niwrap-freesurfer 0.5.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_jacobian.py

@@ -0,0 +1,290 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_JACOBIAN_METADATA = Metadata(
+    id="261fa5191d385d242b16ec1808b1a5ac51b44bc2.boutiques",
+    name="mri_jacobian",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriJacobianParameters = typing.TypedDict('MriJacobianParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_jacobian"],
+    "morph_file": InputPathType,
+    "template_vol": InputPathType,
+    "output_vol": str,
+    "atlas_coord": bool,
+    "write_area_vols": bool,
+    "log_jacobian": bool,
+    "smooth_sigma": typing.NotRequired[float | None],
+    "zero_mean_log": bool,
+    "tm3d": bool,
+    "help2": bool,
+    "dt": bool,
+    "debug_voxel": typing.NotRequired[list[float] | None],
+    "remove": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_jacobian": mri_jacobian_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "mri_jacobian": mri_jacobian_outputs,
+    }.get(t)
+
+
+class MriJacobianOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_jacobian(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    result_vol: OutputPathType
+    """Resulting volume file after Jacobian computation"""
+
+
+def mri_jacobian_params(
+    morph_file: InputPathType,
+    template_vol: InputPathType,
+    output_vol: str,
+    atlas_coord: bool = False,
+    write_area_vols: bool = False,
+    log_jacobian: bool = False,
+    smooth_sigma: float | None = None,
+    zero_mean_log: bool = False,
+    tm3d: bool = False,
+    help2: bool = False,
+    dt: bool = False,
+    debug_voxel: list[float] | None = None,
+    remove: bool = False,
+) -> MriJacobianParameters:
+    """
+    Build parameters.
+    
+    Args:
+        morph_file: 3D morph input file.
+        template_vol: Template volume file.
+        output_vol: Output volume file.
+        atlas_coord: Output is written in atlas coordinate system.
+        write_area_vols: Writing area volumes.
+        log_jacobian: Taking log of Jacobian values before saving.
+        smooth_sigma: Smoothing Jacobian volume with sigma.
+        zero_mean_log: Make log Jacobian zero mean.
+        tm3d: The input morph (m3z) originated from tm3d (mri_cvs_register).
+        help2: Writing out help.
+        dt: DT option (description not provided in help text).
+        debug_voxel: Debug voxel with specified Gx, Gy, Gz coordinates.
+        remove: Remove option (description not provided in help text).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_jacobian",
+        "morph_file": morph_file,
+        "template_vol": template_vol,
+        "output_vol": output_vol,
+        "atlas_coord": atlas_coord,
+        "write_area_vols": write_area_vols,
+        "log_jacobian": log_jacobian,
+        "zero_mean_log": zero_mean_log,
+        "tm3d": tm3d,
+        "help2": help2,
+        "dt": dt,
+        "remove": remove,
+    }
+    if smooth_sigma is not None:
+        params["smooth_sigma"] = smooth_sigma
+    if debug_voxel is not None:
+        params["debug_voxel"] = debug_voxel
+    return params
+
+
+def mri_jacobian_cargs(
+    params: MriJacobianParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_jacobian")
+    cargs.append(execution.input_file(params.get("morph_file")))
+    cargs.append(execution.input_file(params.get("template_vol")))
+    cargs.append(params.get("output_vol"))
+    if params.get("atlas_coord"):
+        cargs.append("-a")
+    if params.get("write_area_vols"):
+        cargs.append("-w")
+    if params.get("log_jacobian"):
+        cargs.append("-l")
+    if params.get("smooth_sigma") is not None:
+        cargs.extend([
+            "-s",
+            str(params.get("smooth_sigma"))
+        ])
+    if params.get("zero_mean_log"):
+        cargs.append("-z")
+    if params.get("tm3d"):
+        cargs.append("-tm3d")
+    if params.get("help2"):
+        cargs.append("-u")
+    if params.get("dt"):
+        cargs.append("-dt")
+    if params.get("debug_voxel") is not None:
+        cargs.extend([
+            "-debug_voxel",
+            *map(str, params.get("debug_voxel"))
+        ])
+    if params.get("remove"):
+        cargs.append("-remove")
+    return cargs
+
+
+def mri_jacobian_outputs(
+    params: MriJacobianParameters,
+    execution: Execution,
+) -> MriJacobianOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriJacobianOutputs(
+        root=execution.output_file("."),
+        result_vol=execution.output_file(params.get("output_vol")),
+    )
+    return ret
+
+
+def mri_jacobian_execute(
+    params: MriJacobianParameters,
+    execution: Execution,
+) -> MriJacobianOutputs:
+    """
+    Compute the Jacobian of a morph with FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriJacobianOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_jacobian_cargs(params, execution)
+    ret = mri_jacobian_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_jacobian(
+    morph_file: InputPathType,
+    template_vol: InputPathType,
+    output_vol: str,
+    atlas_coord: bool = False,
+    write_area_vols: bool = False,
+    log_jacobian: bool = False,
+    smooth_sigma: float | None = None,
+    zero_mean_log: bool = False,
+    tm3d: bool = False,
+    help2: bool = False,
+    dt: bool = False,
+    debug_voxel: list[float] | None = None,
+    remove: bool = False,
+    runner: Runner | None = None,
+) -> MriJacobianOutputs:
+    """
+    Compute the Jacobian of a morph with FreeSurfer.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        morph_file: 3D morph input file.
+        template_vol: Template volume file.
+        output_vol: Output volume file.
+        atlas_coord: Output is written in atlas coordinate system.
+        write_area_vols: Writing area volumes.
+        log_jacobian: Taking log of Jacobian values before saving.
+        smooth_sigma: Smoothing Jacobian volume with sigma.
+        zero_mean_log: Make log Jacobian zero mean.
+        tm3d: The input morph (m3z) originated from tm3d (mri_cvs_register).
+        help2: Writing out help.
+        dt: DT option (description not provided in help text).
+        debug_voxel: Debug voxel with specified Gx, Gy, Gz coordinates.
+        remove: Remove option (description not provided in help text).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriJacobianOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_JACOBIAN_METADATA)
+    params = mri_jacobian_params(
+        morph_file=morph_file,
+        template_vol=template_vol,
+        output_vol=output_vol,
+        atlas_coord=atlas_coord,
+        write_area_vols=write_area_vols,
+        log_jacobian=log_jacobian,
+        smooth_sigma=smooth_sigma,
+        zero_mean_log=zero_mean_log,
+        tm3d=tm3d,
+        help2=help2,
+        dt=dt,
+        debug_voxel=debug_voxel,
+        remove=remove,
+    )
+    return mri_jacobian_execute(params, execution)
+
+
+__all__ = [
+    "MRI_JACOBIAN_METADATA",
+    "MriJacobianOutputs",
+    "MriJacobianParameters",
+    "mri_jacobian",
+    "mri_jacobian_params",
+]

