mosamatic2 2.0.6__tar.gz → 2.0.8__tar.gz

{mosamatic2-2.0.6 → mosamatic2-2.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mosamatic2
-Version: 2.0.6
+Version: 2.0.8
 Summary: 
 Author: Ralph Brecheisen
 Author-email: r.brecheisen@maastrichtuniversity.nl

{mosamatic2-2.0.6 → mosamatic2-2.0.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mosamatic2"
-version = "2.0.6"
+version = "2.0.8"
 description = ""
 authors = [
     {name = "Ralph Brecheisen", email = "r.brecheisen@maastrichtuniversity.nl"}

{mosamatic2-2.0.6 → mosamatic2-2.0.8}/src/mosamatic2/cli.py

@@ -6,6 +6,7 @@ from mosamatic2.commands import (
     createpngsfromsegmentations,
     dicom2nifti,
     selectslicefromscans,
+    createdicomsummary,
 )
 from mosamatic2.core.utils import show_doc_command
 
@@ -33,4 +34,5 @@ main.add_command(segmentmusclefatl3tensorflow.segmentmusclefatl3tensorflow)
 main.add_command(createpngsfromsegmentations.createpngsfromsegmentations)
 main.add_command(dicom2nifti.dicom2nifti)
 main.add_command(selectslicefromscans.selectslicefromscans)
+main.add_command(createdicomsummary.createdicomsummary)
 main.add_command(show_doc_command(main)) # Special command to show long description for command

mosamatic2-2.0.8/src/mosamatic2/commands/createdicomsummary.py

@@ -0,0 +1,61 @@
+import click
+
+from mosamatic2.core.tasks import CreateDicomSummaryTask
+
+
+@click.command(help='Creates a DICOM summary inside a root directory')
+@click.option(
+    '--directory', 
+    required=True, 
+    type=click.Path(exists=True), 
+    help='Root directory with DICOM images (can be multiple scans)',
+)
+@click.option(
+    '--output', 
+    required=True, 
+    type=click.Path(), 
+    help='Output directory'
+)
+@click.option(
+    '--overwrite', 
+    type=click.BOOL, 
+    default=False, 
+    help='Overwrite [true|false]'
+)
+def createdicomsummary(directory, output, overwrite):
+    """
+    Creates a DICOM summary inside a root directory. Each patient should have
+    its own directory. Inside each patient's directory, there can be multiple
+    scans (called series) and multiple DICOM files per scan. The output of this
+    command is a file summary.txt (stored in the output directory) that contains
+    the following information:
+
+    - A list of patient directory names with the number of scans inside each
+      patient directory
+    - For each patient directory and scan directory the following information:
+        - Nr. of DICOM images in the scan
+        - Modality (e.g., CT or MRI)
+        - Image type (e.g., for Dixon scans can be in-phase, opposite-phase, 
+          water or fat images)
+        - Rows/columns (size of the images)
+        - Pixel spacing (size of each pixel in mm^2)
+        - Slice thickness: (thickness of each image slice)
+
+    Parameters
+    ----------
+    --directory : str
+        Root directory with patient directories, scans and DICOM images
+
+    --output : str
+        Path to output directory
+
+    --overwrite : bool
+        Overwrite contents output directory [true|false]
+    """
+    task = CreateDicomSummaryTask(
+        inputs={'directory': directory},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()

mosamatic2-2.0.8/src/mosamatic2/core/pipelines/__init__.py

@@ -0,0 +1 @@
+from mosamatic2.core.pipelines.defaultpipeline.defaultpipeline import DefaultPipeline

{mosamatic2-2.0.6 → mosamatic2-2.0.8}/src/mosamatic2/core/tasks/__init__.py

@@ -3,4 +3,5 @@ from mosamatic2.core.tasks.segmentmusclefatl3tensorflowtask.segmentmusclefatl3te
 from mosamatic2.core.tasks.calculatescorestask.calculatescorestask import CalculateScoresTask
 from mosamatic2.core.tasks.createpngsfromsegmentationstask.createpngsfromsegmentationstask import CreatePngsFromSegmentationsTask
 from mosamatic2.core.tasks.dicom2niftitask.dicom2niftitask import Dicom2NiftiTask
-from mosamatic2.core.tasks.selectslicefromscanstask.selectslicefromscanstask import SelectSliceFromScansTask
+from mosamatic2.core.tasks.selectslicefromscanstask.selectslicefromscanstask import SelectSliceFromScansTask
+from mosamatic2.core.tasks.createdicomsummarytask.createdicomsummarytask import CreateDicomSummaryTask

