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petersej (Jens Petersen)
User

Projects (9)

User Details

User Since
Aug 1 2016, 12:10 PM (115 w, 2 d)

Recent Activity

Tue, Oct 2

petersej added a member for MIC: full.
Tue, Oct 2, 9:17 AM

Sep 14 2018

petersej added a member for BVM: thomass.
Sep 14 2018, 4:49 PM

Aug 29 2018

petersej triaged T25314: Clean threading for trixi as High priority.
Aug 29 2018, 10:48 AM · Restricted Project, trixi
petersej added a comment to T24634: Clear all visdom environments.

Please provide more info. Do you mean a utility function that clears all environments? Why do we need that?

Aug 29 2018, 10:31 AM · trixi
petersej closed T24865: Renaming and Starring for trixi as Resolved.
Aug 29 2018, 10:29 AM · trixi
petersej added a comment to T25059: Make tag and label consistent in counter and show_value etc.

@zimmerer please close if this is resolved to your satisfaction

Aug 29 2018, 10:29 AM · trixi
petersej closed T24695: How to handle "big data" in experiment viewer as Resolved.

Current solution works alright for now, closing

Aug 29 2018, 10:27 AM · trixi

Aug 28 2018

petersej triaged T25309: Unify API for Numpy- & PytorchPlotFileLogger as High priority.
Aug 28 2018, 10:05 AM · Restricted Project, trixi

Jun 13 2018

petersej moved T24865: Renaming and Starring for trixi from Resolved to In Progress on the trixi board.
Jun 13 2018, 3:01 PM · trixi
petersej closed T24674: Show log files in experiment browser as Resolved.
Jun 13 2018, 3:00 PM · trixi
petersej closed T24657: Add state to experiment log (and experiment browser) as Resolved.
Jun 13 2018, 3:00 PM · trixi
petersej closed T24616: Vislogger fix/inspect error log as Resolved.
Jun 13 2018, 2:59 PM · trixi
petersej placed T20047: Single method for status bar update up for grabs.
Jun 13 2018, 2:48 PM · MITK
petersej placed T19724: Feature processor for classification up for grabs.
Jun 13 2018, 2:48 PM · Bugzilla, MITK
petersej placed T19011: DICOM Browser: Scanning empty directory causes Import dialog to stay open forever up for grabs.
Jun 13 2018, 2:48 PM · MITK, Bugzilla
petersej placed T19600: Active Learning Module & Plugin up for grabs.
Jun 13 2018, 2:47 PM · Bugzilla, MITK
petersej placed T19310: Add bulk retrieval to DICOM plugin up for grabs.
Jun 13 2018, 2:47 PM · Bugzilla, MITK

Apr 24 2018

petersej closed T24693: Hierachical Config as Resolved.
Apr 24 2018, 5:02 PM · trixi
petersej moved T24693: Hierachical Config from Backlog to In Progress on the trixi board.
Apr 24 2018, 12:52 PM · trixi

Apr 21 2018

petersej triaged T24695: How to handle "big data" in experiment viewer as Normal priority.
Apr 21 2018, 7:08 PM · trixi
petersej triaged T24694: Make plots in experiment view removable as Wishlist priority.
Apr 21 2018, 7:05 PM · trixi

Apr 20 2018

petersej triaged T24693: Hierachical Config as Wishlist priority.
Apr 20 2018, 3:22 PM · trixi

Apr 11 2018

petersej closed T24587: NumpyVisdomLogger crashes with segmentation fault as Resolved.
Apr 11 2018, 11:12 AM · trixi
petersej added a comment to T24587: NumpyVisdomLogger crashes with segmentation fault.

I did two things that apparently solved the problem (>50k episodes without issue). 1. Move matplotlib.use("agg") to the __init__.py, because I was actually using Qt5Agg. This is a necessary fix regardless of this particular problem. 2. I "un-threaded" the saving of figures. This is likely the fix, but I still don't know why... Will mark as resolved regardless.

Apr 11 2018, 11:12 AM · trixi
petersej moved T24587: NumpyVisdomLogger crashes with segmentation fault from Backlog to In Progress on the trixi board.
Apr 11 2018, 10:59 AM · trixi

Apr 8 2018

petersej added a comment to T24587: NumpyVisdomLogger crashes with segmentation fault.

Idea: Currently we're making .savefig threaded, maybe creating a little helper that does .savefig and then .clear in a thread could help?

Apr 8 2018, 5:18 PM · trixi
petersej added a comment to T24587: NumpyVisdomLogger crashes with segmentation fault.

