fix: Fix checking if channel requested by MeasurementProfile exists (#…

…1165)

fix PARTSEG-VA

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

## Summary by CodeRabbit

- **New Features**
- Introduced a method to check the existence of channels, enhancing
validation during measurements.
- Updated handling of channel identifiers to accept both `Channel`
objects and strings for improved flexibility.
- Improved dialog functionality by allowing it to have a parent widget
for better user experience.
- Enhanced the measurement profile structure for clarity and
functionality, focusing on ROI measurements.

- **Bug Fixes**
- Enhanced error messaging for channel validity to align with user
input, improving usability.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

package/PartSeg/_roi_analysis/advanced_window.py

@@ -805,7 +805,7 @@ def import_measurement_profiles(self):
             if err:
                 QMessageBox.warning(self, "Import error", "error during importing, part of data were filtered.")
             measurement_dict = self.settings.measurement_profiles
-            imp = ImportDialog(stat, measurement_dict, StringViewer, MeasurementProfile)
+            imp = ImportDialog(stat, measurement_dict, StringViewer, MeasurementProfile, parent=self)
             if not imp.exec_():
                 return
             for original_name, final_name in imp.get_import_list():

package/PartSeg/_roi_analysis/measurement_widget.py

@@ -367,11 +367,11 @@ def append_measurement_result(self):
         units = self.units_choose.currentEnum()
 
         for num in compute_class.get_channels_num():
-            if num >= self.settings.image.channels:
+            if not self.settings.image.has_channel(num):
                 QMessageBox.warning(
                     self,
                     "Measurement error",
-                    f"Cannot calculate this measurement because image do not have channel {num+1}",
+                    f"Cannot calculate this measurement because image do not have channel {num}",
                 )
                 return
 

package/PartSeg/common_gui/napari_image_view.py

@@ -413,7 +413,7 @@ def mask_opacity(self) -> float:
     def mask_color(self) -> ColorInfo:
         """Get mask marking color"""
         color = Color(np.divide(self.settings.get_from_profile("mask_presentation_color", [255, 255, 255]), 255))
-        return {0: (0, 0, 0, 0), 1: color.rgba}
+        return {0: (0, 0, 0, 0), 1: color.rgba, None: (0, 0, 0, 0)}
 
     def get_image(self, image: Optional[Image]) -> Image:
         if image is not None:

package/PartSeg/plugins/napari_widgets/measurement_widget.py

@@ -14,6 +14,7 @@
 from PartSeg.plugins.napari_widgets._settings import get_settings
 from PartSeg.plugins.napari_widgets.utils import NapariFormDialog, generate_image
 from PartSegCore.roi_info import ROIInfo
+from PartSegImage import Channel
 
 if TYPE_CHECKING:
     from PartSegCore.analysis.measurement_calculation import MeasurementProfile, MeasurementResult
@@ -58,11 +59,13 @@ def append_measurement_result(self):
         if self.channels_chose.value is None:
             return
         for name in compute_class.get_channels_num():
-            if name not in self.napari_viewer.layers:
+            if name.value not in self.napari_viewer.layers:
                 show_info(f"Cannot calculate this measurement because image do not have layer {name}")
                 return
         units = self.units_choose.currentEnum()
-        image = generate_image(self.napari_viewer, self.channels_chose.value.name, *compute_class.get_channels_num())
+        image = generate_image(
+            self.napari_viewer, Channel(self.channels_chose.value.name), *compute_class.get_channels_num()
+        )
         if self.mask_chose.value is not None:
             image.set_mask(self.mask_chose.value.data)
         roi_info = ROIInfo(self.roi_chose.value.data).fit_to_image(image)