niwrap_freesurfer/freesurfer/mri_joint_density.py

@@ -0,0 +1,192 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+MRI_JOINT_DENSITY_METADATA = Metadata(
+    id="95c3248976aa45e74859871185ad767414270ee1.boutiques",
+    name="mri_joint_density",
+    package="freesurfer",
+    container_image_tag="freesurfer/freesurfer:7.4.1",
+)
+
+
+MriJointDensityParameters = typing.TypedDict('MriJointDensityParameters', {
+    "__STYX_TYPE__": typing.Literal["mri_joint_density"],
+    "vol1": InputPathType,
+    "vol2": InputPathType,
+    "output_density_file": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "mri_joint_density": mri_joint_density_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "mri_joint_density": mri_joint_density_outputs,
+    }.get(t)
+
+
+class MriJointDensityOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `mri_joint_density(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output file containing the computed joint density"""
+
+
+def mri_joint_density_params(
+    vol1: InputPathType,
+    vol2: InputPathType,
+    output_density_file: str,
+) -> MriJointDensityParameters:
+    """
+    Build parameters.
+    
+    Args:
+        vol1: First input volume.
+        vol2: Second input volume.
+        output_density_file: Output joint density file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "mri_joint_density",
+        "vol1": vol1,
+        "vol2": vol2,
+        "output_density_file": output_density_file,
+    }
+    return params
+
+
+def mri_joint_density_cargs(
+    params: MriJointDensityParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("mri_joint_density")
+    cargs.append(execution.input_file(params.get("vol1")))
+    cargs.append(execution.input_file(params.get("vol2")))
+    cargs.append(params.get("output_density_file"))
+    return cargs
+
+
+def mri_joint_density_outputs(
+    params: MriJointDensityParameters,
+    execution: Execution,
+) -> MriJointDensityOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = MriJointDensityOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_density_file")),
+    )
+    return ret
+
+
+def mri_joint_density_execute(
+    params: MriJointDensityParameters,
+    execution: Execution,
+) -> MriJointDensityOutputs:
+    """
+    Tool for computing joint density from two volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `MriJointDensityOutputs`).
+    """
+    params = execution.params(params)
+    cargs = mri_joint_density_cargs(params, execution)
+    ret = mri_joint_density_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def mri_joint_density(
+    vol1: InputPathType,
+    vol2: InputPathType,
+    output_density_file: str,
+    runner: Runner | None = None,
+) -> MriJointDensityOutputs:
+    """
+    Tool for computing joint density from two volumes.
+    
+    Author: FreeSurfer Developers
+    
+    URL: https://github.com/freesurfer/freesurfer
+    
+    Args:
+        vol1: First input volume.
+        vol2: Second input volume.
+        output_density_file: Output joint density file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `MriJointDensityOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_JOINT_DENSITY_METADATA)
+    params = mri_joint_density_params(
+        vol1=vol1,
+        vol2=vol2,
+        output_density_file=output_density_file,
+    )
+    return mri_joint_density_execute(params, execution)
+
+
+__all__ = [
+    "MRI_JOINT_DENSITY_METADATA",
+    "MriJointDensityOutputs",
+    "MriJointDensityParameters",
+    "mri_joint_density",
+    "mri_joint_density_params",
+]