types import model
-from ome_types.units import _quantity_property  # noqa
-
-from .. import AbstractReader
-
-
-def lazy_property(function, field, *arg_fields):
-    def lazy(self):
-        if self.__dict__.get(field) is None:
-            self.__dict__[field] = function(*[getattr(self, arg_field) for arg_field in arg_fields])
-            try:
-                self.model_fields_set.add(field)
-            except Exception:  # noqa
-                pass
-        return self.__dict__[field]
-    return property(lazy)
-
-
-class Plane(model.Plane):
-    """ Lazily retrieve delta_t from metadata """
-    def __init__(self, t0, file, **kwargs):  # noqa
-        super().__init__(**kwargs)
-        # setting fields here because they would be removed by ome_types/pydantic after class definition
-        setattr(self.__class__, 'delta_t', lazy_property(self.get_delta_t, 'delta_t', 't0', 'file'))
-        setattr(self.__class__, 'delta_t_quantity', _quantity_property('delta_t'))
-        self.__dict__['t0'] = t0  # noqa
-        self.__dict__['file'] = file  # noqa
-
-    @staticmethod
-    def get_delta_t(t0, file):
-        with tifffile.TiffFile(file) as tif:
-            info = yaml.safe_load(tif.pages[0].tags[50839].value['Info'])
-        return float((datetime.strptime(info['Time'], '%Y-%m-%d %H:%M:%S %z') - t0).seconds)
-
-
-class Reader(AbstractReader, ABC):
-    priority = 10
-
-    @staticmethod
-    def _can_open(path):
-        pat = re.compile(r'(?:\d+-)?Pos.*', re.IGNORECASE)
-        return (isinstance(path, Path) and path.is_dir() and
-                (pat.match(path.name) or any(file.is_dir() and pat.match(file.stem) for file in path.iterdir())))
-
-    def get_ome(self):
-        ome = model.OME()
-        with tifffile.TiffFile(self.filedict[0, 0, 0]) as tif:
-            metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
-        ome.experimenters.append(
-            model.Experimenter(id='Experimenter:0', user_name=metadata['Info']['Summary']['UserName']))
-        objective_str = metadata['Info']['ZeissObjectiveTurret-Label']
-        ome.instruments.append(model.Instrument())
-        ome.instruments[0].objectives.append(
-            model.Objective(
-                id='Objective:0', manufacturer='Zeiss', model=objective_str,
-                nominal_magnification=float(re.findall(r'(\d+)x', objective_str)[0]),
-                lens_na=float(re.findall(r'/(\d\.\d+)', objective_str)[0]),
-                immersion=model.Objective_Immersion.OIL if 'oil' in objective_str.lower() else None))
-        tubelens_str = metadata['Info']['ZeissOptovar-Label']
-        ome.instruments[0].objectives.append(
-            model.Objective(
-                id='Objective:Tubelens:0', manufacturer='Zeiss', model=tubelens_str,
-                nominal_magnification=float(re.findall(r'\d?\d*[,.]?\d+(?=x$)', tubelens_str)[0].replace(',', '.'))))
-        ome.instruments[0].detectors.append(
-            model.Detector(
-                id='Detector:0', amplification_gain=100))
-        ome.instruments[0].filter_sets.append(
-            model.FilterSet(id='FilterSet:0', model=metadata['Info']['ZeissReflectorTurret-Label']))
-
-        pxsize = metadata['Info']['PixelSizeUm']
-        pxsize_cam = 6.5 if 'Hamamatsu' in metadata['Info']['Core-Camera'] else None
-        if pxsize == 0:
-            pxsize = pxsize_cam / ome.instruments[0].objectives[0].nominal_magnification
-        pixel_type = metadata['Info']['PixelType'].lower()
-        if pixel_type.startswith('gray'):
-            pixel_type = 'uint' + pixel_type[4:]
-        else:
-            pixel_type = 'uint16'  # assume
-
-        size_c, size_z, size_t = (max(i) + 1 for i in zip(*self.filedict.keys()))
-        t0 = datetime.strptime(metadata['Info']['Time'], '%Y-%m-%d %H:%M:%S %z')
-        ome.images.append(
-            model.Image(
-                pixels=model.Pixels(
-                    size_c=size_c, size_z=size_z, size_t=size_t,
-                    size_x=metadata['Info']['Width'], size_y=metadata['Info']['Height'],
-                    dimension_order='XYCZT',  # type: ignore
-                    type=pixel_type, physical_size_x=pxsize, physical_size_y=pxsize,
-                    physical_size_z=metadata['Info']['Summary']['z-step_um']),
-                objective_settings=model.ObjectiveSettings(id='Objective:0')))
-
-        for c, z, t in product(range(size_c), range(size_z), range(size_t)):
-            ome.images[0].pixels.planes.append(
-                Plane(t0, self.filedict[c, z, t],
-                      the_c=c, the_z=z, the_t=t, exposure_time=metadata['Info']['Exposure-ms'] / 1000))
-
-        # compare channel names from metadata with filenames
-        pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$', re.IGNORECASE)
-        for c in range(size_c):
-            ome.images[0].pixels.channels.append(
-                model.Channel(
-                    id=f'Channel:{c}', name=pattern_c.findall(self.filedict[c, 0, 0].stem)[0],
-                    detector_settings=model.DetectorSettings(
-                        id='Detector:0', binning=metadata['Info']['Hamamatsu_sCMOS-Binning']),
-                    filter_set_ref=model.FilterSetRef(id='FilterSet:0')))
-        return ome
-
-    def open(self):
-        # /some_path/Pos4: path = /some_path, series = 4
-        # /some_path/5-Pos_001_005: path = /some_path/5-Pos_001_005, series = 0
-        if re.match(r'(?:\d+-)?Pos.*', self.path.name, re.IGNORECASE) is None:
-            pat = re.compile(rf'^(?:\d+-)?Pos{self.series}$', re.IGNORECASE)
-            files = sorted(file for file in self.path.iterdir() if pat.match(file.name))
-            if len(files):
-                path = files[0]
-            else:
-                raise FileNotFoundError(self.path / pat.pattern)
-        else:
-            path = self.path
-
-        pat = re.compile(r'^img_\d{3,}.*\d{3,}.*\.tif$', re.IGNORECASE)
-        filelist = sorted([file for file in path.iterdir() if pat.search(file.name)])
-        with tifffile.TiffFile(self.path / filelist[0]) as tif:
-            metadata = {key: yaml.safe_load(value) for key, value in tif.pages[0].tags[50839].value.items()}
-
-        # compare channel names from metadata with filenames
-        cnamelist = metadata['Info']['Summary']['ChNames']
-        cnamelist = [c for c in cnamelist if any([c in f.name for f in filelist])]
-
-        pattern_c = re.compile(r'img_\d{3,}_(.*)_\d{3,}$', re.IGNORECASE)
-        pattern_z = re.compile(r'(\d{3,})$')
-        pattern_t = re.compile(r'img_(\d{3,})', re.IGNORECASE)
-        self.filedict = {(cnamelist.index(pattern_c.findall(file.stem)[0]),  # noqa
-                          int(pattern_z.findall(file.stem)[0]),
-                          int(pattern_t.findall(file.stem)[0])): file for file in filelist}
-
-    def __frame__(self, c=0, z=0, t=0):
-        return tifffile.imread(self.path / self.filedict[(c, z, t)])

ndbioimage/readers/tifread.py

@@ -1,85 +0,0 @@
-from abc import ABC
-from functools import cached_property
-from itertools import product
-from pathlib import Path
-
-import numpy as np
-import tifffile
-import yaml
-from ome_types import model
-
-from .. import AbstractReader
-
-
-class Reader(AbstractReader, ABC):
-    priority = 0
-    do_not_pickle = 'reader'
-
-    @staticmethod
-    def _can_open(path):
-        if isinstance(path, Path) and path.suffix in ('.tif', '.tiff'):
-            with tifffile.TiffFile(path) as tif:
-                return tif.is_imagej and tif.pages[-1]._nextifd() == 0  # noqa
-        else:
-            return False
-
-    @cached_property
-    def metadata(self):
-        return {key: yaml.safe_load(value) if isinstance(value, str) else value
-                for key, value in self.reader.imagej_metadata.items()}
-
-    def get_ome(self):
-        page = self.reader.pages[0]
-        size_y = page.imagelength
-        size_x = page.imagewidth
-        if self.p_ndim == 3:
-            size_c = page.samplesperpixel
-            size_t = self.metadata.get('frames', 1)  # // C
-        else:
-            size_c = self.metadata.get('channels', 1)
-            size_t = self.metadata.get('frames', 1)
-        size_z = self.metadata.get('slices', 1)
-        if 282 in page.tags and 296 in page.tags and page.tags[296].value == 1:
-            f = page.tags[282].value
-            pxsize = f[1] / f[0]
-        else:
-            pxsize = None
-
-        dtype = page.dtype.name
-        if dtype not in ('int8', 'int16', 'int32', 'uint8', 'uint16', 'uint32',
-                         'float', 'double', 'complex', 'double-complex', 'bit'):
-            dtype = 'float'
-
-        interval_t = self.metadata.get('interval', 0)
-
-        ome = model.OME()
-        ome.instruments.append(model.Instrument(id='Instrument:0'))
-        ome.instruments[0].objectives.append(model.Objective(id='Objective:0'))
-        ome.images.append(
-            model.Image(
-                id='Image:0',
-                pixels=model.Pixels(
-                    id='Pixels:0',
-                    size_c=size_c, size_z=size_z, size_t=size_t, size_x=size_x, size_y=size_y,
-                    dimension_order='XYCZT', type=dtype,  # type: ignore
-                    physical_size_x=pxsize, physical_size_y=pxsize),
-                objective_settings=model.ObjectiveSettings(id='Objective:0')))
-        for c, z, t in product(range(size_c), range(size_z), range(size_t)):
-            ome.images[0].pixels.planes.append(model.Plane(the_c=c, the_z=z, the_t=t, delta_t=interval_t * t))
-        return ome
-
-    def open(self):
-        self.reader = tifffile.TiffFile(self.path)
-        page = self.reader.pages[0]
-        self.p_ndim = page.ndim  # noqa
-        if self.p_ndim == 3:
-            self.p_transpose = [i for i in [page.axes.find(j) for j in 'SYX'] if i >= 0]  # noqa
-
-    def close(self):
-        self.reader.close()
-
-    def __frame__(self, c, z, t):
-        if self.p_ndim == 3:
-            return np.transpose(self.reader.asarray(z + t * self.base_shape['z']), self.p_transpose)[c]
-        else:
-            return self.reader.asarray(c + z * self.base_shape['c'] + t * self.base_shape['c'] * self.base_shape['z'])

py/ndbioimage/__init__.py

@@ -0,0 +1,624 @@
+from __future__ import annotations
+
+import os
+import warnings
+from abc import ABC
+from argparse import ArgumentParser
+from collections import OrderedDict
+from functools import cached_property, wraps
+from importlib.metadata import version
+from itertools import product
+from pathlib import Path
+from typing import Any, Callable, Optional, Sequence, TypeVar
+
+import numpy as np
+from numpy.typing import ArrayLike, DTypeLike
+from tiffwrite import FrameInfo, IJTiffParallel
+from tqdm.auto import tqdm
+
+from ome_metadata import Ome
+from ome_metadata.ome_metadata_rs import Length  # noqa
+from . import ndbioimage_rs as rs  # noqa
+from .transforms import Transform, Transforms  # noqa: F401
+
+try:
+    __version__ = version(Path(__file__).parent.name)
+except Exception:  # noqa
+    __version__ = "unknown"
+
+try:
+    with open(Path(__file__).parent.parent / ".git" / "HEAD") as g:
+        head = g.read().split(":")[1].strip()
+    with open(Path(__file__).parent.parent / ".git" / head) as h:
+        __git_commit_hash__ = h.read().rstrip("\n")
+except Exception:  # noqa
+    __git_commit_hash__ = "unknown"
+
+warnings.filterwarnings("ignore", "Reference to unknown ID")
+Number = int | float | np.integer | np.floating
+
+
+for dep_file in (Path(__file__).parent / "deps").glob("*_"):
+    dep_file.rename(str(dep_file)[:-1])
+
+if not list((Path(__file__).parent / "jassets").glob("bioformats*.jar")):
+    rs.download_bioformats(True)
+
+
+class ReaderNotFoundError(Exception):
+    pass
+
+
+class TransformTiff(IJTiffParallel):
+    """transform frames in a parallel process to speed up saving"""
+
+    def __init__(self, image: Imread, *args: Any, **kwargs: Any) -> None:
+        self.image = image
+        super().__init__(*args, **kwargs)
+
+    def parallel(self, frame: tuple[int, int, int]) -> tuple[FrameInfo]:
+        return ((np.asarray(self.image(*frame)), 0, 0, 0),)
+
+
+class DequeDict(OrderedDict):
+    def __init__(self, maxlen: int = None, *args: Any, **kwargs: Any) -> None:
+        self.maxlen = maxlen
+        super().__init__(*args, **kwargs)
+
+    def __setitem__(self, *args: Any, **kwargs: Any) -> None:
+        super().__setitem__(*args, **kwargs)
+        self.truncate()
+
+    def truncate(self) -> None:
+        if self.maxlen is not None:
+            while len(self) > self.maxlen:
+                self.popitem(False)
+
+    def update(self, *args: Any, **kwargs: Any) -> None:
+        super().update(*args, **kwargs)  # type: ignore
+        self.truncate()
+
+
+def find(obj: Sequence[Any], **kwargs: Any) -> Any:
+    for item in obj:
+        try:
+            if all([getattr(item, key) == value for key, value in kwargs.items()]):
+                return item
+        except AttributeError:
+            pass
+    return None
+
+
+R = TypeVar("R")
+
+
+def try_default(fun: Callable[..., R], default: Any, *args: Any, **kwargs: Any) -> R:
+    try:
+        return fun(*args, **kwargs)
+    except Exception:  # noqa
+        return default
+
+
+class Shape(tuple):
+    def __new__(cls, shape: Sequence[int] | Shape, axes: str = "yxczt") -> Shape:
+        if isinstance(shape, Shape):
+            axes = shape.axes  # type: ignore
+        new = super().__new__(cls, shape)
+        new.axes = axes.lower()
+        return new  # type: ignore
+
+    def __getitem__(self, n: int | str) -> int | tuple[int]:
+        if isinstance(n, str):
+            if len(n) == 1:
+                return self[self.axes.find(n.lower())] if n.lower() in self.axes else 1
+            else:
+                return tuple(self[i] for i in n)  # type: ignore
+        return super().__getitem__(n)
+
+    @cached_property
+    def yxczt(self) -> tuple[int, int, int, int, int]:
+        return tuple(self[i] for i in "yxczt")  # type: ignore
+
+
+class OmeCache(DequeDict):
+    """prevent (potentially expensive) rereading of ome data by caching"""
+
+    instance = None
+
+    def __new__(cls) -> OmeCache:
+        if cls.instance is None:
+            cls.instance = super().__new__(cls)
+        return cls.instance
+
+    def __init__(self) -> None:
+        super().__init__(64)
+
+    def __reduce__(self) -> tuple[type, tuple]:
+        return self.__class__, ()
+
+    def __getitem__(self, path: Path | str | tuple) -> Ome:
+        if isinstance(path, tuple):
+            return super().__getitem__(path)
+        else:
+            return super().__getitem__(self.path_and_lstat(path))
+
+    def __setitem__(self, path: Path | str | tuple, value: Ome) -> None:
+        if isinstance(path, tuple):
+            super().__setitem__(path, value)
+        else:
+            super().__setitem__(self.path_and_lstat(path), value)
+
+    def __contains__(self, path: Path | str | tuple) -> bool:
+        if isinstance(path, tuple):
+            return super().__contains__(path)
+        else:
+            return super().__contains__(self.path_and_lstat(path))
+
+    @staticmethod
+    def path_and_lstat(
+        path: str | Path,
+    ) -> tuple[Path, Optional[os.stat_result], Optional[os.stat_result]]:
+        path = Path(path)
+        return (
+            path,
+            (path.lstat() if path.exists() else None),
+            (
+                path.with_suffix(".ome.xml").lstat()
+                if path.with_suffix(".ome.xml").exists()
+                else None
+            ),
+        )
+
+
+def get_positions(path: str | Path) -> Optional[list[int]]:  # noqa
+    # TODO
+    return None
+
+
+class Imread(rs.View, np.lib.mixins.NDArrayOperatorsMixin, ABC):
+    """class to read image files, while taking good care of important metadata,
+    currently optimized for .czi files, but can open anything that bioformats can handle
+        path: path to the image file
+        optional:
+        axes: order of axes, default: cztyx, but omitting any axes with lenght 1
+        dtype: datatype to be used when returning frames
+
+        Examples:
+            >> im = Imread('/path/to/file.image', axes='czt)
+            >> im
+             << shows summary
+            >> im.shape
+             << (15, 26, 1000, 1000)
+            >> im.axes
+             << 'ztyx'
+            >> plt.imshow(im[1, 0])
+             << plots frame at position z=1, t=0 (python type indexing)
+            >> plt.imshow(im[:, 0].max('z'))
+             << plots max-z projection at t=0
+            >> im.pxsize
+             << 0.09708737864077668 image-plane pixel size in um
+            >> im.laserwavelengths
+             << [642, 488]
+            >> im.laserpowers
+             << [0.02, 0.0005] in %
+
+            See __init__ and other functions for more ideas.
+
+            # TODO: argmax, argmin, nanmax, nanmin, nanmean, nansum, nanstd, nanvar, std, var, squeeze
+    """
+
+    def __getitem__(self, item):
+        new = super().__getitem__(item)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def __copy__(self):
+        Imread(super().__copy__())
+
+    def copy(self):
+        Imread(super().copy())
+
+    def astype(self):
+        Imread(super().astype())
+
+    def squeeze(self):
+        new = super().squeeze()
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def min(self, *args, **kwargs) -> Imread | float:
+        new = super().min(*args, **kwargs)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def max(self, *args, **kwargs) -> Imread | float:
+        new = super().max(*args, **kwargs)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def mean(self, *args, **kwargs) -> Imread | float:
+        new = super().mean(*args, **kwargs)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def sum(self, *args, **kwargs) -> Imread | float:
+        new = super().sum(*args, **kwargs)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def transpose(self, *args, **kwargs) -> Imread | float:
+        new = super().transpose(*args, **kwargs)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    def swap_axes(self, *args, **kwargs) -> Imread | float:
+        new = super().swap_axes(*args, **kwargs)
+        return Imread(new) if isinstance(new, rs.View) else new
+
+    @property
+    def T(self) -> Imread | float:
+        return Imread(super().T)
+
+    @staticmethod
+    def get_positions(path: str | Path) -> Optional[list[int]]:  # noqa
+        # TODO
+        return None
+
+    @staticmethod
+    def as_axis(axis):
+        if axis is None:
+            return None
+        elif isinstance(axis, int):
+            return axis
+        else:
+            return str(axis)
+
+    @wraps(np.moveaxis)
+    def moveaxis(self, source, destination):
+        raise NotImplementedError("moveaxis is not implemented")
+
+    @wraps(np.ndarray.flatten)
+    def flatten(self, *args, **kwargs) -> np.ndarray:
+        return np.asarray(self).flatten(*args, **kwargs)
+
+    @wraps(np.ndarray.reshape)
+    def reshape(self, *args, **kwargs) -> np.ndarray:
+        return np.asarray(self).reshape(*args, **kwargs)  # noqa
+
+    def as_array(self) -> np.ndarray:
+        return self.__array__()
+
+    @wraps(np.ndarray.astype)
+    def astype(self, dtype: DTypeLike, *_, **__) -> Imread:
+        return Imread(super().astype(str(np.dtype(dtype))))
+
+    @staticmethod
+    def fix_ome(ome: Ome) -> Ome:
+        # fix ome if necessary
+        for image in ome.image:
+            try:
+                if (
+                    image.pixels.physical_size_z is None
+                    and len(set([plane.the_z for plane in image.pixels.planes])) > 1
+                ):
+                    z = np.array(
+                        [
+                            (
+                                plane.position_z_unit.convert("um", plane.position_z),
+                                plane.the_z,
+                            )
+                            for plane in image.pixels.planes
+                            if plane.the_c == 0 and plane.the_t == 0
+                        ]
+                    )
+                    i = np.argsort(z[:, 1])
+                    image.pixels.physical_size_z = (
+                        np.nanmean(np.true_divide(*np.diff(z[i], axis=0).T)) * 1e6
+                    )
+                    image.pixels.physical_size_z_unit = Length("um")  # type: ignore
+            except Exception:  # noqa
+                pass
+        return ome
+
+    @staticmethod
+    def read_ome(path: str | Path) -> Optional[Ome]:
+        path = Path(path)  # type: ignore
+        if path.with_suffix(".ome.xml").exists():
+            return Ome.from_xml(path.with_suffix(".ome.xml").read_text())
+        return None
+
+    def get_ome(self) -> Ome:
+        """OME metadata structure"""
+        return Ome.from_xml(self.get_ome_xml())
+
+    @cached_property
+    def ome(self) -> Ome:
+        cache = OmeCache()
+        if self.path not in cache:
+            ome = self.read_ome(self.path)
+            if ome is None:
+                ome = self.get_ome()
+            cache[self.path] = self.fix_ome(ome)
+        return cache[self.path]
+
+    def is_noise(self, volume: ArrayLike = None) -> bool:
+        """True if volume only has noise"""
+        if volume is None:
+            volume = self
+        fft = np.fft.fftn(volume)
+        corr = np.fft.fftshift(np.fft.ifftn(fft * fft.conj()).real / np.sum(volume**2))
+        return 1 - corr[tuple([0] * corr.ndim)] < 0.0067
+
+    @staticmethod
+    def kill_vm() -> None:
+        pass
+
+    def save_as_movie(
+        self,
+        fname: Path | str = None,
+        c: int | Sequence[int] = None,  # noqa
+        z: int | Sequence[int] = None,  # noqa
+        t: str | int | Sequence[int] = None,  # noqa
+        colors: tuple[str] = None,
+        brightnesses: tuple[float] = None,
+        scale: int = None,
+        bar: bool = True,
+    ) -> None:
+        """saves the image as a mp4 or mkv file"""
+        from matplotlib.colors import to_rgb
+        from skvideo.io import FFmpegWriter
+
+        if t is None:
+            t = np.arange(self.shape["t"])
+        elif isinstance(t, str):
+            t = eval(f"np.arange(self.shape['t'])[{t}]")
+        elif np.isscalar(t):
+            t = (t,)
+
+        def get_ab(
+            tyx: Imread, p: tuple[float, float] = (1, 99)
+        ) -> tuple[float, float]:
+            s = tyx.flatten()
+            s = s[s > 0]
+            a, b = np.percentile(s, p)
+            if a == b:
+                a, b = np.min(s), np.max(s)
+            if a == b:
+                a, b = 0, 1
+            return a, b
+
+        def cframe(
+            frame: ArrayLike,
+            color: str,
+            a: float,
+            b: float,
+            scale: float = 1,  # noqa
+        ) -> np.ndarray:
+            color = to_rgb(color)
+            frame = (frame - a) / (b - a)
+            frame = np.dstack([255 * frame * i for i in color])
+            return np.clip(np.round(frame), 0, 255).astype("uint8")
+
+        ab = list(zip(*[get_ab(i) for i in self.transpose("cztyx")]))  # type: ignore
+        colors = colors or ("r", "g", "b")[: self.shape["c"]] + max(
+            0, self.shape["c"] - 3
+        ) * ("w",)
+        brightnesses = brightnesses or (1,) * self.shape["c"]
+        scale = scale or 1
+        shape_x = 2 * ((self.shape["x"] * scale + 1) // 2)
+        shape_y = 2 * ((self.shape["y"] * scale + 1) // 2)
+
+        with FFmpegWriter(
+            str(fname).format(name=self.path.stem, path=str(self.path.parent)),
+            outputdict={
+                "-vcodec": "libx264",
+                "-preset": "veryslow",
+                "-pix_fmt": "yuv420p",
+                "-r": "7",
+                "-vf": f"setpts={25 / 7}*PTS,scale={shape_x}:{shape_y}:flags=neighbor",
+            },
+        ) as movie:
+            im = self.transpose("tzcyx")  # type: ignore
+            for ti in tqdm(t, desc="Saving movie", disable=not bar):
+                movie.writeFrame(
+                    np.max(
+                        [
+                            cframe(yx, c, a, b / s, scale)
+                            for yx, a, b, c, s in zip(
+                                im[ti].max("z"), *ab, colors, brightnesses
+                            )
+                        ],
+                        0,
+                    )
+                )
+
+    def save_as_tiff(
+        self,
+        fname: Path | str = None,
+        c: int | Sequence[int] = None,
+        z: int | Sequence[int] = None,
+        t: int | Sequence[int] = None,
+        split: bool = False,
+        bar: bool = True,
+        pixel_type: str = "uint16",
+        **kwargs: Any,
+    ) -> None:
+        """saves the image as a tif file
+        split: split channels into different files"""
+        fname = Path(str(fname).format(name=self.path.stem, path=str(self.path.parent)))
+        if fname is None:
+            fname = self.path.with_suffix(".tif")
+            if fname == self.path:
+                raise FileExistsError(f"File {fname} exists already.")
+        if not isinstance(fname, Path):
+            fname = Path(fname)
+        if split:
+            for i in range(self.shape["c"]):
+                if self.timeseries:
+                    self.save_as_tiff(
+                        fname.with_name(f"{fname.stem}_C{i:01d}").with_suffix(".tif"),
+                        i,
+                        0,
+                        None,
+                        False,
+                        bar,
+                        pixel_type,
+                    )
+                else:
+                    self.save_as_tiff(
+                        fname.with_name(f"{fname.stem}_C{i:01d}").with_suffix(".tif"),
+                        i,
+                        None,
+                        0,
+                        False,
+                        bar,
+                        pixel_type,
+                    )
+        else:
+            n = [c, z, t]
+            for i, ax in enumerate("czt"):
+                if n[i] is None:
+                    n[i] = range(self.shape[ax])
+                elif not isinstance(n[i], (tuple, list)):
+                    n[i] = (n[i],)
+
+            shape = [len(i) for i in n]
+            with TransformTiff(
+                self,
+                fname.with_suffix(".tif"),
+                dtype=pixel_type,
+                pxsize=self.pxsize,
+                deltaz=self.deltaz,
+                **kwargs,
+            ) as tif:
+                for i, m in tqdm(  # noqa
+                    zip(product(*[range(s) for s in shape]), product(*n)),  # noqa
+                    total=np.prod(shape),
+                    desc="Saving tiff",
+                    disable=not bar,
+                ):
+                    tif.save(m, *i)  # type: ignore
+
+    def with_transform(
+        self,
+        channels: bool = True,
+        drift: bool = False,
+        file: Path | str = None,
+        bead_files: Sequence[Path | str] = (),
+    ) -> Imread:
+        """returns a view where channels and/or frames are registered with an affine transformation
+        channels: True/False register channels using bead_files
+        drift: True/False register frames to correct drift
+        file: load registration from file with name file, default: transform.yml in self.path.parent
+        bead_files: files used to register channels, default: files in self.path.parent,
+            with names starting with 'beads'
+        """
+        raise NotImplementedError("transforms are not yet implemented")
+        # view = self.copy()
+        # if file is None:
+        #     file = Path(view.path.parent) / 'transform.yml'
+        # else:
+        #     file = Path(file)
+        # if not bead_files:
+        #     try:
+        #         bead_files = Transforms.get_bead_files(view.path.parent)
+        #     except Exception:  # noqa
+        #         if not file.exists():
+        #             raise Exception('No transform file and no bead file found.')
+        #         bead_files = ()
+        #
+        # if channels:
+        #     try:
+        #         view.transform = Transforms.from_file(file, T=drift)
+        #     except Exception:  # noqa
+        #         view.transform = Transforms().with_beads(view.cyllens, bead_files)
+        #         if drift:
+        #             view.transform = view.transform.with_drift(view)
+        #         view.transform.save(file.with_suffix('.yml'))
+        #         view.transform.save_channel_transform_tiff(bead_files, file.with_suffix('.tif'))
+        # elif drift:
+        #     try:
+        #         view.transform = Transforms.from_file(file, C=False)
+        #     except Exception:  # noqa
+        #         view.transform = Transforms().with_drift(self)
+        # view.transform.adapt(view.frameoffset, view.shape.yxczt, view.channel_names)
+        # return view
+
+
+def main() -> None:
+    parser = ArgumentParser(description="Display info and save as tif")
+    parser.add_argument("-v", "--version", action="version", version=__version__)
+    parser.add_argument("file", help="image_file", type=str, nargs="*")
+    parser.add_argument(
+        "-w",
+        "--write",
+        help="path to tif/movie out, {folder}, {name} and {ext} take this from file in",
+        type=str,
+        default=None,
+    )
+    parser.add_argument(
+        "-o", "--extract_ome", help="extract ome to xml file", action="store_true"
+    )
+    parser.add_argument(
+        "-r", "--register", help="register channels", action="store_true"
+    )
+    parser.add_argument("-c", "--channel", help="channel", type=int, default=None)
+    parser.add_argument("-z", "--zslice", help="z-slice", type=int, default=None)
+    parser.add_argument(
+        "-t",
+        "--time",
+        help="time (frames) in python slicing notation",
+        type=str,
+        default=None,
+    )
+    parser.add_argument("-s", "--split", help="split channels", action="store_true")
+    parser.add_argument("-f", "--force", help="force overwrite", action="store_true")
+    parser.add_argument(
+        "-C", "--movie-colors", help="colors for channels in movie", type=str, nargs="*"
+    )
+    parser.add_argument(
+        "-B",
+        "--movie-brightnesses",
+        help="scale brightness of each channel",
+        type=float,
+        nargs="*",
+    )
+    parser.add_argument(
+        "-S", "--movie-scale", help="upscale movie xy size, int", type=float
+    )
+    args = parser.parse_args()
+
+    for file in tqdm(args.file, desc="operating on files", disable=len(args.file) == 1):
+        file = Path(file)
+        with Imread(file) as im:  # noqa
+            if args.register:
+                im = im.with_transform()  # noqa
+            if args.write:
+                write = Path(
+                    args.write.format(
+                        folder=str(file.parent), name=file.stem, ext=file.suffix
+                    )
+                ).absolute()  # noqa
+                write.parent.mkdir(parents=True, exist_ok=True)
+                if write.exists() and not args.force:
+                    print(
+                        f"File {args.write} exists already, add the -f flag if you want to overwrite it."
+                    )
+                elif write.suffix in (".mkv", ".mp4"):
+                    im.save_as_movie(
+                        write,
+                        args.channel,
+                        args.zslice,
+                        args.time,
+                        args.movie_colors,
+                        args.movie_brightnesses,
+                        args.movie_scale,
+                        bar=len(args.file) == 1,
+                    )
+                else:
+                    im.save_as_tiff(
+                        write,
+                        args.channel,
+                        args.zslice,
+                        args.time,
+                        args.split,
+                        bar=len(args.file) == 1,
+                    )
+            if args.extract_ome:
+                with open(im.path.with_suffix(".ome.xml"), "w") as f:
+                    f.write(im.ome.to_xml())
+            if len(args.file) == 1:
+                print(im.summary)

