Add obsep support and minor fixes (#230)

azure-pipelines.yml

@@ -165,7 +165,7 @@ stages:
             displayName: TestBuild
 
       - job: pyinstaller
-        condition: not(startsWith(variables['Build.SourceBranch'], 'refs/heads/feature'))
+        # condition: not(startsWith(variables['Build.SourceBranch'], 'refs/heads/feature'))
         strategy:
           matrix:
             macos:

build_utils/minimal-req.txt

@@ -10,8 +10,8 @@ defusedxml==0.6.0
 h5py==2.8.0
 imagecodecs==2020.5.30
 imageio==2.5.0
-napari==0.4.2
-numpy==1.16.0
+napari==0.4.3
+numpy==1.16.5
 oiffile==2019.1.1
 openpyxl==2.4.9
 packaging==17.1
@@ -24,6 +24,5 @@ sympy==1.1.1
 tifffile==2020.2.16
 xlrd==1.1.0
 xlsxwriter
-dataclasses==0.7 ;python_version < '3.7'
-typing-extensions==3.7.4 ;python_version < '3.8'
+typing-extensions==3.7.4.2 ;python_version < '3.8'
 PyQt5!=5.15.0,==5.12.3

launcher.spec

@@ -56,7 +56,25 @@ napari.plugins.plugin_manager.discover()
 
 hiddenimports = ["imagecodecs._" + x for x in imagecodecs._extensions()] +\
                 ["imagecodecs._shared"] + [x.__name__ for x in napari.plugins.plugin_manager.plugins.values()] + \
-                ["pkg_resources.py2_warn", "scipy.special.cython_special", "ipykernel.datapub"]
+                ["pkg_resources.py2_warn", "scipy.special.cython_special", "ipykernel.datapub"] + [
+                    "numpy.core._dtype_ctypes",
+                    "sentry_sdk.integrations.logging",
+                    "sentry_sdk.integrations.stdlib",
+                    "sentry_sdk.integrations.excepthook",
+                    "sentry_sdk.integrations.dedupe",
+                    "sentry_sdk.integrations.atexit",
+                    "sentry_sdk.integrations.modules",
+                    "sentry_sdk.integrations.argv",
+                    "sentry_sdk.integrations.threading",
+                    "numpy.random.common",
+                    "numpy.random.bounded_integers",
+                    "numpy.random.entropy",
+                    "PartSegCore.register",
+                    "defusedxml.cElementTree",
+                    "vispy.app.backends._pyqt5",
+                    "scipy.spatial.transform._rotation_groups",
+                    "magicgui.backends._qtpy",
+                ]
 
 try:
     from sentry_sdk.integrations import _AUTO_ENABLING_INTEGRATIONS
@@ -106,25 +124,7 @@ a = Analysis(
     + collect_data_files("vispy")
     + collect_data_files("napari")
     + pyzmq_data,
-    hiddenimports=hiddenimports
-    + [
-        "numpy.core._dtype_ctypes",
-        "sentry_sdk.integrations.logging",
-        "sentry_sdk.integrations.stdlib",
-        "sentry_sdk.integrations.excepthook",
-        "sentry_sdk.integrations.dedupe",
-        "sentry_sdk.integrations.atexit",
-        "sentry_sdk.integrations.modules",
-        "sentry_sdk.integrations.argv",
-        "sentry_sdk.integrations.threading",
-        "numpy.random.common",
-        "numpy.random.bounded_integers",
-        "numpy.random.entropy",
-        "PartSegCore.register",
-        "defusedxml.cElementTree",
-        "vispy.app.backends._pyqt5",
-        "scipy.spatial.transform._rotation_groups"
-    ],
+    hiddenimports=hiddenimports,
     # + ["plugins." + x.name for x in plugins.get_plugins()],
     hookspath=[],
     runtime_hooks=[],

package/PartSeg/common_gui/algorithms_description.py

@@ -82,7 +82,10 @@ def recursive_get_values(self):
 
     def set_value(self, val):
         """set value of widget """
-        return self._setter(self._widget, val)
+        try:
+            return self._setter(self._widget, val)
+        except TypeError:
+            pass
 
     def get_field(self) -> QWidget:
         """

