niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__fat_tract_colorize.py

@@ -0,0 +1,267 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__FAT_TRACT_COLORIZE_METADATA = Metadata(
+    id="08df2223341e8a3953edfe06cc72302451f3e2c8.boutiques",
+    name="@fat_tract_colorize",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFatTractColorizeParameters = typing.TypedDict('VFatTractColorizeParameters', {
+    "__STYX_TYPE__": typing.Literal["@fat_tract_colorize"],
+    "in_fa": InputPathType,
+    "in_v1": InputPathType,
+    "in_tracts": str,
+    "prefix": str,
+    "in_ulay": typing.NotRequired[InputPathType | None],
+    "no_view": bool,
+    "only_view": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@fat_tract_colorize": v__fat_tract_colorize_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 {
+        "@fat_tract_colorize": v__fat_tract_colorize_outputs,
+    }.get(t)
+
+
+class VFatTractColorizeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__fat_tract_colorize(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_hue_volume: OutputPathType
+    """HSL coloration volume file with four bricks from the V1 and FA volumes:
+    Hue, Saturation, Luminosity, and Brightness"""
+    output_iso_surface: OutputPathType
+    """Slightly smoothed isosurface file made by IsoSurface"""
+    output_iso_spec: OutputPathType
+    """Spec file made by quickspec"""
+    output_proj_surface: OutputPathType
+    """Projection of appropriate coloration onto the surface"""
+
+
+def v__fat_tract_colorize_params(
+    in_fa: InputPathType,
+    in_v1: InputPathType,
+    in_tracts: str,
+    prefix: str,
+    in_ulay: InputPathType | None = None,
+    no_view: bool = False,
+    only_view: bool = False,
+) -> VFatTractColorizeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_fa: FA values of the DT fitting, used to modulate the brightness of\
+            the RGB coloration.
+        in_v1: First eigenvector of the DT fitting. A unit vector volume with 3\
+            components (0-1 range).
+        in_tracts: The INDIMAP or PAIRMAP file output by 3dTrackID, specifying\
+            the subbrick if >1 (e.g., NAME_INDIMAP+orig'[0]').
+        prefix: Prefix for all output files.
+        in_ulay: Optional underlay dataset for AFNI/SUMA viewing. Default is to\
+            use the FA dataset.
+        no_view: Turn off auto-running of AFNI_SUMA commands to view the output\
+            immediately.
+        only_view: Only view the data with AFNI+SUMA, assuming the command has\
+            been run before.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@fat_tract_colorize",
+        "in_fa": in_fa,
+        "in_v1": in_v1,
+        "in_tracts": in_tracts,
+        "prefix": prefix,
+        "no_view": no_view,
+        "only_view": only_view,
+    }
+    if in_ulay is not None:
+        params["in_ulay"] = in_ulay
+    return params
+
+
+def v__fat_tract_colorize_cargs(
+    params: VFatTractColorizeParameters,
+    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("@fat_tract_colorize")
+    cargs.extend([
+        "-in_fa",
+        execution.input_file(params.get("in_fa"))
+    ])
+    cargs.extend([
+        "-in_v1",
+        execution.input_file(params.get("in_v1"))
+    ])
+    cargs.extend([
+        "-in_tracts",
+        params.get("in_tracts")
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("in_ulay") is not None:
+        cargs.extend([
+            "-in_ulay",
+            execution.input_file(params.get("in_ulay"))
+        ])
+    if params.get("no_view"):
+        cargs.append("-no_view")
+    if params.get("only_view"):
+        cargs.append("-only_view")
+    return cargs
+
+
+def v__fat_tract_colorize_outputs(
+    params: VFatTractColorizeParameters,
+    execution: Execution,
+) -> VFatTractColorizeOutputs:
+    """
+    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 = VFatTractColorizeOutputs(
+        root=execution.output_file("."),
+        output_hue_volume=execution.output_file(params.get("prefix") + "_RGB_HUE.nii.gz"),
+        output_iso_surface=execution.output_file(params.get("prefix") + "_RGB_iso.ply"),
+        output_iso_spec=execution.output_file(params.get("prefix") + "_RGB_iso.spec"),
+        output_proj_surface=execution.output_file(params.get("prefix") + "_RGB.niml.dset"),
+    )
+    return ret
+
+
+def v__fat_tract_colorize_execute(
+    params: VFatTractColorizeParameters,
+    execution: Execution,
+) -> VFatTractColorizeOutputs:
+    """
+    Visualize tractographic output from 3dTrackID, particularly in probabilistic
+    mode.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFatTractColorizeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__fat_tract_colorize_cargs(params, execution)
+    ret = v__fat_tract_colorize_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__fat_tract_colorize(
+    in_fa: InputPathType,
+    in_v1: InputPathType,
+    in_tracts: str,
+    prefix: str,
+    in_ulay: InputPathType | None = None,
+    no_view: bool = False,
+    only_view: bool = False,
+    runner: Runner | None = None,
+) -> VFatTractColorizeOutputs:
+    """
+    Visualize tractographic output from 3dTrackID, particularly in probabilistic
+    mode.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_fa: FA values of the DT fitting, used to modulate the brightness of\
+            the RGB coloration.
+        in_v1: First eigenvector of the DT fitting. A unit vector volume with 3\
+            components (0-1 range).
+        in_tracts: The INDIMAP or PAIRMAP file output by 3dTrackID, specifying\
+            the subbrick if >1 (e.g., NAME_INDIMAP+orig'[0]').
+        prefix: Prefix for all output files.
+        in_ulay: Optional underlay dataset for AFNI/SUMA viewing. Default is to\
+            use the FA dataset.
+        no_view: Turn off auto-running of AFNI_SUMA commands to view the output\
+            immediately.
+        only_view: Only view the data with AFNI+SUMA, assuming the command has\
+            been run before.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFatTractColorizeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FAT_TRACT_COLORIZE_METADATA)
+    params = v__fat_tract_colorize_params(
+        in_fa=in_fa,
+        in_v1=in_v1,
+        in_tracts=in_tracts,
+        prefix=prefix,
+        in_ulay=in_ulay,
+        no_view=no_view,
+        only_view=only_view,
+    )
+    return v__fat_tract_colorize_execute(params, execution)
+
+
+__all__ = [
+    "VFatTractColorizeOutputs",
+    "VFatTractColorizeParameters",
+    "V__FAT_TRACT_COLORIZE_METADATA",
+    "v__fat_tract_colorize",
+    "v__fat_tract_colorize_params",
+]