py/ndbioimage/ome.py

@@ -0,0 +1,39 @@
+from __future__ import annotations
+
+from ome_metadata import ome_metadata_rs as rs  # noqa
+from collections import UserDict, UserList
+
+
+class Ome(UserDict):
+    @staticmethod
+    def from_xml(xml: str) -> Ome:
+        """Create the OME structure from an XML string"""
+        new = Ome()
+        new.update(rs.ome(str(xml)))
+        return new
+
+    def __dir__(self) -> list[str]:
+        return list(self.keys()) + list(super().__dir__())
+
+    def __getattr__(self, key: str) -> Ome | OmeList | int | float | str:
+        try:
+            new = self.__getitem__(key)
+        except KeyError:
+            raise AttributeError(f"'Ome' object has no attribute '{key}'")
+        if isinstance(new, dict):
+            return Ome(**new)
+        elif isinstance(new, list):
+            return OmeList(new)
+        else:
+            return new
+
+
+class OmeList(UserList):
+    def __getitem__(self, item: int) -> Ome | OmeList | int | float | str:
+        new = super().__getitem__(item)
+        if isinstance(new, dict):
+            return Ome(**new)
+        elif isinstance(new, list):
+            return OmeList(new)
+        else:
+            return new

py/ndbioimage/transforms.py

@@ -21,7 +21,7 @@ except ImportError:
     DataFrame, Series, concat = None, None, None
 
 
-if hasattr(yaml, 'full_load'):
+if hasattr(yaml, "full_load"):
     yamlload = yaml.full_load
 else:
     yamlload = yaml.load
@@ -34,7 +34,7 @@ class Transforms(dict):
 
     @classmethod
     def from_file(cls, file, C=True, T=True):
-        with open(Path(file).with_suffix('.yml')) as f:
+        with open(Path(file).with_suffix(".yml")) as f:
             return cls.from_dict(yamlload(f), C, T)
 
     @classmethod
@@ -42,7 +42,9 @@ class Transforms(dict):
         new = cls()
         for key, value in d.items():
             if isinstance(key, str) and C:
-                new[key.replace(r'\:', ':').replace('\\\\', '\\')] = Transform.from_dict(value)
+                new[key.replace(r"\:", ":").replace("\\\\", "\\")] = (
+                    Transform.from_dict(value)
+                )
             elif T:
                 new[key] = Transform.from_dict(value)
         return new
@@ -69,11 +71,19 @@ class Transforms(dict):
             return new
 
     def asdict(self):
-        return {key.replace('\\', '\\\\').replace(':', r'\:') if isinstance(key, str) else key: value.asdict()
-                for key, value in self.items()}
+        return {
+            key.replace("\\", "\\\\").replace(":", r"\:")
+            if isinstance(key, str)
+            else key: value.asdict()
+            for key, value in self.items()
+        }
 
     def __getitem__(self, item):
-        return np.prod([self[i] for i in item[::-1]]) if isinstance(item, tuple) else super().__getitem__(item)
+        return (
+            np.prod([self[i] for i in item[::-1]])
+            if isinstance(item, tuple)
+            else super().__getitem__(item)
+        )
 
     def __missing__(self, key):
         return self.default
@@ -88,7 +98,7 @@ class Transforms(dict):
         return hash(frozenset((*self.__dict__.items(), *self.items())))
 
     def save(self, file):
-        with open(Path(file).with_suffix('.yml'), 'w') as f:
+        with open(Path(file).with_suffix(".yml"), "w") as f:
             yaml.safe_dump(self.asdict(), f, default_flow_style=None)
 
     def copy(self):
@@ -109,8 +119,10 @@ class Transforms(dict):
         transform_channels = {key for key in self.keys() if isinstance(key, str)}
         if set(channel_names) - transform_channels:
             mapping = key_map(channel_names, transform_channels)
-            warnings.warn(f'The image file and the transform do not have the same channels,'
-                          f' creating a mapping: {mapping}')
+            warnings.warn(
+                f"The image file and the transform do not have the same channels,"
+                f" creating a mapping: {mapping}"
+            )
             for key_im, key_t in mapping.items():
                 self[key_im] = self[key_t]
 
@@ -124,37 +136,54 @@ class Transforms(dict):
 
     def coords_pandas(self, array, channel_names, columns=None):
         if isinstance(array, DataFrame):
-            return concat([self.coords_pandas(row, channel_names, columns) for _, row in array.iterrows()], axis=1).T
+            return concat(
+                [
+                    self.coords_pandas(row, channel_names, columns)
+                    for _, row in array.iterrows()
+                ],
+                axis=1,
+            ).T
         elif isinstance(array, Series):
             key = []
-            if 'C' in array:
-                key.append(channel_names[int(array['C'])])
-            if 'T' in array:
-                key.append(int(array['T']))
+            if "C" in array:
+                key.append(channel_names[int(array["C"])])
+            if "T" in array:
+                key.append(int(array["T"]))
             return self[tuple(key)].coords(array, columns)
         else:
-            raise TypeError('Not a pandas DataFrame or Series.')
+            raise TypeError("Not a pandas DataFrame or Series.")
 
     def with_beads(self, cyllens, bead_files):
-        assert len(bead_files) > 0, 'At least one file is needed to calculate the registration.'
-        transforms = [self.calculate_channel_transforms(file, cyllens) for file in bead_files]
+        assert len(bead_files) > 0, (
+            "At least one file is needed to calculate the registration."
+        )
+        transforms = [
+            self.calculate_channel_transforms(file, cyllens) for file in bead_files
+        ]
         for key in {key for transform in transforms for key in transform.keys()}:
-            new_transforms = [transform[key] for transform in transforms if key in transform]
+            new_transforms = [
+                transform[key] for transform in transforms if key in transform
+            ]
             if len(new_transforms) == 1:
                 self[key] = new_transforms[0]
             else:
                 self[key] = Transform()
-                self[key].parameters = np.mean([t.parameters for t in new_transforms], 0)
-                self[key].dparameters = (np.std([t.parameters for t in new_transforms], 0) /
-                                        np.sqrt(len(new_transforms))).tolist()
+                self[key].parameters = np.mean(
+                    [t.parameters for t in new_transforms], 0
+                )
+                self[key].dparameters = (
+                    np.std([t.parameters for t in new_transforms], 0)
+                    / np.sqrt(len(new_transforms))
+                ).tolist()
         return self
 
     @staticmethod
     def get_bead_files(path):
         from . import Imread
+
         files = []
         for file in path.iterdir():
-            if file.name.lower().startswith('beads'):
+            if file.name.lower().startswith("beads"):
                 try:
                     with Imread(file):
                         files.append(file)
@@ -162,32 +191,36 @@ class Transforms(dict):
                     pass
         files = sorted(files)
         if not files:
-            raise Exception('No bead file found!')
+            raise Exception("No bead file found!")
         checked_files = []
         for file in files:
             try:
                 if file.is_dir():
-                    file /= 'Pos0'
+                    file /= "Pos0"
                 with Imread(file):  # check for errors opening the file
                     checked_files.append(file)
             except (Exception,):
                 continue
         if not checked_files:
-            raise Exception('No bead file found!')
+            raise Exception("No bead file found!")
         return checked_files
 
     @staticmethod
     def calculate_channel_transforms(bead_file, cyllens):
-        """ When no channel is not transformed by a cylindrical lens, assume that the image is scaled by a factor 1.162
-            in the horizontal direction """
+        """When no channel is not transformed by a cylindrical lens, assume that the image is scaled by a factor 1.162
+        in the horizontal direction"""
         from . import Imread
 
-        with Imread(bead_file, axes='zcyx') as im:  # noqa
-            max_ims = im.max('z')
+        with Imread(bead_file, axes="zcyx") as im:  # noqa
+            max_ims = im.max("z")
             goodch = [c for c, max_im in enumerate(max_ims) if not im.is_noise(max_im)]
             if not goodch:
                 goodch = list(range(len(max_ims)))
-            untransformed = [c for c in range(im.shape['c']) if cyllens[im.detector[c]].lower() == 'none']
+            untransformed = [
+                c
+                for c in range(im.shape["c"])
+                if cyllens[im.detector[c]].lower() == "none"
+            ]
 
             good_and_untrans = sorted(set(goodch) & set(untransformed))
             if good_and_untrans:
@@ -200,54 +233,81 @@ class Transforms(dict):
                 matrix[0, 0] = 0.86
                 transform.matrix = matrix
             transforms = Transforms()
-            for c in tqdm(goodch, desc='Calculating channel transforms'):  # noqa
+            for c in tqdm(goodch, desc="Calculating channel transforms"):  # noqa
                 if c == masterch:
                     transforms[im.channel_names[c]] = transform
                 else:
-                    transforms[im.channel_names[c]] = Transform.register(max_ims[masterch], max_ims[c]) * transform
+                    transforms[im.channel_names[c]] = (
+                        Transform.register(max_ims[masterch], max_ims[c]) * transform
+                    )
         return transforms
 
     @staticmethod
     def save_channel_transform_tiff(bead_files, tiffile):
         from . import Imread
+
         n_channels = 0
         for file in bead_files:
             with Imread(file) as im:
-                n_channels = max(n_channels, im.shape['c'])
+                n_channels = max(n_channels, im.shape["c"])
         with IJTiffFile(tiffile) as tif:
             for t, file in enumerate(bead_files):
                 with Imread(file) as im:
                     with Imread(file).with_transform() as jm:
-                        for c in range(im.shape['c']):
-                            tif.save(np.hstack((im(c=c, t=0).max('z'), jm(c=c, t=0).max('z'))), c, 0, t)
+                        for c in range(im.shape["c"]):
+                            tif.save(
+                                np.hstack(
+                                    (im(c=c, t=0).max("z"), jm(c=c, t=0).max("z"))
+                                ),
+                                c,
+                                0,
+                                t,
+                            )
 
     def with_drift(self, im):
-        """ Calculate shifts relative to the first frame
-            divide the sequence into groups,
-            compare each frame to the frame in the middle of the group and compare these middle frames to each other
+        """Calculate shifts relative to the first frame
+        divide the sequence into groups,
+        compare each frame to the frame in the middle of the group and compare these middle frames to each other
         """
-        im = im.transpose('tzycx')
-        t_groups = [list(chunk) for chunk in Chunks(range(im.shape['t']), size=round(np.sqrt(im.shape['t'])))]
+        im = im.transpose("tzycx")
+        t_groups = [
+            list(chunk)
+            for chunk in Chunks(
+                range(im.shape["t"]), size=round(np.sqrt(im.shape["t"]))
+            )
+        ]
         t_keys = [int(np.round(np.mean(t_group))) for t_group in t_groups]
-        t_pairs = [(int(np.round(np.mean(t_group))), frame) for t_group in t_groups for frame in t_group]
+        t_pairs = [
+            (int(np.round(np.mean(t_group))), frame)
+            for t_group in t_groups
+            for frame in t_group
+        ]
         t_pairs.extend(zip(t_keys, t_keys[1:]))
-        fmaxz_keys = {t_key: filters.gaussian(im[t_key].max('z'), 5) for t_key in t_keys}
+        fmaxz_keys = {
+            t_key: filters.gaussian(im[t_key].max("z"), 5) for t_key in t_keys
+        }
 
         def fun(t_key_t, im, fmaxz_keys):
             t_key, t = t_key_t
             if t_key == t:
                 return 0, 0
             else:
-                fmaxz = filters.gaussian(im[t].max('z'), 5)
-                return Transform.register(fmaxz_keys[t_key], fmaxz, 'translation').parameters[4:]
+                fmaxz = filters.gaussian(im[t].max("z"), 5)
+                return Transform.register(
+                    fmaxz_keys[t_key], fmaxz, "translation"
+                ).parameters[4:]
 
-        shifts = np.array(pmap(fun, t_pairs, (im, fmaxz_keys), desc='Calculating image shifts.'))
+        shifts = np.array(
+            pmap(fun, t_pairs, (im, fmaxz_keys), desc="Calculating image shifts.")
+        )
         shift_keys_cum = np.zeros(2)
-        for shift_keys, t_group in zip(np.vstack((-shifts[0], shifts[im.shape['t']:])), t_groups):
+        for shift_keys, t_group in zip(
+            np.vstack((-shifts[0], shifts[im.shape["t"] :])), t_groups
+        ):
             shift_keys_cum += shift_keys
             shifts[t_group] += shift_keys_cum
 
-        for i, shift in enumerate(shifts[:im.shape['t']]):
+        for i, shift in enumerate(shifts[: im.shape["t"]]):
             self[i] = Transform.from_shift(shift)
         return self
 
@@ -257,9 +317,11 @@ class Transform:
         if sitk is None:
             self.transform = None
         else:
-            self.transform = sitk.ReadTransform(str(Path(__file__).parent / 'transform.txt'))
-        self.dparameters = [0., 0., 0., 0., 0., 0.]
-        self.shape = [512., 512.]
+            self.transform = sitk.ReadTransform(
+                str(Path(__file__).parent / "transform.txt")
+            )
+        self.dparameters = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        self.shape = [512.0, 512.0]
         self.origin = [255.5, 255.5]
         self._last, self._inverse = None, None
 
@@ -274,12 +336,14 @@ class Transform:
 
     @classmethod
     def register(cls, fix, mov, kind=None):
-        """ kind: 'affine', 'translation', 'rigid' """
+        """kind: 'affine', 'translation', 'rigid'"""
         if sitk is None:
-            raise ImportError('SimpleElastix is not installed: '
-                              'https://simpleelastix.readthedocs.io/GettingStarted.html')
+            raise ImportError(
+                "SimpleElastix is not installed: "
+                "https://simpleelastix.readthedocs.io/GettingStarted.html"
+            )
         new = cls()
-        kind = kind or 'affine'
+        kind = kind or "affine"
         new.shape = fix.shape
         fix, mov = new.cast_image(fix), new.cast_image(mov)
         # TODO: implement RigidTransform
@@ -290,16 +354,18 @@ class Transform:
         tfilter.SetParameterMap(sitk.GetDefaultParameterMap(kind))
         tfilter.Execute()
         transform = tfilter.GetTransformParameterMap()[0]
-        if kind == 'affine':
-            new.parameters = [float(t) for t in transform['TransformParameters']]
-            new.shape = [float(t) for t in transform['Size']]
-            new.origin = [float(t) for t in transform['CenterOfRotationPoint']]
-        elif kind == 'translation':
-            new.parameters = [1.0, 0.0, 0.0, 1.0] + [float(t) for t in transform['TransformParameters']]
-            new.shape = [float(t) for t in transform['Size']]
+        if kind == "affine":
+            new.parameters = [float(t) for t in transform["TransformParameters"]]
+            new.shape = [float(t) for t in transform["Size"]]
+            new.origin = [float(t) for t in transform["CenterOfRotationPoint"]]
+        elif kind == "translation":
+            new.parameters = [1.0, 0.0, 0.0, 1.0] + [
+                float(t) for t in transform["TransformParameters"]
+            ]
+            new.shape = [float(t) for t in transform["Size"]]
             new.origin = [(t - 1) / 2 for t in new.shape]
         else:
-            raise NotImplementedError(f'{kind} tranforms not implemented (yet)')
+            raise NotImplementedError(f"{kind} tranforms not implemented (yet)")
         new.dparameters = 6 * [np.nan]
         return new
 
@@ -315,16 +381,35 @@ class Transform:
 
     @classmethod
     def from_file(cls, file):
-        with open(Path(file).with_suffix('.yml')) as f:
+        with open(Path(file).with_suffix(".yml")) as f:
             return cls.from_dict(yamlload(f))
 
     @classmethod
     def from_dict(cls, d):
         new = cls()
-        new.origin = [float(i) for i in d['CenterOfRotationPoint']]
-        new.parameters = [float(i) for i in d['TransformParameters']]
-        new.dparameters = [float(i) for i in d['dTransformParameters']] if 'dTransformParameters' in d else 6 * [np.nan]
-        new.shape = [float(i) for i in d['Size']]
+        new.origin = (
+            None
+            if d["CenterOfRotationPoint"] is None
+            else [float(i) for i in d["CenterOfRotationPoint"]]
+        )
+        new.parameters = (
+            (1.0, 0.0, 0.0, 1.0, 0.0, 0.0)
+            if d["TransformParameters"] is None
+            else [float(i) for i in d["TransformParameters"]]
+        )
+        new.dparameters = (
+            [
+                (0.0, 0.0, 0.0, 0.0, 0.0, 0.0) if i is None else float(i)
+                for i in d["dTransformParameters"]
+            ]
+            if "dTransformParameters" in d
+            else 6 * [np.nan] and d["dTransformParameters"] is not None
+        )
+        new.shape = (
+            None
+            if d["Size"] is None
+            else [None if i is None else float(i) for i in d["Size"]]
+        )
         return new
 
     def __mul__(self, other):  # TODO: take care of dmatrix
@@ -357,9 +442,13 @@ class Transform:
 
