voxelops 0.1.0__py3-none-any.whl

voxelops/schemas/qsiparc.py

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+"""QSIParc schemas: inputs, outputs, and defaults."""
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Optional
+
+from parcellate.interfaces.models import AtlasDefinition
+
+
+@dataclass
+class QSIParcInputs:
+    """Required inputs for QSIParc parcellation.
+
+    Parameters
+    ----------
+    qsirecon_dir : Path
+        QSIRecon output directory.
+    participant : str
+        Participant label (without 'sub-' prefix).
+    output_dir : Optional[Path], optional
+        Output directory, by default None.
+        If None, defaults to qsirecon_dir parent.
+    session : Optional[str], optional
+        Session label (without 'ses-' prefix), by default None.
+    atlases : Optional[list[AtlasDefinition]], optional
+        List of atlas definitions, by default None.
+    n_jobs : Optional[int], optional
+        Number of jobs to run in parallel, by default None.
+    n_procs : Optional[int], optional
+        Number of processors to use, by default None.
+    """
+
+    qsirecon_dir: Path
+    participant: str
+    output_dir: Optional[Path] = None
+    session: Optional[str] = None
+    atlases: Optional[list[AtlasDefinition]] = None
+    n_jobs: Optional[int] = None
+    n_procs: Optional[int] = None
+
+    def __post_init__(self):
+        """Ensure paths are Path objects."""
+        self.qsirecon_dir = Path(self.qsirecon_dir)
+        if self.output_dir:
+            self.output_dir = Path(self.output_dir)
+
+
+@dataclass
+class QSIParcOutputs:
+    """Expected outputs from QSIParc.
+
+    Parameters
+    ----------
+    output_dir : Path
+        Parcellation output directory.
+    """
+
+    output_dir: Path
+
+    @classmethod
+    def from_inputs(cls, inputs: QSIParcInputs, output_dir: Path):
+        """Generate expected output paths from inputs.
+
+        Parameters
+        ----------
+        inputs : QSIParcInputs
+            QSIParcInputs instance.
+        output_dir : Path
+            Resolved output directory.
+
+        Returns
+        -------
+        QSIParcOutputs
+            QSIParcOutputs with expected paths.
+        """
+        return cls(output_dir=output_dir)
+
+
+@dataclass
+class QSIParcDefaults:
+    """Default configuration for QSIParc (brain bank standards).
+
+    Parameters
+    ----------
+    mask : Optional[str], optional
+        Mask to apply during parcellation ("gm", "wm", "brain", or path), by default "gm".
+    force : bool, optional
+        Whether to overwrite existing outputs, by default False.
+    background_label : int, optional
+        Label value for background voxels, by default 0.
+    resampling_target : Optional[str], optional
+        Resampling strategy ("data", "labels", "atlas", or None), by default "data".
+    log_level : str, optional
+        Logging verbosity (e.g., "INFO", "DEBUG"), by default "INFO".
+    n_jobs : Optional[int], optional
+        Number of jobs to run in parallel, by default 1.
+    n_procs : Optional[int], optional
+        Number of processors to use, by default 1.
+    """
+
+    mask: Optional[str] = "gm"
+    force: bool = False
+    background_label: int = 0
+    resampling_target: Optional[str] = "data"
+    log_level: str = "INFO"
+    n_jobs: Optional[int] = 1
+    n_procs: Optional[int] = 1

