Skip to content

Commit 8bbb532

Browse files
davidmeunier79davidmeunier79
authored
Add itk debias clean Dockerfiles (#299)
itk_debias + clean Dockerfile
1 parent 051da82 commit 8bbb532

File tree

16 files changed

+276
-190
lines changed

16 files changed

+276
-190
lines changed

‎.github/workflows/build_on_prerelease.yml‎

Lines changed: 56 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ jobs:
6767
uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
6868
with:
6969
context: .
70-
file: Dockerfile_testpypi_nomcr
70+
file: Dockerfile_testpypi
7171
push: true
7272
tags: ${{ steps.meta.outputs.tags }}
7373
labels: ${{ steps.meta.outputs.labels }}
@@ -161,7 +161,7 @@ jobs:
161161
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results
162162

163163
run-pretest-ants-marmo:
164-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg marmo)
164+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo)
165165
needs: docker-build
166166
runs-on: ubuntu-latest
167167
timeout-minutes: 1440
@@ -187,9 +187,9 @@ jobs:
187187
ls macapype_CI_v2.1/cerimed_marmo
188188
echo ""
189189
190-
- name: Running test pipeline cerimed_marmo ANTS_robustreg_noseg T1 T2
190+
- name: Running test pipeline cerimed_marmo ANTS_noseg T1 T2
191191
run: |
192-
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
192+
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
193193
194194
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/
195195
@@ -206,7 +206,7 @@ jobs:
206206
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
207207

208208
run-pretest-ants-marmoT2:
209-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS marmo T2)
209+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo T2)
210210
needs: docker-build
211211
runs-on: ubuntu-latest
212212
timeout-minutes: 1440
@@ -250,7 +250,7 @@ jobs:
250250
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
251251

252252
run-pretest-ants-baboon:
253-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
253+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
254254
needs: docker-build
255255
runs-on: ubuntu-latest
256256
timeout-minutes: 1440
@@ -294,7 +294,7 @@ jobs:
294294
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results
295295

296296
run-pretest-ants-baboon3:
297-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
297+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
298298
needs: docker-build
299299
runs-on: ubuntu-latest
300300
timeout-minutes: 1440
@@ -338,7 +338,7 @@ jobs:
338338
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3
339339

340340
run-pretest-ants-baboon2:
341-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
341+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
342342
needs: docker-build
343343
runs-on: ubuntu-latest
344344
timeout-minutes: 1440
@@ -382,7 +382,7 @@ jobs:
382382
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2
383383

384384
run-pretest-ants-baboon1:
385-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
385+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
386386
needs: docker-build
387387
runs-on: ubuntu-latest
388388
timeout-minutes: 1440
@@ -425,6 +425,50 @@ jobs:
425425
run:
426426
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1
427427

428+
run-pretest-ants-baboon0:
429+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
430+
needs: docker-build
431+
runs-on: ubuntu-latest
432+
timeout-minutes: 1440
433+
434+
steps:
435+
- name: Pull latest docker image
436+
run:
437+
docker pull macatools/macapype:latest
438+
439+
- name: Download dataset
440+
run: |
441+
442+
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
443+
444+
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
445+
446+
pwd
447+
echo ""
448+
449+
ls macapype_CI_v2.1
450+
echo ""
451+
452+
ls macapype_CI_v2.1/cerimed_baboon
453+
echo ""
454+
455+
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
456+
run: |
457+
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results0 -soft ANTS_robustreg_prep -species baboon0 -sub Prune -ses 0 -deriv -pad -dt T1 T2
458+
459+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/
460+
461+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/
462+
463+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/
464+
465+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/sub-Prune/ses-0/anat/
466+
echo ""
467+
468+
- name: Cleaning dataset
469+
run:
470+
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0
471+
428472
run-pretest-ants-baboon3-0p6:
429473
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
430474
needs: docker-build
@@ -452,7 +496,7 @@ jobs:
452496
ls macapype_CI_v2.1/cerimed_baboon
453497
echo ""
454498
455-
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
499+
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
456500
run: |
457501
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_robustreg -species baboon3_0p6 -sub Prune -ses 3 -deriv -pad -dt T1 T2
458502
@@ -496,7 +540,7 @@ jobs:
496540
ls macapype_CI_v2.1/cerimed_baboon
497541
echo ""
498542
499-
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
543+
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
500544
run: |
501545
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_robustreg -species baboon2_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
502546
@@ -540,7 +584,7 @@ jobs:
540584
ls macapype_CI_v2.1/cerimed_baboon
541585
echo ""
542586
543-
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
587+
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
544588
run: |
545589
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_robustreg -species baboon1_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
546590

‎.github/workflows/build_on_release.yml‎

Lines changed: 56 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ jobs:
6666
with:
6767
context: .
6868

69-
file: Dockerfile_nomcr
69+
file: Dockerfile
7070
push: true
7171
tags: ${{ steps.meta.outputs.tags }}
7272
labels: ${{ steps.meta.outputs.labels }}
@@ -161,7 +161,7 @@ jobs:
161161
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_macaque/results
162162

