Merge pull request #87 from sebi06/work_in_progress

Work in progress 0.8.0 - merge to main

Author: sebi06

.gitignore

@@ -182,3 +182,4 @@ data/nuc_small_green.czi
 data/nuc_small.czi
 data/Tumor_HE_Orig_small_disp.czi
 data/Tumor_HE_RGB_disp.czi
+.pylintrc

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = czitools
-version = 0.7.6
+version = 0.8.0
 author = Sebastian Rhode
 author_email = sebrhode@gmail.com
 url = https://github.com/sebi06/czitools

src/czitools/__init__.py

@@ -1,3 +1,3 @@
 # __init__.py
 # version of the czitools package
-__version__ = "0.7.6"
+__version__ = "0.8.0"

src/czitools/_tests/test_channelinfo.py

@@ -10,14 +10,15 @@
 
 
 @pytest.mark.parametrize(
-    "czifile, clims, colors, gamma, names, dyes, ch_disp, is_rgb, is_consistent, pxtypes",
+    "czifile, clims, colors, gamma, names, dyes, dyes_short, ch_disp, is_rgb, is_consistent, pxtypes",
     [
         (
             "Tumor_HE_Orig_small.czi",
             [[0.0, 0.5]],
             ["#80808000"],
             [0.85],
             ["CH1"],
+            ["TL Brightfield"],
             ["Brigh"],
             {
                 0: pyczi.ChannelDisplaySettingsDataClass(
@@ -38,6 +39,7 @@
             ["#FFFF7E00", "#FF00FF33"],
             [0.7999999999999998, 0.7999999999999998],
             ["LED555", "LED470"],
+            ["LED555", "LED470"],
             ["AF555", "AF488"],
             {
                 0: pyczi.ChannelDisplaySettingsDataClass(
@@ -65,6 +67,7 @@
             ["#80808000"],
             [0.85],
             ["CH1"],
+            ["C1"],
             ["Dye-CH1"],
             {
                 0: pyczi.ChannelDisplaySettingsDataClass(
@@ -89,6 +92,7 @@
             [0.7999999999999998, 0.7999999999999998],
             ["AF568", "AF488"],
             ["AF568", "AF488"],
+            ["AF568", "AF488"],
             {
                 0: pyczi.ChannelDisplaySettingsDataClass(
                     True,
@@ -118,6 +122,7 @@ def test_channelinfo(
     gamma: List[float],
     names: List[str],
     dyes: List[str],
+    dyes_short: List[str],
     ch_disp: Dict[int, pyczi.ChannelDisplaySettingsDataClass],
     is_rgb: Dict[int, bool],
     is_consistent: bool,
@@ -132,6 +137,7 @@ def test_channelinfo(
     assert czi_channels.gamma == gamma
     assert czi_channels.names == names
     assert czi_channels.dyes == dyes
+    assert czi_channels.dyes_short == dyes_short
     assert czi_channels.czi_disp_settings == ch_disp
     assert czi_channels.isRGB == is_rgb
     assert czi_channels.consistent_pixeltypes == is_consistent

src/czitools/metadata_tools/channel.py

@@ -27,6 +27,8 @@ class CziChannelInfo:
         czisource (Union[str, os.PathLike[str], Box]): The source of the CZI image data.
         names (List[str]): List of channel names.
         dyes (List[str]): List of dye names.
+        dyes_short (List[str]): List of short dye names.
+        channel_descriptions (List[str]): List of channel descriptions.
         colors (List[str]): List of channel colors.
         clims (List[List[float]]): List of channel intensity limits.
         gamma (List[float]): List of gamma values for each channel.
@@ -48,6 +50,8 @@ class CziChannelInfo:
     czisource: Union[str, os.PathLike[str], Box]
     names: List[str] = field(init=False, default_factory=lambda: [])
     dyes: List[str] = field(init=False, default_factory=lambda: [])
+    dyes_short: List[str] = field(init=False, default_factory=lambda: [])
+    channel_descriptions: List[str] = field(init=False, default_factory=lambda: [])
     colors: List[str] = field(init=False, default_factory=lambda: [])
     clims: List[List[float]] = field(init=False, default_factory=lambda: [])
     gamma: List[float] = field(init=False, default_factory=lambda: [])
@@ -131,8 +135,18 @@ def _get_channel_info(self, display: Box):
         if display is not None:
             (
                 self.dyes.append("Dye-CH1")
+                if display.Name is None
+                else self.dyes.append(display.Name)
+            )
+            (
+                self.dyes_short.append("Dye-CH1")
+                if display.ShortName is None
+                else self.dyes_short.append(display.ShortName)
+            )
+            (
+                self.channel_descriptions.append("")
                 if display.ShortName is None
-                else self.dyes.append(display.ShortName)
+                else self.channel_descriptions.append(display.Description)
             )
             (
                 self.colors.append("#80808000")

src/czitools/metadata_tools/czi_metadata.py

@@ -425,8 +425,10 @@ def create_md_dict_red(
         "ScaleRatio_XYZ": metadata.scale.ratio,
         "ChannelNames": metadata.channelinfo.names,
         "ChannelDyes": metadata.channelinfo.dyes,
+        "ChannelDyesShort": metadata.channelinfo.dyes_short,
         "ChannelColors": metadata.channelinfo.colors,
         "WellArrayNames": metadata.sample.well_array_names,
+        "ChannelDescriptions": metadata.channelinfo.channel_descriptions,
         "WellIndicies": metadata.sample.well_indices,
         "WellPositionNames": metadata.sample.well_position_names,
         "WellRowID": metadata.sample.well_rowID,