Merge pull request #134 from GalKepler/base_workflow

Base workflow

pyproject.toml

@@ -25,7 +25,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.dependencies]
 python = "^3.10"
-nipype = "^1.8.6"
+nipype = {git = "https://github.com/nipy/nipype.git"}
 templateflow = "^23.0.0"
 psutil = "^5.9.5"
 niworkflows = "^1.8.1"

src/kepost/atlases/utils.py

@@ -11,6 +11,29 @@
 ]
 
 
+def get_atlas_properties(atlas: str):
+    """
+    A simple function to get the properties of an atlas.
+
+    Parameters
+    ----------
+    atlas : str
+        The name of the atlas.
+
+    Returns
+    -------
+    dict
+        A dictionary with the properties of the atlas.
+    """
+    from kepost.atlases.available_atlases.available_atlases import AVAILABLE_ATLASES
+
+    nifti, description, region_col, index_col = [
+        AVAILABLE_ATLASES.get(atlas).get(key)  # type: ignore[union-attr]
+        for key in ["nifti", "description_file", "region_col", "index_col"]
+    ]
+    return nifti, description, region_col, index_col
+
+
 def generate_gm_mask_from_smriprep(
     gm_probseg: Union[str, Path], out_file: Union[str, Path], force: bool = False
 ):

src/kepost/config.py

@@ -252,7 +252,7 @@ class nipype(_Config):
     """Estimation in GB of the RAM this workflow can allocate at any given time."""
     nprocs = os.cpu_count()
     """Number of processes (compute tasks) that can be run in parallel (multiprocessing only)."""
-    omp_nthreads = None
+    omp_nthreads = 8
     """Number of CPUs a single process can access for multithreaded execution."""
     plugin = "MultiProc"
     """NiPype's execution plugin."""
@@ -385,6 +385,9 @@ def init(cls):
             cls.keprep_database_dir = _db_path
         cls.layout = cls._layout
 
+        if cls.participant_label is None:
+            cls.participant_label = cls.layout.get_subjects()
+
         if "all" in cls.debug:
             cls.debug = list(DEBUG_MODES)
 
@@ -394,6 +397,9 @@ def init(cls):
             if Path(cls.output_dir).name != "kepost":
                 cls.output_dir = Path(cls.output_dir) / "kepost"
 
+        if cls.fs_subjects_dir is None:
+            cls.fs_subjects_dir = Path(cls.keprep_dir).parent / "freesurfer"
+
 
 # These variables are not necessary anymore
 del _fs_license
@@ -409,8 +415,10 @@ def init(cls):
 class workflow(_Config):
     """Configure the particular execution graph of this workflow."""
 
-    anat_only = False
-    """Execute the anatomical preprocessing only."""
+    five_tissue_type_algorithm = "hsvs"
+    """Algorithm to use for the generation of the five-tissue-type image. Available algorithms are: `hsvs`, `fsl`."""
+    gm_probseg_threshold = 0.0001
+    """Threshold for the probabilistic segmentation of the gray matter."""
     atlases: list = ["all"]
     """Parcellation atlas(es) to use for the parcellation step. Available atlases are: `all`, `fan2016`, `huang2022`, `schaefer2018_{n_regions}_{n_networks}`."""
     dipy_reconstruction_method = "NLLS"

src/kepost/interfaces/bids/__init__.py

@@ -0,0 +1 @@
+from kepost.interfaces.bids.bids import DerivativesDataSink  # noqa: F401