- remove all readers but bioformats

- open folder with sequence

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ndbioimage"
-version = "2025.2.2"
+version = "2025.2.3"
 edition = "2021"
 rust-version = "1.78.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]

py/ndbioimage/__init__.py

@@ -1,10 +1,9 @@
 from __future__ import annotations
 
-import multiprocessing
 import os
 import re
 import warnings
-from abc import ABC, ABCMeta, abstractmethod
+from abc import ABC
 from argparse import ArgumentParser
 from collections import OrderedDict
 from datetime import datetime
@@ -18,11 +17,12 @@ from typing import Any, Callable, Generator, Iterable, Optional, Sequence, TypeV
 import numpy as np
 import yaml
 from numpy.typing import ArrayLike, DTypeLike
-from ome_types import OME, from_xml, model, ureg
+from ome_types import OME, from_xml, ureg
 from pint import set_application_registry
 from tiffwrite import FrameInfo, IJTiffParallel
 from tqdm.auto import tqdm
 
+from .ndbioimage_rs import Reader, download_bioformats  # noqa
 from .transforms import Transform, Transforms  # noqa: F401
 
 try:
@@ -44,8 +44,11 @@ warnings.filterwarnings('ignore', 'Reference to unknown ID')
 Number = int | float | np.integer | np.floating
 
 
-class ReaderNotFoundError(Exception):
-    pass
+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")):
+    download_bioformats(True)
 
 
 class TransformTiff(IJTiffParallel):
@@ -96,12 +99,6 @@ def try_default(fun: Callable[..., R], default: Any, *args: Any, **kwargs: Any)
         return default
 
 
-def bioformats_ome(path: str | Path) -> OME:
-    from .rs import Reader
-    reader = Reader(str(path), 0)
-    return from_xml(reader.get_ome_xml(), parser='lxml')
-
-
 class Shape(tuple):
     def __new__(cls, shape: Sequence[int] | Shape, axes: str = 'yxczt') -> Shape:
         if isinstance(shape, Shape):
@@ -164,9 +161,9 @@ class OmeCache(DequeDict):
                 (path.with_suffix('.ome.xml').lstat() if path.with_suffix('.ome.xml').exists() else None))
 
 
-def get_positions(path: str | Path) -> Optional[list[int]]:
-    subclass = AbstractReader.get_subclass(path)
-    return subclass.get_positions(AbstractReader.split_path_series(path)[0])
+def get_positions(path: str | Path) -> Optional[list[int]]:  # noqa
+    # TODO
+    return None
 
 
 class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
@@ -203,89 +200,181 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
                  << [0.02, 0.0005] in %
 
                 See __init__ and other functions for more ideas.
-
-            Subclassing:
-                Subclass AbstractReader to add more file types. A subclass should always have at least the following
-                methods:
-                    staticmethod _can_open(path): returns True when the subclass can open the image in path
-                    __frame__(self, c, z, t): this should return a single frame at channel c, slice z and time t
-                    optional open(self): code to be run during initialization, e.g. to open a file handle
-                    optional close(self): close the file in a proper way
-                    optional class field priority: subclasses with lower priority will be tried first, default = 99
-                    optional get_ome(self) -> OME: return an OME structure with metadata,
-                        if not present bioformats will be used to generate an OME
-                    Any other method can be overridden as needed
     """
 
-    isclosed: Optional[bool]
-    channel_names: Optional[list[str]]
-    series: Optional[int]
-    pxsize_um: Optional[float]
-    deltaz_um: Optional[float]
-    exposuretime_s: Optional[list[float]]
-    timeinterval: Optional[float]
-    binning: Optional[list[int]]
-    laserwavelengths: Optional[list[tuple[float]]]
-    laserpowers: Optional[list[tuple[float]]]
-    objective: Optional[model.Objective]
-    magnification: Optional[float]
-    tubelens: Optional[model.Objective]
-    filter: Optional[str]
-    powermode: Optional[str]
-    collimator: Optional[str]
-    tirfangle: Optional[list[float]]
-    gain: Optional[list[float]]
-    pcf: Optional[list[float]]
-    path: Path
-    __frame__: Callable[[int, int, int], np.ndarray]
+    do_not_pickle = 'cache', 'reader'
+    ureg = ureg
+
+    def close(self) -> None:
+        self.reader.close()
 
