niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3dresample.py

@@ -0,0 +1,256 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DRESAMPLE_METADATA = Metadata(
+    id="0d87d38a4f7c77290f6d466ec9698d61440eb3e2.boutiques",
+    name="3dresample",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dresampleParameters = typing.TypedDict('V3dresampleParameters', {
+    "__STYX_TYPE__": typing.Literal["3dresample"],
+    "in_file": InputPathType,
+    "master": typing.NotRequired[InputPathType | None],
+    "orientation": typing.NotRequired[typing.Literal["AIL", "AIR", "ASL", "ASR", "PIL", "PIR", "PSL", "PSR", "ALI", "ALS", "ARI", "ARS", "PLI", "PLS", "PRI", "PRS", "IAL", "IAR", "IPL", "IPR", "SAL", "SAR", "SPL", "SPR", "ILA", "ILP", "IRA", "IRP", "SLA", "SLP", "SRA", "SRP", "LAI", "LAS", "LPI", "LPS", "RAI", "RAS", "RPI", "RPS", "LIA", "LIP", "LSA", "LSP", "RIA", "RIP", "RSA", "RSP"] | None],
+    "prefix": str,
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+    "resample_mode": typing.NotRequired[typing.Literal["NN", "Li", "Cu", "Bk"] | None],
+    "voxel_size": typing.NotRequired[list[float] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dresample": v_3dresample_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 {
+        "3dresample": v_3dresample_outputs,
+    }.get(t)
+
+
+class V3dresampleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dresample(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+
+
+def v_3dresample_params(
+    in_file: InputPathType,
+    prefix: str,
+    master: InputPathType | None = None,
+    orientation: typing.Literal["AIL", "AIR", "ASL", "ASR", "PIL", "PIR", "PSL", "PSR", "ALI", "ALS", "ARI", "ARS", "PLI", "PLS", "PRI", "PRS", "IAL", "IAR", "IPL", "IPR", "SAL", "SAR", "SPL", "SPR", "ILA", "ILP", "IRA", "IRP", "SLA", "SLP", "SRA", "SRP", "LAI", "LAS", "LPI", "LPS", "RAI", "RAS", "RPI", "RPS", "LIA", "LIP", "LSA", "LSP", "RIA", "RIP", "RSA", "RSP"] | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    resample_mode: typing.Literal["NN", "Li", "Cu", "Bk"] | None = None,
+    voxel_size: list[float] | None = None,
+) -> V3dresampleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3dresample.
+        prefix: required prefix for output dataset.
+        master: Align dataset grid to a reference file.
+        orientation: New orientation code.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        resample_mode: 'nn' or 'li' or 'cu' or 'bk'. Resampling method from set\
+            {"nn", "li", "cu", "bk"}. these are for "nearest neighbor", "linear",\
+            "cubic" and "blocky"interpolation, respectively. default is nn.
+        voxel_size: (a float, a float, a float). Resample to new dx, dy and dz.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dresample",
+        "in_file": in_file,
+        "prefix": prefix,
+    }
+    if master is not None:
+        params["master"] = master
+    if orientation is not None:
+        params["orientation"] = orientation
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    if resample_mode is not None:
+        params["resample_mode"] = resample_mode
+    if voxel_size is not None:
+        params["voxel_size"] = voxel_size
+    return params
+
+
+def v_3dresample_cargs(
+    params: V3dresampleParameters,
+    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("3dresample")
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("in_file"))
+    ])
+    if params.get("master") is not None:
+        cargs.extend([
+            "-master",
+            execution.input_file(params.get("master"))
+        ])
+    if params.get("orientation") is not None:
+        cargs.extend([
+            "-orient",
+            params.get("orientation")
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    if params.get("resample_mode") is not None:
+        cargs.extend([
+            "-rmode",
+            params.get("resample_mode")
+        ])
+    if params.get("voxel_size") is not None:
+        cargs.extend([
+            "-dxyz",
+            *map(str, params.get("voxel_size"))
+        ])
+    return cargs
+
+
+def v_3dresample_outputs(
+    params: V3dresampleParameters,
+    execution: Execution,
+) -> V3dresampleOutputs:
+    """
+    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 = V3dresampleOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(params.get("prefix")),
+    )
+    return ret
+
+
+def v_3dresample_execute(
+    params: V3dresampleParameters,
+    execution: Execution,
+) -> V3dresampleOutputs:
+    """
+    Resample or reorient an image using AFNI 3dresample command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dresampleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dresample_cargs(params, execution)
+    ret = v_3dresample_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dresample(
+    in_file: InputPathType,
+    prefix: str,
+    master: InputPathType | None = None,
+    orientation: typing.Literal["AIL", "AIR", "ASL", "ASR", "PIL", "PIR", "PSL", "PSR", "ALI", "ALS", "ARI", "ARS", "PLI", "PLS", "PRI", "PRS", "IAL", "IAR", "IPL", "IPR", "SAL", "SAR", "SPL", "SPR", "ILA", "ILP", "IRA", "IRP", "SLA", "SLP", "SRA", "SRP", "LAI", "LAS", "LPI", "LPS", "RAI", "RAS", "RPI", "RPS", "LIA", "LIP", "LSA", "LSP", "RIA", "RIP", "RSA", "RSP"] | None = None,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    resample_mode: typing.Literal["NN", "Li", "Cu", "Bk"] | None = None,
+    voxel_size: list[float] | None = None,
+    runner: Runner | None = None,
+) -> V3dresampleOutputs:
+    """
+    Resample or reorient an image using AFNI 3dresample command.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3dresample.
