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Author SHA1 Message Date
w.pomp
e5eac07b7b - bugfix 2026-01-26 17:22:11 +01:00
w.pomp
8ff52f5af5 - main_channel and default_transform arguments for Imread.with_transform 2026-01-26 17:03:27 +01:00
w.pomp
066a39719a - match ome.tif sequence metadata based on position number, with backup by taking any metadata found (with warning) 2026-01-16 11:32:00 +01:00
w.pomp
776b5204c4 - remove python 3.14 test as SimpleITK-SimpleElastix is not yet available 2025-11-27 15:45:55 +01:00
w.pomp
e27a0f2657 - cziread: deal with missing exposure times 2025-11-26 17:24:48 +01:00
Wim Pomp
7fe1d189e5 - fix reading time interval when defined not in s in ome 
- search all ome.tif for metadata in order
 2025-10-15 20:29:07 +02:00
w.pomp
1b5febc35b - add option to skip autoscaling brightness when saving as mp4 
- let coords_pandas also deal with polars dataframes
 2025-09-25 15:20:00 +02:00
Wim Pomp
1fe3b3c824 - Make bioformats optional because jpype can cause problems 
- Ruff format
 2025-08-06 11:03:03 +02:00
Wim Pomp
3346ed3a48 - Can pycharm please stop adding wrong imports please? 2025-03-19 16:14:28 +01:00
Wim Pomp
b7dadb645e - read metadata from first file in ome tiff sequence 2025-03-19 16:06:07 +01:00
Wim Pomp
0ac22aff87 - pyproject towards PEP621 
- catch errors reading metadata in tifread
- read dimension order from ome
 2025-03-19 15:04:57 +01:00
Wim Pomp
6daa372ccf - allow None in Transform.from_dict 
- None transform parameters -> unit parameters/matrix
 2025-02-14 15:45:43 +01:00
Wim Pomp
cb52e77c34 - allow None in Transform.from_dict 2025-02-14 15:00:55 +01:00
39 changed files with 4030 additions and 6241 deletions
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22
.github/workflows/pytest.yml vendored Normal file
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name: PyTest
on: [workflow_call, push, pull_request]
jobs:
pytest:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.10", "3.11", "3.12", "3.13"]
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

86
.gitignore vendored
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/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
._*
*.pyc
/build/
*.egg-info
/venv/
.idea
/.pytest_cache/
/ndbioimage/_version.py
/ndbioimage/jars
/tests/files/*
/poetry.lock
/dist/
/uv.lock

70
Cargo.toml
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[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"]

687
LICENSE
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@@ -1,19 +1,674 @@
Copyright (c) 2025 Wim Pomp
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contain the covered work, unless you entered into that arrangement,
or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
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not convey it at all. For example, if you agree to terms that obligate you
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the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Use with the GNU Affero General Public License.
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permission to link or combine any covered work with a work licensed
under version 3 of the GNU Affero General Public License into a single
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section 13, concerning interaction through a network will apply to the
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14. Revised Versions of this License.
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option of following the terms and conditions either of that numbered
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If the Program specifies that a proxy can decide which future
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above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
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
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(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.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<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>.

74
README.md
View File

@@ -1,9 +1,6 @@
# ndbioimage
[![Pytest](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
## 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/)
# ndbioimage
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
@@ -12,21 +9,23 @@ Additionally, it can automatically calculate an affine transform that corrects f
it on the fly to the image.
Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything
[bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
[bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
## Installation
One of:
```
pip install ndbioimage
```
### Installation with option to write mp4 or mkv:
Work in progress! Make sure ffmpeg is installed.
```
pip install ndbioimage[bioformats]
pip install ndbioimage[write]
pip install ndbioimage[bioformats, write]
```
- bioformats: use [bio-formats](https://www.openmicroscopy.org/bio-formats/)
as fallback when other readers cannot open a file.
- write: write an image file into a mp4 or mkv file. Work in progress! Make sure ffmpeg is installed.
## Usage
### Python
@@ -38,7 +37,7 @@ from ndbioimage import Imread
with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
plt.imshow(im[2, 1])
```
- Showing some image metadata
```
@@ -68,37 +67,30 @@ 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

