Page MenuHomePhabricator

gaoh (Hanno Gao)
User

Projects

User Details

User Since
Sep 3 2018, 11:01 AM (306 w, 3 d)

Recent Activity

Wed, Jul 10

gaoh added a comment to T30359: MITK MiniApps in Kaapana.

What is with MitkCLGlobalImageFeatures, it is not expected to be part of MITK anymore? Or is it still part of it?

Wed, Jul 10, 3:30 PM · MITK

Mar 7 2024

gaoh added a comment to T30359: MITK MiniApps in Kaapana.

If I haven't missed something we can directly replace MitkCLResampleImageToReference with MitkMapImage. I can patch the according Kaapana files as soon as we have the new MITK installer. Do we have tests for the containers?

Mar 7 2024, 11:40 AM · MITK

Mar 6 2024

gaoh assigned T30359: MITK MiniApps in Kaapana to floca.
Mar 6 2024, 11:34 AM · MITK
gaoh created T30359: MITK MiniApps in Kaapana.
Mar 6 2024, 11:34 AM · MITK

Feb 27 2024

gaoh removed a member for Kaapana (internal): j860d.
Feb 27 2024, 10:31 AM
gaoh removed a member for Kaapana (internal): kochch.
Feb 27 2024, 10:31 AM
gaoh removed a member for Kaapana (internal): k688h.
Feb 27 2024, 10:31 AM
gaoh removed a member for Kaapana (internal): maerz.
Feb 27 2024, 10:31 AM
gaoh removed a member for Kaapana (internal): dmichael.
Feb 27 2024, 10:31 AM
gaoh removed a member for Kaapana (internal): kleina.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): thomass.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): onogur.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): rosst.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): graf.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): m139l.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): m564f.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): s429r.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): kausch.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): e249r.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): petersej.
Feb 27 2024, 10:30 AM
gaoh removed a member for Kaapana (internal): r738v.
Feb 27 2024, 10:29 AM
gaoh removed a member for Kaapana (internal): t543a.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): r010a.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): j562r.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): kleesiek.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): schererj.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): kalali.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): k656s.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): goetzm.
Feb 27 2024, 10:28 AM
gaoh removed a member for Kaapana (internal): j162k.
Feb 27 2024, 10:27 AM
gaoh added a member for Kaapana (internal): m395c.
Feb 27 2024, 10:27 AM

Dec 11 2023

gaoh added a comment to T30293: Introduce new interoperability/developer-friendly scene file format (including reader).

Thank you! Yes this would already be really helpful. Allowing to only create 1 file, and if needed, just change a few properties in it, makes it much more useable.

Dec 11 2023, 11:56 AM · MITK (v2024.12)

Aug 2 2023

gaoh added a comment to T30148: MITK FlowBench v2023.04 - crashes on "Accept segmentation".

So I can store files as nrrd and then use the mitkfileconverter to convert them to dcm? And this is better, then directly storeing the files as dcm?

Aug 2 2023, 9:39 AM · MITK (v2023.12)

Aug 1 2023

gaoh added a comment to T30148: MITK FlowBench v2023.04 - crashes on "Accept segmentation".

Ok, since this issue made it impossible to use v2023.04 in Kaapaana mitk-flow, I am still on the previous release, where it kind of works?
So I would stay on this previous release until there is a new MITK version addressing these DICOM issues.
For now we are highly dependent on dicoms, so we don't have the option to just store the files in another file format...

Aug 1 2023, 5:10 PM · MITK (v2023.12)

Jul 4 2023

gaoh created T30148: MITK FlowBench v2023.04 - crashes on "Accept segmentation".
Jul 4 2023, 11:12 AM · MITK (v2023.12)

Jun 27 2023

gaoh updated subscribers of T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem.

@k656s has an example dataset. I am still at the release version before (I think 2022.10?) but I will update to the current release. Could this already help?
If not, I would vote for the task list view reinit after loading opiton.

Jun 27 2023, 11:05 AM · Next Milestone, Request for Discussion, MITK

Jun 22 2023

gaoh created T29650: mitk-flow " Please reinitialize the selected segmentation image!" problem.
Jun 22 2023, 3:49 PM · Next Milestone, Request for Discussion, MITK

Mar 27 2023

gaoh closed T28884: MITK Flowbench -Save Seg not working, due to file naming issues as Invalid.

theoretically yes, but I guess it is not relevant. Since we now use the tasklist feature. And before that, I used the described workaround. So this is not needed anymore.

