niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_par2_afni.py

@@ -0,0 +1,244 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_PAR2_AFNI_METADATA = Metadata(
+    id="955afce507c339e4fbf43caaf056ad39a659f439.boutiques",
+    name="3dPAR2AFNI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dPar2AfniParameters = typing.TypedDict('V3dPar2AfniParameters', {
+    "__STYX_TYPE__": typing.Literal["3dPAR2AFNI"],
+    "input_file": InputPathType,
+    "skip_outliers_test": bool,
+    "output_analyze": bool,
+    "output_dir": typing.NotRequired[str | None],
+    "verbose_flag": bool,
+    "gzip_files": bool,
+    "byte_swap_4": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dPAR2AFNI": v_3d_par2_afni_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 {
+        "3dPAR2AFNI": v_3d_par2_afni_outputs,
+    }.get(t)
+
+
+class V3dPar2AfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_par2_afni(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_files: OutputPathType
+    """Converted output files"""
+
+
+def v_3d_par2_afni_params(
+    input_file: InputPathType,
+    skip_outliers_test: bool = False,
+    output_analyze: bool = False,
+    output_dir: str | None = None,
+    verbose_flag: bool = False,
+    gzip_files: bool = False,
+    byte_swap_4: bool = False,
+) -> V3dPar2AfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input PAR file (e.g., subject1.PAR).
+        skip_outliers_test: Skip the outliers test when converting 4D files.\
+            The default is to perform the outliers test.
+        output_analyze: Output ANALYZE files instead of HEAD/BRIK.
+        output_dir: The name of the directory where the created files should be\
+            placed. If this directory does not exist, the program exits without\
+            performing any conversion.
+        verbose_flag: Be verbose in operation.
+        gzip_files: Gzip the files created. The default is not to gzip the\
+            files.
+        byte_swap_4: 4-Byte-swap the files created. The default is not to 4\
+            byte-swap.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dPAR2AFNI",
+        "input_file": input_file,
+        "skip_outliers_test": skip_outliers_test,
+        "output_analyze": output_analyze,
+        "verbose_flag": verbose_flag,
+        "gzip_files": gzip_files,
+        "byte_swap_4": byte_swap_4,
+    }
+    if output_dir is not None:
+        params["output_dir"] = output_dir
+    return params
+
+
+def v_3d_par2_afni_cargs(
+    params: V3dPar2AfniParameters,
+    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("3dPAR2AFNI.pl")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("skip_outliers_test"):
+        cargs.append("-s")
+    if params.get("output_analyze"):
+        cargs.append("-a")
+    if params.get("output_dir") is not None:
+        cargs.extend([
+            "-o",
+            params.get("output_dir")
+        ])
+    if params.get("verbose_flag"):
+        cargs.append("-v")
+    if params.get("gzip_files"):
+        cargs.append("-g")
+    if params.get("byte_swap_4"):
+        cargs.append("-4")
+    return cargs
+
+
+def v_3d_par2_afni_outputs(
+    params: V3dPar2AfniParameters,
+    execution: Execution,
+) -> V3dPar2AfniOutputs:
+    """
+    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 = V3dPar2AfniOutputs(
+        root=execution.output_file("."),
+        output_files=execution.output_file(pathlib.Path(params.get("input_file")).name + "_converted"),
+    )
+    return ret
+
+
+def v_3d_par2_afni_execute(
+    params: V3dPar2AfniParameters,
+    execution: Execution,
+) -> V3dPar2AfniOutputs:
+    """
+    Convert Philips PAR/REC files to AFNI's BRIK/HEAD, NIfTI, or ANALYZE format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dPar2AfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_par2_afni_cargs(params, execution)
+    ret = v_3d_par2_afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_par2_afni(
+    input_file: InputPathType,
+    skip_outliers_test: bool = False,
+    output_analyze: bool = False,
+    output_dir: str | None = None,
+    verbose_flag: bool = False,
+    gzip_files: bool = False,
+    byte_swap_4: bool = False,
+    runner: Runner | None = None,
+) -> V3dPar2AfniOutputs:
+    """
+    Convert Philips PAR/REC files to AFNI's BRIK/HEAD, NIfTI, or ANALYZE format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input PAR file (e.g., subject1.PAR).