     @staticmethod
-    def get_subclass(path: Path | str | Any):
-        if len(AbstractReader.__subclasses__()) == 0:
-            raise Exception('Restart python kernel please!')
-        path, _ = AbstractReader.split_path_series(path)
-        for subclass in sorted(AbstractReader.__subclasses__(), key=lambda subclass_: subclass_.priority):
-            if subclass._can_open(path):  # noqa
-                do_not_pickle = (AbstractReader.do_not_pickle,) if isinstance(AbstractReader.do_not_pickle, str) \
-                    else AbstractReader.do_not_pickle
-                subclass_do_not_pickle = (subclass.do_not_pickle,) if isinstance(subclass.do_not_pickle, str) \
-                    else subclass.do_not_pickle if hasattr(subclass, 'do_not_pickle') else ()
-                subclass.do_not_pickle = set(do_not_pickle).union(set(subclass_do_not_pickle))
-                return subclass
-        raise ReaderNotFoundError(f'No reader found for {path}.')
+    def get_positions(path: str | Path) -> Optional[list[int]]:  # noqa
+        # TODO
+        return None
 
-
-    def __new__(cls, path: Path | str | Imread | Any = None, dtype: DTypeLike = None, axes: str = None) -> Imread:
-        if cls is not Imread:
-            return super().__new__(cls)
+    def __init__(self, path: Path | str | Imread | Any = None, dtype: DTypeLike = None, axes: str = None) -> None:
+        super().__init__()
         if isinstance(path, Imread):
-            return path
-        subclass = cls.get_subclass(path)
-        do_not_pickle = (AbstractReader.do_not_pickle,) if isinstance(AbstractReader.do_not_pickle, str) \
-            else AbstractReader.do_not_pickle
-        subclass_do_not_pickle = (subclass.do_not_pickle,) if isinstance(subclass.do_not_pickle, str) \
-            else subclass.do_not_pickle if hasattr(subclass, 'do_not_pickle') else ()
-        subclass.do_not_pickle = set(do_not_pickle).union(set(subclass_do_not_pickle))
-        return super().__new__(subclass)
+            self.base = path.base or path
+        else:
+            self.base = self
+            self.isclosed = False
+            if isinstance(path, str):
+                path = Path(path)
+            self.path, self.series = self.split_path_series(path)
+            self.reader = Reader(str(self.path), int(self.series))
+            self.frame_decorator = None
+            self.transform = Transforms()
+            if isinstance(path, Path) and path.exists():
+                self.title = self.path.name
+                self.acquisitiondate = datetime.fromtimestamp(self.path.stat().st_mtime).strftime('%y-%m-%dT%H:%M:%S')
+            else:  # ndarray
+                self.title = self.__class__.__name__
+                self.acquisitiondate = 'now'
 
-    def __init__(self, *args: Any, **kwargs: Any):
-        def parse(base: Imread = None,  # noqa
-                  slice: tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray] = None,  # noqa
-                  shape: tuple[int, ...] = (0, 0, 0, 0, 0),  # noqa
-                  dtype: DTypeLike = None,  # noqa
-                  frame_decorator: Callable[[Imread, np.ndarray, int, int, int], np.ndarray] = None  # noqa
-                  ) -> tuple[Any, ...]:
-            return base, slice, shape, dtype, frame_decorator
+            self.pcf = None
+            self.powermode = None
+            self.collimator = None
+            self.tirfangle = None
+            self.cyllens = ['None', 'None']
+            self.duolink = 'None'
+            self.detector = [0, 1]
+            self.track = [0]
+            self.cache = DequeDict(16)
+            self.frameoffset = 0, 0  # how far apart the centers of frame and sensor are
 