Running python -m pdb myscript.py now gave out the following RuntimeWarning:

Apr 8 2018, 5:09 PM · trixi
petersej added a comment to T24587: NumpyVisdomLogger crashes with segmentation fault.

I can confirm that the segfault is in fact the problem. Running without visdom logging still results in segfault, but much later (sample size 1, ca. 13000 episodes). The EOFError is then only the result of the dead sender. Random idea from the internet: Stack memory limit too low? Mine is currently at 8192MB (ulimit -s)

Apr 8 2018, 1:59 PM · trixi

Apr 6 2018

petersej triaged T24587: NumpyVisdomLogger crashes with segmentation fault as High priority.
Apr 6 2018, 1:52 PM · trixi
petersej triaged T24586: NumpyPlotFileLogger savefig with IndexError as Normal priority.
Apr 6 2018, 1:40 PM · trixi
petersej added a watcher for trixi: petersej.
Apr 6 2018, 1:29 PM

Mar 27 2018

petersej added a parent task for T23174: Add Example and readme to vislogger package: Unknown Object (Maniphest Task).
Mar 27 2018, 4:50 PM · trixi
petersej added a comment to T23174: Add Example and readme to vislogger package.

Simple README not sufficient, Jupyter notebook better alternative.

Mar 27 2018, 3:56 PM · trixi
petersej reassigned T23174: Add Example and readme to vislogger package from isensee to koehlerg.
Mar 27 2018, 3:55 PM · trixi

Jan 18 2018

petersej closed T23171: Make vislogger package as Resolved.
Jan 18 2018, 5:25 PM · Deep Learning
petersej closed T23171: Make vislogger package, a subtask of T23156: Visdom visualization package, as Resolved.
Jan 18 2018, 5:25 PM · Restricted Project, Deep Learning
petersej added a comment to T23155: Provide a Python Style Guide.

More or less ready, waiting for new wiki

Jan 18 2018, 5:24 PM · Deep Learning, MITK

Nov 6 2017

petersej closed T23634: Batchgenerators API improvements as Resolved.
Nov 6 2017, 11:43 AM · Deep Learning

Nov 2 2017

petersej created T23634: Batchgenerators API improvements.
Nov 2 2017, 5:58 PM · Deep Learning

Sep 29 2017

petersej created T23470: Markdown for Python Example Project.
Sep 29 2017, 2:59 PM · MITK

Aug 9 2017

petersej reassigned T23156: Visdom visualization package from petersej to zimmerer.
Aug 9 2017, 11:27 AM · Restricted Project, Deep Learning

Aug 3 2017

petersej added a project to T23156: Visdom visualization package: Restricted Project.
Aug 3 2017, 3:08 PM · Restricted Project, Deep Learning
petersej added a project to T23155: Provide a Python Style Guide: Deep Learning.
Aug 3 2017, 3:07 PM · Deep Learning, MITK
petersej created T23156: Visdom visualization package.
Aug 3 2017, 3:00 PM · Restricted Project, Deep Learning
petersej created T23155: Provide a Python Style Guide.
Aug 3 2017, 2:35 PM · Deep Learning, MITK

Apr 4 2017

petersej committed rMITK67a391cd0871: Logging works (authored by petersej).
Logging works
Apr 4 2017, 9:52 AM

Mar 30 2017

petersej committed rMITK29003b990cfd: Implement interaction logger (authored by petersej).
Implement interaction logger
Mar 30 2017, 7:01 PM
petersej added a comment to T19600: Active Learning Module & Plugin.

Pushed new branch T19600-ActiveLearning-Backup.

Mar 30 2017, 11:05 AM · Bugzilla, MITK
petersej committed rMITK5343ea1db706: Remove presets for now (authored by petersej).
Remove presets for now
Mar 30 2017, 11:04 AM
petersej committed rMITKdf2a285ec489: Add missing declaration (authored by petersej).
Add missing declaration
Mar 30 2017, 11:04 AM
petersej committed rMITK90bb124781c4: Merge branch 'T19600-ActiveLearning' into T19600-ActiveLearning-new-master (authored by petersej).
Merge branch 'T19600-ActiveLearning' into T19600-ActiveLearning-new-master
Mar 30 2017, 11:04 AM
petersej added a comment to T19600: Active Learning Module & Plugin.

Pushed new branch T19600-ActiveLearning-new-master.