niwrap_afni/afni/v__find_afni_dset_path.py

@@ -0,0 +1,199 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__FIND_AFNI_DSET_PATH_METADATA = Metadata(
+    id="f180e5877075d554456c8f3bc0bb390ac06654a3.boutiques",
+    name="@FindAfniDsetPath",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFindAfniDsetPathParameters = typing.TypedDict('VFindAfniDsetPathParameters', {
+    "__STYX_TYPE__": typing.Literal["@FindAfniDsetPath"],
+    "dsetname": str,
+    "append_file": bool,
+    "full_path": bool,
+    "help": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@FindAfniDsetPath": v__find_afni_dset_path_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 VFindAfniDsetPathOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__find_afni_dset_path(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__find_afni_dset_path_params(
+    dsetname: str,
+    append_file: bool = False,
+    full_path: bool = False,
+    help_: bool = False,
+) -> VFindAfniDsetPathParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dsetname: Name of the dataset to search for.
+        append_file: Show the file appended to (even with atlas name).
+        full_path: Print full path instead of '.'.
+        help_: Display help message.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@FindAfniDsetPath",
+        "dsetname": dsetname,
+        "append_file": append_file,
+        "full_path": full_path,
+        "help": help_,
+    }
+    return params
+
+
+def v__find_afni_dset_path_cargs(
+    params: VFindAfniDsetPathParameters,
+    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("@FindAfniDsetPath")
+    cargs.append(params.get("dsetname"))
+    if params.get("append_file"):
+        cargs.append("-append_file")
+    if params.get("full_path"):
+        cargs.append("-full_path")
+    if params.get("help"):
+        cargs.append("-help")
+    return cargs
+
+
+def v__find_afni_dset_path_outputs(
+    params: VFindAfniDsetPathParameters,
+    execution: Execution,
+) -> VFindAfniDsetPathOutputs:
+    """
+    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 = VFindAfniDsetPathOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__find_afni_dset_path_execute(
+    params: VFindAfniDsetPathParameters,
+    execution: Execution,
+) -> VFindAfniDsetPathOutputs:
+    """
+    Searches various AFNI directories for a specified dataset and returns its path.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFindAfniDsetPathOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__find_afni_dset_path_cargs(params, execution)
+    ret = v__find_afni_dset_path_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__find_afni_dset_path(
+    dsetname: str,
+    append_file: bool = False,
+    full_path: bool = False,
+    help_: bool = False,
+    runner: Runner | None = None,
+) -> VFindAfniDsetPathOutputs:
+    """
+    Searches various AFNI directories for a specified dataset and returns its path.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dsetname: Name of the dataset to search for.
+        append_file: Show the file appended to (even with atlas name).
+        full_path: Print full path instead of '.'.
+        help_: Display help message.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFindAfniDsetPathOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FIND_AFNI_DSET_PATH_METADATA)
+    params = v__find_afni_dset_path_params(
+        dsetname=dsetname,
+        append_file=append_file,
+        full_path=full_path,
+        help_=help_,
+    )
+    return v__find_afni_dset_path_execute(params, execution)
+
+
+__all__ = [
+    "VFindAfniDsetPathOutputs",
+    "VFindAfniDsetPathParameters",
+    "V__FIND_AFNI_DSET_PATH_METADATA",
+    "v__find_afni_dset_path",
+    "v__find_afni_dset_path_params",
+]

