Page MenuHomePhabricator

schererj (Jonas Scherer)
User

User Details

User Since
Feb 21 2017, 11:10 AM (224 w, 6 d)

Recent Activity

Mon, May 17

schererj added a comment to T28232: Shapemodels.

Ok, but this makes not a big difference, right?
Here's what I think would be good for us:

  • A single Dockerfile build-able without any local files
  • The needed source-code should be downloaded via a direct git clone within the Dockerfile
  • Internal usage would allow to pass credentials as build-args to git
  • Models should be downloaded via curl during the build-process as well
  • There should be two stages:
    1. Download and build source-code + download and unzip models
    2. Execution environment (incl. the models) - but without build dependencies, build tree etc
Mon, May 17, 11:21 AM · Kaapana (internal), Request for Discussion, MITK

May 14 2021

schererj committed rKAAPANA304068318187: added external mint model send (authored by schererj).
added external mint model send
May 14 2021, 10:35 AM
schererj committed rKAAPANAfa58acec850b: racoon-platform installer 14.05.21 (authored by schererj).
racoon-platform installer 14.05.21
May 14 2021, 10:00 AM

May 12 2021

schererj added a comment to T28232: Shapemodels.

The problem is the MBI branch, which is afaik not public.
If there is a working Dockerfile, which can be publicly build, I'm happy to include it.
Additionally the models need to be put somewhere to be downloaded (also public in this case).
Hope this helps.

May 12 2021, 4:53 PM · Kaapana (internal), Request for Discussion, MITK
schererj committed rKAAPANA7f408e671f74: reset api version (authored by schererj).
reset api version
May 12 2021, 4:04 PM
schererj committed rKAAPANAce79ced300b8: debug. (authored by schererj).
debug.
May 12 2021, 2:46 PM
schererj committed rKAAPANA430a24db0d15: new kube apis (authored by schererj).
new kube apis
May 12 2021, 2:46 PM
schererj committed rKAAPANA907f5ccfd5e0: debug. (authored by schererj).
debug.
May 12 2021, 2:46 PM
schererj committed rKAAPANAe500eb658d5e: kubernetes 1.20 adjustments (authored by schererj).
kubernetes 1.20 adjustments
May 12 2021, 11:59 AM
schererj committed rKAAPANAd89c3145f697: adjustments (authored by schererj).
adjustments
May 12 2021, 11:55 AM

May 11 2021

schererj committed rKAAPANA6d89ed6cc955: adjusted ensemble to find fitting models (authored by schererj).
adjusted ensemble to find fitting models
May 11 2021, 11:46 PM
schererj committed rKAAPANA366fc0191c27: small adjustments (authored by schererj).
small adjustments
May 11 2021, 6:04 PM
schererj committed rKAAPANA375acecc3b95: radiomics workflow gui-parameters (authored by schererj).
radiomics workflow gui-parameters
May 11 2021, 11:29 AM
schererj committed rKAAPANAf701d572bbb8: ohif link fix (authored by schererj).
ohif link fix
May 11 2021, 9:57 AM

May 10 2021

schererj committed rKAAPANAededa34b272d: small adjustments (authored by schererj).
small adjustments
May 10 2021, 5:35 PM
schererj committed rKAAPANAba3cd1a89bb2: removed skipping for empty segmentations (authored by schererj).
removed skipping for empty segmentations
May 10 2021, 4:42 PM
schererj committed rKAAPANA85f83fb33620: algname change (authored by schererj).
algname change
May 10 2021, 2:38 PM
schererj committed rKAAPANAaacdea031fa5: LocalSortGtOperator included (authored by schererj).
LocalSortGtOperator included
May 10 2021, 1:30 PM

May 9 2021

schererj committed rKAAPANAcc835e4b59b9: label collect fix and logging cleanup (authored by schererj).
label collect fix and logging cleanup
May 9 2021, 5:46 PM
schererj committed rKAAPANA68b87de28f68: test sat (authored by schererj).
test sat
May 9 2021, 1:22 AM

May 8 2021

schererj committed rKAAPANAd919ebe5ad83: progress (authored by schererj).
progress
May 8 2021, 11:18 AM
schererj committed rKAAPANAafd1a3a476b1: included delete series fix (authored by schererj).
included delete series fix
May 8 2021, 10:26 AM
schererj committed rKAAPANA0e9067785680: new workflow layout (authored by schererj).
new workflow layout
May 8 2021, 10:26 AM