131
build.rs
View File

@@ -1,131 +0,0 @@
#[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(())
}

1614
ndbioimage/__init__.py Executable file
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File diff suppressed because it is too large Load Diff

81
ndbioimage/jvm.py Normal file
View File

@@ -0,0 +1,81 @@
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

6
ndbioimage/readers/__init__.py Normal file
View File

@@ -0,0 +1,6 @@
from .. import JVM
if JVM is None:
__all__ = "cziread", "fijiread", "ndread", "seqread", "tifread", "metaseriesread"
else:
__all__ = "bfread", "cziread", "fijiread", "ndread", "seqread", "tifread", "metaseriesread"

213
ndbioimage/readers/bfread.py Normal file
View File

@@ -0,0 +1,213 @@
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()

677
ndbioimage/readers/cziread.py Normal file
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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[min(c, len(exposure_times) - 1)] if len(exposure_times) > 0 else None,
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

68
ndbioimage/readers/fijiread.py Normal file
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@@ -0,0 +1,68 @@
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

88
ndbioimage/readers/metaseriesread.py Normal file
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@@ -0,0 +1,88 @@
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")

62
ndbioimage/readers/ndread.py Normal file
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@@ -0,0 +1,62 @@
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

183
ndbioimage/readers/seqread.py Normal file
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@@ -0,0 +1,183 @@
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)])

170
ndbioimage/readers/tifread.py Normal file
View File

@@ -0,0 +1,170 @@
import re
import warnings
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 from_xml, model
from .. import AbstractReader, try_default
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: try_default(yaml.safe_load, value, value) if isinstance(value, str) else value
for key, value in self.reader.imagej_metadata.items()
}
def get_ome(self):
if self.reader.is_ome:
pos_number_pat = re.compile(r"\d+")
def get_pos_number(s):
return [int(i) for i in pos_number_pat.findall(s)]
match = re.match(r"^(.*)(pos[\d_]+)(.*)$", self.path.name, flags=re.IGNORECASE)
if match is not None and len(match.groups()) == 3:
a, b, c = match.groups()
pat = re.compile(f"^{re.escape(a)}" + re.sub(r"\d+", r"\\d+", b) + f"{re.escape(c)}$")
backup_ome = []
backup_backup_ome = []
pos_number = get_pos_number(b)
for file in sorted(self.path.parent.iterdir(), key=lambda i: (len(i.name), i.name)):
if pat.match(file.name):
with tifffile.TiffFile(file) as tif:
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=UserWarning)
ome = from_xml(tif.ome_metadata)
backup_backup_ome.extend(ome.images)
try:
backup_ome.extend(
[
image
for image in ome.images
if pos_number == get_pos_number(image.stage_label.name)
]
)
except ValueError:
pass
ome.images = [image for image in ome.images if b == image.stage_label.name]
if ome.images:
return ome
if backup_ome:
ome.images = [backup_ome[0]]
warnings.warn(
"could not find the ome.tif file containing the metadata with an exact match, "
f"matched {ome.images[0].stage_label.name} with {b} instead, "
"did you rename the file?"
)
return ome
if backup_backup_ome:
ome.images = [backup_backup_ome[0]]
warnings.warn(
"could not find the ome.tif file containing the metadata, "
f"used metadata from {ome.images[0].name} instead, "
"did you rename the file"
)
return ome
warnings.warn("could not find the ome.tif file containing the metadata")
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.first
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
else:
self.p_transpose = [i for i in [page.axes.find(j) for j in "YX"] if i >= 0] # noqa
def close(self):
self.reader.close()
def __frame__(self, c: int, z: int, t: int):
dimension_order = self.ome.images[0].pixels.dimension_order.value
if self.p_ndim == 3:
axes = "".join([ax.lower() for ax in dimension_order if ax.lower() in "zt"])
ct = {"z": z, "t": t}
n = sum([ct[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
return np.transpose(self.reader.asarray(int(n)), self.p_transpose)[int(c)]
else:
axes = "".join([ax.lower() for ax in dimension_order if ax.lower() in "czt"])
czt = {"c": c, "z": z, "t": t}
n = sum([czt[ax] * np.prod(self.base_shape[axes[:i]]) for i, ax in enumerate(axes)])
return np.transpose(self.reader.asarray(int(n)), self.p_transpose)