niwrap_afni/afni/v__fix_fssphere.py

@@ -0,0 +1,236 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__FIX_FSSPHERE_METADATA = Metadata(
+    id="b742177d5b0ebe3a73650e2f92bfe87238f0bcca.boutiques",
+    name="@fix_FSsphere",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFixFssphereParameters = typing.TypedDict('VFixFssphereParameters', {
+    "__STYX_TYPE__": typing.Literal["@fix_FSsphere"],
+    "spec_file": InputPathType,
+    "sphere_file": InputPathType,
+    "num_iterations": typing.NotRequired[int | None],
+    "extent_lim": typing.NotRequired[float | None],
+    "project_first": bool,
+    "keep_temp": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@fix_FSsphere": v__fix_fssphere_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 {
+        "@fix_FSsphere": v__fix_fssphere_outputs,
+    }.get(t)
+
+
+class VFixFssphereOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__fix_fssphere(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    corrected_surface: OutputPathType
+    """Corrected surface"""
+
+
+def v__fix_fssphere_params(
+    spec_file: InputPathType,
+    sphere_file: InputPathType,
+    num_iterations: int | None = None,
+    extent_lim: float | None = None,
+    project_first: bool = False,
+    keep_temp: bool = False,
+) -> VFixFssphereParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: Spec file.
+        sphere_file: SPHERE.asc is the sphere to be used.
+        num_iterations: Number of local smoothing operations. Default is 3000.
+        extent_lim: Extent, in mm, by which troubled sections are fattened.\
+            Default is 6.
+        project_first: Project to a sphere, before smoothing. Default is 0.
+        keep_temp: Keep temporary files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@fix_FSsphere",
+        "spec_file": spec_file,
+        "sphere_file": sphere_file,
+        "project_first": project_first,
+        "keep_temp": keep_temp,
+    }
+    if num_iterations is not None:
+        params["num_iterations"] = num_iterations
+    if extent_lim is not None:
+        params["extent_lim"] = extent_lim
+    return params
+
+
+def v__fix_fssphere_cargs(
+    params: VFixFssphereParameters,
+    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("@fix_FSsphere")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("spec_file"))
+    ])
+    cargs.extend([
+        "-sphere",
+        execution.input_file(params.get("sphere_file"))
+    ])
+    if params.get("num_iterations") is not None:
+        cargs.extend([
+            "-niter",
+            str(params.get("num_iterations"))
+        ])
+    if params.get("extent_lim") is not None:
+        cargs.extend([
+            "-lim",
+            str(params.get("extent_lim"))
+        ])
+    if params.get("project_first"):
+        cargs.append("-project_first")
+    if params.get("keep_temp"):
+        cargs.append("-keep_temp")
+    return cargs
+
+
+def v__fix_fssphere_outputs(
+    params: VFixFssphereParameters,
+    execution: Execution,
+) -> VFixFssphereOutputs:
+    """
+    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 = VFixFssphereOutputs(
+        root=execution.output_file("."),
+        corrected_surface=execution.output_file("[SPHERE]_fxd.asc"),
+    )
+    return ret
+
+
+def v__fix_fssphere_execute(
+    params: VFixFssphereParameters,
+    execution: Execution,
+) -> VFixFssphereOutputs:
+    """
+    Tool for fixing errors in FreeSurfer spherical surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFixFssphereOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__fix_fssphere_cargs(params, execution)
+    ret = v__fix_fssphere_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__fix_fssphere(
+    spec_file: InputPathType,
+    sphere_file: InputPathType,
+    num_iterations: int | None = None,
+    extent_lim: float | None = None,
+    project_first: bool = False,
+    keep_temp: bool = False,
+    runner: Runner | None = None,
+) -> VFixFssphereOutputs:
+    """
+    Tool for fixing errors in FreeSurfer spherical surfaces.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: Spec file.
+        sphere_file: SPHERE.asc is the sphere to be used.
+        num_iterations: Number of local smoothing operations. Default is 3000.
+        extent_lim: Extent, in mm, by which troubled sections are fattened.\
+            Default is 6.
+        project_first: Project to a sphere, before smoothing. Default is 0.
+        keep_temp: Keep temporary files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFixFssphereOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FIX_FSSPHERE_METADATA)
+    params = v__fix_fssphere_params(
+        spec_file=spec_file,
+        sphere_file=sphere_file,
+        num_iterations=num_iterations,
+        extent_lim=extent_lim,
+        project_first=project_first,
+        keep_temp=keep_temp,
+    )
+    return v__fix_fssphere_execute(params, execution)
+
+
+__all__ = [
+    "VFixFssphereOutputs",
+    "VFixFssphereParameters",
+    "V__FIX_FSSPHERE_METADATA",
+    "v__fix_fssphere",
+    "v__fix_fssphere_params",
+]