niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v__radial_correlate.py

@@ -0,0 +1,407 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__RADIAL_CORRELATE_METADATA = Metadata(
+    id="1cbb44d20d4e3ca23ba7981bb4c49932fce75bf0.boutiques",
+    name="@radial_correlate",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VRadialCorrelateParameters = typing.TypedDict('VRadialCorrelateParameters', {
+    "__STYX_TYPE__": typing.Literal["@radial_correlate"],
+    "input_files": list[InputPathType],
+    "results_dir": typing.NotRequired[str | None],
+    "do_corr": typing.NotRequired[str | None],
+    "do_clust": typing.NotRequired[str | None],
+    "mask_dset": typing.NotRequired[InputPathType | None],
+    "cthresh": typing.NotRequired[float | None],
+    "frac_limit": typing.NotRequired[float | None],
+    "sphere_rad": typing.NotRequired[float | None],
+    "use_3dmerge": typing.NotRequired[str | None],
+    "percentile": typing.NotRequired[float | None],
+    "min_thr": typing.NotRequired[float | None],
+    "nfirst": typing.NotRequired[float | None],
+    "ver": bool,
+    "verbose": bool,
+    "help": bool,
+    "hist": bool,
+    "corr_mask": typing.NotRequired[str | None],
+    "do_clean": typing.NotRequired[str | None],
+    "polort": typing.NotRequired[float | None],
+    "merge_frad": 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 {
+        "@radial_correlate": v__radial_correlate_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 {
+        "@radial_correlate": v__radial_correlate_outputs,
+    }.get(t)
+
+
+class VRadialCorrelateOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__radial_correlate(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    corr_volumes: OutputPathType | None
+    """Directory containing correlation volumes"""
+
+
+def v__radial_correlate_params(
+    input_files: list[InputPathType],
+    results_dir: str | None = None,
+    do_corr: str | None = None,
+    do_clust: str | None = None,
+    mask_dset: InputPathType | None = None,
+    cthresh: float | None = None,
+    frac_limit: float | None = None,
+    sphere_rad: float | None = None,
+    use_3dmerge: str | None = None,
+    percentile: float | None = None,
+    min_thr: float | None = None,
+    nfirst: float | None = None,
+    ver: bool = False,
+    verbose: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    corr_mask: str | None = None,
+    do_clean: str | None = None,
+    polort: float | None = None,
+    merge_frad: float | None = None,
+) -> VRadialCorrelateParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: A list of EPI datasets.
+        results_dir: Results directory for correlations.
+        do_corr: Create correlation volumes (yes/no).
+        do_clust: Cluster correlation volumes (yes/no).
+        mask_dset: Specify a mask dataset to replace automask.
+        cthresh: Threshold on correlation values.
+        frac_limit: Minimum mask fraction surviving cluster.
+        sphere_rad: Generate correlations within voxel spheres.
+        use_3dmerge: Use 3dmerge rather than 3dLocalstat (yes/no).
+        percentile: Percentile to use as threshold.
+        min_thr: Minimum percentile threshold to be considered.
+        nfirst: Number of initial TRs to remove.
+        ver: Show version number.
+        verbose: Make verbose: set echo.
+        help_: Show help.
+        hist: Show modification history.
+        corr_mask: Mask time series before correlation blurring (yes/no).
+        do_clean: Clean up at end, leaving only correlations (yes/no).
+        polort: Detrend time series with given polynomial degree.
