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Maniphest T28886

MITK Flowbench - Reopen created segmentation not working
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Description

MITK v2021.10 - Use MITK Flow to create a segmentation. Afterwards I tried to reopen it with MITK Flow, to "change" it.
But MITK Flow does not open anymore:

   "BodyPartExamined" : "ABDOMEN",
   "ClinicalTrialCoordinatingCenterName" : "Unknown",
   "ClinicalTrialSeriesID" : "Session 1",
   "ClinicalTrialTimePointID" : "0",
   "ContentCreatorName" : "MITK",
   "InstanceNumber" : "1",
   "SeriesDescription" : "MITK Segmentation",
   "SeriesNumber" : "00",
   "segmentAttributes" : [
      [
         {
            "SegmentAlgorithmName" : "MITK Segmentation",
            "SegmentAlgorithmType" : "SEMIAUTOMATIC",
            "SegmentDescription" : "Kidney",
            "SegmentLabel" : "Kidney",
            "SegmentedPropertyCategoryCodeSequence" : {
               "CodeMeaning" : "Anatomical Structure",
               "CodeValue" : "T-D000A",
               "CodingSchemeDesignator" : "SRT"
            },
            "SegmentedPropertyTypeCodeSequence" : {
               "CodeMeaning" : "Kidney",
               "CodeValue" : "T-71000",
               "CodingSchemeDesignator" : "SRT"
            },
            "labelID" : 1,
            "recommendedDisplayRGBValue" : [ 185, 102, 83 ]
         }
      ]
   ]
}
qt.svg: Cannot open file ':/org_mitk_icons/icons/awesome/scalable/actions/document-save.svg', because: No such file or directory
qt.svg: Cannot open file ':/org_mitk_icons/icons/awesome/scalable/actions/document-save.svg', because: No such file or directory
qt.svg: Cannot open file ':/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg', because: No such file or directory
qt.svg: Cannot open file ':/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg', because: No such file or directory
!12.858! WARNING: Could not read :/org_mitk_icons/icons/awesome/scalable/actions/document-save.svg
!12.858! WARNING: Could not read :/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg
Aborted (core dumped)

Opening the same data with an older version of MITK Flow GUI works. I tried in kaapana and directly in Linux.
As testdataset I used E130-Personal\Gao\mitk-flow-211130133218128483\batch\1.2.276.0.7230010.3.1.3.17483548.639.1638271264.889404\

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gaoh created this task.Nov 30 2021, 4:48 PM
gaoh added a project: Kaapana (internal).
gaoh added a subscriber: floca.
floca added a project: Missing Info.Nov 30 2021, 6:17 PM

can you provide the files necessary to reproduce the problem outside of a container? (so at least image, seg and the scene file you generate automatically, and the call of MITK Workbench you use.)

floca edited projects, added MITK (v2022.04); removed MITK.Nov 30 2021, 6:17 PM
gaoh added a comment.Nov 30 2021, 8:16 PM

Yes, sorry I didn't highlight it ;):

As testdataset I used E130-Personal\Gao\mitk-flow-211130133218128483\batch\1.2.276.0.7230010.3.1.3.17483548.639.1638271264.889404\

floca mentioned this in T28903: [Segmentation] Monitoring of segmentation nodes in views is error prone/ not safe..Dec 6 2021, 9:02 PM
floca added a comment.EditedDec 6 2021, 9:55 PM

Found the problem in the code. Will be solved by T28903

Work around: add the following line to your segmentation_props file:

<property key="visible" type="BoolProperty"><bool value="true"/></property>

But be warned your example data still does not work due to the slice error also meantioned in T28900. (But there I also have found the reason)

kislinsk triaged this task as Normal priority.Jan 11 2022, 6:47 AM
kislinsk added a subtask: T28903: [Segmentation] Monitoring of segmentation nodes in views is error prone/ not safe..
kislinsk added a subtask: Restricted Maniphest Task.
kalali closed subtask T28903: [Segmentation] Monitoring of segmentation nodes in views is error prone/ not safe. as Resolved.Jan 25 2022, 1:32 PM
kalali added a subscriber: kalali.Jan 25 2022, 5:05 PM

Please check if the problem persists now with T28903: [Segmentation] Monitoring of segmentation nodes in views is error prone/ not safe. merged into develop.

gaoh added a comment.Jan 27 2022, 1:08 PM
In T28886#232894, @kalali wrote:

Please check if the problem persists now with T28903: [Segmentation] Monitoring of segmentation nodes in views is error prone/ not safe. merged into develop.

ok, I will check again, as soon there is a new snapshot with the changes available...

In T28886#231897, @floca wrote:

Found the problem in the code. Will be solved by T28903

Work around: add the following line to your segmentation_props file:

<property key="visible" type="BoolProperty"><bool value="true"/></property>

But be warned your example data still does not work due to the slice error also meantioned in T28900. (But there I also have found the reason)

by enabling this, the flow-bench opens, the segmentation is also visible in the data manager, but still it is not part of the "Data Selection":

image.png (189×727 px, 69 KB)

kislinsk edited projects, added Next Milestone, MITK; removed MITK (v2022.04).Apr 29 2022, 1:38 PM
floca edited projects, added MITK (v2022.10); removed MITK, Next Milestone.May 13 2022, 2:35 PM

@gaoh Would you be so kind and verify that the problem still exists? Thanks.

floca moved this task from Backlog to Segmentation on the MITK (v2022.10) board.May 16 2022, 12:31 PM
floca added a comment.Sep 21 2022, 9:07 AM

@gaoh Ping

gaoh added a comment.Sep 21 2022, 9:28 AM

oh so I forgot to send it: But this is, what my browser had cashed: "Yes, so I recently tested it, with the current release."
But also, if I remember correctly, this was due to the Phantom dataset we have as the default dataset:
I removed a few slices at the end, and now it is working.

So I guess, the problem was the dataset and this can be closed? Or should MITK also be able to handle such "broken" datasets?

floca closed this task as Invalid.Sep 21 2022, 9:36 AM

To make our live a bit easier. I would say it is a data problem ;).

If our assessment changes, we can reopen it.

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