Integration tests

.github/workflows/build_macos.yml

@@ -15,7 +15,7 @@ env:
 jobs:
   build:
     name: Build packages
-    runs-on: macos-12
+    runs-on: macos-13
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
@@ -54,8 +54,8 @@ jobs:
       env:
         DISPLAY: ':99.0'
       run: |
-          pip install pytest-qt pytest-cov
-          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests
+          pip install pytest-qt pytest-cov pytest-timeout
+          pytest -vvv --cov=gui --cov=utils ${{github.workspace}}/integration_tests --timeout=60 --log-cli-level=DEBUG
 
     - name: Build software
       run: |

.github/workflows/build_macos_arm.yml

@@ -55,8 +55,8 @@ jobs:
       run: |
           cd ${{github.workspace}}
           source tmp/venv/bin/activate
-          pip3 install pytest-qt pytest-cov
-          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests
+          pip3 install pytest-qt pytest-cov pytest-timeout
+          pytest -vvv --cov=gui --cov=utils ${{github.workspace}}/integration_tests --timeout=60 --log-cli-level=DEBUG
           deactivate
 
     - name: Build software

.github/workflows/build_ubuntu.yml

@@ -81,9 +81,9 @@ jobs:
       env:
         DISPLAY: ':99.0'
       run: |
-          pip install pytest-qt pytest-cov
+          pip install pytest-qt pytest-cov pytest-timeout
           /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX
-          pytest --cov=gui --cov=utils ${{github.workspace}}/integration_tests --cov-report=xml
+          pytest -vvv --cov=gui --cov=utils ${{github.workspace}}/integration_tests --cov-report=xml --timeout=60 --log-cli-level=DEBUG
 
     - name: Build software
       run: |

.gitignore

@@ -38,3 +38,5 @@ quickpkg/
 *.tar.gz
 assets/Raidionics_ubuntu/usr/local/bin
 .coverage
+*.raidionics
+integrationtests/

gui/RaidionicsMainWindow.py

@@ -522,7 +522,7 @@ def on_process_log_message(self, log_msg: str) -> None:
         aware of it (in case they don't have the reflex to check the log file).
         """
         cases = ["[Software warning]", "[Software error]", "[Backend warning]", "[Backend error]"]
-        if True in [x in log_msg for x in cases]:
+        if True in [x in log_msg for x in cases] and not UserPreferencesStructure.getInstance().disable_modal_warnings:
             diag = QErrorMessage(self)
             diag.setWindowTitle("Error or warning identified!")
             diag.showMessage(log_msg + "<br><br>Please visit the log file (Settings > Logs)")
@@ -540,6 +540,9 @@ def standardOutputWritten(self, text):
             self.batch_mode_widget.standardOutputWritten(text)
 
     def on_clear_scene(self):
+        """
+
+        """
         logging.info("[RaidionicsMainWindow] Interface clean-up. Removing all loaded patients and studies.")
         self.batch_study_widget.on_clear_scene()
         self.single_patient_widget.on_clear_scene()

gui/SinglePatientComponent/CentralDisplayArea/CentralDisplayAreaWidget.py

@@ -191,24 +191,28 @@ def on_volume_layer_toggled(self, volume_uid, state):
         if not self.current_patient_parameters:
             self.current_patient_parameters = SoftwareConfigResources.getInstance().get_active_patient()
 
