Remove sdcflows and model ASLPrep on fMRIPrep/next (#338)

* Try this. * keep working. * Update plotting.py * Update base.py * Update base.py * Update. * Update plotting.py * Update plotting.py * fix. * Update plotting.py * Update plotting.py * Update plotting.py * Update. * Update cbf.py * Update cbf.py * Update cbf.py * Update cbf.py * Set Infs to 0. The Philips M0 scan has values of zero for some in-mask voxels, which, when used to calculate CBF, results in Infs. * Try just using standard ASL preproc pipeline. * Try that. * Update tests.py * Update outputs.py * Update base.py * Update base.py * More work. * More work. * More work. * Update utility.py * More work. * Run black and isort. * Update. * Update. * More work. * Update. * Fix. * Update gecbf.py * Update. * Update misc.py * Update fit.py * Update. * Update. * Fix? * Update fit.py * Update fit.py * Update fit.py * Update reference.py * Update reference.py * Update fit.py * Update fit.py * Whoops! * Update fit.py * Update fit.py * Update fit.py * Update fit.py * Update fit.py * Lots of changes. * Update config.py * Update base.py * Update base.py * Update base.py * Update base.py * Update. * Update base.py * Update. * Update. * Update base.py * Update confounds.py * Update. * Update base.py * Update. * Update confounds.py * Update. * Update. * Update. * Update workflows.rst * Update fit.py * Use new fMRIPrep! * Update. * Update. * update. * Update reference.py * Update. * Fix some things. * Fix many things. * Try 3.10. * Update. * Bump build Docker image version. * Update. * Update lint.yml * Update. * Update run.py * Update test_cli.py * Update test_cli.py * Update parser.py * Update parser.py * Update parser.py * Update parser.py * Update. * Update base.py * Update base.py * Update fit.py * Update fit.py * Update base.py * Update qc.py * Update apply.py * Update base.py * Update reference.py * Update base.py * Update base.py * Fix connections. * Make ApplyTransforms calls verbose. * Fix ApplyTransforms calls. * Try that. * Update. * Try fixing m0scan_native. * Try that then. * Try that then. * Update cbf.py * Update test_cli.py * Update aslprep_bids_config.json * Update test_cli.py * Write out native-space derivatives. * Update outputs.py * Update expected outputs. * Update base.py * Update expected outputs. * Update. * Parcellate data no matter what. * More cleanup. * Try adding numpy to build requirements. * Run isort. * Update __init__.py * Deal with style issues. * Add precomputed (will be empty). * Ignore unused parameter. * Try fixing install. * precomputed is a dictionary. * Outsource more workflows to fmriprep. * Try to implement functional cache. * Update BASIL output names. * Update base.py * Update hmc.py * Update bids.py * Remove GE workflows. * Try to fix GE HMC. * Whoops! * Run isort. * Update hmc.py * Update hmc.py * Update expected outputs. * Write out QC file. * Update utility.py * Add outputnode back in. * Try to debug motion params more. * Support single-volume motion parameters. * Add source to docstring. * Keep cleaning up GE processing. * Set confounds min volumes to 2. * Update confounds.py * Make QC calculations flexible. * Remove unused import. * Remove unused data files. * Write out QC file correctly. * Rename QC json filename. * Add confounds to GE outputs. * Drop unused functions and classes. * Try fixing tests. * Use GenericLabel instead of MultiLabel. * Use fMRIPrep's resampling interfaces. * Remove unnecessary comment. * Outsource more workflows to fMRIPrep. * Update expected_outputs_test_002.txt * Update expected outputs. * Update expected_outputs_test_001.txt * Don't use FixHeadersApplyTransforms. * Fix some connections in fit. * Add checks. * Fix logger name. * Retain niftis for now. * Override DDS for some workflow calls. * Disable aslref-space outputs unless requested Copies nipreps/fmriprep#3159. * Pass FLAIR images to anatomical workflow builder Copied from nipreps/fmriprep#3146. * Tag memory estimates in resamplers Copied from nipreps/fmriprep#3150. * Use M0 scan for reference for GE data. * Try to fix transform name. * Add reference image smoothing step. * Give smoothing output a BIDS-ish name. * Update fit.py * Remove unused modules. * Pin sMRIPrep version. * Reduce mask. * Squeeze masks before merging. * Fix module name. * Drop niftis from test outputs. * Update workflows.rst * Improve documentation. * Update api.rst * Update workflows.rst * Update citations. * More documentation improvements. * Remove dropped coverage files from expected outputs. * Update license and output docs. * Fix issues with CIFTI connections. * Update base Docker image. The new version has MSM. * Add level testing jobs. * Update expected outputs. * Try fixing more issues. * Draft workflow to produce CIFTI CBF maps. * Keep working on CIFTI CBF workflow. * Keep working on CIFTI CBF workflow. * Add reference images. * Update outputs.py * Address multiple bugs with GIFTI outputs. * Try outputting fsaverage. * Add docstrings. * Ignore unused argument. * Update tests. * Fix! * Update test_002 cache (it was already v3). * Update. * Update test_cli.py * Update config.yml * Update config.yml * Fix things. * Update test_cli.py * Update config.yml * Combine QC and confounds modules. * Remove unused functions/interfaces. * Remove another unused function. * Remove unused interface function. * Bump anatomical test data version. * Fix import. * Update expected outputs. * Create expected_outputs_qtab.txt * Grab MNI152NLin2009cAsym xfm for resampling. * Update expected outputs. * Add topup to boilerplate BibTeX file. * Revert some changes. * Update expected outputs. * Move asl_anat_wf from resampling to full. * Try outputting CIFTI for one test. * Add updated fsLR workflow from fMRIPrep. * Update resampling.py * Speed up test_003. * Use internal version of init_bold_surf_wf. * Fix style issues. * Remove unused script. * Fix typos. * Drop CIFTI test and sort expected outputs.
PennLINC · Dec 6, 2023 · 8c80d31 · 8c80d31
1 parent 10fc6ba
commit 8c80d31
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Showing 116 changed files with 9,632 additions and 12,022 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: [3.8]
+        python-version: ['3.10']
 