-        base, slice, shape, dtype, frame_decorator = parse(*args, **kwargs)  # noqa
-        self.base = base or self
-        self.slice = slice
-        self._shape = Shape(shape)
-        self.dtype = dtype
-        self.frame_decorator = frame_decorator
-        self.transform = Transforms()
-        self.flags = dict(C_CONTIGUOUS=False, F_CONTIGUOUS=False, OWNDATA=False, WRITEABLE=False,
-                          ALIGNED=False, WRITEBACKIFCOPY=False, UPDATEIFCOPY=False)
+            # extract some metadata from ome
+            instrument = self.ome.instruments[0] if self.ome.instruments else None
+            image = self.ome.images[self.series if len(self.ome.images) > 1 else 0]
+            pixels = image.pixels
+            self._shape = Shape((pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t),
+                                'yxczt')
+            self.base_shape = Shape((pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t),
+                                    'yxczt')
+            self.dtype = pixels.type.value if dtype is None else dtype
+            self.pxsize = pixels.physical_size_x_quantity
+            try:
+                self.exposuretime = tuple(find(image.pixels.planes, the_c=c).exposure_time_quantity
+                                          for c in range(self.shape['c']))
+            except AttributeError:
+                self.exposuretime = ()
+
+            if self.zstack:
+                self.deltaz = image.pixels.physical_size_z_quantity
+                self.deltaz_um = None if self.deltaz is None else self.deltaz.to(self.ureg.um).m
+            else:
+                self.deltaz = self.deltaz_um = None
+            if image.objective_settings:
+                self.objective = find(instrument.objectives, id=image.objective_settings.id)
+            else:
+                self.objective = None
+            try:
+                t0 = find(image.pixels.planes, the_c=0, the_t=0, the_z=0).delta_t
+                t1 = find(image.pixels.planes, the_c=0, the_t=self.shape['t'] - 1, the_z=0).delta_t
+                self.timeinterval = (t1 - t0) / (self.shape['t'] - 1) if self.shape['t'] > 1 and t1 > t0 else None
+            except AttributeError:
+                self.timeinterval = None
+            try:
+                self.binning = [int(i) for i in image.pixels.channels[0].detector_settings.binning.value.split('x')]
+                if self.pxsize is not None:
+                    self.pxsize *= self.binning[0]
+            except (AttributeError, IndexError, ValueError):
+                self.binning = None
+            self.channel_names = [channel.name for channel in image.pixels.channels]
+            self.channel_names += [chr(97 + i) for i in range(len(self.channel_names), self.shape['c'])]
+            self.cnamelist = self.channel_names
+            try:
+                optovars = [objective for objective in instrument.objectives if 'tubelens' in objective.id.lower()]
+            except AttributeError:
+                optovars = []
+            if len(optovars) == 0:
+                self.tubelens = None
+            else:
+                self.tubelens = optovars[0]
+            if self.objective:
+                if self.tubelens:
+                    self.magnification = self.objective.nominal_magnification * self.tubelens.nominal_magnification
+                else:
+                    self.magnification = self.objective.nominal_magnification
+                self.NA = self.objective.lens_na
+            else:
+                self.magnification = None
+                self.NA = None
+
+            self.gain = [find(instrument.detectors, id=channel.detector_settings.id).amplification_gain
+                         for channel in image.pixels.channels
+                         if channel.detector_settings
+                         and find(instrument.detectors, id=channel.detector_settings.id).amplification_gain]
+            self.laserwavelengths = [(channel.excitation_wavelength_quantity.to(self.ureg.nm).m,)
+                                     for channel in pixels.channels if channel.excitation_wavelength_quantity]
+            self.laserpowers = try_default(lambda: [(1 - channel.light_source_settings.attenuation,)
+                                                    for channel in pixels.channels], [])
+            self.filter = try_default(  # type: ignore
+                lambda: [find(instrument.filter_sets, id=channel.filter_set_ref.id).model
+                         for channel in image.pixels.channels], None)
+            self.pxsize_um = None if self.pxsize is None else self.pxsize.to(self.ureg.um).m
+            self.exposuretime_s = [None if i is None else i.to(self.ureg.s).m for i in self.exposuretime]
+
+            if axes is None:
+                self.axes = ''.join(i for i in 'cztyx' if self.shape[i] > 1)
+            elif axes.lower() == 'full':
+                self.axes = 'cztyx'
+            else:
+                self.axes = axes
+            self.slice = [np.arange(s, dtype=int) for s in self.shape.yxczt]
+
+            m = self.extrametadata
+            if m is not None:
+                try:
+                    self.cyllens = m['CylLens']
+                    self.duolink = m['DLFilterSet'].split(' & ')[m['DLFilterChannel']]
+                    if 'FeedbackChannels' in m:
+                        self.feedback = m['FeedbackChannels']
+                    else:
+                        self.feedback = m['FeedbackChannel']
+                except Exception:  # noqa
+                    self.cyllens = ['None', 'None']
+                    self.duolink = 'None'
+                    self.feedback = []
+            try:
+                self.cyllenschannels = np.where([self.cyllens[self.detector[c]].lower() != 'none'
+                                                 for c in range(self.shape['c'])])[0].tolist()
+            except Exception:  # noqa
+                pass
+            try:
+                s = int(re.findall(r'_(\d{3})_', self.duolink)[0]) * ureg.nm
+            except Exception:  # noqa
+                s = 561 * ureg.nm
+            try:
+                sigma = []
+                for c, d in enumerate(self.detector):
+                    emission = (np.hstack(self.laserwavelengths[c]) + 22) * ureg.nm
+                    sigma.append([emission[emission > s].max(initial=0), emission[emission < s].max(initial=0)][d])
+                sigma = np.hstack(sigma)
+                sigma[sigma == 0] = 600 * ureg.nm
+                sigma /= 2 * self.NA * self.pxsize
+                self.sigma = sigma.magnitude.tolist()  # type: ignore
+            except Exception:  # noqa
+                self.sigma = [2] * self.shape['c']
+            if not self.NA:
+                self.immersionN = 1
+            elif 1.5 < self.NA:
+                self.immersionN = 1.661
+            elif 1.3 < self.NA < 1.5:
+                self.immersionN = 1.518
+            elif 1 < self.NA < 1.3:
+                self.immersionN = 1.33
+            else:
+                self.immersionN = 1
+
+            p = re.compile(r'(\d+):(\d+)$')
+            try:
+                self.track, self.detector = zip(*[[int(i) for i in p.findall(find(
+                    self.ome.images[self.series].pixels.channels, id=f'Channel:{c}').detector_settings.id)[0]]
+                                                  for c in range(self.shape['c'])])
+            except Exception:  # noqa
+                pass
 
