niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1dfft.py

@@ -0,0 +1,269 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DFFT_METADATA = Metadata(
+    id="1b882371fd5c103972dacb7d40e09d3d66d4ad04.boutiques",
+    name="1dfft",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dfftParameters = typing.TypedDict('V1dfftParameters', {
+    "__STYX_TYPE__": typing.Literal["1dfft"],
+    "infile": InputPathType,
+    "outfile": str,
+    "ignore": typing.NotRequired[float | None],
+    "use": typing.NotRequired[float | None],
+    "nfft": typing.NotRequired[float | None],
+    "tocx": bool,
+    "fromcx": bool,
+    "hilbert": bool,
+    "nodetrend": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dfft": v_1dfft_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 {
+        "1dfft": v_1dfft_outputs,
+    }.get(t)
+
+
+class V1dfftOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1dfft(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_fft: OutputPathType
+    """Output file with the absolute value of the FFT of the input columns."""
+
+
+def v_1dfft_params(
+    infile: InputPathType,
+    outfile: str,
+    ignore: float | None = None,
+    use: float | None = None,
+    nfft: float | None = None,
+    tocx: bool = False,
+    fromcx: bool = False,
+    hilbert: bool = False,
+    nodetrend: bool = False,
+) -> V1dfftParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input .1D file containing an ASCII list of numbers arranged in\
+            columns.
+        outfile: Output file to store the FFT results.
+        ignore: Skip the first 'sss' lines in the input file. [default = no\
+            skipping].
+        use: Use only 'uuu' lines of the input file. [default = use them all].
+        nfft: Set FFT length to 'nnn'. [default = length of data (# of lines\
+            used)].
+        tocx: Save Re and Im parts of transform in 2 columns.
+        fromcx: Convert 2 column complex input into 1 column real output. Note:\
+            This will not work if the original data FFT length was an odd number.
+        hilbert: When -fromcx is used, the inverse FFT will do the Hilbert\
+            transform instead.
+        nodetrend: Skip the detrending of the input.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dfft",
+        "infile": infile,
+        "outfile": outfile,
+        "tocx": tocx,
+        "fromcx": fromcx,
+        "hilbert": hilbert,
+        "nodetrend": nodetrend,
+    }
+    if ignore is not None:
+        params["ignore"] = ignore
+    if use is not None:
+        params["use"] = use
+    if nfft is not None:
+        params["nfft"] = nfft
+    return params
+
+
+def v_1dfft_cargs(
+    params: V1dfftParameters,
+    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("1dfft")
+    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(params.get("outfile"))
+    if params.get("ignore") is not None:
+        cargs.extend([
+            "-ignore",
+            str(params.get("ignore"))
+        ])
+    if params.get("use") is not None:
+        cargs.extend([
+            "-use",
+            str(params.get("use"))
+        ])
+    if params.get("nfft") is not None:
+        cargs.extend([
+            "-nfft",
+            str(params.get("nfft"))
+        ])
+    if params.get("tocx"):
+        cargs.append("-tocx")
+    if params.get("fromcx"):
+        cargs.append("-fromcx")
+    if params.get("hilbert"):
+        cargs.append("-hilbert")
+    if params.get("nodetrend"):
+        cargs.append("-nodetrend")
+    return cargs
+
+
+def v_1dfft_outputs(
+    params: V1dfftParameters,
+    execution: Execution,
+) -> V1dfftOutputs:
+    """
+    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 = V1dfftOutputs(
+        root=execution.output_file("."),
+        out_fft=execution.output_file(params.get("outfile")),
+    )
+    return ret
+
+
+def v_1dfft_execute(
+    params: V1dfftParameters,
+    execution: Execution,
+) -> V1dfftOutputs:
+    """
+    Compute the absolute value of the FFT of input columns from an AFNI 1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dfftOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1dfft_cargs(params, execution)
+    ret = v_1dfft_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1dfft(
+    infile: InputPathType,
+    outfile: str,
+    ignore: float | None = None,
+    use: float | None = None,
+    nfft: float | None = None,
+    tocx: bool = False,
+    fromcx: bool = False,
+    hilbert: bool = False,
+    nodetrend: bool = False,
+    runner: Runner | None = None,
+) -> V1dfftOutputs:
+    """
+    Compute the absolute value of the FFT of input columns from an AFNI 1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input .1D file containing an ASCII list of numbers arranged in\
+            columns.
+        outfile: Output file to store the FFT results.
+        ignore: Skip the first 'sss' lines in the input file. [default = no\
+            skipping].
