mosamatic2 2.0.14__tar.gz → 2.0.16__tar.gz

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.14
+Version: 2.0.16
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.14"
+version = "2.0.16"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/src/mosamatic2/core/utils.py

@@ -363,5 +363,9 @@ def is_docker_running():
         return False
     
 
+def is_path_docker_compatible(path):
+    return not ' ' in path
+
+
 def to_unix_path(path):
     return path.replace("\\", "/").replace(" ", "\\ ")

mosamatic2-2.0.16/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.16 

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/src/mosamatic2/ui/widgets/panels/pipelines/boadockerpipelinepanel.py

@@ -16,6 +16,7 @@ from PySide6.QtCore import (
 )
 
 from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_docker_running, is_path_docker_compatible
 from mosamatic2.ui.widgets.panels.pipelines.pipelinepanel import PipelinePanel
 from mosamatic2.ui.settings import Settings
 from mosamatic2.ui.utils import is_macos
@@ -127,6 +128,15 @@ class BoaDockerPipelinePanel(PipelinePanel):
             self.settings().set('last_directory', directory)
 
     def handle_run_pipeline_button(self):
+        if not is_docker_running():
+            QMessageBox.information(self, 'Error', 'Docker is not running. Please start Docker Desktop first')
+            return
+        if not is_path_docker_compatible(self.scans_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to scans directory contains spaces and is not Docker compatible')
+            return
+        if not is_path_docker_compatible(self.output_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to output directory contains spaces and is not Docker compatible')
+            return
         errors = self.check_inputs_and_parameters()
         if len(errors) > 0:
             error_message = 'Following errors were encountered:\n'

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/src/mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py

@@ -18,6 +18,7 @@ from PySide6.QtCore import (
 )
 
 from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_docker_running, is_path_docker_compatible
 from mosamatic2.ui.widgets.panels.pipelines.pipelinepanel import PipelinePanel
 from mosamatic2.ui.settings import Settings
 from mosamatic2.ui.utils import is_macos
@@ -223,6 +224,18 @@ class DefaultDockerPipelinePanel(PipelinePanel):
             self.model_type_combobox().setCurrentText('pytorch')
 
     def handle_run_pipeline_button(self):
+        if not is_docker_running():
+            QMessageBox.information(self, 'Error', 'Docker is not running. Please start Docker Desktop first')
+            return
+        if not is_path_docker_compatible(self.images_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to images directory contains spaces and is not Docker compatible')
+            return
+        if not is_path_docker_compatible(self.model_files_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to model files directory contains spaces and is not Docker compatible')
+            return
+        if not is_path_docker_compatible(self.output_dir_line_edit().text()):
+            QMessageBox.information(self, 'Error', 'Path to output directory contains spaces and is not Docker compatible')
+            return
         errors = self.check_inputs_and_parameters()
         if len(errors) > 0:
             error_message = 'Following errors were encountered:\n'

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/custominteractorstyle.py

@@ -14,6 +14,8 @@ class CustomInteractorStyle(vtk.vtkInteractorStyleImage):
         self.status_actor = status_actor
         self.slice_obj = slice_obj
         self.orientation = orientation
+        self._color_window = 0
+        self._color_level = 0
 
         xmin, xmax, ymin, ymax, zmin, zmax = image_data.GetExtent()
         if orientation == "axial":
@@ -29,6 +31,22 @@ class CustomInteractorStyle(vtk.vtkInteractorStyleImage):
         self.slice_mapper.SetSliceNumber(self.slice)
         self.update_status_message()
 
+    def color_window(self):
+        return self._color_window
+
+    def set_color_window(self, color_window):
+        self._color_window = color_window
+        self.slice_obj.GetProperty().SetColorWindow(self._color_window)
+        self.GetInteractor().GetRenderWindow().Render()
+
+    def color_level(self):
+        return self._color_level
+
+    def set_color_level(self, color_level):
+        self._color_level = color_level
+        self.slice_obj.GetProperty().SetColorLevel(self._color_level)
+        self.GetInteractor().GetRenderWindow().Render()
+
     def update_status_message(self):
         window = int(self.slice_obj.GetProperty().GetColorWindow())
         level = int(self.slice_obj.GetProperty().GetColorLevel())

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/sliceviewer.py

@@ -11,10 +11,12 @@ IMAGE_SHIFT_SCALE = -1000
 
 
 class SliceViewer(QWidget):
-    def __init__(self):
+    def __init__(self, color_window=COLOR_WINDOW, color_level=COLOR_LEVEL):
         super(SliceViewer, self).__init__()
         self._nifti_file_or_dicom_dir = None
         self._view_orientation = 'axial'
+        self._color_window = color_window
+        self._color_level = color_level
         self._vtk_widget = QVTKRenderWindowInteractor(self)
         self._render_window = self._vtk_widget.GetRenderWindow()
         self._interactor = self._render_window.GetInteractor()
@@ -27,6 +29,22 @@ class SliceViewer(QWidget):
         self._render_window.AddRenderer(self._default_renderer)
         self._render_window.Render()
 
