Atlas space display

.github/workflows/build_macos.yml

@@ -15,7 +15,7 @@ env:
 jobs:
   build:
     name: Build packages
-    runs-on: macos-11
+    runs-on: macos-12
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python 3.8
@@ -72,8 +72,8 @@ jobs:
     - name: Make installer
       run: |
         git clone https://github.com/dbouget/quickpkg.git
-        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.2.3-macOS.pkg
-        cp -r Raidionics-1.2.3-macOS.pkg dist/Raidionics-1.2.3-macOS-x86_64.pkg
+        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.2.4-macOS.pkg
+        cp -r Raidionics-1.2.4-macOS.pkg dist/Raidionics-1.2.4-macOS-x86_64.pkg
 
     - name: Upload package
       uses: actions/upload-artifact@v4

.github/workflows/build_macos_arm.yml

@@ -18,7 +18,7 @@ jobs:
         cd tmp
         python3 -m virtualenv -p python3 venv --clear
         source venv/bin/activate
-        python3 -m pip install wheel setuptools
+        python3 -m pip install wheel setuptools==69.5.1
         deactivate
 
     - name: Install dependencies
@@ -67,8 +67,8 @@ jobs:
     - name: Make installer
       run: |
         git clone https://github.com/dbouget/quickpkg.git
-        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.2.3-macOS.pkg
-        cp -r Raidionics-1.2.3-macOS.pkg dist/Raidionics-1.2.3-macOS-arm64.pkg
+        quickpkg/quickpkg dist/Raidionics.app --output Raidionics-1.2.4-macOS.pkg
+        cp -r Raidionics-1.2.4-macOS.pkg dist/Raidionics-1.2.4-macOS-arm64.pkg
 
     - name: Upload package
       uses: actions/upload-artifact@v4

.github/workflows/build_ubuntu.yml

@@ -108,7 +108,7 @@ jobs:
         cp -r dist/Raidionics assets/Raidionics_ubuntu/usr/local/bin
         dpkg-deb --build --root-owner-group assets/Raidionics_ubuntu
         ls -la
-        cp -r assets/Raidionics_ubuntu.deb dist/Raidionics-1.2.3-ubuntu.deb
+        cp -r assets/Raidionics_ubuntu.deb dist/Raidionics-1.2.4-ubuntu.deb
 
     - name: Upload package
       uses: actions/upload-artifact@v4

.github/workflows/build_windows.yml

@@ -62,7 +62,7 @@ jobs:
     - name: Make installer
       run: |
         makensis.exe assets/Raidionics.nsi
-        cp -r assets/Raidionics-1.2.3-win.exe dist/Raidionics-1.2.3-win.exe
+        cp -r assets/Raidionics-1.2.4-win.exe dist/Raidionics-1.2.4-win.exe
 
     - name: Upload package
       uses: actions/upload-artifact@v4

assets/Raidionics.nsi

@@ -2,7 +2,7 @@
 !define COMP_NAME "SINTEF"
 !define VERSION "1.2.2"
 !define DESCRIPTION "Application"
-!define INSTALLER_NAME "Raidionics-1.2.3-win.exe"
+!define INSTALLER_NAME "Raidionics-1.2.4-win.exe"
 !define MAIN_APP_EXE "Raidionics.exe"
 !define INSTALL_TYPE "SetShellVarContext current"
 !define REG_ROOT "HKLM"

assets/main.spec

@@ -85,7 +85,7 @@ if sys.platform == "darwin":
                     'CFBundleIdentifier': 'Raidionics',
                     'CFBundleInfoDictionaryVersion': '6.0',
                     'CFBundleName': 'Raidionics',
-                    'CFBundleVersion': '1.2.3',
+                    'CFBundleVersion': '1.2.4',
                     'CFBundlePackageType': 'APPL',
                     'LSBackgroundOnly': 'false',
                 },

assets/main_arm.spec

@@ -84,7 +84,7 @@ if sys.platform == "darwin":
                     'CFBundleIdentifier': 'Raidionics',
                     'CFBundleInfoDictionaryVersion': '6.0',
                     'CFBundleName': 'Raidionics',
-                    'CFBundleVersion': '1.2.3',
+                    'CFBundleVersion': '1.2.4',
                     'CFBundlePackageType': 'APPL',
                     'LSBackgroundOnly': 'false',
                 },