     @property
     def matrix(self):
-        return np.array(((*self.parameters[:2], self.parameters[4]),
-                         (*self.parameters[2:4], self.parameters[5]),
-                         (0, 0, 1)))
+        return np.array(
+            (
+                (*self.parameters[:2], self.parameters[4]),
+                (*self.parameters[2:4], self.parameters[5]),
+                (0, 0, 1),
+            )
+        )
 
     @matrix.setter
     def matrix(self, value):
@@ -368,9 +457,13 @@ class Transform:
 
     @property
     def dmatrix(self):
-        return np.array(((*self.dparameters[:2], self.dparameters[4]),
-                         (*self.dparameters[2:4], self.dparameters[5]),
-                         (0, 0, 0)))
+        return np.array(
+            (
+                (*self.dparameters[:2], self.dparameters[4]),
+                (*self.dparameters[2:4], self.dparameters[5]),
+                (0, 0, 0),
+            )
+        )
 
     @dmatrix.setter
     def dmatrix(self, value):
@@ -381,6 +474,8 @@ class Transform:
     def parameters(self):
         if self.transform is not None:
             return list(self.transform.GetParameters())
+        else:
+            return [1.0, 0.0, 0.0, 1.0, 0.0, 0.0]
 
     @parameters.setter
     def parameters(self, value):
@@ -416,43 +511,62 @@ class Transform:
         self.shape = shape[:2]
 
     def asdict(self):
-        return {'CenterOfRotationPoint': self.origin, 'Size': self.shape, 'TransformParameters': self.parameters,
-                'dTransformParameters': np.nan_to_num(self.dparameters, nan=1e99).tolist()}
+        return {
+            "CenterOfRotationPoint": self.origin,
+            "Size": self.shape,
+            "TransformParameters": self.parameters,
+            "dTransformParameters": np.nan_to_num(self.dparameters, nan=1e99).tolist(),
+        }
 
     def frame(self, im, default=0):
         if self.is_unity():
             return im
         else:
             if sitk is None:
-                raise ImportError('SimpleElastix is not installed: '
-                                  'https://simpleelastix.readthedocs.io/GettingStarted.html')
+                raise ImportError(
+                    "SimpleElastix is not installed: "
+                    "https://simpleelastix.readthedocs.io/GettingStarted.html"
+                )
             dtype = im.dtype
-            im = im.astype('float')
-            intp = sitk.sitkBSpline if np.issubdtype(dtype, np.floating) else sitk.sitkNearestNeighbor
-            return self.cast_array(sitk.Resample(self.cast_image(im), self.transform, intp, default)).astype(dtype)
+            im = im.astype("float")
+            intp = (
+                sitk.sitkBSpline
+                if np.issubdtype(dtype, np.floating)
+                else sitk.sitkNearestNeighbor
+            )
+            return self.cast_array(
+                sitk.Resample(self.cast_image(im), self.transform, intp, default)
+            ).astype(dtype)
 
     def coords(self, array, columns=None):
-        """ Transform coordinates in 2 column numpy array,
-            or in pandas DataFrame or Series objects in columns ['x', 'y']
+        """Transform coordinates in 2 column numpy array,
+        or in pandas DataFrame or Series objects in columns ['x', 'y']
         """
         if self.is_unity():
             return array.copy()
         elif DataFrame is not None and isinstance(array, (DataFrame, Series)):
-            columns = columns or ['x', 'y']
+            columns = columns or ["x", "y"]
             array = array.copy()
             if isinstance(array, DataFrame):
                 array[columns] = self.coords(np.atleast_2d(array[columns].to_numpy()))
             elif isinstance(array, Series):
-                array[columns] = self.coords(np.atleast_2d(array[columns].to_numpy()))[0]
+                array[columns] = self.coords(np.atleast_2d(array[columns].to_numpy()))[
+                    0
+                ]
             return array
         else:  # somehow we need to use the inverse here to get the same effect as when using self.frame
-            return np.array([self.inverse.transform.TransformPoint(i.tolist()) for i in np.asarray(array)])
+            return np.array(
+                [
+                    self.inverse.transform.TransformPoint(i.tolist())
+                    for i in np.asarray(array)
+                ]
+            )
 
     def save(self, file):
-        """ save the parameters of the transform calculated
-            with affine_registration to a yaml file
+        """save the parameters of the transform calculated
+        with affine_registration to a yaml file
         """
-        if not file[-3:] == 'yml':
-            file += '.yml'
-        with open(file, 'w') as f:
+        if not file[-3:] == "yml":
+            file += ".yml"
+        with open(file, "w") as f:
             yaml.safe_dump(self.asdict(), f, default_flow_style=None)

pyproject.toml

@@ -1,54 +1,56 @@
-[tool.poetry]
+[build-system]
+requires = ["maturin>=1.8,<2.0"]
+build-backend = "maturin"
+
+[project]
 name = "ndbioimage"
-version = "2025.1.2"
 description = "Bio image reading, metadata and some affine registration."
-authors = ["W. Pomp <w.pomp@nki.nl>"]
-license = "GPLv3"
+authors = [
+    { name = "W. Pomp", email = "w.pomp@nki.nl" }
+]
+license = "MIT"
 readme = "README.md"
 keywords = ["bioformats", "imread", "numpy", "metadata"]
-include = ["transform.txt"]
-repository = "https://github.com/wimpomp/ndbioimage"
-exclude = ["ndbioimage/jars"]
-
-[tool.poetry.dependencies]
-python = "^3.10"
-numpy = ">=1.20.0"
-pandas = "*"
-tifffile = "*"
-czifile = "2019.7.2"
-tiffwrite = ">=2024.12.1"
-ome-types = ">=0.4.0"
-pint = "*"
-tqdm = "*"
-lxml = "*"
-pyyaml = "*"
-parfor = ">=2025.1.0"
-JPype1 = "*"
-SimpleITK-SimpleElastix = [
-    { version = "*", python = "<3.12" },
-    { version = "*", python = ">=3.12", markers = "sys_platform != 'darwin'" },
-    { version = "*", python = ">=3.12", markers = "platform_machine == 'aarch64'" },
+requires-python = ">=3.10"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Rust",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+]
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "tiffwrite",
+    "ome-metadata >= 0.2.1",
+    "tqdm",
 ]
-scikit-image = "*"
-imagecodecs = "*"
-xsdata = "^23"  # until pydantic is up-to-date
-matplotlib = { version = "*", optional = true }
-scikit-video = { version = "*", optional = true }
-pytest = { version = "*", optional = true }
 
-[tool.poetry.extras]
+[project.optional-dependencies]
 test = ["pytest"]
 write = ["matplotlib", "scikit-video"]
 
-[tool.poetry.scripts]
+[project.urls]
+Repository = "https://github.com/wimpomp/ndbioimage/tree/rs"
+
+[project.scripts]
 ndbioimage = "ndbioimage:main"
 
 [tool.pytest.ini_options]
 filterwarnings = ["ignore:::(colorcet)"]
 
+[tool.maturin]
+python-source = "py"
+features = ["pyo3/extension-module", "python", "gpl-formats"]
+module-name = "ndbioimage.ndbioimage_rs"
+exclude = ["py/ndbioimage/jassets/*", "py/ndbioimage/deps/*"]
+strip = true
+
 [tool.isort]
 line_length = 119
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"

src/axes.rs

@@ -0,0 +1,251 @@
+use crate::error::Error;
+use crate::stats::MinMax;
+use ndarray::{Array, Dimension, Ix2, SliceInfo, SliceInfoElem};
+use serde::{Deserialize, Deserializer, Serialize, Serializer};
+use serde_with::{DeserializeAs, SerializeAs};
+use std::fmt::{Display, Formatter};
+use std::hash::{Hash, Hasher};
+use std::str::FromStr;
+
+/// a trait to find axis indices from any object
+pub trait Ax {
+    /// C: 0, Z: 1, T: 2, Y: 3, X: 4
+    fn n(&self) -> usize;
+
+    /// the indices of axes in self.axes, which always has all of CZTYX
+    fn pos(&self, axes: &[Axis], slice: &[SliceInfoElem]) -> Result<usize, Error>;
+
+    /// the indices of axes in self.axes, which always has all of CZTYX, but skip axes with an operation
+    fn pos_op(
+        &self,
+        axes: &[Axis],
+        slice: &[SliceInfoElem],
+        op_axes: &[Axis],
+    ) -> Result<usize, Error>;
+}
+
+/// Enum for CZTYX axes or a new axis
+#[derive(Clone, Copy, Debug, Eq, Ord, PartialOrd, Serialize, Deserialize)]
+pub enum Axis {
+    C,
+    Z,
+    T,
+    Y,
+    X,
+    New,
+}
+
+impl Hash for Axis {
+    fn hash<H: Hasher>(&self, state: &mut H) {
+        (*self as usize).hash(state);
+    }
+}
+
+impl FromStr for Axis {
+    type Err = Error;
+
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        match s.to_uppercase().as_str() {
+            "C" => Ok(Axis::C),
+            "Z" => Ok(Axis::Z),
+            "T" => Ok(Axis::T),
+            "Y" => Ok(Axis::Y),
+            "X" => Ok(Axis::X),
+            "NEW" => Ok(Axis::New),
+            _ => Err(Error::InvalidAxis(s.to_string())),
+        }
+    }
+}
+
+impl Display for Axis {
+    fn fmt(&self, f: &mut Formatter<'_>) -> std::fmt::Result {
+        let s = match self {
+            Axis::C => "C",
+            Axis::Z => "Z",
+            Axis::T => "T",
+            Axis::Y => "Y",
+            Axis::X => "X",
+            Axis::New => "N",
+        };
+        write!(f, "{}", s)
+    }
+}
+
+impl Ax for Axis {
+    fn n(&self) -> usize {
+        *self as usize
+    }
+
+    fn pos(&self, axes: &[Axis], _slice: &[SliceInfoElem]) -> Result<usize, Error> {
+        if let Some(pos) = axes.iter().position(|a| a == self) {
+            Ok(pos)
+        } else {
+            Err(Error::AxisNotFound(
+                format!("{:?}", self),
+                format!("{:?}", axes),
+            ))
+        }
+    }
+
+    fn pos_op(
+        &self,
+        axes: &[Axis],
+        _slice: &[SliceInfoElem],
+        _op_axes: &[Axis],
+    ) -> Result<usize, Error> {
+        self.pos(axes, _slice)
+    }
+}
+
+impl Ax for usize {
+    fn n(&self) -> usize {
+        *self
+    }
+
+    fn pos(&self, _axes: &[Axis], slice: &[SliceInfoElem]) -> Result<usize, Error> {
+        let idx: Vec<_> = slice
+            .iter()
+            .enumerate()
+            .filter_map(|(i, s)| if s.is_index() { None } else { Some(i) })
+            .collect();
+        Ok(idx[*self])
+    }
+
+    fn pos_op(
+        &self,
+        axes: &[Axis],
+        slice: &[SliceInfoElem],
+        op_axes: &[Axis],
+    ) -> Result<usize, Error> {
+        let idx: Vec<_> = axes
+            .iter()
+            .zip(slice.iter())
+            .enumerate()
+            .filter_map(|(i, (ax, s))| {
+                if s.is_index() | op_axes.contains(ax) {
+                    None
+                } else {
+                    Some(i)
+                }
+            })
+            .collect();
+        debug_assert!(*self < idx.len(), "self: {}, idx: {:?}", self, idx);
+        Ok(idx[*self])
+    }
+}
+
+#[derive(Clone, Debug, Serialize, Deserialize)]
+pub(crate) enum Operation {
+    Max,
+    Min,
+    Sum,
+    Mean,
+}
+
+impl Operation {
+    pub(crate) fn operate<T, D>(
+        &self,
+        array: Array<T, D>,
+        axis: usize,
+    ) -> Result<<Array<T, D> as MinMax>::Output, Error>
+    where
+        D: Dimension,
+        Array<T, D>: MinMax,
+    {
+        match self {
+            Operation::Max => array.max(axis),
+            Operation::Min => array.min(axis),
+            Operation::Sum => array.sum(axis),
+            Operation::Mean => array.mean(axis),
+        }
+    }
+}
+
+impl PartialEq for Axis {
+    fn eq(&self, other: &Self) -> bool {
+        (*self as u8) == (*other as u8)
+    }
+}
+
+pub(crate) fn slice_info<D: Dimension>(
+    info: &[SliceInfoElem],
+) -> Result<SliceInfo<&[SliceInfoElem], Ix2, D>, Error> {
+    match info.try_into() {
+        Ok(slice) => Ok(slice),
+        Err(err) => Err(Error::TryInto(err.to_string())),
+    }
+}
+
+#[derive(Serialize, Deserialize)]
+#[serde(remote = "SliceInfoElem")]
+pub(crate) enum SliceInfoElemDef {
+    Slice {
+        start: isize,
+        end: Option<isize>,
+        step: isize,
+    },
+    Index(isize),
+    NewAxis,
+}
+
+impl SerializeAs<SliceInfoElem> for SliceInfoElemDef {
+    fn serialize_as<S>(source: &SliceInfoElem, serializer: S) -> Result<S::Ok, S::Error>
+    where
+        S: Serializer,
+    {
+        SliceInfoElemDef::serialize(source, serializer)
+    }
+}
+
+impl<'de> DeserializeAs<'de, SliceInfoElem> for SliceInfoElemDef {
+    fn deserialize_as<D>(deserializer: D) -> Result<SliceInfoElem, D::Error>
+    where
+        D: Deserializer<'de>,
+    {
+        SliceInfoElemDef::deserialize(deserializer)
+    }
+}
+
+#[derive(Clone, Debug)]
+pub(crate) struct Slice {
+    start: isize,
+    end: isize,
+    step: isize,
+}
+
+impl Slice {
+    pub(crate) fn new(start: isize, end: isize, step: isize) -> Self {
+        Self { start, end, step }
+    }
+
+    pub(crate) fn empty() -> Self {
+        Self {
+            start: 0,
+            end: 0,
+            step: 1,
+        }
+    }
+}
+
+impl Iterator for Slice {
+    type Item = isize;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        if self.end - self.start >= self.step {
+            let r = self.start;
+            self.start += self.step;
+            Some(r)
+        } else {
+            None
+        }
+    }
+}
+
+impl IntoIterator for &Slice {
+    type Item = isize;
+    type IntoIter = Slice;
+
+    fn into_iter(self) -> Self::IntoIter {
+        self.clone()
+    }
+}

src/bioformats.rs

@@ -0,0 +1,230 @@
+use crate::error::Error;
+use j4rs::{Instance, InvocationArg, Jvm, JvmBuilder};
+use std::cell::OnceCell;
+use std::rc::Rc;
+
+thread_local! {
+    static JVM: OnceCell<Rc<Jvm>> = const { OnceCell::new() }
+}
+
+/// Ensure 1 jvm per thread
+fn jvm() -> Rc<Jvm> {
+    JVM.with(|cell| {
+        cell.get_or_init(move || {
+            #[cfg(feature = "python")]
+            let path = crate::py::ndbioimage_file();
+
+            #[cfg(not(feature = "python"))]
+            let path = std::env::current_exe()
+                .unwrap()
+                .parent()
+                .unwrap()
+                .to_path_buf();
+
+            let class_path = if path.join("jassets").exists() {
+                path.as_path()
+            } else {
+                path.parent().unwrap()
+            };
+            if !class_path.join("jassets").exists() {
+                panic!(
+                    "jassets directory does not exist in {}",
+                    class_path.display()
+                );
+            }
+
+            Rc::new(
+                JvmBuilder::new()
+                    .skip_setting_native_lib()
+                    .with_base_path(class_path.to_str().unwrap())
+                    .build()
+                    .expect("Failed to build JVM"),
+            )
+        })
+        .clone()
+    })
+}
+
+pub fn download_bioformats(gpl_formats: bool) -> Result<(), Error> {
+    #[cfg(feature = "python")]
+    let path = crate::py::ndbioimage_file();
+
+    #[cfg(not(feature = "python"))]
+    let path = std::env::current_exe()?.parent().unwrap().to_path_buf();
+
+    let class_path = path.parent().unwrap();
+    let jassets = class_path.join("jassets");
+    if !jassets.exists() {
+        std::fs::create_dir_all(jassets)?;
+    }
+    println!("installing jassets in {}", class_path.display());
+    let jvm = JvmBuilder::new()
+        .skip_setting_native_lib()
+        .with_base_path(class_path.to_str().unwrap())
+        .with_maven_settings(j4rs::MavenSettings::new(vec![
+            j4rs::MavenArtifactRepo::from(
+                "openmicroscopy::https://artifacts.openmicroscopy.org/artifactory/ome.releases",
+            ),
+        ]))
+        .build()?;
+
+    jvm.deploy_artifact(&j4rs::MavenArtifact::from("ome:bioformats_package:8.3.0"))?;
+
+    if gpl_formats {
+        jvm.deploy_artifact(&j4rs::MavenArtifact::from("ome:formats-gpl:8.3.0"))?;
+    }
+
+    Ok(())
+}
+
+macro_rules! method_return {
+    ($R:ty$(|c)?) => { Result<$R, Error> };
+    () => { Result<(), Error> };
+}
+
+macro_rules! method_arg {
+    ($n:tt: $t:ty|p) => {
+        InvocationArg::try_from($n)?.into_primitive()?
+    };
+    ($n:tt: $t:ty) => {
+        InvocationArg::try_from($n)?
+    };
+}
+
+macro_rules! method {
+    ($name:ident, $method:expr $(,[$($n:tt: $t:ty$(|$p:tt)?),*])? $(=> $tt:ty$(|$c:tt)?)?) => {
+        #[allow(dead_code)]
+        pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
+            let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?];
+            let _result = jvm().invoke(&self.0, $method, &args)?;
+
+            macro_rules! method_result {
+                ($R:ty|c) => {
+                    Ok(jvm().to_rust(_result)?)
+                };
+                ($R:ty|d) => {
+                    Ok(jvm().to_rust_deserialized(_result)?)
+                };
+                ($R:ty) => {
+                    Ok(_result)
+                };
+                () => {
+                    Ok(())
+                };
+            }
+
+            method_result!($($tt$(|$c)?)?)
+        }
+    };
+}
+
+fn transmute_vec<T, U>(vec: Vec<T>) -> Vec<U> {
+    unsafe {
+        // Ensure the original vector is not dropped.
+        let mut v_clone = std::mem::ManuallyDrop::new(vec);
+        Vec::from_raw_parts(
+            v_clone.as_mut_ptr() as *mut U,
+            v_clone.len(),
+            v_clone.capacity(),
+        )
+    }
+}
+
+/// Wrapper around bioformats java class loci.common.DebugTools
+pub struct DebugTools;
+
+impl DebugTools {
+    /// set debug root level: ERROR, DEBUG, TRACE, INFO, OFF
+    pub fn set_root_level(level: &str) -> Result<(), Error> {
+        jvm().invoke_static(
+            "loci.common.DebugTools",
+            "setRootLevel",
+            &[InvocationArg::try_from(level)?],
+        )?;
+        Ok(())
+    }
+}
+
+/// Wrapper around bioformats java class loci.formats.ChannelSeparator
+pub(crate) struct ChannelSeparator(Instance);
+
+impl ChannelSeparator {
+    pub(crate) fn new(image_reader: &ImageReader) -> Result<Self, Error> {
+        let jvm = jvm();
+        let channel_separator = jvm.create_instance(
+            "loci.formats.ChannelSeparator",
+            &[InvocationArg::from(jvm.clone_instance(&image_reader.0)?)],
+        )?;
+        Ok(ChannelSeparator(channel_separator))
+    }
+
+    pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>, Error> {
+        Ok(transmute_vec(self.open_bi8(index)?))
+    }
+
+    method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
+    method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
+}
+
+/// Wrapper around bioformats java class loci.formats.ImageReader
+pub struct ImageReader(Instance);
+
+impl Drop for ImageReader {
+    fn drop(&mut self) {
+        self.close().unwrap()
+    }
+}
+
+impl ImageReader {
+    pub(crate) fn new() -> Result<Self, Error> {
+        let reader = jvm().create_instance("loci.formats.ImageReader", InvocationArg::empty())?;
+        Ok(ImageReader(reader))
+    }
+
+    pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>, Error> {
+        Ok(transmute_vec(self.open_bi8(index)?))
+    }
+
+    pub(crate) fn ome_xml(&self) -> Result<String, Error> {
+        let mds = self.get_metadata_store()?;
+        Ok(jvm()
+            .chain(&mds)?
+            .cast("loci.formats.ome.OMEPyramidStore")?
+            .invoke("dumpXML", InvocationArg::empty())?
+            .to_rust()?)
+    }
+
+    method!(set_metadata_store, "setMetadataStore", [ome_data: Instance]);
+    method!(get_metadata_store, "getMetadataStore" => Instance);
+    method!(set_id, "setId", [id: &str]);
+    method!(set_series, "setSeries", [series: i32|p]);
+    method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
+    method!(get_size_x, "getSizeX" => i32|c);
+    method!(get_size_y, "getSizeY" => i32|c);
+    method!(get_size_c, "getSizeC" => i32|c);
+    method!(get_size_t, "getSizeT" => i32|c);
+    method!(get_size_z, "getSizeZ" => i32|c);
+    method!(get_pixel_type, "getPixelType" => i32|c);
+    method!(is_little_endian, "isLittleEndian" => bool|c);
+    method!(is_rgb, "isRGB" => bool|c);
+    method!(is_interleaved, "isInterleaved" => bool|c);
+    method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
+    method!(get_rgb_channel_count, "getRGBChannelCount" => i32|c);
+    method!(is_indexed, "isIndexed" => bool|c);
+    method!(get_8bit_lookup_table, "get8BitLookupTable" => Instance);
+    method!(get_16bit_lookup_table, "get16BitLookupTable" => Instance);
+    method!(close, "close");
+}
+
+/// Wrapper around bioformats java class loci.formats.MetadataTools
+pub(crate) struct MetadataTools(Instance);
+
+impl MetadataTools {
+    pub(crate) fn new() -> Result<Self, Error> {
+        let meta_data_tools =
+            jvm().create_instance("loci.formats.MetadataTools", InvocationArg::empty())?;
+        Ok(MetadataTools(meta_data_tools))
+    }
+
+    method!(create_ome_xml_metadata, "createOMEXMLMetadata" => Instance);
+}

