feat: widget to deal with region of interest

src/napari_locan/_tests/test_widget_roi.py

@@ -1,25 +1,298 @@
+from pathlib import Path
+
+import locan as lc
+import napari
+import numpy as np
+import pytest
+
 from napari_locan import RoiQWidget
-from napari_locan.data_model._locdata import SmlmData
+from napari_locan.data_model.smlm_data import SmlmData
 
 
 class TestRoiQWidgetQWidget:
-    def test_RoiQWidget_init(self, make_napari_viewer):
+    def test_RoiQWidget_init(self, make_napari_viewer, locdata_2d):
         smlm_data = SmlmData()
         viewer = make_napari_viewer()
         my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
-        assert not my_widget._locdatas_combobox.isEditable()
+
+        assert len(my_widget._regions) == 0
+        assert len(my_widget._rois) == 0
+
+        assert my_widget._regions_combobox.count() == 0
+        assert my_widget._regions_combobox.currentIndex() == -1
+        assert my_widget._regions_text_edit.toPlainText() == ""
+
+        assert my_widget._reference_combobox.count() == 4
+        assert my_widget._reference_combobox.currentIndex() == 0
+
         assert my_widget._locdatas_combobox.currentIndex() == -1
-        assert my_widget._locdatas_combobox.currentText() == ""
+        assert my_widget._loc_properties_x_combobox.currentIndex() == -1
+        assert my_widget._loc_properties_y_combobox.currentIndex() == -1
 
-        # todo:
-        # make shapes layer
-        # load file with path
-        # check text for rois
-        # save in temp directory
+        assert not my_widget._rois_combobox.isEditable()
+        assert my_widget._rois_combobox.currentIndex() == -1
+        assert my_widget._rois_combobox.currentText() == ""
+        assert my_widget._roi_text_edit.toPlainText() == ""
 