+        merge_frad: Specify a radius fraction for 3dmerge blurring.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@radial_correlate",
+        "input_files": input_files,
+        "ver": ver,
+        "verbose": verbose,
+        "help": help_,
+        "hist": hist,
+    }
+    if results_dir is not None:
+        params["results_dir"] = results_dir
+    if do_corr is not None:
+        params["do_corr"] = do_corr
+    if do_clust is not None:
+        params["do_clust"] = do_clust
+    if mask_dset is not None:
+        params["mask_dset"] = mask_dset
+    if cthresh is not None:
+        params["cthresh"] = cthresh
+    if frac_limit is not None:
+        params["frac_limit"] = frac_limit
+    if sphere_rad is not None:
+        params["sphere_rad"] = sphere_rad
+    if use_3dmerge is not None:
+        params["use_3dmerge"] = use_3dmerge
+    if percentile is not None:
+        params["percentile"] = percentile
+    if min_thr is not None:
+        params["min_thr"] = min_thr
+    if nfirst is not None:
+        params["nfirst"] = nfirst
+    if corr_mask is not None:
+        params["corr_mask"] = corr_mask
+    if do_clean is not None:
+        params["do_clean"] = do_clean
+    if polort is not None:
+        params["polort"] = polort
+    if merge_frad is not None:
+        params["merge_frad"] = merge_frad
+    return params
+
+
+def v__radial_correlate_cargs(
+    params: VRadialCorrelateParameters,
+    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("@radial_correlate")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("results_dir") is not None:
+        cargs.extend([
+            "-rdir",
+            params.get("results_dir")
+        ])
+    if params.get("do_corr") is not None:
+        cargs.extend([
+            "-do_corr",
+            params.get("do_corr")
+        ])
+    if params.get("do_clust") is not None:
+        cargs.extend([
+            "-do_clust",
+            params.get("do_clust")
+        ])
+    if params.get("mask_dset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dset"))
+        ])
+    if params.get("cthresh") is not None:
+        cargs.extend([
+            "-cthresh",
+            str(params.get("cthresh"))
+        ])
+    if params.get("frac_limit") is not None:
+        cargs.extend([
+            "-frac_limit",
+            str(params.get("frac_limit"))
+        ])
+    if params.get("sphere_rad") is not None:
+        cargs.extend([
+            "-sphere_rad",
+            str(params.get("sphere_rad"))
+        ])
+    if params.get("use_3dmerge") is not None:
+        cargs.extend([
+            "-use_3dmerge",
+            params.get("use_3dmerge")
+        ])
+    if params.get("percentile") is not None:
+        cargs.extend([
+            "-percentile",
+            str(params.get("percentile"))
+        ])
+    if params.get("min_thr") is not None:
+        cargs.extend([
+            "-min_thr",
+            str(params.get("min_thr"))
+        ])
+    if params.get("nfirst") is not None:
+        cargs.extend([
+            "-nfirst",
+            str(params.get("nfirst"))
+        ])
+    if params.get("ver"):
+        cargs.append("-ver")
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("corr_mask") is not None:
+        cargs.extend([
+            "-corr_mask",
+            params.get("corr_mask")
+        ])
+    if params.get("do_clean") is not None:
+        cargs.extend([
+            "-do_clean",
+            params.get("do_clean")
+        ])
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polort"))
+        ])
+    if params.get("merge_frad") is not None:
+        cargs.extend([
+            "-merge_frad",
+            str(params.get("merge_frad"))
+        ])
+    return cargs
+
+
+def v__radial_correlate_outputs(
+    params: VRadialCorrelateParameters,
+    execution: Execution,
+) -> VRadialCorrelateOutputs:
+    """
+    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 = VRadialCorrelateOutputs(
+        root=execution.output_file("."),
+        corr_volumes=execution.output_file(params.get("results_dir") + "/correlation_volumes") if (params.get("results_dir") is not None) else None,
+    )
+    return ret
+
+
+def v__radial_correlate_execute(
+    params: VRadialCorrelateParameters,
+    execution: Execution,
+) -> VRadialCorrelateOutputs:
+    """
+    Check datasets for correlation artifacts.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VRadialCorrelateOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__radial_correlate_cargs(params, execution)
+    ret = v__radial_correlate_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__radial_correlate(
+    input_files: list[InputPathType],
+    results_dir: str | None = None,
+    do_corr: str | None = None,
+    do_clust: str | None = None,
+    mask_dset: InputPathType | None = None,
+    cthresh: float | None = None,
+    frac_limit: float | None = None,
+    sphere_rad: float | None = None,
+    use_3dmerge: str | None = None,
+    percentile: float | None = None,
+    min_thr: float | None = None,
+    nfirst: float | None = None,
+    ver: bool = False,
+    verbose: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    corr_mask: str | None = None,
+    do_clean: str | None = None,
+    polort: float | None = None,
+    merge_frad: float | None = None,
+    runner: Runner | None = None,
+) -> VRadialCorrelateOutputs:
+    """
+    Check datasets for correlation artifacts.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: A list of EPI datasets.
+        results_dir: Results directory for correlations.
+        do_corr: Create correlation volumes (yes/no).
+        do_clust: Cluster correlation volumes (yes/no).
