niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_compare_affine.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_COMPARE_AFFINE_METADATA = Metadata(
+    id="05a5d8e8f58b82dd3d94b8878f12307d386f682c.boutiques",
+    name="3dCompareAffine",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dCompareAffineParameters = typing.TypedDict('V3dCompareAffineParameters', {
+    "__STYX_TYPE__": typing.Literal["3dCompareAffine"],
+    "mask": typing.NotRequired[str | None],
+    "dset": typing.NotRequired[InputPathType | None],
+    "affine": typing.NotRequired[list[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 {
+        "3dCompareAffine": v_3d_compare_affine_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 {
+        "3dCompareAffine": v_3d_compare_affine_outputs,
+    }.get(t)
+
+
+class V3dCompareAffineOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_compare_affine(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output file containing comparison results of affine transformations"""
+
+
+def v_3d_compare_affine_params(
+    mask: str | None = None,
+    dset: InputPathType | None = None,
+    affine: list[str] | None = None,
+) -> V3dCompareAffineParameters:
+    """
+    Build parameters.
+    
+    Args:
+        mask: Dataset containing non-zero voxels used as the region over which\
+            to compare the affine transformations.
+        dset: Dataset to compute an automask from it and use that mask as the\
+            spatial region for comparison.
+        affine: Input an affine transformation (file or 'MATRIX'). Multiple\
+            '-affine' options can be used to input multiple files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dCompareAffine",
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if dset is not None:
+        params["dset"] = dset
+    if affine is not None:
+        params["affine"] = affine
+    return params
+
+
+def v_3d_compare_affine_cargs(
+    params: V3dCompareAffineParameters,
+    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("3dCompareAffine")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask")
+        ])
+    if params.get("dset") is not None:
+        cargs.extend([
+            "-dset",
+            execution.input_file(params.get("dset"))
+        ])
+    if params.get("affine") is not None:
+        cargs.extend([
+            "-affine",
+            *params.get("affine")
+        ])
+    return cargs
+
+
+def v_3d_compare_affine_outputs(
+    params: V3dCompareAffineParameters,
+    execution: Execution,
+) -> V3dCompareAffineOutputs:
+    """
+    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 = V3dCompareAffineOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("[OUTPUT_PREFIX]_comparison.txt"),
+    )
+    return ret
+
+
+def v_3d_compare_affine_execute(
+    params: V3dCompareAffineParameters,
+    execution: Execution,
+) -> V3dCompareAffineOutputs:
+    """
+    Compares two (or more) affine spatial transformations on a dataset and outputs
+    measurements of their differences in spatial displacements.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dCompareAffineOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_compare_affine_cargs(params, execution)
+    ret = v_3d_compare_affine_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_compare_affine(
+    mask: str | None = None,
+    dset: InputPathType | None = None,
+    affine: list[str] | None = None,
+    runner: Runner | None = None,
+) -> V3dCompareAffineOutputs:
+    """
+    Compares two (or more) affine spatial transformations on a dataset and outputs
+    measurements of their differences in spatial displacements.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        mask: Dataset containing non-zero voxels used as the region over which\
+            to compare the affine transformations.
+        dset: Dataset to compute an automask from it and use that mask as the\
+            spatial region for comparison.
+        affine: Input an affine transformation (file or 'MATRIX'). Multiple\
+            '-affine' options can be used to input multiple files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dCompareAffineOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_COMPARE_AFFINE_METADATA)
+    params = v_3d_compare_affine_params(
+        mask=mask,
+        dset=dset,
+        affine=affine,
+    )
+    return v_3d_compare_affine_execute(params, execution)
+
+
+__all__ = [
+    "V3dCompareAffineOutputs",
+    "V3dCompareAffineParameters",
+    "V_3D_COMPARE_AFFINE_METADATA",
+    "v_3d_compare_affine",
+    "v_3d_compare_affine_params",
+]

