niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__make_plug_diff.py

@@ -0,0 +1,237 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__MAKE_PLUG_DIFF_METADATA = Metadata(
+    id="ed24df6f541e54eb4e1231d905483a763eecd72f.boutiques",
+    name="@make_plug_diff",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VMakePlugDiffParameters = typing.TypedDict('VMakePlugDiffParameters', {
+    "__STYX_TYPE__": typing.Literal["@make_plug_diff"],
+    "vtk_dir": str,
+    "xm_dir": str,
+    "afni_src_dir": str,
+    "afni_bin_dir": str,
+    "comments": bool,
+    "linux": bool,
+    "diff_dir": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@make_plug_diff": v__make_plug_diff_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 {
+    }.get(t)
+
+
+class VMakePlugDiffOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__make_plug_diff(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__make_plug_diff_params(
+    vtk_dir: str,
+    xm_dir: str,
+    afni_src_dir: str,
+    afni_bin_dir: str,
+    diff_dir: str,
+    comments: bool = False,
+    linux: bool = False,
+) -> VMakePlugDiffParameters:
+    """
+    Build parameters.
+    
+    Args:
+        vtk_dir: Directory where vtk is installed.
+        xm_dir: Directory where motif is installed.
+        afni_src_dir: Full path to AFNI's src/ directory.
+        afni_bin_dir: Path, relative to ASRCDIR, to abin.
+        diff_dir: Name of directory containing diffusion code.
+        comments: Output comments only.
+        linux: Flag for doing linuxy things.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@make_plug_diff",
+        "vtk_dir": vtk_dir,
+        "xm_dir": xm_dir,
+        "afni_src_dir": afni_src_dir,
+        "afni_bin_dir": afni_bin_dir,
+        "comments": comments,
+        "linux": linux,
+        "diff_dir": diff_dir,
+    }
+    return params
+
+
+def v__make_plug_diff_cargs(
+    params: VMakePlugDiffParameters,
+    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("@make_plug_diff")
+    cargs.extend([
+        "-vtk",
+        params.get("vtk_dir")
+    ])
+    cargs.extend([
+        "-xm",
+        params.get("xm_dir")
+    ])
+    cargs.extend([
+        "-asrc",
+        params.get("afni_src_dir")
+    ])
+    cargs.extend([
+        "-abin",
+        params.get("afni_bin_dir")
+    ])
+    if params.get("comments"):
+        cargs.append("-comments")
+    if params.get("linux"):
+        cargs.append("-linux")
+    cargs.extend([
+        "-diff",
+        params.get("diff_dir")
+    ])
+    return cargs
+
+
+def v__make_plug_diff_outputs(
+    params: VMakePlugDiffParameters,
+    execution: Execution,
+) -> VMakePlugDiffOutputs:
+    """
+    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 = VMakePlugDiffOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__make_plug_diff_execute(
+    params: VMakePlugDiffParameters,
+    execution: Execution,
+) -> VMakePlugDiffOutputs:
+    """
+    Compiles AFNI's diffusion plugin.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VMakePlugDiffOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__make_plug_diff_cargs(params, execution)
+    ret = v__make_plug_diff_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__make_plug_diff(
+    vtk_dir: str,
+    xm_dir: str,
+    afni_src_dir: str,
+    afni_bin_dir: str,
+    diff_dir: str,
+    comments: bool = False,
+    linux: bool = False,
+    runner: Runner | None = None,
+) -> VMakePlugDiffOutputs:
+    """
+    Compiles AFNI's diffusion plugin.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        vtk_dir: Directory where vtk is installed.
+        xm_dir: Directory where motif is installed.
+        afni_src_dir: Full path to AFNI's src/ directory.
+        afni_bin_dir: Path, relative to ASRCDIR, to abin.
+        diff_dir: Name of directory containing diffusion code.
+        comments: Output comments only.