+        mask_dset: Specify a mask dataset to replace automask.
+        cthresh: Threshold on correlation values.
+        frac_limit: Minimum mask fraction surviving cluster.
+        sphere_rad: Generate correlations within voxel spheres.
+        use_3dmerge: Use 3dmerge rather than 3dLocalstat (yes/no).
+        percentile: Percentile to use as threshold.
+        min_thr: Minimum percentile threshold to be considered.
+        nfirst: Number of initial TRs to remove.
+        ver: Show version number.
+        verbose: Make verbose: set echo.
+        help_: Show help.
+        hist: Show modification history.
+        corr_mask: Mask time series before correlation blurring (yes/no).
+        do_clean: Clean up at end, leaving only correlations (yes/no).
+        polort: Detrend time series with given polynomial degree.
+        merge_frad: Specify a radius fraction for 3dmerge blurring.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VRadialCorrelateOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__RADIAL_CORRELATE_METADATA)
+    params = v__radial_correlate_params(
+        input_files=input_files,
+        results_dir=results_dir,
+        do_corr=do_corr,
+        do_clust=do_clust,
+        mask_dset=mask_dset,
+        cthresh=cthresh,
+        frac_limit=frac_limit,
+        sphere_rad=sphere_rad,
+        use_3dmerge=use_3dmerge,
+        percentile=percentile,
+        min_thr=min_thr,
+        nfirst=nfirst,
+        ver=ver,
+        verbose=verbose,
+        help_=help_,
+        hist=hist,
+        corr_mask=corr_mask,
+        do_clean=do_clean,
+        polort=polort,
+        merge_frad=merge_frad,
+    )
+    return v__radial_correlate_execute(params, execution)
+
+
+__all__ = [
+    "VRadialCorrelateOutputs",
+    "VRadialCorrelateParameters",
+    "V__RADIAL_CORRELATE_METADATA",
+    "v__radial_correlate",
+    "v__radial_correlate_params",
+]

niwrap_afni/afni/v__rename_panga.py

@@ -0,0 +1,279 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V__RENAME_PANGA_METADATA = Metadata(
+    id="fc436284e4d19008103d6e31378b12da7948cb1f.boutiques",
+    name="@RenamePanga",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+VRenamePangaParameters = typing.TypedDict('VRenamePangaParameters', {
+    "__STYX_TYPE__": typing.Literal["@RenamePanga"],
+    "dir_number": str,
+    "first_image_number": str,
+    "num_slices": float,
+    "num_reps": float,
+    "output_root": str,
+    "keep_prefix": bool,
+    "interactive": bool,
+    "outliers_check": bool,
+    "slice_pattern": typing.NotRequired[str | None],
+    "output_directory": 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 {
+        "@RenamePanga": v__rename_panga_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 {
+        "@RenamePanga": v__rename_panga_outputs,
+    }.get(t)
+
+
+class VRenamePangaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v__rename_panga(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    head_file: OutputPathType | None
+    """Main output file (HEAD)"""
+    brik_file: OutputPathType | None
+    """Main output file (BRIK)"""
+    log_file: OutputPathType | None
+    """Log file created in the current directory"""
+
+
+def v__rename_panga_params(
+    dir_number: str,
+    first_image_number: str,
+    num_slices: float,
+    num_reps: float,
+    output_root: str,
+    keep_prefix: bool = False,
+    interactive: bool = False,
+    outliers_check: bool = False,
+    slice_pattern: str | None = None,
+    output_directory: str | None = None,
+) -> VRenamePangaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dir_number: The directory number where the first image of the series is\
+            stored.
+        first_image_number: The number of the first image in the series.
+        num_slices: The number of slices making up the imaged volume.
+        num_reps: The number of samples in your time series.
+        output_root: The prefix for the output brick.
+        keep_prefix: Forces @RenamePanga to use the prefix you designate\
+            without modification.
+        interactive: Launches to3d in interactive mode. This allows you to\
+            double check the automated settings.
+        outliers_check: Performs outliers check and writes the outliers to a\
+            .1D file placed in the output directory.
+        slice_pattern: Sets the slice acquisition pattern. The default option\
+            is alt+z.
