niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_pvmap.py

@@ -0,0 +1,221 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_PVMAP_METADATA = Metadata(
+    id="55dba5084ade4c336efba69e81addccf3e2d93a3.boutiques",
+    name="3dPVmap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dPvmapParameters = typing.TypedDict('V3dPvmapParameters', {
+    "__STYX_TYPE__": typing.Literal["3dPVmap"],
+    "prefix": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "inputdataset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dPVmap": v_3d_pvmap_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 {
+        "3dPVmap": v_3d_pvmap_outputs,
+    }.get(t)
+
+
+class V3dPvmapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_pvmap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outbrik: OutputPathType | None
+    """Output PVmap file"""
+    outhead: OutputPathType | None
+    """Output PVmap header file"""
+    pc_vectors: OutputPathType | None
+    """Principal component time series vectors"""
+
+
+def v_3d_pvmap_params(
+    inputdataset: InputPathType,
+    prefix: str | None = None,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+) -> V3dPvmapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        inputdataset: Input dataset (e.g., fred.nii).
+        prefix: Output prefix for generated files.
+        mask: Mask dataset (e.g., brainmask.nii).
+        automask: Automatically generate a mask from the input dataset.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dPVmap",
+        "automask": automask,
+        "inputdataset": inputdataset,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if mask is not None:
+        params["mask"] = mask
+    return params
+
+
+def v_3d_pvmap_cargs(
+    params: V3dPvmapParameters,
+    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("3dPVmap")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    cargs.append(execution.input_file(params.get("inputdataset")))
+    return cargs
+
+
+def v_3d_pvmap_outputs(
+    params: V3dPvmapParameters,
+    execution: Execution,
+) -> V3dPvmapOutputs:
+    """
+    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 = V3dPvmapOutputs(
+        root=execution.output_file("."),
+        outbrik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        outhead=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        pc_vectors=execution.output_file(params.get("prefix") + ".1D") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_pvmap_execute(
+    params: V3dPvmapParameters,
+    execution: Execution,
+) -> V3dPvmapOutputs:
+    """
+    Computes the first two principal component vectors of a time series dataset,
+    then outputs the R-squared coefficient of each voxel time series with these
+    first two components.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dPvmapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_pvmap_cargs(params, execution)
+    ret = v_3d_pvmap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_pvmap(
+    inputdataset: InputPathType,
+    prefix: str | None = None,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    runner: Runner | None = None,
+) -> V3dPvmapOutputs:
+    """
+    Computes the first two principal component vectors of a time series dataset,
+    then outputs the R-squared coefficient of each voxel time series with these
+    first two components.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        inputdataset: Input dataset (e.g., fred.nii).
+        prefix: Output prefix for generated files.
+        mask: Mask dataset (e.g., brainmask.nii).
+        automask: Automatically generate a mask from the input dataset.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dPvmapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PVMAP_METADATA)
+    params = v_3d_pvmap_params(
+        prefix=prefix,
+        mask=mask,
+        automask=automask,
+        inputdataset=inputdataset,
+    )
+    return v_3d_pvmap_execute(params, execution)
+
+
+__all__ = [
+    "V3dPvmapOutputs",
+    "V3dPvmapParameters",
+    "V_3D_PVMAP_METADATA",
+    "v_3d_pvmap",
+    "v_3d_pvmap_params",
+]

niwrap_afni/afni/v_3d_qwarp.py

@@ -0,0 +1,359 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_QWARP_METADATA = Metadata(
+    id="b31e14a7b7123e83340819abf222feefbe217a71.boutiques",
