Parallelize parcellation and replace atlases

.circleci/run_local_tests.py

@@ -0,0 +1,92 @@
+#!/usr/bin/env python3
+"""Run tests locally."""
+import argparse
+import os
+import subprocess
+
+
+def _get_parser():
+    """Parse command line inputs for tests.
+
+    Returns
+    -------
+    parser.parse_args() : argparse dict
+    """
+    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        "-k",
+        dest="test_regex",
+        metavar="PATTERN",
+        type=str,
+        help="Test pattern.",
+        required=False,
+        default=None,
+    )
+    parser.add_argument(
+        "-m",
+        dest="test_mark",
+        metavar="LABEL",
+        type=str,
+        help="Test mark label.",
+        required=False,
+        default=None,
+    )
+    return parser
+
+
+def run_command(command, env=None):
+    """Run a given shell command with certain environment variables set."""
+    merged_env = os.environ
+    if env:
+        merged_env.update(env)
+    process = subprocess.Popen(
+        command,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        shell=True,
+        env=merged_env,
+    )
+    while True:
+        line = process.stdout.readline()
+        line = str(line, "utf-8")[:-1]
+        print(line)
+        if line == "" and process.poll() is not None:
+            break
+
+    if process.returncode != 0:
+        raise RuntimeError(
+            f"Non zero return code: {process.returncode}\n" f"{command}\n\n{process.stdout.read()}"
+        )
+
+
+def run_tests(test_regex, test_mark):
+    """Run the tests."""
+    local_patch = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+    mounted_code = "/usr/local/miniconda/lib/python3.8/site-packages/aslprep"
+    run_str = "docker run --rm -ti "
+    run_str += f"-v {local_patch}:/usr/local/miniconda/lib/python3.8/site-packages/aslprep "
+    run_str += "--entrypoint pytest "
+    run_str += "pennlinc/aslprep:unstable "
+    run_str += (
+        f"{mounted_code}/aslprep "
+        f"--data_dir={mounted_code}/aslprep/tests/data/test_data "
+        f"--output_dir={mounted_code}/aslprep/tests/data/test_data/run_pytests/out "
+        f"--working_dir={mounted_code}/aslprep/tests/data/test_data/run_pytests/work "
+    )
+    if test_regex:
+        run_str += f"-k {test_regex} "
+    elif test_mark:
+        run_str += f"-rP -o log_cli=true -m {test_mark} "
+
+    run_command(run_str)
+
+
+def _main(argv=None):
+    """Run the tests."""
+    options = _get_parser().parse_args(argv)
+    kwargs = vars(options)
+    run_tests(**kwargs)
+
+
+if __name__ == "__main__":
+    _main()

.gitignore

@@ -1,3 +1,4 @@
+aslprep/tests/data/test_data
 .circleci/local_aslprep_path.txt
 
 .DS_Store

aslprep/data/aslprep_bids_config.json

@@ -13,11 +13,19 @@
     {
       "name": "measure",
       "pattern": "(?:^|_)measure-([a-zA-Z0-9]+)"
+    },
+    {
+      "name": "resolution",
+      "pattern": "res-([a-zA-Z0-9]+)"
+    },
+    {
+      "name": "density",
+      "pattern": "den-([a-zA-Z0-9]+)"
     }
   ],
   "default_path_patterns": [
-    "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
-    "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
+    "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
+    "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{density}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",