+        prefix: required prefix for output dataset.
+        master: Align dataset grid to a reference file.
+        orientation: New orientation code.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        resample_mode: 'nn' or 'li' or 'cu' or 'bk'. Resampling method from set\
+            {"nn", "li", "cu", "bk"}. these are for "nearest neighbor", "linear",\
+            "cubic" and "blocky"interpolation, respectively. default is nn.
+        voxel_size: (a float, a float, a float). Resample to new dx, dy and dz.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dresampleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DRESAMPLE_METADATA)
+    params = v_3dresample_params(
+        in_file=in_file,
+        master=master,
+        orientation=orientation,
+        prefix=prefix,
+        outputtype=outputtype,
+        resample_mode=resample_mode,
+        voxel_size=voxel_size,
+    )
+    return v_3dresample_execute(params, execution)
+
+
+__all__ = [
+    "V3dresampleOutputs",
+    "V3dresampleParameters",
+    "V_3DRESAMPLE_METADATA",
+    "v_3dresample",
+    "v_3dresample_params",
+]

niwrap_afni/afni/v_3dretroicor.py

@@ -0,0 +1,296 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3DRETROICOR_METADATA = Metadata(
+    id="0b8e3bbd9eaa6f16498a0393158cdcd367502347.boutiques",
+    name="3dretroicor",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dretroicorParameters = typing.TypedDict('V3dretroicorParameters', {
+    "__STYX_TYPE__": typing.Literal["3dretroicor"],
+    "ignore": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "card": typing.NotRequired[InputPathType | None],
+    "cardphase": typing.NotRequired[str | None],
+    "threshold": typing.NotRequired[float | None],
+    "resp": typing.NotRequired[InputPathType | None],
+    "respphase": typing.NotRequired[str | None],
+    "order": typing.NotRequired[float | None],
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dretroicor": v_3dretroicor_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 {
+        "3dretroicor": v_3dretroicor_outputs,
+    }.get(t)
+
+
+class V3dretroicorOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3dretroicor(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    corrected_dataset: OutputPathType | None
+    """Corrected dataset output."""
+    output_cardiac_phase: OutputPathType | None
+    """Cardiac phase output file."""
+    output_resp_phase: OutputPathType | None
+    """Respiratory phase output file."""
+
+
+def v_3dretroicor_params(
+    dataset: InputPathType,
+    ignore: float | None = None,
+    prefix: str | None = None,
+    card: InputPathType | None = None,
+    cardphase: str | None = None,
+    threshold: float | None = None,
+    resp: InputPathType | None = None,
+    respphase: str | None = None,
+    order: float | None = None,
+) -> V3dretroicorParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: 3D+time dataset to process.
+        ignore: The number of initial timepoints to ignore in the input. These\
+            points will be passed through uncorrected.
+        prefix: Prefix for new, corrected dataset.
+        card: 1D cardiac data file for cardiac correction.
+        cardphase: Filename for 1D cardiac phase output.
+        threshold: Threshold for detection of R-wave peaks in input. Make sure\
+            it's above the background noise level; try 3/4 or 4/5 times range plus\
+            minimum.
+        resp: 1D respiratory waveform data for correction.