Mar 27 2023, 5:11 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)

Jan 25 2023

gaoh added a comment to T29431: [worklist] mitk-flow: save changed dicom segmentation not possible.

thanks again, for solving this issue! So in the current kaapana develop the tasklist feature is now integrated!

Jan 25 2023, 9:13 AM · MITK

Dec 12 2022

gaoh triaged T29432: [worklist] mitk-flow preload first task as Wishlist priority.
Dec 12 2022, 10:52 AM · MITK
gaoh triaged T29431: [worklist] mitk-flow: save changed dicom segmentation not possible as Normal priority.
Dec 12 2022, 10:46 AM · MITK

Dec 6 2022

gaoh triaged T29428: Creating scene file with image properties can result in missing LevelWindowbar as Normal priority.
Dec 6 2022, 4:42 PM · MITK
gaoh created T29428: Creating scene file with image properties can result in missing LevelWindowbar.
Dec 6 2022, 4:42 PM · MITK
gaoh triaged T29427: FlowBench mitkscene structure has changed. as Normal priority.
Dec 6 2022, 2:58 PM · MITK

Nov 25 2022

gaoh added a comment to T27189: REST API for data storage.

So the last changes in the branch, are basically the changes I made, so that she could modify the code, already used for the dicomweb/kaapana interaction, to simply apply it for this modul. Since it would have been quite similar. I guess, when the changes of the rest module are done: We (AIH-Cluster will take care of restarting the MITK-Kaapana interaction). I think this could be then a not so complicated add-on.

Nov 25 2022, 12:16 PM · MITK (v2024.12), Restricted Project, Request for Discussion
gaoh added a comment to T27189: REST API for data storage.

Oh yes, I also forgot about this, the final state was, as I remember correctly, that she did not succeed in producing meaningful results.

Nov 25 2022, 12:12 PM · MITK (v2024.12), Restricted Project, Request for Discussion

Sep 21 2022

gaoh added a comment to T28886: MITK Flowbench - Reopen created segmentation not working.

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.

Sep 21 2022, 9:28 AM · MITK (v2022.10), Missing Info, Kaapana (internal)

Jul 22 2022

gaoh added a comment to T29243: nnUNet in MITK: Downloading pre-trained models in Kaapana context.

ok, but then the GPU problem is also feasible! If it is for a pre-known time-limited usage, like in an interactive session, I don't see a problem assigning a GPU to the container.

Jul 22 2022, 2:26 PM · MITK (v2024.12), Kaapana (internal)
gaoh added a comment to T29243: nnUNet in MITK: Downloading pre-trained models in Kaapana context.

To point 1, in Kubernetes you can mount any path/volume to the desired mounting point. So I could just mount the directory in the MITK container in e.g. /models

Jul 22 2022, 1:49 PM · MITK (v2024.12), Kaapana (internal)

Jun 1 2022

gaoh added a member for MIC: l597s.
Jun 1 2022, 12:52 PM
gaoh added a member for Kaapana (internal): l597s.
Jun 1 2022, 12:52 PM

May 17 2022

gaoh added a comment to T28884: MITK Flowbench -Save Seg not working, due to file naming issues.

yes, that will help. Also, this worklist will be quite helpful, allowing a new form of "batch-processing".

May 17 2022, 3:34 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)

May 16 2022

gaoh lowered the priority of T28884: MITK Flowbench -Save Seg not working, due to file naming issues from Normal to Low.

Yes, so I changed it already, and I am using the seriesUID as name for the images. Additionally, I had to add the layer property: Because by introducing the image name property, somehow the layer is also set (to a high number, probably). When I create a new SEG without setting the layer of the image to 0, the SEG is only put on top, when opening the data manager.

May 16 2022, 10:02 AM · MITK (v2023.04), Request for Discussion, Kaapana (internal)

Mar 25 2022

gaoh triaged T29062: MITK Flow as High priority.
Mar 25 2022, 2:28 PM · Cleared, MITK (v2022.04)

Jan 27 2022

gaoh added a comment to T28886: MITK Flowbench - Reopen created segmentation not working.