mosamatic2-2.0.8/src/mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py

@@ -0,0 +1,60 @@
+import os
+import json
+from mosamatic2.core.tasks.task import Task
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.core.utils import is_dicom, load_dicom
+
+LOG = LogManager()
+
+
+class CreateDicomSummaryTask(Task):
+    INPUTS = ['directory']
+    PARAMS = []
+
+    def __init__(self, inputs, params, output, overwrite):
+        super(CreateDicomSummaryTask, self).__init__(inputs, params, output, overwrite)
+
+    def run(self):
+        nr_steps = len(os.listdir(self.input('directory'))) * 2
+        LOG.info('Collecting data...')
+        data = {}
+        step = 0
+        for patient_dir_name in os.listdir(self.input('directory')):
+            data[patient_dir_name] = {}
+            patient_dir_path = os.path.join(self.input('directory'), patient_dir_name)
+            for root, dirs, files in os.walk(patient_dir_path):
+                for f in files:
+                    f_path = os.path.join(root, f)
+                    if is_dicom(f_path):
+                        p = load_dicom(f_path, stop_before_pixels=True)
+                        series_instance_uid = p.SeriesInstanceUID
+                        if not series_instance_uid in data[patient_dir_name].keys():
+                            data[patient_dir_name][series_instance_uid] = []
+                        data[patient_dir_name][series_instance_uid].append(p)
+            self.set_progress(step, nr_steps)
+            step += 1
+        LOG.info('Building summary...')
+        summary = {
+            'nr_series_per_patient': {},
+        }
+        # Calculate nr. of series per patient
+        for patient_dir_name in data.keys():
+            summary['nr_series_per_patient'][patient_dir_name] = len(data[patient_dir_name].keys())
+        # Summarize series data per patient
+        for patient_dir_name in data.keys():
+            summary[patient_dir_name] = {}
+            for series_instance_uid in data[patient_dir_name].keys():
+                summary[patient_dir_name][series_instance_uid] = {
+                    'nr_images': len(data[patient_dir_name][series_instance_uid]),
+                    'modality': data[patient_dir_name][series_instance_uid][0].Modality,
+                    'image_type': str(data[patient_dir_name][series_instance_uid][0].ImageType),
+                    'rows': data[patient_dir_name][series_instance_uid][0].Rows,
+                    'columns': data[patient_dir_name][series_instance_uid][0].Columns,
+                    'pixel_spacing': str(data[patient_dir_name][series_instance_uid][0].PixelSpacing),
+                    'slice_thickness': data[patient_dir_name][series_instance_uid][0].SliceThickness,
+                }
+            self.set_progress(step, nr_steps)
+            step += 1
+        LOG.info('Exporting summary...')
+        with open(os.path.join(self.output(), 'summary.txt'), 'w') as f:
+            json.dump(summary, f, indent=4)

{mosamatic2-2.0.6 → mosamatic2-2.0.8}/src/mosamatic2/server.py

@@ -7,6 +7,7 @@ from mosamatic2.core.tasks import CalculateScoresTask
 from mosamatic2.core.tasks import CreatePngsFromSegmentationsTask
 from mosamatic2.core.tasks import Dicom2NiftiTask
 from mosamatic2.core.tasks import SelectSliceFromScansTask
+from mosamatic2.core.tasks import CreateDicomSummaryTask
 
 app = Flask(__name__)
 
@@ -122,6 +123,21 @@ def run_selectslicefromscans():
     return 'PASSED'
 
 
+@app.route('/createdicomsummary')
+def run_createdicomsummary():
+    directory = request.args.get('directory')
+    output = request.args.get('output')
+    overwrite = request.args.get('overwrite', default=True, type=bool)
+    task = CreateDicomSummaryTask(
+        inputs={'directory': directory},
+        params=None,
+        output=output,
+        overwrite=overwrite,
+    )
+    task.run()
+    return 'PASSED'
+
+
 def main():
     parser = argparse.ArgumentParser()
     parser.add_argument('--port', type=int, default=constants.MOSAMATIC2_SERVER_PORT)

{mosamatic2-2.0.6 → mosamatic2-2.0.8}/src/mosamatic2/ui/mainwindow.py

@@ -19,6 +19,7 @@ from mosamatic2.ui.widgets.panels.tasks.segmentmusclefatl3tensorflowtaskpanel im
 from mosamatic2.ui.widgets.panels.tasks.createpngsfromsegmentationstaskpanel import CreatePngsFromSegmentationsTaskPanel
 from mosamatic2.ui.widgets.panels.tasks.calculatescorestaskpanel import CalculateScoresTaskPanel
 from mosamatic2.ui.widgets.panels.tasks.dicom2niftitaskpanel import Dicom2NiftiTaskPanel
+from mosamatic2.ui.widgets.panels.tasks.createdicomsummarytaskpanel import CreateDicomSummaryTaskPanel
 from mosamatic2.ui.widgets.panels.tasks.selectslicefromscanstaskpanel import SelectSliceFromScansTaskPanel
 from mosamatic2.ui.widgets.panels.pipelines.defaultpipelinepanel import DefaultPipelinePanel
 from mosamatic2.ui.widgets.panels.visualizations.slicevisualization.slicevisualization import SliceVisualization
@@ -38,6 +39,7 @@ class MainWindow(QMainWindow):
         self._create_pngs_from_segmentations_task_panel = None
         self._calculate_scores_task_panel = None
         self._dicom2nifti_task_panel = None
+        self._create_dicom_summary_task_panel = None
         self._select_slice_from_scans_task_panel = None
         self._default_pipeline_panel = None
         self._slice_visualization = None
@@ -80,6 +82,8 @@ class MainWindow(QMainWindow):
         create_pngs_from_segmentations_task_action.triggered.connect(self.handle_create_pngs_from_segmentations_task_action)
         dicom2nifti_task_action = QAction('Dicom2NiftiTask', self)
         dicom2nifti_task_action.triggered.connect(self.handle_dicom2nifti_task_action)
+        create_dicom_summary_task_action = QAction('CreateDicomSummaryTask', self)
+        create_dicom_summary_task_action.triggered.connect(self.handle_create_dicom_summary_task_action)
         select_slice_from_scans_task_action = QAction('SelectSliceFromScansTask', self)
         select_slice_from_scans_task_action.triggered.connect(self.handle_select_slice_from_scans_task_action)
         tasks_menu = self.menuBar().addMenu('Tasks')
@@ -88,6 +92,7 @@ class MainWindow(QMainWindow):
         tasks_menu.addAction(calculate_scores_task_action)
         tasks_menu.addAction(create_pngs_from_segmentations_task_action)
         tasks_menu.addAction(dicom2nifti_task_action)
+        tasks_menu.addAction(create_dicom_summary_task_action)
         tasks_menu.addAction(select_slice_from_scans_task_action)
 
     def init_pipelines_menu(self):
@@ -120,6 +125,7 @@ class MainWindow(QMainWindow):
             self._main_panel.add_panel(self.create_pngs_from_segmentations_task_panel(), 'createpngsfromsegmentationstaskpanel')
             self._main_panel.add_panel(self.calculate_scores_task_panel(), 'calculatescorestaskpanel')
             self._main_panel.add_panel(self.dicom2nifti_task_panel(), 'dicom2niftitaskpanel')
+            self._main_panel.add_panel(self.create_dicom_summary_task_panel(), 'createdicomsummarytaskpanel')
             self._main_panel.add_panel(self.select_slice_from_scans_task_panel(), 'selectslicefromscanstaskpanel')
             self._main_panel.add_panel(self.default_pipeline_panel(), 'defaultpipelinepanel')
             self._main_panel.add_panel(self.slice_visualization(), 'slicevisualization')
@@ -158,6 +164,11 @@ class MainWindow(QMainWindow):
         if not self._dicom2nifti_task_panel:
             self._dicom2nifti_task_panel = Dicom2NiftiTaskPanel()
         return self._dicom2nifti_task_panel
+    
+    def create_dicom_summary_task_panel(self):
+        if not self._create_dicom_summary_task_panel:
+            self._create_dicom_summary_task_panel = CreateDicomSummaryTaskPanel()
+        return self._create_dicom_summary_task_panel
 
     def select_slice_from_scans_task_panel(self):
         if not self._select_slice_from_scans_task_panel:
@@ -196,6 +207,9 @@ class MainWindow(QMainWindow):
     def handle_dicom2nifti_task_action(self):
         self.main_panel().select_panel('dicom2niftitaskpanel')
 
+    def handle_create_dicom_summary_task_action(self):
+        self.main_panel().select_panel('createdicomsummarytaskpanel')
+
     def handle_select_slice_from_scans_task_action(self):
         self.main_panel().select_panel('selectslicefromscanstaskpanel')
 
@@ -216,6 +230,7 @@ class MainWindow(QMainWindow):
         self.create_pngs_from_segmentations_task_panel().save_inputs_and_parameters()
         self.calculate_scores_task_panel().save_inputs_and_parameters()
         self.dicom2nifti_task_panel().save_inputs_and_parameters()
+        self.create_dicom_summary_task_panel().save_inputs_and_parameters()
         self.select_slice_from_scans_task_panel().save_inputs_and_parameters()
         self.default_pipeline_panel().save_inputs_and_parameters()
         self.slice_visualization().save_inputs_and_parameters()

mosamatic2-2.0.8/src/mosamatic2/ui/resources/VERSION

@@ -0,0 +1 @@
+2.0.8 

mosamatic2-2.0.8/src/mosamatic2/ui/widgets/panels/tasks/createdicomsummarytaskpanel.py

@@ -0,0 +1,183 @@
+import os
+
+from PySide6.QtWidgets import (
+    QLineEdit,
+    QCheckBox,
+    QSpinBox,
+    QHBoxLayout,
+    QVBoxLayout,
+    QFormLayout,
+    QPushButton,
+    QFileDialog,
+    QMessageBox,
+)
+from PySide6.QtCore import (
+    QThread, 
+    Slot,
+)
+
+from mosamatic2.core.managers.logmanager import LogManager
+from mosamatic2.ui.widgets.panels.tasks.taskpanel import TaskPanel
+from mosamatic2.ui.settings import Settings
+from mosamatic2.ui.utils import is_macos
+from mosamatic2.ui.worker import Worker
+from mosamatic2.core.tasks import CreateDicomSummaryTask
+
+LOG = LogManager()
+
+PANEL_TITLE = 'CreateDicomSummaryTaskPanel'
+PANEL_NAME = 'createdicomsummarytaskpanel'
+
+
+class CreateDicomSummaryTaskPanel(TaskPanel):
+    def __init__(self):
+        super(CreateDicomSummaryTaskPanel, self).__init__()
+        self.set_title(PANEL_TITLE)
+        self._images_dir_line_edit = None
+        self._images_dir_select_button = None
+        self._output_dir_line_edit = None
+        self._output_dir_select_button = None
+        self._overwrite_checkbox = None
+        self._form_layout = None
+        self._run_task_button = None
+        self._settings = None
+        self._task = None
+        self._worker = None
+        self._thread = None
+        self.init_layout()
+
+    def images_dir_line_edit(self):
+        if not self._images_dir_line_edit:
+            self._images_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/images_dir'))
+        return self._images_dir_line_edit
+    
+    def images_dir_select_button(self):
+        if not self._images_dir_select_button:
+            self._images_dir_select_button = QPushButton('Select')
+            self._images_dir_select_button.clicked.connect(self.handle_images_dir_select_button)
+        return self._images_dir_select_button
+    
+    def output_dir_line_edit(self):
+        if not self._output_dir_line_edit:
+            self._output_dir_line_edit = QLineEdit(self.settings().get(f'{PANEL_NAME}/output_dir'))
+        return self._output_dir_line_edit
+    
+    def output_dir_select_button(self):
+        if not self._output_dir_select_button:
+            self._output_dir_select_button = QPushButton('Select')
+            self._output_dir_select_button.clicked.connect(self.handle_output_dir_select_button)
+        return self._output_dir_select_button
+    
+    def overwrite_checkbox(self):
+        if not self._overwrite_checkbox:
+            self._overwrite_checkbox = QCheckBox('')
+            self._overwrite_checkbox.setChecked(self.settings().get_bool(f'{PANEL_NAME}/overwrite', True))
+        return self._overwrite_checkbox
+    
+    def form_layout(self):
+        if not self._form_layout:
+            self._form_layout = QFormLayout()
+            if is_macos():
+                self._form_layout.setFieldGrowthPolicy(QFormLayout.ExpandingFieldsGrow)
+        return self._form_layout
+    
+    def run_task_button(self):
+        if not self._run_task_button:
+            self._run_task_button = QPushButton('Run task')
+            self._run_task_button.clicked.connect(self.handle_run_task_button)
+        return self._run_task_button
+    
+    def settings(self):
+        if not self._settings:
+            self._settings = Settings()
+        return self._settings
+    
+    def init_layout(self):
+        images_dir_layout = QHBoxLayout()
+        images_dir_layout.addWidget(self.images_dir_line_edit())
+        images_dir_layout.addWidget(self.images_dir_select_button())
+        output_dir_layout = QHBoxLayout()
+        output_dir_layout.addWidget(self.output_dir_line_edit())
+        output_dir_layout.addWidget(self.output_dir_select_button())
+        self.form_layout().addRow('Images directory', images_dir_layout)
+        self.form_layout().addRow('Output directory', output_dir_layout)
+        self.form_layout().addRow('Overwrite', self.overwrite_checkbox())
+        layout = QVBoxLayout()
+        layout.addLayout(self.form_layout())
+        layout.addWidget(self.run_task_button())
+        self.setLayout(layout)
+        self.setObjectName(PANEL_NAME)
+
+    def handle_images_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.images_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_output_dir_select_button(self):
+        last_directory = self.settings().get('last_directory')
+        directory = QFileDialog.getExistingDirectory(dir=last_directory)
+        if directory:
+            self.output_dir_line_edit().setText(directory)
+            self.settings().set('last_directory', directory)
+
+    def handle_run_task_button(self):
+        errors = self.check_inputs_and_parameters()
+        if len(errors) > 0:
+            error_message = 'Following errors were encountered:\n'
+            for error in errors:
+                error_message += f' - {error}\n'
+            QMessageBox.information(self, 'Error', error_message)
+        else:
+            LOG.info('Running task...')
+            self.run_task_button().setEnabled(False)
+            self.save_inputs_and_parameters()
+            self._task = CreateDicomSummaryTask(
+                inputs={'directory': self.images_dir_line_edit().text()},
+                params=None,
+                output=self.output_dir_line_edit().text(),
+                overwrite=self.overwrite_checkbox().isChecked(),
+            )
+            self._worker = Worker(self._task)
+            self._thread = QThread()
+            self._worker.moveToThread(self._thread)
+            self._thread.started.connect(self._worker.run)
+            self._worker.progress.connect(self.handle_progress)
+            self._worker.status.connect(self.handle_status)
+            self._worker.finished.connect(self.handle_finished)
+            self._worker.finished.connect(self._thread.quit)
+            self._worker.finished.connect(self._worker.deleteLater)
+            self._thread.finished.connect(self._thread.deleteLater)
+            self._thread.start()
+
+    @Slot(int)
+    def handle_progress(self, progress):
+        LOG.info(f'Progress: {progress} / 100%')
+
+    @Slot(str)
+    def handle_status(self, status):
+        LOG.info(f'Status: {status}')
+
+    @Slot()
+    def handle_finished(self):
+        self.run_task_button().setEnabled(True)
+
+    # HELPERS
+
+    def check_inputs_and_parameters(self):
+        errors = []
+        if self.images_dir_line_edit().text() == '':
+            errors.append('Empty images directory path')
+        if not os.path.isdir(self.images_dir_line_edit().text()):
+            errors.append('Images directory does not exist')
+        if self.output_dir_line_edit().text() == '':
+            errors.append('Empty output directory path')
+        if os.path.isdir(self.output_dir_line_edit().text()) and not self.overwrite_checkbox().isChecked():
+            errors.append('Output directory exists but overwrite=False. Please remove output directory first')
+        return errors
+    
+    def save_inputs_and_parameters(self):
+        self.settings().set(f'{PANEL_NAME}/images_dir', self.images_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/output_dir', self.output_dir_line_edit().text())
+        self.settings().set(f'{PANEL_NAME}/overwrite', self.overwrite_checkbox().isChecked())

mosamatic2-2.0.6/src/mosamatic2/core/pipelines/__init__.py

@@ -1 +0,0 @@
-from mosamatic2.core.pipelines.defaultpipeline import DefaultPipeline

mosamatic2-2.0.6/src/mosamatic2/ui/resources/VERSION

@@ -1 +0,0 @@
-2.0.6