-    def test_RoiQWidget_(self, make_napari_viewer, locdata_2d):
         smlm_data = SmlmData(locdatas=[locdata_2d])
         viewer = make_napari_viewer()
         my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        assert len(my_widget._regions) == 0
+        assert len(my_widget._rois) == 0
+
+        assert my_widget._regions_combobox.count() == 0
+        assert my_widget._regions_combobox.currentIndex() == -1
+        assert my_widget._regions_text_edit.toPlainText() == ""
+
+        assert my_widget._reference_combobox.count() == 4
+        assert my_widget._reference_combobox.currentIndex() == 0
+
         assert my_widget._locdatas_combobox.currentIndex() == 0
-        assert my_widget._locdatas_combobox.currentText() != ""
+        assert my_widget._loc_properties_x_combobox.currentIndex() == 0
+        assert my_widget._loc_properties_y_combobox.currentIndex() == 1
+
+        assert not my_widget._rois_combobox.isEditable()
+        assert my_widget._rois_combobox.currentIndex() == -1
+        assert my_widget._rois_combobox.currentText() == ""
+        assert my_widget._roi_text_edit.toPlainText() == ""
+
+    def test_RoiQWidget_regions(self, make_napari_viewer, locdata_2d):
+        smlm_data = SmlmData(locdatas=[locdata_2d])
+        viewer = make_napari_viewer()
+        my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        shape_data = [
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "rectangle"),
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "ellipse"),
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "polygon"),
+        ]
+        viewer.add_shapes(shape_data)
+
+        my_widget._scale_layer_button_on_click()
+
+        my_widget._get_regions_button_on_click()
+        assert len(my_widget._regions) == 3
+        assert my_widget._regions_combobox.count() == 3
+        assert my_widget._regions_combobox.currentIndex() == 2
+        assert (
+            my_widget._regions_text_edit.toPlainText()
+            != "Rectangle((0.0, 0.0), 3.1, 2.5, 0)"
+        )
+
+        my_widget._delete_regions_button_on_click()
+        assert len(my_widget._regions) == 2
+        assert my_widget._regions_combobox.count() == 2
+        assert my_widget._regions_combobox.currentIndex() == 1
+        assert my_widget._regions_text_edit.toPlainText() != ""
+
+    @pytest.mark.skip("requires user interaction")
+    def test_RoiQWidget_regions_delete_all(self, make_napari_viewer, locdata_2d):
+        smlm_data = SmlmData(locdatas=[locdata_2d])
+        viewer = make_napari_viewer()
+        my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        shape_data = [
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "rectangle"),
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "ellipse"),
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "polygon"),
+        ]
+        viewer.add_shapes(shape_data)
+
+        my_widget._get_regions_button_on_click()
+        assert len(my_widget._regions) == 3
+        assert my_widget._regions_combobox.count() == 3
+        assert my_widget._regions_combobox.currentIndex() == 2
+
+        # requires user interaction
+        my_widget._delete_all_regions_button_on_click()
+        assert len(my_widget._regions) == 0
+        assert my_widget._regions_combobox.count() == 0
+        assert my_widget._regions_combobox.currentIndex() == -1
+
+    def test_RoiQWidget_rois(self, make_napari_viewer, locdata_2d):
+        smlm_data = SmlmData(locdatas=[locdata_2d])
+        viewer = make_napari_viewer()
+        my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        smlm_data.locdata.meta.file.path = "locdata_2d.txt"
+        smlm_data.locdata.meta.file.type = "RAPIDSTORM"
+
+        shape_data = [
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "rectangle"),
+        ]
+        viewer.add_shapes(shape_data)
+
+        my_widget._get_regions_button_on_click()
+        assert len(my_widget._regions) == 1
+
+        my_widget._reference_combobox.setCurrentIndex(0)
+        assert my_widget._reference_combobox.currentText() == "None"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 1
+        assert my_widget._rois_combobox.count() == 1
+        assert my_widget._rois_combobox.currentIndex() == 0
+        assert my_widget._rois[0].reference is None
+        assert my_widget._rois[0].region == my_widget._regions[0]
+        assert my_widget._rois[0].loc_properties == ["position_x", "position_y"]
+        assert my_widget._roi_text_edit.toPlainText() != ""
+
+        my_widget._reference_combobox.setCurrentIndex(1)
+        assert my_widget._reference_combobox.currentText() == "SmlmData"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 2
+        assert my_widget._rois_combobox.count() == 2
+        assert my_widget._rois_combobox.currentIndex() == 1
+        assert my_widget._rois[1].reference is my_widget.smlm_data.locdata
+        assert my_widget._rois[1].region == my_widget._regions[0]
+        assert my_widget._rois[1].loc_properties == ["position_x", "position_y"]
+        assert my_widget._roi_text_edit.toPlainText() != ""
+
+        my_widget._reference_combobox.setCurrentIndex(2)
+        assert my_widget._reference_combobox.currentText() == "File reference"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 3
+        assert my_widget._rois_combobox.count() == 3
+        assert my_widget._rois_combobox.currentIndex() == 2
+        assert isinstance(my_widget._rois[2].reference, lc.data.metadata_pb2.Metadata)
+        assert (
+            my_widget._rois[2].reference.file.path == smlm_data.locdata.meta.file.path