May 7 2021

schererj committed rKAAPANA79bb014e6337: progress (authored by schererj).
progress
May 7 2021, 9:14 PM
schererj committed rKAAPANA742aa9b26fdc: added ensemble combination method (authored by schererj).
added ensemble combination method
May 7 2021, 1:02 PM
schererj committed rKAAPANA890dc330a624: working ensemble evaluation with new workflow (authored by schererj).
working ensemble evaluation with new workflow
May 7 2021, 8:52 AM
schererj committed rKAAPANAbadf1da11fb8: dice evaluation container (authored by schererj).
dice evaluation container
May 7 2021, 8:52 AM

May 6 2021

schererj committed rKAAPANA45b9f7cfc2cc: new tensor-based evaluation operator (authored by schererj).
new tensor-based evaluation operator
May 6 2021, 2:11 AM

May 5 2021

schererj committed rKAAPANA2dd0afa7069d: new resample concept (authored by schererj).
new resample concept
May 5 2021, 3:52 PM
schererj committed rKAAPANAe16604a59f3b: getInputData bugfix (authored by schererj).
getInputData bugfix
May 5 2021, 3:52 PM
schererj committed rKAAPANA1c22a8fc36fa: getInputData with elastic support (authored by schererj).
getInputData with elastic support
May 5 2021, 10:44 AM
schererj committed rKAAPANA48f455ebff79: ensemble adjustments (authored by schererj).
ensemble adjustments
May 5 2021, 10:44 AM

May 4 2021

schererj committed rKAAPANA20f3c3382e16: adjustments (authored by schererj).
adjustments
May 4 2021, 10:42 AM
schererj committed rKAAPANAfc4b543bd8fd: added conf to auto-trigger configuration (authored by schererj).
added conf to auto-trigger configuration
May 4 2021, 12:46 AM
schererj committed rKAAPANA50307be847e9: lots of small improvements (authored by schererj).
lots of small improvements
May 4 2021, 12:18 AM

May 3 2021

schererj committed rKAAPANA14b0d43a3066: added dicom send script (authored by schererj).
added dicom send script
May 3 2021, 2:29 PM
schererj committed rKAAPANA830a35f87296: added dicom send script (authored by schererj).
added dicom send script
May 3 2021, 2:29 PM
schererj committed rKAAPANA9138a8006d3e: Merge branch 'feature/racoon-platform' of https://phabricator.mitk. (authored by schererj).
Merge branch 'feature/racoon-platform' of https://phabricator.mitk.
May 3 2021, 2:29 PM
schererj committed rKAAPANAc5425ec8e5c8: single_label organ seg label fix (authored by schererj).
single_label organ seg label fix
May 3 2021, 2:29 PM
schererj committed rKAAPANA5d4a1ec9b10d: single_label organ seg label fix (authored by schererj).
single_label organ seg label fix
May 3 2021, 1:28 PM
schererj committed rKAAPANAbf0c12c13a69: Merge branch 'feature/racoon-platform' of https://phabricator.mitk. (authored by schererj).
Merge branch 'feature/racoon-platform' of https://phabricator.mitk.
May 3 2021, 12:57 PM
schererj committed rKAAPANA95eb9f3e9ccd: added body_part form entry to nnunet-train (authored by schererj).
added body_part form entry to nnunet-train
May 3 2021, 12:57 PM
schererj committed rKAAPANAd64794ad1942: added body-part-extraction from original dicom for DCMQI (authored by schererj).
added body-part-extraction from original dicom for DCMQI
May 3 2021, 12:45 PM
schererj committed rKAAPANAe047404a931a: chnaged max-active-runs shapemodels to 15 (authored by schererj).
chnaged max-active-runs shapemodels to 15
May 3 2021, 12:33 PM
schererj committed rKAAPANA240b1ffe03a8: Merge branch 'feature/racoon-platform' of https://phabricator.mitk. (authored by schererj).
Merge branch 'feature/racoon-platform' of https://phabricator.mitk.
May 3 2021, 12:01 PM
schererj committed rKAAPANA9033e2cd51c9: sorted seg list (authored by schererj).
sorted seg list
May 3 2021, 12:01 PM
schererj committed rKAAPANA98532827da2a: progress (authored by schererj).
progress
May 3 2021, 12:01 PM
schererj committed rKAAPANA40f172b72806: typo (authored by schererj).
typo
May 3 2021, 12:45 AM
schererj committed rKAAPANA1822bc866795: removed seg-labels from default dashboard (authored by schererj).
removed seg-labels from default dashboard
May 3 2021, 12:43 AM
schererj committed rKAAPANAe504c5759f2b: landing-page sort dashboaards + 2 new default dashboards (segmentation +… (authored by schererj).
landing-page sort dashboaards + 2 new default dashboards (segmentation +…
May 3 2021, 12:22 AM
schererj committed rKAAPANAcda21f78a56c: changed default interpolation_order to 1 (authored by schererj).
changed default interpolation_order to 1
May 3 2021, 12:22 AM