src/colors.rs

@@ -0,0 +1,207 @@
+use crate::error::Error;
+use lazy_static::lazy_static;
+use std::collections::HashMap;
+use std::fmt::Display;
+use std::str::FromStr;
+
+lazy_static! {
+    static ref COLORS: HashMap<String, String> = {
+        HashMap::from([
+            ("b".to_string(), "#0000FF".to_string()),
+            ("g".to_string(), "#008000".to_string()),
+            ("r".to_string(), "#FF0000".to_string()),
+            ("c".to_string(), "#00BFBF".to_string()),
+            ("m".to_string(), "#BF00BF".to_string()),
+            ("y".to_string(), "#BFBF00".to_string()),
+            ("k".to_string(), "#000000".to_string()),
+            ("w".to_string(), "#FFFFFF".to_string()),
+            ("aliceblue".to_string(), "#F0F8FF".to_string()),
+            ("antiquewhite".to_string(), "#FAEBD7".to_string()),
+            ("aqua".to_string(), "#00FFFF".to_string()),
+            ("aquamarine".to_string(), "#7FFFD4".to_string()),
+            ("azure".to_string(), "#F0FFFF".to_string()),
+            ("beige".to_string(), "#F5F5DC".to_string()),
+            ("bisque".to_string(), "#FFE4C4".to_string()),
+            ("black".to_string(), "#000000".to_string()),
+            ("blanchedalmond".to_string(), "#FFEBCD".to_string()),
+            ("blue".to_string(), "#0000FF".to_string()),
+            ("blueviolet".to_string(), "#8A2BE2".to_string()),
+            ("brown".to_string(), "#A52A2A".to_string()),
+            ("burlywood".to_string(), "#DEB887".to_string()),
+            ("cadetblue".to_string(), "#5F9EA0".to_string()),
+            ("chartreuse".to_string(), "#7FFF00".to_string()),
+            ("chocolate".to_string(), "#D2691E".to_string()),
+            ("coral".to_string(), "#FF7F50".to_string()),
+            ("cornflowerblue".to_string(), "#6495ED".to_string()),
+            ("cornsilk".to_string(), "#FFF8DC".to_string()),
+            ("crimson".to_string(), "#DC143C".to_string()),
+            ("cyan".to_string(), "#00FFFF".to_string()),
+            ("darkblue".to_string(), "#00008B".to_string()),
+            ("darkcyan".to_string(), "#008B8B".to_string()),
+            ("darkgoldenrod".to_string(), "#B8860B".to_string()),
+            ("darkgray".to_string(), "#A9A9A9".to_string()),
+            ("darkgreen".to_string(), "#006400".to_string()),
+            ("darkgrey".to_string(), "#A9A9A9".to_string()),
+            ("darkkhaki".to_string(), "#BDB76B".to_string()),
+            ("darkmagenta".to_string(), "#8B008B".to_string()),
+            ("darkolivegreen".to_string(), "#556B2F".to_string()),
+            ("darkorange".to_string(), "#FF8C00".to_string()),
+            ("darkorchid".to_string(), "#9932CC".to_string()),
+            ("darkred".to_string(), "#8B0000".to_string()),
+            ("darksalmon".to_string(), "#E9967A".to_string()),
+            ("darkseagreen".to_string(), "#8FBC8F".to_string()),
+            ("darkslateblue".to_string(), "#483D8B".to_string()),
+            ("darkslategray".to_string(), "#2F4F4F".to_string()),
+            ("darkslategrey".to_string(), "#2F4F4F".to_string()),
+            ("darkturquoise".to_string(), "#00CED1".to_string()),
+            ("darkviolet".to_string(), "#9400D3".to_string()),
+            ("deeppink".to_string(), "#FF1493".to_string()),
+            ("deepskyblue".to_string(), "#00BFFF".to_string()),
+            ("dimgray".to_string(), "#696969".to_string()),
+            ("dimgrey".to_string(), "#696969".to_string()),
+            ("dodgerblue".to_string(), "#1E90FF".to_string()),
+            ("firebrick".to_string(), "#B22222".to_string()),
+            ("floralwhite".to_string(), "#FFFAF0".to_string()),
+            ("forestgreen".to_string(), "#228B22".to_string()),
+            ("fuchsia".to_string(), "#FF00FF".to_string()),
+            ("gainsboro".to_string(), "#DCDCDC".to_string()),
+            ("ghostwhite".to_string(), "#F8F8FF".to_string()),
+            ("gold".to_string(), "#FFD700".to_string()),
+            ("goldenrod".to_string(), "#DAA520".to_string()),
+            ("gray".to_string(), "#808080".to_string()),
+            ("green".to_string(), "#008000".to_string()),
+            ("greenyellow".to_string(), "#ADFF2F".to_string()),
+            ("grey".to_string(), "#808080".to_string()),
+            ("honeydew".to_string(), "#F0FFF0".to_string()),
+            ("hotpink".to_string(), "#FF69B4".to_string()),
+            ("indianred".to_string(), "#CD5C5C".to_string()),
+            ("indigo".to_string(), "#4B0082".to_string()),
+            ("ivory".to_string(), "#FFFFF0".to_string()),
+            ("khaki".to_string(), "#F0E68C".to_string()),
+            ("lavender".to_string(), "#E6E6FA".to_string()),
+            ("lavenderblush".to_string(), "#FFF0F5".to_string()),
+            ("lawngreen".to_string(), "#7CFC00".to_string()),
+            ("lemonchiffon".to_string(), "#FFFACD".to_string()),
+            ("lightblue".to_string(), "#ADD8E6".to_string()),
+            ("lightcoral".to_string(), "#F08080".to_string()),
+            ("lightcyan".to_string(), "#E0FFFF".to_string()),
+            ("lightgoldenrodyellow".to_string(), "#FAFAD2".to_string()),
+            ("lightgray".to_string(), "#D3D3D3".to_string()),
+            ("lightgreen".to_string(), "#90EE90".to_string()),
+            ("lightgrey".to_string(), "#D3D3D3".to_string()),
+            ("lightpink".to_string(), "#FFB6C1".to_string()),
+            ("lightsalmon".to_string(), "#FFA07A".to_string()),
+            ("lightseagreen".to_string(), "#20B2AA".to_string()),
+            ("lightskyblue".to_string(), "#87CEFA".to_string()),
+            ("lightslategray".to_string(), "#778899".to_string()),
+            ("lightslategrey".to_string(), "#778899".to_string()),
+            ("lightsteelblue".to_string(), "#B0C4DE".to_string()),
+            ("lightyellow".to_string(), "#FFFFE0".to_string()),
+            ("lime".to_string(), "#00FF00".to_string()),
+            ("limegreen".to_string(), "#32CD32".to_string()),
+            ("linen".to_string(), "#FAF0E6".to_string()),
+            ("magenta".to_string(), "#FF00FF".to_string()),
+            ("maroon".to_string(), "#800000".to_string()),
+            ("mediumaquamarine".to_string(), "#66CDAA".to_string()),
+            ("mediumblue".to_string(), "#0000CD".to_string()),
+            ("mediumorchid".to_string(), "#BA55D3".to_string()),
+            ("mediumpurple".to_string(), "#9370DB".to_string()),
+            ("mediumseagreen".to_string(), "#3CB371".to_string()),
+            ("mediumslateblue".to_string(), "#7B68EE".to_string()),
+            ("mediumspringgreen".to_string(), "#00FA9A".to_string()),
+            ("mediumturquoise".to_string(), "#48D1CC".to_string()),
+            ("mediumvioletred".to_string(), "#C71585".to_string()),
+            ("midnightblue".to_string(), "#191970".to_string()),
+            ("mintcream".to_string(), "#F5FFFA".to_string()),
+            ("mistyrose".to_string(), "#FFE4E1".to_string()),
+            ("moccasin".to_string(), "#FFE4B5".to_string()),
+            ("navajowhite".to_string(), "#FFDEAD".to_string()),
+            ("navy".to_string(), "#000080".to_string()),
+            ("oldlace".to_string(), "#FDF5E6".to_string()),
+            ("olive".to_string(), "#808000".to_string()),
+            ("olivedrab".to_string(), "#6B8E23".to_string()),
+            ("orange".to_string(), "#FFA500".to_string()),
+            ("orangered".to_string(), "#FF4500".to_string()),
+            ("orchid".to_string(), "#DA70D6".to_string()),
+            ("palegoldenrod".to_string(), "#EEE8AA".to_string()),
+            ("palegreen".to_string(), "#98FB98".to_string()),
+            ("paleturquoise".to_string(), "#AFEEEE".to_string()),
+            ("palevioletred".to_string(), "#DB7093".to_string()),
+            ("papayawhip".to_string(), "#FFEFD5".to_string()),
+            ("peachpuff".to_string(), "#FFDAB9".to_string()),
+            ("peru".to_string(), "#CD853F".to_string()),
+            ("pink".to_string(), "#FFC0CB".to_string()),
+            ("plum".to_string(), "#DDA0DD".to_string()),
+            ("powderblue".to_string(), "#B0E0E6".to_string()),
+            ("purple".to_string(), "#800080".to_string()),
+            ("rebeccapurple".to_string(), "#663399".to_string()),
+            ("red".to_string(), "#FF0000".to_string()),
+            ("rosybrown".to_string(), "#BC8F8F".to_string()),
+            ("royalblue".to_string(), "#4169E1".to_string()),
+            ("saddlebrown".to_string(), "#8B4513".to_string()),
+            ("salmon".to_string(), "#FA8072".to_string()),
+            ("sandybrown".to_string(), "#F4A460".to_string()),
+            ("seagreen".to_string(), "#2E8B57".to_string()),
+            ("seashell".to_string(), "#FFF5EE".to_string()),
+            ("sienna".to_string(), "#A0522D".to_string()),
+            ("silver".to_string(), "#C0C0C0".to_string()),
+            ("skyblue".to_string(), "#87CEEB".to_string()),
+            ("slateblue".to_string(), "#6A5ACD".to_string()),
+            ("slategray".to_string(), "#708090".to_string()),
+            ("slategrey".to_string(), "#708090".to_string()),
+            ("snow".to_string(), "#FFFAFA".to_string()),
+            ("springgreen".to_string(), "#00FF7F".to_string()),
+            ("steelblue".to_string(), "#4682B4".to_string()),
+            ("tan".to_string(), "#D2B48C".to_string()),
+            ("teal".to_string(), "#008080".to_string()),
+            ("thistle".to_string(), "#D8BFD8".to_string()),
+            ("tomato".to_string(), "#FF6347".to_string()),
+            ("turquoise".to_string(), "#40E0D0".to_string()),
+            ("violet".to_string(), "#EE82EE".to_string()),
+            ("wheat".to_string(), "#F5DEB3".to_string()),
+            ("white".to_string(), "#FFFFFF".to_string()),
+            ("whitesmoke".to_string(), "#F5F5F5".to_string()),
+            ("yellow".to_string(), "#FFFF00".to_string()),
+            ("yellowgreen".to_string(), "#9ACD32".to_string()),
+        ])
+    };
+}
+
+#[derive(Clone, Debug)]
+pub struct Color {
+    r: u8,
+    g: u8,
+    b: u8,
+}
+
+impl FromStr for Color {
+    type Err = Error;
+
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        let s = if !s.starts_with("#") {
+            if let Some(s) = COLORS.get(s) {
+                s
+            } else {
+                return Err(Error::InvalidColor(s.to_string()));
+            }
+        } else {
+            s
+        };
+        let r = u8::from_str_radix(&s[1..3], 16)?;
+        let g = u8::from_str_radix(&s[3..5], 16)?;
+        let b = u8::from_str_radix(&s[5..], 16)?;
+        Ok(Self { r, g, b })
+    }
+}
+
+impl Display for Color {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        write!(f, "#{:02X}{:02X}{:02X}", self.r, self.g, self.b)
+    }
+}
+
+impl Color {
+    pub fn to_rgb(&self) -> Vec<u8> {
+        vec![self.r, self.g, self.b]
+    }
+}

src/error.rs

@@ -0,0 +1,65 @@
+use thiserror::Error;
+
+#[derive(Debug, Error)]
+pub enum Error {
+    #[error(transparent)]
+    IO(#[from] std::io::Error),
+    #[error(transparent)]
+    Shape(#[from] ndarray::ShapeError),
+    #[error(transparent)]
+    J4rs(#[from] j4rs::errors::J4RsError),
+    #[error(transparent)]
+    Infallible(#[from] std::convert::Infallible),
+    #[error(transparent)]
+    ParseIntError(#[from] std::num::ParseIntError),
+    #[error(transparent)]
+    Ome(#[from] ome_metadata::error::Error),
+    #[cfg(feature = "tiff")]
+    #[error(transparent)]
+    TemplateError(#[from] indicatif::style::TemplateError),
+    #[cfg(feature = "tiff")]
+    #[error(transparent)]
+    TiffWrite(#[from] tiffwrite::error::Error),
+    #[error("invalid axis: {0}")]
+    InvalidAxis(String),
+    #[error("axis {0} not found in axes {1}")]
+    AxisNotFound(String, String),
+    #[error("conversion error: {0}")]
+    TryInto(String),
+    #[error("file already exists {0}")]
+    FileAlreadyExists(String),
+    #[error("could not download ffmpeg: {0}")]
+    Ffmpeg(String),
+    #[error("index {0} out of bounds {1}")]
+    OutOfBounds(isize, isize),
+    #[error("axis {0} has length {1}, but was not included")]
+    OutOfBoundsAxis(String, usize),
+    #[error("dimensionality mismatch: {0} != {0}")]
+    DimensionalityMismatch(usize, usize),
+    #[error("axis {0}: {1} is already operated on!")]
+    AxisAlreadyOperated(usize, String),
+    #[error("not enough free dimensions")]
+    NotEnoughFreeDimensions,
+    #[error("cannot cast {0} to {1}")]
+    Cast(String, String),
+    #[error("empty view")]
+    EmptyView,
+    #[error("invalid color: {0}")]
+    InvalidColor(String),
+    #[error("no image or pixels found")]
+    NoImageOrPixels,
+    #[error("invalid attenuation value: {0}")]
+    InvalidAttenuation(String),
+    #[error("not a valid file name")]
+    InvalidFileName,
+    #[error("unknown pixel type {0}")]
+    UnknownPixelType(String),
+    #[error("no mean")]
+    NoMean,
+    #[error("tiff is locked")]
+    TiffLock,
+    #[error("not implemented: {0}")]
+    NotImplemented(String),
+    #[error("cannot parse: {0}")]
+    Parse(String),
+}

src/lib.rs

@@ -0,0 +1,414 @@
+#![cfg_attr(docsrs, feature(doc_auto_cfg))]
+
+mod bioformats;
+
+pub mod axes;
+pub mod metadata;
+#[cfg(feature = "python")]
+mod py;
+pub mod reader;
+pub mod stats;
+pub mod view;
+
+pub mod colors;
+pub mod error;
+#[cfg(feature = "movie")]
+pub mod movie;
+#[cfg(feature = "tiff")]
+pub mod tiff;
+
+pub use bioformats::download_bioformats;
+
+#[cfg(test)]
+mod tests {
+    use crate::axes::Axis;
+    use crate::error::Error;
+    use crate::reader::{Frame, Reader};
+    use crate::stats::MinMax;
+    use crate::view::Item;
+    use downloader::{Download, Downloader};
+    use ndarray::{Array, Array4, Array5, NewAxis};
+    use ndarray::{Array2, s};
+    use rayon::prelude::*;
+
+    fn open(file: &str) -> Result<Reader, Error> {
+        let path = std::env::current_dir()?
+            .join("tests")
+            .join("files")
+            .join(file);
+        Reader::new(&path, 0)
+    }
+
+    #[test]
+    fn read_ome() -> Result<(), Box<dyn std::error::Error>> {
+        let path = std::env::current_dir()?.join("tests/files/ome");
+        std::fs::create_dir_all(&path)?;
+        let url =
+            "https://downloads.openmicroscopy.org/images/OME-TIFF/2016-06/bioformats-artificial/";
+        let page = reqwest::blocking::get(url)?.text()?;
+        let pat = regex::Regex::new(
+            r#"<a\s+href\s*=\s*"([^"<>]+)">[^<>]+</a>\s+\d{2}-\w{3}-\d{4}\s+\d{2}:\d{2}\s+(\d+)"#,
+        )?;
+        let mut downloads = Vec::new();
+        let mut files = Vec::new();
+        for line in page.lines() {
+            if let Some(cap) = pat.captures(line) {
+                let link = cap[1].trim().to_string();
+                let size = cap[2].trim().parse::<usize>()?;
+                if size < 10 * 1024usize.pow(2) {
+                    if !path.join(&link).exists() {
+                        downloads.push(Download::new(&format!("{}{}", url, link)));
+                    }
+                    files.push(path.join(link));
+                }
+            }
+        }
+        if !downloads.is_empty() {
+            let mut downloader = Downloader::builder().download_folder(&path).build()?;
+            downloader.download(&downloads)?;
+        }
+        let mut count = 0;
+        for file in files {
+            if let Ok(reader) = Reader::new(&file, 0) {
+                let _ome = reader.get_ome()?;
+                count += 1;
+            }
+        }
+        println!("count: {}", count);
+        assert!(count > 30);
+        Ok(())
+    }
+
+    fn get_pixel_type(file: &str) -> Result<String, Error> {
+        let reader = open(file)?;
+        Ok(format!(
+            "file: {}, pixel type: {:?}",
+            file, reader.pixel_type
+        ))
+    }
+
+    fn get_frame(file: &str) -> Result<Frame, Error> {
+        let reader = open(file)?;
+        reader.get_frame(0, 0, 0)
+    }
+
+    #[test]
+    fn read_ser() -> Result<(), Error> {
+        let file = "Experiment-2029.czi";
+        let reader = open(file)?;
+        println!("size: {}, {}", reader.size_y, reader.size_y);
+        let frame = reader.get_frame(0, 0, 0)?;
+        if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
+            println!("{:?}", arr);
+        } else {
+            println!("could not convert Frame to Array<i8>");
+        }
+        Ok(())
+    }
+
+    #[test]
+    fn read_par() -> Result<(), Error> {
+        let files = vec!["Experiment-2029.czi", "test.tif"];
+        let pixel_type = files
+            .into_par_iter()
+            .map(|file| get_pixel_type(file).unwrap())
+            .collect::<Vec<_>>();
+        println!("{:?}", pixel_type);
+        Ok(())
+    }
+
+    #[test]
+    fn read_frame_par() -> Result<(), Error> {
+        let files = vec!["Experiment-2029.czi", "test.tif"];
+        let frames = files
+            .into_par_iter()
+            .map(|file| get_frame(file).unwrap())
+            .collect::<Vec<_>>();
+        println!("{:?}", frames);
+        Ok(())
+    }
+
+    #[test]
+    fn read_sequence() -> Result<(), Error> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        println!("reader: {:?}", reader);
+        let frame = reader.get_frame(0, 4, 0)?;
+        println!("frame: {:?}", frame);
+        let frame = reader.get_frame(0, 2, 0)?;
+        println!("frame: {:?}", frame);
+        Ok(())
+    }
+
+    #[test]
+    fn read_sequence1() -> Result<(), Error> {
+        let file = "4-Pos_001_002/img_000000000_Cy3-Cy3_filter_000.tif";
+        let reader = open(file)?;
+        println!("reader: {:?}", reader);
+        Ok(())
+    }
+
+    #[test]
+    fn ome_xml() -> Result<(), Error> {
+        let file = "Experiment-2029.czi";
+        let reader = open(file)?;
+        let xml = reader.get_ome_xml()?;
+        println!("{}", xml);
+        Ok(())
+    }
+
+    #[test]
+    fn view() -> Result<(), Error> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        let view = reader.view();
+        let a = view.slice(s![0, 5, 0, .., ..])?;
+        let b = reader.get_frame(0, 5, 0)?;
+        let c: Array2<isize> = a.try_into()?;
+        let d: Array2<isize> = b.try_into()?;
+        assert_eq!(c, d);
+        Ok(())
+    }
+
+    #[test]
+    fn view_shape() -> Result<(), Error> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        let view = reader.view();
+        let a = view.slice(s![0, ..5, 0, .., 100..200])?;
+        let shape = a.shape();
+        assert_eq!(shape, vec![5, 1024, 100]);
+        Ok(())
+    }
+
+    #[test]
+    fn view_new_axis() -> Result<(), Error> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        let view = reader.view();
+        let a = Array5::<u8>::zeros((1, 9, 1, 1024, 1024));
+        let a = a.slice(s![0, ..5, 0, NewAxis, 100..200, ..]);
+        let v = view.slice(s![0, ..5, 0, NewAxis, 100..200, ..])?;
+        assert_eq!(v.shape(), a.shape());
+        let a = a.slice(s![NewAxis, .., .., NewAxis, .., .., NewAxis]);
+        let v = v.slice(s![NewAxis, .., .., NewAxis, .., .., NewAxis])?;
+        assert_eq!(v.shape(), a.shape());
+        Ok(())
+    }
+
+    #[test]
+    fn view_permute_axes() -> Result<(), Error> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        let view = reader.view();
+        let s = view.shape();
+        let mut a = Array5::<u8>::zeros((s[0], s[1], s[2], s[3], s[4]));
+        assert_eq!(view.shape(), a.shape());
+        let b: Array5<usize> = view.clone().try_into()?;
+        assert_eq!(b.shape(), a.shape());
+
+        let view = view.swap_axes(Axis::C, Axis::Z)?;
+        a.swap_axes(0, 1);
+        assert_eq!(view.shape(), a.shape());
+        let b: Array5<usize> = view.clone().try_into()?;
+        assert_eq!(b.shape(), a.shape());
+        let view = view.permute_axes(&[Axis::X, Axis::Z, Axis::Y])?;
+        let a = a.permuted_axes([4, 1, 2, 0, 3]);
+        assert_eq!(view.shape(), a.shape());
+        let b: Array5<usize> = view.clone().try_into()?;
+        assert_eq!(b.shape(), a.shape());
+        Ok(())
+    }
+
+    macro_rules! test_max {
+        ($($name:ident: $b:expr $(,)?)*) => {
+            $(
+                #[test]
+                fn $name() -> Result<(), Error> {
+                    let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+                    let reader = open(file)?;
+                    let view = reader.view();
+                    let array: Array5<usize> = view.clone().try_into()?;
+                    let view = view.max_proj($b)?;
+                    let a: Array4<usize> = view.clone().try_into()?;
+                    let b = array.max($b)?;
+                    assert_eq!(a.shape(), b.shape());
+                    assert_eq!(a, b);
+                    Ok(())
+                }
+            )*
+        };
+    }
+
+    test_max! {
+        max_c: 0
+        max_z: 1
+        max_t: 2
+        max_y: 3
+        max_x: 4
+    }
+
+    macro_rules! test_index {
+        ($($name:ident: $b:expr $(,)?)*) => {
+            $(
+                #[test]
+                fn $name() -> Result<(), Error> {
+                    let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+                    let reader = open(file)?;
+                    let view = reader.view();
+                    let v4: Array<usize, _> = view.slice($b)?.try_into()?;
+                    let a5: Array5<usize> = reader.view().try_into()?;
+                    let a4 = a5.slice($b).to_owned();
+                    assert_eq!(a4, v4);
+                    Ok(())
+                }
+            )*
+        };
+    }
+
+    test_index! {
+        index_0: s![.., .., .., .., ..]
+        index_1: s![0, .., .., .., ..]
+        index_2: s![.., 0, .., .., ..]
+        index_3: s![.., .., 0, .., ..]
+        index_4: s![.., .., .., 0, ..]
+        index_5: s![.., .., .., .., 0]
+        index_6: s![0, 0, .., .., ..]
+        index_7: s![0, .., 0, .., ..]
+        index_8: s![0, .., .., 0, ..]
+        index_9: s![0, .., .., .., 0]
+        index_a: s![.., 0, 0, .., ..]
+        index_b: s![.., 0, .., 0, ..]
+        index_c: s![.., 0, .., .., 0]
+        index_d: s![.., .., 0, 0, ..]
+        index_e: s![.., .., 0, .., 0]
+        index_f: s![.., .., .., 0, 0]
+        index_g: s![0, 0, 0, .., ..]
+        index_h: s![0, 0, .., 0, ..]
+        index_i: s![0, 0, .., .., 0]
+        index_j: s![0, .., 0, 0, ..]
+        index_k: s![0, .., 0, .., 0]
+        index_l: s![0, .., .., 0, 0]
+        index_m: s![0, 0, 0, 0, ..]
+        index_n: s![0, 0, 0, .., 0]
+        index_o: s![0, 0, .., 0, 0]
+        index_p: s![0, .., 0, 0, 0]
+        index_q: s![.., 0, 0, 0, 0]
+        index_r: s![0, 0, 0, 0, 0]
+    }
+
+    #[test]
+    fn dyn_view() -> Result<(), Error> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        let a = reader.view().into_dyn();
+        let b = a.max_proj(1)?;
+        let c = b.slice(s![0, 0, .., ..])?;
+        let d = c.as_array::<usize>()?;
+        assert_eq!(d.shape(), [1024, 1024]);
+        Ok(())
+    }
+
+    #[test]
+    fn item() -> Result<(), Error> {
+        let file = "1xp53-01-AP1.czi";
+        let reader = open(file)?;
+        let view = reader.view();
+        let a = view.slice(s![.., 0, 0, 0, 0])?;
+        let b = a.slice(s![0])?;
+        let item = b.item::<usize>()?;
+        assert_eq!(item, 2);
+        Ok(())
+    }
+
+    #[test]
+    fn slice_cztyx() -> Result<(), Error> {
+        let file = "1xp53-01-AP1.czi";
+        let reader = open(file)?;
+        let view = reader.view().max_proj(Axis::Z)?.into_dyn();
+        println!("view.axes: {:?}", view.get_axes());
+        println!("view.slice: {:?}", view.get_slice());
+        let r = view.reset_axes()?;
+        println!("r.axes: {:?}", r.get_axes());
+        println!("r.slice: {:?}", r.get_slice());
+        let a = view.slice_cztyx(s![0, 0, 0, .., ..])?;
+        println!("a.axes: {:?}", a.get_axes());
+        println!("a.slice: {:?}", a.get_slice());
+        assert_eq!(a.axes(), [Axis::Y, Axis::X]);
+        Ok(())
+    }
+
+    #[test]
+    fn reset_axes() -> Result<(), Error> {
+        let file = "1xp53-01-AP1.czi";
+        let reader = open(file)?;
+        let view = reader.view().max_proj(Axis::Z)?;
+        let view = view.reset_axes()?;
+        assert_eq!(view.axes(), [Axis::C, Axis::New, Axis::T, Axis::Y, Axis::X]);
+        let a = view.as_array::<f64>()?;
+        assert_eq!(a.ndim(), 5);
+        Ok(())
+    }
+
+    #[test]
+    fn reset_axes2() -> Result<(), Error> {
+        let file = "Experiment-2029.czi";
+        let reader = open(file)?;
+        let view = reader.view().squeeze()?;
+        let a = view.reset_axes()?;
+        assert_eq!(a.axes(), [Axis::C, Axis::Z, Axis::T, Axis::Y, Axis::X]);
+        Ok(())
+    }
+
+    #[test]
+    fn reset_axes3() -> Result<(), Error> {
+        let file = "Experiment-2029.czi";
+        let reader = open(file)?;
+        let view4 = reader.view().squeeze()?;
+        let view = view4.max_proj(Axis::Z)?.into_dyn();
+        let slice = view.slice_cztyx(s![0, .., .., .., ..])?.into_dyn();
+        let a = slice.as_array::<u16>()?;
+        assert_eq!(slice.shape(), [1, 10, 1280, 1280]);
+        assert_eq!(a.shape(), [1, 10, 1280, 1280]);
+        let r = slice.reset_axes()?;
+        let b = r.as_array::<u16>()?;
+        assert_eq!(r.shape(), [1, 1, 10, 1280, 1280]);
+        assert_eq!(b.shape(), [1, 1, 10, 1280, 1280]);
+        let q = slice.max_proj(Axis::C)?.max_proj(Axis::T)?;
+        let c = q.as_array::<f64>()?;
+        assert_eq!(q.shape(), [1, 1280, 1280]);
+        assert_eq!(c.shape(), [1, 1280, 1280]);
+        let p = q.reset_axes()?;
+        let d = p.as_array::<u16>()?;
+        println!("axes: {:?}", p.get_axes());
+        println!("operations: {:?}", p.get_operations());
+        println!("slice: {:?}", p.get_slice());
+        assert_eq!(p.shape(), [1, 1, 1, 1280, 1280]);
+        assert_eq!(d.shape(), [1, 1, 1, 1280, 1280]);
+        Ok(())
+    }
+
+    #[test]
+    fn max() -> Result<(), Error> {
+        let file = "Experiment-2029.czi";
+        let reader = open(file)?;
+        let view = reader.view();
+        let m = view.max_proj(Axis::T)?;
+        let a = m.as_array::<u16>()?;
+        assert_eq!(m.shape(), [2, 1, 1280, 1280]);
+        assert_eq!(a.shape(), [2, 1, 1280, 1280]);
+        let mc = view.max_proj(Axis::C)?;
+        let a = mc.as_array::<u16>()?;
+        assert_eq!(mc.shape(), [1, 10, 1280, 1280]);
+        assert_eq!(a.shape(), [1, 10, 1280, 1280]);
+        let mz = mc.max_proj(Axis::Z)?;
+        let a = mz.as_array::<u16>()?;
+        assert_eq!(mz.shape(), [10, 1280, 1280]);
+        assert_eq!(a.shape(), [10, 1280, 1280]);
+        let mt = mz.max_proj(Axis::T)?;
+        let a = mt.as_array::<u16>()?;
+        assert_eq!(mt.shape(), [1280, 1280]);
+        assert_eq!(a.shape(), [1280, 1280]);
+        Ok(())
+    }
+}

