niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/find_variance_lines.py

@@ -0,0 +1,353 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIND_VARIANCE_LINES_METADATA = Metadata(
+    id="400a7e1ff61116676091a1736a0b5ffb08f0a496.boutiques",
+    name="find_variance_lines",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FindVarianceLinesParameters = typing.TypedDict('FindVarianceLinesParameters', {
+    "__STYX_TYPE__": typing.Literal["find_variance_lines"],
+    "input_files": list[InputPathType],
+    "mask": typing.NotRequired[str | None],
+    "min_cvox": typing.NotRequired[int | None],
+    "min_nt": typing.NotRequired[int | None],
+    "nerode": typing.NotRequired[int | None],
+    "nfirst": typing.NotRequired[int | None],
+    "percentile": typing.NotRequired[int | None],
+    "polort": typing.NotRequired[str | None],
+    "output_dir": typing.NotRequired[str | None],
+    "do_clean": typing.NotRequired[int | None],
+    "do_img": typing.NotRequired[int | None],
+    "echo": bool,
+    "help": bool,
+    "hist": bool,
+    "ver": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "find_variance_lines": find_variance_lines_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 {
+        "find_variance_lines": find_variance_lines_outputs,
+    }.get(t)
+
+
+class FindVarianceLinesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `find_variance_lines(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    variance_maps: OutputPathType | None
+    """Variance maps per run"""
+    scaled_variance_maps: OutputPathType | None
+    """Scaled variance maps per run"""
+    cluster_reports: OutputPathType | None
+    """Cluster reports"""
+    jpeg_images: OutputPathType | None
+    """JPEG images showing locations of high variance"""
+
+
+def find_variance_lines_params(
+    input_files: list[InputPathType],
+    mask: str | None = None,
+    min_cvox: int | None = None,
+    min_nt: int | None = None,
+    nerode: int | None = None,
+    nfirst: int | None = None,
+    percentile: int | None = None,
+    polort: str | None = None,
+    output_dir: str | None = None,
+    do_clean: int | None = None,
+    do_img: int | None = None,
+    echo: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    ver: bool = False,
+) -> FindVarianceLinesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input EPI datasets.
+        mask: Mask for computations (default=AUTO).
+        min_cvox: Minimum voxels for valid mask column (default=5).
+        min_nt: Minimum number of time points required (default=10).
+        nerode: How much to erode input or auto-mask (default=0).
+        nfirst: Discard the first VAL time points (default=0).
+        percentile: Percentile of variance values to scale to (default=90).
+        polort: Polynomial detrending degree (default=A).
+        output_dir: Name of the output directory (default=vlines.result).
+        do_clean: Do we clean up a little? (default=1).
+        do_img: Make vline images? (default=1).
+        echo: Run script with shell 'echo' set (default=no).
+        help_: Show this help.
+        hist: Show the version history.
+        ver: Show the current version.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "find_variance_lines",
+        "input_files": input_files,
+        "echo": echo,
+        "help": help_,
+        "hist": hist,
+        "ver": ver,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if min_cvox is not None:
+        params["min_cvox"] = min_cvox
+    if min_nt is not None:
+        params["min_nt"] = min_nt
+    if nerode is not None:
+        params["nerode"] = nerode
+    if nfirst is not None:
+        params["nfirst"] = nfirst
+    if percentile is not None:
+        params["percentile"] = percentile
+    if polort is not None:
+        params["polort"] = polort
+    if output_dir is not None:
+        params["output_dir"] = output_dir
+    if do_clean is not None:
+        params["do_clean"] = do_clean
+    if do_img is not None:
+        params["do_img"] = do_img
+    return params
+
+
+def find_variance_lines_cargs(
+    params: FindVarianceLinesParameters,
+    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("find_variance_lines.tcsh")
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            params.get("mask")
+        ])
+    if params.get("min_cvox") is not None:
+        cargs.extend([
+            "-min_cvox",
+            str(params.get("min_cvox"))
+        ])
+    if params.get("min_nt") is not None:
+        cargs.extend([
+            "-min_nt",
+            str(params.get("min_nt"))
+        ])
+    if params.get("nerode") is not None:
+        cargs.extend([
+            "-nerode",
+            str(params.get("nerode"))
+        ])
+    if params.get("nfirst") is not None:
+        cargs.extend([
+            "-nfirst",
+            str(params.get("nfirst"))
+        ])
+    if params.get("percentile") is not None:
+        cargs.extend([
+            "-perc",
+            str(params.get("percentile"))
+        ])
+    if params.get("polort") is not None:
+        cargs.extend([
+            "-polort",
+            params.get("polort")
+        ])
+    if params.get("output_dir") is not None:
+        cargs.extend([
+            "-rdir",
+            params.get("output_dir")
+        ])
