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Watershed workflow #1437

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Commits on Oct 4, 2016

  1. documentationsfehler reduziert

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  2. part 1: creating workflow and applet

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Commits on Oct 5, 2016

  1. eigenes Threshold hinzugefuegt

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Commits on Oct 6, 2016

  1. watershedsegmentation workflow 0.0

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  2. watershedSegmentation workflow 0.1

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Commits on Oct 7, 2016

  1. applets bessr verstanden

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Commits on Oct 11, 2016

  1. channel selection applet vorbereiten

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  2. channel selection klappt schon recht gut

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Commits on Oct 12, 2016

  1. channel Selection gemacht und geht

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Commits on Oct 13, 2016

  1. visibility completed for channel selection

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  2. channel Selection output is left

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Commits on Oct 19, 2016

  1. troubleshooting included

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Commits on Oct 26, 2016

  1. savety copy and changement

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  2. aufgeraeumt und nun auf der suche nach der position

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Commits on Oct 27, 2016

  1. pixel value works for 3d images with x,y,z tags

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  2. channel selection integrated with pixel value update

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Commits on Oct 28, 2016

  1. preparation for cursor, brusher, eraser; Brushvalue Spinbox finished

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Commits on Nov 2, 2016

  1. fehler gefunden

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Commits on Nov 3, 2016

  1. jetzt geht es nicht mehr weil ganz viel rüberkopiert wurde von 

    pixelClassification. Daher jetzt PixelClassification bearbeiten
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  2. pixelclassification kopiert zum herumprobieren

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  3. brushing statt labeling eingefuehrt, welches meinen zwecken mehr dienen 

    sollte
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Commits on Nov 4, 2016

  1. alles rausgeschmissen was man nicht braucht. als naechstes: ein label 

    immer vorhanden
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  2. am brushing label dran, dass es nicht von anfang alles schwarz ist

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  3. watershed mit pixelvalue zurueck gesetzt ohne brushing aber lauffaehig

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  4. direkt vor fixing von export. noch alles ohne Fehler

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Commits on Nov 7, 2016

  1. export klappt an sich. nur gibt es jetzt beim anklicken von prediciton 

    export eine floating point exception
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Commits on Nov 9, 2016

  1. Direkt vor Umsetzung und Integration von LabelingGui (Labels) in Wate… 

    …rshed Applet und Workflow; keine Aenderungen zum letzten Commit, nur ein Anhaltspunkt
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Commits on Nov 10, 2016

  1. labelingDrawer ist integriert. Schritt 3 steht an

    @shaker6691
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  2. watershedLabeling erstellt aber nichts hinzugefuegt

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Commits on Nov 11, 2016

  1. Enabled to show the value of each label

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  2. 8bit colortable (random 256 diffrent colors) for labels

    @shaker6691
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  3. vixel value integrated into watershedLabelingGui and functionality added 

    in watershedSegementationGui
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Commits on Nov 14, 2016

  1. tried to integrate CorrectedSeedsIn and ...Out (still didn't work)

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Commits on Nov 17, 2016

  1. integrated the import of seeds with labels und resetting them. TODO: 

    same colors on reset
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Commits on Nov 18, 2016

  1. ColorProblem solved; labels adding and deleting works fine except; if 

    label 1 deleted, label 2 remains value 2, but new things drawn with
label 2 have value 1
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Commits on Nov 23, 2016

  1. fixing the bug. now draw with correct number after label deletion

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  2. pixelValueDisplaying as separate class

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  3. export of 'importAndResetLabels' as class nearly finished

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Commits on Nov 24, 2016

  1. importAndResetLabels successfully exported into class

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  2. clean up a little bit

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  3. tidied up the setup layer

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  4. introduction of the watershed-algorithm itself. doesn't work yet

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Commits on Nov 25, 2016

  1. watershed works for one particular dataset

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  2. cleaned up the watershedLabeling folder a little bit

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  3. removed unneccesary applets and workflows with test data.

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  4. data export works

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  5. preparation for automatic controll of watershed, whether 2D, 3D, with or 

    without slices
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Commits on Nov 29, 2016

  1. included automatic slicing (when time is used) in watershed algorithm 

    TODO watershed with inputSlot parameter
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Commits on Nov 30, 2016

  1. parameterinput via slots works

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  2. bug fixes. now it should work better

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  3. another bug

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Commits on Dec 1, 2016

  1. saved the watershed calculations in cache

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  2. new todo tasks

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Commits on Dec 2, 2016

  1. serializer doesn't work. try some things with the pixelclassification… 

    … used serializer
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Commits on Dec 8, 2016

  1. serializer worked on

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Commits on Dec 9, 2016

  1. SerialListSlot with slot level = 1 or higher implemented

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  2. serialization of labelsNames and LabelCache with Level 1

