enh: prepare CLI script to run estimation, add --dry-run

sdcflows/cli/find_estimators.py → sdcflows/cli/main.py

@@ -1,3 +1,26 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Standalone command line executable for estimation of fieldmaps."""
 import argparse
 from pathlib import Path
 
@@ -12,6 +35,13 @@ def _parser():
         formatter_class=argparse.RawDescriptionHelpFormatter,
     )
     parser.add_argument("bids_dir", type=Path, help="The input BIDS directory to parse")
+    parser.add_argument(
+        "-n",
+        "--dry-run",
+        action="store_true",
+        default=False,
+        help="only find estimable fieldmaps (that is, estimation is not triggered)",
+    )
     parser.add_argument(
         "-s",
         "--subjects",
@@ -30,7 +60,7 @@ def _parser():
         metavar="PATH",
         type=Path,
         help="Path to a PyBIDS database folder, for faster indexing (especially "
-             "useful for large datasets). Will be created if not present."
+        "useful for large datasets). Will be created if not present.",
     )
     parser.add_argument(
         "-v",
@@ -54,14 +84,16 @@ def gen_layout(bids_dir, database_dir=None):
             "models",
             "derivatives",
             re.compile(r"^\."),
-            re.compile(r"sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|eeg|ieeg|meg|micr|perf)"),
+            re.compile(
+                r"sub-[a-zA-Z0-9]+(/ses-[a-zA-Z0-9]+)?/(beh|eeg|ieeg|meg|micr|perf)"
+            ),
         ),
     )
 
-    layout_kwargs = {'indexer': _indexer}
+    layout_kwargs = {"indexer": _indexer}
 
     if database_dir:
-        layout_kwargs['database_path'] = database_dir
+        layout_kwargs["database_path"] = database_dir
 
     layout = BIDSLayout(bids_dir, **layout_kwargs)
     return layout
@@ -80,7 +112,7 @@ def main(argv=None):
     bids_dir = pargs.bids_dir.resolve(strict=True)
     layout = gen_layout(bids_dir, pargs.bids_database_dir)
     subjects = collect_participants(layout, pargs.subjects)
-    logger = create_logger('sdcflow.wrangler', level=10 if pargs.verbose else 40)
+    logger = create_logger("sdcflow.wrangler", level=10 if pargs.verbose else 40)
     estimators_record = {}
     for subject in subjects:
         estimators_record[subject] = find_estimators(
@@ -91,18 +123,20 @@ def main(argv=None):
         )
 
     # pretty print results
-    print(f"Estimation for <{str(bids_dir)}> complete. Found:")
-    for subject, estimators in estimators_record.items():
-        print(f"\tsub-{subject}")
-        if not estimators:
-            print("\t\tNo estimators found")
-            continue
-        for estimator in estimators:
-            print(f"\t\t{estimator}")
-            for fl in estimator.sources:
-                fl_relpath = fl.path.relative_to(str(bids_dir / f'sub-{subject}'))
-                pe_dir = fl.metadata.get("PhaseEncodingDirection")
-                print(f"\t\t\t{pe_dir}\t{fl_relpath}")
+    if pargs.dry_run:
+        print(f"Estimation for <{str(bids_dir)}> complete. Found:")
+        for subject, estimators in estimators_record.items():
+            print(f"\tsub-{subject}")
+            if not estimators:
+                print("\t\tNo estimators found")
+                continue
+            for estimator in estimators:
+                print(f"\t\t{estimator}")
+                for fl in estimator.sources:
+                    fl_relpath = fl.path.relative_to(str(bids_dir / f"sub-{subject}"))
+                    pe_dir = fl.metadata.get("PhaseEncodingDirection")
+                    print(f"\t\t\t{pe_dir}\t{fl_relpath}")
+        return
 
 
 if __name__ == "__main__":

sdcflows/cli/tests/test_find_estimators.py

@@ -1,8 +1,31 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Check the CLI."""
 import pytest
 from niworkflows.utils.testing import generate_bids_skeleton
 
-from ..find_estimators import main as find_estimators
-from ...fieldmaps import clear_registry
+from sdcflows.cli.main import main as find_estimators
+from sdcflows.fieldmaps import clear_registry
 
 OUTPUT = """\
 Estimation for <{path}> complete. Found:
@@ -102,12 +125,15 @@
 
 @pytest.mark.parametrize(
     "test_id,config,estimator_id",
-    [("intendedfor", intendedfor_config, "auto_00000"), ("b0field", b0field_config, "pepolar")],
+    [
+        ("intendedfor", intendedfor_config, "auto_00000"),
+        ("b0field", b0field_config, "pepolar"),
+    ],
 )
 def test_find_estimators(tmp_path, capsys, test_id, config, estimator_id):
     path = tmp_path / test_id
     generate_bids_skeleton(path, config)
-    find_estimators([str(path)])
+    find_estimators([str(path), "--dry-run"])
     output = OUTPUT.format(path=path, estimator_id=estimator_id)
     out, _ = capsys.readouterr()
     assert out == output

setup.cfg

@@ -80,7 +80,7 @@ sdcflows =
 
 [options.entry_points]
 console_scripts =
-    sdcflows-find-estimators=sdcflows.cli.find_estimators:main
+    sdcflows=sdcflows.cli.main:main
 
 [flake8]
 max-line-length = 99