niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_blur_to_fwhm.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_3D_BLUR_TO_FWHM_METADATA = Metadata(
+    id="f4b40fc76ce4b806bbbbfa509356f57bb656233d.boutiques",
+    name="3dBlurToFWHM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBlurToFwhmParameters = typing.TypedDict('V3dBlurToFwhmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dBlurToFWHM"],
+    "automask": bool,
+    "blurmaster": typing.NotRequired[InputPathType | None],
+    "fwhm": typing.NotRequired[float | None],
+    "fwhmxy": typing.NotRequired[float | None],
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "prefix": 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 {
+        "3dBlurToFWHM": v_3d_blur_to_fwhm_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 {
+        "3dBlurToFWHM": v_3d_blur_to_fwhm_outputs,
+    }.get(t)
+
+
+class V3dBlurToFwhmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_blur_to_fwhm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output image file name."""
+
+
+def v_3d_blur_to_fwhm_params(
+    in_file: InputPathType,
+    automask: bool = False,
+    blurmaster: InputPathType | None = None,
+    fwhm: float | None = None,
+    fwhmxy: float | None = None,
+    mask: InputPathType | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    prefix: str | None = None,
+) -> V3dBlurToFwhmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: The dataset that will be smoothed.
+        automask: Create an automask from the input dataset.
+        blurmaster: The dataset whose smoothness controls the process.
+        fwhm: Blur until the 3d fwhm reaches this value (in mm).
+        fwhmxy: Blur until the 2d (x,y)-plane fwhm reaches this value (in mm).
+        mask: Mask dataset, if desired. voxels not in mask will be set to zero\
+            in output.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        prefix: Prefix for output dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBlurToFWHM",
+        "automask": automask,
+        "in_file": in_file,
+    }
+    if blurmaster is not None:
+        params["blurmaster"] = blurmaster
+    if fwhm is not None:
+        params["fwhm"] = fwhm
+    if fwhmxy is not None:
+        params["fwhmxy"] = fwhmxy
+    if mask is not None:
+        params["mask"] = mask
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_blur_to_fwhm_cargs(
+    params: V3dBlurToFwhmParameters,
+    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("3dBlurToFWHM")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("blurmaster") is not None:
+        cargs.extend([
+            "-blurmaster",
+            execution.input_file(params.get("blurmaster"))
+        ])
+    if params.get("fwhm") is not None:
+        cargs.extend([
+            "-FWHM",
+            str(params.get("fwhm"))
+        ])
+    if params.get("fwhmxy") is not None:
+        cargs.extend([
+            "-FWHMxy",
+            str(params.get("fwhmxy"))
+        ])
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("in_file"))
+    ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3d_blur_to_fwhm_outputs(
+    params: V3dBlurToFwhmParameters,
+    execution: Execution,
+) -> V3dBlurToFwhmOutputs:
+    """
+    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 = V3dBlurToFwhmOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_blur_to_fwhm_execute(
+    params: V3dBlurToFwhmParameters,
+    execution: Execution,
+) -> V3dBlurToFwhmOutputs:
+    """
+    Blurs a 'master' dataset until it reaches a specified FWHM smoothness
+    (approximately).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBlurToFwhmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_blur_to_fwhm_cargs(params, execution)
+    ret = v_3d_blur_to_fwhm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_blur_to_fwhm(
+    in_file: InputPathType,
+    automask: bool = False,
+    blurmaster: InputPathType | None = None,
+    fwhm: float | None = None,
+    fwhmxy: float | None = None,
+    mask: InputPathType | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dBlurToFwhmOutputs:
+    """
+    Blurs a 'master' dataset until it reaches a specified FWHM smoothness
+    (approximately).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: The dataset that will be smoothed.
+        automask: Create an automask from the input dataset.
+        blurmaster: The dataset whose smoothness controls the process.
+        fwhm: Blur until the 3d fwhm reaches this value (in mm).
+        fwhmxy: Blur until the 2d (x,y)-plane fwhm reaches this value (in mm).
+        mask: Mask dataset, if desired. voxels not in mask will be set to zero\
+            in output.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        prefix: Prefix for output dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dBlurToFwhmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BLUR_TO_FWHM_METADATA)
+    params = v_3d_blur_to_fwhm_params(
+        automask=automask,
+        blurmaster=blurmaster,
+        fwhm=fwhm,
+        fwhmxy=fwhmxy,
+        in_file=in_file,
+        mask=mask,
+        outputtype=outputtype,
+        prefix=prefix,
+    )
+    return v_3d_blur_to_fwhm_execute(params, execution)
+
+
+__all__ = [
+    "V3dBlurToFwhmOutputs",
+    "V3dBlurToFwhmParameters",
+    "V_3D_BLUR_TO_FWHM_METADATA",
+    "v_3d_blur_to_fwhm",
+    "v_3d_blur_to_fwhm_params",
+]

niwrap_afni/afni/v_3d_brain_sync.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_3D_BRAIN_SYNC_METADATA = Metadata(
+    id="5b4873a7460d63bb6ab8b2f718571646d6b0ba3b.boutiques",
+    name="3dBrainSync",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dBrainSyncParameters = typing.TypedDict('V3dBrainSyncParameters', {
+    "__STYX_TYPE__": typing.Literal["3dBrainSync"],
+    "inset1": InputPathType,
+    "inset2": InputPathType,
+    "qprefix": typing.NotRequired[str | None],
+    "pprefix": typing.NotRequired[str | None],
+    "normalize": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "verb": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dBrainSync": v_3d_brain_sync_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 {
+        "3dBrainSync": v_3d_brain_sync_outputs,
+    }.get(t)
+
+
+class V3dBrainSyncOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_brain_sync(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    qprefix_output: OutputPathType | None
+    """Output dataset after orthogonal matrix transformation"""
+    pprefix_output: OutputPathType | None
+    """Output dataset after permutation transformation"""
+    qprefix_sval: OutputPathType | None
+    """Singular values from the BC' decomposition"""
+    qprefix_qmat: OutputPathType | None
+    """Q matrix"""
+    pprefix_perm: OutputPathType | None
+    """Permutation indexes p(i)"""
+
+
+def v_3d_brain_sync_params(
+    inset1: InputPathType,
+    inset2: InputPathType,
+    qprefix: str | None = None,
+    pprefix: str | None = None,
+    normalize: bool = False,
+    mask: InputPathType | None = None,
+    verb: bool = False,
+) -> V3dBrainSyncParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inset1: Reference dataset.