src/main.rs

@@ -0,0 +1,194 @@
+use clap::{Parser, Subcommand};
+#[cfg(feature = "movie")]
+use ndarray::SliceInfoElem;
+use ndbioimage::error::Error;
+#[cfg(feature = "movie")]
+use ndbioimage::movie::MovieOptions;
+use ndbioimage::reader::{split_path_and_series, Reader};
+#[cfg(feature = "tiff")]
+use ndbioimage::tiff::TiffOptions;
+use ndbioimage::view::View;
+use std::path::PathBuf;
+
+#[derive(Parser)]
+#[command(arg_required_else_help = true, version, about, long_about = None, propagate_version = true)]
+struct Cli {
+    #[command(subcommand)]
+    command: Commands,
+}
+
+#[derive(Subcommand)]
+enum Commands {
+    /// Print some metadata
+    Info {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+    },
+    /// save ome metadata as xml
+    ExtractOME {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+    },
+    /// Save the image as tiff file
+    #[cfg(feature = "tiff")]
+    Tiff {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+        #[arg(short, long, value_name = "COLOR", num_args(1..))]
+        colors: Vec<String>,
+        #[arg(short, long, value_name = "OVERWRITE")]
+        overwrite: bool,
+    },
+    /// Save the image as mp4 file
+    #[cfg(feature = "movie")]
+    Movie {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+        #[arg(short, long, value_name = "VELOCITY", default_value = "3.6")]
+        velocity: f64,
+        #[arg(short, long, value_name = "BRIGHTNESS", num_args(1..))]
+        brightness: Vec<f64>,
+        #[arg(short, long, value_name = "SCALE", default_value = "1.0")]
+        scale: f64,
+        #[arg(short = 'C', long, value_name = "COLOR", num_args(1..))]
+        colors: Vec<String>,
+        #[arg(short, long, value_name = "OVERWRITE")]
+        overwrite: bool,
+        #[arg(short, long, value_name = "REGISTER")]
+        register: bool,
+        #[arg(short, long, value_name = "CHANNEL")]
+        channel: Option<isize>,
+        #[arg(short, long, value_name = "ZSLICE")]
+        zslice: Option<String>,
+        #[arg(short, long, value_name = "TIME")]
+        time: Option<String>,
+        #[arg(short, long, value_name = "NO-SCALE-BRIGHTNESS")]
+        no_scaling: bool,
+    },
+    /// Download the BioFormats jar into the correct folder
+    DownloadBioFormats {
+        #[arg(short, long, value_name = "GPL_FORMATS")]
+        gpl_formats: bool,
+    },
+}
+
+#[cfg(feature = "movie")]
+fn parse_slice(s: &str) -> Result<SliceInfoElem, Error> {
+    let mut t = s
+        .trim()
+        .replace("..", ":")
+        .split(":")
+        .map(|i| i.parse().ok())
+        .collect::<Vec<Option<isize>>>();
+    if t.len() > 3 {
+        return Err(Error::Parse(s.to_string()));
+    }
+    while t.len() < 3 {
+        t.push(None);
+    }
+    match t[..] {
+        [Some(start), None, None] => Ok(SliceInfoElem::Index(start)),
+        [Some(start), end, None] => Ok(SliceInfoElem::Slice {
+            start,
+            end,
+            step: 1,
+        }),
+        [Some(start), end, Some(step)] => Ok(SliceInfoElem::Slice { start, end, step }),
+        [None, end, None] => Ok(SliceInfoElem::Slice {
+            start: 0,
+            end,
+            step: 1,
+        }),
+        [None, end, Some(step)] => Ok(SliceInfoElem::Slice {
+            start: 0,
+            end,
+            step,
+        }),
+        _ => Err(Error::Parse(s.to_string())),
+    }
+}
+
+pub(crate) fn main() -> Result<(), Error> {
+    let cli = Cli::parse();
+    match &cli.command {
+        Commands::Info { file } => {
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let view = View::from_path(path, series.unwrap_or(0))?.squeeze()?;
+                println!("{}", view.summary()?);
+            }
+        }
+        Commands::ExtractOME { file } => {
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let reader = Reader::new(&path, series.unwrap_or(0))?;
+                let xml = reader.get_ome_xml()?;
+                std::fs::write(path.with_extension("xml"), xml)?;
+            }
+        }
+        #[cfg(feature = "tiff")]
+        Commands::Tiff {
+            file,
+            colors,
+            overwrite,
+        } => {
+            let mut options = TiffOptions::new(true, None, colors.clone(), *overwrite)?;
+            options.enable_bar()?;
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let view = View::from_path(path, series.unwrap_or(0))?;
+                view.save_as_tiff(f.with_extension("tiff"), &options)?;
+            }
+        }
+        #[cfg(feature = "movie")]
+        Commands::Movie {
+            file,
+            velocity: speed,
+            brightness,
+            scale,
+            colors,
+            overwrite,
+            register,
+            channel,
+            zslice,
+            time,
+            no_scaling,
+        } => {
+            let options = MovieOptions::new(
+                *speed,
+                brightness.to_vec(),
+                *scale,
+                colors.to_vec(),
+                *overwrite,
+                *register,
+                *no_scaling,
+            )?;
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let view = View::from_path(path, series.unwrap_or(0))?;
+                let mut s = [SliceInfoElem::Slice {
+                    start: 0,
+                    end: None,
+                    step: 1,
+                }; 5];
+                if let Some(channel) = channel {
+                    s[0] = SliceInfoElem::Index(*channel);
+                };
+                if let Some(zslice) = zslice {
+                    s[1] = parse_slice(zslice)?;
+                }
+                if let Some(time) = time {
+                    s[2] = parse_slice(time)?;
+                }
+                view.into_dyn()
+                    .slice(s.as_slice())?
+                    .save_as_movie(f.with_extension("mp4"), &options)?;
+            }
+        }
+        Commands::DownloadBioFormats { gpl_formats } => {
+            ndbioimage::download_bioformats(*gpl_formats)?
+        }
+    }
+
+    Ok(())
+}

src/metadata.rs

@@ -0,0 +1,363 @@
+use crate::error::Error;
+use itertools::Itertools;
+use ome_metadata::Ome;
+use ome_metadata::ome::{
+    BinningType, Convert, Image, Instrument, Objective, Pixels, UnitsLength, UnitsTime,
+};
+
+impl Metadata for Ome {
+    fn get_instrument(&self) -> Option<&Instrument> {
+        let instrument_id = self.get_image()?.instrument_ref.as_ref()?.id.clone();
+        self.instrument
+            .iter()
+            .find(|i| i.id == instrument_id)
+    }
+
+    fn get_image(&self) -> Option<&Image> {
+        if let Some(image) = &self.image.first() {
+            Some(&image)
+        } else {
+            None
+        }
+    }
+}
+
+pub trait Metadata {
+    fn get_instrument(&self) -> Option<&Instrument>;
+    fn get_image(&self) -> Option<&Image>;
+
+    fn get_pixels(&self) -> Option<&Pixels> {
+        if let Some(image) = self.get_image() {
+            Some(&image.pixels)
+        } else {
+            None
+        }
+    }
+
+    fn get_objective(&self) -> Option<&Objective> {
+        let objective_id = self.get_image()?.objective_settings.as_ref()?.id.clone();
+        self.get_instrument()?
+            .objective
+            .iter()
+            .find(|o| o.id == objective_id)
+    }
+
+    fn get_tube_lens(&self) -> Option<Objective> {
+        Some(Objective {
+            manufacturer: None,
+            model: Some("Unknown".to_string()),
+            serial_number: None,
+            lot_number: None,
+            id: "TubeLens:1".to_string(),
+            correction: None,
+            immersion: None,
+            lens_na: None,
+            nominal_magnification: Some(1.0),
+            calibrated_magnification: None,
+            working_distance: None,
+            working_distance_unit: UnitsLength::um,
+            iris: None,
+            annotation_ref: vec![],
+        })
+    }
+
+    /// shape of the data along cztyx axes
+    fn shape(&self) -> Result<(usize, usize, usize, usize, usize), Error> {
+        if let Some(pixels) = self.get_pixels() {
+            Ok((
+                pixels.size_c as usize,
+                pixels.size_z as usize,
+                pixels.size_t as usize,
+                pixels.size_y as usize,
+                pixels.size_x as usize,
+            ))
+        } else {
+            Err(Error::NoImageOrPixels)
+        }
+    }
+
+    /// pixel size in nm
+    fn pixel_size(&self) -> Result<Option<f64>, Error> {
+        if let Some(pixels) = self.get_pixels() {
+            match (pixels.physical_size_x, pixels.physical_size_y) {
+                (Some(x), Some(y)) => Ok(Some(
+                    (pixels
+                        .physical_size_x_unit
+                        .convert(&UnitsLength::nm, x as f64)?
+                        + pixels
+                            .physical_size_y_unit
+                            .convert(&UnitsLength::nm, y as f64)?)
+                        / 2f64,
+                )),
+                (Some(x), None) => Ok(Some(
+                    pixels
+                        .physical_size_x_unit
+                        .convert(&UnitsLength::nm, x as f64)?
+                        .powi(2),
+                )),
+                (None, Some(y)) => Ok(Some(
+                    pixels
+                        .physical_size_y_unit
+                        .convert(&UnitsLength::nm, y as f64)?
+                        .powi(2),
+                )),
+                _ => Ok(None),
+            }
+        } else {
+            Ok(None)
+        }
+    }
+
+    /// distance between planes in z-stack in nm
+    fn delta_z(&self) -> Result<Option<f64>, Error> {
+        if let Some(pixels) = self.get_pixels() {
+            if let Some(z) = pixels.physical_size_z {
+                return Ok(Some(
+                    pixels
+                        .physical_size_z_unit
+                        .convert(&UnitsLength::nm, z as f64)?,
+                ));
+            }
+        }
+        Ok(None)
+    }
+
+    /// time interval in seconds for time-lapse images
+    fn time_interval(&self) -> Result<Option<f64>, Error> {
+        if let Some(pixels) = self.get_pixels() {
+            if let Some(t) = pixels.plane.iter().map(|p| p.the_t).max() {
+                if t > 0 {
+                    let plane_a = pixels.plane
+                        .iter()
+                        .find(|p| (p.the_c == 0) && (p.the_z == 0) && (p.the_t == 0));
+                    let plane_b = pixels.plane
+                        .iter()
+                        .find(|p| (p.the_c == 0) && (p.the_z == 0) && (p.the_t == t));
+                    if let (Some(a), Some(b)) = (plane_a, plane_b) {
+                        if let (Some(a_t), Some(b_t)) = (a.delta_t, b.delta_t) {
+                            return Ok(Some(
+                                (b.delta_t_unit.convert(&UnitsTime::s, b_t as f64)?
+                                    - a.delta_t_unit.convert(&UnitsTime::s, a_t as f64)?)
+                                .abs()
+                                    / (t as f64),
+                            ));
+                        }
+                    }
+                }
+            }
+        }
+        Ok(None)
+    }
+
+    /// exposure time for channel, z=0 and t=0
+    fn exposure_time(&self, channel: usize) -> Result<Option<f64>, Error> {
+        let c = channel as i32;
+        if let Some(pixels) = self.get_pixels() {
+            if let Some(p) = pixels.plane
+                .iter()
+                .find(|p| (p.the_c == c) && (p.the_z == 0) && (p.the_t == 0))
+            {
+                if let Some(t) = p.exposure_time {
+                    return Ok(Some(p.exposure_time_unit.convert(&UnitsTime::s, t as f64)?));
+                }
+            }
+        }
+        Ok(None)
+    }
+
+    fn binning(&self, channel: usize) -> Option<usize> {
+        match self
+            .get_pixels()?
+            .channel
+            .get(channel)?
+            .detector_settings
+            .as_ref()?
+            .binning
+            .as_ref()?
+        {
+            BinningType::_1X1 => Some(1),
+            BinningType::_2X2 => Some(2),
+            BinningType::_4X4 => Some(4),
+            BinningType::_8X8 => Some(8),
+            BinningType::Other => None,
+        }
+    }
+
+    fn laser_wavelengths(&self, channel: usize) -> Result<Option<f64>, Error> {
+        if let Some(pixels) = self.get_pixels() {
+            if let Some(channel) = pixels.channel.get(channel) {
+                if let Some(w) = channel.excitation_wavelength {
+                    return Ok(Some(
+                        channel
+                            .excitation_wavelength_unit
+                            .convert(&UnitsLength::nm, w as f64)?,
+                    ));
+                }
+            }
+        }
+        Ok(None)
+    }
+
+    fn laser_powers(&self, channel: usize) -> Result<Option<f64>, Error> {
+        if let Some(pixels) = self.get_pixels() {
+            if let Some(channel) = pixels.channel.get(channel) {
+                if let Some(ls) = &channel.light_source_settings {
+                    if let Some(a) = ls.attenuation {
+                        return if (0. ..=1.).contains(&a) {
+                            Ok(Some(1f64 - (a as f64)))
+                        } else {
+                            Err(Error::InvalidAttenuation(a.to_string()))
+                        };
+                    }
+                }
+            }
+        }
+        Ok(None)
+    }
+
+    fn objective_name(&self) -> Option<String> {
+        Some(self.get_objective()?.model.as_ref()?.clone())
+    }
+
+    fn magnification(&self) -> Option<f64> {
+        Some(
+            (self.get_objective()?.nominal_magnification? as f64)
+                * (self.get_tube_lens()?.nominal_magnification? as f64),
+        )
+    }
+
+    fn tube_lens_name(&self) -> Option<String> {
+        self.get_tube_lens()?.model.clone()
+    }
+
+    fn filter_set_name(&self, channel: usize) -> Option<String> {
+        let filter_set_id = self
+            .get_pixels()?
+            .channel
+            .get(channel)?
+            .filter_set_ref
+            .as_ref()?
+            .id
+            .clone();
+        self.get_instrument()
+            .as_ref()?
+            .filter_set
+            .iter()
+            .find(|f| f.id == filter_set_id)?
+            .model
+            .clone()
+    }
+
+    fn gain(&self, channel: usize) -> Option<f64> {
+        if let Some(pixels) = self.get_pixels() {
+            Some(
+                *pixels
+                    .channel
+                    .get(channel)?
+                    .detector_settings
+                    .as_ref()?
+                    .gain
+                    .as_ref()? as f64,
+            )
+        } else {
+            None
+        }
+    }
+
+    fn summary(&self) -> Result<String, Error> {
+        let size_c = if let Some(pixels) = self.get_pixels() {
+            pixels.channel.len()
+        } else {
+            0
+        };
+        let mut s = "".to_string();
+        if let Ok(Some(pixel_size)) = self.pixel_size() {
+            s.push_str(&format!("pixel size:    {pixel_size:.2} nm\n"));
+        }
+        if let Ok(Some(delta_z)) = self.delta_z() {
+            s.push_str(&format!("z-interval:    {delta_z:.2} nm\n"))
+        }
+        if let Ok(Some(time_interval)) = self.time_interval() {
+            s.push_str(&format!("time interval: {time_interval:.2} s\n"))
+        }
+        let exposure_time = (0..size_c)
+            .map(|c| self.exposure_time(c))
+            .collect::<Result<Vec<_>, Error>>()?
+            .into_iter()
+            .flatten()
+            .collect::<Vec<_>>();
+        if !exposure_time.is_empty() {
+            s.push_str(&format!(
+                "exposure time: {}\n",
+                exposure_time.into_iter().join(" | ")
+            ));
+        }
+        if let Some(magnification) = self.magnification() {
+            s.push_str(&format!("magnification: {magnification}x\n"))
+        }
+        if let Some(objective_name) = self.objective_name() {
+            s.push_str(&format!("objective:     {objective_name}\n"))
+        }
+        if let Some(tube_lens_name) = self.tube_lens_name() {
+            s.push_str(&format!("tube lens:     {tube_lens_name}\n"))
+        }
+        let filter_set_name = (0..size_c)
+            .map(|c| self.filter_set_name(c))
+            .collect::<Vec<_>>()
+            .into_iter()
+            .flatten()
+            .collect::<Vec<_>>();
+        if !filter_set_name.is_empty() {
+            s.push_str(&format!(
+                "filter set:    {}\n",
+                filter_set_name.into_iter().join(" | ")
+            ));
+        }
+        let gain = (0..size_c)
+            .map(|c| self.gain(c))
+            .collect::<Vec<_>>()
+            .into_iter()
+            .flatten()
+            .collect::<Vec<_>>();
+        if !gain.is_empty() {
+            s.push_str(&format!("gain:          {}\n", gain.into_iter().join(" ")));
+        }
+        let laser_wavelengths = (0..size_c)
+            .map(|c| self.laser_wavelengths(c))
+            .collect::<Result<Vec<_>, Error>>()?
+            .into_iter()
+            .flatten()
+            .collect::<Vec<_>>();
+        if !laser_wavelengths.is_empty() {
+            s.push_str(&format!(
+                "laser colors:  {} nm\n",
+                laser_wavelengths.into_iter().join(" | ")
+            ));
+        }
+        let laser_powers = (0..size_c)
+            .map(|c| self.laser_powers(c))
+            .collect::<Result<Vec<_>, Error>>()?
+            .into_iter()
+            .flatten()
+            .collect::<Vec<_>>();
+        if !laser_powers.is_empty() {
+            s.push_str(&format!(
+                "laser powers:   {}\n",
+                laser_powers.into_iter().join(" | ")
+            ));
+        }
+        let binning = (0..size_c)
+            .map(|c| self.binning(c))
+            .collect::<Vec<_>>()
+            .into_iter()
+            .flatten()
+            .collect::<Vec<_>>();
+        if !binning.is_empty() {
+            s.push_str(&format!(
+                "binning:       {}\n",
+                binning.into_iter().join(" | ")
+            ));
+        }
+        Ok(s.to_string())
+    }
+}

