niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__measure_erosion_thick.py

@@ -0,0 +1,328 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__MEASURE_EROSION_THICK_METADATA = Metadata(
+    id="80ee03f3fb5d8279762f2ef41bc06131e413b576.boutiques",
+    name="@measure_erosion_thick",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VMeasureErosionThickParameters = typing.TypedDict('VMeasureErosionThickParameters', {
+    "__STYX_TYPE__": typing.Literal["@measure_erosion_thick"],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": typing.NotRequired[str | None],
+    "resample": typing.NotRequired[str | None],
+    "surfsmooth": typing.NotRequired[float | None],
+    "smoothmm": typing.NotRequired[float | None],
+    "maxthick": typing.NotRequired[float | None],
+    "depthsearch": typing.NotRequired[float | None],
+    "keep_temp_files": bool,
+    "surfsmooth_method": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@measure_erosion_thick": v__measure_erosion_thick_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 {
+        "@measure_erosion_thick": v__measure_erosion_thick_outputs,
+    }.get(t)
+
+
+class VMeasureErosionThickOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__measure_erosion_thick(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    erosion_depth: OutputPathType
+    """Depth dataset."""
+    erosion_thick: OutputPathType
+    """Volumetric thickness dataset."""
+    erosion_thick_smooth: OutputPathType
+    """Smoothed volumetric thickness dataset."""
+    erosion_thick_niml: OutputPathType
+    """Unsmoothed thickness mapped to surface nodes."""
+    erosion_thick_smooth_niml: OutputPathType
+    """Smoothed thickness mapped to surface nodes."""
+    maskset_output: OutputPathType
+    """Mask dataset."""
+    resampled_maskset: OutputPathType
+    """Resampled mask dataset."""
+    anat_gii: OutputPathType
+    """Surface representation of mask volume."""
+    quick_spec: OutputPathType
+    """Simple specification file for surface to use with suma commands."""
+
+
+def v__measure_erosion_thick_params(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str | None = None,
+    resample: str | None = None,
+    surfsmooth: float | None = None,
+    smoothmm: float | None = None,
+    maxthick: float | None = None,
+    depthsearch: float | None = None,
+    keep_temp_files: bool = False,
+    surfsmooth_method: str | None = None,
+) -> VMeasureErosionThickParameters:
+    """
+    Build parameters.
+    
+    Args:
+        maskset: Mask dataset for input.
+        surfset: Surface dataset onto which to map thickness (probably a\
+            pial/gray matter surface).
+        outdir: Output directory. If not specified, erosion_thickdir is used.
+        resample: Resample input to mm in millimeters (put a number here).\
+            Recommended for most 1mm data.
+        surfsmooth: Smooth surface map of thickness by mm millimeters. Default\
+            is 8 mm.
+        smoothmm: Smooth volume by mm FWHM in mask. Default is 2*voxelsize of\
+            mask or resampled mask.
+        maxthick: Search for maximum thickness value of mm millimeters. Default\
+            is 6 mm.
+        depthsearch: Map to surface by looking for max along mm millimeter\
+            normal vectors. Default is 3 mm.
+        keep_temp_files: Do not delete the intermediate files (for testing).
+        surfsmooth_method: Heat method used for smoothing surfaces. Default is\
+            HEAT_07 but HEAT_05 is also useful for models.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@measure_erosion_thick",
+        "maskset": maskset,
+        "surfset": surfset,
+        "keep_temp_files": keep_temp_files,
+    }
+    if outdir is not None:
+        params["outdir"] = outdir
+    if resample is not None:
+        params["resample"] = resample
+    if surfsmooth is not None:
+        params["surfsmooth"] = surfsmooth
+    if smoothmm is not None:
+        params["smoothmm"] = smoothmm
+    if maxthick is not None:
+        params["maxthick"] = maxthick
+    if depthsearch is not None:
+        params["depthsearch"] = depthsearch
+    if surfsmooth_method is not None:
+        params["surfsmooth_method"] = surfsmooth_method
+    return params
+
+
+def v__measure_erosion_thick_cargs(
+    params: VMeasureErosionThickParameters,
+    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("@measure_erosion_thick")
+    cargs.extend([
+        "-maskset",
+        execution.input_file(params.get("maskset"))
+    ])
+    cargs.extend([
+        "-surfset",
+        execution.input_file(params.get("surfset"))
+    ])
+    if params.get("outdir") is not None:
+        cargs.extend([
+            "-outdir",
+            params.get("outdir")
+        ])
+    if params.get("resample") is not None:
+        cargs.extend([
+            "-resample",
+            params.get("resample")
+        ])
+    if params.get("surfsmooth") is not None:
+        cargs.extend([
+            "-surfsmooth",
