niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_tsort.py

@@ -0,0 +1,267 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TSORT_METADATA = Metadata(
+    id="28c28b79e328ac59d8297a59e0298ad19fb48796.boutiques",
+    name="3dTsort",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTsortParameters = typing.TypedDict('V3dTsortParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTsort"],
+    "input_file": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "dec": bool,
+    "rank": bool,
+    "ind": bool,
+    "val": bool,
+    "random": bool,
+    "ranfft": bool,
+    "randft": bool,
+    "datum": 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 {
+        "3dTsort": v_3d_tsort_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 {
+        "3dTsort": v_3d_tsort_outputs,
+    }.get(t)
+
+
+class V3dTsortOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tsort(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_dataset: OutputPathType | None
+    """Main default output of 3dTsort"""
+
+
+def v_3d_tsort_params(
+    input_file: InputPathType,
+    prefix: str | None = None,
+    dec: bool = False,
+    rank: bool = False,
+    ind: bool = False,
+    val: bool = False,
+    random_: bool = False,
+    ranfft: bool = False,
+    randft: bool = False,
+    datum: str | None = None,
+) -> V3dTsortParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input dataset to be sorted.
+        prefix: Prefix for the output dataset.
+        dec: Sort into decreasing order.
+        rank: Output rank instead of sorted values; ranks range from 1 to Nvals.
+        ind: Output sorting index (0 to Nvals -1).
+        val: Output sorted values (default).
+        random_: Randomly shuffle (permute) the time points in each voxel.
+        ranfft: Randomize each time series by scrambling the FFT phase.
+        randft: Randomize each time series by scrambling the DFT phase.
+        datum: Coerce the output data to be stored as the given type (byte,\
+            short, or float).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTsort",
+        "input_file": input_file,
+        "dec": dec,
+        "rank": rank,
+        "ind": ind,
+        "val": val,
+        "random": random_,
+        "ranfft": ranfft,
+        "randft": randft,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if datum is not None:
+        params["datum"] = datum
+    return params
+
+
+def v_3d_tsort_cargs(
+    params: V3dTsortParameters,
+    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("3dTsort")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("dec"):
+        cargs.append("-dec")
+    if params.get("rank"):
+        cargs.append("-rank")
+    if params.get("ind"):
+        cargs.append("-ind")
+    if params.get("val"):
+        cargs.append("-val")
+    if params.get("random"):
+        cargs.append("-random")
+    if params.get("ranfft"):
+        cargs.append("-ranFFT")
+    if params.get("randft"):
+        cargs.append("-ranDFT")
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    return cargs
+
+
+def v_3d_tsort_outputs(
+    params: V3dTsortParameters,
+    execution: Execution,
+) -> V3dTsortOutputs:
+    """
+    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 = V3dTsortOutputs(
+        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_tsort_execute(
+    params: V3dTsortParameters,
+    execution: Execution,
+) -> V3dTsortOutputs:
+    """
+    Sorts each voxel in a dataset and produces a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsortOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tsort_cargs(params, execution)
+    ret = v_3d_tsort_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tsort(
+    input_file: InputPathType,
+    prefix: str | None = None,
+    dec: bool = False,
+    rank: bool = False,
+    ind: bool = False,
+    val: bool = False,
+    random_: bool = False,
+    ranfft: bool = False,
+    randft: bool = False,
+    datum: str | None = None,
+    runner: Runner | None = None,
+) -> V3dTsortOutputs:
+    """
+    Sorts each voxel in a dataset and produces a new dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input dataset to be sorted.
+        prefix: Prefix for the output dataset.
+        dec: Sort into decreasing order.
+        rank: Output rank instead of sorted values; ranks range from 1 to Nvals.
+        ind: Output sorting index (0 to Nvals -1).
+        val: Output sorted values (default).
+        random_: Randomly shuffle (permute) the time points in each voxel.
+        ranfft: Randomize each time series by scrambling the FFT phase.
+        randft: Randomize each time series by scrambling the DFT phase.
+        datum: Coerce the output data to be stored as the given type (byte,\
+            short, or float).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsortOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSORT_METADATA)
+    params = v_3d_tsort_params(
+        input_file=input_file,
+        prefix=prefix,
+        dec=dec,
+        rank=rank,
+        ind=ind,
+        val=val,
+        random_=random_,
+        ranfft=ranfft,
+        randft=randft,
+        datum=datum,
+    )
+    return v_3d_tsort_execute(params, execution)
+
+
+__all__ = [
+    "V3dTsortOutputs",
+    "V3dTsortParameters",
+    "V_3D_TSORT_METADATA",
+    "v_3d_tsort",
+    "v_3d_tsort_params",
+]

