Diffusion MITK 9dc1b99b0cb7

Segment Anything Tool
9dc1b99b0cb7
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Description

Segment Anything Tool

Summary: SAM tool UI & backend code changes including modifications to SegWithPreviewTool class

Test Plan: Coming Soon

Reviewers: floca, kislinsk, O1 MITK Reviewer Group I

Reviewed By: floca, O1 MITK Reviewer Group I

Maniphest Tasks: T29604, T30153

Differential Revision: https://phabricator.mitk.org/D847

Details

Provenance

a178n	Authored on Oct 13 2023, 2:13 PM
a178n	Pushed on Oct 13 2023, 3:41 PM

Reviewer

O1: MITK Reviewer Group I

Differential Revision

Restricted Differential Revision

Parents

rMITKebc6c339724f: Merge branch 'develop' into feature/T29604-sam-tool-2
rMITKa10a1c236d4d: Remove numeric PK models.

Branches

Unknown

Tags

Unknown

Tasks

T29604: SAM as 2D Tool in MITK- iteration 2
T30153: SAM tool: Add caching support for Cross-hair rotated image views

Event Timeline

a178n committed rMITK9dc1b99b0cb7: Segment Anything Tool (authored by a178n).Oct 13 2023, 3:41 PM

a178n added tasks: T30153: SAM tool: Add caching support for Cross-hair rotated image views, T29604: SAM as 2D Tool in MITK- iteration 2.

a178n added an edge: Restricted Differential Revision.

kislinsk mentioned this in T30248: 2023 Week 46 (Mid November).Nov 13 2023, 4:23 PM

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

ebc6c339724f Merge branch 'develop' into feature/T29604-sam-tool-2
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a178n
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fda96a0189cd Adding locale switch to writer for consistency
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a178n
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3b69a0ef5732 Changing SAM runner git url
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a178n
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7bb192083536 Update itkTypeMacro
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a178n
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4ff22142545d Improve documentation and null check
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a178n
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72504a2fc713 Code cleanup
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a178n
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a3c9484bce54 SAM tool will now reinit after timed out
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a178n
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3b1b4dfa6d88 SAM tool: Introducing timeout for python process comms
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a178n
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ce918dfa2126 Merge branch 'develop' into feature/T29604-sam-tool-2
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a178n
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0b574ff4f211 Avoid deep copy from ITK window filter to MITK image in SAM tool
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a178n
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3245b3ca6b90 SAM tool Code refactoring changes
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a178n
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10f6ed0de3f5 2D RGB image bugfix in SAM tool
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a178n
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328bd55da9d2 Ubuntu build fixes
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a178n
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d2b0b156bc2e Adding optimized ITK-based file writer for SAM tool
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a178n
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e831e8c5a6fe Levelwindowfilter now applied to images for SAM tool
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a178n
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943c448c1353 SAM tool: Update hash logic for robustness
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a178n
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678147e40e8a SAM tool now fully support cross hair rotated images : Hashing logic change
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a178n
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35cb316d276b SAM tool Minor code changes
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a178n
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7c87988922d4 Merge branch 'develop' into feature/T29604-sam-tool-2
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a178n
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6efa5580b99e Bugfix: SAM preference gpu box won't be white anymore
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a178n
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e9343bbcfc5a SAM tool won't download models anymore. Qt5 Network dependency removed
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a178n
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5178ed355957 Minor code update for Ubuntu build
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a178n
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ffb81898d5af Tool API Bugfix: Seg tools in 2D mode can confirm on arbitrary steps correctly
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a178n
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8ce0afe14a46 Adding support for 2D images
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a178n
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e299172911b1 SAM Tool: Better UX changes
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a178n
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9709514e5e0c Force install pytorch v2.0.0 and torchvision 0.15
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a178n
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504cc0a24aad SAM tool won't show pop when no GPU was found
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a178n
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eaa8b7302816 SAMtool: Rename "Activate" to "Initialize"
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a178n
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cc4ae71813c2 Linux/Mac build fixes
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a178n
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370d9a358960 Better GPU vs CPU UX with redundancy for SAM tool
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a178n
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1d993a6c0303 SAM tool now supports CPU inferencing
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a178n
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e1e2e3914c25 Adding Preference change listener to SAM tool
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b5659e85568a SAM tool will now use nrrd file for python interaction.
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a178n
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04cce0bac84d Rename SAM to Segment Anything
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a178n
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805eecf6a32e Confirm segmentation works now
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a178n
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b5aea9d23a3d SegWithPreviewTool feature update: Adding ConfirmCleanUp virtual function to…
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a178n
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36ed77ecfe00 Add doc strings for SAM tool functions
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a178n
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a43bc92e2885 SAM tool Code clean up
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a178n
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cbe41a9e63b4 SAM tool: code updates for better status update on UI
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511cbe2c3947 SAM tool Ubuntu build fixes
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fde7c40a6029 Move SAM tool Preferences to dedicated UI page
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28d42b2f66d4 Update Install: SAM wrapper can be now pip installed
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f17b28a70fa1 SAM Tool: Minor code cleanup
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9c581076d539 Adding live status messages from tool class to GUI
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c82bcb145830 Adding SAM model selection tip for users
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4e7bc874a68d GPU name parsing bugfix
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198eb50374b6 Moving GPU selection into MITK Preferences from SAM tool UI
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eb253d085c61 SAM tool can now handle cuda out of memory situation and throw error message
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34a7d3b3077e Code cleanup: Installer & model selection not part of SAM GUI anymore
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6e78a214df0d SAM Python class code refactoring
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Changes (23)

