niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1d_astrip.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_ASTRIP_METADATA = Metadata(
+    id="ea5f26ed07e83433aaff1882a3ae80d4c15231c8.boutiques",
+    name="1dAstrip",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dAstripParameters = typing.TypedDict('V1dAstripParameters', {
+    "__STYX_TYPE__": typing.Literal["1dAstrip"],
+    "infile": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dAstrip": v_1d_astrip_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 {
+        "1dAstrip": v_1d_astrip_outputs,
+    }.get(t)
+
+
+class V1dAstripOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_astrip(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output file with only numeric characters."""
+
+
+def v_1d_astrip_params(
+    infile: InputPathType,
+) -> V1dAstripParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input file from which non-numeric characters will be stripped.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dAstrip",
+        "infile": infile,
+    }
+    return params
+
+
+def v_1d_astrip_cargs(
+    params: V1dAstripParameters,
+    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("1dAstrip")
+    cargs.append("< " + execution.input_file(params.get("infile")))
+    return cargs
+
+
+def v_1d_astrip_outputs(
+    params: V1dAstripParameters,
+    execution: Execution,
+) -> V1dAstripOutputs:
+    """
+    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 = V1dAstripOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("[OUTPUT_FILE]"),
+    )
+    return ret
+
+
+def v_1d_astrip_execute(
+    params: V1dAstripParameters,
+    execution: Execution,
+) -> V1dAstripOutputs:
+    """
+    Strips non-numeric characters from a file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dAstripOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_astrip_cargs(params, execution)
+    ret = v_1d_astrip_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_astrip(
+    infile: InputPathType,
+    runner: Runner | None = None,
+) -> V1dAstripOutputs:
+    """
+    Strips non-numeric characters from a file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input file from which non-numeric characters will be stripped.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dAstripOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_ASTRIP_METADATA)
+    params = v_1d_astrip_params(
+        infile=infile,
+    )
+    return v_1d_astrip_execute(params, execution)
+
+
+__all__ = [
+    "V1dAstripOutputs",
+    "V1dAstripParameters",
+    "V_1D_ASTRIP_METADATA",
+    "v_1d_astrip",
+    "v_1d_astrip_params",
+]

niwrap_afni/afni/v_1d_bandpass.py

@@ -0,0 +1,238 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_BANDPASS_METADATA = Metadata(
+    id="69b4e08ff33a85a01f56df929195839c7c7f9208.boutiques",
+    name="1dBandpass",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dBandpassParameters = typing.TypedDict('V1dBandpassParameters', {
+    "__STYX_TYPE__": typing.Literal["1dBandpass"],
+    "fbot": float,
+    "ftop": float,
+    "infile": InputPathType,
+    "timestep": typing.NotRequired[float | None],
+    "ortfile": typing.NotRequired[InputPathType | None],
+    "nodetrend": bool,
+    "norm": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dBandpass": v_1d_bandpass_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 {
+    }.get(t)
+
+
+class V1dBandpassOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_bandpass(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_1d_bandpass_params(
+    fbot: float,
+    ftop: float,
+    infile: InputPathType,
+    timestep: float | None = None,
+    ortfile: InputPathType | None = None,
+    nodetrend: bool = False,
+    norm: bool = False,
+) -> V1dBandpassParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fbot: Lowest frequency in the passband, in Hz (must be greater than or\
+            equal to 0).
+        ftop: Highest frequency in the passband, in Hz (must be greater than\
+            FBOT).
+        infile: Input AFNI *.1D file; each column is processed.
+        timestep: Set time step to 'dd' sec (default is 1.0).
+        ortfile: Also orthogonalize input to columns in specified *.1D file\
+            (only one '-ort' option is allowed).
+        nodetrend: Skip the quadratic detrending of the input.