+        )
+        assert (
+            my_widget._rois[2].reference.file.type == smlm_data.locdata.meta.file.type
+        )
+        assert my_widget._rois[2].region == my_widget._regions[0]
+        assert my_widget._rois[2].loc_properties == ["position_x", "position_y"]
+        assert my_widget._roi_text_edit.toPlainText() != ""
+
+        my_widget._reference_combobox.setCurrentIndex(0)
+        assert my_widget._reference_combobox.currentText() == "None"
+        my_widget._create_roi_button_on_click()
+        with pytest.raises(AttributeError):
+            my_widget._apply_roi_button_on_click()
+        assert len(my_widget.smlm_data.locdatas) == 1
+
+        my_widget._delete_roi_button_on_click()
+        assert len(my_widget._rois) == 3
+        assert my_widget._rois_combobox.currentIndex() == 2
+
+        my_widget._reference_combobox.setCurrentIndex(1)
+        assert my_widget._reference_combobox.currentText() == "SmlmData"
+        my_widget._create_roi_button_on_click()
+        my_widget._apply_roi_button_on_click()
+        assert len(my_widget.smlm_data.locdatas) == 2
+
+    @pytest.mark.skip("requires user interactions")
+    def test_RoiQWidget_reference_file_dialog_and_delete_all(
+        self, make_napari_viewer, locdata_2d
+    ):
+        smlm_data = SmlmData(locdatas=[locdata_2d])
+        viewer = make_napari_viewer()
+        my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        shape_data = [
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "rectangle"),
+        ]
+        viewer.add_shapes(shape_data)
+
+        my_widget._get_regions_button_on_click()
+        assert len(my_widget._regions) == 1
+
+        my_widget._reference_combobox.setCurrentIndex(3)
+        assert my_widget._reference_combobox.currentText() == "File dialog"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 1
+        assert my_widget._rois_combobox.count() == 1
+        assert my_widget._rois_combobox.currentIndex() == 0
+        print(my_widget._rois[0].reference)
+        assert my_widget._rois[0].reference.file.path != ""
+        assert my_widget._rois[0].reference.file.type != ""
+
+        # requires user interaction
+        my_widget._delete_all_roi_button_on_click()
+        assert len(my_widget._rois) == 0
+        assert my_widget._rois_combobox.count() == 0
+        assert my_widget._rois_combobox.currentIndex() == -1
+
+    def test_RoiQWidget_save_rois(self, make_napari_viewer, locdata_2d, tmp_path):
+        smlm_data = SmlmData(locdatas=[locdata_2d])
+        viewer = make_napari_viewer()
+        my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        smlm_data.locdata.meta.file.path = str(tmp_path / "locdata_2d.txt")
+        smlm_data.locdata.meta.file.type = "RAPIDSTORM"
+
+        shape_data = [
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "rectangle"),
+        ]
+        viewer.add_shapes(shape_data)
+
+        my_widget._get_regions_button_on_click()
+        my_widget._reference_combobox.setCurrentIndex(1)
+        assert my_widget._reference_combobox.currentText() == "SmlmData"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 1
+        assert my_widget._rois_combobox.currentIndex() == 0
+        with pytest.raises(AttributeError):
+            my_widget._save_roi_button_on_click()
+
+        my_widget._reference_combobox.setCurrentIndex(2)
+        assert my_widget._reference_combobox.currentText() == "File reference"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 2
+        assert my_widget._rois_combobox.currentIndex() == 1
+
+        my_widget._save_roi_button_on_click()
+        roi_file = (
+            tmp_path / f"locdata_2d_{my_widget._rois_combobox.currentText()}.yaml"
+        )
+        assert roi_file.exists()
+
+        my_widget._load_roi_button_on_click(file_path=roi_file)
+        assert len(my_widget._rois) == 3
+        assert my_widget._rois_combobox.currentIndex() == 2
+
+    @pytest.mark.skip("need user interaction")
+    def test_RoiQWidget_save_and_load_rois_gui(
+        self, make_napari_viewer, locdata_2d, tmp_path
+    ):
+        smlm_data = SmlmData()
+        viewer = make_napari_viewer()
+        my_widget = RoiQWidget(viewer, smlm_data=smlm_data)
+
+        shape_data = [
+            (np.array([[0, 0], [0, 2.5], [3.1, 2.5], [3.1, 0]]), "rectangle"),
+        ]
+        viewer.add_shapes(shape_data)
+
+        my_widget._get_regions_button_on_click()
+        my_widget._reference_combobox.setCurrentIndex(3)
+        assert my_widget._reference_combobox.currentText() == "File dialog"
+        my_widget._create_roi_button_on_click()
+        assert len(my_widget._rois) == 1
+        assert my_widget._rois_combobox.currentIndex() == 0
+
+        my_widget._save_roi_button_on_click()
+
+        roi_file = Path(my_widget._rois[0].reference.file.path)
+        roi_file = roi_file.with_name(roi_file.stem + "_roi_0.yaml")
+        my_widget._load_roi_button_on_click(file_path=roi_file)
+        assert len(my_widget._rois) == 2
+        assert my_widget._rois_combobox.currentIndex() == 1
+
+
+@pytest.mark.napari
+def test_run_napari():
+    viewer = napari.Viewer()
+    viewer.open_sample("napari-locan", "tubulin_image")
+    viewer.add_shapes(data=None, text="ROI shapes")
+    viewer.window.add_plugin_dock_widget(
+        plugin_name="napari-locan", widget_name="SMLM data"
+    )
+    viewer.window.add_plugin_dock_widget(
+        plugin_name="napari-locan", widget_name="Show metadata"
+    )
+    viewer.window.add_plugin_dock_widget(
+        plugin_name="napari-locan", widget_name="Region of interest"
+    )
+    napari.run()