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Commits on Dec 12, 2016

  1. 2 bug fixes for saving and resetting

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  2. 1 bug fix for getting the higher dimension right

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Commits on Dec 19, 2016

  1. documentation errors solved with pyqt 4 vs pyqt5

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  2. applet_api.RST and applet_library.RST have a compiling error, therefore 

    not integrated in this docu, because otherwise debugging is extremly
difficult
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Commits on Dec 20, 2016

  1. fixing 2 bugs in the documentation, where classes that didn't exist 

    anymore are now excluded from the documentation
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  2. removed all warnings and bugs

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  3. documentation for a single applet

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Commits on Dec 21, 2016

  1. added interesting 'nice to know' facts

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Commits on Dec 22, 2016

  1. expanded the docu with labelingGui

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Commits on Jan 9, 2017

  1. Merge branch 'watershed_workflow' 

    Added the the watershed_workflow parts to the master, but didn't remove
anything from the original code
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  2. seeds new applet; not working right now

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Commits on Jan 10, 2017

  1. layout for seeds applet added

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  2. Added all seeds parameter to sync and broadcasting. Still no computation

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Commits on Jan 11, 2017

  1. working on the smoothing and generating of seeds

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  2. main thing works but distance transform needs to be used from anna

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  3. cleaned up seedgeneration and connected to gui

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Commits on Jan 12, 2017

  1. seeds and watershed together with slots and with bugs

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Commits on Jan 13, 2017

  1. corrected dt and make reset seeds faster. 

    TODO: all button actions with execut
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Commits on Jan 16, 2017

  1. applet Seeds working with execute right now, but not perfect

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Commits on Jan 17, 2017

  1. directly before reorderaxis. seeds works with propagate dirty

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Commits on Jan 18, 2017

  1. before: integrate z,t in generateSeeds

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  2. before reorderaxis and execute in watershed

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  3. watershed applet works with execute. now the reset and reload of the 

    labels has to be done automatically if the seeds have changed
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Commits on Jan 19, 2017

  1. made all ready

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Commits on Feb 1, 2017

  1. reorderaxis in the workflow in the data selection

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  2. OpSeeds: Removed unused slot

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  3. OpSeeds: Use 'ready' notifications instead of 'metaChanged' notificat… 

    …ions
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  4. OpSeeds: Remove unnecessary calls to setDirty()

    @stuarteberg
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  5. SeedsGui: Initialize combo boxes BEFORE initializing their callbacks.

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  6. WatershedSegmentationGui: Clean up notification callbacks during shut… 

    …down
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  7. OpWatershedSegmentation: Removed an unnecessary call to setDirty()

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  8. Use OpCompressedCache, not _OpCacheWrapper

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  9. OpSeeds: Minor clean up in execute()

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  10. SeedsGui: Fix initial seeds display

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  11. OpWatershedSegmentation: Moved Seeds dirty handling from a notifyDirt… 

    …y callback to propagateDirty() instead
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  12. OpWatershedSegmentationCalculation: Simplify propagateDirty()

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Commits on Feb 2, 2017

  1. wasn't that important

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Commits on Feb 3, 2017

  1. time problem with cache solved by setting the blocksize for cache

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  2. time cache fixed in ws applet as well

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  3. fixed the reset bug, so that the ws labels are reset only when applet is 

    active
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  4. fixed some bugs

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Commits on Feb 7, 2017

  1. changed ResetLabelsToSlot to InputSeedsChanged

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Commits on Feb 13, 2017

  1. changed seeds gui

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Commits on Feb 14, 2017

  1. implemented the clear label functionality

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  2. labeling always in the seeds applet

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Commits on Feb 20, 2017

  1. serializer tests added

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  2. watershed segmentation test serializer corrected

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Commits on Feb 24, 2017

  1. Begin of the pixel classification workflow

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Commits on Mar 6, 2017

  1. removed all unused applets and workflows as well as some ununsed code 

    snippets
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Commits on Mar 9, 2017

  1. added license header to all watershed files

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    shaker6691 committed Mar 9, 2017
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  2. Tests for OpSeeds created and all are successful

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    shaker6691 committed Mar 9, 2017
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Commits on Mar 10, 2017

  1. beginning of OpWSCalculation tests and some corrections

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  2. tests for opWSCalc for 3D, 2 is outstanding

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    shaker6691 committed Mar 10, 2017
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  3. completed test for opWatershedSegmentationCalculation

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    shaker6691 committed Mar 10, 2017
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  4. removed all print statements; watershed workflow is finished

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    shaker6691 committed Mar 10, 2017
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Commits on Mar 24, 2017

  1. Merge branch 'master' of githubL:ilastik/ilastik into watershed_workflow 

    to integrate the changes in the master in the watershed_workflow branch
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    shaker6691 committed Mar 24, 2017
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