voxelops/schemas/qsiprep.py

@@ -0,0 +1,140 @@
+"""QSIPrep schemas: inputs, outputs, and defaults."""
+
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import List, Optional
+
+
+@dataclass
+class QSIPrepInputs:
+    """Required inputs for QSIPrep diffusion preprocessing.
+
+    Parameters
+    ----------
+    bids_dir : Path
+        BIDS dataset directory.
+    participant : str
+        Participant label (without 'sub-' prefix).
+    output_dir : Optional[Path], optional
+        Output directory, by default None.
+        If None, defaults to bids_dir/../derivatives/qsiprep.
+    work_dir : Optional[Path], optional
+        Working directory, by default None.
+        If None, defaults to output_dir/../work/qsiprep.
+    bids_filters : Optional[Path], optional
+        Path to BIDS filters JSON file, by default None.
+    """
+
+    bids_dir: Path
+    participant: str
+    output_dir: Optional[Path] = None
+    work_dir: Optional[Path] = None
+    bids_filters: Optional[Path] = None  # Path to BIDS filters JSON file
+
+    def __post_init__(self):
+        """Ensure paths are Path objects."""
+        self.bids_dir = Path(self.bids_dir)
+        if self.output_dir:
+            self.output_dir = Path(self.output_dir)
+        if self.work_dir:
+            self.work_dir = Path(self.work_dir)
+        if self.bids_filters:
+            self.bids_filters = Path(self.bids_filters)
+
+
+@dataclass
+class QSIPrepOutputs:
+    """Expected outputs from QSIPrep.
+
+    Parameters
+    ----------
+    qsiprep_dir : Path
+        QSIPrep output directory.
+    participant_dir : Path
+        Participant-specific directory.
+    html_report : Path
+        HTML report file.
+    work_dir : Path
+        Working directory.
+    figures_dir : Path
+        QC figures directory.
+    """
+
+    qsiprep_dir: Path
+    participant_dir: Path
+    html_report: Path
+    work_dir: Path
+    figures_dir: Path
+
+    @classmethod
+    def from_inputs(cls, inputs: QSIPrepInputs, output_dir: Path, work_dir: Path):
+        """Generate expected output paths from inputs.
+
+        Parameters
+        ----------
+        inputs : QSIPrepInputs
+            QSIPrepInputs instance.
+        output_dir : Path
+            Resolved output directory.
+        work_dir : Path
+            Resolved work directory.
+
+        Returns
+        -------
+        QSIPrepOutputs
+            QSIPrepOutputs with expected paths.
+        """
+        qsiprep_dir = output_dir / "qsiprep"
+        participant_dir = qsiprep_dir / f"sub-{inputs.participant}"
+
+        return cls(
+            qsiprep_dir=qsiprep_dir,
+            participant_dir=participant_dir,
+            html_report=qsiprep_dir / f"sub-{inputs.participant}.html",
+            work_dir=work_dir,
+            figures_dir=participant_dir / "figures",
+        )
+
+
+@dataclass
+class QSIPrepDefaults:
+    """Default configuration for QSIPrep (brain bank standards).
+
+    Parameters
+    ----------
+    nprocs : int, optional
+        Number of parallel processes, by default 8.
+    mem_gb : int, optional
+        Memory limit in GB, by default 16000.
+    output_resolution : float, optional
+        Output resolution in mm, by default 1.6.
+    anatomical_template : List[str], optional
+        List of output spaces, by default ["MNI152NLin2009cAsym"].
+    longitudinal : bool, optional
+        Enable longitudinal processing, by default False.
+    subject_anatomical_reference : str, optional
+        Anatomical reference for longitudinal processing, by default "unbiased".
+    skip_bids_validation : bool, optional
+        Skip BIDS validation, by default False.
+    fs_license : Optional[Path], optional
+        Path to FreeSurfer license file, by default None.
+    docker_image : str, optional
+        Docker image to use, by default "pennlinc/qsiprep:latest".
+    """
+
+    nprocs: int = 8
+    mem_mb: int = 16000
+    output_resolution: float = 1.6
+    anatomical_template: List[str] = field(
+        default_factory=lambda: ["MNI152NLin2009cAsym"]
+    )
+    longitudinal: bool = False
+    subject_anatomical_reference: str = "unbiased"
+    skip_bids_validation: bool = False
+    fs_license: Optional[Path] = None
+    docker_image: str = "pennlinc/qsiprep:latest"
+
+    def __post_init__(self):
+        """Ensure fs_license is Path object if provided."""
+        if self.fs_license:
+            self.fs_license = Path(self.fs_license)