-        if state:
-            self.reset_overlay()  # Until the time there is a co-registration option between input MRI volumes.
-            self.displayed_image = self.current_patient_parameters.get_mri_by_uid(volume_uid).get_display_volume()
-            self.displayed_image_uid = volume_uid
-
-            # Reset to the view-point, until the time there's co-registration or MNI space, where we can keep it.
-            # @FIXME. Is the center of the volume actually correct? Looks fishy
-            self.point_clicker_position = [int(self.displayed_image.shape[0] / 2),
-                                           int(self.displayed_image.shape[1] / 2),
-                                           int(self.displayed_image.shape[2] / 2)]
-            self.update_viewers_image()
-        else:  # If all images have been removed by the user, should display an empty view
-            self.displayed_image = np.zeros(shape=(150, 150, 150), dtype='uint8')
-            self.displayed_image_uid = None
-            self.point_clicker_position = [int(self.displayed_image.shape[0] / 2),
-                                           int(self.displayed_image.shape[1] / 2),
-                                           int(self.displayed_image.shape[2] / 2)]
-            self.update_viewers_image()
+        try:
+            if state:
+                self.reset_overlay()  # Until the time there is a co-registration option between input MRI volumes.
+                self.displayed_image = self.current_patient_parameters.get_mri_by_uid(volume_uid).get_display_volume()
+                self.displayed_image_uid = volume_uid
+
+                # Reset to the view-point, until the time there's co-registration or MNI space, where we can keep it.
+                # @FIXME. Is the center of the volume actually correct? Looks fishy
+                self.point_clicker_position = [int(self.displayed_image.shape[0] / 2),
+                                               int(self.displayed_image.shape[1] / 2),
+                                               int(self.displayed_image.shape[2] / 2)]
+                self.update_viewers_image()
+            else:  # If all images have been removed by the user, should display an empty view
+                self.displayed_image = np.zeros(shape=(150, 150, 150), dtype='uint8')
+                self.displayed_image_uid = None
+                self.point_clicker_position = [int(self.displayed_image.shape[0] / 2),
+                                               int(self.displayed_image.shape[1] / 2),
+                                               int(self.displayed_image.shape[2] / 2)]
+                self.update_viewers_image()
+        except Exception as e:
+            logging.error("[Software error][CentralDisplayAreaWidget] Issue trying to toggle the view for a volume.")
+            logging.info("Collected: {}\n {}".format(e, traceback.format_exc()))
 
     def on_volume_contrast_changed(self, volume_uid):
         # @TODO. Should group the viewer calls into another function somewhere, since all three above methods use it.

gui/SinglePatientComponent/LayersInteractorSidePanel/AnnotationLayersInteractor/AnnotationSingleLayerWidget.py

@@ -7,6 +7,7 @@
 from gui.UtilsWidgets.CustomQGroupBox.QCollapsibleGroupBox import QCollapsibleGroupBox
 
 from utils.software_config import SoftwareConfigResources
+from utils.data_structures.UserPreferencesStructure import UserPreferencesStructure
 
 
 class AnnotationSingleLayerWidget(QWidget):
@@ -534,16 +535,18 @@ def __on_annotation_type_changed(self):
         params.set_annotation_class_type(self.annotation_type_combobox.currentText())
 
     def __on_parent_mri_changed(self, index: int) -> None:
-        code = QMessageBox.warning(self, "Parent MRI change warning.",
+
+        if not UserPreferencesStructure.getInstance().disable_modal_warnings:
+            code = QMessageBox.warning(self, "Parent MRI change warning.",
                                    "Are you sure you want to proceed with the change of parent MRI?",
                                    QMessageBox.Ok | QMessageBox.Cancel, QMessageBox.Ok)
-        if code == QMessageBox.StandardButton.Cancel:  # Change canceled
-            self.parent_image_combobox.blockSignals(True)
-            parent_mri_display_name = SoftwareConfigResources.getInstance().get_active_patient().get_mri_by_uid(
-                SoftwareConfigResources.getInstance().get_active_patient().get_annotation_by_uid(self.uid).get_parent_mri_uid()).display_name
-            self.parent_image_combobox.setCurrentText(parent_mri_display_name)
-            self.parent_image_combobox.blockSignals(False)
-            return
+            if code == QMessageBox.StandardButton.Cancel:  # Change canceled
+                self.parent_image_combobox.blockSignals(True)
+                parent_mri_display_name = SoftwareConfigResources.getInstance().get_active_patient().get_mri_by_uid(
+                    SoftwareConfigResources.getInstance().get_active_patient().get_annotation_by_uid(self.uid).get_parent_mri_uid()).display_name
+                self.parent_image_combobox.setCurrentText(parent_mri_display_name)
+                self.parent_image_combobox.blockSignals(False)
+                return
 
         params = SoftwareConfigResources.getInstance().get_active_patient().get_annotation_by_uid(self.uid)
         old_mri_parent = params.get_parent_mri_uid()

gui/SinglePatientComponent/LayersInteractorSidePanel/AnnotationLayersInteractor/AnnotationsLayersInteractor.py

@@ -87,14 +87,17 @@ def reset(self):
             self.volumes_widget.pop(w)
         self.header.collapse()
 