+        linux: Flag for doing linuxy things.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VMakePlugDiffOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MAKE_PLUG_DIFF_METADATA)
+    params = v__make_plug_diff_params(
+        vtk_dir=vtk_dir,
+        xm_dir=xm_dir,
+        afni_src_dir=afni_src_dir,
+        afni_bin_dir=afni_bin_dir,
+        comments=comments,
+        linux=linux,
+        diff_dir=diff_dir,
+    )
+    return v__make_plug_diff_execute(params, execution)
+
+
+__all__ = [
+    "VMakePlugDiffOutputs",
+    "VMakePlugDiffParameters",
+    "V__MAKE_PLUG_DIFF_METADATA",
+    "v__make_plug_diff",
+    "v__make_plug_diff_params",
+]

niwrap_afni/afni/v__measure_bb_thick.py

@@ -0,0 +1,352 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__MEASURE_BB_THICK_METADATA = Metadata(
+    id="261dd15d9b87b8820a89a7b2a53c5bb9a97c42a1.boutiques",
+    name="@measure_bb_thick",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VMeasureBbThickParameters = typing.TypedDict('VMeasureBbThickParameters', {
+    "__STYX_TYPE__": typing.Literal["@measure_bb_thick"],
+    "maskset": InputPathType,
+    "surfset": InputPathType,
+    "outdir": typing.NotRequired[str | None],
+    "resample": typing.NotRequired[str | None],
+    "increment": typing.NotRequired[float | None],
+    "surfsmooth": typing.NotRequired[float | None],
+    "smoothmm": typing.NotRequired[float | None],
+    "maxthick": typing.NotRequired[float | None],
+    "depth_search": typing.NotRequired[float | None],
+    "keep_temp_files": bool,
+    "balls_only": 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_bb_thick": v__measure_bb_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_bb_thick": v__measure_bb_thick_outputs,
+    }.get(t)
+
+
+class VMeasureBbThickOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__measure_bb_thick(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    maxfill: OutputPathType | None
+    """Thickness/depth dataset"""
+    bb_thick: OutputPathType | None
+    """Volumetric thickness dataset"""
+    bb_thick_smooth: OutputPathType | None
+    """Smoothed volumetric thickness dataset"""
+    bb_thick_niml: OutputPathType | None
+    """Unsmoothed thickness mapped to surface nodes"""
+    bb_thick_smooth_niml: OutputPathType | None
+    """Smoothed thickness mapped to surface nodes"""
+    maskset_output: OutputPathType | None
+    """Mask dataset"""
+    maskset_resampled: OutputPathType | None
+    """Resampled mask dataset"""
+    anat_surface: OutputPathType | None
+    """Surface representation of mask volume"""
+    quick_spec: OutputPathType | None
+    """Simple specification file for surface to use with suma commands"""
+
+
+def v__measure_bb_thick_params(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str | None = None,
+    resample: str | None = None,
+    increment: float | None = None,
+    surfsmooth: float | None = None,
+    smoothmm: float | None = None,
+    maxthick: float | None = None,
+    depth_search: float | None = None,
+    keep_temp_files: bool = False,
+    balls_only: bool = False,
+    surfsmooth_method: str | None = None,
+) -> VMeasureBbThickParameters:
+    """
+    Build parameters.
+    
+    Args:
+        maskset: Mask dataset for input.
+        surfset: Surface dataset onto which to map thickness (e.g., pial/gray\
+            matter surface).
+        outdir: Output directory.
+        resample: Resample input to mm in millimeters (e.g., half a voxel or\
+            'auto'). No resampling is done by default.
+        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.
+        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.
+        depth_search: 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).
+        balls_only: Calculate only with spheres and skip boxes.