2
py/ndbioimage/transform.txt → ndbioimage/transform.txt
View File

@@ -1,6 +1,4 @@
#Insight Transform File V1.0
#Transform 0
Transform: CompositeTransform_double_2_2
#Transform 1
Transform: AffineTransform_double_2_2
Parameters: 1 0 0 1 0 0

212
py/ndbioimage/transforms.py → ndbioimage/transforms.py
View File

@@ -16,9 +16,14 @@ except ImportError:
sitk = None
try:
from pandas import DataFrame, Series, concat
import pandas as pd
except ImportError:
DataFrame, Series, concat = None, None, None
pd = None
try:
import polars as pl
except ImportError:
pl = None
if hasattr(yaml, "full_load"):
@@ -42,9 +47,7 @@ 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
@@ -72,18 +75,12 @@ class Transforms(dict):
def asdict(self):
return {
key.replace("\\", "\\\\").replace(":", r"\:")
if isinstance(key, str)
else key: value.asdict()
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
@@ -120,8 +117,7 @@ class Transforms(dict):
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}"
f"The image file and the transform do not have the same channels, creating a mapping: {mapping}"
)
for key_im, key_t in mapping.items():
self[key_im] = self[key_t]
@@ -135,15 +131,13 @@ class Transforms(dict):
return inverse
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,
if pd is None:
raise ImportError("pandas is not available")
if isinstance(array, pd.DataFrame):
return pd.concat(
[self.coords_pandas(row, channel_names, columns) for _, row in array.iterrows()], axis=1
).T
elif isinstance(array, Series):
elif isinstance(array, pd.Series):
key = []
if "C" in array:
key.append(channel_names[int(array["C"])])
@@ -153,27 +147,20 @@ class Transforms(dict):
else:
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."
)
def with_beads(self, cyllens, bead_files, main_channel=None, default_transform=None):
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
self.calculate_channel_transforms(file, cyllens, main_channel, default_transform) 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].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))
np.std([t.parameters for t in new_transforms], 0) / np.sqrt(len(new_transforms))
).tolist()
return self
@@ -206,7 +193,7 @@ class Transforms(dict):
return checked_files
@staticmethod
def calculate_channel_transforms(bead_file, cyllens):
def calculate_channel_transforms(bead_file, cyllens, main_channel=None, default_transform=None):
"""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
@@ -216,34 +203,32 @@ class Transforms(dict):
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:
masterch = good_and_untrans[0]
else:
masterch = goodch[0]
if main_channel is None:
if good_and_untrans:
main_channel = good_and_untrans[0]
else:
main_channel = goodch[0]
transform = Transform()
if not good_and_untrans:
matrix = transform.matrix
matrix = transform.matrix
if default_transform is None:
matrix[0, 0] = 0.86
transform.matrix = matrix
else:
for i, t in zip(((0, 0), (0, 1), (1, 0), (1, 1), (0, 2), (1, 2)), default_transform):
matrix[i] = t
transform.matrix = matrix
transforms = Transforms()
for c in tqdm(goodch, desc="Calculating channel transforms"): # noqa
if c == masterch:
if c == main_channel:
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[main_channel], max_ims[c]) * transform
return transforms
@staticmethod
def save_channel_transform_tiff(bead_files, tiffile):
def save_channel_transform_tiff(bead_files, tiffile, default_transform=None):
from . import Imread
n_channels = 0
@@ -253,16 +238,9 @@ class Transforms(dict):