Mar 30 2017, 11:04 AM · Bugzilla, MITK

Jan 20 2017

petersej committed rMITKc9d736a2ff7d: Merge branch 'T2662-darkStyle2017' of https://phabricator.mitk. (authored by petersej).
Merge branch 'T2662-darkStyle2017' of https://phabricator.mitk.
Jan 20 2017, 5:26 PM
petersej committed rMITK99fa0dacfc66: Start implementing dark icon theme (authored by petersej).
Start implementing dark icon theme
Jan 20 2017, 5:26 PM

Nov 11 2016

petersej committed rMITKca218a062650: Region grower no longer overwrites locked labels (authored by petersej).
Region grower no longer overwrites locked labels
Nov 11 2016, 3:12 PM
petersej committed rMITKce5325553b8e: Fix paint and wipe tools (authored by petersej).
Fix paint and wipe tools
Nov 11 2016, 2:38 PM
petersej committed rMITK38840f59435f: Fix subtract and correction tools (authored by petersej).
Fix subtract and correction tools
Nov 11 2016, 2:19 PM
petersej added a comment to T22098: Multilabel segmentation tools not working correctly.

Pushed new branch T22098-Multilabel-Segmentation-Tools.

Nov 11 2016, 2:19 PM · MITK (2016-11)
petersej created T22098: Multilabel segmentation tools not working correctly.
Nov 11 2016, 2:13 PM · MITK (2016-11)
petersej created T22088: Synchronize node color with color of active label in LabelSetImage.
Nov 11 2016, 9:13 AM · MITK (2016-11)

Nov 3 2016

petersej created T20223: MITK does not load RGB and RGBA test images.
Nov 3 2016, 10:09 AM · MITK (2016-11)

Oct 28 2016

petersej committed rMITKafde4cca8a70: Implement status bar method to display image info (authored by petersej).
Implement status bar method to display image info
Oct 28 2016, 3:02 PM
petersej added a revision to T20047: Single method for status bar update: Unknown Object (Differential Revision).
Oct 28 2016, 1:52 PM · MITK

Oct 9 2016

petersej committed rMITK3db9f26c1153: Merge branch 'T19600-ActiveLearning' of https://phabricator.mitk. (authored by petersej).
Merge branch 'T19600-ActiveLearning' of https://phabricator.mitk.
Oct 9 2016, 5:51 PM
petersej committed rMITKf23fe824de1c: Start implementing presets (authored by petersej).
Start implementing presets
Oct 9 2016, 5:51 PM
petersej committed rMITK6a97e976ab42: Change region opacity and pixel type (authored by petersej).
Change region opacity and pixel type
Oct 9 2016, 5:51 PM

Oct 6 2016

petersej committed rMITK80a77518cfdb: Add opening filter, needs testing (authored by petersej).
Add opening filter, needs testing
Oct 6 2016, 5:40 PM

Oct 5 2016

petersej committed rMITK8331a8eaefcb: Multiply sigma by mean spacing (authored by petersej).
Multiply sigma by mean spacing
Oct 5 2016, 4:52 PM

Oct 4 2016

petersej committed rMITK2f35f35c0de2: Set structure tensor outer scale to 1.3 * inner (authored by petersej).
Set structure tensor outer scale to 1.3 * inner
Oct 4 2016, 7:15 PM
petersej created T20047: Single method for status bar update.
Oct 4 2016, 2:12 PM · MITK
petersej committed rMITK3012cc49fdbf: Synchronize image navigator and status bar (authored by petersej).
Synchronize image navigator and status bar
Oct 4 2016, 1:54 PM
petersej closed T19849: Pixel Value not updated for 3D+t image as Resolved by committing rMITK3012cc49fdbf: Synchronize image navigator and status bar.
Oct 4 2016, 1:54 PM · MITK (2016-11)
petersej added a comment to T20023: Visual Studio 2015 compile crashes during superbuild of HDF5 library.

HDF 1.8.14 doesn't support VS2015, see
https://support.hdfgroup.org/ftp/HDF5/releases/ReleaseFiles/hdf5-1.8.14-RELEASE.txt
We could upgrade to 1.8.17 and when we move to ITK 4.11 with HDF 1.8.17 just get rid of our own third party HDF!?
According to HDF release notes the first version with VS2015 support is 1.8.16.