src/movie.rs

@@ -0,0 +1,285 @@
+use crate::axes::Axis;
+use crate::colors::Color;
+use crate::error::Error;
+use crate::reader::PixelType;
+use crate::view::View;
+use ffmpeg_sidecar::command::FfmpegCommand;
+use ffmpeg_sidecar::download::auto_download;
+use ffmpeg_sidecar::event::{FfmpegEvent, LogLevel};
+use itertools::Itertools;
+use ndarray::{Array2, Array3, Dimension, IxDyn, s, stack};
+use ordered_float::OrderedFloat;
+use std::io::Write;
+use std::path::Path;
+use std::thread;
+
+pub struct MovieOptions {
+    velocity: f64,
+    brightness: Vec<f64>,
+    scale: f64,
+    colors: Option<Vec<Vec<u8>>>,
+    overwrite: bool,
+    register: bool,
+    no_scaling: bool,
+}
+
+impl Default for MovieOptions {
+    fn default() -> Self {
+        Self {
+            velocity: 3.6,
+            brightness: Vec::new(),
+            scale: 1.0,
+            colors: None,
+            overwrite: false,
+            register: false,
+            no_scaling: false,
+        }
+    }
+}
+
+impl MovieOptions {
+    pub fn new(
+        velocity: f64,
+        brightness: Vec<f64>,
+        scale: f64,
+        colors: Vec<String>,
+        overwrite: bool,
+        register: bool,
+        no_scaling: bool,
+    ) -> Result<Self, Error> {
+        let colors = if colors.is_empty() {
+            None
+        } else {
+            let colors = colors
+                .iter()
+                .map(|c| c.parse::<Color>())
+                .collect::<Result<Vec<_>, Error>>()?;
+            Some(colors.into_iter().map(|c| c.to_rgb()).collect())
+        };
+        Ok(Self {
+            velocity,
+            brightness,
+            scale,
+            colors,
+            overwrite,
+            register,
+            no_scaling,
+        })
+    }
+
+    pub fn set_velocity(&mut self, velocity: f64) {
+        self.velocity = velocity;
+    }
+
+    pub fn set_brightness(&mut self, brightness: Vec<f64>) {
+        self.brightness = brightness;
+    }
+
+    pub fn set_scale(&mut self, scale: f64) {
+        self.scale = scale;
+    }
+
+    pub fn set_colors(&mut self, colors: &[String]) -> Result<(), Error> {
+        let colors = colors
+            .iter()
+            .map(|c| c.parse::<Color>())
+            .collect::<Result<Vec<_>, Error>>()?;
+        self.colors = Some(colors.into_iter().map(|c| c.to_rgb()).collect());
+        Ok(())
+    }
+
+    pub fn set_overwrite(&mut self, overwrite: bool) {
+        self.overwrite = overwrite;
+    }
+}
+
+fn get_ab(tyx: View<IxDyn>) -> Result<(f64, f64), Error> {
+    let s = tyx
+        .as_array::<f64>()?
+        .iter()
+        .filter_map(|&i| {
+            if i == 0.0 || !i.is_finite() {
+                None
+            } else {
+                Some(OrderedFloat::from(i))
+            }
+        })
+        .sorted_unstable()
+        .map(f64::from)
+        .collect::<Vec<_>>();
+
+    let n = s.len();
+    let mut a = s[n / 100];
+    let mut b = s[n - n / 100 - 1];
+    if a == b {
+        a = s[0];
+        b = s[n - 1];
+    }
+    if a == b {
+        a = 0.0;
+        b = 1.0;
+    }
+    Ok((a, b))
+}
+
+fn cframe(frame: Array2<f64>, color: &[u8], a: f64, b: f64) -> Array3<f64> {
+    let frame = ((frame - a) / (b - a)).clamp(0.0, 1.0);
+    let color = color
+        .iter()
+        .map(|&c| (c as f64) / 255.0)
+        .collect::<Vec<_>>();
+    let frame = color
+        .iter()
+        .map(|&c| (c * &frame).to_owned())
+        .collect::<Vec<Array2<f64>>>();
+    let view = frame.iter().map(|c| c.view()).collect::<Vec<_>>();
+    stack(ndarray::Axis(2), &view).unwrap()
+}
+
+impl<D> View<D>
+where
+    D: Dimension,
+{
+    pub fn save_as_movie<P>(&self, path: P, options: &MovieOptions) -> Result<(), Error>
+    where
+        P: AsRef<Path>,
+    {
+        if options.register {
+            return Err(Error::NotImplemented("register".to_string()));
+        }
+        let path = path.as_ref().to_path_buf();
+        if path.exists() {
+            if options.overwrite {
+                std::fs::remove_file(&path)?;
+            } else {
+                return Err(Error::FileAlreadyExists(path.display().to_string()));
+            }
+        }
+        let view = self.max_proj(Axis::Z)?.reset_axes()?;
+        let velocity = options.velocity;
+        let mut brightness = options.brightness.clone();
+        let scale = options.scale;
+        let shape = view.shape();
+        let size_c = shape[0];
+        let size_t = shape[2];
+        let size_y = shape[3];
+        let size_x = shape[4];
+        let shape_y = 2 * (((size_y as f64 * scale) / 2.).round() as usize);
+        let shape_x = 2 * (((size_x as f64 * scale) / 2.).round() as usize);
+
+        while brightness.len() < size_c {
+            brightness.push(1.0);
+        }
+        let mut colors = if let Some(colors) = options.colors.as_ref() {
+            colors.to_vec()
+        } else {
+            Vec::new()
+        };
+        while colors.len() < size_c {
+            colors.push(vec![255, 255, 255]);
+        }
+
+        if let Err(e) = auto_download() {
+            return Err(Error::Ffmpeg(e.to_string()));
+        }
+
+        let mut movie = FfmpegCommand::new()
+            .args([
+                "-f",
+                "rawvideo",
+                "-pix_fmt",
+                "rgb24",
+                "-s",
+                &format!("{size_x}x{size_y}"),
+            ])
+            .input("-")
+            .args([
+                "-vcodec",
+                "libx264",
+                "-preset",
+                "veryslow",
+                "-pix_fmt",
+                "yuv420p",
+                "-r",
+                "7",
+                "-vf",
+                &format!("setpts={velocity}*PTS,scale={shape_x}:{shape_y}:flags=neighbor"),
+            ])
+            .output(path.to_str().expect("path cannot be converted to string"))
+            .spawn()?;
+        let mut stdin = movie.take_stdin().unwrap();
+
+        let ab = if options.no_scaling {
+            vec![
+                match view.pixel_type {
+                    PixelType::I8 => (i8::MIN as f64, i8::MAX as f64),
+                    PixelType::U8 => (u8::MIN as f64, u8::MAX as f64),
+                    PixelType::I16 => (i16::MIN as f64, i16::MAX as f64),
+                    PixelType::U16 => (u16::MIN as f64, u16::MAX as f64),
+                    PixelType::I32 => (i32::MIN as f64, i32::MAX as f64),
+                    PixelType::U32 => (u32::MIN as f64, u32::MAX as f64),
+                    PixelType::I64 => (i64::MIN as f64, i64::MAX as f64),
+                    PixelType::U64 => (u64::MIN as f64, u64::MAX as f64),
+                    _ => (0.0, 1.0),
+                };
+                view.size_c
+            ]
+        } else {
+            (0..size_c)
+                .map(|c| match view.slice(s![c, .., .., .., ..]) {
+                    Ok(slice) => get_ab(slice.into_dyn()),
+                    Err(e) => Err(e),
+                })
+                .collect::<Result<Vec<_>, Error>>()?
+        };
+
+        thread::spawn(move || {
+            for t in 0..size_t {
+                let mut frame = Array3::<f64>::zeros((size_y, size_x, 3));
+                for c in 0..size_c {
+                    frame = frame
+                        + cframe(
+                            view.get_frame(c, 0, t).unwrap(),
+                            &colors[c],
+                            ab[c].0,
+                            ab[c].1 / brightness[c],
+                        );
+                }
+                let frame = (frame.clamp(0.0, 1.0) * 255.0).round().mapv(|i| i as u8);
+                let bytes: Vec<_> = frame.flatten().into_iter().collect();
+                stdin.write_all(&bytes).unwrap();
+            }
+        });
+
+        movie
+            .iter()
+            .map_err(|e| Error::Ffmpeg(e.to_string()))?
+            .for_each(|e| match e {
+                FfmpegEvent::Log(LogLevel::Error, e) => println!("Error: {}", e),
+                FfmpegEvent::Progress(p) => println!("Progress: {} / 00:00:15", p.time),
+                _ => {}
+            });
+        Ok(())
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::reader::Reader;
+
+    #[test]
+    fn movie() -> Result<(), Error> {
+        let file = "1xp53-01-AP1.czi";
+        let path = std::env::current_dir()?
+            .join("tests")
+            .join("files")
+            .join(file);
+        let reader = Reader::new(&path, 0)?;
+        let view = reader.view();
+        let mut options = MovieOptions::default();
+        options.set_overwrite(true);
+        view.save_as_movie("/home/wim/tmp/movie.mp4", &options)?;
+        Ok(())
+    }
+}

src/py.rs

@@ -0,0 +1,989 @@
+use crate::axes::Axis;
+use crate::bioformats::download_bioformats;
+use crate::error::Error;
+use crate::metadata::Metadata;
+use crate::reader::{PixelType, Reader};
+use crate::view::{Item, View};
+use itertools::Itertools;
+use ndarray::{Ix0, IxDyn, SliceInfoElem};
+use numpy::IntoPyArray;
+use ome_metadata::Ome;
+use pyo3::IntoPyObjectExt;
+use pyo3::exceptions::{PyNotImplementedError, PyValueError};
+use pyo3::prelude::*;
+use pyo3::types::{PyEllipsis, PyInt, PyList, PySlice, PySliceMethods, PyString, PyTuple};
+use serde::{Deserialize, Serialize};
+use serde_json::{from_str, to_string};
+use std::path::PathBuf;
+use std::sync::Arc;
+
+impl From<crate::error::Error> for PyErr {
+    fn from(err: crate::error::Error) -> PyErr {
+        PyErr::new::<PyValueError, _>(err.to_string())
+    }
+}
+
+#[pyclass(module = "ndbioimage.ndbioimage_rs")]
+struct ViewConstructor;
+
+#[pymethods]
+impl ViewConstructor {
+    #[new]
+    fn new() -> Self {
+        Self
+    }
+
+    fn __getnewargs__<'py>(&self, py: Python<'py>) -> Bound<'py, PyTuple> {
+        PyTuple::empty(py)
+    }
+
+    #[staticmethod]
+    fn __call__(state: String) -> PyResult<PyView> {
+        if let Ok(new) = from_str(&state) {
+            Ok(new)
+        } else {
+            Err(PyErr::new::<PyValueError, _>(
+                "cannot parse state".to_string(),
+            ))
+        }
+    }
+}
+
+#[pyclass(subclass, module = "ndbioimage.ndbioimage_rs")]
+#[pyo3(name = "View")]
+#[derive(Clone, Debug, Serialize, Deserialize)]
+struct PyView {
+    view: View<IxDyn>,
+    dtype: PixelType,
+    ome: Arc<Ome>,
+}
+
+#[pymethods]
+impl PyView {
+    /// new view on a file at path, open series #, open as dtype: (u)int(8/16/32) or float(32/64)
+    #[new]
+    #[pyo3(signature = (path, series = 0, dtype = "uint16", axes = "cztyx"))]
+    fn new<'py>(
+        py: Python<'py>,
+        path: Bound<'py, PyAny>,
+        series: usize,
+        dtype: &str,
+        axes: &str,
+    ) -> PyResult<Self> {
+        if path.is_instance_of::<Self>() {
+            Ok(path.cast_into::<Self>()?.extract::<Self>()?)
+        } else {
+            let builtins = PyModule::import(py, "builtins")?;
+            let mut path = PathBuf::from(
+                builtins
+                    .getattr("str")?
+                    .call1((path,))?
+                    .cast_into::<PyString>()?
+                    .extract::<String>()?,
+            );
+            if path.is_dir() {
+                for file in path.read_dir()?.flatten() {
+                    let p = file.path();
+                    if file.path().is_file() && (p.extension() == Some("tif".as_ref())) {
+                        path = p;
+                        break;
+                    }
+                }
+            }
+            let axes = axes
+                .chars()
+                .map(|a| a.to_string().parse())
+                .collect::<Result<Vec<Axis>, Error>>()?;
+            let reader = Reader::new(&path, series)?;
+            let view = View::new_with_axes(Arc::new(reader), axes)?;
+            let dtype = dtype.parse()?;
+            let ome = Arc::new(view.get_ome()?);
+            Ok(Self { view, dtype, ome })
+        }
+    }
+
+    fn squeeze<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
+        let view = self.view.squeeze()?;
+        if view.ndim() == 0 {
+            Ok(match self.dtype {
+                PixelType::I8 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i8>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U8 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u8>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I16 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i16>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U16 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u16>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I32 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i32>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U32 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u32>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I64 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U64 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I128 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U128 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::F32 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<f32>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::F64 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<f64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::F128 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<f64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+            })
+        } else {
+            PyView {
+                view,
+                dtype: self.dtype.clone(),
+                ome: self.ome.clone(),
+            }
+            .into_bound_py_any(py)
+        }
+    }
+
+    /// close the file: does nothing as this is handled automatically
+    fn close(&self) -> PyResult<()> {
+        Ok(())
+    }
+
+    /// change the data type of the view: (u)int(8/16/32) or float(32/64)
+    fn as_type(&self, dtype: &str) -> PyResult<PyView> {
+        Ok(PyView {
+            view: self.view.clone(),
+            dtype: dtype.parse()?,
+            ome: self.ome.clone(),
+        })
+    }
+
+    /// change the data type of the view: (u)int(8/16/32) or float(32/64)
+    fn astype(&self, dtype: &str) -> PyResult<PyView> {
+        self.as_type(dtype)
+    }
+
+    /// slice the view and return a new view or a single number
+    fn __getitem__<'py>(
+        &self,
+        py: Python<'py>,
+        n: Bound<'py, PyAny>,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        let slice: Vec<_> = if n.is_instance_of::<PyTuple>() {
+            n.cast_into::<PyTuple>()?.into_iter().collect()
+        } else if n.is_instance_of::<PyList>() {
+            n.cast_into::<PyList>()?.into_iter().collect()
+        } else {
+            vec![n]
+        };
+        let mut new_slice = Vec::new();
+        let mut ellipsis = None;
+        let shape = self.view.shape();
+        for (i, (s, t)) in slice.iter().zip(shape.iter()).enumerate() {
+            if s.is_instance_of::<PyInt>() {
+                new_slice.push(SliceInfoElem::Index(s.cast::<PyInt>()?.extract::<isize>()?));
+            } else if s.is_instance_of::<PySlice>() {
+                let u = s.cast::<PySlice>()?.indices(*t as isize)?;
+                new_slice.push(SliceInfoElem::Slice {
+                    start: u.start,
+                    end: Some(u.stop),
+                    step: u.step,
+                });
+            } else if s.is_instance_of::<PyEllipsis>() {
+                if ellipsis.is_some() {
+                    return Err(PyErr::new::<PyValueError, _>(
+                        "cannot have more than one ellipsis".to_string(),
+                    ));
+                }
+                let _ = ellipsis.insert(i);
+            } else {
+                return Err(PyErr::new::<PyValueError, _>(format!(
+                    "cannot convert {:?} to slice",
+                    s
+                )));
+            }
+        }
+        if new_slice.len() > shape.len() {
+            return Err(PyErr::new::<PyValueError, _>(format!(
+                "got more indices ({}) than dimensions ({})",
+                new_slice.len(),
+                shape.len()
+            )));
+        }
+        while new_slice.len() < shape.len() {
+            if let Some(i) = ellipsis {
+                new_slice.insert(
+                    i,
+                    SliceInfoElem::Slice {
+                        start: 0,
+                        end: None,
+                        step: 1,
+                    },
+                )
+            } else {
+                new_slice.push(SliceInfoElem::Slice {
+                    start: 0,
+                    end: None,
+                    step: 1,
+                })
+            }
+        }
+        let view = self.view.slice(new_slice.as_slice())?;
+        if view.ndim() == 0 {
+            Ok(match self.dtype {
+                PixelType::I8 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i8>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U8 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u8>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I16 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i16>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U16 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u16>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I32 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i32>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U32 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u32>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::F32 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<f32>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::F64 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<f64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I64 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U64 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::I128 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<i128>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::U128 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<u128>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+                PixelType::F128 => view
+                    .into_dimensionality::<Ix0>()?
+                    .item::<f64>()?
+                    .into_pyobject(py)?
+                    .into_any(),
+            })
+        } else {
+            PyView {
+                view,
+                dtype: self.dtype.clone(),
+                ome: self.ome.clone(),
+            }
+            .into_bound_py_any(py)
+        }
+    }
+
+    #[pyo3(signature = (dtype = None))]
+    fn __array__<'py>(&self, py: Python<'py>, dtype: Option<&str>) -> PyResult<Bound<'py, PyAny>> {
+        if let Some(dtype) = dtype {
+            self.as_type(dtype)?.as_array(py)
+        } else {
+            self.as_array(py)
+        }
+    }
+
+    fn __contains__(&self, _item: Bound<PyAny>) -> PyResult<bool> {
+        Err(PyNotImplementedError::new_err("contains not implemented"))
+    }
+
+    fn __enter__<'py>(slf: PyRef<'py, Self>) -> PyResult<PyRef<'py, Self>> {
+        Ok(slf)
+    }
+
+    #[allow(unused_variables)]
+    #[pyo3(signature = (exc_type=None, exc_val=None, exc_tb=None))]
+    fn __exit__(
+        &self,
+        exc_type: Option<Bound<PyAny>>,
+        exc_val: Option<Bound<PyAny>>,
+        exc_tb: Option<Bound<PyAny>>,
+    ) -> PyResult<()> {
+        self.close()
+    }
+
+    fn __reduce__(&self) -> PyResult<(ViewConstructor, (String,))> {
+        if let Ok(s) = to_string(self) {
+            Ok((ViewConstructor, (s,)))
+        } else {
+            Err(PyErr::new::<PyValueError, _>(
+                "cannot get state".to_string(),
+            ))
+        }
+    }
+
+    fn __copy__(&self) -> Self {
+        Self {
+            view: self.view.clone(),
+            dtype: self.dtype.clone(),
+            ome: self.ome.clone(),
+        }
+    }
+
+    fn copy(&self) -> Self {
+        Self {
+            view: self.view.clone(),
+            dtype: self.dtype.clone(),
+            ome: self.ome.clone(),
+        }
+    }
+
+    fn __len__(&self) -> PyResult<usize> {
+        Ok(self.view.len())
+    }
+
+    fn __repr__(&self) -> PyResult<String> {
+        Ok(self.view.summary()?)
+    }
+
+    fn __str__(&self) -> PyResult<String> {
+        Ok(self.view.path.display().to_string())
+    }
+
+    /// retrieve a single frame at czt, sliced accordingly
+    fn get_frame<'py>(
+        &self,
+        py: Python<'py>,
+        c: isize,
+        z: isize,
+        t: isize,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        Ok(match self.dtype {
+            PixelType::I8 => self
+                .view
+                .get_frame::<i8, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::U8 => self
+                .view
+                .get_frame::<u8, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::I16 => self
+                .view
+                .get_frame::<i16, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::U16 => self
+                .view
+                .get_frame::<u16, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::I32 => self
+                .view
+                .get_frame::<i32, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::U32 => self
+                .view
+                .get_frame::<u32, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::F32 => self
+                .view
+                .get_frame::<f32, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::F64 => self
+                .view
+                .get_frame::<f64, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::I64 => self
+                .view
+                .get_frame::<i64, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::U64 => self
+                .view
+                .get_frame::<u64, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::I128 => self
+                .view
+                .get_frame::<i64, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::U128 => self
+                .view
+                .get_frame::<u64, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+            PixelType::F128 => self
+                .view
+                .get_frame::<f64, _>(c, z, t)?
+                .into_pyarray(py)
+                .into_any(),
+        })
+    }
+
+    fn flatten<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
+        Ok(match self.dtype {
+            PixelType::I8 => self.view.flatten::<i8>()?.into_pyarray(py).into_any(),
+            PixelType::U8 => self.view.flatten::<u8>()?.into_pyarray(py).into_any(),
+            PixelType::I16 => self.view.flatten::<i16>()?.into_pyarray(py).into_any(),
+            PixelType::U16 => self.view.flatten::<u16>()?.into_pyarray(py).into_any(),
+            PixelType::I32 => self.view.flatten::<i32>()?.into_pyarray(py).into_any(),
+            PixelType::U32 => self.view.flatten::<u32>()?.into_pyarray(py).into_any(),
+            PixelType::F32 => self.view.flatten::<f32>()?.into_pyarray(py).into_any(),
+            PixelType::F64 => self.view.flatten::<f64>()?.into_pyarray(py).into_any(),
+            PixelType::I64 => self.view.flatten::<i64>()?.into_pyarray(py).into_any(),
+            PixelType::U64 => self.view.flatten::<u64>()?.into_pyarray(py).into_any(),
+            PixelType::I128 => self.view.flatten::<i64>()?.into_pyarray(py).into_any(),
+            PixelType::U128 => self.view.flatten::<u64>()?.into_pyarray(py).into_any(),
+            PixelType::F128 => self.view.flatten::<f64>()?.into_pyarray(py).into_any(),
+        })
+    }
+
+    fn to_bytes(&self) -> PyResult<Vec<u8>> {
+        Ok(match self.dtype {
+            PixelType::I8 => self.view.to_bytes::<i8>()?,
+            PixelType::U8 => self.view.to_bytes::<u8>()?,
+            PixelType::I16 => self.view.to_bytes::<i16>()?,
+            PixelType::U16 => self.view.to_bytes::<u16>()?,
+            PixelType::I32 => self.view.to_bytes::<i32>()?,
+            PixelType::U32 => self.view.to_bytes::<u32>()?,
+            PixelType::F32 => self.view.to_bytes::<f32>()?,
+            PixelType::F64 => self.view.to_bytes::<f64>()?,
+            PixelType::I64 => self.view.to_bytes::<i64>()?,
+            PixelType::U64 => self.view.to_bytes::<u64>()?,
+            PixelType::I128 => self.view.to_bytes::<i64>()?,
+            PixelType::U128 => self.view.to_bytes::<u64>()?,
+            PixelType::F128 => self.view.to_bytes::<f64>()?,
+        })
+    }
+
+    fn tobytes(&self) -> PyResult<Vec<u8>> {
+        self.to_bytes()
+    }
+
+    /// retrieve the ome metadata as an XML string
+    fn get_ome_xml(&self) -> PyResult<String> {
+        Ok(self.view.get_ome_xml()?)
+    }
+
+    /// the file path
+    #[getter]
+    fn path(&self) -> PyResult<String> {
+        Ok(self.view.path.display().to_string())
+    }
+
+    /// the series in the file
+    #[getter]
+    fn series(&self) -> PyResult<usize> {
+        Ok(self.view.series)
+    }
+
+    /// the axes in the view
+    #[getter]
+    fn axes(&self) -> String {
+        self.view.axes().iter().map(|a| format!("{:?}", a)).join("")
+    }
+
+    /// the shape of the view
+    #[getter]
+    fn shape(&self) -> Vec<usize> {
+        self.view.shape()
+    }
+
+    #[getter]
+    fn slice(&self) -> PyResult<Vec<String>> {
+        Ok(self
+            .view
+            .get_slice()
+            .iter()
+            .map(|s| format!("{:#?}", s))
+            .collect())
+    }
+
+    /// the number of pixels in the view
+    #[getter]
+    fn size(&self) -> usize {
+        self.view.size()
+    }
+
+    /// the number of dimensions in the view
+    #[getter]
+    fn ndim(&self) -> usize {
+        self.view.ndim()
+    }
+
+    /// find the position of an axis
+    #[pyo3(text_signature = "axis: str | int")]
+    fn get_ax(&self, axis: Bound<PyAny>) -> PyResult<usize> {
+        if axis.is_instance_of::<PyString>() {
+            let axis = axis
+                .cast_into::<PyString>()?
+                .extract::<String>()?
+                .parse::<Axis>()?;
+            self.view
+                .axes()
+                .iter()
+                .position(|a| *a == axis)
+                .ok_or_else(|| {
+                    PyErr::new::<PyValueError, _>(format!("cannot find axis {:?}", axis))
+                })
+        } else if axis.is_instance_of::<PyInt>() {
+            Ok(axis.cast_into::<PyInt>()?.extract::<usize>()?)
+        } else {
+            Err(PyErr::new::<PyValueError, _>(
+                "cannot convert to axis".to_string(),
+            ))
+        }
+    }
+
+    /// swap two axes
+    #[pyo3(text_signature = "ax0: str | int, ax1: str | int")]
+    fn swap_axes(&self, ax0: Bound<PyAny>, ax1: Bound<PyAny>) -> PyResult<Self> {
+        let ax0 = self.get_ax(ax0)?;
+        let ax1 = self.get_ax(ax1)?;
+        let view = self.view.swap_axes(ax0, ax1)?;
+        Ok(PyView {
+            view,
+            dtype: self.dtype.clone(),
+            ome: self.ome.clone(),
+        })
+    }
+
+    /// permute the order of the axes
+    #[pyo3(signature = (axes = None), text_signature = "axes: list[str | int] = None")]
+    fn transpose(&self, axes: Option<Vec<Bound<PyAny>>>) -> PyResult<Self> {
+        let view = if let Some(axes) = axes {
+            let ax = axes
+                .into_iter()
+                .map(|a| self.get_ax(a))
+                .collect::<Result<Vec<_>, _>>()?;
+            self.view.permute_axes(&ax)?
+        } else {
+            self.view.transpose()?
+        };
+        Ok(PyView {
+            view,
+            dtype: self.dtype.clone(),
+            ome: self.ome.clone(),
+        })
+    }
+
+    #[allow(non_snake_case)]
+    #[getter]
+    fn T(&self) -> PyResult<Self> {
+        self.transpose(None)
+    }
+
+    /// collect data into a numpy array
+    fn as_array<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
+        Ok(match self.dtype {
+            PixelType::I8 => self.view.as_array_dyn::<i8>()?.into_pyarray(py).into_any(),
+            PixelType::U8 => self.view.as_array_dyn::<u8>()?.into_pyarray(py).into_any(),
+            PixelType::I16 => self.view.as_array_dyn::<i16>()?.into_pyarray(py).into_any(),
+            PixelType::U16 => self.view.as_array_dyn::<u16>()?.into_pyarray(py).into_any(),
+            PixelType::I32 => self.view.as_array_dyn::<i32>()?.into_pyarray(py).into_any(),
+            PixelType::U32 => self.view.as_array_dyn::<u32>()?.into_pyarray(py).into_any(),
+            PixelType::F32 => self.view.as_array_dyn::<f32>()?.into_pyarray(py).into_any(),
+            PixelType::F64 => self.view.as_array_dyn::<f64>()?.into_pyarray(py).into_any(),
+            PixelType::I64 => self.view.as_array_dyn::<i64>()?.into_pyarray(py).into_any(),
+            PixelType::U64 => self.view.as_array_dyn::<u64>()?.into_pyarray(py).into_any(),
+            PixelType::I128 => self.view.as_array_dyn::<i64>()?.into_pyarray(py).into_any(),
+            PixelType::U128 => self.view.as_array_dyn::<u64>()?.into_pyarray(py).into_any(),
+            PixelType::F128 => self.view.as_array_dyn::<f64>()?.into_pyarray(py).into_any(),
+        })
+    }
+
+    #[getter]
+    fn get_dtype(&self) -> PyResult<&str> {
+        Ok(match self.dtype {
+            PixelType::I8 => "int8",
+            PixelType::U8 => "uint8",
+            PixelType::I16 => "int16",
+            PixelType::U16 => "uint16",
+            PixelType::I32 => "int32",
+            PixelType::U32 => "uint32",
+            PixelType::F32 => "float32",
+            PixelType::F64 => "float64",
+            PixelType::I64 => "int64",
+            PixelType::U64 => "uint64",
+            PixelType::I128 => "int128",
+            PixelType::U128 => "uint128",
+            PixelType::F128 => "float128",
+        })
+    }
+
+    #[setter]
+    fn set_dtype(&mut self, dtype: String) -> PyResult<()> {
+        self.dtype = dtype.parse()?;
+        Ok(())
+    }
+
+    /// get the maximum overall or along a given axis
+    #[allow(clippy::too_many_arguments)]
+    #[pyo3(signature = (axis=None, dtype=None, out=None, keepdims=false, initial=0, r#where=true), text_signature = "axis: str | int")]
+    fn max<'py>(
+        &self,
+        py: Python<'py>,
+        axis: Option<Bound<'py, PyAny>>,
+        dtype: Option<Bound<'py, PyAny>>,
+        out: Option<Bound<'py, PyAny>>,
+        keepdims: bool,
+        initial: Option<usize>,
+        r#where: bool,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        if let Some(i) = initial
+            && i != 0
+        {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        if dtype.is_some() || out.is_some() || keepdims || !r#where {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        if let Some(axis) = axis {
+            PyView {
+                dtype: self.dtype.clone(),
+                view: self.view.max_proj(self.get_ax(axis)?)?,
+                ome: self.ome.clone(),
+            }
+            .into_bound_py_any(py)
+        } else {
+            Ok(match self.dtype {
+                PixelType::I8 => self.view.max::<i8>()?.into_pyobject(py)?.into_any(),
+                PixelType::U8 => self.view.max::<u8>()?.into_pyobject(py)?.into_any(),
+                PixelType::I16 => self.view.max::<i16>()?.into_pyobject(py)?.into_any(),
+                PixelType::U16 => self.view.max::<u16>()?.into_pyobject(py)?.into_any(),
+                PixelType::I32 => self.view.max::<i32>()?.into_pyobject(py)?.into_any(),
+                PixelType::U32 => self.view.max::<u32>()?.into_pyobject(py)?.into_any(),
+                PixelType::F32 => self.view.max::<f32>()?.into_pyobject(py)?.into_any(),
+                PixelType::F64 => self.view.max::<f64>()?.into_pyobject(py)?.into_any(),
+                PixelType::I64 => self.view.max::<i64>()?.into_pyobject(py)?.into_any(),
+                PixelType::U64 => self.view.max::<u64>()?.into_pyobject(py)?.into_any(),
+                PixelType::I128 => self.view.max::<i64>()?.into_pyobject(py)?.into_any(),
+                PixelType::U128 => self.view.max::<u64>()?.into_pyobject(py)?.into_any(),
+                PixelType::F128 => self.view.max::<f64>()?.into_pyobject(py)?.into_any(),
+            })
+        }
+    }
+
+    /// get the minimum overall or along a given axis
+    #[allow(clippy::too_many_arguments)]
+    #[pyo3(signature = (axis=None, dtype=None, out=None, keepdims=false, initial=0, r#where=true), text_signature = "axis: str | int")]
+    fn min<'py>(
+        &self,
+        py: Python<'py>,
+        axis: Option<Bound<'py, PyAny>>,
+        dtype: Option<Bound<'py, PyAny>>,
+        out: Option<Bound<'py, PyAny>>,
+        keepdims: bool,
+        initial: Option<usize>,
+        r#where: bool,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        if let Some(i) = initial
+            && i != 0
+        {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        if dtype.is_some() || out.is_some() || keepdims || !r#where {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        if let Some(axis) = axis {
+            PyView {
+                dtype: self.dtype.clone(),
+                view: self.view.min_proj(self.get_ax(axis)?)?,
+                ome: self.ome.clone(),
+            }
+            .into_bound_py_any(py)
+        } else {
+            Ok(match self.dtype {
+                PixelType::I8 => self.view.min::<i8>()?.into_pyobject(py)?.into_any(),
+                PixelType::U8 => self.view.min::<u8>()?.into_pyobject(py)?.into_any(),
+                PixelType::I16 => self.view.min::<i16>()?.into_pyobject(py)?.into_any(),
+                PixelType::U16 => self.view.min::<u16>()?.into_pyobject(py)?.into_any(),
+                PixelType::I32 => self.view.min::<i32>()?.into_pyobject(py)?.into_any(),
+                PixelType::U32 => self.view.min::<u32>()?.into_pyobject(py)?.into_any(),
+                PixelType::F32 => self.view.min::<f32>()?.into_pyobject(py)?.into_any(),
+                PixelType::F64 => self.view.min::<f64>()?.into_pyobject(py)?.into_any(),
+                PixelType::I64 => self.view.min::<i64>()?.into_pyobject(py)?.into_any(),
+                PixelType::U64 => self.view.min::<u64>()?.into_pyobject(py)?.into_any(),
+                PixelType::I128 => self.view.min::<i64>()?.into_pyobject(py)?.into_any(),
+                PixelType::U128 => self.view.min::<u64>()?.into_pyobject(py)?.into_any(),
+                PixelType::F128 => self.view.min::<f64>()?.into_pyobject(py)?.into_any(),
+            })
+        }
+    }
+
+    #[pyo3(signature = (axis=None, dtype=None, out=None, keepdims=false, *, r#where=true), text_signature = "axis: str | int")]
+    fn mean<'py>(
+        &self,
+        py: Python<'py>,
+        axis: Option<Bound<'py, PyAny>>,
+        dtype: Option<Bound<'py, PyAny>>,
+        out: Option<Bound<'py, PyAny>>,
+        keepdims: bool,
+        r#where: bool,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        if dtype.is_some() || out.is_some() || keepdims || !r#where {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        if let Some(axis) = axis {
+            let dtype = if let PixelType::F32 = self.dtype {
+                PixelType::F32
+            } else {
+                PixelType::F64
+            };
+            PyView {
+                dtype,
+                view: self.view.mean_proj(self.get_ax(axis)?)?,
+                ome: self.ome.clone(),
+            }
+            .into_bound_py_any(py)
+        } else {
+            Ok(match self.dtype {
+                PixelType::F32 => self.view.mean::<f32>()?.into_pyobject(py)?.into_any(),
+                _ => self.view.mean::<f64>()?.into_pyobject(py)?.into_any(),
+            })
+        }
+    }
+
+    /// get the sum overall or along a given axis
+    #[allow(clippy::too_many_arguments)]
+    #[pyo3(signature = (axis=None, dtype=None, out=None, keepdims=false, initial=0, r#where=true), text_signature = "axis: str | int")]
+    fn sum<'py>(
+        &self,
+        py: Python<'py>,
+        axis: Option<Bound<'py, PyAny>>,
+        dtype: Option<Bound<'py, PyAny>>,
+        out: Option<Bound<'py, PyAny>>,
+        keepdims: bool,
+        initial: Option<usize>,
+        r#where: bool,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        if let Some(i) = initial
+            && i != 0
+        {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        if dtype.is_some() || out.is_some() || keepdims || !r#where {
+            Err(Error::NotImplemented(
+                "arguments beyond axis are not implemented".to_string(),
+            ))?;
+        }
+        let dtype = match self.dtype {
+            PixelType::I8 => PixelType::I16,
+            PixelType::U8 => PixelType::U16,
+            PixelType::I16 => PixelType::I32,
+            PixelType::U16 => PixelType::U32,
+            PixelType::I32 => PixelType::I64,
+            PixelType::U32 => PixelType::U64,
+            PixelType::F32 => PixelType::F32,
+            PixelType::F64 => PixelType::F64,
+            PixelType::I64 => PixelType::I128,
+            PixelType::U64 => PixelType::U128,
+            PixelType::I128 => PixelType::I128,
+            PixelType::U128 => PixelType::U128,
+            PixelType::F128 => PixelType::F128,
+        };
+        if let Some(axis) = axis {
+            PyView {
+                dtype,
+                view: self.view.sum_proj(self.get_ax(axis)?)?,
+                ome: self.ome.clone(),
+            }
+            .into_bound_py_any(py)
+        } else {
+            Ok(match self.dtype {
+                PixelType::F32 => self.view.sum::<f32>()?.into_pyobject(py)?.into_any(),
+                PixelType::F64 => self.view.sum::<f64>()?.into_pyobject(py)?.into_any(),
+                PixelType::I64 => self.view.sum::<i64>()?.into_pyobject(py)?.into_any(),
+                PixelType::U64 => self.view.sum::<u64>()?.into_pyobject(py)?.into_any(),
+                PixelType::I128 => self.view.sum::<i64>()?.into_pyobject(py)?.into_any(),
+                PixelType::U128 => self.view.sum::<u64>()?.into_pyobject(py)?.into_any(),
+                PixelType::F128 => self.view.sum::<f64>()?.into_pyobject(py)?.into_any(),
+                _ => self.view.sum::<i64>()?.into_pyobject(py)?.into_any(),
+            })
+        }
+    }
+
+    #[getter]
+    fn z_stack(&self) -> PyResult<bool> {
+        if let Some(s) = self.view.size_ax(Axis::Z) {
+            Ok(s > 1)
+        } else {
+            Ok(false)
+        }
+    }
+
+    #[getter]
+    fn time_series(&self) -> PyResult<bool> {
+        if let Some(s) = self.view.size_ax(Axis::T) {
+            Ok(s > 1)
+        } else {
+            Ok(false)
+        }
+    }
+
+    #[getter]
+    fn pixel_size(&self) -> PyResult<Option<f64>> {
+        Ok(self.ome.pixel_size()?)
+    }
+
+    #[getter]
+    fn delta_z(&self) -> PyResult<Option<f64>> {
+        Ok(self.ome.delta_z()?)
+    }
+
+    #[getter]
+    fn time_interval(&self) -> PyResult<Option<f64>> {
+        Ok(self.ome.time_interval()?)
+    }
+
+    fn exposure_time(&self, channel: usize) -> PyResult<Option<f64>> {
+        Ok(self.ome.exposure_time(channel)?)
+    }
+
+    fn binning(&self, channel: usize) -> Option<usize> {
+        self.ome.binning(channel)
+    }
+
+    fn laser_wavelengths(&self, channel: usize) -> PyResult<Option<f64>> {
+        Ok(self.ome.laser_wavelengths(channel)?)
+    }
+
+    fn laser_power(&self, channel: usize) -> PyResult<Option<f64>> {
+        Ok(self.ome.laser_powers(channel)?)
+    }
+
+    #[getter]
+    fn objective_name(&self) -> Option<String> {
+        self.ome.objective_name()
+    }
+
+    #[getter]
+    fn magnification(&self) -> Option<f64> {
+        self.ome.magnification()
+    }
+
+    #[getter]
+    fn tube_lens_name(&self) -> Option<String> {
+        self.ome.tube_lens_name()
+    }
+
+    fn filter_set_name(&self, channel: usize) -> Option<String> {
+        self.ome.filter_set_name(channel)
+    }
+
+    fn gain(&self, channel: usize) -> Option<f64> {
+        self.ome.gain(channel)
+    }
+
+    /// gives a helpful summary of the recorded experiment
+    fn summary(&self) -> PyResult<String> {
+        Ok(self.view.summary()?)
+    }
+}
+
+pub(crate) fn ndbioimage_file() -> PathBuf {
+    let file = Python::attach(|py| {
+        py.import("ndbioimage")
+            .unwrap()
+            .filename()
+            .unwrap()
+            .to_string()
+    });
+    PathBuf::from(file)
+}
+
+#[pyfunction]
+#[pyo3(name = "download_bioformats")]
+fn py_download_bioformats(gpl_formats: bool) -> PyResult<()> {
+    download_bioformats(gpl_formats)?;
+    Ok(())
+}
+
+#[pymodule]
+#[pyo3(name = "ndbioimage_rs")]
+fn ndbioimage_rs(m: &Bound<PyModule>) -> PyResult<()> {
+    m.add_class::<PyView>()?;
+    m.add_class::<ViewConstructor>()?;
+    m.add_function(wrap_pyfunction!(py_download_bioformats, m)?)?;
+    Ok(())
+}