with IJTiffFile(tiffile) as tif:
for t, file in enumerate(bead_files):
with Imread(file) as im:
with Imread(file).with_transform() as jm:
with Imread(file).with_transform(default_transform=default_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,
)
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
@@ -270,22 +248,11 @@ class Transforms(dict):
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"]))
)
]
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
@@ -293,17 +260,11 @@ class Transforms(dict):
return 0, 0
else:
fmaxz = filters.gaussian(im[t].max("z"), 5)
return Transform.register(
fmaxz_keys[t_key], fmaxz, "translation"
).parameters[4:]
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
@@ -317,9 +278,7 @@ class Transform:
if sitk is None:
self.transform = None
else:
self.transform = sitk.ReadTransform(
str(Path(__file__).parent / "transform.txt")
)
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]
@@ -339,8 +298,7 @@ class Transform:
"""kind: 'affine', 'translation', 'rigid'"""
if sitk is None:
raise ImportError(
"SimpleElastix is not installed: "
"https://simpleelastix.readthedocs.io/GettingStarted.html"
"SimpleElastix is not installed: https://simpleelastix.readthedocs.io/GettingStarted.html"
)
new = cls()
kind = kind or "affine"
@@ -359,13 +317,11 @@ class Transform:
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.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} transforms not implemented (yet)")
new.dparameters = 6 * [np.nan]
return new
@@ -387,29 +343,18 @@ class Transform:
@classmethod
def from_dict(cls, d):
new = cls()
new.origin = (
None
if d["CenterOfRotationPoint"] is None
else [float(i) for i in d["CenterOfRotationPoint"]]
)
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"]
]
[(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"]]
)
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
@@ -443,11 +388,7 @@ 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),
)
((*self.parameters[:2], self.parameters[4]), (*self.parameters[2:4], self.parameters[5]), (0, 0, 1))
)
@matrix.setter
@@ -458,11 +399,7 @@ 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),
)
((*self.dparameters[:2], self.dparameters[4]), (*self.dparameters[2:4], self.dparameters[5]), (0, 0, 0))
)
@dmatrix.setter
@@ -524,19 +461,12 @@ class Transform:
else:
if sitk is None:
raise ImportError(
"SimpleElastix is not installed: "
"https://simpleelastix.readthedocs.io/GettingStarted.html"
"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)
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,
@@ -544,23 +474,23 @@ class Transform:
"""
if self.is_unity():
return array.copy()
elif DataFrame is not None and isinstance(array, (DataFrame, Series)):
elif pd is not None and isinstance(array, (pd.DataFrame, pd.Series)):
columns = columns or ["x", "y"]
array = array.copy()
if isinstance(array, DataFrame):
if isinstance(array, pd.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
]
elif isinstance(array, pd.Series):
array[columns] = self.coords(np.atleast_2d(array[columns].to_numpy()))[0]
return array
elif pl is not None and isinstance(array, (pl.DataFrame, pl.LazyFrame)):
columns = columns or ["x", "y"]
if isinstance(array, pl.DataFrame):
xy = self.coords(np.atleast_2d(array.select(columns).to_numpy()))
elif isinstance(array, pl.LazyFrame):
xy = self.coords(np.atleast_2d(array.select(columns).collect().to_numpy()))
return array.with_columns(**{c: i for c, i in zip(columns, xy.T)})
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