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

Jan 27 2022, 1:08 PM · MITK (v2022.10), Missing Info, Kaapana (internal)

Jan 26 2022

gaoh added a comment to T28946: MITK Flow - Save Segmentation - Error/Exception Handling.

Input data to reproduce the error:

Jan 26 2022, 12:50 PM · Auto-closed, Kaapana (internal), MITK
gaoh triaged T28946: MITK Flow - Save Segmentation - Error/Exception Handling as Normal priority.

We discussed in the meeting:

  1. Exception handling is a good idea and should be the way to handle it. So mitk has to throw the exception and not show a success.
  2. Since in the input image a required tag is missing, MITK cannot provide a fix, allowing a success in dcmqi
Jan 26 2022, 11:40 AM · Auto-closed, Kaapana (internal), MITK
gaoh updated the task description for T28946: MITK Flow - Save Segmentation - Error/Exception Handling.
Jan 26 2022, 9:53 AM · Auto-closed, Kaapana (internal), MITK
gaoh created T28946: MITK Flow - Save Segmentation - Error/Exception Handling.
Jan 26 2022, 9:51 AM · Auto-closed, Kaapana (internal), MITK

Jan 25 2022

gaoh closed Restricted Maniphest Task, a subtask of T27968: CTP gets stuck on large import, as Resolved.
Jan 25 2022, 12:57 PM · Kaapana (internal)

Dec 1 2021

gaoh triaged T28889: [Installer] Ubuntu 20.04 missing required package to start GUI as Normal priority.
Dec 1 2021, 11:13 AM · Auto-closed, MITK

Nov 30 2021

gaoh added a comment to T28886: MITK Flowbench - Reopen created segmentation not working.

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

Nov 30 2021, 8:16 PM · MITK (v2022.10), Missing Info, Kaapana (internal)
gaoh added a project to T28886: MITK Flowbench - Reopen created segmentation not working: Kaapana (internal).
Nov 30 2021, 4:49 PM · MITK (v2022.10), Missing Info, Kaapana (internal)
gaoh created T28886: MITK Flowbench - Reopen created segmentation not working.
Nov 30 2021, 4:48 PM · MITK (v2022.10), Missing Info, Kaapana (internal)
gaoh added a project to T28884: MITK Flowbench -Save Seg not working, due to file naming issues: Kaapana (internal).
Nov 30 2021, 1:38 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)
gaoh created T28884: MITK Flowbench -Save Seg not working, due to file naming issues.
Nov 30 2021, 1:37 PM · MITK (v2023.04), Request for Discussion, Kaapana (internal)

Nov 3 2021

gaoh removed a project from T28159: Officially support MITK using system Qt: Kaapana (internal).
Nov 3 2021, 3:07 PM · Auto-closed, CI, Request for Discussion, MITK

Oct 29 2021

gaoh added a comment to T27968: CTP gets stuck on large import.

In the current setup, the transfer is handled from airflow. This is also the case in the wDB-gateway. This stress test should therefore perform the same way and work. I have also a different test with random data, that work up to a limit. The system has now different recovery possibilities and can therefore handle large (random sorted) datasets better. I guess that there are sometimes sill errors, but since the system then restarts, no-one notices it. But there are still limits (depending mainly on the server (RAM)).
So I would also say this ticket is resolved for now. On a long run, changing the whole import process could remain a valid option.

Oct 29 2021, 9:45 AM · Kaapana (internal)

Sep 10 2021

gaoh added a comment to T28600: Kaapana containerd version is 1.2.5 which is 2 years old: Need to update that.

so, this is what we have tried so far:
helm updated to 3.6
microk9s to 1.22
first problem: v1beta1 version cannot be used anymore --> changed to v1 in the repo
next problem: our treafik is not compatible anymore (with 1.22)

Sep 10 2021, 12:18 PM · Request for Discussion, Kaapana (internal)
gaoh lowered the priority of T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch from Normal to Low.
Sep 10 2021, 9:20 AM · Request for Discussion, Kaapana (internal)

Aug 3 2021

gaoh added a member for MIC: metzger.
Aug 3 2021, 1:49 PM

Jul 19 2021

gaoh added a comment to T28529: Replace Elasticsearch and Kibana with apache-licensed opensearch.

