niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__float_fix.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__FLOAT_FIX_METADATA = Metadata(
+    id="69c8566d3c52dcfb93a135adaaa38398077c4bc6.boutiques",
+    name="@float_fix",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFloatFixParameters = typing.TypedDict('VFloatFixParameters', {
+    "__STYX_TYPE__": typing.Literal["@float_fix"],
+    "input_files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@float_fix": v__float_fix_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 VFloatFixOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__float_fix(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__float_fix_params(
+    input_files: list[InputPathType],
+) -> VFloatFixParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input files to be checked for illegal IEEE floating point\
+            values. Wildcards can be used, but filenames must end with .HEAD.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@float_fix",
+        "input_files": input_files,
+    }
+    return params
+
+
+def v__float_fix_cargs(
+    params: VFloatFixParameters,
+    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("@float_fix")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def v__float_fix_outputs(
+    params: VFloatFixParameters,
+    execution: Execution,
+) -> VFloatFixOutputs:
+    """
+    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 = VFloatFixOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__float_fix_execute(
+    params: VFloatFixParameters,
+    execution: Execution,
+) -> VFloatFixOutputs:
+    """
+    Check whether the input files have any IEEE floating point numbers for illegal
+    values: infinities and not-a-number (NaN) values.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFloatFixOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__float_fix_cargs(params, execution)
+    ret = v__float_fix_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__float_fix(
+    input_files: list[InputPathType],
+    runner: Runner | None = None,
+) -> VFloatFixOutputs:
+    """
+    Check whether the input files have any IEEE floating point numbers for illegal
+    values: infinities and not-a-number (NaN) values.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input files to be checked for illegal IEEE floating point\
+            values. Wildcards can be used, but filenames must end with .HEAD.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFloatFixOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FLOAT_FIX_METADATA)
+    params = v__float_fix_params(
+        input_files=input_files,
+    )
+    return v__float_fix_execute(params, execution)
+
+
+__all__ = [
+    "VFloatFixOutputs",
+    "VFloatFixParameters",
+    "V__FLOAT_FIX_METADATA",
+    "v__float_fix",
+    "v__float_fix_params",
+]

niwrap_afni/afni/v__from_rai.py

@@ -0,0 +1,186 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__FROM_RAI_METADATA = Metadata(
+    id="34d0b2acd8f2be090b2dfad6b13f248d55bc3857.boutiques",
+    name="@FromRAI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFromRaiParameters = typing.TypedDict('VFromRaiParameters', {
+    "__STYX_TYPE__": typing.Literal["@FromRAI"],
+    "rai_coordinates": list[float],
+    "orientation": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "@FromRAI": v__from_rai_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 VFromRaiOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__from_rai(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__from_rai_params(
+    rai_coordinates: list[float],
+    orientation: str,
+) -> VFromRaiParameters:
+    """
+    Build parameters.
+    
+    Args:
+        rai_coordinates: RAI coordinates X, Y, and Z.
+        orientation: Orientation format.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@FromRAI",
+        "rai_coordinates": rai_coordinates,
+        "orientation": orientation,
+    }
+    return params
+
+
+def v__from_rai_cargs(
+    params: VFromRaiParameters,
+    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("@FromRAI")
+    cargs.extend([
+        "-xyz",
+        *map(str, params.get("rai_coordinates"))
+    ])
+    cargs.extend([
+        "-or",
+        params.get("orientation")
+    ])
+    return cargs
+
+
+def v__from_rai_outputs(
+    params: VFromRaiParameters,
+    execution: Execution,
+) -> VFromRaiOutputs:
+    """
+    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 = VFromRaiOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__from_rai_execute(
+    params: VFromRaiParameters,
+    execution: Execution,
+) -> VFromRaiOutputs:
+    """
+    Changes the RAI coordinates to the specified orientation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFromRaiOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__from_rai_cargs(params, execution)
+    ret = v__from_rai_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__from_rai(
+    rai_coordinates: list[float],
+    orientation: str,
+    runner: Runner | None = None,
+) -> VFromRaiOutputs:
+    """
+    Changes the RAI coordinates to the specified orientation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        rai_coordinates: RAI coordinates X, Y, and Z.
