niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_fdr.py

@@ -0,0 +1,325 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_FDR_METADATA = Metadata(
+    id="052b0ab8a12acc2def2e27ee40fa90c4b23263c0.boutiques",
+    name="3dFDR",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dFdrParameters = typing.TypedDict('V3dFdrParameters', {
+    "__STYX_TYPE__": typing.Literal["3dFDR"],
+    "input_file": InputPathType,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "mask_threshold": typing.NotRequired[float | None],
+    "constant_type": typing.NotRequired[typing.Literal["cind", "cdep"] | None],
+    "quiet": bool,
+    "list": bool,
+    "prefix": str,
+    "mode_option": typing.NotRequired[typing.Literal["old", "new"] | None],
+    "pmask": bool,
+    "nopmask": bool,
+    "force": bool,
+    "float": bool,
+    "qval": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dFDR": v_3d_fdr_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 {
+        "3dFDR": v_3d_fdr_outputs,
+    }.get(t)
+
+
+class V3dFdrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_fdr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_brik: OutputPathType
+    """Output dataset in BRIK format"""
+    output_head: OutputPathType
+    """Output dataset in HEAD format"""
+    output_1d: OutputPathType
+    """Output list of voxel q-values"""
+
+
+def v_3d_fdr_params(
+    input_file: InputPathType,
+    prefix: str,
+    mask_file: InputPathType | None = None,
+    mask_threshold: float | None = None,
+    constant_type: typing.Literal["cind", "cdep"] | None = None,
+    quiet: bool = False,
+    list_: bool = False,
+    mode_option: typing.Literal["old", "new"] | None = None,
+    pmask: bool = False,
+    nopmask: bool = False,
+    force: bool = False,
+    float_: bool = False,
+    qval: bool = False,
+) -> V3dFdrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input 3D functional dataset filename.
+        prefix: Use 'pname' for the output dataset prefix name.
+        mask_file: Use mask values from file mname. If file mname contains more\
+            than 1 sub-brick, the mask sub-brick must be specified. Generally\
+            should be used to avoid counting non-brain voxels.
+        mask_threshold: Only voxels whose corresponding mask value is greater\
+            than or equal to the specified value in absolute terms will be\
+            considered. Default is 1.
+        constant_type: Set constant c(N): 1 for independent p-values (default)\
+            or sum(1/i, i=1,...,N) for any joint distribution.
+        quiet: Suppress screen output.
+        list_: Write sorted list of voxel q-values to screen.
+        mode_option: Use the old or new mode of operation. 'new' is now the\
+            default.
+        pmask: Ignore p=1 voxels (default in new mode).
+        nopmask: Count p=1 voxels (default in old mode).
+        force: Force conversion of all sub-bricks, treating them as p-values.
+        float_: Force the output of z-scores in floating point format.
+        qval: Force the output of q-values rather than z-scores.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dFDR",
+        "input_file": input_file,
+        "quiet": quiet,
+        "list": list_,
+        "prefix": prefix,
+        "pmask": pmask,
+        "nopmask": nopmask,
+        "force": force,
+        "float": float_,
+        "qval": qval,
+    }
+    if mask_file is not None:
+        params["mask_file"] = mask_file
+    if mask_threshold is not None:
+        params["mask_threshold"] = mask_threshold
+    if constant_type is not None:
+        params["constant_type"] = constant_type
+    if mode_option is not None:
+        params["mode_option"] = mode_option
+    return params
+
+
+def v_3d_fdr_cargs(
+    params: V3dFdrParameters,
+    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("3dFDR")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("mask_file") is not None:
+        cargs.extend([
+            "-mask_file",
+            execution.input_file(params.get("mask_file"))
+        ])
+    if params.get("mask_threshold") is not None:
+        cargs.extend([
+            "-mask_thr",
+            str(params.get("mask_threshold"))
+        ])
+    if params.get("constant_type") is not None:
+        cargs.extend([
+            "-c",
+            params.get("constant_type")
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("list"):
+        cargs.append("-list")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("mode_option") is not None:
+        cargs.extend([
+            "-",
+            params.get("mode_option")
+        ])
+    if params.get("pmask"):
+        cargs.append("-pmask")
+    if params.get("nopmask"):
+        cargs.append("-nopmask")
+    if params.get("force"):
+        cargs.append("-force")
+    if params.get("float"):
+        cargs.append("-float")
+    if params.get("qval"):
+        cargs.append("-qval")
+    return cargs
+
+
+def v_3d_fdr_outputs(
+    params: V3dFdrParameters,
+    execution: Execution,
+) -> V3dFdrOutputs:
+    """
+    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 = V3dFdrOutputs(
+        root=execution.output_file("."),
+        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        output_1d=execution.output_file(params.get("prefix") + ".1D"),
+    )
+    return ret
+
+
+def v_3d_fdr_execute(
+    params: V3dFdrParameters,
+    execution: Execution,
+) -> V3dFdrOutputs:
+    """
+    A tool for applying False Discovery Rate (FDR) thresholding to voxelwise
+    statistics in 3D functional datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dFdrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_fdr_cargs(params, execution)
+    ret = v_3d_fdr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_fdr(
+    input_file: InputPathType,
+    prefix: str,
+    mask_file: InputPathType | None = None,
+    mask_threshold: float | None = None,
+    constant_type: typing.Literal["cind", "cdep"] | None = None,
+    quiet: bool = False,
+    list_: bool = False,
+    mode_option: typing.Literal["old", "new"] | None = None,
+    pmask: bool = False,
+    nopmask: bool = False,
+    force: bool = False,
+    float_: bool = False,
+    qval: bool = False,
+    runner: Runner | None = None,
+) -> V3dFdrOutputs:
+    """
+    A tool for applying False Discovery Rate (FDR) thresholding to voxelwise
+    statistics in 3D functional datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input 3D functional dataset filename.