     def __call__(self, c: int = None, z: int = None, t: int = None, x: int = None, y: int = None) -> np.ndarray:
         """ same as im[] but allowing keyword axes, but slices need to made with slice() or np.s_ """
@@ -359,7 +448,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
 
         # TODO: check output dimensionality when requested shape in some dimension is 1
         if all([isinstance(s, Number) or a < 0 and s.size == 1 for s, a in zip(new_slice, axes_idx)]):
-            return self.block(*new_slice).item()
+            return self.block(*new_slice).item()  # type: ignore
         else:
             new = View(self)
             new.slice = new_slice
@@ -381,8 +470,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
     def __setstate__(self, state: dict[str, Any]) -> None:
         """ What happens during unpickling """
         self.__dict__.update({key: value for key, value in state.items() if key != 'cache_size'})
-        if isinstance(self, AbstractReader):
-            self.open()
+        self.reader = Reader(str(self.path), int(self.series))
         self.cache = DequeDict(state.get('cache_size', 16))
 
     def __str__(self) -> str:
@@ -406,7 +494,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
         if dtype is not None:
             block = block.astype(dtype)
         if block.ndim == 0:
-            return block.item()
+            return block.item()  # type: ignore
         axes = ''.join(j for i, j in enumerate('yxczt') if i not in axes_squeeze)
         return block.transpose([axes.find(i) for i in self.shape.axes if i in axes])
 
@@ -415,6 +503,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
         """ frame-wise application of np.argmin and np.argmax """
         if axis is None:
             value = arg = None
+            axes = ''.join(i for i in self.axes if i in 'yx') + 'czt'
             for idx in product(range(self.shape['c']), range(self.shape['z']), range(self.shape['t'])):
                 yxczt = (slice(None), slice(None)) + idx
                 in_idx = tuple(yxczt['yxczt'.find(i)] for i in self.axes)
@@ -424,16 +513,20 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
                 if value is None:
                     arg = new_arg + idx
                     value = new_value
+                elif value == new_value:
+                    a = np.ravel_multi_index([arg[axes.find(i)] for i in self.axes], self.shape)
+                    b = np.ravel_multi_index([(new_arg + idx)[axes.find(i)] for i in self.axes], self.shape)
+                    if b < a:
+                        arg = new_arg + idx
                 else:
                     i = fun((value, new_value))  # type: ignore
                     arg = (arg, new_arg + idx)[i]
                     value = (value, new_value)[i]
-            axes = ''.join(i for i in self.axes if i in 'yx') + 'czt'
             arg = np.ravel_multi_index([arg[axes.find(i)] for i in self.axes], self.shape)
             if out is None:
                 return arg
             else:
-                out.itemset(arg)
+                out[:] = arg
                 return out
         else:
             if isinstance(axis, str):
@@ -508,7 +601,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
             if out is None:
                 return res
             else:
-                out.itemset(res)
+                out[:] = res
                 return out
         else:
             if isinstance(axis, str):
@@ -613,8 +706,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
     def summary(self) -> str:
         """ gives a helpful summary of the recorded experiment """
         s = [f'path/filename: {self.path}',
-             f'series/pos:    {self.series}',
-             f"reader:        {self.base.__class__.__module__.split('.')[-1]}"]
+             f'series/pos:    {self.series}']
         s.extend((f'dtype:         {self.dtype}',
                   f'shape ({self.axes}):'.ljust(15) + f"{' x '.join(str(i) for i in self.shape)}"))
         if self.pxsize_um:
@@ -754,7 +846,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
 