May 2 2021

schererj committed rKAAPANA024e329f3e31: removed seg-filter from default kibana dashboard (authored by schererj).
removed seg-filter from default kibana dashboard
May 2 2021, 3:58 PM
schererj committed rKAAPANAec9d8f5909bf: new init-dicom test container working v0.1.1-vdev (authored by schererj).
new init-dicom test container working v0.1.1-vdev
May 2 2021, 3:56 PM
schererj committed rKAAPANA87f68f81f6dd: dcmqi body_part for segmentations (authored by schererj).
dcmqi body_part for segmentations
May 2 2021, 1:54 AM
schererj committed rKAAPANAd2c1a7c7b8ac: seg-check working + Kibana Dashboard update (authored by schererj).
seg-check working + Kibana Dashboard update
May 2 2021, 12:59 AM

May 1 2021

schererj committed rKAAPANA2d0d5031dbfb: node_uid fix (authored by schererj).
node_uid fix
May 1 2021, 9:17 PM
schererj committed rKAAPANA84b879e521d9: Merge branch 'feature/racoon-platform' of https://phabricator.mitk. (authored by schererj).
Merge branch 'feature/racoon-platform' of https://phabricator.mitk.
May 1 2021, 9:17 PM
schererj committed rKAAPANAfedced75c03a: new segmenation merging operator (authored by schererj).
new segmenation merging operator
May 1 2021, 9:17 PM

Apr 29 2021

schererj moved T28458: Airflow-App from Discussion to In Progress on the Kaapana (internal) board.
Apr 29 2021, 9:14 AM · Kaapana (internal)
schererj committed rKAAPANA5d7280be9032: limited active_runs for extract metadata to 20 (authored by schererj).
limited active_runs for extract metadata to 20
Apr 29 2021, 9:13 AM

Apr 28 2021

schererj committed rKAAPANA2a5f69a3e860: incereased dcmsend timeout (authored by schererj).
incereased dcmsend timeout
Apr 28 2021, 8:59 PM
schererj committed rKAAPANA0aa5c2c4de39: 3d_lowres as default for training (authored by schererj).
3d_lowres as default for training
Apr 28 2021, 7:05 PM
schererj committed rKAAPANA93638a3b691c: removed all_selectable_tasks (authored by schererj).
removed all_selectable_tasks
Apr 28 2021, 2:59 PM
schererj committed rKAAPANAe39b8febd871: init (authored by schererj).
init
Apr 28 2021, 2:52 PM
schererj committed rKAAPANAab7b6e04e04f: re-added nnunet inference (authored by schererj).
re-added nnunet inference
Apr 28 2021, 2:52 PM
schererj committed rKAAPANAff440a1b2bff: switched train_network to model (authored by schererj).
switched train_network to model
Apr 28 2021, 1:47 PM
schererj committed rKAAPANA5015372a869f: switched train_network to model (authored by schererj).
switched train_network to model
Apr 28 2021, 1:47 PM
schererj committed rKAAPANAbeb5118eb2b3: increased waiting-time for reverse-proxy restart (authored by schererj).
increased waiting-time for reverse-proxy restart
Apr 28 2021, 1:46 PM
schererj committed rKAAPANA15cac706b3a7: prediction without dataset.json fix (authored by schererj).
prediction without dataset.json fix
Apr 28 2021, 11:33 AM
schererj committed rKAAPANA7cca4c336dfd: set use_nifti_encoding to false per default + mini improvements (authored by schererj).
set use_nifti_encoding to false per default + mini improvements
Apr 28 2021, 10:49 AM
schererj committed rKAAPANAa888486cbdef: dice evaluation single plot export + DCMQI seg-filter bugfix (authored by schererj).
dice evaluation single plot export + DCMQI seg-filter bugfix
Apr 28 2021, 10:37 AM

