niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_despike.py

@@ -0,0 +1,191 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DESPIKE_METADATA = Metadata(
+    id="724be608ea12115bb59f6e6981f0905bfd860c95.boutiques",
+    name="3dDespike",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDespikeParameters = typing.TypedDict('V3dDespikeParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDespike"],
+    "prefix": typing.NotRequired[str | None],
+    "in_file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dDespike": v_3d_despike_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 {
+        "3dDespike": v_3d_despike_outputs,
+    }.get(t)
+
+
+class V3dDespikeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_despike(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType | None
+    """Output file."""
+
+
+def v_3d_despike_params(
+    in_file: InputPathType,
+    prefix: str | None = None,
+) -> V3dDespikeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3ddespike.
+        prefix: Prefix for output file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDespike",
+        "in_file": in_file,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_despike_cargs(
+    params: V3dDespikeParameters,
+    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("3dDespike")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    cargs.append(execution.input_file(params.get("in_file")))
+    return cargs
+
+
+def v_3d_despike_outputs(
+    params: V3dDespikeParameters,
+    execution: Execution,
+) -> V3dDespikeOutputs:
+    """
+    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 = V3dDespikeOutputs(
+        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_despike_execute(
+    params: V3dDespikeParameters,
+    execution: Execution,
+) -> V3dDespikeOutputs:
+    """
+    Removes 'spikes' from the 3D+time input dataset and writes a new dataset with
+    the spike values replaced by something more pleasing to the eye.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDespikeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_despike_cargs(params, execution)
+    ret = v_3d_despike_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_despike(
+    in_file: InputPathType,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dDespikeOutputs:
+    """
+    Removes 'spikes' from the 3D+time input dataset and writes a new dataset with
+    the spike values replaced by something more pleasing to the eye.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3ddespike.
+        prefix: Prefix for output file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDespikeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DESPIKE_METADATA)
+    params = v_3d_despike_params(
+        prefix=prefix,
+        in_file=in_file,
+    )
+    return v_3d_despike_execute(params, execution)
+
+
+__all__ = [
+    "V3dDespikeOutputs",
+    "V3dDespikeParameters",
+    "V_3D_DESPIKE_METADATA",
+    "v_3d_despike",
+    "v_3d_despike_params",
+]

niwrap_afni/afni/v_3d_detrend.py

@@ -0,0 +1,191 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DETREND_METADATA = Metadata(
+    id="e1acbbed353dee123a530befb4df733e98383a20.boutiques",
+    name="3dDetrend",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDetrendParameters = typing.TypedDict('V3dDetrendParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDetrend"],
+    "in_file": InputPathType,
+    "outputtype": typing.NotRequired[typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dDetrend": v_3d_detrend_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 {
+        "3dDetrend": v_3d_detrend_outputs,
+    }.get(t)
+
+
+class V3dDetrendOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_detrend(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_file: OutputPathType
+    """Output image file name."""
+    out_file_: OutputPathType
+    """Output file."""
+
+
+def v_3d_detrend_params(
+    in_file: InputPathType,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+) -> V3dDetrendParameters:
+    """
+    Build parameters.
+    
+    Args:
+        in_file: Input file to 3ddetrend.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDetrend",
+        "in_file": in_file,
+    }
+    if outputtype is not None:
+        params["outputtype"] = outputtype
+    return params
+
+
+def v_3d_detrend_cargs(
+    params: V3dDetrendParameters,
+    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("3dDetrend")
+    cargs.append(execution.input_file(params.get("in_file")))
+    if params.get("outputtype") is not None:
+        cargs.append(params.get("outputtype"))
+    return cargs
+
+
+def v_3d_detrend_outputs(
+    params: V3dDetrendParameters,
+    execution: Execution,
+) -> V3dDetrendOutputs:
+    """
+    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 = V3dDetrendOutputs(
+        root=execution.output_file("."),
+        out_file=execution.output_file(pathlib.Path(params.get("in_file")).name + "_detrend"),
+        out_file_=execution.output_file("out_file"),
+    )
+    return ret
+
+
+def v_3d_detrend_execute(
+    params: V3dDetrendParameters,
+    execution: Execution,
+) -> V3dDetrendOutputs:
+    """
+    This program removes components from voxel time series using linear least
+    squares.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDetrendOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_detrend_cargs(params, execution)
+    ret = v_3d_detrend_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_detrend(
+    in_file: InputPathType,
+    outputtype: typing.Literal["NIFTI", "AFNI", "NIFTI_GZ"] | None = None,
+    runner: Runner | None = None,
+) -> V3dDetrendOutputs:
+    """
+    This program removes components from voxel time series using linear least
+    squares.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        in_file: Input file to 3ddetrend.
+        outputtype: 'nifti' or 'afni' or 'nifti_gz'. Afni output filetype.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDetrendOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DETREND_METADATA)
+    params = v_3d_detrend_params(
+        in_file=in_file,
+        outputtype=outputtype,
+    )
+    return v_3d_detrend_execute(params, execution)
+
+
+__all__ = [
+    "V3dDetrendOutputs",
+    "V3dDetrendParameters",
+    "V_3D_DETREND_METADATA",
+    "v_3d_detrend",
+    "v_3d_detrend_params",
+]