package/PartSeg/common_gui/main_window.py

@@ -1,3 +1,4 @@
+import dataclasses
 import os
 from pathlib import Path
 from typing import List, Optional, Type
@@ -72,7 +73,7 @@ def set_data(self, data):
             if image:
                 if isinstance(image, Image):
                     # noinspection PyProtectedMember
-                    data = data._replace(image=image)
+                    data = dataclasses.replace(data, image=image)
             else:
                 return
         if data is None:

package/PartSeg/plugins/__init__.py

@@ -33,6 +33,7 @@ def get_plugins():
         napari.plugins.plugin_manager.register(load_roi_project)
         napari.plugins.plugin_manager.register(napari_plugin_engine)
         napari.plugins.plugin_manager.register(save_mask_roi)
+
     else:
         packages = pkgutil.iter_modules(__path__, __name__ + ".")
     packages2 = itertools.chain(

package/PartSegCore/mask/io_functions.py

@@ -410,7 +410,7 @@ class LoadStackImage(LoadBase):
 
     @classmethod
     def get_name(cls):
-        return "Image(*.tif *.tiff *.lsm *.czi *.oib *.oif)"
+        return "Image(*.tif *.tiff *.lsm *.czi *.oib *.oif *.obsep)"
 
     @classmethod
     def get_short_name(cls):

package/PartSegCore/napari_plugins/save_mask_roi.py

@@ -5,6 +5,7 @@
 from napari_plugin_engine import napari_hook_implementation
 
 from PartSegCore.mask.io_functions import MaskProjectTuple, SaveROI
+from PartSegImage.image import NAPARI_SCALING
 
 
 @napari_hook_implementation
@@ -14,5 +15,5 @@ def napari_write_labels(path: str, data: Any, meta: dict) -> Optional[str]:
     ext = os.path.splitext(path)[1]
     if ext in SaveROI.get_extensions():
         project = MaskProjectTuple(file_path="", image=None, roi=data)
-        SaveROI.save(path, project, parameters={})
+        SaveROI.save(path, project, parameters={"spacing": numpy.divide(meta["scale"], NAPARI_SCALING)[-3:]})
         return path

package/PartSegImage/__init__.py

@@ -3,7 +3,14 @@
 
 from . import tifffile_fixes  # noqa: F401
 from .image import Image
-from .image_reader import CziImageReader, GenericImageReader, OifImagReader, TiffFileException, TiffImageReader
+from .image_reader import (
+    CziImageReader,
+    GenericImageReader,
+    ObsepImageReader,
+    OifImagReader,
+    TiffFileException,
+    TiffImageReader,
+)
 from .image_writer import ImageWriter
 
 __all__ = (
@@ -13,6 +20,7 @@
     "TiffFileException",
     "CziImageReader",
     "OifImagReader",
+    "ObsepImageReader",
     "GenericImageReader",
 )
 

package/PartSegImage/image.py

@@ -1,3 +1,4 @@
+import re
 import typing
 import warnings
 from collections.abc import Iterable
@@ -10,6 +11,8 @@
 _DEF = object()
 FRAME_THICKNESS = 2
 
+NAPARI_SCALING = 10 ** 9
+
 
 def minimal_dtype(val: int):
     """
@@ -158,13 +161,18 @@ def merge(self, image: "Image", axis: typing.Union[str, int]) -> "Image":
         data = self.reorder_axes(image.get_data(), image.axis_order)
         data = np.concatenate((self.get_data(), data), axis=axis)
         channel_names = self.channel_names
+        reg = re.compile(r"channel \d+")
         for name in image.channel_names:
+            match = reg.match(name)
             new_name = name
+            if match:
+                name = "channel"
+                new_name = f"channel {len(channel_names) + 1}"
             i = 1
             while new_name in channel_names:
-                new_name = f"{new_name} ({i})"
+                new_name = f"{name} ({i})"
                 i += 1
-                if i > 10000:
+                if i > 10000:  # pragma: no cover
                     raise ValueError("fail when try to fix channel name")
             channel_names.append(new_name)
 
@@ -482,7 +490,7 @@ def spacing(self) -> Spacing:
             return tuple(self._image_spacing[1:])
         return self._image_spacing
 