+        prefix: Use 'pname' for the output dataset prefix name.
+        mask_file: Use mask values from file mname. If file mname contains more\
+            than 1 sub-brick, the mask sub-brick must be specified. Generally\
+            should be used to avoid counting non-brain voxels.
+        mask_threshold: Only voxels whose corresponding mask value is greater\
+            than or equal to the specified value in absolute terms will be\
+            considered. Default is 1.
+        constant_type: Set constant c(N): 1 for independent p-values (default)\
+            or sum(1/i, i=1,...,N) for any joint distribution.
+        quiet: Suppress screen output.
+        list_: Write sorted list of voxel q-values to screen.
+        mode_option: Use the old or new mode of operation. 'new' is now the\
+            default.
+        pmask: Ignore p=1 voxels (default in new mode).
+        nopmask: Count p=1 voxels (default in old mode).
+        force: Force conversion of all sub-bricks, treating them as p-values.
+        float_: Force the output of z-scores in floating point format.
+        qval: Force the output of q-values rather than z-scores.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dFdrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FDR_METADATA)
+    params = v_3d_fdr_params(
+        input_file=input_file,
+        mask_file=mask_file,
+        mask_threshold=mask_threshold,
+        constant_type=constant_type,
+        quiet=quiet,
+        list_=list_,
+        prefix=prefix,
+        mode_option=mode_option,
+        pmask=pmask,
+        nopmask=nopmask,
+        force=force,
+        float_=float_,
+        qval=qval,
+    )
+    return v_3d_fdr_execute(params, execution)
+
+
+__all__ = [
+    "V3dFdrOutputs",
+    "V3dFdrParameters",
+    "V_3D_FDR_METADATA",
+    "v_3d_fdr",
+    "v_3d_fdr_params",
+]

niwrap_afni/afni/v_3d_fft.py

@@ -0,0 +1,307 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_FFT_METADATA = Metadata(
+    id="346ceaa099cde8147ff4ea8529349b8671ac8691.boutiques",
+    name="3dFFT",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dFftParameters = typing.TypedDict('V3dFftParameters', {
+    "__STYX_TYPE__": typing.Literal["3dFFT"],
+    "dataset": InputPathType,
+    "abs": bool,
+    "phase": bool,
+    "complex": bool,
+    "inverse": bool,
+    "Lx": typing.NotRequired[float | None],
+    "Ly": typing.NotRequired[float | None],
+    "Lz": typing.NotRequired[float | None],
+    "altIN": bool,
+    "altOUT": bool,
+    "input": typing.NotRequired[InputPathType | None],
+    "prefix": 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 {
+        "3dFFT": v_3d_fft_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 {
+        "3dFFT": v_3d_fft_outputs,
+    }.get(t)
+
+
+class V3dFftOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_fft(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Output dataset generated by 3dFFT."""
+
+
+def v_3d_fft_params(
+    dataset: InputPathType,
+    abs_: bool = False,
+    phase: bool = False,
+    complex_: bool = False,
+    inverse: bool = False,
+    lx: float | None = None,
+    ly: float | None = None,
+    lz: float | None = None,
+    alt_in: bool = False,
+    alt_out: bool = False,
+    input_: InputPathType | None = None,
+    prefix: str | None = None,
+) -> V3dFftParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dataset: Input dataset (e.g., dataset.nii).
+        abs_: Outputs the magnitude of the FFT (default).
+        phase: Outputs the phase of the FFT (-PI..PI).
+        complex_: Outputs the complex-valued FFT.
+        inverse: Does the inverse FFT instead of the forward FFT.
+        lx: Use FFT of length 'xx' in the x-direction.