     @wraps(np.ndarray.reshape)
     def reshape(self, *args, **kwargs):
-        return np.asarray(self).reshape(*args, **kwargs)
+        return np.asarray(self).reshape(*args, **kwargs)  # noqa
 
     @wraps(np.ndarray.squeeze)
     def squeeze(self, axes=None):
@@ -859,7 +951,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
             self.cache.move_to_end(key)
             f = self.cache[key]
         else:
-            f = self.transform[self.channel_names[c], t].frame(self.__frame__(c, z, t))
+            f = self.transform[self.channel_names[c], t].frame(self.reader.get_frame(int(c), int(z), int(t)))
             if self.frame_decorator is not None:
                 f = self.frame_decorator(self, f, c, z, t)
             if self.cache.maxlen:
@@ -915,12 +1007,6 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
                 czt.append([k % self.shape[i] for k in n])
         return [self.get_channel(c) for c in czt[0]], *czt[1:3]  # type: ignore
 
-    @staticmethod
-    def bioformats_ome(path: [str, Path]) -> OME:
-        """ Use java BioFormats to make an ome metadata structure. """
-        with multiprocessing.get_context('spawn').Pool(1) as pool:
-            return pool.map(bioformats_ome, (path,))[0]
-
     @staticmethod
     def fix_ome(ome: OME) -> OME:
         # fix ome if necessary
@@ -945,8 +1031,8 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
             return OME.from_xml(path.with_suffix('.ome.xml'))
 
     def get_ome(self) -> OME:
-        """ overload this """
-        return self.bioformats_ome(self.path)
+        """ OME metadata structure """
+        return from_xml(self.reader.get_ome_xml(), parser='lxml')
 
     @cached_property
     def ome(self) -> OME:
@@ -1116,8 +1202,14 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
 
 class View(Imread, ABC):
     def __init__(self, base: Imread, dtype: DTypeLike = None) -> None:
-        super().__init__(base.base, base.slice, base.shape, dtype or base.dtype, base.frame_decorator)
+        super().__init__(base)
+        self.dtype = dtype or base.dtype
+        self.slice = base.slice
+        self._shape = Shape(base.shape)
+        self.frame_decorator = base.frame_decorator
         self.transform = base.transform
+        self.flags = dict(C_CONTIGUOUS=False, F_CONTIGUOUS=False, OWNDATA=False, WRITEABLE=False,
+                          ALIGNED=False, WRITEBACKIFCOPY=False, UPDATEIFCOPY=False)
 
     def __getattr__(self, item: str) -> Any:
         if not hasattr(self.base, item):
@@ -1125,194 +1217,6 @@ class View(Imread, ABC):
         return self.base.__getattribute__(item)
 