package/PartSeg/plugins/napari_widgets/utils.py

@@ -61,8 +61,10 @@ def __init__(self, *args, **kwargs):
 def generate_image(viewer: Viewer, *layer_names):
     axis_order = Image.axis_order.replace("C", "")
     image_list = []
+    if isinstance(layer_names[0], str):
+        layer_names = [Channel(el) for el in layer_names]
     for name in dict.fromkeys(layer_names):
-        image_layer = viewer.layers[name]
+        image_layer = viewer.layers[name.value]
         data_scale = image_layer.scale[-3:] / UNIT_SCALE[Units.nm.value]
         image_list.append(
             Image(

package/PartSegCore/analysis/measurement_base.py

@@ -395,7 +395,13 @@ def calculate_property(
 
     @classmethod
     def get_starting_leaf(cls) -> Leaf:
-        """This leaf is put on default list"""
+        """This leaf is put on a default list"""
+        if (
+            hasattr(cls, "__argument_class__")
+            and cls.__argument_class__ is not None
+            and cls.__argument_class__ is not BaseModel
+        ):
+            return Leaf(name=cls._display_name(), parameters=cls.__argument_class__())
         return Leaf(name=cls._display_name())
 
     @classmethod

package/PartSegImage/image.py

@@ -526,8 +526,11 @@ def get_data_by_axis(self, **kwargs) -> np.ndarray:
         axis_pos = self.get_array_axis_positions()
         if "c" in kwargs:
             kwargs["C"] = kwargs.pop("c")
-        if "C" in kwargs and isinstance(kwargs["C"], str):
-            kwargs["C"] = self.channel_names.index(kwargs["C"])
+        if "C" in kwargs:
+            if isinstance(kwargs["C"], Channel):
+                kwargs["C"] = kwargs["C"].value
+            if isinstance(kwargs["C"], str):
+                kwargs["C"] = self.channel_names.index(kwargs["C"])
 
         channel = kwargs.pop("C", slice(None) if "C" in self.axis_order else 0)
         if isinstance(channel, Channel):
@@ -571,6 +574,14 @@ def get_channel(self, num: int | str | Channel) -> np.ndarray:
         """
         return self.get_data_by_axis(c=num)
 
+    def has_channel(self, num: int | str | Channel) -> bool:
+        if isinstance(num, Channel):
+            num = num.value
+
+        if isinstance(num, str):
+            return num in self.channel_names
+        return 0 <= num < self.channels
+
     def get_layer(self, time: int, stack: int) -> np.ndarray:
         """
         return single layer contains data for all channel

package/tests/conftest.py

@@ -12,7 +12,12 @@
 from PartSegCore.algorithm_describe_base import ROIExtractionProfile
 from PartSegCore.analysis import ProjectTuple, SegmentationPipeline, SegmentationPipelineElement
 from PartSegCore.analysis.measurement_base import AreaType, MeasurementEntry, PerComponent
-from PartSegCore.analysis.measurement_calculation import ComponentsNumber, MeasurementProfile, Volume
+from PartSegCore.analysis.measurement_calculation import (
+    ColocalizationMeasurement,
+    ComponentsNumber,
+    MeasurementProfile,
+    Volume,
+)
 from PartSegCore.image_operations import RadiusType
 from PartSegCore.mask.io_functions import MaskProjectTuple
 from PartSegCore.mask_create import MaskProperty
@@ -69,15 +74,15 @@ def image2d(tmp_path):
 
 @pytest.fixture()
 def stack_image():
-    data = np.zeros([20, 40, 40], dtype=np.uint8)
+    data = np.zeros([20, 40, 40, 2], dtype=np.uint8)
     for x, y in itertools.product([0, 20], repeat=2):
         data[1:-1, x + 2 : x + 18, y + 2 : y + 18] = 100
     for x, y in itertools.product([0, 20], repeat=2):
         data[3:-3, x + 4 : x + 16, y + 4 : y + 16] = 120
     for x, y in itertools.product([0, 20], repeat=2):
         data[5:-5, x + 6 : x + 14, y + 6 : y + 14] = 140
 