+        ly: Use FFT of length 'yy' in the y-direction.
+        lz: Use FFT of length 'zz' in the z-direction.
+        alt_in: Alternate signs of input data before FFT to bring zero\
+            frequency from edge of FFT-space to center of grid for cosmetic\
+            purposes.
+        alt_out: Alternate signs of output data after FFT. Use '-altOUT' with\
+            '-altIN' on the forward transform to get the signs of the recovered\
+            image correct.
+        input_: Read the input dataset from specified file instead of from the\
+            last argument on the command line.
+        prefix: Use specified prefix for the output dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dFFT",
+        "dataset": dataset,
+        "abs": abs_,
+        "phase": phase,
+        "complex": complex_,
+        "inverse": inverse,
+        "altIN": alt_in,
+        "altOUT": alt_out,
+    }
+    if lx is not None:
+        params["Lx"] = lx
+    if ly is not None:
+        params["Ly"] = ly
+    if lz is not None:
+        params["Lz"] = lz
+    if input_ is not None:
+        params["input"] = input_
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_fft_cargs(
+    params: V3dFftParameters,
+    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("3dFFT")
+    cargs.append(execution.input_file(params.get("dataset")))
+    if params.get("abs"):
+        cargs.append("--abs")
+    if params.get("phase"):
+        cargs.append("--phase")
+    if params.get("complex"):
+        cargs.append("--complex")
+    if params.get("inverse"):
+        cargs.append("--inverse")
+    if params.get("Lx") is not None:
+        cargs.extend([
+            "--Lx",
+            str(params.get("Lx"))
+        ])
+    if params.get("Ly") is not None:
+        cargs.extend([
+            "--Ly",
+            str(params.get("Ly"))
+        ])
+    if params.get("Lz") is not None:
+        cargs.extend([
+            "--Lz",
+            str(params.get("Lz"))
+        ])
+    if params.get("altIN"):
+        cargs.append("--altIN")
+    if params.get("altOUT"):
+        cargs.append("--altOUT")
+    if params.get("input") is not None:
+        cargs.extend([
+            "--input",
+            execution.input_file(params.get("input"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "--prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3d_fft_outputs(
+    params: V3dFftParameters,
+    execution: Execution,
+) -> V3dFftOutputs:
+    """
+    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 = V3dFftOutputs(
+        root=execution.output_file("."),
+        output_dataset=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_fft_execute(
+    params: V3dFftParameters,
+    execution: Execution,
+) -> V3dFftOutputs:
+    """
+    Performs the FFT of the input dataset in 3 directions (x, y, z) and produces the
+    output dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dFftOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_fft_cargs(params, execution)
+    ret = v_3d_fft_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_fft(
+    dataset: InputPathType,
+    abs_: bool = False,
+    phase: bool = False,
+    complex_: bool = False,
+    inverse: bool = False,
+    lx: float | None = None,
+    ly: float | None = None,
+    lz: float | None = None,
+    alt_in: bool = False,
+    alt_out: bool = False,
+    input_: InputPathType | None = None,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dFftOutputs:
+    """
+    Performs the FFT of the input dataset in 3 directions (x, y, z) and produces the
+    output dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dataset: Input dataset (e.g., dataset.nii).
+        abs_: Outputs the magnitude of the FFT (default).
+        phase: Outputs the phase of the FFT (-PI..PI).
+        complex_: Outputs the complex-valued FFT.
+        inverse: Does the inverse FFT instead of the forward FFT.
+        lx: Use FFT of length 'xx' in the x-direction.
+        ly: Use FFT of length 'yy' in the y-direction.
+        lz: Use FFT of length 'zz' in the z-direction.
+        alt_in: Alternate signs of input data before FFT to bring zero\
+            frequency from edge of FFT-space to center of grid for cosmetic\
+            purposes.
+        alt_out: Alternate signs of output data after FFT. Use '-altOUT' with\
+            '-altIN' on the forward transform to get the signs of the recovered\
+            image correct.
+        input_: Read the input dataset from specified file instead of from the\
+            last argument on the command line.
+        prefix: Use specified prefix for the output dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dFftOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_FFT_METADATA)
+    params = v_3d_fft_params(
+        dataset=dataset,
+        abs_=abs_,
+        phase=phase,
+        complex_=complex_,
+        inverse=inverse,
+        lx=lx,
+        ly=ly,
+        lz=lz,
+        alt_in=alt_in,
+        alt_out=alt_out,
+        input_=input_,
+        prefix=prefix,
+    )
+    return v_3d_fft_execute(params, execution)
+
+
+__all__ = [
+    "V3dFftOutputs",
+    "V3dFftParameters",
+    "V_3D_FFT_METADATA",
+    "v_3d_fft",
+    "v_3d_fft_params",
+]