 
-class AbstractReader(Imread, metaclass=ABCMeta):
-    priority = 99
-    do_not_pickle = 'cache'
-    ureg = ureg
-
-    @staticmethod
-    @abstractmethod
-    def _can_open(path: Path | str) -> bool:
-        """ Override this method, and return true when the subclass can open the file """
-        return False
-
-    @staticmethod
-    def get_positions(path: str | Path) -> Optional[list[int]]:
-        return None
-
-    @abstractmethod
-    def __frame__(self, c: int, z: int, t: int) -> np.ndarray:
-        """ Override this, return the frame at c, z, t """
-        return np.random.randint(0, 255, self.shape['yx'])
-
-    def open(self) -> None:
-        """ Optionally override this, open file handles etc.
-            filehandles cannot be pickled and should be marked such by setting do_not_pickle = 'file_handle_name' """
-        return
-
-    def close(self) -> None:
-        """ Optionally override this, close file handles etc. """
-        return
-
-    def __init__(self, path: Path | str | Imread | Any = None, dtype: DTypeLike = None, axes: str = None) -> None:
-        if isinstance(path, Imread):
-            return
-        super().__init__()
-        self.isclosed = False
-        if isinstance(path, str):
-            path = Path(path)
-        self.path, self.series = self.split_path_series(path)
-        if isinstance(path, Path) and path.exists():
-            self.title = self.path.name
-            self.acquisitiondate = datetime.fromtimestamp(self.path.stat().st_mtime).strftime('%y-%m-%dT%H:%M:%S')
-        else:  # ndarray
-            self.title = self.__class__.__name__
-            self.acquisitiondate = 'now'
-
-        self.reader = None
-        self.pcf = None
-        self.powermode = None
-        self.collimator = None
-        self.tirfangle = None
-        self.cyllens = ['None', 'None']
-        self.duolink = 'None'
-        self.detector = [0, 1]
-        self.track = [0]
-        self.cache = DequeDict(16)
-        self.frameoffset = 0, 0  # how far apart the centers of frame and sensor are
-
-        self.open()
-        # extract some metadata from ome
-        instrument = self.ome.instruments[0] if self.ome.instruments else None
-        image = self.ome.images[self.series if len(self.ome.images) > 1 else 0]
-        pixels = image.pixels
-        self.shape = pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t
-        self.base_shape = Shape((pixels.size_y, pixels.size_x, pixels.size_c, pixels.size_z, pixels.size_t), 'yxczt')
-        self.dtype = pixels.type.value if dtype is None else dtype
-        self.pxsize = pixels.physical_size_x_quantity
-        try:
-            self.exposuretime = tuple(find(image.pixels.planes, the_c=c).exposure_time_quantity
-                                      for c in range(self.shape['c']))
-        except AttributeError:
-            self.exposuretime = ()
-
-        if self.zstack:
-            self.deltaz = image.pixels.physical_size_z_quantity
-            self.deltaz_um = None if self.deltaz is None else self.deltaz.to(self.ureg.um).m
-        else:
-            self.deltaz = self.deltaz_um = None
-        if image.objective_settings:
-            self.objective = find(instrument.objectives, id=image.objective_settings.id)
-        else:
-            self.objective = None
-        try:
-            t0 = find(image.pixels.planes, the_c=0, the_t=0, the_z=0).delta_t
-            t1 = find(image.pixels.planes, the_c=0, the_t=self.shape['t'] - 1, the_z=0).delta_t
-            self.timeinterval = (t1 - t0) / (self.shape['t'] - 1) if self.shape['t'] > 1 and t1 > t0 else None
-        except AttributeError:
-            self.timeinterval = None
-        try:
-            self.binning = [int(i) for i in image.pixels.channels[0].detector_settings.binning.value.split('x')]
-            if self.pxsize is not None:
-                self.pxsize *= self.binning[0]
-        except (AttributeError, IndexError, ValueError):
-            self.binning = None
-        self.channel_names = [channel.name for channel in image.pixels.channels]
-        self.channel_names += [chr(97 + i) for i in range(len(self.channel_names), self.shape['c'])]
-        self.cnamelist = self.channel_names
-        try:
-            optovars = [objective for objective in instrument.objectives if 'tubelens' in objective.id.lower()]
-        except AttributeError:
-            optovars = []
-        if len(optovars) == 0:
-            self.tubelens = None
-        else:
-            self.tubelens = optovars[0]
-        if self.objective:
-            if self.tubelens:
-                self.magnification = self.objective.nominal_magnification * self.tubelens.nominal_magnification
-            else:
-                self.magnification = self.objective.nominal_magnification
-            self.NA = self.objective.lens_na
-        else:
-            self.magnification = None
-            self.NA = None
-
-        self.gain = [find(instrument.detectors, id=channel.detector_settings.id).amplification_gain
-                     for channel in image.pixels.channels
-                     if channel.detector_settings
-                     and find(instrument.detectors, id=channel.detector_settings.id).amplification_gain]
-        self.laserwavelengths = [(channel.excitation_wavelength_quantity.to(self.ureg.nm).m,)
-                                 for channel in pixels.channels if channel.excitation_wavelength_quantity]
-        self.laserpowers = try_default(lambda: [(1 - channel.light_source_settings.attenuation,)
-                                                for channel in pixels.channels], [])
-        self.filter = try_default(  # type: ignore
-            lambda: [find(instrument.filter_sets, id=channel.filter_set_ref.id).model
-                     for channel in image.pixels.channels], None)
-        self.pxsize_um = None if self.pxsize is None else self.pxsize.to(self.ureg.um).m
-        self.exposuretime_s = [None if i is None else i.to(self.ureg.s).m for i in self.exposuretime]
-
-        if axes is None:
-            self.axes = ''.join(i for i in 'cztyx' if self.shape[i] > 1)
-        elif axes.lower() == 'full':
-            self.axes = 'cztyx'
-        else:
-            self.axes = axes
-        self.slice = [np.arange(s, dtype=int) for s in self.shape.yxczt]
-
-        m = self.extrametadata
-        if m is not None:
-            try:
-                self.cyllens = m['CylLens']
-                self.duolink = m['DLFilterSet'].split(' & ')[m['DLFilterChannel']]
-                if 'FeedbackChannels' in m:
-                    self.feedback = m['FeedbackChannels']
-                else:
-                    self.feedback = m['FeedbackChannel']
-            except Exception:  # noqa
-                self.cyllens = ['None', 'None']
-                self.duolink = 'None'
-                self.feedback = []
-        try:
-            self.cyllenschannels = np.where([self.cyllens[self.detector[c]].lower() != 'none'
-                                             for c in range(self.shape['c'])])[0].tolist()
-        except Exception:  # noqa
-            pass
-        try:
-            s = int(re.findall(r'_(\d{3})_', self.duolink)[0]) * ureg.nm
-        except Exception:  # noqa
-            s = 561 * ureg.nm
-        try:
-            sigma = []
-            for c, d in enumerate(self.detector):
-                emission = (np.hstack(self.laserwavelengths[c]) + 22) * ureg.nm
-                sigma.append([emission[emission > s].max(initial=0), emission[emission < s].max(initial=0)][d])
-            sigma = np.hstack(sigma)
-            sigma[sigma == 0] = 600 * ureg.nm
-            sigma /= 2 * self.NA * self.pxsize
-            self.sigma = sigma.magnitude.tolist()  # type: ignore
-        except Exception:  # noqa
-            self.sigma = [2] * self.shape['c']
-        if not self.NA:
-            self.immersionN = 1
-        elif 1.5 < self.NA:
-            self.immersionN = 1.661
-        elif 1.3 < self.NA < 1.5:
-            self.immersionN = 1.518
-        elif 1 < self.NA < 1.3:
-            self.immersionN = 1.33
-        else:
-            self.immersionN = 1
-
-        p = re.compile(r'(\d+):(\d+)$')
-        try:
-            self.track, self.detector = zip(*[[int(i) for i in p.findall(find(
-                self.ome.images[self.series].pixels.channels, id=f'Channel:{c}').detector_settings.id)[0]]
-                                              for c in range(self.shape['c'])])
-        except Exception:  # noqa
-            pass
-
-
 def main() -> None:
     parser = ArgumentParser(description='Display info and save as tif')
     parser.add_argument('-v', '--version', action='version', version=__version__)
@@ -1352,6 +1256,3 @@ def main() -> None:
                     f.write(im.ome.to_xml())
             if len(args.file) == 1:
                 print(im.summary)
-
-
-from .readers import *  # noqa