+    def get_layer_widget_length(self) -> int:
+        return len(self.volumes_widget)
+
     def get_layer_widget_by_index(self, index: int) -> AnnotationSingleLayerWidget:
         if index >= len(self.volumes_widget):
             raise ValueError("[AnnotationsLayerInteractor] Trying to retrieve an Annotation layer widget with an out-of-bound index value.")
         return self.volumes_widget[list(self.volumes_widget.keys())[index]]
 
     def get_layer_widget_by_visible_name(self, name: str) -> AnnotationSingleLayerWidget:
         for w in list(self.volumes_widget.keys()):
-            if self.volumes_widget[w].visible_name == name:
+            if self.volumes_widget[w].display_name_lineedit.text() == name:
                 return self.volumes_widget[w]
         raise ValueError("[AnnotationsLayerInteractor] Trying to retrieve a non-existing Annotation layer widget by visible name with: {}.".format(name))
 

gui/SinglePatientComponent/LayersInteractorSidePanel/AtlasLayersInteractor/AtlasesLayersInteractor.py

@@ -91,14 +91,18 @@ def reset(self):
             self.volumes_widget.pop(w)
         self.header.collapse()
 
+
+    def get_layer_widget_length(self) -> int:
+        return len(self.volumes_widget)
+
     def get_layer_widget_by_index(self, index: int) -> AtlasSingleLayerWidget:
         if index >= len(self.volumes_widget):
             raise ValueError("[AtlasesLayerInteractor] Trying to retrieve an Atlas layer widget with an out-of-bound index value.")
         return self.volumes_widget[list(self.volumes_widget.keys())[index]]
 
     def get_layer_widget_by_visible_name(self, name: str) -> AtlasSingleLayerWidget:
         for w in list(self.volumes_widget.keys()):
-            if self.volumes_widget[w].visible_name == name:
+            if self.volumes_widget[w].display_name_lineedit.text() == name:
                 return self.volumes_widget[w]
         raise ValueError("[AtlasesLayerInteractor] Trying to retrieve a non-existing Atlas layer widget by visible name with: {}.".format(name))
 

gui/SinglePatientComponent/LayersInteractorSidePanel/MRIVolumesInteractor/MRISeriesLayerWidget.py

@@ -9,6 +9,7 @@
 from gui.UtilsWidgets.CustomQGroupBox.QCollapsibleGroupBox import QCollapsibleGroupBox
 from gui.UtilsWidgets.CustomQDialog.ContrastAdjustmentDialog import ContrastAdjustmentDialog
 from gui.UtilsWidgets.CustomQDialog.DisplayDICOMMetadataDialog import DisplayMetadataDICOMDialog
+from utils.data_structures.UserPreferencesStructure import UserPreferencesStructure
 
 from utils.software_config import SoftwareConfigResources
 from utils.data_structures.MRIVolumeStructure import MRISequenceType
@@ -294,7 +295,7 @@ def __on_delete_layer(self):
         """
         linked_annos = SoftwareConfigResources.getInstance().get_active_patient().get_all_annotations_for_mri(self.uid)
         linked_atlases = SoftwareConfigResources.getInstance().get_active_patient().get_all_atlases_for_mri(self.uid)
-        if (len(linked_annos) + len(linked_atlases)) != 0:
+        if (len(linked_annos) + len(linked_atlases)) != 0 and not UserPreferencesStructure.getInstance().disable_modal_warnings:
             code = QMessageBox.warning(self, "MRI volume layer deletion warning.",
                                        "Deleting an MRI volume will also remove all other files linked to it (e.g., annotations).",
                                        QMessageBox.Ok | QMessageBox.Cancel, QMessageBox.Ok)

gui/SinglePatientComponent/LayersInteractorSidePanel/MRIVolumesInteractor/MRIVolumesLayerInteractor.py

@@ -90,14 +90,17 @@ def reset(self) -> None:
             self.volumes_widget.pop(w)
         self.header.collapse()
 
