improve docstrings

package/PartSeg/_roi_mask/stack_settings.py

@@ -210,9 +210,9 @@ def transform_state(
 
         :param MaskProjectTuple state: state to be transformed
         :param ROIInfo new_roi_info: roi description
-        :param typing.Dict[int, typing.Optional[ROIExtractionProfile]] new_roi_extraction_parameters:
+        :param dict[int, typing.Optional[ROIExtractionProfile]] new_roi_extraction_parameters:
             Parameters used to extract roi
-        :param typing.List[int] list_of_components: list of components from new_roi which should be selected
+        :param list[int] list_of_components: list of components from new_roi which should be selected
         :param bool save_chosen: if save currently selected components
         :return: new state
         """

package/PartSegCore/algorithm_describe_base.py

@@ -4,6 +4,7 @@
 import typing
 import warnings
 from abc import ABC, ABCMeta, abstractmethod
+from collections.abc import MutableMapping
 from functools import wraps
 from importlib.metadata import version
 from typing import Annotated
@@ -535,13 +536,13 @@ def pretty_print(self, algorithm_dict):
         )
 
     @classmethod
-    def _pretty_print(cls, values: typing.MutableMapping, translate_dict: dict[str, AlgorithmProperty], indent=0):
-        if not isinstance(values, typing.MutableMapping):
+    def _pretty_print(cls, values: MutableMapping, translate_dict: dict[str, AlgorithmProperty], indent=0):
+        if not isinstance(values, MutableMapping):
             return textwrap.indent(str(values), " " * indent)
         res = ""
         for k, v in values.items():
             if k not in translate_dict:
-                if isinstance(v, typing.MutableMapping):
+                if isinstance(v, MutableMapping):
                     res += " " * indent + f"{k}: {cls._pretty_print(v, {}, indent + 2)}\n"
                 else:
                     res += " " * indent + f"{k}: {v}\n"
@@ -561,7 +562,7 @@ def _pretty_print(cls, values: typing.MutableMapping, translate_dict: dict[str,
                 if values_:
                     res += "\n"
                     res += cls._pretty_print(values_, desc.possible_values[name].get_fields_dict(), indent + 2)
-            elif isinstance(v, typing.MutableMapping):
+            elif isinstance(v, MutableMapping):
                 res += cls._pretty_print(v, {}, indent + 2)
             else:
                 res += str(v)

package/PartSegCore/analysis/calculation_plan.py

@@ -404,7 +404,7 @@ class Calculation(BaseCalculation):
     :ivar CalculationPlan ~.calculation_plan: plan of calculation
     :ivar str uuid: ~.uuid of whole calculation
     :ivar ~.voxel_size: default voxel size (for files which do not contains this information in metadata
-    :ivar typing.List[str] ~.file_list: list of files to be proceed
+    :ivar list[str] ~.file_list: list of files to be proceed
     """
 
     def __init__(

package/PartSegCore/analysis/measurement_base.py

@@ -129,7 +129,7 @@ def get_channel_num(self, measurement_dict: dict[str, "MeasurementMethodBase"])
         """
         Get set with number of channels needed for calculate this measurement
 
-        :param measurement_dict: dict with all measurementh method.
+        :param measurement_dict: dict with all measurement methods.
         :return: set of channels num
         """
         resp = set()
@@ -380,9 +380,6 @@ def calculate_property(
         Main function for calculating measurement
 
         :param channel: main channel selected for measurement
-        :param channel_{i}: for channel requested using :py:meth:`get_fields`
-            ``AlgorithmProperty("channel", "Channel", 0, value_type=Channel)``
-        :param area_array: array representing current area returned by :py:meth:`area_type`
         :param roi: array representing roi
         :param mask: array representing mask (upper level roi)
         :param voxel_size: size of single voxel in meters

package/PartSegCore/mask/io_functions.py

@@ -69,10 +69,10 @@ class MaskProjectTuple(ProjectInfoBase):
     :ivar typing.Optional[np.ndarray] ~.mask: Mask limiting segmentation area.
     :ivar ROIInfo ~.roi_info: ROI information.
     :ivar SegmentationInfo ~.roi_info: ROI description
-    :ivar typing.List[int] ~.selected_components: list of selected components
-    :ivar typing.Dict[int,typing.Optional[SegmentationProfile]] ~.segmentation_parameters:
+    :ivar list[int] ~.selected_components: list of selected components
+    :ivar dict[int,typing.Optional[SegmentationProfile]] ~.segmentation_parameters:
         For each component description set of parameters used for segmentation
-    :ivar typing.List[HistoryElement] history: list of operations needed to create :py:attr:`mask`
+    :ivar list[HistoryElement] history: list of operations needed to create :py:attr:`mask`
     :ivar str ~.errors: information about problems meet during calculation
     :ivar typing.Optional[typing.List[float]] ~.spacing: information about spacing when image is missed.
         For napari read plugin

package/PartSegCore/mask_create.py

@@ -115,7 +115,7 @@ def calculate_mask(
     :param typing.Optional[np.ndarray] old_mask: if in mask_description there is set to crop and old_mask is not None
         then final mask is clipped to this area
     :param typing.Iterable[typing.Union[float,int]] spacing: spacing of image. Needed for calculating radius of dilate
-    :param typing.Optional[typing.List[int]] components: If present inform which components
+    :param typing.Optional[list[int]] components: If present inform which components
         should be used when calculation mask, otherwise use all.
     :param typing.Optional[int] time_axis: which axis of array should be treated as time. IF none then none.
     :return: new mask