+        skip_outliers_test: Skip the outliers test when converting 4D files.\
+            The default is to perform the outliers test.
+        output_analyze: Output ANALYZE files instead of HEAD/BRIK.
+        output_dir: The name of the directory where the created files should be\
+            placed. If this directory does not exist, the program exits without\
+            performing any conversion.
+        verbose_flag: Be verbose in operation.
+        gzip_files: Gzip the files created. The default is not to gzip the\
+            files.
+        byte_swap_4: 4-Byte-swap the files created. The default is not to 4\
+            byte-swap.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dPar2AfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PAR2_AFNI_METADATA)
+    params = v_3d_par2_afni_params(
+        input_file=input_file,
+        skip_outliers_test=skip_outliers_test,
+        output_analyze=output_analyze,
+        output_dir=output_dir,
+        verbose_flag=verbose_flag,
+        gzip_files=gzip_files,
+        byte_swap_4=byte_swap_4,
+    )
+    return v_3d_par2_afni_execute(params, execution)
+
+
+__all__ = [
+    "V3dPar2AfniOutputs",
+    "V3dPar2AfniParameters",
+    "V_3D_PAR2_AFNI_METADATA",
+    "v_3d_par2_afni",
+    "v_3d_par2_afni_params",
+]

niwrap_afni/afni/v_3d_periodogram.py

@@ -0,0 +1,220 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_PERIODOGRAM_METADATA = Metadata(
+    id="9a68bd8e7aa1c6c39962b274d89b8ea010ab603e.boutiques",
+    name="3dPeriodogram",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dPeriodogramParameters = typing.TypedDict('V3dPeriodogramParameters', {
+    "__STYX_TYPE__": typing.Literal["3dPeriodogram"],
+    "prefix": typing.NotRequired[str | None],
+    "taper": typing.NotRequired[float | None],
+    "nfft": typing.NotRequired[float | None],
+    "dataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dPeriodogram": v_3d_periodogram_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 {
+        "3dPeriodogram": v_3d_periodogram_outputs,
+    }.get(t)
+
+
+class V3dPeriodogramOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_periodogram(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_header: OutputPathType | None
+    """Output dataset header file"""
+    output_brick: OutputPathType | None
+    """Output dataset brick file"""
+
+
+def v_3d_periodogram_params(
+    dataset: InputPathType,
+    prefix: str | None = None,
+    taper: float | None = None,
+    nfft: float | None = None,
+) -> V3dPeriodogramParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset.
+        prefix: Prefix for the output dataset.
+        taper: Fraction of data to taper.
+        nfft: Set FFT length to a specific number of points.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dPeriodogram",
+        "dataset": dataset,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if taper is not None:
+        params["taper"] = taper
+    if nfft is not None:
+        params["nfft"] = nfft
+    return params
+
+
+def v_3d_periodogram_cargs(
+    params: V3dPeriodogramParameters,
+    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("3dPeriodogram")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("taper") is not None:
+        cargs.extend([
+            "-taper",
+            str(params.get("taper"))
+        ])
+    if params.get("nfft") is not None:
+        cargs.extend([
+            "-nfft",
+            str(params.get("nfft"))
+        ])
+    cargs.append(execution.input_file(params.get("dataset")))
+    return cargs
+
+
+def v_3d_periodogram_outputs(
+    params: V3dPeriodogramParameters,
+    execution: Execution,
+) -> V3dPeriodogramOutputs:
+    """
+    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 = V3dPeriodogramOutputs(
+        root=execution.output_file("."),
+        output_header=execution.output_file(params.get("prefix") + ".HEAD") if (params.get("prefix") is not None) else None,
+        output_brick=execution.output_file(params.get("prefix") + ".BRIK") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_periodogram_execute(
+    params: V3dPeriodogramParameters,
+    execution: Execution,
+) -> V3dPeriodogramOutputs:
+    """
+    Computes the periodogram of each voxel time series. The periodogram is a crude
+    estimate of the power spectrum.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dPeriodogramOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_periodogram_cargs(params, execution)
+    ret = v_3d_periodogram_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_periodogram(
+    dataset: InputPathType,
+    prefix: str | None = None,
+    taper: float | None = None,
+    nfft: float | None = None,
+    runner: Runner | None = None,
+) -> V3dPeriodogramOutputs:
+    """
+    Computes the periodogram of each voxel time series. The periodogram is a crude
+    estimate of the power spectrum.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset.