+    name="3dQwarp",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dQwarpParameters = typing.TypedDict('V3dQwarpParameters', {
+    "__STYX_TYPE__": typing.Literal["3dQwarp"],
+    "base_dataset": InputPathType,
+    "source_dataset": InputPathType,
+    "prefix": str,
+    "no_warp": bool,
+    "inverse_warp": bool,
+    "no_dataset": bool,
+    "a_warp": bool,
+    "pcl": bool,
+    "pear": bool,
+    "hel": bool,
+    "mi": bool,
+    "nmi": bool,
+    "lpc": bool,
+    "lpa": bool,
+    "noneg": bool,
+    "nopenalty": bool,
+    "minpatch": typing.NotRequired[float | None],
+    "maxlev": typing.NotRequired[float | None],
+    "verbose": bool,
+    "quiet": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dQwarp": v_3d_qwarp_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 {
+        "3dQwarp": v_3d_qwarp_outputs,
+    }.get(t)
+
+
+class V3dQwarpOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_qwarp(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    warped_dataset: OutputPathType
+    """Warped dataset"""
+    warp_dataset: OutputPathType
+    """Warp dataset"""
+    inverse_warp_dataset: OutputPathType
+    """Inverse warp dataset"""
+
+
+def v_3d_qwarp_params(
+    base_dataset: InputPathType,
+    source_dataset: InputPathType,
+    prefix: str,
+    no_warp: bool = False,
+    inverse_warp: bool = False,
+    no_dataset: bool = False,
+    a_warp: bool = False,
+    pcl: bool = False,
+    pear: bool = False,
+    hel: bool = False,
+    mi: bool = False,
+    nmi: bool = False,
+    lpc: bool = False,
+    lpa: bool = False,
+    noneg: bool = False,
+    nopenalty: bool = False,
+    minpatch: float | None = None,
+    maxlev: float | None = None,
+    verbose: bool = False,
+    quiet: bool = False,
+) -> V3dQwarpParameters:
+    """
+    Build parameters.
+    
+    Args:
+        base_dataset: Base dataset.
+        source_dataset: Source dataset.
+        prefix: Prefix for the output datasets.
+        no_warp: Do not save the _WARP file.
+        inverse_warp: Compute and save the _WARPINV file.
+        no_dataset: Do not save the warped source dataset.
+        a_warp: Output the nonlinear warp when -allineate is used.
+        pcl: Clipped Pearson correlation (default method).
+        pear: Use strict Pearson correlation for matching.
+        hel: Use Hellinger metric for matching.
+        mi: Use Mutual Information for matching.
+        nmi: Use Normalized Mutual Information for matching.
+        lpc: Use Local Pearson correlation (signed) for matching.
+        lpa: Use Local Pearson correlation (absolute value) for matching.
+        noneg: Replace negative values in either input volume with 0.
+        nopenalty: Don't use a penalty on the cost functional.
+        minpatch: Set the minimum patch size for warp searching.
+        maxlev: Set the maximum refinement level.
+        verbose: Print out very verbose progress messages.
+        quiet: Cut out most progress messages.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dQwarp",
+        "base_dataset": base_dataset,
+        "source_dataset": source_dataset,
+        "prefix": prefix,
+        "no_warp": no_warp,
+        "inverse_warp": inverse_warp,
+        "no_dataset": no_dataset,
+        "a_warp": a_warp,
+        "pcl": pcl,
+        "pear": pear,
+        "hel": hel,
+        "mi": mi,
+        "nmi": nmi,
+        "lpc": lpc,
+        "lpa": lpa,
+        "noneg": noneg,
+        "nopenalty": nopenalty,
+        "verbose": verbose,
+        "quiet": quiet,
+    }
+    if minpatch is not None:
+        params["minpatch"] = minpatch
+    if maxlev is not None:
+        params["maxlev"] = maxlev
+    return params
+
+
+def v_3d_qwarp_cargs(
+    params: V3dQwarpParameters,
+    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("3dQwarp")
+    cargs.append(execution.input_file(params.get("base_dataset")))
+    cargs.append(execution.input_file(params.get("source_dataset")))
+    cargs.append(params.get("prefix"))
+    if params.get("no_warp"):
+        cargs.append("-nowarp")
+    if params.get("inverse_warp"):
+        cargs.append("-iwarp")
+    if params.get("no_dataset"):
+        cargs.append("-nodset")
+    if params.get("a_warp"):
+        cargs.append("-awarp")
+    if params.get("pcl"):
+        cargs.append("-pcl")
+    if params.get("pear"):
+        cargs.append("-pear")
+    if params.get("hel"):