src/reader.rs

@@ -0,0 +1,487 @@
+use crate::axes::Axis;
+use crate::bioformats;
+use crate::bioformats::{DebugTools, ImageReader, MetadataTools};
+use crate::error::Error;
+use crate::view::View;
+use ndarray::{Array2, Ix5, s};
+use num::{FromPrimitive, Zero};
+use ome_metadata::Ome;
+use serde::{Deserialize, Serialize};
+use std::any::type_name;
+use std::fmt::Debug;
+use std::ops::Deref;
+use std::path::{Path, PathBuf};
+use std::str::FromStr;
+use std::sync::Arc;
+use thread_local::ThreadLocal;
+
+pub fn split_path_and_series<P>(path: P) -> Result<(PathBuf, Option<usize>), Error>
+where
+    P: Into<PathBuf>,
+{
+    let path = path.into();
+    let file_name = path
+        .file_name()
+        .ok_or(Error::InvalidFileName)?
+        .to_str()
+        .ok_or(Error::InvalidFileName)?;
+    if file_name.to_lowercase().starts_with("pos") {
+        if let Some(series) = file_name.get(3..) {
+            if let Ok(series) = series.parse::<usize>() {
+                return Ok((path, Some(series)));
+            }
+        }
+    }
+    Ok((path, None))
+}
+
+/// Pixel types (u)int(8/16/32) or float(32/64), (u/i)(64/128) are not included in bioformats
+#[allow(clippy::upper_case_acronyms)]
+#[derive(Clone, Debug, Serialize, Deserialize)]
+pub enum PixelType {
+    I8,
+    U8,
+    I16,
+    U16,
+    I32,
+    U32,
+    F32,
+    F64,
+    I64,
+    U64,
+    I128,
+    U128,
+    F128,
+}
+
+impl TryFrom<i32> for PixelType {
+    type Error = Error;
+
+    fn try_from(value: i32) -> Result<Self, Self::Error> {
+        match value {
+            0 => Ok(PixelType::I8),
+            1 => Ok(PixelType::U8),
+            2 => Ok(PixelType::I16),
+            3 => Ok(PixelType::U16),
+            4 => Ok(PixelType::I32),
+            5 => Ok(PixelType::U32),
+            6 => Ok(PixelType::F32),
+            7 => Ok(PixelType::F64),
+            8 => Ok(PixelType::I64),
+            9 => Ok(PixelType::U64),
+            10 => Ok(PixelType::I128),
+            11 => Ok(PixelType::U128),
+            12 => Ok(PixelType::F128),
+            _ => Err(Error::UnknownPixelType(value.to_string())),
+        }
+    }
+}
+
+impl FromStr for PixelType {
+    type Err = Error;
+
+    fn from_str(s: &str) -> Result<Self, Self::Err> {
+        match s.to_lowercase().as_str() {
+            "int8" | "i8" => Ok(PixelType::I8),
+            "uint8" | "u8" => Ok(PixelType::U8),
+            "int16" | "i16" => Ok(PixelType::I16),
+            "uint16" | "u16" => Ok(PixelType::U16),
+            "int32" | "i32" => Ok(PixelType::I32),
+            "uint32" | "u32" => Ok(PixelType::U32),
+            "float" | "f32" | "float32" => Ok(PixelType::F32),
+            "double" | "f64" | "float64" => Ok(PixelType::F64),
+            "int64" | "i64" => Ok(PixelType::I64),
+            "uint64" | "u64" => Ok(PixelType::U64),
+            "int128" | "i128" => Ok(PixelType::I128),
+            "uint128" | "u128" => Ok(PixelType::U128),
+            "extended" | "f128" => Ok(PixelType::F128),
+            _ => Err(Error::UnknownPixelType(s.to_string())),
+        }
+    }
+}
+
+/// Struct containing frame data in one of eight pixel types. Cast to `Array2<T>` using try_into.
+#[allow(clippy::upper_case_acronyms)]
+#[derive(Clone, Debug)]
+pub enum Frame {
+    I8(Array2<i8>),
+    U8(Array2<u8>),
+    I16(Array2<i16>),
+    U16(Array2<u16>),
+    I32(Array2<i32>),
+    U32(Array2<u32>),
+    F32(Array2<f32>),
+    F64(Array2<f64>),
+    I64(Array2<i64>),
+    U64(Array2<u64>),
+    I128(Array2<i128>),
+    U128(Array2<u128>),
+    F128(Array2<f64>), // f128 is nightly
+}
+
+macro_rules! impl_frame_cast {
+    ($($t:tt: $s:ident $(,)?)*) => {
+        $(
+            impl From<Array2<$t>> for Frame {
+                fn from(value: Array2<$t>) -> Self {
+                    Frame::$s(value)
+                }
+            }
+        )*
+    };
+}
+
+impl_frame_cast! {
+    u8: U8
+    i8: I8
+    i16: I16
+    u16: U16
+    i32: I32
+    u32: U32
+    f32: F32
+    f64: F64
+    i64: I64
+    u64: U64
+    i128: I128
+    u128: U128
+}
+
+#[cfg(target_pointer_width = "32")]
+impl_frame_cast! {
+    usize: UINT32
+    isize: INT32
+}
+
+impl<T> TryInto<Array2<T>> for Frame
+where
+    T: FromPrimitive + Zero + 'static,
+{
+    type Error = Error;
+
+    fn try_into(self) -> Result<Array2<T>, Self::Error> {
+        let mut err = Ok(());
+        let arr = match self {
+            Frame::I8(v) => v.mapv_into_any(|x| {
+                T::from_i8(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::U8(v) => v.mapv_into_any(|x| {
+                T::from_u8(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::I16(v) => v.mapv_into_any(|x| {
+                T::from_i16(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::U16(v) => v.mapv_into_any(|x| {
+                T::from_u16(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::I32(v) => v.mapv_into_any(|x| {
+                T::from_i32(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::U32(v) => v.mapv_into_any(|x| {
+                T::from_u32(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::F32(v) => v.mapv_into_any(|x| {
+                T::from_f32(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::F64(v) | Frame::F128(v) => v.mapv_into_any(|x| {
+                T::from_f64(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::I64(v) => v.mapv_into_any(|x| {
+                T::from_i64(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::U64(v) => v.mapv_into_any(|x| {
+                T::from_u64(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::I128(v) => v.mapv_into_any(|x| {
+                T::from_i128(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+            Frame::U128(v) => v.mapv_into_any(|x| {
+                T::from_u128(x).unwrap_or_else(|| {
+                    err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
+                    T::zero()
+                })
+            }),
+        };
+        match err {
+            Err(err) => Err(err),
+            Ok(()) => Ok(arr),
+        }
+    }
+}
+
+/// Reader interface to file. Use get_frame to get data.
+#[derive(Serialize, Deserialize)]
+pub struct Reader {
+    #[serde(skip)]
+    image_reader: ThreadLocal<ImageReader>,
+    /// path to file
+    pub path: PathBuf,
+    /// which (if more than 1) of the series in the file to open
+    pub series: usize,
+    /// size x (horizontal)
+    pub size_x: usize,
+    /// size y (vertical)
+    pub size_y: usize,
+    /// size c (# channels)
+    pub size_c: usize,
+    /// size z (# slices)
+    pub size_z: usize,
+    /// size t (# time/frames)
+    pub size_t: usize,
+    /// pixel type ((u)int(8/16/32) or float(32/64))
+    pub pixel_type: PixelType,
+    little_endian: bool,
+}
+
+impl Deref for Reader {
+    type Target = ImageReader;
+
+    fn deref(&self) -> &Self::Target {
+        self.get_reader().unwrap()
+    }
+}
+
+impl Clone for Reader {
+    fn clone(&self) -> Self {
+        Reader::new(&self.path, self.series).unwrap()
+    }
+}
+
+impl Debug for Reader {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        f.debug_struct("Reader")
+            .field("path", &self.path)
+            .field("series", &self.series)
+            .field("size_x", &self.size_x)
+            .field("size_y", &self.size_y)
+            .field("size_c", &self.size_c)
+            .field("size_z", &self.size_z)
+            .field("size_t", &self.size_t)
+            .field("pixel_type", &self.pixel_type)
+            .field("little_endian", &self.little_endian)
+            .finish()
+    }
+}
+
+impl Reader {
+    /// Create a new reader for the image file at a path, and open series #.
+    pub fn new<P>(path: P, series: usize) -> Result<Self, Error>
+    where
+        P: AsRef<Path>,
+    {
+        DebugTools::set_root_level("ERROR")?;
+        let mut reader = Reader {
+            image_reader: ThreadLocal::default(),
+            path: path.as_ref().to_path_buf(),
+            series,
+            size_x: 0,
+            size_y: 0,
+            size_c: 0,
+            size_z: 0,
+            size_t: 0,
+            pixel_type: PixelType::I8,
+            little_endian: false,
+        };
+        reader.set_reader()?;
+        reader.size_x = reader.get_size_x()? as usize;
+        reader.size_y = reader.get_size_y()? as usize;
+        reader.size_c = reader.get_size_c()? as usize;
+        reader.size_z = reader.get_size_z()? as usize;
+        reader.size_t = reader.get_size_t()? as usize;
+        reader.pixel_type = PixelType::try_from(reader.get_pixel_type()?)?;
+        reader.little_endian = reader.is_little_endian()?;
+        Ok(reader)
+    }
+
+    fn get_reader(&self) -> Result<&ImageReader, Error> {
+        self.image_reader.get_or_try(|| {
+            let reader = ImageReader::new()?;
+            let meta_data_tools = MetadataTools::new()?;
+            let ome_meta = meta_data_tools.create_ome_xml_metadata()?;
+            reader.set_metadata_store(ome_meta)?;
+            reader.set_id(self.path.to_str().ok_or(Error::InvalidFileName)?)?;
+            reader.set_series(self.series as i32)?;
+            Ok(reader)
+        })
+    }
+
+    pub fn set_reader(&self) -> Result<(), Error> {
+        self.get_reader().map(|_| ())
+    }
+
+    /// Get ome metadata as ome structure
+    pub fn get_ome(&self) -> Result<Ome, Error> {
+        let mut ome = self.ome_xml()?.parse::<Ome>()?;
+        if ome.image.len() > 1 {
+            ome.image = vec![ome.image[self.series].clone()];
+        }
+        Ok(ome)
+    }
+
+    /// Get ome metadata as xml string
+    pub fn get_ome_xml(&self) -> Result<String, Error> {
+        self.ome_xml()
+    }
+
+    fn deinterleave(&self, bytes: Vec<u8>, channel: usize) -> Result<Vec<u8>, Error> {
+        let chunk_size = match self.pixel_type {
+            PixelType::I8 => 1,
+            PixelType::U8 => 1,
+            PixelType::I16 => 2,
+            PixelType::U16 => 2,
+            PixelType::I32 => 4,
+            PixelType::U32 => 4,
+            PixelType::F32 => 4,
+            PixelType::F64 => 8,
+            PixelType::I64 => 8,
+            PixelType::U64 => 8,
+            PixelType::I128 => 16,
+            PixelType::U128 => 16,
+            PixelType::F128 => 8,
+        };
+        Ok(bytes
+            .chunks(chunk_size)
+            .skip(channel)
+            .step_by(self.size_c)
+            .flat_map(|a| a.to_vec())
+            .collect())
+    }
+
+    /// Retrieve fame at channel c, slize z and time t.
+    #[allow(clippy::if_same_then_else)]
+    pub fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
+        let bytes = if self.is_rgb()? && self.is_interleaved()? {
+            let index = self.get_index(z as i32, 0, t as i32)?;
+            self.deinterleave(self.open_bytes(index)?, c)?
+        } else if self.get_rgb_channel_count()? > 1 {
+            let channel_separator = bioformats::ChannelSeparator::new(self)?;
+            let index = channel_separator.get_index(z as i32, c as i32, t as i32)?;
+            channel_separator.open_bytes(index)?
+        } else if self.is_indexed()? {
+            let index = self.get_index(z as i32, c as i32, t as i32)?;
+            self.open_bytes(index)?
+            // TODO: apply LUT
+            // let _bytes_lut = match self.pixel_type {
+            //     PixelType::INT8 | PixelType::UINT8 => {
+            //         let _lut = self.image_reader.get_8bit_lookup_table()?;
+            //     }
+            //     PixelType::INT16 | PixelType::UINT16 => {
+            //         let _lut = self.image_reader.get_16bit_lookup_table()?;
+            //     }
+            //     _ => {}
+            // };
+        } else {
+            let index = self.get_index(z as i32, c as i32, t as i32)?;
+            self.open_bytes(index)?
+        };
+        self.bytes_to_frame(bytes)
+    }
+
+    fn bytes_to_frame(&self, bytes: Vec<u8>) -> Result<Frame, Error> {
+        macro_rules! get_frame {
+            ($t:tt, <$n:expr) => {
+                Ok(Frame::from(Array2::from_shape_vec(
+                    (self.size_y, self.size_x),
+                    bytes
+                        .chunks($n)
+                        .map(|x| $t::from_le_bytes(x.try_into().unwrap()))
+                        .collect(),
+                )?))
+            };
+            ($t:tt, >$n:expr) => {
+                Ok(Frame::from(Array2::from_shape_vec(
+                    (self.size_y, self.size_x),
+                    bytes
+                        .chunks($n)
+                        .map(|x| $t::from_be_bytes(x.try_into().unwrap()))
+                        .collect(),
+                )?))
+            };
+        }
+
+        match (&self.pixel_type, self.little_endian) {
+            (PixelType::I8, true) => get_frame!(i8, <1),
+            (PixelType::U8, true) => get_frame!(u8, <1),
+            (PixelType::I16, true) => get_frame!(i16, <2),
+            (PixelType::U16, true) => get_frame!(u16, <2),
+            (PixelType::I32, true) => get_frame!(i32, <4),
+            (PixelType::U32, true) => get_frame!(u32, <4),
+            (PixelType::F32, true) => get_frame!(f32, <4),
+            (PixelType::F64, true) => get_frame!(f64, <8),
+            (PixelType::I64, true) => get_frame!(i64, <8),
+            (PixelType::U64, true) => get_frame!(u64, <8),
+            (PixelType::I128, true) => get_frame!(i128, <16),
+            (PixelType::U128, true) => get_frame!(u128, <16),
+            (PixelType::F128, true) => get_frame!(f64, <8),
+            (PixelType::I8, false) => get_frame!(i8, >1),
+            (PixelType::U8, false) => get_frame!(u8, >1),
+            (PixelType::I16, false) => get_frame!(i16, >2),
+            (PixelType::U16, false) => get_frame!(u16, >2),
+            (PixelType::I32, false) => get_frame!(i32, >4),
+            (PixelType::U32, false) => get_frame!(u32, >4),
+            (PixelType::F32, false) => get_frame!(f32, >4),
+            (PixelType::F64, false) => get_frame!(f64, >8),
+            (PixelType::I64, false) => get_frame!(i64, >8),
+            (PixelType::U64, false) => get_frame!(u64, >8),
+            (PixelType::I128, false) => get_frame!(i128, >16),
+            (PixelType::U128, false) => get_frame!(u128, >16),
+            (PixelType::F128, false) => get_frame!(f64, >8),
+        }
+    }
+
+    /// get a sliceable view on the image file
+    pub fn view(&self) -> View<Ix5> {
+        let slice = s![
+            0..self.size_c,
+            0..self.size_z,
+            0..self.size_t,
+            0..self.size_y,
+            0..self.size_x
+        ];
+        View::new(
+            Arc::new(self.clone()),
+            slice.as_ref().to_vec(),
+            vec![Axis::C, Axis::Z, Axis::T, Axis::Y, Axis::X],
+        )
+    }
+}
+
+impl Drop for Reader {
+    fn drop(&mut self) {
+        if let Ok(reader) = self.get_reader() {
+            reader.close().unwrap();
+        }
+    }
+}