-    return MaskProjectTuple("test_path", Image(data, (2, 1, 1), axes_order="ZYX", file_path="test_path"))
+    return MaskProjectTuple("test_path", Image(data, (2, 1, 1), axes_order="ZYXC", file_path="test_path"))
 
 
 @pytest.fixture()
@@ -201,8 +206,18 @@ def measurement_profiles():
             calculation_tree=Volume.get_starting_leaf().replace_(area=AreaType.Mask, per_component=PerComponent.No),
         ),
     ]
-    return MeasurementProfile(name="statistic1", chosen_fields=statistics), MeasurementProfile(
-        name="statistic2", chosen_fields=statistics + statistics2
+    statistics3 = [
+        MeasurementEntry(
+            name="Colocalisation",
+            calculation_tree=ColocalizationMeasurement.get_starting_leaf().replace_(
+                per_component=PerComponent.No, area=AreaType.ROI
+            ),
+        ),
+    ]
+    return (
+        MeasurementProfile(name="statistic1", chosen_fields=statistics),
+        MeasurementProfile(name="statistic2", chosen_fields=statistics + statistics2),
+        MeasurementProfile(name="statistic3", chosen_fields=statistics + statistics2 + statistics3),
     )
 
 

package/tests/test_PartSeg/conftest.py

@@ -12,14 +12,14 @@
 
 
 @pytest.fixture()
-def base_settings(image, tmp_path, measurement_profiles, qapp):
+def base_settings(image, tmp_path, measurement_profiles):
     settings = BaseSettings(tmp_path)
     settings.image = image
     return settings
 
 
 @pytest.fixture()
-def part_settings(image, tmp_path, measurement_profiles, qapp):
+def part_settings(image, tmp_path, measurement_profiles):
     settings = PartSettings(tmp_path)
     settings.image = image
     for el in measurement_profiles:
@@ -28,7 +28,7 @@ def part_settings(image, tmp_path, measurement_profiles, qapp):
 
 
 @pytest.fixture()
-def stack_settings(tmp_path, image, qapp):
+def stack_settings(tmp_path, image):
     settings = StackSettings(tmp_path)
     settings.image = image
     chose = ChosenComponents()
@@ -38,7 +38,7 @@ def stack_settings(tmp_path, image, qapp):
 
 
 @pytest.fixture()
-def part_settings_with_project(image, analysis_segmentation2, tmp_path, qapp):
+def part_settings_with_project(image, analysis_segmentation2, tmp_path):
     settings = PartSettings(tmp_path)
     settings.image = image
     settings.set_project_info(analysis_segmentation2)

package/tests/test_PartSeg/roi_analysis/test_advanced_window.py

@@ -148,10 +148,10 @@ def test_base_steep(self, qtbot, part_settings):
             widget.profile_name.setText("test")
         assert widget.save_butt.isEnabled()
 
-        assert len(part_settings.measurement_profiles) == 2
+        assert len(part_settings.measurement_profiles) == 3
         with qtbot.waitSignal(widget.save_butt.clicked):
             widget.save_butt.click()
-        assert len(part_settings.measurement_profiles) == 3
+        assert len(part_settings.measurement_profiles) == 4
 
         with qtbot.waitSignal(widget.profile_name.textChanged):
             widget.profile_name.setText("")

package/tests/test_PartSeg/test_analysis.py

@@ -18,7 +18,7 @@ def test_missed_mask(self, qmessagebox_path, qtbot, analysis_segmentation, part_
         widget = MeasurementWidget(part_settings)
         qtbot.addWidget(widget)
 
-        assert widget.measurement_type.count() == 3
+        assert widget.measurement_type.count() == 4
         part_settings.set_project_info(analysis_segmentation)
 
         with qtbot.waitSignal(widget.measurement_type.currentIndexChanged):
@@ -34,7 +34,7 @@ def test_base(self, qtbot, analysis_segmentation, part_settings):
         widget = MeasurementWidget(part_settings)
         qtbot.addWidget(widget)
 