niwrap_afni/afni/v_3d_conformist.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_3D_CONFORMIST_METADATA = Metadata(
+    id="f609f1b815cd20fa63c94e47456124184827cae8.boutiques",
+    name="3dConformist",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dConformistParameters = typing.TypedDict('V3dConformistParameters', {
+    "__STYX_TYPE__": typing.Literal["3dConformist"],
+    "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 {
+        "3dConformist": v_3d_conformist_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 {
+        "3dConformist": v_3d_conformist_outputs,
+    }.get(t)
+
+
+class V3dConformistOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_conformist(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """Zero padded output dataset files"""
+
+
+def v_3d_conformist_params(
+    input_files: list[InputPathType],
+) -> V3dConformistParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input datasets to be zero padded to the same size.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dConformist",
+        "input_files": input_files,
+    }
+    return params
+
+
+def v_3d_conformist_cargs(
+    params: V3dConformistParameters,
+    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("3dConformist")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def v_3d_conformist_outputs(
+    params: V3dConformistParameters,
+    execution: Execution,
+) -> V3dConformistOutputs:
+    """
+    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 = V3dConformistOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_conformist_execute(
+    params: V3dConformistParameters,
+    execution: Execution,
+) -> V3dConformistOutputs:
+    """
+    Program to conform a collection of datasets to the same size by zero padding.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dConformistOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_conformist_cargs(params, execution)
+    ret = v_3d_conformist_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_conformist(
+    input_files: list[InputPathType],
+    runner: Runner | None = None,
+) -> V3dConformistOutputs:
+    """
+    Program to conform a collection of datasets to the same size by zero padding.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input datasets to be zero padded to the same size.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dConformistOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CONFORMIST_METADATA)
+    params = v_3d_conformist_params(
+        input_files=input_files,
+    )
+    return v_3d_conformist_execute(params, execution)
+
+
+__all__ = [
+    "V3dConformistOutputs",
+    "V3dConformistParameters",
+    "V_3D_CONFORMIST_METADATA",
+    "v_3d_conformist",
+    "v_3d_conformist_params",
+]

niwrap_afni/afni/v_3d_convolve.py

@@ -0,0 +1,197 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CONVOLVE_METADATA = Metadata(
+    id="98f37303338db7321cbe065f60581ee844d011e4.boutiques",
+    name="3dConvolve",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dConvolveParameters = typing.TypedDict('V3dConvolveParameters', {
+    "__STYX_TYPE__": typing.Literal["3dConvolve"],
+    "infile": InputPathType,
+    "outfile": str,
+    "options": 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 {
+        "3dConvolve": v_3d_convolve_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 {
+        "3dConvolve": v_3d_convolve_outputs,
+    }.get(t)
+
+
+class V3dConvolveOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_convolve(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Main output file of 3dConvolve"""
+
+
+def v_3d_convolve_params(
+    infile: InputPathType,
+    outfile: str,
+    options: str | None = None,
+) -> V3dConvolveParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input file for 3dConvolve.
+        outfile: Output file for 3dConvolve.
+        options: Additional options for 3dConvolve.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dConvolve",
+        "infile": infile,
+        "outfile": outfile,
+    }
+    if options is not None:
+        params["options"] = options
+    return params
+
+
+def v_3d_convolve_cargs(
+    params: V3dConvolveParameters,
+    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("3dConvolve")
+    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(params.get("outfile"))
+    if params.get("options") is not None:
+        cargs.extend([
+            "-options",
+            params.get("options")
+        ])
+    return cargs
+
+
+def v_3d_convolve_outputs(
+    params: V3dConvolveParameters,
+    execution: Execution,
+) -> V3dConvolveOutputs:
+    """
+    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 = V3dConvolveOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("outfile")),
+    )
+    return ret
+
+
+def v_3d_convolve_execute(
+    params: V3dConvolveParameters,
+    execution: Execution,
+) -> V3dConvolveOutputs:
+    """
+    3dConvolve is no longer supported in AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dConvolveOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_convolve_cargs(params, execution)
+    ret = v_3d_convolve_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_convolve(
+    infile: InputPathType,
+    outfile: str,
+    options: str | None = None,
+    runner: Runner | None = None,
+) -> V3dConvolveOutputs:
+    """
+    3dConvolve is no longer supported in AFNI.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input file for 3dConvolve.
+        outfile: Output file for 3dConvolve.
+        options: Additional options for 3dConvolve.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dConvolveOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CONVOLVE_METADATA)
+    params = v_3d_convolve_params(
+        infile=infile,
+        outfile=outfile,
+        options=options,
+    )
+    return v_3d_convolve_execute(params, execution)
+
+
+__all__ = [
+    "V3dConvolveOutputs",
+    "V3dConvolveParameters",
+    "V_3D_CONVOLVE_METADATA",
+    "v_3d_convolve",
+    "v_3d_convolve_params",
+]