Merge pull request #34 from Medical-Image-Analysis-Laboratory/28_refe…

…rence_stack

[ENH] Automatic reference/stacks ordering

.circleci/test-01_outputs.txt

@@ -21,11 +21,19 @@ nipype/sub-01/rec-1/srr_pipeline/data_sinker/_inputs.pklz
 nipype/sub-01/rec-1/srr_pipeline/data_sinker/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/data_sinker/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/data_sinker/result_data_sinker.pklz
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/_node.pklz
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/_report/report.rst
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/result_filenames_gen.pklz
 nipype/sub-01/rec-1/srr_pipeline/graph1.json
 nipype/sub-01/rec-1/srr_pipeline/graph.dot
 nipype/sub-01/rec-1/srr_pipeline/graph.json
 nipype/sub-01/rec-1/srr_pipeline/graph.png
 nipype/sub-01/rec-1/srr_pipeline/index.html
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/_node.pklz
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/_report/report.rst
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/result_masks_filtered.pklz
 nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/_inputs.pklz
 nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/nlmDenoise/_report/report.rst
@@ -154,17 +162,25 @@ nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_inputs.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/result_srtkTVSuperResolution.pklz
+nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.json
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.nii.gz
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/_node.pklz
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/_report/report.rst
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/result_t2ws_filtered.pklz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SR_id-1_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SR_id-1_T2w.json
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SR_id-1_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-1_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-1_id-1_desc-preprocSR_T2w.nii.gz
+pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-1_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-3_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-3_id-1_desc-preprocSR_T2w.nii.gz
+pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-3_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-5_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-5_id-1_desc-preprocSR_T2w.nii.gz
+pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-5_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
 pymialsrtk-2.0.0b1/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
 pymialsrtk-2.0.0b1/sub-01/xfm/sub-01_run-5_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt

.circleci/test-02_outputs.txt

@@ -8,11 +8,19 @@ nipype/sub-01/rec-1/srr_pipeline/data_sinker/_inputs.pklz
 nipype/sub-01/rec-1/srr_pipeline/data_sinker/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/data_sinker/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/data_sinker/result_data_sinker.pklz
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/_node.pklz
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/_report/report.rst
+nipype/sub-01/rec-1/srr_pipeline/filenames_gen/result_filenames_gen.pklz
 nipype/sub-01/rec-1/srr_pipeline/graph1.json
 nipype/sub-01/rec-1/srr_pipeline/graph.dot
 nipype/sub-01/rec-1/srr_pipeline/graph.json
 nipype/sub-01/rec-1/srr_pipeline/graph.png
 nipype/sub-01/rec-1/srr_pipeline/index.html
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/_node.pklz
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/_report/report.rst
+nipype/sub-01/rec-1/srr_pipeline/masks_filtered/result_masks_filtered.pklz
 nipype/sub-01/rec-1/srr_pipeline/Multiple_Brain_extraction/_inputs.pklz
 nipype/sub-01/rec-1/srr_pipeline/Multiple_Brain_extraction/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/Multiple_Brain_extraction/_report/report.rst
@@ -151,23 +159,25 @@ nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_inputs.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_node.pklz
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/_report/report.rst
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/result_srtkTVSuperResolution.pklz
+nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.json
 nipype/sub-01/rec-1/srr_pipeline/srtkTVSuperResolution/SRTV_sub-01_3V_rad1.nii.gz
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/_inputs.pklz
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/_node.pklz
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/_report/report.rst
+nipype/sub-01/rec-1/srr_pipeline/t2ws_filtered/result_t2ws_filtered.pklz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SDI_id-1_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SR_id-1_T2w_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SR_id-1_T2w.json
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_rec-SR_id-1_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-1_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-1_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-1_id-1_desc-preprocSR_T2w.nii.gz
-pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-2_T2w_brainMask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-3_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-3_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-3_id-1_desc-preprocSR_T2w.nii.gz
-pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-4_T2w_brainMask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-5_desc-brain_mask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-5_id-1_desc-preprocSDI_T2w.nii.gz
 pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-5_id-1_desc-preprocSR_T2w.nii.gz
-pymialsrtk-2.0.0b1/sub-01/anat/sub-01_run-6_T2w_brainMask.nii.gz
 pymialsrtk-2.0.0b1/sub-01/xfm/sub-01_run-1_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
 pymialsrtk-2.0.0b1/sub-01/xfm/sub-01_run-3_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt
 pymialsrtk-2.0.0b1/sub-01/xfm/sub-01_run-5_id-1_T2w_from-origin_to-SDI_mode-image_xfm.txt

