niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_lomb_scargle.py

@@ -0,0 +1,307 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LOMB_SCARGLE_METADATA = Metadata(
+    id="ec1cdb90b6faac538a25b9943b1823c8bc7afa27.boutiques",
+    name="3dLombScargle",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLombScargleParameters = typing.TypedDict('V3dLombScargleParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLombScargle"],
+    "prefix": str,
+    "inset": InputPathType,
+    "censor_1d": typing.NotRequired[InputPathType | None],
+    "censor_string": typing.NotRequired[str | None],
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "out_pow_spec": bool,
+    "nyquist_multiplier": typing.NotRequired[int | None],
+    "nifti": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dLombScargle": v_3d_lomb_scargle_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 {
+        "3dLombScargle": v_3d_lomb_scargle_outputs,
+    }.get(t)
+
+
+class V3dLombScargleOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_lomb_scargle(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    time_points: OutputPathType
+    """1D file of the sampled time points (in units of seconds) of the analyzed
+    data set"""
+    frequency_points: OutputPathType
+    """1D file of the frequency sample points (in units of 1/seconds) of the
+    output periodogram/spectrum data set"""
+    amplitude_spectrum: OutputPathType
+    """Volumetric data set containing a LS-derived amplitude spectrum"""
+    power_spectrum: OutputPathType
+    """Volumetric data set containing a LS-derived power spectrum"""
+
+
+def v_3d_lomb_scargle_params(
+    prefix: str,
+    inset: InputPathType,
+    censor_1d: InputPathType | None = None,
+    censor_string: str | None = None,
+    mask_file: InputPathType | None = None,
+    out_pow_spec: bool = False,
+    nyquist_multiplier: int | None = None,
+    nifti: bool = False,
+) -> V3dLombScargleParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output prefix name for data volume, time point 1D file, and\
+            frequency 1D file.
+        inset: Time series of volumes, a 4D volumetric data set.
+        censor_1d: Single row or column of 1s (keep) and 0s (censored)\
+            describing which volumes of FILE are kept in the sampling and which are\
+            censored out, respectively. The length of the list of numbers must be\
+            of the same length as the number of volumes in FILE. If not entered,\
+            then the program will look for subbricks of all-zeros and assume those\
+            are censored out.
+        censor_string: AFNI-style selector string of volumes to *keep* in the\
+            analysis. Such as: '[0..4,7,10..$]'.
+        mask_file: Optional, mask of volume to analyze; additionally, any voxel\
+            with uniformly zero values across time will produce a zero-spectrum.
+        out_pow_spec: Switch to output the amplitude spectrum of the freqs\
+            instead of the periodogram. In the formulation used here, for a time\
+            series of length N, the power spectral value S is related to the\
+            amplitude value X as: S = (X)**2. (Without this opt, default output is\
+            amplitude spectrum.).
+        nyquist_multiplier: L-S periodograms can include frequencies above what\
+            would typically be considered Nyquist. By default, the maximum\
+            frequency will be what f_N *would* have been if no censoring of points\
+            had occurred. Acceptable values are >0. (This sets the 'hifac'\
+            parameter).
+        nifti: Switch to output *.nii.gz volume file (default format is\
+            BRIK/HEAD).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLombScargle",
+        "prefix": prefix,
+        "inset": inset,
+        "out_pow_spec": out_pow_spec,
+        "nifti": nifti,
+    }
+    if censor_1d is not None:
+        params["censor_1d"] = censor_1d
+    if censor_string is not None:
+        params["censor_string"] = censor_string
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if nyquist_multiplier is not None:
+        params["nyquist_multiplier"] = nyquist_multiplier
+    return params
+
+
+def v_3d_lomb_scargle_cargs(
+    params: V3dLombScargleParameters,
+    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("3dLombScargle")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.extend([
+        "-inset",
+        execution.input_file(params.get("inset"))
+    ])
+    if params.get("censor_1d") is not None:
+        cargs.extend([
+            "-censor_1D",