+        prefix: Prefix for the output dataset.
+        taper: Fraction of data to taper.
+        nfft: Set FFT length to a specific number of points.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dPeriodogramOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PERIODOGRAM_METADATA)
+    params = v_3d_periodogram_params(
+        prefix=prefix,
+        taper=taper,
+        nfft=nfft,
+        dataset=dataset,
+    )
+    return v_3d_periodogram_execute(params, execution)
+
+
+__all__ = [
+    "V3dPeriodogramOutputs",
+    "V3dPeriodogramParameters",
+    "V_3D_PERIODOGRAM_METADATA",
+    "v_3d_periodogram",
+    "v_3d_periodogram_params",
+]

niwrap_afni/afni/v_3d_pfm.py

@@ -0,0 +1,248 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_PFM_METADATA = Metadata(
+    id="c5e5e30b454a1a81f02535de2e794be7d716492a.boutiques",
+    name="3dPFM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dPfmParameters = typing.TypedDict('V3dPfmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dPFM"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dPFM": v_3d_pfm_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 {
+        "3dPFM": v_3d_pfm_outputs,
+    }.get(t)
+
+
+class V3dPfmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_pfm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    beta: OutputPathType
+    """Prefix for the neuronal-related (i.e. deconvolved) time series."""
+    betafitts: OutputPathType
+    """Prefix of the convolved neuronal-related time series."""
+    fitts: OutputPathType
+    """Prefix for the fitted time series."""
+    resid: OutputPathType
+    """Prefix for the residuals of the fit to the data."""
+    mean: OutputPathType
+    """Prefix for the intercept of the model."""
+    lhsest: OutputPathType
+    """Prefix for the estimates of the LHS parameters."""
+    lhsfitts: OutputPathType
+    """Prefix for the fitted time series of the LHS parameters."""
+    lambda_: OutputPathType
+    """Prefix for output volume with the regularization parameter of the
+    deconvolution of each voxel."""
+    costs: OutputPathType
+    """Prefix for output volume of the cost function used to select the
+    regularization parameter according to the selected criteria."""
+    tstats_beta: OutputPathType
+    """Prefix for the T-statistics of beta at each time point."""
+    tdf_beta: OutputPathType
+    """Prefix for degrees of freedom of the T-statistics of beta."""
+    z_tstats_beta: OutputPathType
+    """Prefix for (normalized) z-scores of the T-statistics of beta."""
+    fstats_beta: OutputPathType
+    """Prefix for the F-statistics of the deconvolved component."""
+    fdf_beta: OutputPathType
+    """Prefix for degrees of freedom of Fstats_beta."""
+    z_fstats_beta: OutputPathType
+    """Prefix for (normalized) z-scores of the Fstats_beta."""
+    tstats_lhs: OutputPathType
+    """Prefix for T-statistics of LHS regressors at each time point."""
+    tdf_lhs: OutputPathType
+    """Prefix for degrees of freedom of the Tstats_LHS."""
+    z_tstats_lhs: OutputPathType
+    """Prefix for (normalized) z-scores of the Tstats_LHS."""
+    fstats_lhs: OutputPathType
+    """Prefix for the F-statistics of the LHS regressors."""
+    fdf_lhs: OutputPathType
+    """Prefix for degrees of freedom of Fstats_LHS."""