.gitignore

@@ -85,8 +85,9 @@ dist
 data/derivatives/mialsrtk*
 data/derivatives/nipype*
 data/derivatives/pymialsrtk*
+data/derivatives/manual_masks*
+data/sub-ctrl*
 
 # Editors  #
 #####################
 .idea/*
-

docker/bidsapp/run.py

@@ -159,7 +159,7 @@ def main(bids_dir, output_dir, subject, p_stacksOrder, session, paramTV=None, nu
     session <string>
         Session ID if applicable (in the form ``ses-YY``)
 
-    paramTV dict<'deltatTV': float, 'lambdaTV': float, 'primal_dual_loops': int>>
+    paramTV dict <'deltatTV': float, 'lambdaTV': float, 'primal_dual_loops': int>>
         Dictionary of Total-Variation super-resolution optimizer parameters
 
     number_of_cores <int>
@@ -236,9 +236,10 @@ def main(bids_dir, output_dir, subject, p_stacksOrder, session, paramTV=None, nu
                 for sr_params in sr_list:
 
                     ses = sr_params["session"] if "session" in sr_params.keys() else None
+                    stacks_order = sr_params['stacksOrder'] if 'stacksOrder' in sr_params.keys() else None
 
                     print('sr_params')
-                    if ("stacksOrder" not in sr_params.keys()) or ("sr-id" not in sr_params.keys()):
+                    if ("sr-id" not in sr_params.keys()):
                         print('Do not process subjects %s because of missing parameters.' % sub)
                         continue
 
@@ -247,7 +248,7 @@ def main(bids_dir, output_dir, subject, p_stacksOrder, session, paramTV=None, nu
                         res = main(bids_dir=args.bids_dir,
                                    output_dir=args.output_dir,
                                    subject=sub,
-                                   p_stacksOrder=sr_params['stacksOrder'],
+                                   p_stacksOrder=stacks_order,
                                    session=ses,
                                    paramTV=sr_params['paramTV'],
                                    srID=sr_params['sr-id'],
@@ -261,7 +262,7 @@ def main(bids_dir, output_dir, subject, p_stacksOrder, session, paramTV=None, nu
                         res = main(bids_dir=args.bids_dir,
                                    output_dir=args.output_dir,
                                    subject=sub,
-                                   p_stacksOrder=sr_params['stacksOrder'],
+                                   p_stacksOrder=stacks_order,
                                    session=ses,
                                    srID=sr_params['sr-id'],
                                    use_manual_masks=args.manual,

docker/jupyter/Dockerfile

@@ -32,10 +32,13 @@ COPY . /app/notebooks
 
 WORKDIR /app/notebooks
 
-RUN printf '#!/bin/bash \n %s && jupyter-notebook --allow-root --no-browser --ip=\"0.0.0.0\" --NotebookApp.token=\'mial\'' "$CONDA_ACTIVATE" > /app/launch_jupyter_notebook.sh
-RUN chmod 755 /app/launch_jupyter_notebook.sh
+# RUN printf "#!/bin/bash \n %s && jupyter-notebook --allow-root --no-browser --ip=\"0.0.0.0\" --NotebookApp.token=\'mial\'" "$CONDA_ACTIVATE" > /app/launch_jupyter_notebook.sh
+RUN printf "#!/bin/bash \n %s && jupyter-lab --allow-root --no-browser --ip=\"0.0.0.0\" --NotebookApp.token=\'mial\'" "$CONDA_ACTIVATE" > /app/launch_jupyter_lab.sh
+# RUN chmod 755 /app/launch_jupyter_notebook.sh
+RUN chmod 755 /app/launch_jupyter_lab.sh
 
-ENTRYPOINT ["/app/launch_jupyter_notebook.sh"]
+# ENTRYPOINT ["/app/launch_jupyter_notebook.sh"]
+ENTRYPOINT ["/app/launch_jupyter_lab.sh"]
 
 #ENTRYPOINT ["/opt/mialsuperresolutiontoolkit/run.py"]
 

examples/run_docker_jupyter.sh

@@ -5,7 +5,7 @@ data_dir="/home/hkebiri/mialsuperresolutiontoolkit/data"
 
 port=8888
 
-version=v2.0.0-beta-20190906
+version=v2.0.0
 
 cmd="docker run --rm"
 cmd="$cmd -v "${mialsrtk_dir}/notebooks":/app/notebooks"