+        orientation: Orientation format.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFromRaiOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FROM_RAI_METADATA)
+    params = v__from_rai_params(
+        rai_coordinates=rai_coordinates,
+        orientation=orientation,
+    )
+    return v__from_rai_execute(params, execution)
+
+
+__all__ = [
+    "VFromRaiOutputs",
+    "VFromRaiParameters",
+    "V__FROM_RAI_METADATA",
+    "v__from_rai",
+    "v__from_rai_params",
+]

niwrap_afni/afni/v__fs_roi_label.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 *
+
+V__FS_ROI_LABEL_METADATA = Metadata(
+    id="1309e970f178ba30ffa735edd056d5c550b135f1.boutiques",
+    name="@FS_roi_label",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VFsRoiLabelParameters = typing.TypedDict('VFsRoiLabelParameters', {
+    "__STYX_TYPE__": typing.Literal["@FS_roi_label"],
+    "label_int": typing.NotRequired[float | None],
+    "lab_flag": typing.NotRequired[float | None],
+    "rank_int": typing.NotRequired[float | None],
+    "rankmap_file": typing.NotRequired[InputPathType | None],
+    "name": typing.NotRequired[str | None],
+    "labeltable_file": typing.NotRequired[InputPathType | None],
+    "surf_annot_cmap": typing.NotRequired[InputPathType | None],
+    "slab_int": typing.NotRequired[float | None],
+    "sname_name": 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 {
+        "@FS_roi_label": v__fs_roi_label_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 VFsRoiLabelOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__fs_roi_label(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v__fs_roi_label_params(
+    label_int: float | None = None,
+    lab_flag: float | None = None,
+    rank_int: float | None = None,
+    rankmap_file: InputPathType | None = None,
+    name: str | None = None,
+    labeltable_file: InputPathType | None = None,
+    surf_annot_cmap: InputPathType | None = None,
+    slab_int: float | None = None,
+    sname_name: str | None = None,
+) -> VFsRoiLabelParameters:
+    """
+    Build parameters.
+    
+    Args:
+        label_int: Integer labeled area in FreeSurfer's parcellation.
+        lab_flag: Return the name of an integer labeled area in FreeSurfer's\
+            parcellation.
+        rank_int: Return the name of ranked integer labeled area from the\
+            output of 3dRank or 3dmerge -1rank.
+        rankmap_file: Path to the rank map file.
+        name: Return entries matching NAME (case insensitive, partial match)\
+            from FreeSurfer's FreeSurferColorLUT.txt.
+        labeltable_file: Path to the label table file.
+        surf_annot_cmap: CMAP file output by FSread_annot's -roi_1D option.
+        slab_int: Return the name of an integer labeled area in FreeSurfer's\
+            surface-based annotation.