+    def get_layer_widget_length(self) -> int:
+        return len(self.volumes_widget)
+
     def get_layer_widget_by_index(self, index: int) -> MRISeriesLayerWidget:
         if index >= len(self.volumes_widget):
             raise ValueError("[MRIVolumeLayerInteractor] Trying to retrieve an MRI Layer widget with an out-of-bound index value.")
         return self.volumes_widget[list(self.volumes_widget.keys())[index]]
 
     def get_layer_widget_by_visible_name(self, name: str) -> MRISeriesLayerWidget:
         for w in list(self.volumes_widget.keys()):
-            if self.volumes_widget[w].visible_name == name:
+            if self.volumes_widget[w].display_name_lineedit.text() == name:
                 return self.volumes_widget[w]
         raise ValueError("[TimestampsLayerInteractor] Trying to retrieve a non-existing MRI layer widget by visible name with: {}.".format(name))
 

gui/SinglePatientComponent/LayersInteractorSidePanel/SinglePatientLayersWidget.py

@@ -7,9 +7,6 @@
 import logging
 
 from gui.SinglePatientComponent.LayersInteractorSidePanel.TimestampsInteractor.TimestampsLayerInteractor import TimestampsLayerInteractor
-from gui.SinglePatientComponent.LayersInteractorSidePanel.MRIVolumesInteractor.MRIVolumesLayerInteractor import MRIVolumesLayerInteractor
-from gui.SinglePatientComponent.LayersInteractorSidePanel.AnnotationLayersInteractor.AnnotationsLayersInteractor import AnnotationsLayersInteractor
-from gui.SinglePatientComponent.LayersInteractorSidePanel.AtlasLayersInteractor.AtlasesLayersInteractor import AtlasesLayersInteractor
 from gui.SinglePatientComponent.LayersInteractorSidePanel.ActionsInteractor.ActionsInteractorWidget import ActionsInteractorWidget
 from utils.software_config import SoftwareConfigResources
 
@@ -78,10 +75,6 @@ def __set_interface(self):
         self.main_tabwidget.addTab(self.execution_actions_widget, "Actions")
         self.overall_scrollarea_layout.addWidget(self.main_tabwidget)
 
-        self.volumes_collapsiblegroupbox = MRIVolumesLayerInteractor(self)
-        self.annotations_collapsiblegroupbox = AnnotationsLayersInteractor(self)
-        self.atlases_collapsiblegroupbox = AtlasesLayersInteractor(self)
-
         self.overall_scrollarea_layout.addStretch(1)
         self.overall_scrollarea_dummy_widget.setLayout(self.overall_scrollarea_layout)
         self.overall_scrollarea.setWidget(self.overall_scrollarea_dummy_widget)
@@ -113,10 +106,6 @@ def __set_connections(self):
         self.execution_actions_widget.pipeline_execution_requested.connect(self.pipeline_execution_requested)
         self.main_tabwidget.currentChanged.connect(self.__on_main_tab_changed)
 
-        # @TODO. Can be removed, deprecated?
-        self.import_data_triggered.connect(self.volumes_collapsiblegroupbox.on_import_data)
-        self.import_data_triggered.connect(self.annotations_collapsiblegroupbox.on_import_data)
-
     def __set_stylesheets(self):
         software_ss = SoftwareConfigResources.getInstance().stylesheet_components
         font_color = software_ss["Color7"]
@@ -186,8 +175,6 @@ def on_mri_volume_removed(self, uid):
         objects_uids, error_msg = SoftwareConfigResources.getInstance().get_active_patient().remove_mri_volume(volume_uid=uid)
         if SoftwareConfigResources.getInstance().get_active_patient().get_patient_mri_volumes_number() == 0:
             self.volume_view_toggled.emit(uid, False)
-            self.annotations_collapsiblegroupbox.reset()
-            self.atlases_collapsiblegroupbox.reset()
         # logging.info("[SinglePatientLayersWidget] on_mri_volume_removed took {} seconds.".format(time.time() - start))
 
     def on_annotation_volume_import(self, uid):
@@ -210,9 +197,6 @@ def on_patient_selected(self, patient_uid: str) -> None:
         patient_uid : str
             The unique identifier of the newly selected active patient.
         """
-        # self.volumes_collapsiblegroupbox.reset()
-        # self.annotations_collapsiblegroupbox.reset()
-        # self.atlases_collapsiblegroupbox.reset()
         self.patient_view_toggled.emit(patient_uid)
 
     def on_import_patient(self, patient_uid: str) -> None:
@@ -237,9 +221,6 @@ def on_reset_interface(self) -> None:
         Sets all inner widgets to their default states.
         """
         self.timestamp_layer_widget.reset()
-        self.volumes_collapsiblegroupbox.reset()
-        self.annotations_collapsiblegroupbox.reset()
-        self.atlases_collapsiblegroupbox.reset()
         self.execution_actions_widget.reset()
 
     def on_batch_process_started(self) -> None:

gui/SinglePatientComponent/PatientResultsSidePanel/PatientResultsSinglePatientSidePanelWidget.py

