niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mema.py

@@ -0,0 +1,171 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MEMA_METADATA = Metadata(
+    id="3e49aad2d71d54e4f942b7cc6311a0fe4225ef3f.boutiques",
+    name="3dMEMA",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMemaParameters = typing.TypedDict('V3dMemaParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMEMA"],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMEMA": v_3d_mema_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 {
+        "3dMEMA": v_3d_mema_outputs,
+    }.get(t)
+
+
+class V3dMemaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mema(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output file from the analysis"""
+
+
+def v_3d_mema_params(
+) -> V3dMemaParameters:
+    """
+    Build parameters.
+    
+    Args:
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMEMA",
+    }
+    return params
+
+
+def v_3d_mema_cargs(
+    params: V3dMemaParameters,
+    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("3dMEMA")
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v_3d_mema_outputs(
+    params: V3dMemaParameters,
+    execution: Execution,
+) -> V3dMemaOutputs:
+    """
+    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 = V3dMemaOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("[PREFIX].nii.gz"),
+    )
+    return ret
+
+
+def v_3d_mema_execute(
+    params: V3dMemaParameters,
+    execution: Execution,
+) -> V3dMemaOutputs:
+    """
+    3dMEMA is a program for performing Mixed Effects Meta Analysis at group level
+    that models both within- and across-subjects variability.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMemaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mema_cargs(params, execution)
+    ret = v_3d_mema_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mema(
+    runner: Runner | None = None,
+) -> V3dMemaOutputs:
+    """
+    3dMEMA is a program for performing Mixed Effects Meta Analysis at group level
+    that models both within- and across-subjects variability.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMemaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEMA_METADATA)
+    params = v_3d_mema_params(
+    )
+    return v_3d_mema_execute(params, execution)
+
+
+__all__ = [
+    "V3dMemaOutputs",
+    "V3dMemaParameters",
+    "V_3D_MEMA_METADATA",
+    "v_3d_mema",
+    "v_3d_mema_params",
+]