+        cargs.append("-hel")
+    if params.get("mi"):
+        cargs.append("-mi")
+    if params.get("nmi"):
+        cargs.append("-nmi")
+    if params.get("lpc"):
+        cargs.append("-lpc")
+    if params.get("lpa"):
+        cargs.append("-lpa")
+    if params.get("noneg"):
+        cargs.append("-noneg")
+    if params.get("nopenalty"):
+        cargs.append("-nopenalty")
+    if params.get("minpatch") is not None:
+        cargs.extend([
+            "-minpatch",
+            str(params.get("minpatch"))
+        ])
+    if params.get("maxlev") is not None:
+        cargs.extend([
+            "-maxlev",
+            str(params.get("maxlev"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    return cargs
+
+
+def v_3d_qwarp_outputs(
+    params: V3dQwarpParameters,
+    execution: Execution,
+) -> V3dQwarpOutputs:
+    """
+    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 = V3dQwarpOutputs(
+        root=execution.output_file("."),
+        warped_dataset=execution.output_file("{PREFIX}+tlrc"),
+        warp_dataset=execution.output_file("{PREFIX}_WARP+tlrc"),
+        inverse_warp_dataset=execution.output_file("{PREFIX}_WARPINV+tlrc"),
+    )
+    return ret
+
+
+def v_3d_qwarp_execute(
+    params: V3dQwarpParameters,
+    execution: Execution,
+) -> V3dQwarpOutputs:
+    """
+    Computes a nonlinearly warped version of source_dataset to match base_dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dQwarpOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_qwarp_cargs(params, execution)
+    ret = v_3d_qwarp_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_qwarp(
+    base_dataset: InputPathType,
+    source_dataset: InputPathType,
+    prefix: str,
+    no_warp: bool = False,
+    inverse_warp: bool = False,
+    no_dataset: bool = False,
+    a_warp: bool = False,
+    pcl: bool = False,
+    pear: bool = False,
+    hel: bool = False,
+    mi: bool = False,
+    nmi: bool = False,
+    lpc: bool = False,
+    lpa: bool = False,
+    noneg: bool = False,
+    nopenalty: bool = False,
+    minpatch: float | None = None,
+    maxlev: float | None = None,
+    verbose: bool = False,
+    quiet: bool = False,
+    runner: Runner | None = None,
+) -> V3dQwarpOutputs:
+    """
+    Computes a nonlinearly warped version of source_dataset to match base_dataset.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        base_dataset: Base dataset.
+        source_dataset: Source dataset.
+        prefix: Prefix for the output datasets.
+        no_warp: Do not save the _WARP file.
+        inverse_warp: Compute and save the _WARPINV file.
+        no_dataset: Do not save the warped source dataset.
+        a_warp: Output the nonlinear warp when -allineate is used.
+        pcl: Clipped Pearson correlation (default method).
+        pear: Use strict Pearson correlation for matching.
+        hel: Use Hellinger metric for matching.
+        mi: Use Mutual Information for matching.
+        nmi: Use Normalized Mutual Information for matching.
+        lpc: Use Local Pearson correlation (signed) for matching.
+        lpa: Use Local Pearson correlation (absolute value) for matching.
+        noneg: Replace negative values in either input volume with 0.
+        nopenalty: Don't use a penalty on the cost functional.
+        minpatch: Set the minimum patch size for warp searching.
+        maxlev: Set the maximum refinement level.
+        verbose: Print out very verbose progress messages.
+        quiet: Cut out most progress messages.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dQwarpOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_QWARP_METADATA)
+    params = v_3d_qwarp_params(
+        base_dataset=base_dataset,
+        source_dataset=source_dataset,
+        prefix=prefix,
+        no_warp=no_warp,
+        inverse_warp=inverse_warp,
+        no_dataset=no_dataset,
+        a_warp=a_warp,
+        pcl=pcl,
+        pear=pear,
+        hel=hel,
+        mi=mi,
+        nmi=nmi,
+        lpc=lpc,
+        lpa=lpa,
+        noneg=noneg,
+        nopenalty=nopenalty,
+        minpatch=minpatch,
+        maxlev=maxlev,
+        verbose=verbose,
+        quiet=quiet,
+    )
+    return v_3d_qwarp_execute(params, execution)
+
+
+__all__ = [
+    "V3dQwarpOutputs",
+    "V3dQwarpParameters",
+    "V_3D_QWARP_METADATA",
+    "v_3d_qwarp",
+    "v_3d_qwarp_params",
+]