py/ndbioimage/readers/__init__.py

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

py/ndbioimage/readers/bfread.py

@@ -1,37 +0,0 @@
-from __future__ import annotations
-
-from abc import ABC
-from pathlib import Path
-
-import numpy as np
-
-from .. import rs
-from .. import AbstractReader
-
-for file in (Path(__file__).parent / "deps").glob("*_"):
-    file.rename(str(file)[:-1])
-
-if not list((Path(__file__).parent / "jassets").glob("bioformats*.jar")):
-    rs.download_bioformats(True)
-
-
-class Reader(AbstractReader, ABC):
-    priority = 99  # panic and open with BioFormats
-    do_not_pickle = 'reader'
-
-    @staticmethod
-    def _can_open(path: Path) -> bool:
-        try:
-            _ = rs.Reader(path)
-            return True
-        except Exception:
-            return False
-
-    def open(self) -> None:
-        self.reader = rs.Reader(str(self.path), int(self.series))
-
-    def __frame__(self, c: int, z: int, t: int) -> np.ndarray:
-        return self.reader.get_frame(int(c), int(z), int(t))
-
-    def close(self) -> None:
-        self.reader.close()

py/ndbioimage/readers/cziread.py

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

py/ndbioimage/readers/fijiread.py

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

py/ndbioimage/readers/metaseriesread.py

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

py/ndbioimage/readers/ndread.py

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

py/ndbioimage/readers/seqread.py

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

py/ndbioimage/readers/tifread.py

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

py/ndbioimage/rs.py

@@ -1,9 +0,0 @@
-from .ndbioimage_rs import Reader, download_bioformats  # noqa
-from pathlib import Path
-
-
-if not list((Path(__file__).parent / "jassets").glob("bioformats*.jar")):
-    download_bioformats(True)
-
-for file in (Path(__file__).parent / "deps").glob("*_"):
-    file.rename(str(file)[:-1])

