niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/fim2.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 *
+
+FIM2_METADATA = Metadata(
+    id="dc4766ddbc19de164de7f967033e9406b2958bcf.boutiques",
+    name="fim2",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+Fim2Parameters = typing.TypedDict('Fim2Parameters', {
+    "__STYX_TYPE__": typing.Literal["fim2"],
+    "image_files": list[InputPathType],
+    "pcnt": typing.NotRequired[float | None],
+    "pcthresh": typing.NotRequired[float | None],
+    "im1": typing.NotRequired[int | None],
+    "num": typing.NotRequired[int | None],
+    "non": bool,
+    "coef": typing.NotRequired[float | None],
+    "ort": typing.NotRequired[list[InputPathType] | None],
+    "ideal": typing.NotRequired[list[InputPathType] | None],
+    "polref": typing.NotRequired[int | None],
+    "fimfile": typing.NotRequired[str | None],
+    "corr": bool,
+    "corfile": typing.NotRequired[str | None],
+    "cnrfile": typing.NotRequired[str | None],
+    "sigfile": typing.NotRequired[str | None],
+    "fitfile": typing.NotRequired[str | None],
+    "subort": typing.NotRequired[str | None],
+    "flim": bool,
+    "clean": bool,
+    "clip": bool,
+    "q": bool,
+    "dfspace": bool,
+    "regbase": 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 {
+        "fim2": fim2_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 {
+        "fim2": fim2_outputs,
+    }.get(t)
+
+
+class Fim2Outputs(typing.NamedTuple):
+    """
+    Output object returned when calling `fim2(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    activation_magnitudes: OutputPathType | None
+    """Activation magnitudes output file"""
+    correlation_image: OutputPathType | None
+    """Correlation image output file"""
+    contrast_to_noise_image: OutputPathType | None
+    """Contrast-to-noise image output file"""
+    std_deviation_image: OutputPathType | None
+    """Standard deviation image output file"""
+    ls_fit_coefficients: OutputPathType | None
+    """Least squares fit coefficients image files"""
+    subtracted_references: OutputPathType | None
+    """Subtracted ortho reference time series images"""
+
+
+def fim2_params(
+    image_files: list[InputPathType],
+    pcnt: float | None = None,
+    pcthresh: float | None = None,
+    im1: int | None = None,
+    num: int | None = None,
+    non: bool = False,
+    coef: float | None = None,
+    ort: list[InputPathType] | None = None,
+    ideal: list[InputPathType] | None = None,
+    polref: int | None = None,
+    fimfile: str | None = None,
+    corr: bool = False,
+    corfile: str | None = None,
+    cnrfile: str | None = None,
+    sigfile: str | None = None,
+    fitfile: str | None = None,
+    subort: str | None = None,
+    flim: bool = False,
+    clean: bool = False,
+    clip: bool = False,
+    q: bool = False,
+    dfspace: bool = False,
+    regbase: str | None = None,
+) -> Fim2Parameters:
+    """
+    Build parameters.
+    
+    Args:
+        image_files: Input MRI image files.
+        pcnt: Correlation coefficient threshold will be 1 - 0.01 * #.
+        pcthresh: Correlation coefficient threshold will be #.
+        im1: Index of image file to use as first in time series; default is 1.
+        num: Number of images to actually use; default is to use all images.
+        non: Turn off default normalization of the output activation image.
+        coef: Scaling factor to convert the activation output from floats to\
+            short ints.
+        ort: Filename of a time series to which the image data will be\
+            orthogonalized before correlations are computed.
+        ideal: Filename of a time series to which the image data is to be\
+            correlated.
+        polref: Use polynomials of order 0..# as extra 'orts'; default is 0.
+        fimfile: Filename to save activation magnitudes in.
+        corr: Indicates to write correlation output to image file\
+            'fimfile.CORR'.
+        corfile: Filename to save correlation image in.
+        cnrfile: Filename to save contrast-to-noise image in.
+        sigfile: Filename to save standard deviation image in.
+        fitfile: Image files of the least squares fit coefficients of all the\
+            -ort and -polref time series.
+        subort: Filename of the new timeseries of images with the orts and\
+            polrefs subtracted out.
+        flim: Write outputs in mrilib 'float' format.
+        clean: Output images won't have the +/- 10000 values forced into their\
+            corners for scaling purposes.
+        clip: Set to zero regions of low intensity in output correlations, etc.