+        respphase: Filename for 1D respiratory phase output.
+        order: The order of the correction. Higher-order terms yield little\
+            improvement according to Glover et al.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dretroicor",
+        "dataset": dataset,
+    }
+    if ignore is not None:
+        params["ignore"] = ignore
+    if prefix is not None:
+        params["prefix"] = prefix
+    if card is not None:
+        params["card"] = card
+    if cardphase is not None:
+        params["cardphase"] = cardphase
+    if threshold is not None:
+        params["threshold"] = threshold
+    if resp is not None:
+        params["resp"] = resp
+    if respphase is not None:
+        params["respphase"] = respphase
+    if order is not None:
+        params["order"] = order
+    return params
+
+
+def v_3dretroicor_cargs(
+    params: V3dretroicorParameters,
+    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("3dretroicor")
+    if params.get("ignore") is not None:
+        cargs.extend([
+            "-ignore",
+            str(params.get("ignore"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("card") is not None:
+        cargs.extend([
+            "-card",
+            execution.input_file(params.get("card"))
+        ])
+    if params.get("cardphase") is not None:
+        cargs.extend([
+            "-cardphase",
+            params.get("cardphase")
+        ])
+    if params.get("threshold") is not None:
+        cargs.extend([
+            "-threshold",
+            str(params.get("threshold"))
+        ])
+    if params.get("resp") is not None:
+        cargs.extend([
+            "-resp",
+            execution.input_file(params.get("resp"))
+        ])
+    if params.get("respphase") is not None:
+        cargs.extend([
+            "-respphase",
+            params.get("respphase")
+        ])
+    if params.get("order") is not None:
+        cargs.extend([
+            "-order",
+            str(params.get("order"))
+        ])
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3dretroicor_outputs(
+    params: V3dretroicorParameters,
+    execution: Execution,
+) -> V3dretroicorOutputs:
+    """
+    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 = V3dretroicorOutputs(
+        root=execution.output_file("."),
+        corrected_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+        output_cardiac_phase=execution.output_file(params.get("cardphase")) if (params.get("cardphase") is not None) else None,
+        output_resp_phase=execution.output_file(params.get("respphase")) if (params.get("respphase") is not None) else None,
+    )
+    return ret
+
+
+def v_3dretroicor_execute(
+    params: V3dretroicorParameters,
+    execution: Execution,
+) -> V3dretroicorOutputs:
+    """
+    Performs Retrospective Image Correction for physiological motion effects using a
+    modified RETROICOR algorithm.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dretroicorOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3dretroicor_cargs(params, execution)
+    ret = v_3dretroicor_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3dretroicor(
+    dataset: InputPathType,
+    ignore: float | None = None,
+    prefix: str | None = None,
+    card: InputPathType | None = None,
+    cardphase: str | None = None,
+    threshold: float | None = None,
+    resp: InputPathType | None = None,
+    respphase: str | None = None,
+    order: float | None = None,
+    runner: Runner | None = None,
+) -> V3dretroicorOutputs:
+    """
+    Performs Retrospective Image Correction for physiological motion effects using a
+    modified RETROICOR algorithm.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: 3D+time dataset to process.
+        ignore: The number of initial timepoints to ignore in the input. These\
+            points will be passed through uncorrected.
+        prefix: Prefix for new, corrected dataset.
+        card: 1D cardiac data file for cardiac correction.
+        cardphase: Filename for 1D cardiac phase output.
+        threshold: Threshold for detection of R-wave peaks in input. Make sure\
+            it's above the background noise level; try 3/4 or 4/5 times range plus\
+            minimum.
+        resp: 1D respiratory waveform data for correction.
+        respphase: Filename for 1D respiratory phase output.
+        order: The order of the correction. Higher-order terms yield little\
+            improvement according to Glover et al.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dretroicorOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3DRETROICOR_METADATA)
+    params = v_3dretroicor_params(
+        ignore=ignore,
+        prefix=prefix,
+        card=card,
+        cardphase=cardphase,
+        threshold=threshold,
+        resp=resp,
+        respphase=respphase,
+        order=order,
+        dataset=dataset,
+    )
+    return v_3dretroicor_execute(params, execution)
+
+
+__all__ = [
+    "V3dretroicorOutputs",
+    "V3dretroicorParameters",
+    "V_3DRETROICOR_METADATA",
+    "v_3dretroicor",
+    "v_3dretroicor_params",
+]