-    def normalized_scaling(self, factor=10 ** 9) -> Spacing:
+    def normalized_scaling(self, factor=NAPARI_SCALING) -> Spacing:
         if self.is_2d:
             return (1, 1) + tuple(np.multiply(self.spacing, factor))
         return (1,) + tuple(np.multiply(self.spacing, factor))
@@ -498,7 +506,7 @@ def set_spacing(self, value: Spacing):
             return
         if self.is_2d and len(value) + 1 == len(self._image_spacing):
             value = (1.0,) + tuple(value)
-        if len(value) != len(self._image_spacing):
+        if len(value) != len(self._image_spacing):  # pragma: no cover
             raise ValueError("Correction of spacing fail.")
         self._image_spacing = tuple(value)
 

package/PartSegImage/image_reader.py

@@ -9,6 +9,7 @@
 import numpy as np
 import tifffile.tifffile
 from czifile.czifile import CziFile
+from defusedxml import ElementTree
 from oiffile import OifFile
 from tifffile import TiffFile
 
@@ -149,7 +150,7 @@ class GenericImageReader(BaseImageReader):
 
     def read(self, image_path: typing.Union[str, BytesIO, Path], mask_path=None, ext=None) -> Image:
         if ext is None:
-            if isinstance(image_path, str):
+            if isinstance(image_path, (str, Path)):
                 ext = os.path.splitext(image_path)[1]
             else:
                 ext = ".tif"
@@ -158,6 +159,8 @@ def read(self, image_path: typing.Union[str, BytesIO, Path], mask_path=None, ext
             return CziImageReader.read_image(image_path, mask_path, self.callback_function, self.default_spacing)
         if ext in [".oif", ".oib"]:
             return OifImagReader.read_image(image_path, mask_path, self.callback_function, self.default_spacing)
+        if ext == ".obsep":
+            return ObsepImageReader.read_image(image_path, mask_path, self.callback_function, self.default_spacing)
         return TiffImageReader.read_image(image_path, mask_path, self.callback_function, self.default_spacing)
 
 
@@ -238,6 +241,52 @@ def update_array_shape(cls, array: np.ndarray, axes: str):
         return super().update_array_shape(array, axes)
 
 
+class ObsepImageReader(BaseImageReader):
+    def read(self, image_path: typing.Union[str, BytesIO, Path], mask_path=None, ext=None) -> Image:
+        directory = Path(os.path.dirname(image_path))
+        xml_doc = ElementTree.parse(image_path).getroot()
+        channels = xml_doc.findall("net/node/node/attribute[@name='image type']")
+        if not channels:
+            raise ValueError("Information about channel images not found")
+        possible_extensions = [".tiff", ".tif", ".TIFF", ".TIF"]
+        channel_list = []
+        for channel in channels:
+            try:
+                name = next(iter(channel)).attrib["val"]
+            except StopIteration:  # pragma: no cover
+                raise ValueError("Missed information about channel name in obsep file")
+            for ex in possible_extensions:
+                if (directory / (name + ex)).exists():
+                    name += ex
+                    break
+            else:  # pragma: no cover
+                raise ValueError(f"Not found file for key {name}")
+            channel_list.append(TiffImageReader.read_image(directory / name, default_spacing=self.default_spacing))
+        for channel in channels:
+            try:
+                name = next(iter(channel)).attrib["val"] + "_deconv"
+            except StopIteration:  # pragma: no cover
+                raise ValueError("Missed information about channel name in obsep file")
+            for ex in possible_extensions:
+                if (directory / (name + ex)).exists():
+                    name += ex
+                    break
+            if (directory / name).exists():
+                channel_list.append(TiffImageReader.read_image(directory / name, default_spacing=self.default_spacing))
+
+        image = channel_list[0]
+        for el in channel_list[1:]:
+            image = image.merge(el, "C")
+
+        z_spacing = (
+            float(xml_doc.find("net/node/attribute[@name='step width']/double").attrib["val"]) * name_to_scalar["um"]
+        )
+
+        image.set_spacing((z_spacing,) + image.spacing[1:])
+        image.file_path = str(image_path)
+        return image
+
+
 class TiffImageReader(BaseImageReader):
     """
     TIFF/LSM files reader. Base reading with :py:meth:`BaseImageReader.read_image`
@@ -305,7 +354,7 @@ def report_func():
         self.image_file.close()
         if self.mask_file is not None:
             self.mask_file.close()
-        if not isinstance(image_path, str):
+        if not isinstance(image_path, (str, Path)):
             image_path = ""
         return self.image_class(
             image_data,
@@ -332,10 +381,10 @@ def verify_mask(self):
                 continue
             try:
                 j = image_series.axes.index(pos)
-            except ValueError:
+            except ValueError:  # pragma: no cover
                 raise ValueError("Incompatible shape of mask and image (axes)")
                 # TODO add verification if problem with T/Z/I
-            if image_series.shape[j] != mask_series.shape[i]:
+            if image_series.shape[j] != mask_series.shape[i]:  # pragma: no cover
                 raise ValueError("Incompatible shape of mask and image")
             # TODO Add verification if mask have to few dimensions
 