+            execution.input_file(params.get("censor_1d"))
+        ])
+    if params.get("censor_string") is not None:
+        cargs.extend([
+            "-censor_str",
+            params.get("censor_string")
+        ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("out_pow_spec"):
+        cargs.append("-out_pow_spec")
+    if params.get("nyquist_multiplier") is not None:
+        cargs.extend([
+            "-nyq_mult",
+            str(params.get("nyquist_multiplier"))
+        ])
+    if params.get("nifti"):
+        cargs.append("-nifti")
+    return cargs
+
+
+def v_3d_lomb_scargle_outputs(
+    params: V3dLombScargleParameters,
+    execution: Execution,
+) -> V3dLombScargleOutputs:
+    """
+    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 = V3dLombScargleOutputs(
+        root=execution.output_file("."),
+        time_points=execution.output_file(params.get("prefix") + "_time.1D"),
+        frequency_points=execution.output_file(params.get("prefix") + "_freq.1D"),
+        amplitude_spectrum=execution.output_file(params.get("prefix") + "_amp+orig"),
+        power_spectrum=execution.output_file(params.get("prefix") + "_pow+orig"),
+    )
+    return ret
+
+
+def v_3d_lomb_scargle_execute(
+    params: V3dLombScargleParameters,
+    execution: Execution,
+) -> V3dLombScargleOutputs:
+    """
+    Make a periodogram or amplitude-spectrum of a time series that has a
+    non-constant sampling rate.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLombScargleOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_lomb_scargle_cargs(params, execution)
+    ret = v_3d_lomb_scargle_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_lomb_scargle(
+    prefix: str,
+    inset: InputPathType,
+    censor_1d: InputPathType | None = None,
+    censor_string: str | None = None,
+    mask_file: InputPathType | None = None,
+    out_pow_spec: bool = False,
+    nyquist_multiplier: int | None = None,
+    nifti: bool = False,
+    runner: Runner | None = None,
+) -> V3dLombScargleOutputs:
+    """
+    Make a periodogram or amplitude-spectrum of a time series that has a
+    non-constant sampling rate.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output prefix name for data volume, time point 1D file, and\
+            frequency 1D file.
+        inset: Time series of volumes, a 4D volumetric data set.
+        censor_1d: Single row or column of 1s (keep) and 0s (censored)\
+            describing which volumes of FILE are kept in the sampling and which are\
+            censored out, respectively. The length of the list of numbers must be\
+            of the same length as the number of volumes in FILE. If not entered,\
+            then the program will look for subbricks of all-zeros and assume those\
+            are censored out.
+        censor_string: AFNI-style selector string of volumes to *keep* in the\
+            analysis. Such as: '[0..4,7,10..$]'.
+        mask_file: Optional, mask of volume to analyze; additionally, any voxel\
+            with uniformly zero values across time will produce a zero-spectrum.
+        out_pow_spec: Switch to output the amplitude spectrum of the freqs\
+            instead of the periodogram. In the formulation used here, for a time\
+            series of length N, the power spectral value S is related to the\
+            amplitude value X as: S = (X)**2. (Without this opt, default output is\
+            amplitude spectrum.).
+        nyquist_multiplier: L-S periodograms can include frequencies above what\
+            would typically be considered Nyquist. By default, the maximum\
+            frequency will be what f_N *would* have been if no censoring of points\
+            had occurred. Acceptable values are >0. (This sets the 'hifac'\
+            parameter).
+        nifti: Switch to output *.nii.gz volume file (default format is\
+            BRIK/HEAD).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLombScargleOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LOMB_SCARGLE_METADATA)
+    params = v_3d_lomb_scargle_params(
+        prefix=prefix,
+        inset=inset,
+        censor_1d=censor_1d,
+        censor_string=censor_string,
+        mask_file=mask_file,
+        out_pow_spec=out_pow_spec,
+        nyquist_multiplier=nyquist_multiplier,
+        nifti=nifti,
+    )
+    return v_3d_lomb_scargle_execute(params, execution)
+
+
+__all__ = [
+    "V3dLombScargleOutputs",
+    "V3dLombScargleParameters",
+    "V_3D_LOMB_SCARGLE_METADATA",
+    "v_3d_lomb_scargle",
+    "v_3d_lomb_scargle_params",
+]