+            str(params.get("surfsmooth"))
+        ])
+    if params.get("smoothmm") is not None:
+        cargs.extend([
+            "-smoothmm",
+            str(params.get("smoothmm"))
+        ])
+    if params.get("maxthick") is not None:
+        cargs.extend([
+            "-maxthick",
+            str(params.get("maxthick"))
+        ])
+    if params.get("depthsearch") is not None:
+        cargs.extend([
+            "-depthsearch",
+            str(params.get("depthsearch"))
+        ])
+    if params.get("keep_temp_files"):
+        cargs.append("-keep_temp_files")
+    if params.get("surfsmooth_method") is not None:
+        cargs.extend([
+            "-surfsmooth_method",
+            params.get("surfsmooth_method")
+        ])
+    return cargs
+
+
+def v__measure_erosion_thick_outputs(
+    params: VMeasureErosionThickParameters,
+    execution: Execution,
+) -> VMeasureErosionThickOutputs:
+    """
+    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 = VMeasureErosionThickOutputs(
+        root=execution.output_file("."),
+        erosion_depth=execution.output_file("erosion_depth.nii.gz"),
+        erosion_thick=execution.output_file("erosion_thick.nii.gz"),
+        erosion_thick_smooth=execution.output_file("erosion_thick_smooth.nii.gz"),
+        erosion_thick_niml=execution.output_file("erosion_thick.niml.dset"),
+        erosion_thick_smooth_niml=execution.output_file("erosion_thick_smooth_nn_mm.niml.dset"),
+        maskset_output=execution.output_file("maskset.nii.gz"),
+        resampled_maskset=execution.output_file("maskset_rs.nii.gz"),
+        anat_gii=execution.output_file("anat.gii"),
+        quick_spec=execution.output_file("quick.spec"),
+    )
+    return ret
+
+
+def v__measure_erosion_thick_execute(
+    params: VMeasureErosionThickParameters,
+    execution: Execution,
+) -> VMeasureErosionThickOutputs:
+    """
+    Compute thickness of mask using erosion method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VMeasureErosionThickOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__measure_erosion_thick_cargs(params, execution)
+    ret = v__measure_erosion_thick_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__measure_erosion_thick(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str | None = None,
+    resample: str | None = None,
+    surfsmooth: float | None = None,
+    smoothmm: float | None = None,
+    maxthick: float | None = None,
+    depthsearch: float | None = None,
+    keep_temp_files: bool = False,
+    surfsmooth_method: str | None = None,
+    runner: Runner | None = None,
+) -> VMeasureErosionThickOutputs:
+    """
+    Compute thickness of mask using erosion method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        maskset: Mask dataset for input.
+        surfset: Surface dataset onto which to map thickness (probably a\
+            pial/gray matter surface).
+        outdir: Output directory. If not specified, erosion_thickdir is used.
+        resample: Resample input to mm in millimeters (put a number here).\
+            Recommended for most 1mm data.
+        surfsmooth: Smooth surface map of thickness by mm millimeters. Default\
+            is 8 mm.
+        smoothmm: Smooth volume by mm FWHM in mask. Default is 2*voxelsize of\
+            mask or resampled mask.
+        maxthick: Search for maximum thickness value of mm millimeters. Default\
+            is 6 mm.
+        depthsearch: Map to surface by looking for max along mm millimeter\
+            normal vectors. Default is 3 mm.
+        keep_temp_files: Do not delete the intermediate files (for testing).
+        surfsmooth_method: Heat method used for smoothing surfaces. Default is\
+            HEAT_07 but HEAT_05 is also useful for models.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VMeasureErosionThickOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MEASURE_EROSION_THICK_METADATA)
+    params = v__measure_erosion_thick_params(
+        maskset=maskset,
+        surfset=surfset,
+        outdir=outdir,
+        resample=resample,
+        surfsmooth=surfsmooth,
+        smoothmm=smoothmm,
+        maxthick=maxthick,
+        depthsearch=depthsearch,
+        keep_temp_files=keep_temp_files,
+        surfsmooth_method=surfsmooth_method,
+    )
+    return v__measure_erosion_thick_execute(params, execution)
+
+
+__all__ = [
+    "VMeasureErosionThickOutputs",
+    "VMeasureErosionThickParameters",
+    "V__MEASURE_EROSION_THICK_METADATA",
+    "v__measure_erosion_thick",
+    "v__measure_erosion_thick_params",
+]

niwrap_afni/afni/v__measure_in2out.py

@@ -0,0 +1,355 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__MEASURE_IN2OUT_METADATA = Metadata(
+    id="24cc5193feb14e3737f192161109e71637dc1422.boutiques",
+    name="@measure_in2out",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VMeasureIn2outParameters = typing.TypedDict('VMeasureIn2outParameters', {
+    "__STYX_TYPE__": typing.Literal["@measure_in2out"],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": str,