     steps:
       - uses: actions/checkout@v2

diff --git a/.maint/update_authors.py b/.maint/update_authors.py
@@ -37,10 +37,7 @@ def read_md_table(md_text):
     retval = []
     for line in md_text.splitlines():
         if line.strip().startswith("| --- |"):
-            keys = (
-                k.replace("*", "").strip()
-                for k in prev.split("|")
-            )
+            keys = (k.replace("*", "").strip() for k in prev.split("|"))
             keys = [k.lower() for k in keys if k]
             continue
         elif not keys:
@@ -61,19 +58,13 @@ def sort_contributors(entries, git_lines, exclude=None, last=None):
     last = last or []
     sorted_authors = sorted(entries, key=lambda i: i["name"])
 
-    first_last = [
-        " ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors
-    ]
-    first_last_excl = [
-        " ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []
-    ]
+    first_last = [" ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors]
+    first_last_excl = [" ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []]
 
     unmatched = []
     author_matches = []
     for ele in git_lines:
-        matches = process.extract(
-            ele, first_last, scorer=fuzz.token_sort_ratio, limit=2
-        )
+        matches = process.extract(ele, first_last, scorer=fuzz.token_sort_ratio, limit=2)
         # matches is a list [('First match', % Match), ('Second match', % Match)]
         if matches[0][1] > 80:
             val = sorted_authors[first_last.index(matches[0][0])]
@@ -153,8 +144,9 @@ def cli():
 @cli.command()
 @click.option("-z", "--zenodo-file", type=click.Path(exists=True), default=".zenodo.json")
 @click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
-@click.option("-c", "--contributors", type=click.Path(exists=True),
-              default=".maint/CONTRIBUTORS.md")
+@click.option(
+    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+)
 @click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
 @click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
 def zenodo(
@@ -177,15 +169,13 @@ def zenodo(
     )
 
     zen_contributors, miss_contributors = sort_contributors(
-        _namelast(read_md_table(Path(contributors).read_text())),
-        data,
-        exclude=former
+        _namelast(read_md_table(Path(contributors).read_text())), data, exclude=former
     )
 
     zen_pi = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname"))
+            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
         )
     )
 
