niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/spharm_reco.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+SPHARM_RECO_METADATA = Metadata(
+    id="33f63f74ec6a7870069eec599fbb3c35bec65ba8.boutiques",
+    name="SpharmReco",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+SpharmRecoParameters = typing.TypedDict('SpharmRecoParameters', {
+    "__STYX_TYPE__": typing.Literal["SpharmReco"],
+    "input_surface": str,
+    "decomposition_order": float,
+    "bases_prefix": str,
+    "coefficients": list[InputPathType],
+    "output_prefix": typing.NotRequired[str | None],
+    "output_surface": typing.NotRequired[list[str] | None],
+    "debug": typing.NotRequired[float | None],
+    "smoothing": typing.NotRequired[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 {
+        "SpharmReco": spharm_reco_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 SpharmRecoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `spharm_reco(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def spharm_reco_params(
+    input_surface: str,
+    decomposition_order: float,
+    bases_prefix: str,
+    coefficients: list[InputPathType],
+    output_prefix: str | None = None,
+    output_surface: list[str] | None = None,
+    debug: float | None = None,
+    smoothing: float | None = None,
+) -> SpharmRecoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_surface: Surface that provides the topology of the mesh (nodes'\
+            connections). TYPE specifies the input surface type.
+        decomposition_order: Decomposition order.
+        bases_prefix: Prefix of files containing the bases functions (spherical\
+            harmonics). These files are generated with SpharmDeco.
+        coefficients: Coefficients files used to recompose data columns.\
+            Multiple coefficient files can be specified by repeating the option.
+        output_prefix: Write out the reconstructed data into dataset PREFIX.\
+            The output contains N columns; one for each COEF file.
+        output_surface: Write out a new surface with reconstructed coordinates.\
+            Requires N to be a multiple of 3.
+        debug: Debug levels (1-3).
+        smoothing: Smoothing parameter (0 .. 0.001) weighing the contribution\
+            of higher order harmonics.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "SpharmReco",
+        "input_surface": input_surface,
+        "decomposition_order": decomposition_order,
+        "bases_prefix": bases_prefix,
+        "coefficients": coefficients,
+    }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if output_surface is not None:
+        params["output_surface"] = output_surface
+    if debug is not None:
+        params["debug"] = debug
+    if smoothing is not None:
+        params["smoothing"] = smoothing
+    return params
+
+
+def spharm_reco_cargs(
+    params: SpharmRecoParameters,
+    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("SpharmReco")
+    cargs.extend([
+        "-i_TYPE",
+        params.get("input_surface")
+    ])
+    cargs.extend([
+        "-l",
+        str(params.get("decomposition_order"))
+    ])
+    cargs.extend([
+        "-bases_prefix",
+        params.get("bases_prefix")
+    ])
+    cargs.extend([
+        "-coef",
+        *[execution.input_file(f) for f in params.get("coefficients")]
+    ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("output_surface") is not None:
+        cargs.extend([
+            "-o_TYPE",
+            *params.get("output_surface")
+        ])
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("smoothing") is not None:
+        cargs.extend([
+            "-sigma",
+            str(params.get("smoothing"))
+        ])
+    return cargs
+
+
+def spharm_reco_outputs(
+    params: SpharmRecoParameters,
+    execution: Execution,
+) -> SpharmRecoOutputs:
+    """
+    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 = SpharmRecoOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def spharm_reco_execute(
+    params: SpharmRecoParameters,
+    execution: Execution,
+) -> SpharmRecoOutputs:
+    """
+    Spherical Harmonics Reconstruction from a set of harmonics and their
+    corresponding coefficients.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `SpharmRecoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = spharm_reco_cargs(params, execution)
+    ret = spharm_reco_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def spharm_reco(
+    input_surface: str,
+    decomposition_order: float,
+    bases_prefix: str,
+    coefficients: list[InputPathType],
+    output_prefix: str | None = None,
+    output_surface: list[str] | None = None,
+    debug: float | None = None,
+    smoothing: float | None = None,
+    runner: Runner | None = None,
+) -> SpharmRecoOutputs:
+    """
+    Spherical Harmonics Reconstruction from a set of harmonics and their
+    corresponding coefficients.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_surface: Surface that provides the topology of the mesh (nodes'\
+            connections). TYPE specifies the input surface type.
+        decomposition_order: Decomposition order.
+        bases_prefix: Prefix of files containing the bases functions (spherical\
+            harmonics). These files are generated with SpharmDeco.
+        coefficients: Coefficients files used to recompose data columns.\
+            Multiple coefficient files can be specified by repeating the option.
+        output_prefix: Write out the reconstructed data into dataset PREFIX.\
+            The output contains N columns; one for each COEF file.
+        output_surface: Write out a new surface with reconstructed coordinates.\
+            Requires N to be a multiple of 3.
+        debug: Debug levels (1-3).