+    "resample": typing.NotRequired[str | None],
+    "increment": typing.NotRequired[float | None],
+    "surfsmooth": typing.NotRequired[float | None],
+    "maxthick": typing.NotRequired[float | None],
+    "depthsearch": typing.NotRequired[float | None],
+    "maskinoutvals": typing.NotRequired[list[float] | None],
+    "keep_temp_files": bool,
+    "surfsmooth_method": typing.NotRequired[str | None],
+    "fs_cort_dir": typing.NotRequired[str | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@measure_in2out": v__measure_in2out_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 {
+        "@measure_in2out": v__measure_in2out_outputs,
+    }.get(t)
+
+
+class VMeasureIn2outOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__measure_in2out(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    inout_dist: OutputPathType
+    """Volumetric thickness/distance from in to out"""
+    in_and_out: OutputPathType
+    """Volumetric distance to inside and outside in 2 volumes"""
+    inout_thick: OutputPathType
+    """Unsmoothed thickness mapped to surface nodes"""
+    inout_thick_smooth: OutputPathType
+    """Smoothed thickness mapped to surface nodes"""
+    maskset_output: OutputPathType
+    """Mask file"""
+    maskset_rs: OutputPathType
+    """Resampled mask file"""
+    anat_gii: OutputPathType
+    """Surface representation of mask volume"""
+    quick_spec: OutputPathType
+    """Simple specification file for surface to use with suma commands"""
+
+
+def v__measure_in2out_params(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str,
+    resample: str | None = None,
+    increment: float | None = None,
+    surfsmooth: float | None = None,
+    maxthick: float | None = None,
+    depthsearch: float | None = None,
+    maskinoutvals: list[float] | None = None,
+    keep_temp_files: bool = False,
+    surfsmooth_method: str | None = None,
+    fs_cort_dir: str | None = None,
+) -> VMeasureIn2outParameters:
+    """
+    Build parameters.
+    
+    Args:
+        maskset: Mask dataset for input.
+        surfset: Surface dataset onto which to map thickness (probably a\
+            pial/gray matter surface).
+        outdir: Output directory. If not specified, in2out_thickdir is used.
+        resample: Resample input to mm in millimeters (put a number here). Set\
+            this to half a voxel or "auto". No resampling is done by default.\
+            Resampling is highly recommended for most 1mm data.
+        increment: Test thickness at increments of sub-voxel distance. Default\
+            is 1/4 voxel minimum distance (in-plane).
+        surfsmooth: Smooth surface map of thickness by mm millimeters. Default\
+            is 6 mm.
+        maxthick: Search for maximum thickness value of mm millimeters. Default\
+            is 6 mm.
+        depthsearch: Map to surface by looking for max along mm millimeter\
+            normal vectors. Default is 3 mm.
+        maskinoutvals: Use v1 for value of mask, v2 and v3 for inside and\
+            outside mask values (e.g., '1 -2 -1').
+        keep_temp_files: Do not delete the intermediate files (for testing).
+        surfsmooth_method: Heat method used for smoothing surfaces. Default is\
+            HEAT_07 but HEAT_05 is also useful for some models.
+        fs_cort_dir: Use FreeSurfer SUMA directory from @SUMA_Make_Spec_FS for\
+            processing.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@measure_in2out",
+        "maskset": maskset,
+        "surfset": surfset,
+        "outdir": outdir,
+        "keep_temp_files": keep_temp_files,
+    }
+    if resample is not None:
+        params["resample"] = resample
+    if increment is not None:
+        params["increment"] = increment
+    if surfsmooth is not None:
+        params["surfsmooth"] = surfsmooth
+    if maxthick is not None:
+        params["maxthick"] = maxthick
+    if depthsearch is not None:
+        params["depthsearch"] = depthsearch
+    if maskinoutvals is not None:
+        params["maskinoutvals"] = maskinoutvals
+    if surfsmooth_method is not None:
+        params["surfsmooth_method"] = surfsmooth_method
+    if fs_cort_dir is not None:
+        params["fs_cort_dir"] = fs_cort_dir
+    return params
+
+
+def v__measure_in2out_cargs(
+    params: VMeasureIn2outParameters,
+    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("@measure_in2out")
+    cargs.extend([
+        "-maskset",
+        execution.input_file(params.get("maskset"))
+    ])
+    cargs.extend([
+        "-surfset",
+        execution.input_file(params.get("surfset"))
+    ])
+    cargs.extend([
+        "-outdir",
+        params.get("outdir")
+    ])
+    if params.get("resample") is not None:
+        cargs.extend([
+            "-resample",
+            params.get("resample")
+        ])
+    if params.get("increment") is not None:
+        cargs.extend([
+            "-increment",
+            str(params.get("increment"))
+        ])
+    if params.get("surfsmooth") is not None:
