Merge pull request #1 from PennLINC/enh/hcp

HCP ingress

ingress2qsirecon/__init__.py

@@ -1,5 +1,3 @@
-"""Ingress2QSIRecon.
-
-Your description here
 """
-
+Ingress2QSIRecon.
+"""

ingress2qsirecon/cli/__init__.py

@@ -0,0 +1,3 @@
+"""
+Ingress2QSIRecon.
+"""

ingress2qsirecon/cli/main.py

@@ -0,0 +1,75 @@
+from __future__ import annotations
+
+import os
+import shutil
+from pathlib import Path
+
+from beartype import beartype
+
+import ingress2qsirecon
+from ingress2qsirecon.cli.parser import _build_parser
+from ingress2qsirecon.utils.functions import create_layout
+from ingress2qsirecon.utils.workflows import create_ingress2qsirecon_wf
+
+
+@beartype
+def _ingress2qsirecon(**kwargs):
+    """
+    The main function
+
+    This initializes the import directories, then creates and run the nipype workflow.
+    """
+    # Get the command line arguments
+    input_dir = Path(kwargs["input_dir"])
+    output_dir = Path(kwargs["output_dir"])
+    input_pipeline = kwargs["input_pipeline"]
+    participant_label = kwargs["participant_label"]
+    work_dir = Path(kwargs["work_dir"])
+    check_gradients = kwargs["check_gradients"]
+    dry_run = kwargs["dry_run"]
+    symlink = kwargs["symlink"]
+
+    # Raise NotImplemented errors for options not implemented yet
+    if check_gradients or dry_run or symlink:
+        raise NotImplementedError("--check_gradients, --dry_run, and --symlink are not implemented yet.")
+
+    # Create working directory
+    if not work_dir.exists():
+        work_dir.mkdir(parents=True)
+    os.chdir(work_dir)
+
+    # If output_dir doesn't exist, create it
+    if not output_dir.exists():
+        output_dir.mkdir(parents=True)
+
+    # Move BIDS scaffold files to output directory
+    ingress2recon_dir = os.path.dirname(ingress2qsirecon.__file__)
+    if not os.path.exists(os.path.join(output_dir, "dataset_description.json")):
+        shutil.copytree(os.path.join(ingress2recon_dir, "data", "bids_scaffold"), output_dir, dirs_exist_ok=True)
+
+    # If participant_label not defined, make it empty list
+    if participant_label is None:
+        participant_label = []
+
+    # Make list of dictionaries with all information about the ingressions, one dict per subject
+    layouts = create_layout(input_dir, output_dir, input_pipeline, participant_label)
+
+    # Create and run overall workflow, which will be broken down to single subject workflows
+    ingress2qsirecon_wf = create_ingress2qsirecon_wf(layouts, base_dir=work_dir)
+    ingress2qsirecon_wf.run()
+
+
+def main():
+    """
+    The main entry point of the CLI.
+
+    This function is responsible for parsing command line arguments and running the main code.
+    """
+    parser = _build_parser()
+    args = parser.parse_args()
+    args_dict = vars(args)
+    _ingress2qsirecon(**args_dict)
+
+
+if __name__ == '__main__':
+    main()

ingress2qsirecon/cli/parser.py

@@ -0,0 +1,99 @@
+"""Parser."""
+
+
+def _build_parser(**kwargs):
+    """Build parser object.
+
+    ``kwargs`` are passed to ``argparse.ArgumentParser`` (mainly useful for debugging).
+    """
+    import os
+    from argparse import (
+        ArgumentDefaultsHelpFormatter,
+        ArgumentParser,
+    )
+    from functools import partial
+    from pathlib import Path
+
+    def _path_exists(path, parser):
+        """Ensure a given path exists."""
+        if path is None or not Path(path).exists():
+            raise parser.error(f"Path does not exist: <{path}>.")
+        return Path(path).absolute()
+
+    def _drop_sub(value):
+        return value[4:] if value.startswith("sub-") else value
+
+    parser = ArgumentParser(
+        description=f"Ingress2QSIRecon: Restructuring Bespoke Data for Use in QSIRecon",
+        formatter_class=ArgumentDefaultsHelpFormatter,
+        **kwargs,
+    )
+    PathExists = partial(_path_exists, parser=parser)
+
+    # Required, positional arguments
+    parser.add_argument(
+        "input_dir",
+        action="store",
+        type=PathExists,
+        help="Root folder of dataset to ingress, e.g., HCP1200 or UKB. "
+        "Should contain subject folders (e.g., '100307' for HCP).",
+    )
+    parser.add_argument(
+        "output_dir",
+        action="store",
+        type=Path,
+        help="The output path for restructured data.",
+    )
+    parser.add_argument(
+        "input_pipeline",
+        action="store",
+        choices=["hcpya", "ukb"],
+        help="specify which pipeline was used to create the data specified "
+        "in the --input_dir. Current options include 'hcpya' for "
+        "the HCP young adult minimal preprocessing pipeline and 'ukb' for data processed "
+        "with the UK BioBank minimal preprocessing pipeline.",
+    )
+
+    # Optional arguments
+    optional = parser.add_argument_group("Optional arguments")
+    optional.add_argument(
+        "--participant-label",
+        "--participant_label",
+        action="store",
+        nargs="+",
+        type=_drop_sub,
+        help="A space delimited list of subject folder names / identifiers to process "
+        "(e.g., '100307' for HCP). If not specified, all found folders will be processed. "
+        "Currently runs subjects serially.",
+    )
+    optional.add_argument(
+        "--work_dir",
+        "--work-dir",
+        "-w",
+        action="store",
+        type=Path,
+        default=Path(os.getcwd()),
+        help="The working directory for the processing. "
+        "If not specified, the current working directory will be used.",
+    )
+    optional.add_argument(
+        "--check_gradients",
+        "--check-gradients",
+        action="store_true",
+        default=False,
+        help="NOT IMPLEMENTED YET. Run dwigradcheck on gradient table. This adds a lot of time to the processing. ",
+    )
+    optional.add_argument(
+        "--dry-run",
+        "--dry_run",
+        action="store_true",
+        default=False,
+        help="NOT IMPLEMENTED YET. Will return file reorganization mappings without performing the reorganization.",
+    )
+    optional.add_argument(
+        "--symlink",
+        action="store_true",
+        default=False,
+        help="NOT IMPLEMENTED YET. Rather than copying files, create symlinks (shortcuts) in the output directory.",
+    )
+    return parser

ingress2qsirecon/data/bids_scaffold/README

@@ -0,0 +1 @@
+This is an example README file for BIDS validation.

ingress2qsirecon/data/bids_scaffold/dataset_description.json

@@ -0,0 +1,19 @@
+{
+    "Name": "BIDS-ified Data for QSIRecon",
+    "BIDSVersion": "1.9.0",
+    "DatasetType": "derivative",
+    "License": "CC0",
+    "Authors": [
+      "PennLINC",
+      "Your Computer"
+    ],
+    "ReferencesAndLinks": [
+      "https://github.com/PennLINC/ingress2qsirecon"
+    ],
+    "GeneratedBy": [
+      {
+        "Name": "ingress2qsirecon",
+        "Version": "latest"
+        }
+    ]
+  }

ingress2qsirecon/utils/__init__.py

@@ -0,0 +1,3 @@
+"""
+Ingress2QSIRecon.
+"""