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SAM as 2D Tool in MITK- iteration 2
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Description

Next iteration of SAM as 2D Tool in MITK with new UI and python process daemon style backend

Revisions and Commits

rMITK MITK
Restricted Differential RevisionrMITK2fa4cdc39820 SAM backend changes backup
Restricted Differential RevisionrMITK3a66df9945a1 Segment Anything Tool initial commit
Restricted Differential RevisionrMITK64e4a8ca7634 SAM tool UI & backend code changes
Restricted Differential RevisionrMITKc2b3be9dd1be Negative clicks Ahoy!
Restricted Differential RevisionrMITK0a67fe3839d8 Merge branch 'develop' into feature/T29540-sam-2d-tool
Restricted Differential RevisionrMITKd00fc49ec8cd Adding checks to avoid clicks outside image
Restricted Differential RevisionrMITKdf6fef94a552 Merge branch 'develop' into feature/T29540-sam-2d-tool
Restricted Differential RevisionrMITKb2d37df9a7e2 code update with time measurement
Restricted Differential RevisionrMITKebb06baa6b5c SAM tool with daemon working changes
Restricted Differential RevisionrMITKe4f53fdcc0c1 Merge branch 'master' into feature/T29604-sam-tool-2
Restricted Differential RevisionrMITKbf99b967ae7a SAM tool working changes
Restricted Differential RevisionrMITK4948dba75162 SAM installer working changes
Restricted Differential RevisionrMITK6365abecbbf7 Changing click point shape to filled CIRCLE
Restricted Differential RevisionrMITKbdb8197e2a24 Remove Interactive vs Auto radiobutton selection
Restricted Differential RevisionrMITK3cdacd7db9b1 Migrating python related functionalities to dedicated class
Restricted Differential RevisionrMITKe7a8aa8351fe Migrating SAM tool install options into Pref menu: part changes
Restricted Differential RevisionrMITK6e78a214df0d SAM Python class code refactoring
Restricted Differential RevisionrMITK34a7d3b3077e Code cleanup: Installer & model selection not part of SAM GUI anymore
Restricted Differential RevisionrMITKeb253d085c61 SAM tool can now handle cuda out of memory situation and throw error message
Restricted Differential RevisionrMITK198eb50374b6 Moving GPU selection into MITK Preferences from SAM tool UI
Restricted Differential RevisionrMITKc82bcb145830 Adding SAM model selection tip for users
Restricted Differential RevisionrMITK4e7bc874a68d GPU name parsing bugfix
Restricted Differential RevisionrMITKf17b28a70fa1 SAM Tool: Minor code cleanup
Restricted Differential RevisionrMITK9c581076d539 Adding live status messages from tool class to GUI
Restricted Differential RevisionrMITKfde7c40a6029 Move SAM tool Preferences to dedicated UI page
Restricted Differential RevisionrMITK28d42b2f66d4 Update Install: SAM wrapper can be now pip installed
Restricted Differential RevisionrMITK511cbe2c3947 SAM tool Ubuntu build fixes
Restricted Differential RevisionrMITKa43bc92e2885 SAM tool Code clean up
Restricted Differential RevisionrMITKcbe41a9e63b4 SAM tool: code updates for better status update on UI
Restricted Differential RevisionrMITKb5aea9d23a3d SegWithPreviewTool feature update: Adding ConfirmCleanUp virtual function to…
Restricted Differential RevisionrMITK36ed77ecfe00 Add doc strings for SAM tool functions
Restricted Differential RevisionrMITK805eecf6a32e Confirm segmentation works now