niwrap_afni/afni/v_3d_dft.py

@@ -0,0 +1,245 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DFT_METADATA = Metadata(
+    id="a3b7d9976a6067e83188d375554ab6efc38583c7.boutiques",
+    name="3dDFT",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDftParameters = typing.TypedDict('V3dDftParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDFT"],
+    "infile": InputPathType,
+    "prefix": str,
+    "abs_output": bool,
+    "nfft": typing.NotRequired[float | None],
+    "detrend": bool,
+    "taper": typing.NotRequired[float | None],
+    "inverse": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dDFT": v_3d_dft_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 {
+        "3dDFT": v_3d_dft_outputs,
+    }.get(t)
+
+
+class V3dDftOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_dft(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output dataset file"""
+    outheader: OutputPathType
+    """Output dataset header file"""
+
+
+def v_3d_dft_params(
+    infile: InputPathType,
+    prefix: str,
+    abs_output: bool = False,
+    nfft: float | None = None,
+    detrend: bool = False,
+    taper: float | None = None,
+    inverse: bool = False,
+) -> V3dDftParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input dataset (complex- or float-valued).
+        prefix: Prefix for the output file.
+        abs_output: Output float dataset = abs(DFT).
+        nfft: DFT length (must be >= number of time points).
+        detrend: Least-squares remove linear drift before DFT.
+        taper: Fraction (0 <= f <= 1) of data to taper at ends (Hamming taper).
+        inverse: Perform the inverse DFT.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDFT",
+        "infile": infile,
+        "prefix": prefix,
+        "abs_output": abs_output,
+        "detrend": detrend,
+        "inverse": inverse,
+    }
+    if nfft is not None:
+        params["nfft"] = nfft
+    if taper is not None:
+        params["taper"] = taper
+    return params
+
+
+def v_3d_dft_cargs(
+    params: V3dDftParameters,
+    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("3dDFT")
+    cargs.append(execution.input_file(params.get("infile")))
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("abs_output"):
+        cargs.append("-abs")
+    if params.get("nfft") is not None:
+        cargs.extend([
+            "-nfft",
+            str(params.get("nfft"))
+        ])
+    if params.get("detrend"):
+        cargs.append("-detrend")
+    if params.get("taper") is not None:
+        cargs.extend([
+            "-taper",
+            str(params.get("taper"))
+        ])
+    if params.get("inverse"):
+        cargs.append("-inverse")
+    return cargs
+
+
+def v_3d_dft_outputs(
+    params: V3dDftParameters,
+    execution: Execution,
+) -> V3dDftOutputs:
+    """
+    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 = V3dDftOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        outheader=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+    )
+    return ret
+
+
+def v_3d_dft_execute(
+    params: V3dDftParameters,
+    execution: Execution,
+) -> V3dDftOutputs:
+    """
+    Performs Discrete Fourier Transform (DFT) along the time axis of a complex- or
+    float-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dDftOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_dft_cargs(params, execution)
+    ret = v_3d_dft_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_dft(
+    infile: InputPathType,
+    prefix: str,
+    abs_output: bool = False,
+    nfft: float | None = None,
+    detrend: bool = False,
+    taper: float | None = None,
+    inverse: bool = False,
+    runner: Runner | None = None,
+) -> V3dDftOutputs:
+    """
+    Performs Discrete Fourier Transform (DFT) along the time axis of a complex- or
+    float-valued dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input dataset (complex- or float-valued).
+        prefix: Prefix for the output file.
+        abs_output: Output float dataset = abs(DFT).
+        nfft: DFT length (must be >= number of time points).
+        detrend: Least-squares remove linear drift before DFT.
+        taper: Fraction (0 <= f <= 1) of data to taper at ends (Hamming taper).
+        inverse: Perform the inverse DFT.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDftOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DFT_METADATA)
+    params = v_3d_dft_params(
+        infile=infile,
+        prefix=prefix,
+        abs_output=abs_output,
+        nfft=nfft,
+        detrend=detrend,
+        taper=taper,
+        inverse=inverse,
+    )
+    return v_3d_dft_execute(params, execution)
+
+
+__all__ = [
+    "V3dDftOutputs",
+    "V3dDftParameters",
+    "V_3D_DFT_METADATA",
+    "v_3d_dft",
+    "v_3d_dft_params",
+]