Oct 4 2016, 11:47 AM · MITK

Sep 16 2016

petersej added a revision to T19849: Pixel Value not updated for 3D+t image: Unknown Object (Differential Revision).
Sep 16 2016, 2:57 PM · MITK (2016-11)
petersej committed rMITK1090d244ba74: Undo saved changes (authored by petersej).
Undo saved changes
Sep 16 2016, 2:35 PM
petersej committed rMITK80fa6078a851: Merge branch 'T19849-Pixel-value-3DT-image' of https://phabricator.mitk. (authored by petersej).
Merge branch 'T19849-Pixel-value-3DT-image' of https://phabricator.mitk.
Sep 16 2016, 2:35 PM
petersej committed rMITKade77c6724fd: Changes in navigator change status bar (authored by petersej).
Changes in navigator change status bar
Sep 16 2016, 2:35 PM

Sep 13 2016

petersej committed rMITK867e932cc40f: Features all work (authored by petersej).
Features all work
Sep 13 2016, 6:17 PM
petersej committed rMITKff59baccb8e2: Backup before fixing structure tensor (authored by petersej).
Backup before fixing structure tensor
Sep 13 2016, 2:55 PM

Sep 9 2016

petersej committed rMITKcae85debbf3b: Region not working (authored by petersej).
Region not working
Sep 9 2016, 6:58 PM

Sep 8 2016

petersej committed rMITKd2a433d68d40: Size slider, uncertainty method (authored by petersej).
Size slider, uncertainty method
Sep 8 2016, 5:35 PM
petersej committed rMITKd3f3b66818ce: Check geometry before extracting slice again (authored by petersej).
Check geometry before extracting slice again
Sep 8 2016, 5:35 PM

Sep 7 2016

petersej committed rMITK56e416b65b35: Fix brush size (authored by petersej).
Fix brush size
Sep 7 2016, 5:23 PM
petersej committed rMITK58e4dd0db341: Interpolation works (authored by petersej).
Interpolation works
Sep 7 2016, 5:09 PM
petersej committed rMITK067a4da9c63c: Painting works, need refactoring (authored by petersej).
Painting works, need refactoring
Sep 7 2016, 5:09 PM
petersej committed rMITK32d3808f1321: Interactor painting should work (authored by petersej).
Interactor painting should work
Sep 7 2016, 5:09 PM

Sep 6 2016

petersej committed rMITK4b60cf241b27: Implement new interpolation method (authored by petersej).
Implement new interpolation method
Sep 6 2016, 1:56 PM
petersej committed rMITK1f3e1b03640c: Added structure tensor filter from ITK (authored by petersej).
Added structure tensor filter from ITK
Sep 6 2016, 1:56 PM

Sep 2 2016

petersej committed rMITK1669764293ae: Save changes (authored by petersej).
Save changes
Sep 2 2016, 4:26 PM
petersej added a comment to T19849: Pixel Value not updated for 3D+t image.

Pushed new branch T19849-Pixel-value-3DT-image.

Sep 2 2016, 4:26 PM · MITK (2016-11)
petersej claimed T19849: Pixel Value not updated for 3D+t image.
Sep 2 2016, 10:08 AM · MITK (2016-11)

Aug 31 2016

petersej committed rMITK71e3da7de4a7: Implement export (authored by petersej).
Implement export
Aug 31 2016, 6:18 PM

Aug 30 2016

petersej committed rMITKa157c2b795db: MILESTONE: Working version (authored by petersej).
MILESTONE: Working version
Aug 30 2016, 4:24 PM
petersej committed rMITK40c752788a62: Return prediction as image vector (authored by petersej).
Return prediction as image vector
Aug 30 2016, 12:28 PM

Aug 29 2016

petersej created T19907: Changing node data to multicomponent image does not add component slider.
Aug 29 2016, 1:56 PM · MITK

Aug 26 2016

petersej committed rMITK37fbe462f15a: Rendering of vector image crashes (authored by petersej).
Rendering of vector image crashes
Aug 26 2016, 5:19 PM
petersej committed rMITK42847ddb6d07: Threaded prediction works (authored by petersej).
Threaded prediction works
Aug 26 2016, 4:21 PM

Aug 25 2016

petersej committed rMITK84c205d044cf: Start moving prediction to separate thread (authored by petersej).
Start moving prediction to separate thread
Aug 25 2016, 7:16 PM
petersej committed rMITK8e07ff50ce43: Prediction works (authored by petersej).
Prediction works
Aug 25 2016, 4:52 PM

Aug 24 2016

petersej committed rMITK712a0a79b7d3: Moved away from LabelSetImage (authored by petersej).
Moved away from LabelSetImage
Aug 24 2016, 5:36 PM