Restricted Differential RevisionrMITK04cce0bac84d Rename SAM to Segment Anything
Restricted Differential RevisionrMITKb5659e85568a SAM tool will now use nrrd file for python interaction.
Restricted Differential RevisionrMITKe1e2e3914c25 Adding Preference change listener to SAM tool
Restricted Differential RevisionrMITK1d993a6c0303 SAM tool now supports CPU inferencing
Restricted Differential RevisionrMITK370d9a358960 Better GPU vs CPU UX with redundancy for SAM tool
Restricted Differential RevisionrMITKeaa8b7302816 SAMtool: Rename "Activate" to "Initialize"
Audit RequiredRestricted Differential RevisionrMITKcc4ae71813c2 Linux/Mac build fixes
Restricted Differential RevisionrMITK504cc0a24aad SAM tool won't show pop when no GPU was found
Restricted Differential RevisionrMITK9709514e5e0c Force install pytorch v2.0.0 and torchvision 0.15
Restricted Differential RevisionrMITKe299172911b1 SAM Tool: Better UX changes
Restricted Differential RevisionrMITK8ce0afe14a46 Adding support for 2D images
Restricted Differential RevisionrMITKffb81898d5af Tool API Bugfix: Seg tools in 2D mode can confirm on arbitrary steps correctly
Restricted Differential RevisionrMITK5178ed355957 Minor code update for Ubuntu build
Restricted Differential RevisionrMITKe9343bbcfc5a SAM tool won't download models anymore. Qt5 Network dependency removed
Restricted Differential RevisionrMITK6efa5580b99e Bugfix: SAM preference gpu box won't be white anymore
Restricted Differential RevisionrMITK7c87988922d4 Merge branch 'develop' into feature/T29604-sam-tool-2
Restricted Differential RevisionrMITK35cb316d276b SAM tool Minor code changes
Restricted Differential RevisionrMITK678147e40e8a SAM tool now fully support cross hair rotated images : Hashing logic change
Restricted Differential RevisionrMITKe831e8c5a6fe Levelwindowfilter now applied to images for SAM tool
Restricted Differential RevisionrMITKd2b0b156bc2e Adding optimized ITK-based file writer for SAM tool
Restricted Differential RevisionrMITK943c448c1353 SAM tool: Update hash logic for robustness
Restricted Differential RevisionrMITK10f6ed0de3f5 2D RGB image bugfix in SAM tool
Restricted Differential RevisionrMITK328bd55da9d2 Ubuntu build fixes
Restricted Differential RevisionrMITK3245b3ca6b90 SAM tool Code refactoring changes
Restricted Differential RevisionrMITKce918dfa2126 Merge branch 'develop' into feature/T29604-sam-tool-2
Restricted Differential RevisionrMITK0b574ff4f211 Avoid deep copy from ITK window filter to MITK image in SAM tool
Restricted Differential RevisionrMITKa3c9484bce54 SAM tool will now reinit after timed out
Restricted Differential RevisionrMITK3b1b4dfa6d88 SAM tool: Introducing timeout for python process comms
Restricted Differential RevisionrMITK72504a2fc713 Code cleanup
Restricted Differential RevisionrMITK4ff22142545d Improve documentation and null check
Restricted Differential RevisionrMITK7bb192083536 Update itkTypeMacro
Restricted Differential RevisionrMITK3b69a0ef5732 Changing SAM runner git url
Restricted Differential RevisionrMITKfda96a0189cd Adding locale switch to writer for consistency
Restricted Differential RevisionrMITKebc6c339724f Merge branch 'develop' into feature/T29604-sam-tool-2
Restricted Differential RevisionrMITK9dc1b99b0cb7 Segment Anything Tool

