Rename Channel->OmeroChannel and BaseChannel->Channel (ref #404)

tcompa · tcompa · commit d583ebaebe6b · 2023-06-15T10:58:28.000+02:00
diff --git a/fractal_tasks_core/__FRACTAL_MANIFEST__.json b/fractal_tasks_core/__FRACTAL_MANIFEST__.json
@@ -45,9 +45,9 @@
             "title": "Allowed Channels",
             "type": "array",
             "items": {
-              "$ref": "#/definitions/Channel"
+              "$ref": "#/definitions/OmeroChannel"
             },
-            "description": "A list of channel dictionaries, where each channel must include the ``wavelength_id`` key and where the corresponding values should be unique across channels. # TODO: improve after Channel input refactor See issue 386"
+            "description": "A list of ``OmeroChannel``s, where each channel must include the ``wavelength_id`` attribute and where the ``wavelength_id`` values must be unique across the list."
           },
           "num_levels": {
             "title": "Num Levels",
@@ -76,8 +76,8 @@
         ],
         "additionalProperties": false,
         "definitions": {
-          "ChannelWindow": {
-            "title": "ChannelWindow",
+          "Window": {
+            "title": "Window",
             "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n        their values.",
             "type": "object",
             "properties": {
@@ -103,8 +103,8 @@
               "end"
             ]
           },
-          "Channel": {
-            "title": "Channel",
+          "OmeroChannel": {
+            "title": "OmeroChannel",
             "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md)\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
             "type": "object",
             "properties": {
@@ -117,7 +117,7 @@
                 "type": "integer"
               },
               "window": {
-                "$ref": "#/definitions/ChannelWindow"
+                "$ref": "#/definitions/Window"
               },
               "color": {
                 "title": "Color",
@@ -352,11 +352,11 @@
             "description": "Pyramid level of the image to be segmented. Choose 0 to process at full resolution."
           },
           "channel": {
-            "$ref": "#/definitions/BaseChannel",
+            "$ref": "#/definitions/Channel",
             "description": "Primary channel for segmentation; requires either ``wavelength_id`` (e.g. ``A01_C01``) or ``label`` (e.g. ``DAPI``)."
           },
           "channel2": {
-            "$ref": "#/definitions/BaseChannel",
+            "$ref": "#/definitions/Channel",
             "description": "Second channel for segmentation (in the same format as ``channel``). If specified, cellpose runs in dual channel mode.  For dual channel segmentation of cells, the first channel should contain the membrane marker, the second channel should contain the nuclear marker."
           },
           "input_ROI_table": {
@@ -456,8 +456,8 @@
         ],
         "additionalProperties": false,
         "definitions": {
-          "BaseChannel": {
-            "title": "BaseChannel",
+          "Channel": {
+            "title": "Channel",
             "description": "A channel which is specified by either ``wavelength_id`` or ``label``.",
             "type": "object",
             "properties": {
@@ -639,8 +639,8 @@
         ],
         "additionalProperties": false,
         "definitions": {
-          "BaseChannel": {
-            "title": "BaseChannel",
+          "Channel": {
+            "title": "Channel",
             "description": "A channel which is specified by either ``wavelength_id`` or ``label``.",
             "type": "object",
             "properties": {
@@ -672,7 +672,7 @@
                 "type": "string"
               },
               "channel": {
-                "$ref": "#/definitions/BaseChannel"
+                "$ref": "#/definitions/Channel"
               }
             },
             "required": [
@@ -760,10 +760,10 @@
             "additionalProperties": {
               "type": "array",
               "items": {
-                "$ref": "#/definitions/Channel"
+                "$ref": "#/definitions/OmeroChannel"
               }
             },
-            "description": "A dictionary of channel dictionaries, where each channel must include the ``wavelength_id`` key and where the corresponding values should be unique across channels. Values are the integers of the channel order, i.e. ``\"0\"``, ``\"1\"`` etc. # TODO: improve after Channel input refactor https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/386"
+            "description": "A dictionary of lists of ``OmeroChannel``s, where each channel must include the ``wavelength_id`` attribute and where the ``wavelength_id`` values must be unique across each list. Dictionary keys represent channel indices (``\"0\",\"1\",..``)."
           },
           "num_levels": {
             "title": "Num Levels",
@@ -805,8 +805,8 @@
         ],
         "additionalProperties": false,
         "definitions": {
-          "ChannelWindow": {
-            "title": "ChannelWindow",
+          "Window": {
+            "title": "Window",
             "description": "Custom class for Omero-channel window, related to OME-NGFF v0.4\n\nSee https://ngff.openmicroscopy.org/0.4/#omero-md.\nMain difference from the specs:\n\n    1. ``min`` and ``max`` are optional, since we have custom logic to set\n        their values.",
             "type": "object",
             "properties": {
@@ -832,8 +832,8 @@
               "end"
             ]
           },
-          "Channel": {
-            "title": "Channel",
+          "OmeroChannel": {
+            "title": "OmeroChannel",
             "description": "Custom class for Omero channels, related to OME-NGFF v0.4.\n\nDifferences from OME-NGFF v0.4 specs\n(https://ngff.openmicroscopy.org/0.4/#omero-md)\n\n    1. Additional attributes ``wavelength_id`` and ``index``.\n    2. We make ``color`` an optional attribute, since we have custom\n       logic to set its value.\n    3. We make ``window`` an optional attribute, so that we can also\n       process zarr arrays which do not have this attribute.",
             "type": "object",
             "properties": {
@@ -846,7 +846,7 @@
                 "type": "integer"
               },
               "window": {
-                "$ref": "#/definitions/ChannelWindow"
+                "$ref": "#/definitions/Window"
               },
               "color": {
                 "title": "Color",
diff --git a/fractal_tasks_core/lib_channels.py b/fractal_tasks_core/lib_channels.py
@@ -32,7 +32,7 @@
     )
 