+        norm: Make output time series have L2 norm = 1.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dBandpass",
+        "fbot": fbot,
+        "ftop": ftop,
+        "infile": infile,
+        "nodetrend": nodetrend,
+        "norm": norm,
+    }
+    if timestep is not None:
+        params["timestep"] = timestep
+    if ortfile is not None:
+        params["ortfile"] = ortfile
+    return params
+
+
+def v_1d_bandpass_cargs(
+    params: V1dBandpassParameters,
+    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("1dBandpass")
+    cargs.append(str(params.get("fbot")))
+    cargs.append(str(params.get("ftop")))
+    cargs.append(execution.input_file(params.get("infile")))
+    if params.get("timestep") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("timestep"))
+        ])
+    if params.get("ortfile") is not None:
+        cargs.extend([
+            "-ort",
+            execution.input_file(params.get("ortfile"))
+        ])
+    if params.get("nodetrend"):
+        cargs.append("-nodetrend")
+    if params.get("norm"):
+        cargs.append("-norm")
+    return cargs
+
+
+def v_1d_bandpass_outputs(
+    params: V1dBandpassParameters,
+    execution: Execution,
+) -> V1dBandpassOutputs:
+    """
+    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 = V1dBandpassOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_1d_bandpass_execute(
+    params: V1dBandpassParameters,
+    execution: Execution,
+) -> V1dBandpassOutputs:
+    """
+    Bandpass filtering of time series data in AFNI *.1D files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dBandpassOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_bandpass_cargs(params, execution)
+    ret = v_1d_bandpass_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_bandpass(
+    fbot: float,
+    ftop: float,
+    infile: InputPathType,
+    timestep: float | None = None,
+    ortfile: InputPathType | None = None,
+    nodetrend: bool = False,
+    norm: bool = False,
+    runner: Runner | None = None,
+) -> V1dBandpassOutputs:
+    """
+    Bandpass filtering of time series data in AFNI *.1D files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        fbot: Lowest frequency in the passband, in Hz (must be greater than or\
+            equal to 0).
+        ftop: Highest frequency in the passband, in Hz (must be greater than\
+            FBOT).
+        infile: Input AFNI *.1D file; each column is processed.
+        timestep: Set time step to 'dd' sec (default is 1.0).
+        ortfile: Also orthogonalize input to columns in specified *.1D file\
+            (only one '-ort' option is allowed).
+        nodetrend: Skip the quadratic detrending of the input.
+        norm: Make output time series have L2 norm = 1.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dBandpassOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_BANDPASS_METADATA)
+    params = v_1d_bandpass_params(
+        fbot=fbot,
+        ftop=ftop,
+        infile=infile,
+        timestep=timestep,
+        ortfile=ortfile,
+        nodetrend=nodetrend,
+        norm=norm,
+    )
+    return v_1d_bandpass_execute(params, execution)
+
+
+__all__ = [
+    "V1dBandpassOutputs",
+    "V1dBandpassParameters",
+    "V_1D_BANDPASS_METADATA",
+    "v_1d_bandpass",
+    "v_1d_bandpass_params",
+]

niwrap_afni/afni/v_1d_bport.py

@@ -0,0 +1,277 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_BPORT_METADATA = Metadata(
+    id="4be892d519b77ae339eb9adf3a74b7d897d73650.boutiques",
+    name="1dBport",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dBportParameters = typing.TypedDict('V1dBportParameters', {
+    "__STYX_TYPE__": typing.Literal["1dBport"],
+    "band": list[float],
+    "invert": bool,
+    "noconst": bool,
+    "quad": bool,
+    "input_dataset": typing.NotRequired[InputPathType | None],
+    "input_1d_file": typing.NotRequired[InputPathType | None],
+    "nodata": typing.NotRequired[list[float] | None],
+    "tr": typing.NotRequired[float | None],
+    "concat": typing.NotRequired[InputPathType | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dBport": v_1d_bport_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 {
+        "1dBport": v_1d_bport_outputs,
+    }.get(t)
+
+
+class V1dBportOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_bport(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stdout: OutputPathType
+    """Standard output file written by the tool"""
+
+
+def v_1d_bport_params(
+    band: list[float],
+    invert: bool = False,
+    noconst: bool = False,
+    quad: bool = False,
+    input_dataset: InputPathType | None = None,
+    input_1d_file: InputPathType | None = None,
+    nodata: list[float] | None = None,
+    tr: float | None = None,
+    concat: InputPathType | None = None,
+) -> V1dBportParameters:
+    """
+    Build parameters.