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Event Timeline

a178n triaged this task as Normal priority.May 15 2023, 7:27 PM
a178n created this task.
a178n added a comment.May 15 2023, 7:49 PM

Pushed new branch to rMITK MITK: feature/T29604-sam-tool-2.

kislinsk edited projects, added MITK (v2023.12); removed Next Milestone, MITK.May 17 2023, 2:57 PM
kislinsk moved this task from Backlog to Segmentation on the MITK (v2023.12) board.May 17 2023, 3:04 PM
a178n added a subtask: T29648: SAM Python: Improve the wrapper to be used independently without MITK.Jun 26 2023, 7:25 PM
a178n removed a subtask: T29648: SAM Python: Improve the wrapper to be used independently without MITK.Jun 26 2023, 7:27 PM
a178n closed subtask T29635: SAM tool: Cannot Confirm segmentation properly as Resolved.Jun 27 2023, 2:41 PM
a178n added a revision: Restricted Differential Revision.Jul 12 2023, 2:55 PM
a178n moved this task from Segmentation to Cycle on the MITK (v2023.12) board.Jul 19 2023, 10:34 AM
a178n added a commit: rMITK9dc1b99b0cb7: Segment Anything Tool.Oct 13 2023, 3:41 PM
a178n added a commit: rMITKfda96a0189cd: Adding locale switch to writer for consistency.
a178n added a commit: rMITKebc6c339724f: Merge branch 'develop' into feature/T29604-sam-tool-2.
a178n added a commit: rMITK3b69a0ef5732: Changing SAM runner git url.
a178n added a commit: rMITK7bb192083536: Update itkTypeMacro.
a178n added a commit: rMITK4ff22142545d: Improve documentation and null check.
a178n added a commit: rMITK72504a2fc713: Code cleanup.
a178n added a commit: rMITKa3c9484bce54: SAM tool will now reinit after timed out.
a178n added a commit: rMITK3b1b4dfa6d88: SAM tool: Introducing timeout for python process comms.
a178n added a commit: rMITK0b574ff4f211: Avoid deep copy from ITK window filter to MITK image in SAM tool.
a178n added a commit: rMITKce918dfa2126: Merge branch 'develop' into feature/T29604-sam-tool-2.
a178n added a commit: rMITK3245b3ca6b90: SAM tool Code refactoring changes.
a178n added a commit: rMITK10f6ed0de3f5: 2D RGB image bugfix in SAM tool.
a178n added a commit: rMITK328bd55da9d2: Ubuntu build fixes.
a178n added a commit: rMITKd2b0b156bc2e: Adding optimized ITK-based file writer for SAM tool.
a178n added a commit: rMITKe831e8c5a6fe: Levelwindowfilter now applied to images for SAM tool.
a178n added a commit: rMITK943c448c1353: SAM tool: Update hash logic for robustness.
a178n added a commit: rMITK35cb316d276b: SAM tool Minor code changes.
a178n added a commit: rMITK678147e40e8a: SAM tool now fully support cross hair rotated images : Hashing logic change.
a178n added a commit: rMITK6efa5580b99e: Bugfix: SAM preference gpu box won't be white anymore.
a178n added a commit: rMITK7c87988922d4: Merge branch 'develop' into feature/T29604-sam-tool-2.
a178n added a commit: rMITKe9343bbcfc5a: SAM tool won't download models anymore. Qt5 Network dependency removed.
a178n added a commit: rMITKffb81898d5af: Tool API Bugfix: Seg tools in 2D mode can confirm on arbitrary steps correctly.
a178n added a commit: rMITK5178ed355957: Minor code update for Ubuntu build.
a178n added a commit: rMITK8ce0afe14a46: Adding support for 2D images.
a178n added a commit: rMITKe299172911b1: SAM Tool: Better UX changes.
a178n added a commit: rMITK9709514e5e0c: Force install pytorch v2.0.0 and torchvision 0.15.
a178n added a commit: rMITK504cc0a24aad: SAM tool won't show pop when no GPU was found.
a178n added a commit: rMITKeaa8b7302816: SAMtool: Rename "Activate" to "Initialize".
a178n added a commit: rMITKcc4ae71813c2: Linux/Mac build fixes.
