Merge pull request #26 from poldracklab/enh/revise-workflow

ENH: Setup a smoke test on CircleCI + minor improvements to CLI

Author: oesteban

.circleci/config.yml

@@ -118,6 +118,29 @@ jobs:
           paths:
             - /tmp/docker
 
+      - restore_cache:
+          keys:
+            - templateflow-v1-{{ .Branch }}-{{ epoch }}
+            - templateflow-v1-{{ .Branch }}-
+            - templateflow-v1-master-
+            - templateflow-v1-
+          paths:
+            - /tmp/templateflow
+      - run:
+          name: Run on example dataset
+          no_output_timeout: 60m
+          command: |
+            mkdir -p /tmp/templateflow /tmp/workdir
+            docker run -u $( id -u ) --rm -it -v /tmp/templateflow:/home/nirodents/.cache/templateflow \
+                -v $PWD/nirodents/data:/data -v /tmp/workdir:/work -w /work nirodents:latest \
+                artsBrainExtraction /data/15_1_T2_Quick_RAS.nii.gz --sloppy
+      - save_cache:
+          key: templateflow-v1-{{ .Branch }}-{{ epoch }}
+          paths:
+            - /tmp/templateflow
+      - store_artifacts:
+          path: /tmp/workdir
+          destination: interim
 workflows:
   version: 2
   build_test_deploy:

.dockerignore

@@ -0,0 +1,6 @@
+.circleci/
+.maint/
+docs/
+.gitignore
+.mailmap
+.travis.yml

nirodents/cli/brainextraction.py

@@ -14,18 +14,40 @@ def get_parser():
 ANTs-based Rodents ToolS (ARTs) package.\
 """, formatter_class=ArgumentDefaultsHelpFormatter)
 
+    parser.add_argument("input_image", action="store", type=Path,
+                        help="The target image for brain extraction.")
     parser.add_argument("--version", action="version",
                         version="artsBrainExtraction v{}".format(__version__))
-    parser.add_argument("-i", "--input-image", action="store", type=Path,
-                        help="The target image for brain extraction.")
     parser.add_argument("--template", action="store", choices=("WHS", ), default="WHS",
                         help="The TemplateFlow ID of the reference template.")
     parser.add_argument("--omp-nthreads", action="store", type=int, default=cpu_count(),
                         help="Number of CPUs available for multithreading processes.")
     parser.add_argument("--nprocs", action="store", type=int, default=cpu_count(),
                         help="Number of processes that can be run in parallel.")
-    parser.add_argument("--debug", action="store", type=int, default=0, choices=[0,1],
-                        help="Boolean to run debug mode.")
+    parser.add_argument(
+        "-m",
+        "--mri-scheme",
+        action="store",
+        type=str,
+        default="T2w",
+        choices=("T2w", "T1w"),
+        help="select a particular MRI scheme"
+    )
+    parser.add_argument(
+        "-w",
+        "--work-dir",
+        action="store",
+        type=Path,
+        default=Path("work").absolute(),
+        help="path where intermediate results should be stored",
+    )
+    parser.add_argument(
+        "--sloppy",
+        dest="debug",
+        action="store_true",
+        default=False,
+        help="Use low-quality tools for speed - TESTING ONLY",
+    )
     return parser
 
 
@@ -36,17 +58,20 @@ def main():
     opts = get_parser().parse_args()
     be = init_rodent_brain_extraction_wf(
         in_template=opts.template,
+        bids_suffix=opts.mri_scheme,
         omp_nthreads=opts.omp_nthreads,
-        debug=opts.debug
+        debug=opts.debug,
     )
+    be.base_dir = opts.work_dir
     be.inputs.inputnode.in_files = opts.input_image
     nipype_plugin = {"plugin": "Linear"}
     if opts.nprocs > 1:
         nipype_plugin["plugin"] = "MultiProc"
         nipype_plugin["plugin_args"] = {
             "nproc": opts.nprocs,
+            "raise_insufficient": False,
+            "maxtasksperchild": 1,
         }
-    print('input image: ', opts.input_image)
     be.run(**nipype_plugin)
 
 

nirodents/workflows/brainextraction.py

@@ -37,11 +37,9 @@ def init_rodent_brain_extraction_wf(
     final_normalization_quality='precise',
     in_template='WHS',
     init_normalization_quality='3stage',
-    modality='T2w',
     mem_gb=3.0,
     name='rodent_brain_extraction_wf',
     omp_nthreads=None,
-    tpl_suffix='T2star',
     template_spec=None,
     use_float=True,
 ):
@@ -63,7 +61,7 @@ def init_rodent_brain_extraction_wf(
                         name='inputnode')
 
     # Find images in templateFlow
-    tpl_target_path = get_template(in_template, resolution=debug + 1, suffix=tpl_suffix)
+    tpl_target_path = get_template(in_template, resolution=debug + 1, suffix="T2star" if bids_suffix == "T2w" else "T1w")
     tpl_regmask_path = get_template(in_template, resolution=debug + 1, atlas='v3', desc='brain', suffix='mask')
     if tpl_regmask_path:
         inputnode.inputs.in_mask = str(tpl_regmask_path)
@@ -125,7 +123,7 @@ def init_rodent_brain_extraction_wf(
         interpolation='Linear', invert_transform_flags=True), name='warp_mask')
 
     # Set up initial spatial normalization
-    init_settings_file = f'data/brainextraction_{init_normalization_quality}_{modality}.json'
+    init_settings_file = f'data/brainextraction_{init_normalization_quality}_{bids_suffix}.json'
     init_norm = pe.Node(Registration(from_file=pkgr_fn(
         'nirodents', init_settings_file)),
         name='init_norm',
@@ -161,7 +159,7 @@ def init_rodent_brain_extraction_wf(
         skullstrip_tpl.inputs.in_file = tpl_target_path
 
     # Normalise skull-stripped image to brain template
-    final_settings_file = f'data/brainextraction_{final_normalization_quality}_{modality}.json'
+    final_settings_file = f'data/brainextraction_{final_normalization_quality}_{bids_suffix}.json'
     final_norm = pe.Node(Registration(from_file=pkgr_fn(
         'nirodents', final_settings_file)),
         name='final_norm',
@@ -192,7 +190,7 @@ def init_rodent_brain_extraction_wf(
 
     sinker = pe.Node(DataSink(), name='sinker')
 
-    if modality.lower() == 't2w':
+    if bids_suffix.lower() == 't2w':
         wf.connect([
             # resampling, truncation, initial N4, and creation of laplacian
             (inputnode, trunc, [('in_files', 'op1')]),
@@ -271,7 +269,7 @@ def init_rodent_brain_extraction_wf(
         ])
         return wf
 
-    elif modality == 'mp2rage':
+    elif bids_suffix == 't1w':
         wf.connect([
             # resampling and creation of laplacians
             (inputnode, res_target, [('in_files', 'in_file')]),

setup.cfg

@@ -23,7 +23,7 @@ install_requires =
     attrs
     nibabel >= 3.0.1
     nipype @ git+https://github.com/nipy/nipype.git@master
-    niworkflows @ git+https://github.com/oesteban/niworkflows.git@6d2286268d09215045161e534d0bf84dc34f38fc
+    niworkflows @ git+https://github.com/oesteban/niworkflows.git@0f7e42971cf119925b72042db607c9be3f19144a
     templateflow ~= 0.6
 test_requires =
     coverage < 5