Merge pull request #9 from AlanKuurstra/first_echo_bug

fix bug in bids tag order dependency when finding first echo
AlanKuurstra · Apr 16, 2024 · a83a154 · a83a154
2 parents 99f35dd + 9230650
commit a83a154
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Showing 4 changed files with 28 additions and 28 deletions.
diff --git a/.github/workflows/ci-workflow.yml b/.github/workflows/ci-workflow.yml
@@ -55,11 +55,11 @@ jobs:
           reformat(){
             echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g"
           }
-          echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})
-          echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})
+          echo "TEST_IMAGE_BRANCH=$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})" >> "$GITHUB_ENV"
+          echo "TEST_IMAGE_LATEST=$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_LATEST=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG_DOCKERHUB=$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})" >> "$GITHUB_ENV"
 
       - name: login to github package registry
         run: |
@@ -72,6 +72,7 @@ jobs:
           if docker load -i previous_docker_image/prev_image.tar; then
             echo "Loaded docker image from cache."
           else
+            mkdir previous_docker_image
             if docker pull ${TEST_IMAGE_BRANCH}; then
               echo "Pulled ${TEST_IMAGE_BRANCH}"
             else
@@ -116,12 +117,12 @@ jobs:
           # also note the format to make env variables global to other steps: echo::set-env name={name}:{value}
           reformat(){
             echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g"
-          }
-          echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})
-          echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})
+          }          
+          echo "TEST_IMAGE_BRANCH=$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})" >> "$GITHUB_ENV"
+          echo "TEST_IMAGE_LATEST=$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_LATEST=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG_DOCKERHUB=$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})" >> "$GITHUB_ENV"
 
       - name: login to github package registry
         run: |
@@ -165,11 +166,11 @@ jobs:
           reformat(){
             echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g"
           }
-          echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})
-          echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})
+          echo "TEST_IMAGE_BRANCH=$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})" >> "$GITHUB_ENV"
+          echo "TEST_IMAGE_LATEST=$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_LATEST=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG_DOCKERHUB=$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})" >> "$GITHUB_ENV"
 
       - name: login to github package registry
         run: |
@@ -217,11 +218,11 @@ jobs:
           reformat(){
             echo "$1" | tr '[:upper:]' '[:lower:]' | sed -e "s/refs\/heads\///g" | sed -e "s/refs\/tags\///g"
           }
-          echo ::set-env name=TEST_IMAGE_BRANCH::$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})
-          echo ::set-env name=TEST_IMAGE_LATEST::$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_LATEST::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG::$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})
-          echo ::set-env name=BIDSAPP_IMAGE_TAG_DOCKERHUB::$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})
+          echo "TEST_IMAGE_BRANCH=$(reformat ${REGISTRY}/${TEST_IMAGE_BRANCH})" >> "$GITHUB_ENV"
+          echo "TEST_IMAGE_LATEST=$(reformat ${REGISTRY}/${TEST_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_LATEST=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_LATEST})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG=$(reformat ${REGISTRY}/${BIDSAPP_IMAGE_TAG})" >> "$GITHUB_ENV"
+          echo "BIDSAPP_IMAGE_TAG_DOCKERHUB=$(reformat ${BIDSAPP_IMAGE_TAG_DOCKERHUB})" >> "$GITHUB_ENV"
 
       - name: login to github package registry
         run: |

diff --git a/Dockerfile_testing b/Dockerfile_testing
@@ -11,11 +11,10 @@ RUN pip install virtualenv
 #install fsl
 #=============================================
 RUN echo "America/New_York" | sudo tee /etc/timezone && sudo dpkg-reconfigure --frontend noninteractive tzdata
-RUN wget -O- http://neuro.debian.net/lists/trusty.de-md.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
-#sudo apt-key adv --recv-keys --keyserver pgp.mit.edu 2649A5A9
-RUN apt-key adv --recv-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9
+RUN wget -O- http://neuro.debian.net/lists/xenial.cn-bj1.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+RUN apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 0xA5D32F012649A5A9
 RUN sudo apt-get update
-RUN sudo apt-get install -y fsl=5.0.9-5~nd14.04+1
+RUN sudo apt-get install -y fsl=5.0.9-5~nd16.04+1
 #=============================================
 
 #fsl

diff --git a/pipeline_SS_TV_Siemens.py b/pipeline_SS_TV_Siemens.py
@@ -73,14 +73,14 @@ def create_pipeline_SS_TV(bids_dir,
         if layout.get_sessions(subject=subject) == []:
             if sessions == ['.*']:
                 first_echo_files = first_echo_files + layout.get(subject=subject, modality='anat',
-                                                                 extensions='.*part-phase.*echo-0*1.*.nii.*', )
+                                                                 extensions='^(?=.*_part-phase_)(?=.*echo-0*1).*.nii.*', )
             else:
                 print(
                     "Warning: Session filter applied, but subject " + subject + " has no bids session information. This subject has been ignored.")
         else:
             for session in sessions:
                 first_echo_files = first_echo_files + layout.get(subject=subject, session=session, modality='anat',
-                                                                 extensions='.*part-phase.*echo-0*1.*.nii.*', )
+                                                                 extensions='^(?=.*_part-phase_)(?=.*echo-0*1).*.nii.*', )
     anat_folders = []
     for img in first_echo_files:
         full_dirname = os.path.dirname(img.filename)

diff --git a/requirements.txt b/requirements.txt
@@ -5,5 +5,5 @@ numpy==1.16.2
 pybids==0.6.5
 
 # cfmm-nipype-interaces specifies nipype version in dependencies, therefore we do not specify it in this requirements
-git+https://gitlab.com/Kuurstra/[email protected].0
+git+https://gitlab.com/Kuurstra/[email protected].1