So I tried it out. The problem are not the containeres (opensearch and opensearch-dashboard), but our plugin (workflow-trigger).
The plugin workflow-trigger has some package dependencies based on elastic/kibana. These dependencies have to be changed to the once of opensearch-dashboard.
So I tried to change it, but I get some yarn build issues.
So I am having different issues, probably it would be easier to restart the plugin form fresh. But for this, I would like to know, how the current plugin was created, to get an understanding, on how to create a similar one.
So the current issue is, that the package is searching for specific files, probably an opensearch-dashboard has to have a specific dir-order:

Jul 19 2021, 11:37 AM · Request for Discussion, Kaapana (internal)

May 25 2021

gaoh closed T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02 as Resolved.
May 25 2021, 9:26 AM · MITK

May 19 2021

gaoh reopened T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02 as "Open".

The same issue seems to apply to the normal workbench, so this container has also to be updated to the current master

May 19 2021, 11:36 AM · MITK

May 5 2021

gaoh closed T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02 as Resolved.
May 5 2021, 11:27 AM · MITK

Apr 8 2021

gaoh added a member for Kaapana (internal): r738v.
Apr 8 2021, 12:24 PM
gaoh added a member for MIC: r738v.
Apr 8 2021, 12:23 PM

Mar 22 2021

gaoh placed T27968: CTP gets stuck on large import up for grabs.

after tests of the system, the problem might be at the airflow part, this has to be tested

Mar 22 2021, 2:53 PM · Kaapana (internal)

Mar 16 2021

gaoh updated the task description for T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02.
Mar 16 2021, 10:52 AM · MITK
gaoh created T28380: [MultLabel Segmentation, MITK FlowBench] Segmentation not recognized as segmentation in Release v2021.02.
Mar 16 2021, 10:51 AM · MITK

Mar 15 2021

gaoh added a comment to T28374: Workbench crashes after DICOM retrieval .

T28207 describes how to test it without the wDB. When searching for DICOM query retrieve there are already different tasks open with all similar problems

Mar 15 2021, 9:39 AM · Next Milestone, DICOM, MITK

Mar 4 2021

gaoh moved T27968: CTP gets stuck on large import from Discussion to In Progress on the Kaapana (internal) board.
Mar 4 2021, 9:35 AM · Kaapana (internal)
gaoh added a member for Kaapana (internal): d587s.
Mar 4 2021, 9:11 AM

Feb 24 2021

gaoh added a comment to T27968: CTP gets stuck on large import.

I cannot reproduce the error. When sending the data to an instance the data gets imported. When debugging CTP locally there also seems to be no problem. For me also it looks like the problem is not directly in the CTP but in the java library (dcm4che). Did the files got triggered/send to airflow? Did they get stuck in a quarantine folder of the CTP, and if so in which?

Feb 24 2021, 2:09 PM · Kaapana (internal)
gaoh added a comment to T27968: CTP gets stuck on large import.

This is one of my model DICOMs (not 100% sure if this will reproduce it).
If not I can try to make bigger parts.

Download-link from my instance

Just a remark: The download link does not work for me. I get forbidden access. This is also the case, even if I am logged into the platform. But since there is only one folder in minio I also found it without the link:)

Feb 24 2021, 12:26 PM · Kaapana (internal)
gaoh added a comment to T27968: CTP gets stuck on large import.

Can you send me a dataset to reproduce it? I could try to debug CTP, but it looks like it is not even a problem in CTP but in org.dcm4chri

Feb 24 2021, 9:47 AM · Kaapana (internal)

Feb 23 2021

gaoh placed T28207: MITK DicomBrowser q/r Retrieve part crash up for grabs.
Feb 23 2021, 2:33 PM · MITK, Checklist
gaoh added a comment to T28207: MITK DicomBrowser q/r Retrieve part crash.

Get an Openstack instance (e.g. Ubuntu 20.04 DKFZ image,...)

Feb 23 2021, 11:16 AM · MITK, Checklist

Feb 22 2021

gaoh added a comment to T27968: CTP gets stuck on large import.