163163
run-pretest-ants-marmo:
164-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg marmo)
164+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo)
165165
needs: docker-build
166166
runs-on: ubuntu-latest
167167
timeout-minutes: 1440
@@ -187,9 +187,9 @@ jobs:
187187
ls macapype_CI_v2.1/cerimed_marmo
188188
echo ""
189189
190-
- name: Running test pipeline cerimed_marmo ANTS_robustreg_noseg T1 T2
190+
- name: Running test pipeline cerimed_marmo ANTS_noseg T1 T2
191191
run: |
192-
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_robustreg_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
192+
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_marmo -out /data/cerimed_marmo/results -soft ANTS_noseg -species marmo -sub Tresor -ses 01 -deriv -pad -dt T1 T2
193193
194194
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results/
195195
@@ -206,7 +206,7 @@ jobs:
206206
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
207207

208208
run-pretest-ants-marmoT2:
209-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS marmo T2)
209+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_noseg marmo T2)
210210
needs: docker-build
211211
runs-on: ubuntu-latest
212212
timeout-minutes: 1440
@@ -250,7 +250,7 @@ jobs:
250250
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_marmo/results
251251

252252
run-pretest-ants-baboon:
253-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
253+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
254254
needs: docker-build
255255
runs-on: ubuntu-latest
256256
timeout-minutes: 1440
@@ -294,7 +294,7 @@ jobs:
294294
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results
295295

296296
run-pretest-ants-baboon3:
297-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
297+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
298298
needs: docker-build
299299
runs-on: ubuntu-latest
300300
timeout-minutes: 1440
@@ -338,7 +338,7 @@ jobs:
338338
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results3
339339

340340
run-pretest-ants-baboon2:
341-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
341+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
342342
needs: docker-build
343343
runs-on: ubuntu-latest
344344
timeout-minutes: 1440
@@ -382,7 +382,7 @@ jobs:
382382
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results2
383383

384384
run-pretest-ants-baboon1:
385-
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
385+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
386386
needs: docker-build
387387
runs-on: ubuntu-latest
388388
timeout-minutes: 1440
@@ -425,6 +425,50 @@ jobs:
425425
run:
426426
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results1
427427

428+
run-pretest-ants-baboon0:
429+
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg_prep baboon)
430+
needs: docker-build
431+
runs-on: ubuntu-latest
432+
timeout-minutes: 1440
433+
434+
steps:
435+
- name: Pull latest docker image
436+
run:
437+
docker pull macatools/macapype:latest
438+
439+
- name: Download dataset
440+
run: |
441+
442+
curl https://amubox.univ-amu.fr/public.php/dav/files/CoSC5w5ATZextme --output macapype_CI_v2.1.zip
443+
444+
unzip -o macapype_CI_v2.1.zip -d macapype_CI_v2.1
445+
446+
pwd
447+
echo ""
448+
449+
ls macapype_CI_v2.1
450+
echo ""
451+
452+
ls macapype_CI_v2.1/cerimed_baboon
453+
echo ""
454+
455+
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
456+
run: |
457+
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results0 -soft ANTS_robustreg_prep -species baboon0 -sub Prune -ses 0 -deriv -pad -dt T1 T2
458+
459+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/
460+
461+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/
462+
463+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/
464+
465+
ls /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0/derivatives/macapype_ants/sub-Prune/ses-0/anat/
466+
echo ""
467+
468+
- name: Cleaning dataset
469+
run:
470+
sudo rm -rf /home/runner/work/macapype/macapype/macapype_CI_v2.1/cerimed_baboon/results0
471+
428472
run-pretest-ants-baboon3-0p6:
429473
name: Running all existing pipelines in macapype_CI_v2.1.zip (ANTS_robustreg baboon)
430474
needs: docker-build
@@ -452,7 +496,7 @@ jobs:
452496
ls macapype_CI_v2.1/cerimed_baboon
453497
echo ""
454498
455-
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
499+
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
456500
run: |
457501
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results3 -soft ANTS_robustreg -species baboon3_0p6 -sub Prune -ses 3 -deriv -pad -dt T1 T2
458502
@@ -496,7 +540,7 @@ jobs:
496540
ls macapype_CI_v2.1/cerimed_baboon
497541
echo ""
498542
499-
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
543+
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
500544
run: |
501545
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results2 -soft ANTS_robustreg -species baboon2_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
502546
@@ -540,7 +584,7 @@ jobs:
540584
ls macapype_CI_v2.1/cerimed_baboon
541585
echo ""
542586
543-
- name: Running test pipeline cerimed_baboon ANTS_robustreg_prep T1 T2
587+
- name: Running test pipeline cerimed_baboon ANTS_robustreg T1 T2
544588
run: |
545589
docker run -i -v /home/runner/work/macapype/macapype/macapype_CI_v2.1:/data macatools/macapype:latest segment_pnh -data /data/cerimed_baboon -out /data/cerimed_baboon/results1 -soft ANTS_robustreg -species baboon1_0p6 -sub Prune -ses 2 -deriv -pad -dt T1 T2
546590

0 commit comments

Comments
 (0)