+        smoothing: Smoothing parameter (0 .. 0.001) weighing the contribution\
+            of higher order harmonics.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `SpharmRecoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SPHARM_RECO_METADATA)
+    params = spharm_reco_params(
+        input_surface=input_surface,
+        decomposition_order=decomposition_order,
+        bases_prefix=bases_prefix,
+        coefficients=coefficients,
+        output_prefix=output_prefix,
+        output_surface=output_surface,
+        debug=debug,
+        smoothing=smoothing,
+    )
+    return spharm_reco_execute(params, execution)
+
+
+__all__ = [
+    "SPHARM_RECO_METADATA",
+    "SpharmRecoOutputs",
+    "SpharmRecoParameters",
+    "spharm_reco",
+    "spharm_reco_params",
+]

niwrap_afni/afni/stimband.py

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+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+STIMBAND_METADATA = Metadata(
+    id="464e80031a1b4a970344b72621a7160776336ad8.boutiques",
+    name="stimband",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+StimbandParameters = typing.TypedDict('StimbandParameters', {
+    "__STYX_TYPE__": typing.Literal["stimband"],
+    "verbose_flag": bool,
+    "min_freq": typing.NotRequired[float | None],
+    "min_bwidth": typing.NotRequired[float | None],
+    "min_pow": typing.NotRequired[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 {
+        "stimband": stimband_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 {
+        "stimband": stimband_outputs,
+    }.get(t)
+
+
+class StimbandOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `stimband(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_band: OutputPathType
+    """The frequency band covering at least 90% of the power of the stimulus
+    columns."""
+
+
+def stimband_params(
+    verbose_flag: bool = False,
+    min_freq: float | None = None,
+    min_bwidth: float | None = None,
+    min_pow: float | None = None,
+) -> StimbandParameters:
+    """
+    Build parameters.
+    
+    Args:
+        verbose_flag: Print the power band for each individual stimulus column\
+            from each matrix.
+        min_freq: Set the minimum frequency output for the band. Default value\
+            is 0.01.
+        min_bwidth: Set the minimum bandwidth output (top frequency minus\
+            bottom frequency). Default is 0.03.
+        min_pow: Set the minimum power fraction (percentage) to 'ff' instead of\
+            the default 90%. Value must be in the range 50..99.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "stimband",
+        "verbose_flag": verbose_flag,
+    }
+    if min_freq is not None:
+        params["min_freq"] = min_freq
+    if min_bwidth is not None:
+        params["min_bwidth"] = min_bwidth
+    if min_pow is not None:
+        params["min_pow"] = min_pow
+    return params
+
+
+def stimband_cargs(
+    params: StimbandParameters,
+    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("stimband")
+    if params.get("verbose_flag"):
+        cargs.append("-verb")
+    cargs.append("[MATRIXFILES...]")
+    cargs.append("[ADDITIONAL_MATRIXFILES...]")
+    if params.get("min_freq") is not None:
+        cargs.extend([
+            "-min_freq",
+            str(params.get("min_freq"))
+        ])
+    if params.get("min_bwidth") is not None:
+        cargs.extend([
+            "-min_bwidth",
+            str(params.get("min_bwidth"))
+        ])
+    if params.get("min_pow") is not None:
+        cargs.extend([
+            "-min_pow",
+            str(params.get("min_pow"))
+        ])
+    return cargs
+
+
+def stimband_outputs(
+    params: StimbandParameters,
+    execution: Execution,
+) -> StimbandOutputs:
+    """
+    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 = StimbandOutputs(
+        root=execution.output_file("."),
+        output_band=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def stimband_execute(
+    params: StimbandParameters,
+    execution: Execution,
+) -> StimbandOutputs:
+    """
+    Determines frequency band covering at least 90% of the 'power' (|FFT|^2) of
+    stimulus columns from X.nocensor.xmat.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 `StimbandOutputs`).
+    """
+    params = execution.params(params)
+    cargs = stimband_cargs(params, execution)
+    ret = stimband_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def stimband(
+    verbose_flag: bool = False,
+    min_freq: float | None = None,
+    min_bwidth: float | None = None,
+    min_pow: float | None = None,
+    runner: Runner | None = None,
+) -> StimbandOutputs:
+    """
+    Determines frequency band covering at least 90% of the 'power' (|FFT|^2) of
+    stimulus columns from X.nocensor.xmat.1D files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        verbose_flag: Print the power band for each individual stimulus column\
+            from each matrix.
+        min_freq: Set the minimum frequency output for the band. Default value\
+            is 0.01.
+        min_bwidth: Set the minimum bandwidth output (top frequency minus\
+            bottom frequency). Default is 0.03.
+        min_pow: Set the minimum power fraction (percentage) to 'ff' instead of\
+            the default 90%. Value must be in the range 50..99.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `StimbandOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(STIMBAND_METADATA)
+    params = stimband_params(
+        verbose_flag=verbose_flag,
+        min_freq=min_freq,
+        min_bwidth=min_bwidth,
+        min_pow=min_pow,
+    )
+    return stimband_execute(params, execution)
+
+
+__all__ = [
+    "STIMBAND_METADATA",
+    "StimbandOutputs",
+    "StimbandParameters",
+    "stimband",
+    "stimband_params",
+]