+    if params.get("do_clean") is not None:
+        cargs.extend([
+            "-do_clean",
+            str(params.get("do_clean"))
+        ])
+    if params.get("do_img") is not None:
+        cargs.extend([
+            "-do_img",
+            str(params.get("do_img"))
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hist"):
+        cargs.append("-hist")
+    if params.get("ver"):
+        cargs.append("-ver")
+    return cargs
+
+
+def find_variance_lines_outputs(
+    params: FindVarianceLinesParameters,
+    execution: Execution,
+) -> FindVarianceLinesOutputs:
+    """
+    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 = FindVarianceLinesOutputs(
+        root=execution.output_file("."),
+        variance_maps=execution.output_file(params.get("output_dir") + "/variance_map_run*.nii.gz") if (params.get("output_dir") is not None) else None,
+        scaled_variance_maps=execution.output_file(params.get("output_dir") + "/scaled_variance_map_run*.nii.gz") if (params.get("output_dir") is not None) else None,
+        cluster_reports=execution.output_file(params.get("output_dir") + "/cluster_report_run*.txt") if (params.get("output_dir") is not None) else None,
+        jpeg_images=execution.output_file(params.get("output_dir") + "/*.jpg") if (params.get("output_dir") is not None) else None,
+    )
+    return ret
+
+
+def find_variance_lines_execute(
+    params: FindVarianceLinesParameters,
+    execution: Execution,
+) -> FindVarianceLinesOutputs:
+    """
+    Look for bars of high variance that might suggest scanner interference in EPI
+    datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FindVarianceLinesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = find_variance_lines_cargs(params, execution)
+    ret = find_variance_lines_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def find_variance_lines(
+    input_files: list[InputPathType],
+    mask: str | None = None,
+    min_cvox: int | None = None,
+    min_nt: int | None = None,
+    nerode: int | None = None,
+    nfirst: int | None = None,
+    percentile: int | None = None,
+    polort: str | None = None,
+    output_dir: str | None = None,
+    do_clean: int | None = None,
+    do_img: int | None = None,
+    echo: bool = False,
+    help_: bool = False,
+    hist: bool = False,
+    ver: bool = False,
+    runner: Runner | None = None,
+) -> FindVarianceLinesOutputs:
+    """
+    Look for bars of high variance that might suggest scanner interference in EPI
+    datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input EPI datasets.
+        mask: Mask for computations (default=AUTO).
+        min_cvox: Minimum voxels for valid mask column (default=5).
+        min_nt: Minimum number of time points required (default=10).
+        nerode: How much to erode input or auto-mask (default=0).
+        nfirst: Discard the first VAL time points (default=0).
+        percentile: Percentile of variance values to scale to (default=90).
+        polort: Polynomial detrending degree (default=A).
+        output_dir: Name of the output directory (default=vlines.result).
+        do_clean: Do we clean up a little? (default=1).
+        do_img: Make vline images? (default=1).
+        echo: Run script with shell 'echo' set (default=no).
+        help_: Show this help.
+        hist: Show the version history.
+        ver: Show the current version.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FindVarianceLinesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIND_VARIANCE_LINES_METADATA)
+    params = find_variance_lines_params(
+        input_files=input_files,
+        mask=mask,
+        min_cvox=min_cvox,
+        min_nt=min_nt,
+        nerode=nerode,
+        nfirst=nfirst,
+        percentile=percentile,
+        polort=polort,
+        output_dir=output_dir,
+        do_clean=do_clean,
+        do_img=do_img,
+        echo=echo,
+        help_=help_,
+        hist=hist,
+        ver=ver,
+    )
+    return find_variance_lines_execute(params, execution)
+
+
+__all__ = [
+    "FIND_VARIANCE_LINES_METADATA",
+    "FindVarianceLinesOutputs",
+    "FindVarianceLinesParameters",
+    "find_variance_lines",
+    "find_variance_lines_params",
+]

niwrap_afni/afni/firdesign.py

@@ -0,0 +1,235 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+FIRDESIGN_METADATA = Metadata(
+    id="a74504adf0b49ec5a0615bc609bf67d8b73823f0.boutiques",
+    name="FIRdesign",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+FirdesignParameters = typing.TypedDict('FirdesignParameters', {
+    "__STYX_TYPE__": typing.Literal["FIRdesign"],
+    "fbot": float,
+    "ftop": float,
+    "ntap": float,
+    "tr": typing.NotRequired[float | None],
+    "alternative_band": typing.NotRequired[list[float] | None],
+    "alternative_ntap": 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 {
+        "FIRdesign": firdesign_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 FirdesignOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `firdesign(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def firdesign_params(
+    fbot: float,
+    ftop: float,
+    ntap: float,
+    tr: float | None = None,
+    alternative_band: list[float] | None = None,
+    alternative_ntap: float | None = None,
+) -> FirdesignParameters:
+    """
+    Build parameters.