-        assert widget.measurement_type.count() == 3
+        assert widget.measurement_type.count() == 4
         part_settings.set_project_info(analysis_segmentation)
         widget.measurement_type.setCurrentIndex(1)
         assert widget.recalculate_button.isEnabled()
@@ -52,7 +52,7 @@ def test_base2(self, qtbot, analysis_segmentation2, part_settings):
         widget = MeasurementWidget(part_settings)
         qtbot.addWidget(widget)
 
-        assert widget.measurement_type.count() == 3
+        assert widget.measurement_type.count() == 4
         part_settings.set_project_info(analysis_segmentation2)
         widget.measurement_type.setCurrentIndex(2)
         assert widget.recalculate_button.isEnabled()
@@ -64,6 +64,23 @@ def test_base2(self, qtbot, analysis_segmentation2, part_settings):
         assert widget.info_field.columnCount() == 3
         assert widget.info_field.rowCount() == 2
 
+    @pytest.mark.enablethread()
+    @pytest.mark.enabledialog()
+    def test_base_channels(self, qtbot, analysis_segmentation2, part_settings):
+        widget = MeasurementWidget(part_settings)
+        qtbot.addWidget(widget)
+
+        part_settings.set_project_info(analysis_segmentation2)
+        widget.measurement_type.setCurrentIndex(3)
+        assert widget.recalculate_button.isEnabled()
+        widget.recalculate_button.click()
+        assert widget.info_field.columnCount() == 2
+        assert widget.info_field.rowCount() == 4
+        assert widget.info_field.item(1, 1).text() == "4"
+        widget.horizontal_measurement_present.setChecked(True)
+        assert widget.info_field.columnCount() == 4
+        assert widget.info_field.rowCount() == 2
+
 
 class TestSimpleMeasurementsWidget:
     @pytest.mark.enablethread()

package/tests/test_PartSeg/test_napari_widgets.py

@@ -2,7 +2,7 @@
 import gc
 import json
 from importlib.metadata import version
-from unittest.mock import patch
+from unittest.mock import Mock, patch
 
 import numpy as np
 import pandas as pd
@@ -223,16 +223,23 @@ def test_simple_measurement_create(make_napari_viewer, qtbot):
 
 @pytest.mark.enablethread()
 @pytest.mark.enabledialog()
-def test_measurement_create(make_napari_viewer, qtbot, bundle_test_dir):
+@pytest.mark.usefixtures("qtbot")
+def test_measurement_create(make_napari_viewer, bundle_test_dir, monkeypatch):
     from PartSeg.plugins.napari_widgets.measurement_widget import Measurement
 
+    monkeypatch.setattr(
+        "PartSeg.plugins.napari_widgets.measurement_widget.show_info",
+        Mock(side_effect=RuntimeError("should not be called")),
+    )
+
     data = np.zeros((10, 10), dtype=np.uint8)
     data[2:5, 2:-2] = 1
     data[5:-2, 2:-2] = 2
 
     viewer = make_napari_viewer()
     viewer.add_labels(data, name="label")
     viewer.add_image(data, name="image")
+    viewer.add_image(data, name="image2")
     measurement = Measurement(viewer)
     viewer.window.add_dock_widget(measurement)
     measurement.reset_choices()
@@ -243,7 +250,11 @@ def test_measurement_create(make_napari_viewer, qtbot, bundle_test_dir):
     assert measurement.measurement_widget.measurement_type.currentText() == "test"
     assert measurement.measurement_widget.recalculate_button.isEnabled()
     assert measurement.measurement_widget.check_if_measurement_can_be_calculated("test") == "test"
+    assert measurement.measurement_widget.info_field.rowCount() == 0
+    assert measurement.measurement_widget.info_field.columnCount() == 3
     measurement.measurement_widget.append_measurement_result()
+    assert measurement.measurement_widget.info_field.rowCount() == 8
+    assert measurement.measurement_widget.info_field.columnCount() == 3
 