+        output_directory: Directory where the output (bricks and 1D files) will\
+            be stored. The default directory is ./afni.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "@RenamePanga",
+        "dir_number": dir_number,
+        "first_image_number": first_image_number,
+        "num_slices": num_slices,
+        "num_reps": num_reps,
+        "output_root": output_root,
+        "keep_prefix": keep_prefix,
+        "interactive": interactive,
+        "outliers_check": outliers_check,
+    }
+    if slice_pattern is not None:
+        params["slice_pattern"] = slice_pattern
+    if output_directory is not None:
+        params["output_directory"] = output_directory
+    return params
+
+
+def v__rename_panga_cargs(
+    params: VRenamePangaParameters,
+    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("@RenamePanga")
+    cargs.append(params.get("dir_number"))
+    cargs.append(params.get("first_image_number"))
+    cargs.append(str(params.get("num_slices")))
+    cargs.append(str(params.get("num_reps")))
+    cargs.append(params.get("output_root"))
+    if params.get("keep_prefix"):
+        cargs.append("-kp")
+    if params.get("interactive"):
+        cargs.append("-i")
+    if params.get("outliers_check"):
+        cargs.append("-oc")
+    if params.get("slice_pattern") is not None:
+        cargs.extend([
+            "-sp",
+            params.get("slice_pattern")
+        ])
+    if params.get("output_directory") is not None:
+        cargs.extend([
+            "-od",
+            params.get("output_directory")
+        ])
+    return cargs
+
+
+def v__rename_panga_outputs(
+    params: VRenamePangaParameters,
+    execution: Execution,
+) -> VRenamePangaOutputs:
+    """
+    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 = VRenamePangaOutputs(
+        root=execution.output_file("."),
+        head_file=execution.output_file(params.get("output_directory") + "/" + params.get("output_root") + "_r#.HEAD") if (params.get("output_directory") is not None) else None,
+        brik_file=execution.output_file(params.get("output_directory") + "/" + params.get("output_root") + "_r#.BRIK") if (params.get("output_directory") is not None) else None,
+        log_file=execution.output_file(params.get("output_directory") + "/MAPLOG_Panga") if (params.get("output_directory") is not None) else None,
+    )
+    return ret
+
+
+def v__rename_panga_execute(
+    params: VRenamePangaParameters,
+    execution: Execution,
+) -> VRenamePangaOutputs:
+    """
+    Creates AFNI bricks from RealTime GE EPI series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `VRenamePangaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v__rename_panga_cargs(params, execution)
+    ret = v__rename_panga_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v__rename_panga(
+    dir_number: str,
+    first_image_number: str,
+    num_slices: float,
+    num_reps: float,
+    output_root: str,
+    keep_prefix: bool = False,
+    interactive: bool = False,
+    outliers_check: bool = False,
+    slice_pattern: str | None = None,
+    output_directory: str | None = None,
+    runner: Runner | None = None,
+) -> VRenamePangaOutputs:
+    """
+    Creates AFNI bricks from RealTime GE EPI series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dir_number: The directory number where the first image of the series is\
+            stored.
+        first_image_number: The number of the first image in the series.
+        num_slices: The number of slices making up the imaged volume.
+        num_reps: The number of samples in your time series.
+        output_root: The prefix for the output brick.
+        keep_prefix: Forces @RenamePanga to use the prefix you designate\
+            without modification.
+        interactive: Launches to3d in interactive mode. This allows you to\
+            double check the automated settings.
+        outliers_check: Performs outliers check and writes the outliers to a\
+            .1D file placed in the output directory.
+        slice_pattern: Sets the slice acquisition pattern. The default option\
+            is alt+z.
+        output_directory: Directory where the output (bricks and 1D files) will\
+            be stored. The default directory is ./afni.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `VRenamePangaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__RENAME_PANGA_METADATA)
+    params = v__rename_panga_params(
+        dir_number=dir_number,
+        first_image_number=first_image_number,
+        num_slices=num_slices,
+        num_reps=num_reps,
+        output_root=output_root,
+        keep_prefix=keep_prefix,
+        interactive=interactive,
+        outliers_check=outliers_check,
+        slice_pattern=slice_pattern,
+        output_directory=output_directory,
+    )
+    return v__rename_panga_execute(params, execution)
+
+
+__all__ = [
+    "VRenamePangaOutputs",
+    "VRenamePangaParameters",
+    "V__RENAME_PANGA_METADATA",
+    "v__rename_panga",
+    "v__rename_panga_params",
+]