+        use: Use only 'uuu' lines of the input file. [default = use them all].
+        nfft: Set FFT length to 'nnn'. [default = length of data (# of lines\
+            used)].
+        tocx: Save Re and Im parts of transform in 2 columns.
+        fromcx: Convert 2 column complex input into 1 column real output. Note:\
+            This will not work if the original data FFT length was an odd number.
+        hilbert: When -fromcx is used, the inverse FFT will do the Hilbert\
+            transform instead.
+        nodetrend: Skip the detrending of the input.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dfftOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DFFT_METADATA)
+    params = v_1dfft_params(
+        infile=infile,
+        outfile=outfile,
+        ignore=ignore,
+        use=use,
+        nfft=nfft,
+        tocx=tocx,
+        fromcx=fromcx,
+        hilbert=hilbert,
+        nodetrend=nodetrend,
+    )
+    return v_1dfft_execute(params, execution)
+
+
+__all__ = [
+    "V1dfftOutputs",
+    "V1dfftParameters",
+    "V_1DFFT_METADATA",
+    "v_1dfft",
+    "v_1dfft_params",
+]

niwrap_afni/afni/v_1dgen_arma11.py

@@ -0,0 +1,319 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DGEN_ARMA11_METADATA = Metadata(
+    id="9fce1559df8cc31e0d2c99d44319f7a47b38ba76.boutiques",
+    name="1dgenARMA11",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dgenArma11Parameters = typing.TypedDict('V1dgenArma11Parameters', {
+    "__STYX_TYPE__": typing.Literal["1dgenARMA11"],
+    "length_alt": typing.NotRequired[float | None],
+    "num_series": typing.NotRequired[float | None],
+    "param_a": typing.NotRequired[float | None],
+    "param_b": typing.NotRequired[float | None],
+    "param_lam": typing.NotRequired[float | None],
+    "std_dev": typing.NotRequired[float | None],
+    "normalize": bool,
+    "seed": typing.NotRequired[float | None],
+    "corcut": typing.NotRequired[float | None],
+    "arma31": typing.NotRequired[str | None],
+    "arma51": 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 {
+        "1dgenARMA11": v_1dgen_arma11_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 {
+        "1dgenARMA11": v_1dgen_arma11_outputs,
+    }.get(t)
+
+
+class V1dgenArma11Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1dgen_arma11(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output: OutputPathType
+    """Generated ARMA(1,1) time series"""
+
+
+def v_1dgen_arma11_params(
+    length_alt: float | None = None,
+    num_series: float | None = None,
+    param_a: float | None = None,
+    param_b: float | None = None,
+    param_lam: float | None = None,
+    std_dev: float | None = None,
+    normalize: bool = False,
+    seed: float | None = None,
+    corcut: float | None = None,
+    arma31: str | None = None,
+    arma51: str | None = None,
+) -> V1dgenArma11Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        length_alt: Specify the length of the time series vector to generate\
+            (equivalent to -num option).
+        num_series: The number of time series vectors to generate; defaults to\
+            1 if not given.
+        param_a: Specify ARMA(1,1) parameters 'a'.
+        param_b: Specify ARMA(1,1) parameter 'b' directly.
+        param_lam: Specify ARMA(1,1) parameter 'b' indirectly.
+        std_dev: Set standard deviation of results [default=1].
+        normalize: Normalize time series so sum of squares is 1.
+        seed: Set random number seed.
+        corcut: Specify a cutoff for the correlation coefficient r(k) of noise\
+            samples at k units apart. Default is 0.00010.
+        arma31: Specify parameters for a restricted ARMA(3,1) model: -arma31 a\
+            r theta vrat.