Apr 27 2021

schererj committed rKAAPANA120c2d59b3fb: nnunet prediction label adaptions (authored by schererj).
nnunet prediction label adaptions
Apr 27 2021, 10:21 PM
schererj committed rKAAPANA76b72b904f0e: push (authored by schererj).
push
Apr 27 2021, 4:02 PM
schererj committed rKAAPANA687a8dd7d7c5: bug-fixes train_network -> model (authored by schererj).
bug-fixes train_network -> model
Apr 27 2021, 4:02 PM
schererj committed rKAAPANA547b94c5fcf1: before testing (authored by schererj).
before testing
Apr 27 2021, 4:02 PM
schererj committed rKAAPANA4278e55343ad: progress (authored by schererj).
progress
Apr 27 2021, 4:02 PM

Apr 22 2021

schererj committed rKAAPANA25d55af6dd00: dicom port fix for dicom-node-port change (authored by schererj).
dicom port fix for dicom-node-port change
Apr 22 2021, 10:55 AM
schererj reopened T28458: Airflow-App as "Open".
Apr 22 2021, 9:33 AM · Kaapana (internal)
schererj committed rKAAPANA53ac32b5d88e: sort labels (authored by schererj).
sort labels
Apr 22 2021, 12:09 AM

Apr 21 2021

schererj committed rKAAPANA57931f14d590: DICOM port workaround (authored by schererj).
DICOM port workaround
Apr 21 2021, 7:50 PM

Apr 20 2021

schererj committed rKAAPANAf027b0558049: changed MitkSegConverter to Dcmqi (authored by schererj).
changed MitkSegConverter to Dcmqi
Apr 20 2021, 4:46 PM
schererj committed rKAAPANA2b4f524cecb6: increased timeout for dice-evaluation (authored by schererj).
increased timeout for dice-evaluation
Apr 20 2021, 4:11 PM
schererj committed rKAAPANAbfc10f4b6bdd: adjustments (authored by schererj).
adjustments
Apr 20 2021, 2:56 PM
schererj committed rKAAPANA62a9ab97dbd0: small fixes (authored by schererj).
small fixes
Apr 20 2021, 12:28 PM
schererj committed rKAAPANA5369aef907ec: sleep for installer (authored by schererj).
sleep for installer
Apr 20 2021, 12:11 PM
schererj committed rKAAPANAc9453212987a: nnunet update (authored by schererj).
nnunet update
Apr 20 2021, 10:45 AM
schererj committed rKAAPANAcc62ad0d596c: Merge branch 'feature/racoon-platform' of https://phabricator.mitk. (authored by schererj).
Merge branch 'feature/racoon-platform' of https://phabricator.mitk.
Apr 20 2021, 10:45 AM
schererj committed rKAAPANAbf0ef62110e0: before update (authored by schererj).
before update
Apr 20 2021, 10:45 AM

Apr 15 2021

schererj committed rKAAPANAd5fbe4f613a4: racoon-platform adjustments (authored by schererj).
racoon-platform adjustments
Apr 15 2021, 6:06 PM
schererj committed rKAAPANA42d7d1a38232: training adjustments (authored by schererj).
training adjustments
Apr 15 2021, 8:37 AM
schererj committed rKAAPANA2ba957c69603: Merge branch 'feature/training-test' into develop (authored by schererj).
Merge branch 'feature/training-test' into develop
Apr 15 2021, 8:37 AM
schererj committed rKAAPANA9306c2bcf0f3: small adjustments (authored by schererj).
small adjustments
Apr 15 2021, 8:37 AM

Apr 13 2021

schererj committed rKAAPANAf04ce5093188: Merge branch 'feature/racoon-test' into develop (authored by schererj).
Merge branch 'feature/racoon-test' into develop
Apr 13 2021, 10:53 PM
schererj committed rKAAPANA8dd9206d1a70: schedule on big enough gpus only (authored by schererj).
schedule on big enough gpus only
Apr 13 2021, 10:53 PM
schererj committed rKAAPANAee303b55fbc7: gpu scheduling working (authored by schererj).
gpu scheduling working
Apr 13 2021, 10:53 PM
schererj committed rKAAPANA4a6d0c79e293: Task01 fix (authored by schererj).
Task01 fix
Apr 13 2021, 10:53 PM
schererj committed rKAAPANAca5fc1cf996f: formatting (authored by schererj).
formatting
Apr 13 2021, 10:53 PM
schererj committed rKAAPANA0b373340162e: ready for testing (authored by schererj).
ready for testing
Apr 13 2021, 10:53 PM
schererj committed rKAAPANAf82e98f45980: removed max_active_runs from nnunet-inference (authored by schererj).
removed max_active_runs from nnunet-inference
Apr 13 2021, 10:53 PM
schererj committed rKAAPANAfe54e2818c03: gpu scheduling (authored by schererj).
gpu scheduling
Apr 13 2021, 10:53 PM