@@ -195,8 +185,7 @@ def zenodo(
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ "
-            f"files: {', '.join(misses)}",
+            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
@@ -215,15 +204,14 @@ def zenodo(
         if isinstance(creator["affiliation"], list):
             creator["affiliation"] = creator["affiliation"][0]
 
-    Path(zenodo_file).write_text(
-        "%s\n" % json.dumps(zenodo, indent=2)
-    )
+    Path(zenodo_file).write_text("%s\n" % json.dumps(zenodo, indent=2))
 
 
 @cli.command()
 @click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
-@click.option("-c", "--contributors", type=click.Path(exists=True),
-              default=".maint/CONTRIBUTORS.md")
+@click.option(
+    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+)
 @click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
 @click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
 def publication(
@@ -233,9 +221,8 @@ def publication(
     former_file,
 ):
     """Generate the list of authors and affiliations for papers."""
-    members = (
-        _namelast(read_md_table(Path(maintainers).read_text()))
-        + _namelast(read_md_table(Path(contributors).read_text()))
+    members = _namelast(read_md_table(Path(maintainers).read_text())) + _namelast(
+        read_md_table(Path(contributors).read_text())
     )
 
     hits, misses = sort_contributors(
@@ -247,15 +234,12 @@ def publication(
     pi_hits = _namelast(
         sorted(
             read_md_table(Path(pi).read_text()),
-            key=lambda v: (int(v.get("position", -1)), v.get("lastname"))
+            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
         )
     )
 
     pi_names = [pi["name"] for pi in pi_hits]
-    hits = [
-        hit for hit in hits
-        if hit["name"] not in pi_names
-    ] + pi_hits
+    hits = [hit for hit in hits if hit["name"] not in pi_names] + pi_hits
 
     def _aslist(value):
         if isinstance(value, (list, tuple)):
@@ -282,30 +266,22 @@ def _aslist(value):
 
     if misses:
         print(
-            "Some people made commits, but are missing in .maint/ "
-            f"files: {', '.join(misses)}",
+            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
             file=sys.stderr,
         )
 
     print("Authors (%d):" % len(hits))
     print(
         "%s."
-        % "; ".join(
-            [
-                "%s \\ :sup:`%s`\\ " % (i["name"], idx)
-                for i, idx in zip(hits, aff_indexes)
-            ]
-        )
+        % "; ".join(["%s \\ :sup:`%s`\\ " % (i["name"], idx) for i, idx in zip(hits, aff_indexes)])
     )
 
     print(
         "\n\nAffiliations:\n%s"
-        % "\n".join(
-            ["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)]
-        )
+        % "\n".join(["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)])
     )
 
 
 if __name__ == "__main__":
-    """ Install entry-point """
+    """Install entry-point"""
     cli()
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -5,7 +5,7 @@ build:
   apt_packages:
     - graphviz
   tools:
-    python: "3.9"
+    python: "3.10"
 
 sphinx:
   configuration: docs/conf.py

diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -6,7 +6,5 @@
     "[python]": {
         "editor.rulers": [99]
     },
-    "python.linting.flake8Enabled": true,
-    "python.linting.enabled": true,
     "python.analysis.typeCheckingMode": "off",
 }
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM pennlinc/aslprep_build:0.0.4
+FROM pennlinc/aslprep_build:0.0.7
 
 # Install aslprep
 COPY . /src/aslprep