Path

Size

Packages

Modules/

Segmentation/

Interactions/

mitkProcessExecutor.h

O1: MITK Reviewer Group I

mitkSegWithPreviewTool.cpp

O1: MITK Reviewer Group I

mitkSegWithPreviewTool.h

O1: MITK Reviewer Group I

mitkSegmentAnythingProcessExecutor.cpp

O1: MITK Reviewer Group I

mitkSegmentAnythingProcessExecutor.h

O1: MITK Reviewer Group I

mitkSegmentAnythingPythonService.cpp

O1: MITK Reviewer Group I

mitkSegmentAnythingPythonService.h

O1: MITK Reviewer Group I

mitkSegmentAnythingTool.cpp

O1: MITK Reviewer Group I

mitkSegmentAnythingTool.h

O1: MITK Reviewer Group I

files.cmake

O1: MITK Reviewer Group I

SegmentationUI/

Qmitk/

QmitkSegmentAnythingGUIControls.ui

O1: MITK Reviewer Group I

QmitkSegmentAnythingToolGUI.cpp

O1: MITK Reviewer Group I

QmitkSegmentAnythingToolGUI.h

O1: MITK Reviewer Group I

QmitkSetupVirtualEnvUtil.cpp

O1: MITK Reviewer Group I

QmitknnUNetGPU.cpp

O1: MITK Reviewer Group I

files.cmake

O1: MITK Reviewer Group I

Plugins/

org.mitk.gui.qt.segmentation/

files.cmake

O1: MITK Reviewer Group I

plugin.xml

O1: MITK Reviewer Group I

src/

QmitkSegmentAnythingPreferencePage.cpp

O1: MITK Reviewer Group I

QmitkSegmentAnythingPreferencePage.h

O1: MITK Reviewer Group I

QmitkSegmentAnythingPreferencePage.ui

O1: MITK Reviewer Group I

internal/

QmitkSegmentationView.cpp

O1: MITK Reviewer Group I

mitkPluginActivator.cpp

O1: MITK Reviewer Group I

rMITK9dc1b99b0cb7

View Options

Modules/Segmentation/Interactions/mitkProcessExecutor.h

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Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp

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Modules/Segmentation/Interactions/mitkSegWithPreviewTool.h

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Modules/Segmentation/Interactions/mitkSegmentAnythingProcessExecutor.cpp

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Modules/Segmentation/Interactions/mitkSegmentAnythingProcessExecutor.h

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Modules/Segmentation/Interactions/mitkSegmentAnythingPythonService.cpp

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Modules/Segmentation/Interactions/mitkSegmentAnythingPythonService.h

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Modules/Segmentation/Interactions/mitkSegmentAnythingTool.cpp

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Modules/Segmentation/Interactions/mitkSegmentAnythingTool.h

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Modules/Segmentation/files.cmake

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Modules/SegmentationUI/Qmitk/QmitkSegmentAnythingGUIControls.ui

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Modules/SegmentationUI/Qmitk/QmitkSegmentAnythingToolGUI.cpp

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Modules/SegmentationUI/Qmitk/QmitkSegmentAnythingToolGUI.h

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Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp

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Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp

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Modules/SegmentationUI/files.cmake

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Plugins/org.mitk.gui.qt.segmentation/files.cmake

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Plugins/org.mitk.gui.qt.segmentation/plugin.xml

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Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.cpp

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Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.h

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Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.ui

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Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp

View Options

Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp

Segment Anything Tool9dc1b99b0cb7Actions

Description

Details

Event Timeline

Merged Changes

Changes (23)

rMITK9dc1b99b0cb7

Modules/Segmentation/Interactions/mitkProcessExecutor.h

Modules/Segmentation/Interactions/mitkSegWithPreviewTool.cpp

Modules/Segmentation/Interactions/mitkSegWithPreviewTool.h

Modules/Segmentation/Interactions/mitkSegmentAnythingProcessExecutor.cpp

Modules/Segmentation/Interactions/mitkSegmentAnythingProcessExecutor.h

Modules/Segmentation/Interactions/mitkSegmentAnythingPythonService.cpp

Modules/Segmentation/Interactions/mitkSegmentAnythingPythonService.h

Modules/Segmentation/Interactions/mitkSegmentAnythingTool.cpp

Modules/Segmentation/Interactions/mitkSegmentAnythingTool.h

Modules/Segmentation/files.cmake

Modules/SegmentationUI/Qmitk/QmitkSegmentAnythingGUIControls.ui

Modules/SegmentationUI/Qmitk/QmitkSegmentAnythingToolGUI.cpp

Modules/SegmentationUI/Qmitk/QmitkSegmentAnythingToolGUI.h

Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp

Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp

Modules/SegmentationUI/files.cmake

Plugins/org.mitk.gui.qt.segmentation/files.cmake

Plugins/org.mitk.gui.qt.segmentation/plugin.xml

Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.cpp

Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.h

Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentAnythingPreferencePage.ui

Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp

Plugins/org.mitk.gui.qt.segmentation/src/internal/mitkPluginActivator.cpp

Segment Anything Tool
9dc1b99b0cb7
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