 
-class ChannelWindow(BaseModel):
+class Window(BaseModel):
     """
     Custom class for Omero-channel window, related to OME-NGFF v0.4
 
@@ -53,7 +53,7 @@ class ChannelWindow(BaseModel):
     """TBD"""
 
 
-class Channel(BaseModel):
+class OmeroChannel(BaseModel):
     """
     Custom class for Omero channels, related to OME-NGFF v0.4.
 
@@ -74,7 +74,7 @@ class Channel(BaseModel):
     """TBD"""
 
     # From OME-NGFF v0.4 transitional metadata
-    window: Optional[ChannelWindow]
+    window: Optional[Window]
     """TBD"""
     color: Optional[str]
     """TBD"""
@@ -97,7 +97,7 @@ class ChannelNotFoundError(ValueError):
     pass
 
 
-def check_unique_wavelength_ids(channels: List[Channel]):
+def check_unique_wavelength_ids(channels: List[OmeroChannel]):
     """
     Check that the `wavelength_id` attributes of a channel list are unique
     """
@@ -149,7 +149,7 @@ def check_well_channel_labels(*, well_zarr_path: str) -> None:
 
 def get_channel_from_image_zarr(
     *, image_zarr_path: str, label: str = None, wavelength_id: str = None
-) -> Channel:
+) -> OmeroChannel:
     """
     Extract a channel from OME-NGFF zarr attributes
 
@@ -169,7 +169,7 @@ def get_channel_from_image_zarr(
     return channel
 
 
-def get_omero_channel_list(*, image_zarr_path: str) -> List[Channel]:
+def get_omero_channel_list(*, image_zarr_path: str) -> List[OmeroChannel]:
     """
     Extract the list of channels from OME-NGFF zarr attributes
 
@@ -178,13 +178,16 @@ def get_omero_channel_list(*, image_zarr_path: str) -> List[Channel]:
     """
     group = zarr.open_group(image_zarr_path, mode="r+")
     channels_dicts = group.attrs["omero"]["channels"]
-    channels = [Channel(**c) for c in channels_dicts]
+    channels = [OmeroChannel(**c) for c in channels_dicts]
     return channels
 
 
 def get_channel_from_list(
-    *, channels: List[Channel], label: str = None, wavelength_id: str = None
-) -> Channel:
+    *,
+    channels: List[OmeroChannel],
+    label: str = None,
+    wavelength_id: str = None,
+) -> OmeroChannel:
     """
     Find matching channel in a list
 
@@ -245,7 +248,7 @@ def get_channel_from_list(
 
 def define_omero_channels(
     *,
-    channels: List[Channel],
+    channels: List[OmeroChannel],
     bit_depth: int,
     label_prefix: str = None,
 ) -> List[Dict[str, Union[str, int, bool, Dict[str, int]]]]:
diff --git a/fractal_tasks_core/tasks/_input_models.py b/fractal_tasks_core/tasks/_input_models.py
@@ -20,7 +20,7 @@
 from pydantic import validator
 
