feat: Add option to calculate Measurement per Mask component

.github/workflows/test_napari_widgets.yml

@@ -18,8 +18,8 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ ubuntu-20.04 ]
-        python: ['3.8', '3.9']
-        napari_version: [napari411, napari412, napari413, napari414, napari415]
+        python: ['3.9']
+        napari_version: [napari412, napari413, napari414, napari415]
     steps:
       - uses: actions/checkout@v2
 

azure-pipelines.yml

@@ -1,17 +1,10 @@
 trigger:
   branches:
     include:
-    - '*'
-    exclude:
-    - dependabot/*
-    - documentation
-    - release/*
-    - hotfix/*
-    - bugfix/*
-    - sourcery/*
-    - update_requirements
-    - pre-commit-ci-update-config
-    - deepsource*
+    - master
+    - develop
+    - feature/**
+    - main
   tags:
     include:
     - v*

package/PartSeg/_roi_analysis/advanced_window.py

@@ -162,8 +162,8 @@ def profile_chosen(self, text):
                 self.delete_btn.setText("Delete pipeline")
                 self.rename_btn.setText("Rename pipeline")
             else:
-                return
-        except KeyError:
+                return  # pragma: no cover
+        except KeyError:  # pragma: no cover
             return
 
         # TODO update with knowledge from profile dict
@@ -388,7 +388,7 @@ def __init__(self, settings: PartSettings, parent=None):
         self.soft_reset_butt = QPushButton("Remove user parameters")
         self.profile_name = QLineEdit(self)
 
-        self.delete_profile_butt = QPushButton("Delete ")
+        self.delete_profile_butt = QPushButton("Delete")
         self.export_profiles_butt = QPushButton("Export")
         self.import_profiles_butt = QPushButton("Import")
         self.edit_profile_butt = QPushButton("Edit")
@@ -638,9 +638,12 @@ def get_parameters(
         if node.area is None:
             node = node.replace_(area=area)
         if node.per_component is None:
-            node = node.replace_(per_component=component)
+            try:
+                node = node.replace_(per_component=component)
+            except ValueError as e:  # pragma: no cover
+                QMessageBox().warning(self, "Problem in add measurement", str(e))
         with suppress(KeyError):
-            arguments = MEASUREMENT_DICT[str(node.name)].get_fields()
+            arguments = MEASUREMENT_DICT[str(node.name)]._get_fields()  # pylint: disable=protected-access
             if len(arguments) > 0 and not dict(node.parameters):
                 dial = self.form_dialog(arguments)
                 if dial.exec_():
@@ -651,7 +654,7 @@ def get_parameters(
 
     def choose_option(self):
         selected_item = self.profile_options.currentItem()
-        if not isinstance(selected_item, MeasurementListWidgetItem):
+        if not isinstance(selected_item, MeasurementListWidgetItem):  # pragma: no cover
             raise ValueError(f"Current item (type: {type(selected_item)} is not instance of MeasurementListWidgetItem")
         node = deepcopy(selected_item.stat)
         # noinspection PyTypeChecker
@@ -704,6 +707,7 @@ def save_action(self):
         self.settings.measurement_profiles[stat_prof.name] = stat_prof
         self.settings.dump()
         self.export_profiles_butt.setEnabled(True)
+        self.save_butt.setDisabled(True)
 
     def named_save_action(self):
         if self.profile_name.text() in self.settings.measurement_profiles:
@@ -894,11 +898,11 @@ def accept_response(self):
         for name, (type_of, item) in self.object_dict.items():
             if type_of == str:
                 val = str(item.text())
-                if val.strip() != "":
-                    res[name] = val
-                else:
+                if not val.strip():
                     QMessageBox.warning(self, "Not all fields filled", "")
                     return
+                else:
+                    res[name] = val
             else:
                 val = type_of(item.value())
                 res[name] = val

package/PartSeg/_roi_analysis/prepare_plan_widget.py

@@ -292,7 +292,9 @@ def enable_protect(self):
             self.protect = previous
 