src/stats.rs

@@ -0,0 +1,205 @@
+use crate::error::Error;
+use ndarray::{Array, ArrayD, ArrayView, Axis, Dimension, RemoveAxis};
+
+/// a trait to define the min, max, sum and mean operations along an axis
+pub trait MinMax {
+    type Output;
+
+    fn max(self, axis: usize) -> Result<Self::Output, Error>;
+    fn min(self, axis: usize) -> Result<Self::Output, Error>;
+    fn sum(self, axis: usize) -> Result<Self::Output, Error>;
+    fn mean(self, axis: usize) -> Result<Self::Output, Error>;
+}
+
+macro_rules! impl_frame_stats_float_view {
+    ($($t:tt),+ $(,)?) => {
+        $(
+            impl<D> MinMax for ArrayView<'_, $t, D>
+            where
+                D: Dimension + RemoveAxis,
+            {
+                type Output = Array<$t, D::Smaller>;
+
+                fn max(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| {
+                            x.iter()
+                                .fold($t::NEG_INFINITY, |prev, curr| prev.max(*curr))
+                        })
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn min(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| {
+                            x.iter()
+                                .fold($t::INFINITY, |prev, curr| prev.min(*curr))
+                        })
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn sum(self, axis: usize) -> Result<Self::Output, Error> {
+                    Ok(self.sum_axis(Axis(axis)))
+                }
+
+                fn mean(self, axis: usize) -> Result<Self::Output, Error> {
+                    self.mean_axis(Axis(axis)).ok_or(Error::NoMean)
+                }
+            }
+        )*
+    };
+}
+
+macro_rules! impl_frame_stats_int_view {
+    ($($t:tt),+ $(,)?) => {
+        $(
+            impl<D> MinMax for ArrayView<'_, $t, D>
+            where
+                D: Dimension + RemoveAxis,
+            {
+                type Output = Array<$t, D::Smaller>;
+
+                fn max(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| *x.iter().max().unwrap())
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn min(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| *x.iter().min().unwrap())
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn sum(self, axis: usize) -> Result<Self::Output, Error> {
+                    Ok(self.sum_axis(Axis(axis)))
+                }
+
+                fn mean(self, axis: usize) -> Result<Self::Output, Error> {
+                    self.mean_axis(Axis(axis)).ok_or(Error::NoMean)
+                }
+            }
+        )*
+    };
+}
+
+macro_rules! impl_frame_stats_float {
+    ($($t:tt),+ $(,)?) => {
+        $(
+            impl<D> MinMax for Array<$t, D>
+            where
+                D: Dimension + RemoveAxis,
+            {
+                type Output = Array<$t, D::Smaller>;
+
+                fn max(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| {
+                            x.iter()
+                                .fold($t::NEG_INFINITY, |prev, curr| prev.max(*curr))
+                        })
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn min(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| {
+                            x.iter()
+                                .fold($t::INFINITY, |prev, curr| prev.min(*curr))
+                        })
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn sum(self, axis: usize) -> Result<Self::Output, Error> {
+                    Ok(self.sum_axis(Axis(axis)))
+                }
+
+                fn mean(self, axis: usize) -> Result<Self::Output, Error> {
+                    self.mean_axis(Axis(axis)).ok_or(Error::NoMean)
+                }
+            }
+        )*
+    };
+}
+
+macro_rules! impl_frame_stats_int {
+    ($($t:tt),+ $(,)?) => {
+        $(
+            impl<D> MinMax for Array<$t, D>
+            where
+                D: Dimension + RemoveAxis,
+            {
+                type Output = Array<$t, D::Smaller>;
+
+                fn max(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| *x.iter().max().unwrap())
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn min(self, axis: usize) -> Result<Self::Output, Error> {
+                    let a: Vec<_> = self
+                        .lanes(Axis(axis))
+                        .into_iter()
+                        .map(|x| *x.iter().min().unwrap())
+                        .collect();
+                    let mut shape = self.shape().to_vec();
+                    shape.remove(axis);
+                    Ok(ArrayD::from_shape_vec(shape, a)?.into_dimensionality()?)
+                }
+
+                fn sum(self, axis: usize) -> Result<Self::Output, Error> {
+                    Ok(self.sum_axis(Axis(axis)))
+                }
+
+                fn mean(self, axis: usize) -> Result<Self::Output, Error> {
+                    self.mean_axis(Axis(axis)).ok_or(Error::NoMean)
+                }
+            }
+        )*
+    };
+}
+
+impl_frame_stats_float_view!(f32, f64);
+impl_frame_stats_int_view!(
+    u8, i8, u16, i16, u32, i32, u64, i64, u128, i128, usize, isize
+);
+impl_frame_stats_float!(f32, f64);
+impl_frame_stats_int!(
+    u8, i8, u16, i16, u32, i32, u64, i64, u128, i128, usize, isize
+);

src/tiff.rs

@@ -0,0 +1,193 @@
+use crate::colors::Color;
+use crate::error::Error;
+use crate::metadata::Metadata;
+use crate::reader::PixelType;
+use crate::stats::MinMax;
+use crate::view::{Number, View};
+use indicatif::{ProgressBar, ProgressStyle};
+use itertools::iproduct;
+use ndarray::{Array0, Array1, Array2, ArrayD, Dimension};
+use rayon::prelude::*;
+use std::path::Path;
+use std::sync::{Arc, Mutex};
+use tiffwrite::{Bytes, Colors, Compression, IJTiffFile};
+
+#[derive(Clone)]
+pub struct TiffOptions {
+    bar: Option<ProgressStyle>,
+    compression: Compression,
+    colors: Option<Vec<Vec<u8>>>,
+    overwrite: bool,
+}
+
+impl Default for TiffOptions {
+    fn default() -> Self {
+        Self {
+            bar: None,
+            compression: Compression::Zstd(10),
+            colors: None,
+            overwrite: false,
+        }
+    }
+}
+
+impl TiffOptions {
+    pub fn new(
+        bar: bool,
+        compression: Option<Compression>,
+        colors: Vec<String>,
+        overwrite: bool,
+    ) -> Result<Self, Error> {
+        let mut options = Self {
+            bar: None,
+            compression: compression.unwrap_or(Compression::Zstd(10)),
+            colors: None,
+            overwrite,
+        };
+        if bar {
+            options.enable_bar()?;
+        }
+        if !colors.is_empty() {
+            options.set_colors(&colors)?;
+        }
+        Ok(options)
+    }
+
+    /// show a progress bar while saving tiff
+    pub fn enable_bar(&mut self) -> Result<(), Error> {
+        self.bar = Some(ProgressStyle::with_template(
+            "{spinner:.green} [{elapsed_precise}, {percent}%] [{wide_bar:.green/lime}] {pos:>7}/{len:7} ({eta_precise}, {per_sec:<5})",
+        )?.progress_chars("▰▱▱"));
+        Ok(())
+    }
+
+    /// do not show a progress bar while saving tiff
+    pub fn disable_bar(&mut self) {
+        self.bar = None;
+    }
+
+    /// save tiff with zstd compression (default)
+    pub fn set_zstd_compression(&mut self) {
+        self.compression = Compression::Zstd(10)
+    }
+
+    /// save tiff with zstd compression, choose a level between 7..=22
+    pub fn set_zstd_compression_level(&mut self, level: i32) {
+        self.compression = Compression::Zstd(level)
+    }
+
+    /// save tiff with deflate compression
+    pub fn set_deflate_compression(&mut self) {
+        self.compression = Compression::Deflate
+    }
+
+    pub fn set_colors(&mut self, colors: &[String]) -> Result<(), Error> {
+        let colors = colors
+            .iter()
+            .map(|c| c.parse::<Color>())
+            .collect::<Result<Vec<_>, Error>>()?;
+        self.colors = Some(colors.into_iter().map(|c| c.to_rgb()).collect());
+        Ok(())
+    }
+
+    pub fn set_overwrite(&mut self, overwrite: bool) {
+        self.overwrite = overwrite;
+    }
+}
+
+impl<D> View<D>
+where
+    D: Dimension,
+{
+    /// save as tiff with a certain type
+    pub fn save_as_tiff_with_type<T, P>(&self, path: P, options: &TiffOptions) -> Result<(), Error>
+    where
+        P: AsRef<Path>,
+        T: Bytes + Number + Send + Sync,
+        ArrayD<T>: MinMax<Output = ArrayD<T>>,
+        Array1<T>: MinMax<Output = Array0<T>>,
+        Array2<T>: MinMax<Output = Array1<T>>,
+    {
+        let path = path.as_ref().to_path_buf();
+        if path.exists() {
+            if options.overwrite {
+                std::fs::remove_file(&path)?;
+            } else {
+                return Err(Error::FileAlreadyExists(path.display().to_string()));
+            }
+        }
+        let size_c = self.size_c();
+        let size_z = self.size_z();
+        let size_t = self.size_t();
+        let mut tiff = IJTiffFile::new(path)?;
+        tiff.set_compression(options.compression.clone());
+        let ome = self.get_ome()?;
+        tiff.px_size = ome.pixel_size()?.map(|i| i / 1e3);
+        tiff.time_interval = ome.time_interval()?.map(|i| i / 1e3);
+        tiff.delta_z = ome.delta_z()?.map(|i| i / 1e3);
+        tiff.comment = Some(self.ome_xml()?);
+        if let Some(mut colors) = options.colors.clone() {
+            while colors.len() < self.size_c {
+                colors.push(vec![255, 255, 255]);
+            }
+            tiff.colors = Colors::Colors(colors);
+        }
+        let tiff = Arc::new(Mutex::new(tiff));
+        if let Some(style) = &options.bar {
+            let bar = ProgressBar::new((size_c as u64) * (size_z as u64) * (size_t as u64))
+                .with_style(style.clone());
+            iproduct!(0..size_c, 0..size_z, 0..size_t)
+                .collect::<Vec<_>>()
+                .into_par_iter()
+                .map(|(c, z, t)| {
+                    if let Ok(mut tiff) = tiff.lock() {
+                        tiff.save(&self.get_frame::<T, _>(c, z, t)?, c, z, t)?;
+                        bar.inc(1);
+                        Ok(())
+                    } else {
+                        Err(Error::TiffLock)
+                    }
+                })
+                .collect::<Result<(), Error>>()?;
+            bar.finish();
+        } else {
+            iproduct!(0..size_c, 0..size_z, 0..size_t)
+                .collect::<Vec<_>>()
+                .into_par_iter()
+                .map(|(c, z, t)| {
+                    if let Ok(mut tiff) = tiff.lock() {
+                        tiff.save(&self.get_frame::<T, _>(c, z, t)?, c, z, t)?;
+                        Ok(())
+                    } else {
+                        Err(Error::TiffLock)
+                    }
+                })
+                .collect::<Result<(), Error>>()?;
+        };
+        Ok(())
+    }
+
+    /// save as tiff with whatever pixel type the view has
+    pub fn save_as_tiff<P>(&self, path: P, options: &TiffOptions) -> Result<(), Error>
+    where
+        P: AsRef<Path>,
+    {
+        match self.pixel_type {
+            PixelType::I8 => self.save_as_tiff_with_type::<i8, P>(path, options)?,
+            PixelType::U8 => self.save_as_tiff_with_type::<u8, P>(path, options)?,
+            PixelType::I16 => self.save_as_tiff_with_type::<i16, P>(path, options)?,
+            PixelType::U16 => self.save_as_tiff_with_type::<u16, P>(path, options)?,
+            PixelType::I32 => self.save_as_tiff_with_type::<i32, P>(path, options)?,
+            PixelType::U32 => self.save_as_tiff_with_type::<u32, P>(path, options)?,
+            PixelType::F32 => self.save_as_tiff_with_type::<f32, P>(path, options)?,
+            PixelType::F64 => self.save_as_tiff_with_type::<f64, P>(path, options)?,
+            PixelType::I64 => self.save_as_tiff_with_type::<i64, P>(path, options)?,
+            PixelType::U64 => self.save_as_tiff_with_type::<u64, P>(path, options)?,
+            PixelType::I128 => self.save_as_tiff_with_type::<i64, P>(path, options)?,
+            PixelType::U128 => self.save_as_tiff_with_type::<u64, P>(path, options)?,
+            PixelType::F128 => self.save_as_tiff_with_type::<f64, P>(path, options)?,
+        }
+
+        Ok(())
+    }
+}

tests/test_open.py

@@ -1,27 +1,25 @@
 import pickle
-from multiprocessing import active_children
 from pathlib import Path
 
 import pytest
 
-from ndbioimage import Imread, ReaderNotFoundError
+from ndbioimage import Imread
 
 
-@pytest.mark.parametrize('file', (Path(__file__).parent / 'files').iterdir())
+@pytest.mark.parametrize(
+    "file",
+    [
+        file
+        for file in (Path(__file__).parent / "files").iterdir()
+        if not file.suffix == ".pzl"
+    ],
+)
 def test_open(file):
-    try:
-        with Imread(file) as im:
-            mean = im[dict(c=0, z=0, t=0)].mean()
-            b = pickle.dumps(im)
-            jm = pickle.loads(b)
-            assert jm[dict(c=0, z=0, t=0)].mean() == mean
-            v = im.view()
-            assert v[dict(c=0, z=0, t=0)].mean() == mean
-            b = pickle.dumps(v)
-            w = pickle.loads(b)
-            assert w[dict(c=0, z=0, t=0)].mean() == mean
-    except ReaderNotFoundError:
-        assert len(Imread.__subclasses__()), 'No subclasses for Imread found.'
-
-    for child in active_children():
-        child.kill()
+    with Imread(file, axes="cztyx") as im:
+        mean = im[0, 0, 0].mean()
+        b = pickle.dumps(im)
+        jm = pickle.loads(b)
+        assert jm.get_frame(0, 0, 0).mean() == mean
+        b = pickle.dumps(im)
+        jm = pickle.loads(b)
+        assert jm[0, 0, 0].mean() == mean

tests/test_slicing.py

@@ -1,24 +1,41 @@
+import tempfile
 from itertools import combinations_with_replacement
 from numbers import Number
+from pathlib import Path
 
 import numpy as np
 import pytest
+from tiffwrite import tiffwrite
 
 from ndbioimage import Imread
 
-r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
-im = Imread(r)
-a = np.array(im)
+
+@pytest.fixture
+def array():
+    return np.random.randint(0, 255, (64, 64, 2, 3, 4), "uint8")
 
 
-@pytest.mark.parametrize('s', combinations_with_replacement(
-    (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5))
-def test_slicing(s):
-    s_im, s_a = im[s], a[s]
+@pytest.fixture()
+def image(array):
+    with tempfile.TemporaryDirectory() as folder:
+        file = Path(folder) / "test.tif"
+        tiffwrite(file, array, "yxczt")
+        with Imread(file, axes="yxczt") as im:
+            yield im
+
+
+@pytest.mark.parametrize(
+    "s",
+    combinations_with_replacement(
+        (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5
+    ),
+)
+def test_slicing(s, image, array):
+    s_im, s_a = image[s], array[s]
     if isinstance(s_a, Number):
         assert isinstance(s_im, Number)
         assert s_im == s_a
     else:
         assert isinstance(s_im, Imread)
-        assert s_im.shape == s_a.shape
+        assert tuple(s_im.shape) == s_a.shape
         assert np.all(s_im == s_a)

tests/test_ufuncs.py

@@ -1,19 +1,52 @@
+import tempfile
 from itertools import product
+from pathlib import Path
 
 import numpy as np
 import pytest
+from tiffwrite import tiffwrite
 
 from ndbioimage import Imread
 
-r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
-im = Imread(r)
-a = np.array(im)
+
+@pytest.fixture
+def array():
+    return np.random.randint(0, 255, (64, 64, 2, 3, 4), "uint16")
 
 
-@pytest.mark.parametrize('fun_and_axis', product(
-    (np.sum, np.nansum, np.min, np.nanmin, np.max, np.nanmax, np.argmin, np.argmax,
-     np.mean, np.nanmean, np.var, np.nanvar, np.std, np.nanstd), (None, 0, 1, 2, 3, 4)))
-def test_ufuncs(fun_and_axis):
+@pytest.fixture()
+def image(array):
+    with tempfile.TemporaryDirectory() as folder:
+        file = Path(folder) / "test.tif"
+        tiffwrite(file, array, "yxczt")
+        with Imread(file, axes="yxczt") as im:
+            yield im
+
+
+@pytest.mark.parametrize(
+    "fun_and_axis",
+    product(
+        (
+            np.sum,
+            np.nansum,
+            np.min,
+            np.nanmin,
+            np.max,
+            np.nanmax,
+            np.argmin,
+            np.argmax,
+            np.mean,
+            np.nanmean,
+            np.var,
+            np.nanvar,
+            np.std,
+            np.nanstd,
+        ),
+        (None, 0, 1, 2, 3, 4),
+    ),
+)
+def test_ufuncs(fun_and_axis, image, array):
     fun, axis = fun_and_axis
-    assert np.all(np.isclose(fun(im, axis), fun(a, axis))), \
-        f'function {fun.__name__} over axis {axis} does not give the correct result'
+    assert np.all(np.isclose(np.asarray(fun(image, axis)), fun(array, axis))), (
+        f"function {fun.__name__} over axis {axis} does not give the correct result"
+    )