Merge pull request #2 from PennLINC/enh/conform_metadata

Enh/conform metadata

README.md

@@ -2,45 +2,25 @@
 A tool for ingressing outputs from other processing pipelines (e.g., HCP, UKB) for use in QSIRecon.
 
 ## Overview
-Your description here
+This tool can be used to import data from bespoke and widely-used DWI preprocessing pipelines (e.g., Human Connectome Project and UK Biobank) into QSIRecon for post-processing.
 
-## Usage
-This project is set up using poetry. To install the dependencies, run `poetry install` from the root of the project.
-
-```shell
-poetry install
+## Installation
+This project can be installed via PyPi. In your virtual environment run
 ```
-
-To add a new dependency, run `poetry add <dependency>` from the root of the project.
-
-```shell
-poetry add <dependency>
+pip install Ingress2QSIRecon
 ```
-
-### Pre-Commit Hooks
-This project uses [pre-commit](https://pre-commit.com/) to run linting and formatting tools before each commit. To install the pre-commit hooks, run `pre-commit install` from the root of the project.
-
-```shell
-poetry run pre-commit install
+For the master/development branch, you can clone the github repo, and run from within it:
 ```
-
-To run the pre-commit hooks manually, run `pre-commit run --all-files` from the root of the project.
-
-```shell
-poetry run pre-commit run --all-files
+pip install -e .
 ```
 
-
-### Testing
-This project uses [pytest](https://docs.pytest.org/en/stable/) for testing. To run the tests, run `pytest` from the root of the project in the poetry shell.
-
-```shell
-poetry run pytest
-```
-
-There are sensible defaults for pytest setup in the `pyproject.toml` file. You can override these defaults by passing in command line arguments. For example, to run the tests with debug logging enabled, run `pytest --log-cli-level=DEBUG` from the root of the project.
-
-```shell
-poetry run pytest --log-cli-level=DEBUG
+## Usage
+Assuming you have the data to ingress locally availble, you can run the following:
 ```
-
+ingress2qsirecon \
+    /PATH/TO/INPUT/DATA \ # E.g., path to HCP1200 directory
+    /PATH/TO/OUTPUT \ # BIDS directory with ingressed data will be made here
+    PIPELINE_NAME \ # Currently support "hcpya" and "ukb" \
+    -w /PATH/TO/WORKING/DIR \ # Where intermediate files and workflow information will be stored
+    --participant-label 100307 # Name(s) of folder within /PATH/TO/INPUT/DATA. If not specified, will process everyone
+```

ingress2qsirecon/utils/functions.py

@@ -12,6 +12,8 @@
 from pathlib import Path
 from warnings import warn
 
+import nibabel as nb
+
 # Files: file paths relative to subject input folder
 # MNI: MNI template version
 # DIR_PATTERN: regex pattern for subject ID within input folder
@@ -109,13 +111,15 @@ def make_bids_file_paths(subject_layout: dict) -> dict:
     bids_bval_file = os.path.join(bids_base, "dwi", sub_session_string + "_dwi.bval")
     bids_bvec_file = os.path.join(bids_base, "dwi", sub_session_string + "_dwi.bvec")
     bids_b_file = os.path.join(bids_base, "dwi", sub_session_string + "_dwi.b")
+    bids_bmtxt_file = os.path.join(bids_base, "dwi", sub_session_string + "_dwi.bmtxt")
     bids_dwiref_file = os.path.join(bids_base, "dwi", sub_session_string + "_dwiref.nii.gz")
 
     bids_file_paths = {
         "bids_dwi": Path(bids_dwi_file),
         "bids_bvals": Path(bids_bval_file),
         "bids_bvecs": Path(bids_bvec_file),
         "bids_b": Path(bids_b_file),
+        "bids_bmtxt": Path(bids_bmtxt_file),
         "bids_dwiref": Path(bids_dwiref_file),
     }
 
@@ -228,3 +232,19 @@ def create_layout(input_dir: Path, output_dir: Path, input_pipeline: str, partic
         raise ValueError("No subjects found in layout.")
 
     return layout
+
+
+def to_lps(input_img, new_axcodes=("L", "P", "S")):
+    if isinstance(input_img, str):
+        input_img = nb.load(input_img)
+    input_axcodes = nb.aff2axcodes(input_img.affine)
+    # Is the input image oriented how we want?
+    if not input_axcodes == new_axcodes:
+        # Re-orient
+        input_orientation = nb.orientations.axcodes2ornt(input_axcodes)
+        desired_orientation = nb.orientations.axcodes2ornt(new_axcodes)
+        transform_orientation = nb.orientations.ornt_transform(input_orientation, desired_orientation)
+        reoriented_img = input_img.as_reoriented(transform_orientation)
+        return reoriented_img
+    else:
+        return input_img