     @classmethod
-    def refresh_profiles(cls, list_widget: QListWidget, new_values: typing.List[str]):
+    def refresh_profiles(
+        cls, list_widget: typing.Union[QListWidget, SearchableListWidget], new_values: typing.List[str]
+    ):
         index = cls.get_index(list_widget.currentItem(), new_values)
         list_widget.clear()
         list_widget.addItems(new_values)
@@ -840,7 +842,7 @@ def add_roi_extraction(self, roi_extraction: ROIExtractionOp):
 
     def add_roi_extraction_pipeline(self, roi_extraction_pipeline: SegmentationPipeline):
         if self.update_element_chk.isChecked():
-            QMessageBox.warning("Cannot update pipeline", "Cannot update pipeline")
+            QMessageBox.warning(self, "Cannot update pipeline", "Cannot update pipeline")
             return
         pos = self.calculation_plan.current_pos[:]
         old_pos = pos[:]
@@ -1124,7 +1126,7 @@ def _save_roi_profile(self, data: ROIExtractionProfile):
             )
             if not ok:
                 return
-            return self._save_roi_profile(data.copy(update={"name": text}))
+            return self._save_roi_profile(typing.cast(ROIExtractionProfile, data.copy(update={"name": text})))
         self.settings.roi_profiles[data.name] = data
 
     def _save_measurement_profile(self, data: MeasurementProfile):
@@ -1134,7 +1136,7 @@ def _save_measurement_profile(self, data: MeasurementProfile):
             )
             if not ok:
                 return
-            return self._save_measurement_profile(data.copy(update={"name": text}))
+            return self._save_measurement_profile(typing.cast(MeasurementProfile, data.copy(update={"name": text})))
         self.settings.measurement_profiles[data.name] = data
 
     def update_plan_list(self):

package/PartSeg/plugins/napari_widgets/measurement_widget.py

@@ -4,7 +4,7 @@
 from napari import Viewer
 from napari.layers import Image as NapariImage
 from napari.layers import Labels
-from napari.utils.notifications import show_info
+from napari.utils.notifications import notification_manager, show_info
 from qtpy.QtWidgets import QCheckBox, QLabel, QTabWidget
 
 from PartSeg._roi_analysis.advanced_window import MeasurementSettings
@@ -76,14 +76,14 @@ def append_measurement_result(self):
         if "Mask component" in df and self.mask_chose.value is not None:
             df2 = df.groupby("Mask component").mean()
             df2["index"] = df2.index
-            update_properties(df, self.mask_chose.value, self.overwrite.isChecked())
+            update_properties(df2, self.mask_chose.value, self.overwrite.isChecked())
         df["index"] = df.index
-        update_properties(df, self.roi_chose.value, self.overwrite.isChecked())
         if stat is None:
             return
         self.measurements_storage.add_measurements(stat)
         self.previous_profile = compute_class.name
         self.refresh_view()
+        update_properties(df, self.roi_chose.value, self.overwrite.isChecked())
 
     def check_if_measurement_can_be_calculated(self, name):
         if name in (NO_MEASUREMENT_STRING, ""):
@@ -124,8 +124,12 @@ def reset_choices(self, event=None):
 
 
 def update_properties(new_properties, layer: Labels, overwrite):
-    if not overwrite:
-        for key, value in layer.properties.items():
-            if key not in new_properties:
-                new_properties[key] = value
-    layer.properties = new_properties
+    try:
+        if not overwrite:
+            new_properties = new_properties.copy()
+            for key, value in layer.properties.items():
+                if key not in new_properties:
+                    new_properties[key] = value
+        layer.properties = new_properties
+    except Exception as e:  # pylint: disable=broad-except  # pragma: no cover
+        notification_manager.recive_error(e)

package/PartSeg/plugins/napari_widgets/roi_extraction_algorithms.py

@@ -64,7 +64,7 @@ def reset_choices(self, event=None):
         self.form_widget.reset_choices(event)
 
     def get_layer_list(self) -> typing.List[str]:
-        return [x.name for x in self.get_layers().values()]
+        return [x.name for x in self.get_layers().values() if x.name != "mask"]
 
     def get_values(self):
         values = self.form_widget.get_values()
@@ -167,7 +167,7 @@ def profile_dict(self) -> typing.Dict[str, ROIExtractionProfile]:
         return self.settings.get_from_profile(f"{self.prefix()}.profiles", {})
 
     def save_action(self):
-        widget: NapariInteractiveAlgorithmSettingsWidget = self.algorithm_chose.current_widget()
+        widget = typing.cast(NapariInteractiveAlgorithmSettingsWidget, self.algorithm_chose.current_widget())
         profiles = self.profile_dict
         while True:
             text, ok = QInputDialog.getText(self, "Profile Name", "Input profile name here")
@@ -202,14 +202,14 @@ def algorithm_changed(self):
         self.mask_name = ""
 