niwrap_afni/afni/v_3d_tsplit4_d.py

@@ -0,0 +1,209 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TSPLIT4_D_METADATA = Metadata(
+    id="861535b6c29e168191a0da4498bda4b743f855bf.boutiques",
+    name="3dTsplit4D",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTsplit4DParameters = typing.TypedDict('V3dTsplit4DParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTsplit4D"],
+    "prefix": str,
+    "infile": InputPathType,
+    "keep_datum": bool,
+    "digits": 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 {
+        "3dTsplit4D": v_3d_tsplit4_d_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 {
+        "3dTsplit4D": v_3d_tsplit4_d_outputs,
+    }.get(t)
+
+
+class V3dTsplit4DOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tsplit4_d(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfiles: OutputPathType
+    """Multiple 3D single-brick output files"""
+
+
+def v_3d_tsplit4_d_params(
+    prefix: str,
+    infile: InputPathType,
+    keep_datum: bool = False,
+    digits: float | None = None,
+) -> V3dTsplit4DParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Prefix of the output datasets (e.g., out/epi).
+        infile: Input 3D+time dataset (e.g., epi_r1+orig).
+        keep_datum: Output uses original datum (no conversion to float).
+        digits: Number of digits to use for output filenames.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTsplit4D",
+        "prefix": prefix,
+        "infile": infile,
+        "keep_datum": keep_datum,
+    }
+    if digits is not None:
+        params["digits"] = digits
+    return params
+
+
+def v_3d_tsplit4_d_cargs(
+    params: V3dTsplit4DParameters,
+    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("3dTsplit4D")
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    cargs.append(execution.input_file(params.get("infile")))
+    if params.get("keep_datum"):
+        cargs.append("-keep_datum")
+    if params.get("digits") is not None:
+        cargs.extend([
+            "-digits",
+            str(params.get("digits"))
+        ])
+    return cargs
+
+
+def v_3d_tsplit4_d_outputs(
+    params: V3dTsplit4DParameters,
+    execution: Execution,
+) -> V3dTsplit4DOutputs:
+    """
+    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 = V3dTsplit4DOutputs(
+        root=execution.output_file("."),
+        outfiles=execution.output_file(params.get("prefix") + "*"),
+    )
+    return ret
+
+
+def v_3d_tsplit4_d_execute(
+    params: V3dTsplit4DParameters,
+    execution: Execution,
+) -> V3dTsplit4DOutputs:
+    """
+    Convert a 3D+time dataset into multiple 3D single-brick files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsplit4DOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tsplit4_d_cargs(params, execution)
+    ret = v_3d_tsplit4_d_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tsplit4_d(
+    prefix: str,
+    infile: InputPathType,
+    keep_datum: bool = False,
+    digits: float | None = None,
+    runner: Runner | None = None,
+) -> V3dTsplit4DOutputs:
+    """
+    Convert a 3D+time dataset into multiple 3D single-brick files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Prefix of the output datasets (e.g., out/epi).
+        infile: Input 3D+time dataset (e.g., epi_r1+orig).
+        keep_datum: Output uses original datum (no conversion to float).
+        digits: Number of digits to use for output filenames.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsplit4DOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSPLIT4_D_METADATA)
+    params = v_3d_tsplit4_d_params(
+        prefix=prefix,
+        infile=infile,
+        keep_datum=keep_datum,
+        digits=digits,
+    )
+    return v_3d_tsplit4_d_execute(params, execution)
+
+
+__all__ = [
+    "V3dTsplit4DOutputs",
+    "V3dTsplit4DParameters",
+    "V_3D_TSPLIT4_D_METADATA",
+    "v_3d_tsplit4_d",
+    "v_3d_tsplit4_d_params",
+]