@@ -361,7 +410,7 @@ def read_resolution_from_tags(self):
                     scalar = name_to_scalar["centimeter"]
                 elif unit == 2:
                     scalar = name_to_scalar["cal"]
-                else:
+                else:  # pragma: no cover
                     raise KeyError(f"wrong scalar {tags['ResolutionUnit']}, {tags['ResolutionUnit'].value}")
 
             x_spacing = tags["XResolution"].value[1] / tags["XResolution"].value[0] * scalar

package/tests/test_PartSeg/test_main_windows.py

@@ -57,7 +57,7 @@ def test_open_mask(self, qtbot, monkeypatch, tmp_path):
         main_window = LauncherMainWindow("Launcher")
         qtbot.addWidget(main_window)
         main_window._launch_mask()
-        with qtbot.waitSignal(main_window.prepare.finished):
+        with qtbot.waitSignal(main_window.prepare.finished, timeout=10 ** 4):
             main_window.prepare.start()
         # qtbot.addWidget(main_window.wind)
         QCoreApplication.processEvents()

package/tests/test_PartSegImage/test_image_reader.py

@@ -1,12 +1,14 @@
 import math
 import os.path
+import shutil
+from glob import glob
 
 import numpy as np
 import pytest
 import tifffile
 
 import PartSegData
-from PartSegImage import CziImageReader, GenericImageReader, Image, OifImagReader, TiffImageReader
+from PartSegImage import CziImageReader, GenericImageReader, Image, ObsepImageReader, OifImagReader, TiffImageReader
 
 
 class TestImageClass:
@@ -84,6 +86,26 @@ def test_set_spacing(self):
         reader.set_default_spacing((5, 7))
         assert reader.default_spacing == (10 ** -6, 5, 7)
 
+    def test_obsep_read(self, data_test_dir):
+        image = ObsepImageReader.read_image(os.path.join(data_test_dir, "obsep", "test.obsep"))
+        assert image.channels == 2
+        assert np.allclose(image.spacing, (500 * 10 ** -9, 64 * 10 ** -9, 64 * 10 ** -9))
+        assert image.channel_names == ["channel 1", "channel 2"]
+
+    def test_obsep_deconv_read(self, data_test_dir, tmp_path):
+        for el in glob(os.path.join(data_test_dir, "obsep", "*")):
+            shutil.copy(os.path.join(data_test_dir, "obsep", el), tmp_path)
+        image = GenericImageReader.read_image(tmp_path / "test.obsep")
+        assert image.channels == 2
+        assert np.allclose(image.spacing, (500 * 10 ** -9, 64 * 10 ** -9, 64 * 10 ** -9))
+        assert image.channel_names == ["channel 1", "channel 2"]
+        shutil.copy(tmp_path / "Cy5.TIF", tmp_path / "Cy5_decon2.TIF")
+        image = GenericImageReader.read_image(tmp_path / "test.obsep")
+        assert image.channels == 2
+        shutil.copy(tmp_path / "Cy5.TIF", tmp_path / "Cy5_deconv.TIF")
+        image = GenericImageReader.read_image(tmp_path / "test.obsep")
+        assert image.channels == 3
+
 
 class CustomImage(Image):
     axis_order = "TCXYZ"

setup.cfg

@@ -40,8 +40,8 @@ install_requires =
     h5py>=2.8.0
     imagecodecs>=2020.5.30
     imageio>=2.5.0
-    napari>=0.4.2
-    numpy>=1.16.0
+    napari>=0.4.3
+    numpy>=1.16.5
     oiffile>=2019.1.1
     openpyxl>=2.4.9
     packaging>=17.1