+    
+    Args:
+        band: Specify lowest and highest frequencies in the passband.
+        invert: Invert the selection after computing which frequency indexes\
+            correspond to the input band(s).
+        noconst: Same as -nozero. Do NOT generate the 0 frequency (constant)\
+            component when fbot = 0.
+        quad: Add regressors for linear and quadratic trends.
+        input_dataset: Specify the dataset input.
+        input_1d_file: Specify the 1D input file.
+        nodata: Specify the number of time points and optionally TR value for\
+            the simulation.
+        tr: Set the time step duration.
+        concat: Specify the list of start indexes for concatenated runs.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dBport",
+        "band": band,
+        "invert": invert,
+        "noconst": noconst,
+        "quad": quad,
+    }
+    if input_dataset is not None:
+        params["input_dataset"] = input_dataset
+    if input_1d_file is not None:
+        params["input_1d_file"] = input_1d_file
+    if nodata is not None:
+        params["nodata"] = nodata
+    if tr is not None:
+        params["tr"] = tr
+    if concat is not None:
+        params["concat"] = concat
+    return params
+
+
+def v_1d_bport_cargs(
+    params: V1dBportParameters,
+    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("1dBport")
+    cargs.extend([
+        "-band",
+        *map(str, params.get("band"))
+    ])
+    if params.get("invert"):
+        cargs.append("-invert")
+    if params.get("noconst"):
+        cargs.append("-noconst")
+    if params.get("quad"):
+        cargs.append("-quad")
+    if params.get("input_dataset") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_dataset"))
+        ])
+    if params.get("input_1d_file") is not None:
+        cargs.extend([
+            "-input1D",
+            execution.input_file(params.get("input_1d_file"))
+        ])
+    if params.get("nodata") is not None:
+        cargs.extend([
+            "-nodata",
+            *map(str, params.get("nodata"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("tr"))
+        ])
+    if params.get("concat") is not None:
+        cargs.extend([
+            "-concat",
+            execution.input_file(params.get("concat"))
+        ])
+    return cargs
+
+
+def v_1d_bport_outputs(
+    params: V1dBportParameters,
+    execution: Execution,
+) -> V1dBportOutputs:
+    """
+    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 = V1dBportOutputs(
+        root=execution.output_file("."),
+        stdout=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_1d_bport_execute(
+    params: V1dBportParameters,
+    execution: Execution,
+) -> V1dBportOutputs:
+    """
+    Creates a set of columns of sines and cosines for bandpassing via regression.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dBportOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_bport_cargs(params, execution)
+    ret = v_1d_bport_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_bport(
+    band: list[float],
+    invert: bool = False,
+    noconst: bool = False,
+    quad: bool = False,
+    input_dataset: InputPathType | None = None,
+    input_1d_file: InputPathType | None = None,
+    nodata: list[float] | None = None,
+    tr: float | None = None,
+    concat: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> V1dBportOutputs:
+    """
+    Creates a set of columns of sines and cosines for bandpassing via regression.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        band: Specify lowest and highest frequencies in the passband.
+        invert: Invert the selection after computing which frequency indexes\
+            correspond to the input band(s).
+        noconst: Same as -nozero. Do NOT generate the 0 frequency (constant)\
+            component when fbot = 0.
+        quad: Add regressors for linear and quadratic trends.
+        input_dataset: Specify the dataset input.
+        input_1d_file: Specify the 1D input file.
+        nodata: Specify the number of time points and optionally TR value for\
+            the simulation.
+        tr: Set the time step duration.
+        concat: Specify the list of start indexes for concatenated runs.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dBportOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_BPORT_METADATA)
+    params = v_1d_bport_params(
+        band=band,
+        invert=invert,
+        noconst=noconst,
+        quad=quad,
+        input_dataset=input_dataset,
+        input_1d_file=input_1d_file,
+        nodata=nodata,
+        tr=tr,
+        concat=concat,
+    )
+    return v_1d_bport_execute(params, execution)
+
+
+__all__ = [
+    "V1dBportOutputs",
+    "V1dBportParameters",
+    "V_1D_BPORT_METADATA",
+    "v_1d_bport",
+    "v_1d_bport_params",
+]