 
-class BaseChannel(BaseModel):
+class Channel(BaseModel):
     """
     A channel which is specified by either ``wavelength_id`` or ``label``.
     """
@@ -55,7 +55,7 @@ class NapariWorkflowsInput(BaseModel):
 
     type: Literal["image", "label"]
     label_name: Optional[str]
-    channel: Optional[BaseChannel]
+    channel: Optional[Channel]
 
     @validator("label_name", always=True)
     def label_name_is_present(cls, v, values):
diff --git a/fractal_tasks_core/tasks/cellpose_segmentation.py b/fractal_tasks_core/tasks/cellpose_segmentation.py
@@ -36,9 +36,9 @@
 from pydantic.decorator import validate_arguments
 
 import fractal_tasks_core
-from fractal_tasks_core.lib_channels import Channel
 from fractal_tasks_core.lib_channels import ChannelNotFoundError
 from fractal_tasks_core.lib_channels import get_channel_from_image_zarr
+from fractal_tasks_core.lib_channels import OmeroChannel
 from fractal_tasks_core.lib_masked_loading import masked_loading_wrapper
 from fractal_tasks_core.lib_pyramid_creation import build_pyramid
 from fractal_tasks_core.lib_regions_of_interest import (
@@ -53,7 +53,7 @@
 from fractal_tasks_core.lib_ROI_overlaps import get_overlapping_pairs_3D
 from fractal_tasks_core.lib_zattrs_utils import extract_zyx_pixel_sizes
 from fractal_tasks_core.lib_zattrs_utils import rescale_datasets
-from fractal_tasks_core.tasks._input_models import BaseChannel
+from fractal_tasks_core.tasks._input_models import Channel
 
 logger = logging.getLogger(__name__)
 
@@ -154,8 +154,8 @@ def cellpose_segmentation(
     metadata: Dict[str, Any],
     # Task-specific arguments
     level: int,
-    channel: BaseChannel,
-    channel2: Optional[BaseChannel] = None,
+    channel: Channel,
+    channel2: Optional[Channel] = None,
     input_ROI_table: str = "FOV_ROI_table",
     output_ROI_table: Optional[str] = None,
     output_label_name: Optional[str] = None,
@@ -301,7 +301,7 @@ def cellpose_segmentation(
 
     # Find channel index
     try:
-        tmp_channel: Channel = get_channel_from_image_zarr(
+        tmp_channel: OmeroChannel = get_channel_from_image_zarr(
             image_zarr_path=zarrurl,
             wavelength_id=channel.wavelength_id,
             label=channel.label,
@@ -317,7 +317,7 @@ def cellpose_segmentation(
     # Find channel index for second channel, if one is provided
     if channel2:
         try:
-            tmp_channel_c2: Channel = get_channel_from_image_zarr(
+            tmp_channel_c2: OmeroChannel = get_channel_from_image_zarr(
                 image_zarr_path=zarrurl,
                 wavelength_id=channel2.wavelength_id,
                 label=channel2.label,
diff --git a/fractal_tasks_core/tasks/create_ome_zarr.py b/fractal_tasks_core/tasks/create_ome_zarr.py
@@ -27,10 +27,10 @@
 from pydantic.decorator import validate_arguments
 
 import fractal_tasks_core
-from fractal_tasks_core.lib_channels import Channel
 from fractal_tasks_core.lib_channels import check_unique_wavelength_ids
 from fractal_tasks_core.lib_channels import check_well_channel_labels
 from fractal_tasks_core.lib_channels import define_omero_channels
+from fractal_tasks_core.lib_channels import OmeroChannel
 from fractal_tasks_core.lib_glob import glob_with_multiple_patterns
 from fractal_tasks_core.lib_metadata_parsing import parse_yokogawa_metadata
 from fractal_tasks_core.lib_parse_filename_metadata import parse_filename
@@ -54,7 +54,7 @@ def create_ome_zarr(
     metadata: Dict[str, Any],
     image_extension: str = "tif",
     image_glob_patterns: Optional[list[str]] = None,
-    allowed_channels: List[Channel],
+    allowed_channels: List[OmeroChannel],
     num_levels: int = 5,
     coarsening_xy: int = 2,
     metadata_table: str = "mrf_mlf",
@@ -107,12 +107,11 @@ def create_ome_zarr(
     :param coarsening_xy: Linear coarsening factor between subsequent levels.
                           If set to 2, level 1 is 2x downsampled, level 2 is
                           4x downsampled etc.
-    :param allowed_channels: A list of channel dictionaries, where each channel
-                             must include the ``wavelength_id`` key and where
-                             the corresponding values should be unique across
-                             channels.
-                             # TODO: improve after Channel input refactor
-                             See issue 386
+
+    :param allowed_channels: A list of ``OmeroChannel``s, where each channel
+                             must include the ``wavelength_id`` attribute and
+                             where the ``wavelength_id`` values must be unique
+                             across the list.
     :param metadata_table: If equal to ``"mrf_mlf"``, parse Yokogawa metadata
                            from mrf/mlf files in the input_path folder; else,
                            the full path to a csv file containing
diff --git a/fractal_tasks_core/tasks/create_ome_zarr_multiplex.py b/fractal_tasks_core/tasks/create_ome_zarr_multiplex.py
@@ -29,10 +29,10 @@
 from pydantic.decorator import validate_arguments
 