a178n added a commit: rMITK370d9a358960: Better GPU vs CPU UX with redundancy for SAM tool.
a178n added a commit: rMITK1d993a6c0303: SAM tool now supports CPU inferencing.
a178n added a commit: rMITKe1e2e3914c25: Adding Preference change listener to SAM tool.
a178n added a commit: rMITKb5659e85568a: SAM tool will now use nrrd file for python interaction..
a178n added a commit: rMITK04cce0bac84d: Rename SAM to Segment Anything.
a178n added a commit: rMITK805eecf6a32e: Confirm segmentation works now.
a178n added a commit: rMITKb5aea9d23a3d: SegWithPreviewTool feature update: Adding ConfirmCleanUp virtual function to….
a178n added a commit: rMITK36ed77ecfe00: Add doc strings for SAM tool functions.
a178n added a commit: rMITKa43bc92e2885: SAM tool Code clean up.
a178n added a commit: rMITKcbe41a9e63b4: SAM tool: code updates for better status update on UI.
a178n added a commit: rMITK511cbe2c3947: SAM tool Ubuntu build fixes.
a178n added a commit: rMITKfde7c40a6029: Move SAM tool Preferences to dedicated UI page.
a178n added a commit: rMITK28d42b2f66d4: Update Install: SAM wrapper can be now pip installed.
a178n added a commit: rMITKf17b28a70fa1: SAM Tool: Minor code cleanup.
a178n added a commit: rMITK9c581076d539: Adding live status messages from tool class to GUI.
a178n added a commit: rMITKc82bcb145830: Adding SAM model selection tip for users.
a178n added a commit: rMITK4e7bc874a68d: GPU name parsing bugfix.
a178n added a commit: rMITK198eb50374b6: Moving GPU selection into MITK Preferences from SAM tool UI.
a178n added a commit: rMITKeb253d085c61: SAM tool can now handle cuda out of memory situation and throw error message.
a178n added a commit: rMITK34a7d3b3077e: Code cleanup: Installer & model selection not part of SAM GUI anymore.
a178n added a commit: rMITK6e78a214df0d: SAM Python class code refactoring.
a178n added a commit: rMITKe7a8aa8351fe: Migrating SAM tool install options into Pref menu: part changes.
a178n added a commit: rMITK3cdacd7db9b1: Migrating python related functionalities to dedicated class.
a178n added a commit: rMITKbdb8197e2a24: Remove Interactive vs Auto radiobutton selection.
a178n added a commit: rMITK6365abecbbf7: Changing click point shape to filled CIRCLE.
a178n added a commit: rMITKbf99b967ae7a: SAM tool working changes.
a178n added a commit: rMITK4948dba75162: SAM installer working changes.
a178n added a commit: rMITKebb06baa6b5c: SAM tool with daemon working changes.
a178n added a commit: rMITKe4f53fdcc0c1: Merge branch 'master' into feature/T29604-sam-tool-2.
a178n added a commit: rMITKb2d37df9a7e2: code update with time measurement.
a178n added a commit: rMITKdf6fef94a552: Merge branch 'develop' into feature/T29540-sam-2d-tool.
a178n added a commit: rMITK0a67fe3839d8: Merge branch 'develop' into feature/T29540-sam-2d-tool.
a178n added a commit: rMITKd00fc49ec8cd: Adding checks to avoid clicks outside image.
a178n added a commit: rMITKc2b3be9dd1be: Negative clicks Ahoy!.
a178n added a commit: rMITK64e4a8ca7634: SAM tool UI & backend code changes.
a178n added a commit: rMITK3a66df9945a1: Segment Anything Tool initial commit.
a178n added a commit: rMITK2fa4cdc39820: SAM backend changes backup.
kislinsk mentioned this in T30248: 2023 Week 46 (Mid November).Nov 13 2023, 4:23 PM
kislinsk edited projects, added MITK (v2024.06); removed MITK (v2023.12).Dec 5 2023, 10:38 AM
kislinsk moved this task from Backlog to Cycle on the MITK (v2024.06) board.
a178n added a comment.Dec 19 2023, 3:55 PM

Deleted branch from rMITK MITK: feature/T29604-sam-tool-2.

a178n closed this task as Resolved.Mar 6 2024, 9:19 AM
MITK · MIC · IMSY · DKFZ