Can you reproduce the error? If so, we can do something like: https://stackoverflow.com/questions/12096403/java-shutting-down-on-out-of-memory-error

Feb 22 2021, 12:27 PM · Kaapana (internal)

Feb 19 2021

gaoh closed Restricted Maniphest Task, a subtask of T28302: MITK CI jobs for Kaapana, as Resolved.
Feb 19 2021, 11:53 AM · CI, MITK

Feb 18 2021

gaoh added a comment to T28302: MITK CI jobs for Kaapana.

@gaoh

I noticed that the only plugins enabled in the "MitkVolume" configuration are the segmentation plugins. Do you explicitly want to have this "slim" version or is the official WorkbenchRelease configuration more sufficient?

Feb 18 2021, 12:58 PM · CI, MITK

Feb 17 2021

gaoh added a comment to T28302: MITK CI jobs for Kaapana.

And MITK volume (aka the normal workbench) uses the Release build with segmentation=ON

Maybe we should then just label it MITK Workbenches to avoid confusion and reduce (redundant) artefacts.

Feb 17 2021, 11:01 AM · CI, MITK
gaoh added a comment to T28311: MitkFlowBench Naming Issue.

In case of kaapana, the name is currently irrelevant: directly in the next operator, the dcm files are send to the PACs anyway and then the file is deleted.
What would make sense, regading the naming in the PACs and when downloading files, would be to give it the name of the Instance UID.

Feb 17 2021, 9:13 AM · Auto-closed, MITK

Feb 16 2021

gaoh added a comment to T28311: MitkFlowBench Naming Issue.

so maybe a Regex is needed, or just a default file name..

Feb 16 2021, 11:00 AM · Auto-closed, MITK
gaoh created T28311: MitkFlowBench Naming Issue.
Feb 16 2021, 10:58 AM · Auto-closed, MITK

Feb 12 2021

gaoh added a comment to T28302: MITK CI jobs for Kaapana.

Ah so the idea is not to build it, but to directly use a CI binary.
So MITK flow uses:

# Generate Ninja build script for MITK to build a minimum configuration with apps in Release mode into MITK-superbuild directory
RUN cmake -G Ninja -S MITK -B MITK-superbuild
RUN cmake -S MITK -B MITK-superbuild -D CMAKE_BUILD_TYPE:STRING=Release -D BUILD_TESTING:BOOL=OFF -D MITK_BUILD_CONFIGURATION:STRING=FlowBenchSegmentationRelease -D MITK_CUSTOM_REVISION_DESC:STRING=MitkFlow
RUN cmake --build MITK-superbuild
RUN cmake --build MITK-superbuild/MITK-build --target package 
RUN mkdir /opt/final_package
RUN cp /opt/MITK-superbuild/MITK-build/MITK-MitkFlow-linux-x86_64.tar.gz /opt/final_package/MITK-MitkFlow-linux-x86_64.tar.gz

And MITK volume (aka the normal workbench) uses the Release build with segmentation=ON

Feb 12 2021, 10:01 AM · CI, MITK
gaoh added a comment to T28302: MITK CI jobs for Kaapana.

For MITK-flow and MITK-volume I will switch to the new release (release/T28000-v2021.02). It was only on a develop branch, because there were some bug fixes, not yet in a master branch.
But now with the new release...

Feb 12 2021, 9:36 AM · CI, MITK

Feb 1 2021

gaoh added a member for MIC: k688h.
Feb 1 2021, 11:37 AM
gaoh added a member for Kaapana (internal): k688h.
Feb 1 2021, 11:36 AM
gaoh added a comment to T28239: Multilabel Segmentation - 3D Segmentation Confused about required outcome.

To be honest, I just did not understand the checklist correctly. If you know the outcome and read the checklists, they are fine. But for me, it was like a new test starting with loading and testing 3D Data again. So I misunderstood the line Bei den folgenden Aktionen stets mehrere Label, auch auf unterschiedlichen Layern testen. as beeing a new test, because it had of kind of title character. And that is why I thought, I would start with a 3d Image again...

Feb 1 2021, 8:40 AM · MITK-ProjectTemplate, MITK (v2021.02)