 import fractal_tasks_core
-from fractal_tasks_core.lib_channels import Channel
 from fractal_tasks_core.lib_channels import check_unique_wavelength_ids
 from fractal_tasks_core.lib_channels import check_well_channel_labels
 from fractal_tasks_core.lib_channels import define_omero_channels
+from fractal_tasks_core.lib_channels import OmeroChannel
 from fractal_tasks_core.lib_glob import glob_with_multiple_patterns
 from fractal_tasks_core.lib_metadata_parsing import parse_yokogawa_metadata
 from fractal_tasks_core.lib_parse_filename_metadata import parse_filename
@@ -56,7 +56,7 @@ def create_ome_zarr_multiplex(
     metadata: Dict[str, Any],
     image_extension: str = "tif",
     image_glob_patterns: Optional[list[str]] = None,
-    allowed_channels: Dict[str, list[Channel]],
+    allowed_channels: Dict[str, list[OmeroChannel]],
     num_levels: int = 5,
     coarsening_xy: int = 2,
     metadata_table: Union[Literal["mrf_mlf"], Dict[str, str]] = "mrf_mlf",
@@ -107,14 +107,11 @@ def create_ome_zarr_multiplex(
     :param coarsening_xy: Linear coarsening factor between subsequent levels.
                           If set to 2, level 1 is 2x downsampled, level 2 is
                           4x downsampled etc.
-    :param allowed_channels: A dictionary of channel dictionaries, where each
-                             channel must include the ``wavelength_id`` key
-                             and where the corresponding values should be
-                             unique across channels.
-                             Values are the integers of the channel order,
-                             i.e. ``"0"``, ``"1"`` etc.
-                             # TODO: improve after Channel input refactor
-                             https://github.com/fractal-analytics-platform/fractal-tasks-core/issues/386
+    :param allowed_channels: A dictionary of lists of ``OmeroChannel``s, where
+                             each channel must include the ``wavelength_id``
+                             attribute and where the ``wavelength_id`` values
+                             must be unique across each list. Dictionary keys
+                             represent channel indices (``"0","1",..``).
     :param metadata_table: If equal to ``"mrf_mlf"``, parse Yokogawa metadata
                            from mrf/mlf files in the input_path folder;
                            else, a dictionary of key-value pairs like
diff --git a/fractal_tasks_core/tasks/illumination_correction.py b/fractal_tasks_core/tasks/illumination_correction.py
@@ -30,8 +30,8 @@
 from pydantic.decorator import validate_arguments
 from skimage.io import imread
 
-from fractal_tasks_core.lib_channels import Channel
 from fractal_tasks_core.lib_channels import get_omero_channel_list
+from fractal_tasks_core.lib_channels import OmeroChannel
 from fractal_tasks_core.lib_pyramid_creation import build_pyramid
 from fractal_tasks_core.lib_regions_of_interest import (
     convert_ROI_table_to_indices,
@@ -197,7 +197,7 @@ def illumination_correction(
     logger.info(f"  {zarrurl_new=}")
 
     # Read channels from .zattrs
-    channels: list[Channel] = get_omero_channel_list(
+    channels: list[OmeroChannel] = get_omero_channel_list(
         image_zarr_path=zarrurl_old
     )
     num_channels = len(channels)
diff --git a/fractal_tasks_core/tasks/yokogawa_to_ome_zarr.py b/fractal_tasks_core/tasks/yokogawa_to_ome_zarr.py
diff --git a/tests/tasks/test_unit_input_models.py b/tests/tasks/test_unit_input_models.py
diff --git a/tests/test_unit_channels.py b/tests/test_unit_channels.py