niwrap_afni/afni/v_3d_mepfm.py

@@ -0,0 +1,256 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MEPFM_METADATA = Metadata(
+    id="44860000dde3dcae9381914d7a939fdce74cff79.boutiques",
+    name="3dMEPFM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMepfmParameters = typing.TypedDict('V3dMepfmParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMEPFM"],
+    "input_files": list[str],
+    "dbgArgs": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "hrf_model": typing.NotRequired[str | None],
+    "verbosity": typing.NotRequired[int | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMEPFM": v_3d_mepfm_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 {
+        "3dMEPFM": v_3d_mepfm_outputs,
+    }.get(t)
+
+
+class V3dMepfmOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mepfm(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    dr2_output: OutputPathType
+    """Changes in R2* parameter, assumed to represent neuronal-related signal
+    changes"""
+    dr2fit_output: OutputPathType
+    """Convolution of DR2 with HRF, one volume per echo"""
+    ds0_output: OutputPathType
+    """Changes in net magnetization (S0) (if estimated)"""
+    lambda_output: OutputPathType
+    """Regularization parameter"""
+    sigmas_mad_output: OutputPathType
+    """Estimate of the noise standard deviation after wavelet decomposition for
+    each input dataset"""
+    costs_output: OutputPathType
+    """Cost function to select the regularization parameter (lambda) according
+    to selection criterion"""
+
+
+def v_3d_mepfm_params(
+    input_files: list[str],
+    dbg_args: bool = False,
+    mask: InputPathType | None = None,
+    hrf_model: str | None = None,
+    verbosity: int | None = None,
+) -> V3dMepfmParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Dataset to analyze with Multiecho Paradigm Free Mapping,\
+            along with the echo time.
+        dbg_args: Enable R to save the parameters in .3dMEPFM.dbg.AFNI.args in\
+            the current directory.
+        mask: Process voxels inside this mask only. Default is no masking.
+        hrf_model: Haemodynamic response function used for deconvolution.
+        verbosity: Verbosity level. 0 for quiet, 1 (default) or more:\
+            talkative.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMEPFM",
+        "input_files": input_files,
+        "dbgArgs": dbg_args,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if hrf_model is not None:
+        params["hrf_model"] = hrf_model
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def v_3d_mepfm_cargs(
+    params: V3dMepfmParameters,
+    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("3dMEPFM")
+    cargs.extend([
+        "-input",
+        *params.get("input_files")
+    ])
+    if params.get("dbgArgs"):
+        cargs.append("-dbgArgs")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("hrf_model") is not None:
+        cargs.extend([
+            "-hrf",
+            params.get("hrf_model")
+        ])
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    cargs.append("[OTHER_OPTIONS]")
+    return cargs
+
+
+def v_3d_mepfm_outputs(
+    params: V3dMepfmParameters,
+    execution: Execution,
+) -> V3dMepfmOutputs:
+    """
+    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 = V3dMepfmOutputs(
+        root=execution.output_file("."),
+        dr2_output=execution.output_file("DR2_[PREFIX]_*.nii.gz"),
+        dr2fit_output=execution.output_file("DR2fit_[PREFIX]_*.nii.gz"),
+        ds0_output=execution.output_file("DS0_[PREFIX]_*.nii.gz"),
+        lambda_output=execution.output_file("lambda_[PREFIX]_*.nii.gz"),
+        sigmas_mad_output=execution.output_file("sigmas_MAD_[PREFIX]_*.nii.gz"),
+        costs_output=execution.output_file("costs_[PREFIX]_*.nii.gz"),
+    )
+    return ret
+
+
+def v_3d_mepfm_execute(
+    params: V3dMepfmParameters,
+    execution: Execution,
+) -> V3dMepfmOutputs:
+    """
+    Voxelwise deconvolution of Multiecho fMRI data to yield time-varying estimates
+    of changes in transverse relaxation (DR2*) and optionally, net magnetization
+    (DS0).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMepfmOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mepfm_cargs(params, execution)
+    ret = v_3d_mepfm_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mepfm(
+    input_files: list[str],
+    dbg_args: bool = False,
+    mask: InputPathType | None = None,
+    hrf_model: str | None = None,
+    verbosity: int | None = None,
+    runner: Runner | None = None,
+) -> V3dMepfmOutputs:
+    """
+    Voxelwise deconvolution of Multiecho fMRI data to yield time-varying estimates
+    of changes in transverse relaxation (DR2*) and optionally, net magnetization
+    (DS0).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Dataset to analyze with Multiecho Paradigm Free Mapping,\
+            along with the echo time.
+        dbg_args: Enable R to save the parameters in .3dMEPFM.dbg.AFNI.args in\
+            the current directory.
+        mask: Process voxels inside this mask only. Default is no masking.
+        hrf_model: Haemodynamic response function used for deconvolution.
+        verbosity: Verbosity level. 0 for quiet, 1 (default) or more:\
+            talkative.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMepfmOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEPFM_METADATA)
+    params = v_3d_mepfm_params(
+        input_files=input_files,
+        dbg_args=dbg_args,
+        mask=mask,
+        hrf_model=hrf_model,
+        verbosity=verbosity,
+    )
+    return v_3d_mepfm_execute(params, execution)
+
+
+__all__ = [
+    "V3dMepfmOutputs",
+    "V3dMepfmParameters",
+    "V_3D_MEPFM_METADATA",
+    "v_3d_mepfm",
+    "v_3d_mepfm_params",
+]