     def update_mask(self):
-        widget: NapariInteractiveAlgorithmSettingsWidget = self.algorithm_chose.current_widget()
+        widget = typing.cast(NapariInteractiveAlgorithmSettingsWidget, self.algorithm_chose.current_widget())
         mask = widget.get_layers().get("mask", None)
         if getattr(mask, "name", "") != self.mask_name or (widget.mask() is None and mask is not None):
             widget.set_mask(getattr(mask, "data", None))
             self.mask_name = getattr(mask, "name", "")
 
     def update_image(self):
-        widget: NapariInteractiveAlgorithmSettingsWidget = self.algorithm_chose.current_widget()
+        widget = typing.cast(NapariInteractiveAlgorithmSettingsWidget, self.algorithm_chose.current_widget())
         self.settings.last_executed_algorithm = widget.name
         layer_names: typing.List[str] = widget.get_layer_list()
         if layer_names == self.channel_names:
@@ -222,7 +222,7 @@ def update_image(self):
         self.mask_name = ""
 
     def _run_calculation(self):
-        widget: NapariInteractiveAlgorithmSettingsWidget = self.algorithm_chose.current_widget()
+        widget = typing.cast(NapariInteractiveAlgorithmSettingsWidget, self.algorithm_chose.current_widget())
         self.settings.last_executed_algorithm = widget.name
         self.update_image()
         self.update_mask()

package/PartSeg/plugins/napari_widgets/utils.py

@@ -40,11 +40,7 @@ def _element_list(self, fields) -> typing.Iterable[QtAlgorithmProperty]:
         return super()._element_list(itertools.chain([mask], fields))
 
     def get_layers(self):
-        return {
-            name: el.get_value()
-            for name, el in self.widgets_dict.items()
-            if name != "mask" and isinstance(el.get_value(), Layer)
-        }
+        return {name: el.get_value() for name, el in self.widgets_dict.items() if isinstance(el.get_value(), Layer)}
 
     def get_values(self):
         res = {name: el.get_value() for name, el in self.widgets_dict.items() if name != "mask"}

package/PartSegCore/analysis/measurement_base.py

@@ -29,6 +29,7 @@ class PerComponent(Enum):
     No = 1
     Yes = 2
     Mean = 3
+    Per_Mask_component = 4
 
     def __str__(self):
         return self.name.replace("_", " ")
@@ -99,6 +100,14 @@ def _validate_parameters(cls, v, values):  # pylint: disable=R0201
         v = REGISTER.migrate_data(class_to_str(method.__argument_class__), {}, v)
         return method.__argument_class__(**v)
 
+    @validator("per_component")
+    def _validate_per_component(cls, v, values):  # pylint: disable=R0201
+        if not isinstance(v, PerComponent) or "area" not in values or values["area"] is None:
+            return v
+        if v == PerComponent.Per_Mask_component and values["area"] != AreaType.ROI:
+            raise ValueError("Per_Mask_component can be used only with ROI area")
+        return v
+
     def get_channel_num(self, measurement_dict: Dict[str, "MeasurementMethodBase"]) -> Set[Channel]:
         """
         Get set with number of channels needed for calculate this measurement
@@ -171,6 +180,8 @@ def pretty_print(self, measurement_dict: Dict[str, "MeasurementMethodBase"]) ->
         if self.per_component is not None:
             if self.per_component == PerComponent.Yes:
                 resp += " per component "
+            elif self.per_component == PerComponent.Per_Mask_component:
+                resp += " per mask component "
             elif self.per_component == PerComponent.Mean:
                 resp += " mean component "
         resp += self._parameters_string(measurement_dict)
@@ -196,11 +207,14 @@ def get_unit(self, ndim: int) -> Symbol:
 
     def is_per_component(self) -> bool:
         """If measurement return list of result or single value."""
-        return self.per_component == PerComponent.Yes
+        return self.per_component in {PerComponent.Yes, PerComponent.Per_Mask_component}
 
     def need_mask(self) -> bool:
         """If this measurement need mast for proper calculation."""
-        return self.area in [AreaType.Mask, AreaType.Mask_without_ROI]
+        return (
+            self.area in [AreaType.Mask, AreaType.Mask_without_ROI]
+            or self.per_component is PerComponent.Per_Mask_component
+        )
 
 
 def replace(self, **kwargs) -> Leaf: