README.md
pyproject.toml
src/models.py
src/experiments/boamosamatic/buildfilemapping.py
src/experiments/boamosamatic/collectscansandcreateniftis.py
src/experiments/boamosamatic/constants.py
src/experiments/boamosamatic/findl3sforniftis.py
src/experiments/boamosamatic/generatecountsandtimings.py
src/experiments/boamosamatic/utils.py
src/experiments/boamosamatic/old/main.py
src/experiments/boamosamatic/old/utils.py
src/experiments/cocosmit/main.py
src/experiments/contrastsensitivity/lieke/analysis.py
src/experiments/contrastsensitivity/lieke/datapreparation.py
src/experiments/contrastsensitivity/lisa/selectphases.py
src/experiments/copyporschtosandisk/main.py
src/experiments/copyporschtosandisk/utils.py
src/experiments/coronal2axial/coronal2axial.py
src/experiments/dicomdirscan/dicomdirscan.py
src/experiments/dicomseriesfinder/main.py
src/experiments/dockerrunning/main.py
src/experiments/l1tol5analysis/main.py
src/experiments/lauracools/removedotsfromfilenames.py
src/experiments/lauracools/unzipscans.py
src/experiments/lisa/main.py
src/experiments/liversegments3dslicer/main.py
src/experiments/meanvsmedianliver/main.py
src/experiments/moose/main.py
src/experiments/palga/main.py
src/experiments/prepareumcgnicole/copyscansok.py
src/experiments/prepareumcgnicole/main.py
src/experiments/pyside6matplotlib/main.py
src/experiments/pytorcht4/example_pipeline.py
src/experiments/pytorcht4/example_pipeline_l3.py
src/experiments/pytorcht4/example_pipeline_remove_vat.py
src/experiments/pytorcht4/models.py
src/experiments/pytorcht4/param_loader.py
src/experiments/segmentationviewer/__init__.py
src/experiments/segmentationviewer/main.py
src/experiments/segmentationviewer/mainwindow.py
src/experiments/segmentationviewer/widgets/__init__.py
src/experiments/segmentationviewer/widgets/matplotlibcanvas.py
src/experiments/totalsegmentator/totalsegmentator.py
src/experiments/totalsegmentatordixon/totalsegmentatordixon.py
src/experiments/totalsegmentatorgpu/main.py
src/experiments/vtk/liversegments.py
src/experiments/vtk/niftisliceviewer.py
src/experiments/vtk/pyqtgraphbarchart.py
src/experiments/vtk/vtkcone.py
src/experiments/vtk/vtkinfovis.py
src/experiments/vtk/vtkviewports.py
src/experiments/vtkclipping/main.py
src/experiments/vtkmyosteatosis/main.py
src/experiments/vtkmyosteatosis/mainmyosteatosis.py
src/experiments/vtkmyosteatosis/mainnumpy.py
src/experiments/vtksegmentationviewer/main.py
src/experiments/webdavmdr/main.py
src/mosamatic2/__init__.py
src/mosamatic2/app.py
src/mosamatic2/cli.py
src/mosamatic2/constants.py
src/mosamatic2/server.py
src/mosamatic2.egg-info/PKG-INFO
src/mosamatic2.egg-info/SOURCES.txt
src/mosamatic2.egg-info/dependency_links.txt
src/mosamatic2.egg-info/entry_points.txt
src/mosamatic2.egg-info/requires.txt
src/mosamatic2.egg-info/top_level.txt
src/mosamatic2/commands/__init__.py
src/mosamatic2/commands/boadockerpipeline.py
src/mosamatic2/commands/calculatemaskstatistics.py
src/mosamatic2/commands/calculatescores.py
src/mosamatic2/commands/createdicomsummary.py
src/mosamatic2/commands/createpngsfromsegmentations.py
src/mosamatic2/commands/defaultdockerpipeline.py
src/mosamatic2/commands/defaultpipeline.py
src/mosamatic2/commands/dicom2nifti.py
src/mosamatic2/commands/liveranalysispipeline.py
src/mosamatic2/commands/rescaledicomimages.py
src/mosamatic2/commands/segmentmusclefatl3tensorflow.py
src/mosamatic2/commands/selectslicefromscans.py
src/mosamatic2/commands/totalsegmentator.py
src/mosamatic2/core/__init__.py
src/mosamatic2/core/singleton.py
src/mosamatic2/core/utils.py
src/mosamatic2/core/data/__init__.py
src/mosamatic2/core/data/dicomimage.py
src/mosamatic2/core/data/dicomimageseries.py
src/mosamatic2/core/data/dicomloader.py
src/mosamatic2/core/data/dixonseries.py
src/mosamatic2/core/data/filedata.py
src/mosamatic2/core/data/multidicomimage.py
src/mosamatic2/core/data/multiniftiimage.py
src/mosamatic2/core/data/multinumpyimage.py
src/mosamatic2/core/data/niftiimage.py
src/mosamatic2/core/data/numpyimage.py
src/mosamatic2/core/managers/__init__.py
src/mosamatic2/core/managers/logmanager.py
src/mosamatic2/core/managers/logmanagerlistener.py
src/mosamatic2/core/pipelines/__init__.py
src/mosamatic2/core/pipelines/pipeline.py
src/mosamatic2/core/pipelines/boadockerpipeline/__init__.py
src/mosamatic2/core/pipelines/boadockerpipeline/boadockerpipeline.py
src/mosamatic2/core/pipelines/defaultdockerpipeline/__init__.py
src/mosamatic2/core/pipelines/defaultdockerpipeline/defaultdockerpipeline.py
src/mosamatic2/core/pipelines/defaultpipeline/__init__.py
src/mosamatic2/core/pipelines/defaultpipeline/defaultpipeline.py
src/mosamatic2/core/pipelines/liveranalysispipeline/__init__.py
src/mosamatic2/core/pipelines/liveranalysispipeline/liveranalysispipeline.py
src/mosamatic2/core/tasks/__init__.py
src/mosamatic2/core/tasks/task.py
src/mosamatic2/core/tasks/applythresholdtosegmentationstask/__init__.py
src/mosamatic2/core/tasks/applythresholdtosegmentationstask/applythresholdtosegmentationstask.py
src/mosamatic2/core/tasks/calculatemaskstatisticstask/__init__.py
src/mosamatic2/core/tasks/calculatemaskstatisticstask/calculatemaskstatisticstask.py
src/mosamatic2/core/tasks/calculatescorestask/__init__.py
src/mosamatic2/core/tasks/calculatescorestask/calculatescorestask.py
src/mosamatic2/core/tasks/createdicomsummarytask/__init__.py
src/mosamatic2/core/tasks/createdicomsummarytask/createdicomsummarytask.py
src/mosamatic2/core/tasks/createpngsfromsegmentationstask/__init__.py
src/mosamatic2/core/tasks/createpngsfromsegmentationstask/createpngsfromsegmentationstask.py
src/mosamatic2/core/tasks/dicom2niftitask/__init__.py
src/mosamatic2/core/tasks/dicom2niftitask/dicom2niftitask.py
src/mosamatic2/core/tasks/rescaledicomimagestask/__init__.py
src/mosamatic2/core/tasks/rescaledicomimagestask/rescaledicomimagestask.py
src/mosamatic2/core/tasks/segmentationnifti2numpytask/__init__.py
src/mosamatic2/core/tasks/segmentationnifti2numpytask/segmentationnifti2numpytask.py
src/mosamatic2/core/tasks/segmentationnumpy2niftitask/__init__.py
src/mosamatic2/core/tasks/segmentationnumpy2niftitask/segmentationnumpy2niftitask.py
src/mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/__init__.py
src/mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/paramloader.py
src/mosamatic2/core/tasks/segmentmusclefatl3tensorflowtask/segmentmusclefatl3tensorflowtask.py
src/mosamatic2/core/tasks/segmentmusclefatt4pytorchtask/__init__.py
src/mosamatic2/core/tasks/segmentmusclefatt4pytorchtask/paramloader.py
src/mosamatic2/core/tasks/segmentmusclefatt4pytorchtask/segmentmusclefatt4pytorchtask.py
src/mosamatic2/core/tasks/selectslicefromscanstask/__init__.py
src/mosamatic2/core/tasks/selectslicefromscanstask/selectslicefromscanstask.py
src/mosamatic2/core/tasks/totalsegmentatortask/__init__.py
src/mosamatic2/core/tasks/totalsegmentatortask/totalsegmentatortask.py
src/mosamatic2/ui/__init__.py
src/mosamatic2/ui/mainwindow.py
src/mosamatic2/ui/settings.py
src/mosamatic2/ui/utils.py
src/mosamatic2/ui/worker.py
src/mosamatic2/ui/widgets/__init__.py
src/mosamatic2/ui/widgets/splashscreen.py
src/mosamatic2/ui/widgets/dialogs/__init__.py
src/mosamatic2/ui/widgets/dialogs/dialog.py
src/mosamatic2/ui/widgets/dialogs/helpdialog.py
src/mosamatic2/ui/widgets/panels/__init__.py
src/mosamatic2/ui/widgets/panels/defaultpanel.py
src/mosamatic2/ui/widgets/panels/logpanel.py
src/mosamatic2/ui/widgets/panels/mainpanel.py
src/mosamatic2/ui/widgets/panels/settingspanel.py
src/mosamatic2/ui/widgets/panels/stackedpanel.py
src/mosamatic2/ui/widgets/panels/pipelines/__init__.py
src/mosamatic2/ui/widgets/panels/pipelines/boadockerpipelinepanel.py
src/mosamatic2/ui/widgets/panels/pipelines/defaultdockerpipelinepanel.py
src/mosamatic2/ui/widgets/panels/pipelines/defaultpipelinepanel.py
src/mosamatic2/ui/widgets/panels/pipelines/liveranalysispipelinepanel.py
src/mosamatic2/ui/widgets/panels/pipelines/pipelinepanel.py
src/mosamatic2/ui/widgets/panels/tasks/__init__.py
src/mosamatic2/ui/widgets/panels/tasks/applythresholdtosegmentationstaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/calculatemaskstatisticstaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/calculatescorestaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/createdicomsummarytaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/createpngsfromsegmentationstaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/dicom2niftitaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/rescaledicomimagestaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/segmentationnifti2numpytaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/segmentationnumpy2niftitaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/segmentmusclefatl3tensorflowtaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/segmentmusclefatt4pytorchtaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/selectslicefromscanstaskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/taskpanel.py
src/mosamatic2/ui/widgets/panels/tasks/totalsegmentatortaskpanel.py
src/mosamatic2/ui/widgets/panels/tools/__init__.py
src/mosamatic2/ui/widgets/panels/tools/segmentationeditor/document.py
src/mosamatic2/ui/widgets/panels/tools/segmentationeditor/segmentationeditor.py
src/mosamatic2/ui/widgets/panels/tools/segmentationeditor/segmentationeditorcontrols.py
src/mosamatic2/ui/widgets/panels/tools/segmentationeditor/segmentationeditorgraphicsview.py
src/mosamatic2/ui/widgets/panels/tools/segmentationeditor/utils.py
src/mosamatic2/ui/widgets/panels/visualizations/__init__.py
src/mosamatic2/ui/widgets/panels/visualizations/visualization.py
src/mosamatic2/ui/widgets/panels/visualizations/liversegmentvisualization/__init__.py
src/mosamatic2/ui/widgets/panels/visualizations/liversegmentvisualization/liversegmentpicker.py
src/mosamatic2/ui/widgets/panels/visualizations/liversegmentvisualization/liversegmentviewer.py
src/mosamatic2/ui/widgets/panels/visualizations/liversegmentvisualization/liversegmentvisualization.py
src/mosamatic2/ui/widgets/panels/visualizations/musclefatsegmentationuncertaintyvisualization/__init__.py
src/mosamatic2/ui/widgets/panels/visualizations/musclefatsegmentationuncertaintyvisualization/musclefatsegmentationuncertaintyviewer.py
src/mosamatic2/ui/widgets/panels/visualizations/musclefatsegmentationuncertaintyvisualization/musclefatsegmentationuncertaintyvisualization.py
src/mosamatic2/ui/widgets/panels/visualizations/musclefatsegmentationvisualization/__init__.py
src/mosamatic2/ui/widgets/panels/visualizations/musclefatsegmentationvisualization/musclefatsegmentationviewer.py
src/mosamatic2/ui/widgets/panels/visualizations/musclefatsegmentationvisualization/musclefatsegmentationvisualization.py
src/mosamatic2/ui/widgets/panels/visualizations/sliceselectionvisualization/__init__.py
src/mosamatic2/ui/widgets/panels/visualizations/sliceselectionvisualization/sliceselectionviewer.py
src/mosamatic2/ui/widgets/panels/visualizations/sliceselectionvisualization/sliceselectionvisualization.py
src/mosamatic2/ui/widgets/panels/visualizations/sliceselectionvisualization/slicetile.py
src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/__init__.py
src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/custominteractorstyle.py
src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/sliceviewer.py
src/mosamatic2/ui/widgets/panels/visualizations/slicevisualization/slicevisualization.py