niwrap_afni/afni/v_3d_mse.py

@@ -0,0 +1,283 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_MSE_METADATA = Metadata(
+    id="292d17d0d1dc9e4f32f9285cd5defe51b10b115a.boutiques",
+    name="3dMSE",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dMseParameters = typing.TypedDict('V3dMseParameters', {
+    "__STYX_TYPE__": typing.Literal["3dMSE"],
+    "polynomial_order": typing.NotRequired[int | None],
+    "autoclip": bool,
+    "automask": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "scales": typing.NotRequired[float | None],
+    "entwin": typing.NotRequired[float | None],
+    "rthresh": typing.NotRequired[float | None],
+    "dset": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dMSE": v_3d_mse_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 {
+        "3dMSE": v_3d_mse_outputs,
+    }.get(t)
+
+
+class V3dMseOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_mse(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    out_brik: OutputPathType | None
+    """Output dataset in BRIK format."""
+    out_head: OutputPathType | None
+    """Output dataset in HEAD format."""
+
+
+def v_3d_mse_params(
+    dset: InputPathType,
+    polynomial_order: int | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    scales: float | None = None,
+    entwin: float | None = None,
+    rthresh: float | None = None,
+) -> V3dMseParameters:
+    """
+    Build parameters.
+    
+    Args:
+        dset: Input dataset (e.g., dset.nii.gz).
+        polynomial_order: Remove polynomial trend of order 'm' (default is m=1;\
+            m=-1 means no detrending).
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Use automask to clip low-intensity regions.
+        mask: Mask to define 'in-brain' voxels.
+        prefix: Prefix for the output dataset (default is 'MSE').
+        scales: The number of scales to be used in the calculation (default is\
+            5).
+        entwin: The window size used in the calculation (default is 2).
+        rthresh: The radius threshold for determining if values are the same in\
+            the SampleEn calculation, in fractions of the standard deviation\
+            (default is 0.5).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dMSE",
+        "autoclip": autoclip,
+        "automask": automask,
+        "dset": dset,
+    }
+    if polynomial_order is not None:
+        params["polynomial_order"] = polynomial_order
+    if mask is not None:
+        params["mask"] = mask
+    if prefix is not None:
+        params["prefix"] = prefix
+    if scales is not None:
+        params["scales"] = scales
+    if entwin is not None:
+        params["entwin"] = entwin
+    if rthresh is not None:
+        params["rthresh"] = rthresh
+    return params
+
+
+def v_3d_mse_cargs(
+    params: V3dMseParameters,
+    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("3dMSE")
+    if params.get("polynomial_order") is not None:
+        cargs.extend([
+            "-polort",
+            str(params.get("polynomial_order"))
+        ])
+    if params.get("autoclip"):
+        cargs.append("-autoclip")
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("scales") is not None:
+        cargs.extend([
+            "-scales",
+            str(params.get("scales"))
+        ])
+    if params.get("entwin") is not None:
+        cargs.extend([
+            "-entwin",
+            str(params.get("entwin"))
+        ])
+    if params.get("rthresh") is not None:
+        cargs.extend([
+            "-rthresh",
+            str(params.get("rthresh"))
+        ])
+    cargs.append(execution.input_file(params.get("dset")))
+    return cargs
+
+
+def v_3d_mse_outputs(
+    params: V3dMseParameters,
+    execution: Execution,
+) -> V3dMseOutputs:
+    """
+    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 = V3dMseOutputs(
+        root=execution.output_file("."),
+        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_mse_execute(
+    params: V3dMseParameters,
+    execution: Execution,
+) -> V3dMseOutputs:
+    """
+    Computes voxelwise multi-scale entropy.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dMseOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_mse_cargs(params, execution)
+    ret = v_3d_mse_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_mse(
+    dset: InputPathType,
+    polynomial_order: int | None = None,
+    autoclip: bool = False,
+    automask: bool = False,
+    mask: InputPathType | None = None,
+    prefix: str | None = None,
+    scales: float | None = None,
+    entwin: float | None = None,
+    rthresh: float | None = None,
+    runner: Runner | None = None,
+) -> V3dMseOutputs:
+    """
+    Computes voxelwise multi-scale entropy.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        dset: Input dataset (e.g., dset.nii.gz).
+        polynomial_order: Remove polynomial trend of order 'm' (default is m=1;\
+            m=-1 means no detrending).
+        autoclip: Clip off low-intensity regions in the dataset.
+        automask: Use automask to clip low-intensity regions.
+        mask: Mask to define 'in-brain' voxels.
+        prefix: Prefix for the output dataset (default is 'MSE').
+        scales: The number of scales to be used in the calculation (default is\
+            5).
+        entwin: The window size used in the calculation (default is 2).
+        rthresh: The radius threshold for determining if values are the same in\
+            the SampleEn calculation, in fractions of the standard deviation\
+            (default is 0.5).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dMseOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MSE_METADATA)
+    params = v_3d_mse_params(
+        polynomial_order=polynomial_order,
+        autoclip=autoclip,
+        automask=automask,
+        mask=mask,
+        prefix=prefix,
+        scales=scales,
+        entwin=entwin,
+        rthresh=rthresh,
+        dset=dset,
+    )
+    return v_3d_mse_execute(params, execution)
+
+
+__all__ = [
+    "V3dMseOutputs",
+    "V3dMseParameters",
+    "V_3D_MSE_METADATA",
+    "v_3d_mse",
+    "v_3d_mse_params",
+]