@@ -164,6 +164,9 @@ def adjustSize(self) -> None:
         self.patient_list_scrollarea_dummy_widget.setFixedSize(QSize(self.size().width(), actual_height))
         self.repaint()
 
+    def get_patient_results_widget_size(self) -> int:
+        return len(self.patient_results_widgets)
+
     def get_patient_results_widget_by_index(self, index: int) -> SinglePatientResultsWidget:
         if index >= len(self.patient_results_widgets):
             raise ValueError(

gui/SinglePatientComponent/SinglePatientWidget.py

@@ -160,6 +160,7 @@ def __set_cross_connections(self):
         self.import_folder_dialog.patient_imported.connect(self.layers_panel.on_import_patient)
         self.import_dicom_dialog.patient_imported.connect(self.results_panel.on_import_patient)
         self.import_dicom_dialog.mri_volume_imported.connect(self.layers_panel.on_mri_volume_import)
+        self.import_dicom_dialog.annotation_volume_imported.connect(self.layers_panel.on_annotation_volume_import)
         self.layers_panel.import_data_requested.connect(self.__on_import_file_clicked)
         self.layers_panel.import_dicom_requested.connect(self.__on_import_dicom_clicked)
 
@@ -337,4 +338,5 @@ def on_atlas_volume_imported(self, uid: str) -> None:
 
     def on_clear_scene(self):
         for w in list(self.results_panel.patient_results_widgets.keys()):
-            self.results_panel.patient_results_widgets[w].patient_closed.emit(w)
+            self.results_panel.patient_results_widgets[w].patient_closed.emit(w)
+        self.import_dicom_dialog.reset_interface()

gui/StudyBatchComponent/PatientsListingPanel/StudyPatientListingWidget.py

@@ -149,6 +149,24 @@ def adjustSize(self) -> None:
         # logging.debug("Study patient listing scroll area size set to {}.\n".format(QSize(self.size().width(),
         #                                                                                  actual_height)))
 
+    def get_study_patient_widget_length(self) -> int:
+        return len(self.study_patient_widgetitems)
+
+    def get_study_patient_widget_by_index(self, index: int) -> PatientListingWidgetItem:
+        if index >= len(self.study_patient_widgetitems):
+            raise ValueError(
+                "[StudyPatientListingWidget] Trying to retrieve a patient listing widget with an out-of-bound index value.")
+        return self.study_patient_widgetitems[list(self.study_patient_widgetitems.keys())[index]]
+
+    def on_reset_interface(self) -> None:
+        for wid in reversed(list(self.study_patient_widgetitems.keys())):
+            self.patients_list_scrollarea_layout.removeWidget(self.study_patient_widgetitems[wid])
+            self.study_patient_widgetitems[wid].setParent(None)
+            del self.study_patient_widgetitems[wid]
+        self.study_patient_widgetitems = {}
+        self.adjustSize()
+        self.repaint()
+
     def on_patient_imported(self, patient_uid: str) -> None:
         wid = PatientListingWidgetItem(patient_uid=patient_uid, parent=self)
         self.study_patient_widgetitems[patient_uid] = wid
@@ -193,3 +211,10 @@ def on_process_started(self) -> None:
 
     def on_process_finished(self):
         self.patients_refresh_pushbutton.setEnabled(True)
+
+    def on_study_selected(self, uid: str) -> None:
+        """
+        Working on the active study anyway here, so the uid parameter is not used for now.
+        """
+        self.on_reset_interface()
+        self.on_study_imported(uid)

gui/StudyBatchComponent/PatientsSummaryPanel/StudyPatientsContentSummaryPanelWidget.py

@@ -97,6 +97,9 @@ def __set_stylesheets(self):
     def adjustSize(self) -> None:
         pass
 
+    def on_reset_interface(self) -> None:
+        self.content_tree_widget.clear()
+
     def on_patients_import(self) -> None:
         self.content_tree_widget.clear()
         study_patients_uid = SoftwareConfigResources.getInstance().get_active_study().included_patients_uids