voxelops/schemas/qsirecon.py

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+"""QSIRecon schemas: inputs, outputs, and defaults."""
+
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import List, Optional
+
+
+@dataclass
+class QSIReconInputs:
+    """Required inputs for QSIRecon diffusion reconstruction.
+
+    Parameters
+    ----------
+    qsiprep_dir : Path
+        QSIPrep output directory.
+    participant : str
+        Participant label (without 'sub-' prefix).
+    output_dir : Optional[Path], optional
+        Output directory, by default None.
+        If None, defaults to qsiprep_dir/../qsirecon.
+    work_dir : Optional[Path], optional
+        Working directory, by default None.
+        If None, defaults to output_dir/../work/qsirecon.
+    recon_spec : Optional[Path], optional
+        Path to reconstruction spec YAML file, by default None.
+    datasets : Optional[dict[str, Path]], optional
+        Dictionary of dataset names and paths, by default None.
+    atlases : Optional[List[str]], optional
+        List of atlases for connectivity, by default None.
+    """
+
+    qsiprep_dir: Path
+    participant: str
+    output_dir: Optional[Path] = None
+    work_dir: Optional[Path] = None
+    recon_spec: Optional[Path] = None
+    datasets: Optional[dict[str, Path]] = None
+    atlases: Optional[List[str]] = None
+
+
+    def __post_init__(self):
+        """Ensure paths are Path objects."""
+        self.qsiprep_dir = Path(self.qsiprep_dir)
+        if self.output_dir:
+            self.output_dir = Path(self.output_dir)
+        if self.work_dir:
+            self.work_dir = Path(self.work_dir)
+        if self.recon_spec:
+            self.recon_spec = Path(self.recon_spec)
+        if self.datasets:
+            self.datasets = {k: Path(v) for k, v in self.datasets.items()}
+
+
+
+@dataclass
+class QSIReconOutputs:
+    """Expected outputs from QSIRecon.
+
+    Parameters
+    ----------
+    qsirecon_dir : Path
+        QSIRecon output directory.
+    participant_dir : Path
+        Participant-specific directory.
+    html_report : Path
+        HTML report file.
+    work_dir : Path
+        Working directory.
+    """
+
+    qsirecon_dir: Path
+    participant_dir: Path
+    html_report: Path
+    work_dir: Path
+
+    @classmethod
+    def from_inputs(cls, inputs: QSIReconInputs, output_dir: Path, work_dir: Path):
+        """Generate expected output paths from inputs.
+
+        Parameters
+        ----------
+        inputs : QSIReconInputs
+            QSIReconInputs instance.
+        output_dir : Path
+            Resolved output directory.
+        work_dir : Path
+            Resolved work directory.
+
+        Returns
+        -------
+        QSIReconOutputs
+            QSIReconOutputs with expected paths.
+        """
+        qsirecon_dir = output_dir / "qsirecon"
+        participant_dir = qsirecon_dir / f"sub-{inputs.participant}"
+
+        return cls(
+            qsirecon_dir=qsirecon_dir,
+            participant_dir=participant_dir,
+            html_report=qsirecon_dir / f"sub-{inputs.participant}.html",
+            work_dir=work_dir,
+        )
+
+
+@dataclass
+class QSIReconDefaults:
+    """Default configuration for QSIRecon (brain bank standards).
+
+    Parameters
+    ----------
+    nprocs : int, optional
+        Number of parallel processes, by default 8.
+    mem_gb : int, optional
+        Memory limit in GB, by default 16000.
+    atlases : List[str], optional
+        List of atlases for connectivity, by default a long list of atlases.
+    fs_subjects_dir : Optional[Path], optional
+        FreeSurfer subjects directory, by default None.
+    fs_license : Optional[Path], optional
+        Path to FreeSurfer license file, by default None.
+    docker_image : str, optional
+        Docker image to use, by default "pennlinc/qsirecon:latest".
+    """
+
+    nprocs: int = 8
+    mem_mb: int = 16000
+    atlases: List[str] = field(
+        default_factory=lambda: [
+            "4S156Parcels",
+            "4S256Parcels",
+            "4S356Parcels",
+            "4S456Parcels",
+            "4S556Parcels",
+            "4S656Parcels",
+            "4S756Parcels",
+            "4S856Parcels",
+            "4S956Parcels",
+            "4S1056Parcels",
+            "AICHA384Ext",
+            "Brainnetome246Ext",
+            "AAL116",
+            "Gordon333Ext",
+        ]
+    )
+    fs_subjects_dir: Optional[Path] = None
+    fs_license: Optional[Path] = None
+    docker_image: str = "pennlinc/qsirecon:latest"
+
+    def __post_init__(self):
+        """Ensure paths are Path objects if provided."""
+        if self.fs_subjects_dir:
+            self.fs_subjects_dir = Path(self.fs_subjects_dir)
+        if self.fs_license:
+            self.fs_license = Path(self.fs_license)

voxelops/utils/__init__.py

@@ -0,0 +1 @@
+"""Utility modules for VoxelOps."""