+    
+    Args:
+        fbot: Lowest frequency in the pass band.
+        ftop: Highest frequency in the pass band, must be higher than fbot and\
+            <= 0.5/TR.
+        ntap: Number of filter weights (AKA 'taps') to use, must be in the\
+            range 8..2000 (inclusive).
+        tr: Set time grid spacing to 'dd' [default is 1.0].
+        alternative_band: Alternative way to specify the passband.
+        alternative_ntap: Alternative way to specify the number of taps.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "FIRdesign",
+        "fbot": fbot,
+        "ftop": ftop,
+        "ntap": ntap,
+    }
+    if tr is not None:
+        params["tr"] = tr
+    if alternative_band is not None:
+        params["alternative_band"] = alternative_band
+    if alternative_ntap is not None:
+        params["alternative_ntap"] = alternative_ntap
+    return params
+
+
+def firdesign_cargs(
+    params: FirdesignParameters,
+    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("FIRdesign")
+    cargs.append(str(params.get("fbot")))
+    cargs.append(str(params.get("ftop")))
+    cargs.append(str(params.get("ntap")))
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("tr"))
+        ])
+    if params.get("alternative_band") is not None:
+        cargs.extend([
+            "-band",
+            *map(str, params.get("alternative_band"))
+        ])
+    if params.get("alternative_ntap") is not None:
+        cargs.extend([
+            "-ntap",
+            str(params.get("alternative_ntap"))
+        ])
+    return cargs
+
+
+def firdesign_outputs(
+    params: FirdesignParameters,
+    execution: Execution,
+) -> FirdesignOutputs:
+    """
+    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 = FirdesignOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def firdesign_execute(
+    params: FirdesignParameters,
+    execution: Execution,
+) -> FirdesignOutputs:
+    """
+    Uses the Remez algorithm to calculate the FIR filter weights for a bandpass
+    filter; results are written to stdout in an unadorned (no header) column of
+    numbers.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `FirdesignOutputs`).
+    """
+    params = execution.params(params)
+    cargs = firdesign_cargs(params, execution)
+    ret = firdesign_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def firdesign(
+    fbot: float,
+    ftop: float,
+    ntap: float,
+    tr: float | None = None,
+    alternative_band: list[float] | None = None,
+    alternative_ntap: float | None = None,
+    runner: Runner | None = None,
+) -> FirdesignOutputs:
+    """
+    Uses the Remez algorithm to calculate the FIR filter weights for a bandpass
+    filter; results are written to stdout in an unadorned (no header) column of
+    numbers.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        fbot: Lowest frequency in the pass band.
+        ftop: Highest frequency in the pass band, must be higher than fbot and\
+            <= 0.5/TR.
+        ntap: Number of filter weights (AKA 'taps') to use, must be in the\
+            range 8..2000 (inclusive).
+        tr: Set time grid spacing to 'dd' [default is 1.0].
+        alternative_band: Alternative way to specify the passband.
+        alternative_ntap: Alternative way to specify the number of taps.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `FirdesignOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIRDESIGN_METADATA)
+    params = firdesign_params(
+        fbot=fbot,
+        ftop=ftop,
+        ntap=ntap,
+        tr=tr,
+        alternative_band=alternative_band,
+        alternative_ntap=alternative_ntap,
+    )
+    return firdesign_execute(params, execution)
+
+
+__all__ = [
+    "FIRDESIGN_METADATA",
+    "FirdesignOutputs",
+    "FirdesignParameters",
+    "firdesign",
+    "firdesign_params",
+]