+        q: Quiet operation mode.
+        dfspace: Use the 'dfspace' filter to register the images spatially\
+            before filtering.
+        regbase: Read image in file 'fname' as the base image for registration.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "fim2",
+        "image_files": image_files,
+        "non": non,
+        "corr": corr,
+        "flim": flim,
+        "clean": clean,
+        "clip": clip,
+        "q": q,
+        "dfspace": dfspace,
+    }
+    if pcnt is not None:
+        params["pcnt"] = pcnt
+    if pcthresh is not None:
+        params["pcthresh"] = pcthresh
+    if im1 is not None:
+        params["im1"] = im1
+    if num is not None:
+        params["num"] = num
+    if coef is not None:
+        params["coef"] = coef
+    if ort is not None:
+        params["ort"] = ort
+    if ideal is not None:
+        params["ideal"] = ideal
+    if polref is not None:
+        params["polref"] = polref
+    if fimfile is not None:
+        params["fimfile"] = fimfile
+    if corfile is not None:
+        params["corfile"] = corfile
+    if cnrfile is not None:
+        params["cnrfile"] = cnrfile
+    if sigfile is not None:
+        params["sigfile"] = sigfile
+    if fitfile is not None:
+        params["fitfile"] = fitfile
+    if subort is not None:
+        params["subort"] = subort
+    if regbase is not None:
+        params["regbase"] = regbase
+    return params
+
+
+def fim2_cargs(
+    params: Fim2Parameters,
+    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("fim2")
+    cargs.extend([execution.input_file(f) for f in params.get("image_files")])
+    if params.get("pcnt") is not None:
+        cargs.extend([
+            "-pcnt",
+            str(params.get("pcnt"))
+        ])
+    if params.get("pcthresh") is not None:
+        cargs.extend([
+            "-pcthresh",
+            str(params.get("pcthresh"))
+        ])
+    if params.get("im1") is not None:
+        cargs.extend([
+            "-im1",
+            str(params.get("im1"))
+        ])
+    if params.get("num") is not None:
+        cargs.extend([
+            "-num",
+            str(params.get("num"))
+        ])
+    if params.get("non"):
+        cargs.append("-non")
+    if params.get("coef") is not None:
+        cargs.extend([
+            "-coef",
+            str(params.get("coef"))
+        ])
+    if params.get("ort") is not None:
+        cargs.extend([
+            "-ort",
+            *[execution.input_file(f) for f in params.get("ort")]
+        ])
+    if params.get("ideal") is not None:
+        cargs.extend([
+            "-ideal",
+            *[execution.input_file(f) for f in params.get("ideal")]
+        ])
+    if params.get("polref") is not None:
+        cargs.extend([
+            "-polref",
+            str(params.get("polref"))
+        ])
+    if params.get("fimfile") is not None:
+        cargs.extend([
+            "-fimfile",
+            params.get("fimfile")
+        ])
+    if params.get("corr"):
+        cargs.append("-corr")
+    if params.get("corfile") is not None:
+        cargs.extend([
+            "-corfile",
+            params.get("corfile")
+        ])
+    if params.get("cnrfile") is not None:
+        cargs.extend([
+            "-cnrfile",
+            params.get("cnrfile")
+        ])
+    if params.get("sigfile") is not None:
+        cargs.extend([
+            "-sigfile",
+            params.get("sigfile")
+        ])
+    if params.get("fitfile") is not None:
+        cargs.extend([
+            "-fitfile",
+            params.get("fitfile")
+        ])
+    if params.get("subort") is not None:
+        cargs.extend([
+            "-subort",
+            params.get("subort")
+        ])
+    if params.get("flim"):
+        cargs.append("-flim")
+    if params.get("clean"):
+        cargs.append("-clean")
+    if params.get("clip"):
+        cargs.append("-clip")
+    if params.get("q"):
+        cargs.append("-q")
+    if params.get("dfspace"):
+        cargs.append("-dfspace")
+    if params.get("regbase") is not None:
+        cargs.extend([
+            "-regbase",
+            params.get("regbase")
+        ])
+    return cargs
+
+
+def fim2_outputs(
+    params: Fim2Parameters,
+    execution: Execution,
+) -> Fim2Outputs:
+    """
+    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 = Fim2Outputs(
+        root=execution.output_file("."),
+        activation_magnitudes=execution.output_file(params.get("fimfile")) if (params.get("fimfile") is not None) else None,
+        correlation_image=execution.output_file(params.get("corfile")) if (params.get("corfile") is not None) else None,
+        contrast_to_noise_image=execution.output_file(params.get("cnrfile")) if (params.get("cnrfile") is not None) else None,
+        std_deviation_image=execution.output_file(params.get("sigfile")) if (params.get("sigfile") is not None) else None,
+        ls_fit_coefficients=execution.output_file(params.get("fitfile")) if (params.get("fitfile") is not None) else None,
+        subtracted_references=execution.output_file(params.get("subort")) if (params.get("subort") is not None) else None,
+    )
+    return ret
+
+
+def fim2_execute(
+    params: Fim2Parameters,
+    execution: Execution,
+) -> Fim2Outputs:
+    """
+    Functional Imaging Mapping Tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `Fim2Outputs`).