niwrap_afni/afni/v_3d_lrflip.py

@@ -0,0 +1,202 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LRFLIP_METADATA = Metadata(
+    id="b3e8fe43a4546f9996744e159107df5ff817046b.boutiques",
+    name="3dLRflip",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLrflipParameters = typing.TypedDict('V3dLrflipParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLRflip"],
+    "flip_z": bool,
+    "output_prefix": typing.NotRequired[str | None],
+    "datasets": 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 {
+        "3dLRflip": v_3d_lrflip_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 {
+        "3dLRflip": v_3d_lrflip_outputs,
+    }.get(t)
+
+
+class V3dLrflipOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_lrflip(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    flipped_output: OutputPathType | None
+    """Output dataset after flipping"""
+
+
+def v_3d_lrflip_params(
+    datasets: list[InputPathType],
+    flip_z: bool = False,
+    output_prefix: str | None = None,
+) -> V3dLrflipParameters:
+    """
+    Build parameters.
+    
+    Args:
+        datasets: Datasets to flip.
+        flip_z: Flip about the 3rd direction.
+        output_prefix: Prefix to use for output. If multiple datasets are\
+            input, the program will choose a prefix for each output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLRflip",
+        "flip_z": flip_z,
+        "datasets": datasets,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    return params
+
+
+def v_3d_lrflip_cargs(
+    params: V3dLrflipParameters,
+    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("3dLRflip")
+    if params.get("flip_z"):
+        cargs.append("-Z")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("datasets")])
+    return cargs
+
+
+def v_3d_lrflip_outputs(
+    params: V3dLrflipParameters,
+    execution: Execution,
+) -> V3dLrflipOutputs:
+    """
+    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 = V3dLrflipOutputs(
+        root=execution.output_file("."),
+        flipped_output=execution.output_file(params.get("output_prefix") + "*") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_lrflip_execute(
+    params: V3dLrflipParameters,
+    execution: Execution,
+) -> V3dLrflipOutputs:
+    """
+    Flips the rows of a dataset along one of the three axes to correct dataset
+    direction labeling errors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLrflipOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_lrflip_cargs(params, execution)
+    ret = v_3d_lrflip_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_lrflip(
+    datasets: list[InputPathType],
+    flip_z: bool = False,
+    output_prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dLrflipOutputs:
+    """
+    Flips the rows of a dataset along one of the three axes to correct dataset
+    direction labeling errors.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        datasets: Datasets to flip.
+        flip_z: Flip about the 3rd direction.
+        output_prefix: Prefix to use for output. If multiple datasets are\
+            input, the program will choose a prefix for each output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLrflipOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LRFLIP_METADATA)
+    params = v_3d_lrflip_params(
+        flip_z=flip_z,
+        output_prefix=output_prefix,
+        datasets=datasets,
+    )
+    return v_3d_lrflip_execute(params, execution)
+
+
+__all__ = [
+    "V3dLrflipOutputs",
+    "V3dLrflipParameters",
+    "V_3D_LRFLIP_METADATA",
+    "v_3d_lrflip",
+    "v_3d_lrflip_params",
+]

niwrap_afni/afni/v_3d_lss.py

@@ -0,0 +1,175 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_LSS_METADATA = Metadata(
+    id="d793e92300ed18c69c7d31223293711fdbbfaaf7.boutiques",
+    name="3dLSS",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dLssParameters = typing.TypedDict('V3dLssParameters', {
+    "__STYX_TYPE__": typing.Literal["3dLSS"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dLSS": v_3d_lss_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 {
+        "3dLSS": v_3d_lss_outputs,
+    }.get(t)
+
+
+class V3dLssOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_lss(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType
+    """Output dataset containing the LSS estimates of the beta weights for the
+    '-stim_times_IM' stimuli."""
+    save1_d_output: OutputPathType
+    """Estimator vectors saved in a 1D formatted file."""
+
+
+def v_3d_lss_params(
+) -> V3dLssParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dLSS",
+    }
+    return params
+
+
+def v_3d_lss_cargs(
+    params: V3dLssParameters,
+    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("3dLSS")
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v_3d_lss_outputs(
+    params: V3dLssParameters,
+    execution: Execution,
+) -> V3dLssOutputs:
+    """
+    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 = V3dLssOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file("LSSout+orig.HEAD"),
+        save1_d_output=execution.output_file("[SAVE1D]"),
+    )
+    return ret
+
+
+def v_3d_lss_execute(
+    params: V3dLssParameters,
+    execution: Execution,
+) -> V3dLssOutputs:
+    """
+    Least-Squares-Sum (LSS) estimation tool from a -stim_times_IM matrix for
+    multivoxel pattern classification analyses.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dLssOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_lss_cargs(params, execution)
+    ret = v_3d_lss_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_lss(
+    runner: Runner | None = None,
+) -> V3dLssOutputs:
+    """
+    Least-Squares-Sum (LSS) estimation tool from a -stim_times_IM matrix for
+    multivoxel pattern classification analyses.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dLssOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LSS_METADATA)
+    params = v_3d_lss_params(
+    )
+    return v_3d_lss_execute(params, execution)
+
+
+__all__ = [
+    "V3dLssOutputs",
+    "V3dLssParameters",
+    "V_3D_LSS_METADATA",
+    "v_3d_lss",
+    "v_3d_lss_params",
+]