+    def color_window(self):
+        return self._color_window
+
+    def set_color_window(self, color_window):
+        self._color_window = color_window
+        if self._interactor_style:
+            self._interactor_style.set_color_window(self._color_window)
+
+    def color_level(self):
+        return self._color_level
+
+    def set_color_level(self, color_level):
+        self._color_level = color_level
+        if self._interactor_style:
+            self._interactor_style.set_color_level(self._color_level)
+
     def nifti_file_or_dicom_dir(self):
         return self._nifti_file_or_dicom_dir
     
@@ -75,8 +93,8 @@ class SliceViewer(QWidget):
         slice_mapper.SetOrientationToZ()  # axial orientation
         slice_mapper.SetSliceNumber(axial_index)
         slice = vtk.vtkImageSlice()
-        slice.GetProperty().SetColorWindow(400)
-        slice.GetProperty().SetColorLevel(40)
+        slice.GetProperty().SetColorWindow(self.color_window())
+        slice.GetProperty().SetColorLevel(self.color_level())
         slice.SetMapper(slice_mapper)
         slice_text_actor = self.create_text_actor("", 0.01, 0.01, 12, align_bottom=True, normalized=True)
         usage_text_actor = self.create_text_actor(

{mosamatic2-2.0.14 → mosamatic2-2.0.16}/src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/slicevisualization.py

@@ -1,5 +1,7 @@
 from PySide6.QtWidgets import (
     QLineEdit,
+    QLabel,
+    QSpinBox,
     QHBoxLayout,
     QVBoxLayout,
     QFormLayout,
@@ -24,6 +26,9 @@ class SliceVisualization(Visualization):
         self._image_line_edit = None
         self._image_select_button = None
         self._image_dir_select_button = None
+        self._color_window_spinbox = None
+        self._color_level_spinbox = None
+        self._color_window_and_level_reset_button = None
         self._load_image_button = None
         self._slice_viewer = None
         self._form_layout = None
@@ -47,6 +52,22 @@ class SliceVisualization(Visualization):
             self._image_dir_select_button.clicked.connect(self.handle_image_dir_select_button)
         return self._image_dir_select_button
     
+    def color_window_spinbox(self):
+        if not self._color_window_spinbox:
+            self._color_window_spinbox = QSpinBox(self, minimum=0, maximum=1024, value=400)
+        return self._color_window_spinbox
+    
+    def color_level_spinbox(self):
+        if not self._color_level_spinbox:
+            self._color_level_spinbox = QSpinBox(self, minimum=0, maximum=100, value=40)
+        return self._color_level_spinbox
+    
+    def color_window_and_level_reset_button(self):
+        if not self._color_window_and_level_reset_button:
+            self._color_window_and_level_reset_button = QPushButton('Reset')
+            self._color_window_and_level_reset_button.clicked.connect(self.handle_color_window_and_level_reset_button)
+        return self._color_window_and_level_reset_button
+    
     def load_image_button(self):
         if not self._load_image_button:
             self._load_image_button = QPushButton('Load')
@@ -55,7 +76,10 @@ class SliceVisualization(Visualization):
     
     def slice_viewer(self):
         if not self._slice_viewer:
-            self._slice_viewer = SliceViewer()
+            self._slice_viewer = SliceViewer(
+                color_window=self.color_window_spinbox().value(),
+                color_level=self.color_level_spinbox().value(),
+            )
         return self._slice_viewer
 
     def form_layout(self):
@@ -75,7 +99,14 @@ class SliceVisualization(Visualization):
         image_layout.addWidget(self.image_line_edit())
         image_layout.addWidget(self.image_select_button())
         image_layout.addWidget(self.image_dir_select_button())
+        color_window_and_level_layout = QHBoxLayout()
+        color_window_and_level_layout.addWidget(QLabel('Color window'))
+        color_window_and_level_layout.addWidget(self.color_window_spinbox())
+        color_window_and_level_layout.addWidget(QLabel('Color level'))
+        color_window_and_level_layout.addWidget(self.color_level_spinbox())
+        color_window_and_level_layout.addWidget(self.color_window_and_level_reset_button())
         self.form_layout().addRow('NIFTI file or DICOM directory', image_layout)
+        self.form_layout().addRow('', color_window_and_level_layout)
         layout = QVBoxLayout()
         layout.addLayout(self.form_layout())
         layout.addWidget(self.load_image_button())
@@ -97,6 +128,10 @@ class SliceVisualization(Visualization):
             self.image_line_edit().setText(dir_path)
             self.settings().set('last_directory', dir_path)
 
+    def handle_color_window_and_level_reset_button(self):
+        self.slice_viewer().set_color_window(self.color_window_spinbox().value())
+        self.slice_viewer().set_color_level(self.color_level_spinbox().value())
+
     def handle_load_image_button(self):
         self.slice_viewer().set_nifti_file_or_dicom_dir(self.image_line_edit().text())
         # self.slice_viewer().set_view_orientation('axial')

mosamatic2-2.0.14/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.14