gui/RaidionicsMainWindow.py

@@ -1,6 +1,6 @@
 import sys, os
 from PySide6.QtWidgets import QApplication, QLabel, QMainWindow, QMenuBar, QMessageBox,\
-    QHBoxLayout, QVBoxLayout, QStackedWidget, QSizePolicy
+    QHBoxLayout, QVBoxLayout, QStackedWidget, QSizePolicy, QDialog, QErrorMessage
 from PySide6.QtCore import QUrl, QSize, QThread, Signal, Qt
 from PySide6.QtGui import QIcon, QDesktopServices, QCloseEvent, QAction
 import traceback
@@ -9,9 +9,13 @@
 import numpy as np
 import logging
 import warnings
+
+from utils.data_structures.UserPreferencesStructure import UserPreferencesStructure
+
 warnings.simplefilter(action='ignore', category=FutureWarning)
 
 from utils.software_config import SoftwareConfigResources
+from gui.LogReaderThread import LogReaderThread
 from gui.WelcomeWidget import WelcomeWidget
 from gui.SinglePatientComponent.SinglePatientWidget import SinglePatientWidget
 from gui.StudyBatchComponent.StudyBatchWidget import StudyBatchWidget
@@ -39,7 +43,7 @@ def stop(self):
 
 
 class RaidionicsMainWindow(QMainWindow):
-
+    reload_interface = Signal()
     new_patient_clicked = Signal(str)  # Internal unique_id of the clicked patient
 
     def __init__(self, application, *args, **kwargs):
@@ -49,6 +53,8 @@ def __init__(self, application, *args, **kwargs):
         self.app.setWindowIcon(QIcon(os.path.join(os.path.dirname(os.path.realpath(__file__)),
                                                   'Images/raidionics-icon.png')))
         self.app.setStyle("Fusion")  # @TODO: Should we remove Fusion style? Looks strange on macOS
+        self.logs_thread = LogReaderThread()
+        self.logs_thread.start()
         self.__set_interface()
         self.__set_layouts()
         self.__set_stylesheet()
@@ -80,6 +86,7 @@ def __on_exit_software(self) -> None:
         """
         Mirroring of the closeEvent, for when the user press the Quit action in the main menu.
         """
+        self.logs_thread.stop()
         if not SoftwareConfigResources.getInstance().is_patient_list_empty()\
                 and SoftwareConfigResources.getInstance().get_active_patient().has_unsaved_changes():
             dialog = SavePatientChangesDialog()
@@ -322,6 +329,7 @@ def __set_inner_widget_connections(self):
     def __cross_widgets_connections(self):
         self.welcome_widget.left_panel_single_patient_pushbutton.clicked.connect(self.__on_single_patient_clicked)
         self.new_patient_clicked.connect(self.single_patient_widget.on_single_patient_clicked)
+        self.reload_interface.connect(self.single_patient_widget.on_reload_interface)
 
         self.welcome_widget.left_panel_multiple_patients_pushbutton.clicked.connect(self.__on_study_batch_clicked)
         self.welcome_widget.community_clicked.connect(self.__on_community_action_triggered)
@@ -344,6 +352,8 @@ def __cross_widgets_connections(self):
         self.batch_study_widget.patient_report_imported.connect(self.single_patient_widget.patient_report_imported)
         self.batch_study_widget.patient_radiological_sequences_imported.connect(self.single_patient_widget.patient_radiological_sequences_imported)
 
+        self.logs_thread.message.connect(self.on_process_log_message)
+
     def __set_menubar_connections(self):
         self.home_action.triggered.connect(self.__on_home_clicked)
         self.single_use_action.triggered.connect(self.__on_single_patient_clicked)
@@ -427,9 +437,15 @@ def __on_study_batch_clicked(self):
         self.adjustSize()
 
     def __on_settings_preferences_clicked(self):
+        patient_space = UserPreferencesStructure.getInstance().display_space
         diag = SoftwareSettingsDialog(self)
         diag.exec_()
 
+        # Reloading the interface is mainly meant to perform a visual refreshment based on the latest user display choices
+        # For now: changing the display space for viewing a patient images.
+        if UserPreferencesStructure.getInstance().display_space != patient_space:
+            self.reload_interface.emit()
+
     def __on_patient_selected(self, patient_uid: str) -> None:
         """
         A patient has been selected in another module than the single patient one in order to be displayed.
@@ -463,9 +479,9 @@ def __on_help_action_triggered(self) -> None:
     def __on_issues_action_triggered(self) -> None:
         QDesktopServices.openUrl(QUrl("https://github.com/dbouget/Raidionics/issues"))
 
-    def __on_view_logs_triggered(self):
+    def __on_view_logs_triggered(self) -> None:
         """
-        @TODO. Should make a custom widget as text edit to see the content of the raidionics log file.
+        Opens up a pop-up dialog allowing to read through the log file.
         """
         diag = LogsViewerDialog(self)
         diag.exec_()
@@ -485,6 +501,19 @@ def __on_save_file_triggered(self):
     def __on_download_example_data(self):
         QDesktopServices.openUrl(QUrl("https://drive.google.com/file/d/1W3klW_F7Rfge9-utczz9qp7uWh-pVPS1/view?usp=sharing"))
 
