Merge branch 'main' into dev/multi-page-tiff

pims/__version__.py

@@ -16,8 +16,8 @@
 
 # KEEP ENCODING - so that __version__ can be read even if py2.7 is used.
 
-VERSION = (0, 10, 2)
-API_VERSION = (0, 9, 0)
+VERSION = (0, 11, 0)
+API_VERSION = (0, 11, 0)
 
 __title__ = 'pims'
 __description__ = 'Cytomine Python Image Server'

pims/api/metadata.py

@@ -38,6 +38,7 @@
 from pims.files.file import FileRole, FileType, Path
 from pims.formats.utils.structures.metadata import MetadataType
 from pims.processing.image_response import AssociatedResponse
+from pims.utils.dtypes import dtype_to_bits
 
 router = APIRouter()
 api_tags = ['Metadata']
@@ -205,6 +206,10 @@ class ImageInfo(BaseModel):
         ...,
         description='The number of bits within the type storing each pixel that are significant.',
     )
+    bits: conint(ge=1) = Field(
+        ...,
+        description='The number of bits used by the type storing each pixel.'
+    )
 
     @classmethod
     def from_image(cls, image):
@@ -229,6 +234,7 @@ def from_image(cls, image):
                 "description": image.description,
                 "pixel_type": PixelType[str(image.pixel_type)],
                 "significant_bits": image.significant_bits,
+                "bits": dtype_to_bits(image.pixel_type)
             }
         )
 

pims/formats/common/ometiff.py

@@ -246,16 +246,17 @@ def parse_main_metadata(self) -> ImageMetadata:
                     #  information is already extracted.
                     break
 
-                colors = [infer_channel_color(
-                    parse_int(attr.get('Color')),
-                    cc_idx,
-                    shape[axes.index('C')]
-                )] * spp
-
-                if spp == 3 and colors[0] is None:
+                if spp == 3:
+                    # If RGB channel, Color attribute is ignored (Icy behavior)
                     colors = [
                         infer_channel_color(None, i, 3) for i in range(spp)
                     ]
+                else:
+                    colors = [infer_channel_color(
+                        parse_int(attr.get('Color')),
+                        cc_idx,
+                        shape[axes.index('C')]
+                    )] * spp
 
                 names = [attr.get('Name')] * spp
                 if names[0] is None:

pims/importer/listeners.py

@@ -413,13 +413,8 @@ def end_successful_import(self, path: Path, image: Image, *args, **kwargs):
 
         # Cytomine "channels" = number of concrete channels
         ai.channels = image.n_concrete_channels
-        # Cytomine "extrinsicChannels" = number of channels
-        #   (n_concrete_channels * n_samples)
-        ai.extrinsicChannels = image.n_channels
-        # Cytomine "samplePerPixel" = number of samples
-        ai.samplePerPixel = image.n_samples
-        # Cytomine "bitPerSample" = number of bits to store a sample
-        ai.bitPerSample = dtype_to_bits(image.pixel_type)
+        ai.samples = image.n_samples
+        ai.bits = dtype_to_bits(image.pixel_type)
 
         if image.physical_size_x:
             ai.physicalSizeX = round(
@@ -443,19 +438,26 @@ def end_successful_import(self, path: Path, image: Image, *args, **kwargs):
         self.abstract_images.append(ai)
 
         asc = AbstractSliceCollection()
-        set_channel_names = image.n_concrete_channels == image.n_channels
-        for c in range(image.n_concrete_channels):
-            name = None
-            color = None
-            if set_channel_names:
-                name = image.channels[c].suggested_name
-                color = image.channels[c].hex_color
+        for cc in range(image.n_concrete_channels):
+            first_c = cc * image.n_samples
+
+            name = image.channels[first_c].suggested_name
+            color = image.channels[first_c].hex_color
+            if image.n_samples != 1:
+                names = [
+                    image.channels[i].suggested_name
+                    for i in range(first_c, first_c + image.n_samples)
+                ]
+                names = list(dict.fromkeys(names))  # ordered uniqueness
+                name = '|'.join(names)
+                color = None
+
             for z in range(image.depth):
                 for t in range(image.duration):
                     mime = "image/pyrtiff"  # TODO: remove
                     asc.append(
                         AbstractSlice(
-                            ai.id, uf.id, mime, c, z, t,
+                            ai.id, uf.id, mime, cc, z, t,
                             channelName=name, channelColor=color
                         )
                     )

scripts/plugin-list.csv

@@ -1,3 +1,3 @@
 enabled,name,git_url,git_branch
-1,pims-plugin-format-openslide,https://github.com/Cytomine-ULiege/pims-plugin-format-openslide.git,0851dca4ed92bab33ae30200a86ce8e56c655a71
-1,pims-plugin-format-bioformats,https://github.com/Cytomine-ULiege/pims-plugin-format-bioformats.git,c25da92ccf706834adf12e3e0d9fd1362e793c48
+1,pims-plugin-format-openslide,https://github.com/Cytomine-ULiege/pims-plugin-format-openslide.git,5f8a92e37d2a47145f0b375db541b591490361bc
+1,pims-plugin-format-bioformats,https://github.com/Cytomine-ULiege/pims-plugin-format-bioformats.git,f67580116ff21cc994a3d9cfe25c98bd4aaffef9