+        cargs.extend([
+            "-surfsmooth",
+            str(params.get("surfsmooth"))
+        ])
+    if params.get("maxthick") is not None:
+        cargs.extend([
+            "-maxthick",
+            str(params.get("maxthick"))
+        ])
+    if params.get("depthsearch") is not None:
+        cargs.extend([
+            "-depthsearch",
+            str(params.get("depthsearch"))
+        ])
+    if params.get("maskinoutvals") is not None:
+        cargs.extend([
+            "-maskinoutvals",
+            *map(str, params.get("maskinoutvals"))
+        ])
+    if params.get("keep_temp_files"):
+        cargs.append("-keep_temp_files")
+    if params.get("surfsmooth_method") is not None:
+        cargs.extend([
+            "-surfsmooth_method",
+            params.get("surfsmooth_method")
+        ])
+    if params.get("fs_cort_dir") is not None:
+        cargs.extend([
+            "-fs_cort_dir",
+            params.get("fs_cort_dir")
+        ])
+    return cargs
+
+
+def v__measure_in2out_outputs(
+    params: VMeasureIn2outParameters,
+    execution: Execution,
+) -> VMeasureIn2outOutputs:
+    """
+    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 = VMeasureIn2outOutputs(
+        root=execution.output_file("."),
+        inout_dist=execution.output_file("inout_dist.nii.gz"),
+        in_and_out=execution.output_file("in_and_out.nii.gz"),
+        inout_thick=execution.output_file("inout_thick.niml.dset"),
+        inout_thick_smooth=execution.output_file("inout_thick_smooth.niml.dset"),
+        maskset_output=execution.output_file("maskset.nii.gz"),
+        maskset_rs=execution.output_file("maskset_rs.nii.gz"),
+        anat_gii=execution.output_file("anat.gii"),
+        quick_spec=execution.output_file("quick.spec"),
+    )
+    return ret
+
+
+def v__measure_in2out_execute(
+    params: VMeasureIn2outParameters,
+    execution: Execution,
+) -> VMeasureIn2outOutputs:
+    """
+    Compute thickness of mask using in2out method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VMeasureIn2outOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__measure_in2out_cargs(params, execution)
+    ret = v__measure_in2out_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__measure_in2out(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str,
+    resample: str | None = None,
+    increment: float | None = None,
+    surfsmooth: float | None = None,
+    maxthick: float | None = None,
+    depthsearch: float | None = None,
+    maskinoutvals: list[float] | None = None,
+    keep_temp_files: bool = False,
+    surfsmooth_method: str | None = None,
+    fs_cort_dir: str | None = None,
+    runner: Runner | None = None,
+) -> VMeasureIn2outOutputs:
+    """
+    Compute thickness of mask using in2out method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        maskset: Mask dataset for input.
+        surfset: Surface dataset onto which to map thickness (probably a\
+            pial/gray matter surface).
+        outdir: Output directory. If not specified, in2out_thickdir is used.
+        resample: Resample input to mm in millimeters (put a number here). Set\
+            this to half a voxel or "auto". No resampling is done by default.\
+            Resampling is highly recommended for most 1mm data.
+        increment: Test thickness at increments of sub-voxel distance. Default\
+            is 1/4 voxel minimum distance (in-plane).
+        surfsmooth: Smooth surface map of thickness by mm millimeters. Default\
+            is 6 mm.
+        maxthick: Search for maximum thickness value of mm millimeters. Default\
+            is 6 mm.
+        depthsearch: Map to surface by looking for max along mm millimeter\
+            normal vectors. Default is 3 mm.
+        maskinoutvals: Use v1 for value of mask, v2 and v3 for inside and\
+            outside mask values (e.g., '1 -2 -1').
+        keep_temp_files: Do not delete the intermediate files (for testing).
+        surfsmooth_method: Heat method used for smoothing surfaces. Default is\
+            HEAT_07 but HEAT_05 is also useful for some models.
+        fs_cort_dir: Use FreeSurfer SUMA directory from @SUMA_Make_Spec_FS for\
+            processing.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VMeasureIn2outOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MEASURE_IN2OUT_METADATA)
+    params = v__measure_in2out_params(
+        maskset=maskset,
+        surfset=surfset,
+        outdir=outdir,
+        resample=resample,
+        increment=increment,
+        surfsmooth=surfsmooth,
+        maxthick=maxthick,
+        depthsearch=depthsearch,
+        maskinoutvals=maskinoutvals,
+        keep_temp_files=keep_temp_files,
+        surfsmooth_method=surfsmooth_method,
+        fs_cort_dir=fs_cort_dir,
+    )
+    return v__measure_in2out_execute(params, execution)
+
+
+__all__ = [
+    "VMeasureIn2outOutputs",
+    "VMeasureIn2outParameters",
+    "V__MEASURE_IN2OUT_METADATA",
+    "v__measure_in2out",
+    "v__measure_in2out_params",
+]