src/py.rs

@@ -15,7 +15,18 @@ struct PyReader {
 impl PyReader {
     #[new]
     fn new(path: &str, series: usize) -> PyResult<Self> {
-        let path = PathBuf::from(path);
+        let mut path = PathBuf::from(path);
+        if path.is_dir() {
+            for file in path.read_dir()? {
+                if let Ok(f) = file {
+                    let p = f.path();
+                    if f.path().is_file() & (p.extension() == Some("tif".as_ref())) {
+                        path = p;
+                        break;
+                    }
+                }
+            }
+        }
         Ok(PyReader {
             reader: Reader::new(&path, series as i32)?,
         })
@@ -43,6 +54,11 @@ impl PyReader {
     fn get_ome_xml(&self) -> PyResult<String> {
         Ok(self.reader.get_ome_xml()?)
     }
+
+    fn close(&mut self) -> PyResult<()> {
+        self.reader.close()?;
+        Ok(())
+    }
 }
 
 pub(crate) fn ndbioimage_file() -> anyhow::Result<PathBuf> {

tests/test_open.py

@@ -1,27 +1,21 @@
 import pickle
-from multiprocessing import active_children
 from pathlib import Path
 
 import pytest
 
-from ndbioimage import Imread, ReaderNotFoundError
+from ndbioimage import Imread
 
 
-@pytest.mark.parametrize('file', (Path(__file__).parent / 'files').iterdir())
+@pytest.mark.parametrize('file',
+                         [file for file in (Path(__file__).parent / 'files').iterdir() if not file.suffix == '.pzl'])
 def test_open(file):
-    try:
-        with Imread(file) as im:
-            mean = im[dict(c=0, z=0, t=0)].mean()
-            b = pickle.dumps(im)
-            jm = pickle.loads(b)
-            assert jm[dict(c=0, z=0, t=0)].mean() == mean
-            v = im.view()
-            assert v[dict(c=0, z=0, t=0)].mean() == mean
-            b = pickle.dumps(v)
-            w = pickle.loads(b)
-            assert w[dict(c=0, z=0, t=0)].mean() == mean
-    except ReaderNotFoundError:
-        assert len(Imread.__subclasses__()), 'No subclasses for Imread found.'
-
-    for child in active_children():
-        child.kill()
+    with Imread(file) 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

tests/test_slicing.py

@@ -1,20 +1,32 @@
+import tempfile
 from itertools import combinations_with_replacement
 from numbers import Number
+from pathlib import Path
 
 import numpy as np
 import pytest
+from tiffwrite import tiffwrite
 
 from ndbioimage import Imread
 
-r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
-im = Imread(r)
-a = np.array(im)
+
+@pytest.fixture
+def array():
+    return np.random.randint(0, 255, (64, 64, 2, 3, 4), 'uint8')
+
+@pytest.fixture()
+def image(array):
+    with tempfile.TemporaryDirectory() as folder:
+        file = Path(folder) / "test.tif"
+        tiffwrite(file, array, 'yxczt')
+        with Imread(file, axes='yxczt') as im:
+            yield im
 
 
 @pytest.mark.parametrize('s', combinations_with_replacement(
     (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5))
-def test_slicing(s):
-    s_im, s_a = im[s], a[s]
+def test_slicing(s, image, array):
+    s_im, s_a = image[s], array[s]
     if isinstance(s_a, Number):
         assert isinstance(s_im, Number)
         assert s_im == s_a

tests/test_ufuncs.py

@@ -1,19 +1,31 @@
+import tempfile
 from itertools import product
+from pathlib import Path
 
 import numpy as np
 import pytest
+from tiffwrite import tiffwrite
 
 from ndbioimage import Imread
 
-r = np.random.randint(0, 255, (64, 64, 2, 3, 4))
-im = Imread(r)
-a = np.array(im)
+
+@pytest.fixture
+def array():
+    return np.random.randint(0, 255, (64, 64, 2, 3, 4), 'uint16')
+
+@pytest.fixture()
+def image(array):
+    with tempfile.TemporaryDirectory() as folder:
+        file = Path(folder) / "test.tif"
+        tiffwrite(file, array, 'yxczt')
+        with Imread(file, axes='yxczt') as im:
+            yield im
 
 
 @pytest.mark.parametrize('fun_and_axis', product(
     (np.sum, np.nansum, np.min, np.nanmin, np.max, np.nanmax, np.argmin, np.argmax,
      np.mean, np.nanmean, np.var, np.nanvar, np.std, np.nanstd), (None, 0, 1, 2, 3, 4)))
-def test_ufuncs(fun_and_axis):
+def test_ufuncs(fun_and_axis, image, array):
     fun, axis = fun_and_axis
-    assert np.all(np.isclose(fun(im, axis), fun(a, axis))), \
+    assert np.all(np.isclose(fun(image, axis), fun(array, axis))), \
         f'function {fun.__name__} over axis {axis} does not give the correct result'