+        inset2: Dataset to be matched to the reference dataset.
+        qprefix: Specifies the output dataset to be used for the orthogonal\
+            matrix transformation.
+        pprefix: Specifies the output dataset to be used for the permutation\
+            transformation.
+        normalize: Normalize the output dataset(s) so that each time series has\
+            sum-of-squares = 1.
+        mask: Only operate on nonzero voxels in the mask dataset.
+        verb: Print some progress reports and auxiliary information.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dBrainSync",
+        "inset1": inset1,
+        "inset2": inset2,
+        "normalize": normalize,
+        "verb": verb,
+    }
+    if qprefix is not None:
+        params["qprefix"] = qprefix
+    if pprefix is not None:
+        params["pprefix"] = pprefix
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_brain_sync_cargs(
+    params: V3dBrainSyncParameters,
+    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("3dBrainSync")
+    cargs.extend([
+        "-inset1",
+        execution.input_file(params.get("inset1"))
+    ])
+    cargs.extend([
+        "-inset2",
+        execution.input_file(params.get("inset2"))
+    ])
+    if params.get("qprefix") is not None:
+        cargs.extend([
+            "-Qprefix",
+            params.get("qprefix")
+        ])
+    if params.get("pprefix") is not None:
+        cargs.extend([
+            "-Pprefix",
+            params.get("pprefix")
+        ])
+    if params.get("normalize"):
+        cargs.append("-normalize")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("verb"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v_3d_brain_sync_outputs(
+    params: V3dBrainSyncParameters,
+    execution: Execution,
+) -> V3dBrainSyncOutputs:
+    """
+    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 = V3dBrainSyncOutputs(
+        root=execution.output_file("."),
+        qprefix_output=execution.output_file(params.get("qprefix") + ".nii") if (params.get("qprefix") is not None) else None,
+        pprefix_output=execution.output_file(params.get("pprefix") + ".nii") if (params.get("pprefix") is not None) else None,
+        qprefix_sval=execution.output_file(params.get("qprefix") + ".sval.1D") if (params.get("qprefix") is not None) else None,
+        qprefix_qmat=execution.output_file(params.get("qprefix") + ".qmat.1D") if (params.get("qprefix") is not None) else None,
+        pprefix_perm=execution.output_file(params.get("pprefix") + ".perm.1D") if (params.get("pprefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_brain_sync_execute(
+    params: V3dBrainSyncParameters,
+    execution: Execution,
+) -> V3dBrainSyncOutputs:
+    """
+    'Synchronizes' the -inset2 dataset to match the -inset1 dataset, using
+    orthogonal or permutation transformation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dBrainSyncOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_brain_sync_cargs(params, execution)
+    ret = v_3d_brain_sync_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_brain_sync(
+    inset1: InputPathType,
+    inset2: InputPathType,
+    qprefix: str | None = None,
+    pprefix: str | None = None,
+    normalize: bool = False,
+    mask: InputPathType | None = None,
+    verb: bool = False,
+    runner: Runner | None = None,
+) -> V3dBrainSyncOutputs:
+    """
+    'Synchronizes' the -inset2 dataset to match the -inset1 dataset, using
+    orthogonal or permutation transformation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inset1: Reference dataset.
+        inset2: Dataset to be matched to the reference dataset.
+        qprefix: Specifies the output dataset to be used for the orthogonal\
+            matrix transformation.
+        pprefix: Specifies the output dataset to be used for the permutation\
+            transformation.
+        normalize: Normalize the output dataset(s) so that each time series has\
+            sum-of-squares = 1.
+        mask: Only operate on nonzero voxels in the mask dataset.
+        verb: Print some progress reports and auxiliary information.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dBrainSyncOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_BRAIN_SYNC_METADATA)
+    params = v_3d_brain_sync_params(
+        inset1=inset1,
+        inset2=inset2,
+        qprefix=qprefix,
+        pprefix=pprefix,
+        normalize=normalize,
+        mask=mask,
+        verb=verb,
+    )
+    return v_3d_brain_sync_execute(params, execution)
+
+
+__all__ = [
+    "V3dBrainSyncOutputs",
+    "V3dBrainSyncParameters",
+    "V_3D_BRAIN_SYNC_METADATA",
+    "v_3d_brain_sync",
+    "v_3d_brain_sync_params",
+]