+    """
+    params = execution.params(params)
+    cargs = fim2_cargs(params, execution)
+    ret = fim2_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def fim2(
+    image_files: list[InputPathType],
+    pcnt: float | None = None,
+    pcthresh: float | None = None,
+    im1: int | None = None,
+    num: int | None = None,
+    non: bool = False,
+    coef: float | None = None,
+    ort: list[InputPathType] | None = None,
+    ideal: list[InputPathType] | None = None,
+    polref: int | None = None,
+    fimfile: str | None = None,
+    corr: bool = False,
+    corfile: str | None = None,
+    cnrfile: str | None = None,
+    sigfile: str | None = None,
+    fitfile: str | None = None,
+    subort: str | None = None,
+    flim: bool = False,
+    clean: bool = False,
+    clip: bool = False,
+    q: bool = False,
+    dfspace: bool = False,
+    regbase: str | None = None,
+    runner: Runner | None = None,
+) -> Fim2Outputs:
+    """
+    Functional Imaging Mapping Tool.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        image_files: Input MRI image files.
+        pcnt: Correlation coefficient threshold will be 1 - 0.01 * #.
+        pcthresh: Correlation coefficient threshold will be #.
+        im1: Index of image file to use as first in time series; default is 1.
+        num: Number of images to actually use; default is to use all images.
+        non: Turn off default normalization of the output activation image.
+        coef: Scaling factor to convert the activation output from floats to\
+            short ints.
+        ort: Filename of a time series to which the image data will be\
+            orthogonalized before correlations are computed.
+        ideal: Filename of a time series to which the image data is to be\
+            correlated.
+        polref: Use polynomials of order 0..# as extra 'orts'; default is 0.
+        fimfile: Filename to save activation magnitudes in.
+        corr: Indicates to write correlation output to image file\
+            'fimfile.CORR'.
+        corfile: Filename to save correlation image in.
+        cnrfile: Filename to save contrast-to-noise image in.
+        sigfile: Filename to save standard deviation image in.
+        fitfile: Image files of the least squares fit coefficients of all the\
+            -ort and -polref time series.
+        subort: Filename of the new timeseries of images with the orts and\
+            polrefs subtracted out.
+        flim: Write outputs in mrilib 'float' format.
+        clean: Output images won't have the +/- 10000 values forced into their\
+            corners for scaling purposes.
+        clip: Set to zero regions of low intensity in output correlations, etc.
+        q: Quiet operation mode.
+        dfspace: Use the 'dfspace' filter to register the images spatially\
+            before filtering.
+        regbase: Read image in file 'fname' as the base image for registration.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `Fim2Outputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FIM2_METADATA)
+    params = fim2_params(
+        image_files=image_files,
+        pcnt=pcnt,
+        pcthresh=pcthresh,
+        im1=im1,
+        num=num,
+        non=non,
+        coef=coef,
+        ort=ort,
+        ideal=ideal,
+        polref=polref,
+        fimfile=fimfile,
+        corr=corr,
+        corfile=corfile,
+        cnrfile=cnrfile,
+        sigfile=sigfile,
+        fitfile=fitfile,
+        subort=subort,
+        flim=flim,
+        clean=clean,
+        clip=clip,
+        q=q,
+        dfspace=dfspace,
+        regbase=regbase,
+    )
+    return fim2_execute(params, execution)
+
+
+__all__ = [
+    "FIM2_METADATA",
+    "Fim2Outputs",
+    "Fim2Parameters",
+    "fim2",
+    "fim2_params",
+]