 
 def test_update_properties():

package/tests/test_PartSeg/test_roi_analysis_batch.py

@@ -535,7 +535,7 @@ def check_measurement(measurement: prepare_plan_widget.MeasurementCalculate):
 
         widget = prepare_plan_widget.SelectMeasurementOp(part_settings)
         qtbot.addWidget(widget)
-        assert widget.measurements_list.count() == 2
+        assert widget.measurements_list.count() == 3
         with qtbot.assert_not_emitted(widget.set_of_measurement_add):
             widget._measurement_add()
         widget.measurements_list.setCurrentRow(0)

package/tests/test_PartSeg/test_viewer.py

@@ -75,13 +75,13 @@ def test_base(self, image, analysis_segmentation2, tmp_path):
         assert len(viewer.layers) == 2
         settings.image = analysis_segmentation2.image
         viewer.create_initial_layers(True, True, True, True)
-        assert len(viewer.layers) == 1
+        assert len(viewer.layers) == 2
         settings.roi = analysis_segmentation2.roi_info.roi
         viewer.create_initial_layers(True, True, True, True)
-        assert len(viewer.layers) == 2
+        assert len(viewer.layers) == 3
         settings.mask = analysis_segmentation2.mask
         viewer.create_initial_layers(True, True, True, True)
-        assert len(viewer.layers) == 3
+        assert len(viewer.layers) == 4
         viewer.close()
 
     def test_points(self, image, tmp_path, qtbot):

package/tests/test_PartSegCore/test_napari_plugins.py

@@ -27,16 +27,16 @@
 def test_project_to_layers_analysis(analysis_segmentation):
     analysis_segmentation.roi_info.alternative["test"] = np.zeros(analysis_segmentation.image.shape, dtype=np.uint8)
     res = project_to_layers(analysis_segmentation)
-    assert len(res) == 3
+    assert len(res) == 4
     l1 = Layer.create(*res[0])
     assert isinstance(l1, Image)
     assert l1.name == "channel 1"
     assert np.allclose(l1.scale[1:] / 1e9, analysis_segmentation.image.spacing)
-    l2 = Layer.create(*res[1])
+    l2 = Layer.create(*res[2])
     assert isinstance(l2, Labels)
     assert l2.name == "ROI"
     assert np.allclose(l2.scale[1:] / 1e9, analysis_segmentation.image.spacing)
-    l3 = Layer.create(*res[2])
+    l3 = Layer.create(*res[3])
     assert isinstance(l3, Labels)
     assert l3.name == "test"
     assert np.allclose(l3.scale[1:] / 1e9, analysis_segmentation.image.spacing)
@@ -55,7 +55,7 @@ def test_project_to_layers_roi():
 
 def test_project_to_layers_mask(stack_segmentation1):
     res = project_to_layers(stack_segmentation1)
-    assert len(res) == 2
+    assert len(res) == 3
     assert res[0][2] == "image"
 
 

package/tests/test_PartSegImage/test_image.py

@@ -288,9 +288,17 @@ def test_get_channel(self):
         image = self.image_class(
             np.zeros((1, 10, 20, 30, 3), np.uint8), (1, 1, 1), "", axes_order="TZYXC", channel_names=["a", "b", "c"]
         )
+        assert image.has_channel(1)
+        assert image.has_channel(Channel(1))
+        assert not image.has_channel(5)
+        assert not image.has_channel(Channel(5))
         channel = image.get_channel(1)
         assert channel.shape == self.mask_shape((1, 10, 20, 30), "TZYX")
-        channel = image.get_channel("b")
+        assert image.has_channel("b")
+        assert image.has_channel(Channel("b"))
+        assert not image.has_channel("d")
+        assert not image.has_channel(Channel("d"))
+        channel = image.get_channel(Channel("b"))
         assert channel.shape == self.mask_shape((1, 10, 20, 30), "TZYX")
         with pytest.raises(IndexError):
             image.get_channel(4)