624
py/ndbioimage/__init__.py
View File

@@ -1,624 +0,0 @@
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)

39
py/ndbioimage/ome.py
View File

@@ -1,39 +0,0 @@
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

57
pyproject.toml
View File

@@ -1,43 +1,41 @@
[build-system]
requires = ["maturin>=1.8,<2.0"]
build-backend = "maturin"
[project]
name = "ndbioimage"
version = "2026.1.2"
description = "Bio image reading, metadata and some affine registration."
authors = [
{ name = "W. Pomp", email = "w.pomp@nki.nl" }
]
license = "MIT"
license = { text = "GPL-3.0-or-later"}
readme = "README.md"
keywords = ["bioformats", "imread", "numpy", "metadata"]
include = ["transform.txt"]
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"]
exclude = ["ndbioimage/jars"]
dependencies = [
"numpy",
"tiffwrite",
"ome-metadata >= 0.2.1",
"czifile == 2019.7.2",
"imagecodecs",
"lxml",
"numpy >= 1.20",
"ome-types",
"pandas",
"parfor >= 2025.1.0",
"pint",
"pyyaml",
"SimpleITK-SimpleElastix; sys_platform != 'darwin'",
"scikit-image",
"tifffile <= 2025.1.10",
"tiffwrite >= 2024.12.1",
"tqdm",
]
[project.optional-dependencies]
test = ["pytest"]
write = ["matplotlib", "scikit-video"]
bioformats = ["JPype1"]
[project.urls]
Repository = "https://github.com/wimpomp/ndbioimage/tree/rs"
repository = "https://github.com/wimpomp/ndbioimage"
[project.scripts]
ndbioimage = "ndbioimage:main"
@@ -45,12 +43,13 @@ 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
[tool.ruff]
line-length = 119
indent-width = 4
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

251
src/axes.rs
View File

@@ -1,251 +0,0 @@
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()
}
}

230
src/bioformats.rs
View File

@@ -1,230 +0,0 @@
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);
}

207
src/colors.rs
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@@ -1,207 +0,0 @@
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]
}
}

65
src/error.rs
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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),
}

414
src/lib.rs
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#![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(())
}
}

194
src/main.rs
View File

@@ -1,194 +0,0 @@
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(())
}

363
src/metadata.rs
View File

@@ -1,363 +0,0 @@
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())
}
}

285
src/movie.rs
View File

@@ -1,285 +0,0 @@
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(())
}
}

989
src/py.rs
View File

@@ -1,989 +0,0 @@
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(())
}

487
src/reader.rs
View File

@@ -1,487 +0,0 @@
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();
}
}
}

205
src/stats.rs
View File

@@ -1,205 +0,0 @@
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
);

193
src/tiff.rs
View File

@@ -1,193 +0,0 @@
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(())
}
}

1133
src/view.rs
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tests/files/Experiment-2029.czi
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tests/files/test.tif
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36
tests/test_open.py
View File

@@ -1,25 +1,27 @@
import pickle
from multiprocessing import active_children
from pathlib import Path
import pytest
from ndbioimage import Imread
from ndbioimage import Imread, ReaderNotFoundError
@pytest.mark.parametrize(
"file",
[
file
for file in (Path(__file__).parent / "files").iterdir()
if not file.suffix == ".pzl"
],
)
@pytest.mark.parametrize("file", (Path(__file__).parent / "files").iterdir())
def test_open(file):
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
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()

30
tests/test_slicing.py
View File

@@ -1,41 +1,25 @@
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
@pytest.fixture
def array():
return np.random.randint(0, 255, (64, 64, 2, 3, 4), "uint8")
@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
r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
im = Imread(r)
a = np.array(im)
@pytest.mark.parametrize(
"s",
combinations_with_replacement(
(0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5
),
"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]
def test_slicing(s):
s_im, s_a = im[s], a[s]
if isinstance(s_a, Number):
assert isinstance(s_im, Number)
assert s_im == s_a
else:
assert isinstance(s_im, Imread)
assert tuple(s_im.shape) == s_a.shape
assert s_im.shape == s_a.shape
assert np.all(s_im == s_a)

23
tests/test_ufuncs.py
View File

@@ -1,26 +1,13 @@
import tempfile
from itertools import product
from pathlib import Path
import numpy as np
import pytest
from tiffwrite import tiffwrite
from ndbioimage import Imread
@pytest.fixture
def array():
return np.random.randint(0, 255, (64, 64, 2, 3, 4), "uint16")
@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
r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
im = Imread(r)
a = np.array(im)
@pytest.mark.parametrize(
@@ -45,8 +32,8 @@ def image(array):
(None, 0, 1, 2, 3, 4),
),
)
def test_ufuncs(fun_and_axis, image, array):
def test_ufuncs(fun_and_axis):
fun, axis = fun_and_axis
assert np.all(np.isclose(np.asarray(fun(image, axis)), fun(array, 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"
)