+        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_bb_thick",
+        "maskset": maskset,
+        "surfset": surfset,
+        "keep_temp_files": keep_temp_files,
+        "balls_only": balls_only,
+    }
+    if outdir is not None:
+        params["outdir"] = outdir
+    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 smoothmm is not None:
+        params["smoothmm"] = smoothmm
+    if maxthick is not None:
+        params["maxthick"] = maxthick
+    if depth_search is not None:
+        params["depth_search"] = depth_search
+    if surfsmooth_method is not None:
+        params["surfsmooth_method"] = surfsmooth_method
+    return params
+
+
+def v__measure_bb_thick_cargs(
+    params: VMeasureBbThickParameters,
+    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_bb_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("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("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("depth_search") is not None:
+        cargs.extend([
+            "-depthsearch",
+            str(params.get("depth_search"))
+        ])
+    if params.get("keep_temp_files"):
+        cargs.append("-keep_temp_files")
+    if params.get("balls_only"):
+        cargs.append("-balls_only")
+    if params.get("surfsmooth_method") is not None:
+        cargs.extend([
+            "-surfsmooth_method",
+            params.get("surfsmooth_method")
+        ])
+    return cargs
+
+
+def v__measure_bb_thick_outputs(
+    params: VMeasureBbThickParameters,
+    execution: Execution,
+) -> VMeasureBbThickOutputs:
+    """
+    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 = VMeasureBbThickOutputs(
+        root=execution.output_file("."),
+        maxfill=execution.output_file(params.get("outdir") + "/maxfill.nii.gz") if (params.get("outdir") is not None) else None,
+        bb_thick=execution.output_file(params.get("outdir") + "/bb_thick.nii.gz") if (params.get("outdir") is not None) else None,
+        bb_thick_smooth=execution.output_file(params.get("outdir") + "/bb_thick_smooth.nii.gz") if (params.get("outdir") is not None) else None,
+        bb_thick_niml=execution.output_file(params.get("outdir") + "/bb_thick.niml.dset") if (params.get("outdir") is not None) else None,
+        bb_thick_smooth_niml=execution.output_file(params.get("outdir") + "/bb_thick_smooth.niml.dset") if (params.get("outdir") is not None) else None,
+        maskset_output=execution.output_file(params.get("outdir") + "/maskset.nii.gz") if (params.get("outdir") is not None) else None,
+        maskset_resampled=execution.output_file(params.get("outdir") + "/maskset_rs.nii.gz") if (params.get("outdir") is not None) else None,
+        anat_surface=execution.output_file(params.get("outdir") + "/anat.gii") if (params.get("outdir") is not None) else None,
+        quick_spec=execution.output_file(params.get("outdir") + "/quick.spec") if (params.get("outdir") is not None) else None,
+    )
+    return ret
+
+
+def v__measure_bb_thick_execute(
+    params: VMeasureBbThickParameters,
+    execution: Execution,
+) -> VMeasureBbThickOutputs:
+    """
+    Compute thickness of mask using ball and box method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VMeasureBbThickOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__measure_bb_thick_cargs(params, execution)
+    ret = v__measure_bb_thick_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__measure_bb_thick(
+    maskset: InputPathType,
+    surfset: InputPathType,
+    outdir: str | None = None,
+    resample: str | None = None,
+    increment: float | None = None,
+    surfsmooth: float | None = None,
+    smoothmm: float | None = None,
+    maxthick: float | None = None,
+    depth_search: float | None = None,
+    keep_temp_files: bool = False,
+    balls_only: bool = False,
+    surfsmooth_method: str | None = None,
+    runner: Runner | None = None,
+) -> VMeasureBbThickOutputs:
+    """
+    Compute thickness of mask using ball and box method.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        maskset: Mask dataset for input.
+        surfset: Surface dataset onto which to map thickness (e.g., pial/gray\
+            matter surface).
+        outdir: Output directory.
+        resample: Resample input to mm in millimeters (e.g., half a voxel or\
+            'auto'). No resampling is done by default.
+        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.
+        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.
+        depth_search: 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).
+        balls_only: Calculate only with spheres and skip boxes.
+        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 `VMeasureBbThickOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MEASURE_BB_THICK_METADATA)
+    params = v__measure_bb_thick_params(
+        maskset=maskset,
+        surfset=surfset,
+        outdir=outdir,
+        resample=resample,
+        increment=increment,
+        surfsmooth=surfsmooth,
+        smoothmm=smoothmm,
+        maxthick=maxthick,
+        depth_search=depth_search,
+        keep_temp_files=keep_temp_files,
+        balls_only=balls_only,
+        surfsmooth_method=surfsmooth_method,
+    )
+    return v__measure_bb_thick_execute(params, execution)
+
+
+__all__ = [
+    "VMeasureBbThickOutputs",
+    "VMeasureBbThickParameters",
+    "V__MEASURE_BB_THICK_METADATA",
+    "v__measure_bb_thick",
+    "v__measure_bb_thick_params",
+]