+    def on_process_log_message(self, log_msg: str) -> None:
+        """
+        Reading the log file on-the-fly to notify the user in case of software or processing issue to make them
+        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]:
+            diag = QErrorMessage(self)
+            diag.setWindowTitle("Error or warning identified!")
+            diag.showMessage(log_msg + "\nPlease visit the log file (Settings > Logs)")
+            diag.setMinimumSize(QSize(400, 150))
+            diag.exec()
+
     def standardOutputWritten(self, text):
         """
         Redirecting standard output prints to the (correct) displayed widget

gui/SinglePatientComponent/CentralAreaWidget.py

@@ -105,6 +105,9 @@ def __set_layout_dimensions(self):
     def get_widget_name(self):
         return self.widget_name
 
+    def on_reload_interface(self):
+        self.display_area_widget.on_patient_selected()
+
     def on_patient_selected(self, patient_uid):
         self.patient_view_toggled.emit(patient_uid)
 

gui/SinglePatientComponent/CentralDisplayArea/CentralDisplayAreaWidget.py

@@ -162,9 +162,14 @@ def on_patient_selected(self):
 
         # Can only be 0 if the active patient is the default (and empty) temp patient created during initialization.
         if self.current_patient_parameters.get_patient_mri_volumes_number() != 0:
-            self.displayed_image = self.current_patient_parameters.get_mri_by_uid(
-                self.current_patient_parameters.get_all_mri_volumes_uids()[0]).get_display_volume()
-            self.displayed_image_uid = self.current_patient_parameters.get_mri_by_uid(self.current_patient_parameters.get_all_mri_volumes_uids()[0]).unique_id
+            # If updating the central panel after selecting a different display space, the same image as currently
+            # visible should be updated.
+            if self.displayed_image_uid in self.current_patient_parameters.get_all_mri_volumes_uids():
+                self.displayed_image = self.current_patient_parameters.get_mri_by_uid(self.displayed_image_uid).get_display_volume()
+            else:  # If an actual new patient selected, the first available image is displayed
+                self.displayed_image = self.current_patient_parameters.get_mri_by_uid(
+                    self.current_patient_parameters.get_all_mri_volumes_uids()[0]).get_display_volume()
+                self.displayed_image_uid = self.current_patient_parameters.get_mri_by_uid(self.current_patient_parameters.get_all_mri_volumes_uids()[0]).unique_id
             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)]

gui/SinglePatientComponent/CentralDisplayArea/CustomQGraphicsView.py

@@ -89,9 +89,14 @@ def __set_stylesheets(self):
         self.setStyleSheet("QGraphicsView{background-color:rgb(0,0,0);}")
 
     def keyPressEvent(self, event) -> None:
+        """
+        Shortcuts for displaying or hiding elements, only if there is an active patient.
+        S key: display or hide the tumor annotation.
+        """
         if event.key() == Qt.Key_S:
-            logging.info("Changing annotations display state.")
-            self.annotation_display_state_changed.emit()
+            if not SoftwareConfigResources.getInstance().is_patient_list_empty():
+                logging.info("Changing annotations display state.")
+                self.annotation_display_state_changed.emit()
 
     def mousePressEvent(self, event):
         """

gui/SinglePatientComponent/SinglePatientWidget.py

@@ -275,6 +275,14 @@ def __on_patient_selected(self, patient_uid):
         self.top_logo_panel_label_import_dicom_pushbutton.setEnabled(True)
         self.top_logo_panel_statistics_pushbutton.setEnabled(True)
 
+    def on_reload_interface(self) -> None:
+        """
+        In order to generate a new central panel, for example because the display space has changed.
+        """
+        if not SoftwareConfigResources.getInstance().is_patient_list_empty():
+            SoftwareConfigResources.getInstance().get_active_patient().load_in_memory()
+            self.center_panel.on_reload_interface()
+
     def on_patient_selected(self, patient_name):
         self.results_panel.on_external_patient_selection(patient_name)
 
@@ -293,6 +301,7 @@ def on_process_finished(self) -> None:
         self.results_panel.on_process_finished()
         # Hides the process tracking to display back the layers interactor for viewing purposes.
         self.right_panel_stackedwidget.setCurrentIndex(0)
+        self.center_panel.on_reload_interface()
 
     def on_batch_process_started(self) -> None:
         """

gui/UtilsWidgets/CustomQDialog/LogsViewerDialog.py

@@ -9,6 +9,7 @@
 
 class LogsViewerDialog(QDialog):
 
+    error_detected = Signal(str)
     def __init__(self, parent=None):
         super().__init__(parent)
         self.setWindowTitle("Runtime logs")