+    z_fstats_lhs: OutputPathType
+    """Prefix for (normalized) z-scores of Fstats_LHS."""
+    fstats_full: OutputPathType
+    """Prefix for the F-statistics of the full model."""
+    fdf_full: OutputPathType
+    """Prefix for degrees of freedom of Fstats_full."""
+    z_fstats_full: OutputPathType
+    """Prefix for (normalized) z-scores of Fstats_full."""
+    r2_full: OutputPathType
+    """Prefix for R² (coefficient of determination) of the full model."""
+    r2adj_full: OutputPathType
+    """Prefix for Adjusted R² coefficient for the full model."""
+
+
+def v_3d_pfm_params(
+) -> V3dPfmParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dPFM",
+    }
+    return params
+
+
+def v_3d_pfm_cargs(
+    params: V3dPfmParameters,
+    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("3dPFM")
+    cargs.append("[PARAMETERS]")
+    return cargs
+
+
+def v_3d_pfm_outputs(
+    params: V3dPfmParameters,
+    execution: Execution,
+) -> V3dPfmOutputs:
+    """
+    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 = V3dPfmOutputs(
+        root=execution.output_file("."),
+        beta=execution.output_file("[BETA]"),
+        betafitts=execution.output_file("[BETAFITTS]"),
+        fitts=execution.output_file("[FITTS]"),
+        resid=execution.output_file("[RESID]"),
+        mean=execution.output_file("[MEAN]"),
+        lhsest=execution.output_file("[LHSEST]"),
+        lhsfitts=execution.output_file("[LHSFITTS]"),
+        lambda_=execution.output_file("[LAMBDA]"),
+        costs=execution.output_file("[COSTS]"),
+        tstats_beta=execution.output_file("[TSTATS_BETA]"),
+        tdf_beta=execution.output_file("[TDF_BETA]"),
+        z_tstats_beta=execution.output_file("[Z_TSTATS_BETA]"),
+        fstats_beta=execution.output_file("[FSTATS_BETA]"),
+        fdf_beta=execution.output_file("[FDF_BETA]"),
+        z_fstats_beta=execution.output_file("[Z_FSTATS_BETA]"),
+        tstats_lhs=execution.output_file("[TSTATS_LHS]"),
+        tdf_lhs=execution.output_file("[TDF_LHS]"),
+        z_tstats_lhs=execution.output_file("[Z_TSTATS_LHS]"),
+        fstats_lhs=execution.output_file("[FSTATS_LHS]"),
+        fdf_lhs=execution.output_file("[FDF_LHS]"),
+        z_fstats_lhs=execution.output_file("[Z_FSTATS_LHS]"),
+        fstats_full=execution.output_file("[FSTATS_FULL]"),
+        fdf_full=execution.output_file("[FDF_FULL]"),
+        z_fstats_full=execution.output_file("[Z_FSTATS_FULL]"),
+        r2_full=execution.output_file("[R2_FULL]"),
+        r2adj_full=execution.output_file("[R2ADJ_FULL]"),
+    )
+    return ret
+
+
+def v_3d_pfm_execute(
+    params: V3dPfmParameters,
+    execution: Execution,
+) -> V3dPfmOutputs:
+    """
+    Program for identifying brief BOLD events in fMRI time series using Paradigm
+    Free Mapping.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dPfmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_pfm_cargs(params, execution)
+    ret = v_3d_pfm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_pfm(
+    runner: Runner | None = None,
+) -> V3dPfmOutputs:
+    """
+    Program for identifying brief BOLD events in fMRI time series using Paradigm
+    Free Mapping.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dPfmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PFM_METADATA)
+    params = v_3d_pfm_params(
+    )
+    return v_3d_pfm_execute(params, execution)
+
+
+__all__ = [
+    "V3dPfmOutputs",
+    "V3dPfmParameters",
+    "V_3D_PFM_METADATA",
+    "v_3d_pfm",
+    "v_3d_pfm_params",
+]