+        arma51: Specify parameters for a restricted ARMA(5,1) model: -arma51 a\
+            r1 theta1 r2 theta2 vrat.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dgenARMA11",
+        "normalize": normalize,
+    }
+    if length_alt is not None:
+        params["length_alt"] = length_alt
+    if num_series is not None:
+        params["num_series"] = num_series
+    if param_a is not None:
+        params["param_a"] = param_a
+    if param_b is not None:
+        params["param_b"] = param_b
+    if param_lam is not None:
+        params["param_lam"] = param_lam
+    if std_dev is not None:
+        params["std_dev"] = std_dev
+    if seed is not None:
+        params["seed"] = seed
+    if corcut is not None:
+        params["corcut"] = corcut
+    if arma31 is not None:
+        params["arma31"] = arma31
+    if arma51 is not None:
+        params["arma51"] = arma51
+    return params
+
+
+def v_1dgen_arma11_cargs(
+    params: V1dgenArma11Parameters,
+    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("1dgenARMA11")
+    if params.get("length_alt") is not None:
+        cargs.extend([
+            "-len",
+            str(params.get("length_alt"))
+        ])
+    if params.get("num_series") is not None:
+        cargs.extend([
+            "-nvec",
+            str(params.get("num_series"))
+        ])
+    if params.get("param_a") is not None:
+        cargs.extend([
+            "-a",
+            str(params.get("param_a"))
+        ])
+    if params.get("param_b") is not None:
+        cargs.extend([
+            "-b",
+            str(params.get("param_b"))
+        ])
+    if params.get("param_lam") is not None:
+        cargs.extend([
+            "-lam",
+            str(params.get("param_lam"))
+        ])
+    if params.get("std_dev") is not None:
+        cargs.extend([
+            "-sig",
+            str(params.get("std_dev"))
+        ])
+    if params.get("normalize"):
+        cargs.append("-norm")
+    if params.get("seed") is not None:
+        cargs.extend([
+            "-seed",
+            str(params.get("seed"))
+        ])
+    if params.get("corcut") is not None:
+        cargs.extend([
+            "-CORcut",
+            str(params.get("corcut"))
+        ])
+    if params.get("arma31") is not None:
+        cargs.extend([
+            "-arma31",
+            params.get("arma31")
+        ])
+    if params.get("arma51") is not None:
+        cargs.extend([
+            "-arma51",
+            params.get("arma51")
+        ])
+    return cargs
+
+
+def v_1dgen_arma11_outputs(
+    params: V1dgenArma11Parameters,
+    execution: Execution,
+) -> V1dgenArma11Outputs:
+    """
+    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 = V1dgenArma11Outputs(
+        root=execution.output_file("."),
+        output=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_1dgen_arma11_execute(
+    params: V1dgenArma11Parameters,
+    execution: Execution,
+) -> V1dgenArma11Outputs:
+    """
+    Program to generate an ARMA(1,1) time series, for simulation studies. Results
+    are written to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dgenArma11Outputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1dgen_arma11_cargs(params, execution)
+    ret = v_1dgen_arma11_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1dgen_arma11(
+    length_alt: float | None = None,
+    num_series: float | None = None,
+    param_a: float | None = None,
+    param_b: float | None = None,
+    param_lam: float | None = None,
+    std_dev: float | None = None,
+    normalize: bool = False,
+    seed: float | None = None,
+    corcut: float | None = None,
+    arma31: str | None = None,
+    arma51: str | None = None,
+    runner: Runner | None = None,
+) -> V1dgenArma11Outputs:
+    """
+    Program to generate an ARMA(1,1) time series, for simulation studies. Results
+    are written to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        length_alt: Specify the length of the time series vector to generate\
+            (equivalent to -num option).
+        num_series: The number of time series vectors to generate; defaults to\
+            1 if not given.
+        param_a: Specify ARMA(1,1) parameters 'a'.
+        param_b: Specify ARMA(1,1) parameter 'b' directly.
+        param_lam: Specify ARMA(1,1) parameter 'b' indirectly.
+        std_dev: Set standard deviation of results [default=1].
+        normalize: Normalize time series so sum of squares is 1.
+        seed: Set random number seed.
+        corcut: Specify a cutoff for the correlation coefficient r(k) of noise\
+            samples at k units apart. Default is 0.00010.
+        arma31: Specify parameters for a restricted ARMA(3,1) model: -arma31 a\
+            r theta vrat.
+        arma51: Specify parameters for a restricted ARMA(5,1) model: -arma51 a\
+            r1 theta1 r2 theta2 vrat.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dgenArma11Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DGEN_ARMA11_METADATA)
+    params = v_1dgen_arma11_params(
+        length_alt=length_alt,
+        num_series=num_series,
+        param_a=param_a,
+        param_b=param_b,
+        param_lam=param_lam,
+        std_dev=std_dev,
+        normalize=normalize,
+        seed=seed,
+        corcut=corcut,
+        arma31=arma31,
+        arma51=arma51,
+    )
+    return v_1dgen_arma11_execute(params, execution)
+
+
+__all__ = [
+    "V1dgenArma11Outputs",
+    "V1dgenArma11Parameters",
+    "V_1DGEN_ARMA11_METADATA",
+    "v_1dgen_arma11",
+    "v_1dgen_arma11_params",
+]