+        sname_name: Return the entries matching NAME (case insensitive, partial\
+            match) from the CMAP file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@FS_roi_label",
+    }
+    if label_int is not None:
+        params["label_int"] = label_int
+    if lab_flag is not None:
+        params["lab_flag"] = lab_flag
+    if rank_int is not None:
+        params["rank_int"] = rank_int
+    if rankmap_file is not None:
+        params["rankmap_file"] = rankmap_file
+    if name is not None:
+        params["name"] = name
+    if labeltable_file is not None:
+        params["labeltable_file"] = labeltable_file
+    if surf_annot_cmap is not None:
+        params["surf_annot_cmap"] = surf_annot_cmap
+    if slab_int is not None:
+        params["slab_int"] = slab_int
+    if sname_name is not None:
+        params["sname_name"] = sname_name
+    return params
+
+
+def v__fs_roi_label_cargs(
+    params: VFsRoiLabelParameters,
+    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("@FS_roi_label")
+    if params.get("label_int") is not None:
+        cargs.append(str(params.get("label_int")))
+    if params.get("lab_flag") is not None:
+        cargs.extend([
+            "-lab",
+            str(params.get("lab_flag"))
+        ])
+    if params.get("rank_int") is not None:
+        cargs.extend([
+            "-rank",
+            str(params.get("rank_int"))
+        ])
+    if params.get("rankmap_file") is not None:
+        cargs.extend([
+            "-rankmap",
+            execution.input_file(params.get("rankmap_file"))
+        ])
+    if params.get("name") is not None:
+        cargs.extend([
+            "-name",
+            params.get("name")
+        ])
+    if params.get("labeltable_file") is not None:
+        cargs.extend([
+            "-labeltable",
+            execution.input_file(params.get("labeltable_file"))
+        ])
+    if params.get("surf_annot_cmap") is not None:
+        cargs.extend([
+            "-surf_annot_cmap",
+            execution.input_file(params.get("surf_annot_cmap"))
+        ])
+    if params.get("slab_int") is not None:
+        cargs.extend([
+            "-slab",
+            str(params.get("slab_int"))
+        ])
+    if params.get("sname_name") is not None:
+        cargs.extend([
+            "-sname",
+            params.get("sname_name")
+        ])
+    return cargs
+
+
+def v__fs_roi_label_outputs(
+    params: VFsRoiLabelParameters,
+    execution: Execution,
+) -> VFsRoiLabelOutputs:
+    """
+    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 = VFsRoiLabelOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v__fs_roi_label_execute(
+    params: VFsRoiLabelParameters,
+    execution: Execution,
+) -> VFsRoiLabelOutputs:
+    """
+    Tool to get labels associated with FreeSurfer's parcellation and annotation
+    files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VFsRoiLabelOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__fs_roi_label_cargs(params, execution)
+    ret = v__fs_roi_label_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__fs_roi_label(
+    label_int: float | None = None,
+    lab_flag: float | None = None,
+    rank_int: float | None = None,
+    rankmap_file: InputPathType | None = None,
+    name: str | None = None,
+    labeltable_file: InputPathType | None = None,
+    surf_annot_cmap: InputPathType | None = None,
+    slab_int: float | None = None,
+    sname_name: str | None = None,
+    runner: Runner | None = None,
+) -> VFsRoiLabelOutputs:
+    """
+    Tool to get labels associated with FreeSurfer's parcellation and annotation
+    files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        label_int: Integer labeled area in FreeSurfer's parcellation.
+        lab_flag: Return the name of an integer labeled area in FreeSurfer's\
+            parcellation.
+        rank_int: Return the name of ranked integer labeled area from the\
+            output of 3dRank or 3dmerge -1rank.
+        rankmap_file: Path to the rank map file.
+        name: Return entries matching NAME (case insensitive, partial match)\
+            from FreeSurfer's FreeSurferColorLUT.txt.
+        labeltable_file: Path to the label table file.
+        surf_annot_cmap: CMAP file output by FSread_annot's -roi_1D option.
+        slab_int: Return the name of an integer labeled area in FreeSurfer's\
+            surface-based annotation.
+        sname_name: Return the entries matching NAME (case insensitive, partial\
+            match) from the CMAP file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VFsRoiLabelOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FS_ROI_LABEL_METADATA)
+    params = v__fs_roi_label_params(
+        label_int=label_int,
+        lab_flag=lab_flag,
+        rank_int=rank_int,
+        rankmap_file=rankmap_file,
+        name=name,
+        labeltable_file=labeltable_file,
+        surf_annot_cmap=surf_annot_cmap,
+        slab_int=slab_int,
+        sname_name=sname_name,
+    )
+    return v__fs_roi_label_execute(params, execution)
+
+
+__all__ = [
+    "VFsRoiLabelOutputs",
+    "VFsRoiLabelParameters",
+    "V__FS_ROI_LABEL_METADATA",
+    "v__fs_roi_label",
+    "v__fs_roi_label_params",
+]