niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_net_corr.py

@@ -0,0 +1,398 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NET_CORR_METADATA = Metadata(
+    id="958c7038de682b846c408cbd34ee6146fe058e26.boutiques",
+    name="3dNetCorr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNetCorrParameters = typing.TypedDict('V3dNetCorrParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNetCorr"],
+    "prefix": str,
+    "inset": InputPathType,
+    "in_rois": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "fish_z": bool,
+    "part_corr": bool,
+    "ts_out": bool,
+    "ts_label": bool,
+    "ts_indiv": bool,
+    "ts_wb_corr": bool,
+    "ts_wb_Z": bool,
+    "weight_ts": typing.NotRequired[InputPathType | None],
+    "weight_corr": typing.NotRequired[InputPathType | None],
+    "ts_wb_strlabel": bool,
+    "nifti": bool,
+    "output_mask_nonnull": bool,
+    "push_thru_many_zeros": bool,
+    "allow_roi_zeros": bool,
+    "automask_off": bool,
+    "ignore_LT": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNetCorr": v_3d_net_corr_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 {
+        "3dNetCorr": v_3d_net_corr_outputs,
+    }.get(t)
+
+
+class V3dNetCorrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_net_corr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_netcc: OutputPathType
+    """Output correlation matrix file for network 000"""
+    output_netts: OutputPathType
+    """Output mean time series per ROI for network 000"""
+    output_niml: OutputPathType
+    """NIML/SUMA-esque file for visualizing connectivity info in a 3D brain for
+    network 000"""
+    output_roidat: OutputPathType
+    """Columns contain information for each ROI in the used mask."""
+    output_mask_nnull: OutputPathType
+    """Mask of non-null time series"""
+    output_indiv: OutputPathType
+    """Directory containing individual time series files for network 000"""
+    output_binary_mask_nnull: OutputPathType
+    """Binary mask of the non-null time series"""
+
+
+def v_3d_net_corr_params(
+    prefix: str,
+    inset: InputPathType,
+    in_rois: InputPathType,
+    mask: InputPathType | None = None,
+    fish_z: bool = False,
+    part_corr: bool = False,
+    ts_out: bool = False,
+    ts_label: bool = False,
+    ts_indiv: bool = False,
+    ts_wb_corr: bool = False,
+    ts_wb_z: bool = False,
+    weight_ts: InputPathType | None = None,
+    weight_corr: InputPathType | None = None,
+    ts_wb_strlabel: bool = False,
+    nifti: bool = False,
+    output_mask_nonnull: bool = False,
+    push_thru_many_zeros: bool = False,
+    allow_roi_zeros: bool = False,
+    automask_off: bool = False,
+    ignore_lt: bool = False,
+) -> V3dNetCorrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        prefix: Output file name prefix.
+        inset: Time series file (4D data set).
+        in_rois: Input a set of ROIs each labelled with distinct integers.\
+            Multiple subbricks can be input, each will be treated as a separate\
+            network.
+        mask: Whole brain mask within which to calculate correlation.
+        fish_z: Output Fisher Z-transform matrix along with correlation matrix.
+        part_corr: Output the partial correlation matrix.
+        ts_out: Output the mean time series of the ROIs.
+        ts_label: Insert the integer ROI label at the start of each line of the\
+            *.netts file created.
+        ts_indiv: Create a directory for each network that contains the average\
+            time series for each ROI in individual files.
+        ts_wb_corr: Perform whole brain correlation for each ROI's average time\
+            series and output as Pearson 'r' values.
+        ts_wb_z: Perform whole brain correlation for each ROI's average time\
+            series and output as Fisher transformed Z-scores.
+        weight_ts: Input a 1D file of weights to be applied multiplicatively to\
+            each ROI's average time series.
+        weight_corr: Input a 1D file of weights to estimate a weighted Pearson\
+            Correlation.
+        ts_wb_strlabel: Apply string labels to the WB correlation/Z-score\
+            output files.
+        nifti: Output any correlation map files as NIFTI files.
+        output_mask_nonnull: Output mask of non-null time series.
+        push_thru_many_zeros: Push through the calculation even if any ROI\
+            contains more than 10 percent of voxels with null time series.
+        allow_roi_zeros: Allow ROIs to have all-zero time series.
+        automask_off: Disable internal automasking of where time series are not\
+            uniformly zero.
+        ignore_lt: Ignore any label table labels in the '-in_rois' file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNetCorr",
+        "prefix": prefix,
+        "inset": inset,
+        "in_rois": in_rois,
+        "fish_z": fish_z,
+        "part_corr": part_corr,
+        "ts_out": ts_out,
+        "ts_label": ts_label,
+        "ts_indiv": ts_indiv,
+        "ts_wb_corr": ts_wb_corr,
+        "ts_wb_Z": ts_wb_z,
+        "ts_wb_strlabel": ts_wb_strlabel,
+        "nifti": nifti,
+        "output_mask_nonnull": output_mask_nonnull,
+        "push_thru_many_zeros": push_thru_many_zeros,
+        "allow_roi_zeros": allow_roi_zeros,
+        "automask_off": automask_off,
+        "ignore_LT": ignore_lt,
+    }
+    if mask is not None:
+        params["mask"] = mask
+    if weight_ts is not None:
+        params["weight_ts"] = weight_ts
+    if weight_corr is not None:
+        params["weight_corr"] = weight_corr
+    return params
+
+
+def v_3d_net_corr_cargs(
+    params: V3dNetCorrParameters,
+    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("3dNetCorr")
+    cargs.append(params.get("prefix"))
+    cargs.append(execution.input_file(params.get("inset")))
+    cargs.append(execution.input_file(params.get("in_rois")))
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("fish_z"):
+        cargs.append("-fish_z")
+    if params.get("part_corr"):
+        cargs.append("-part_corr")
+    if params.get("ts_out"):
+        cargs.append("-ts_out")
+    if params.get("ts_label"):
+        cargs.append("-ts_label")
+    if params.get("ts_indiv"):
+        cargs.append("-ts_indiv")
+    if params.get("ts_wb_corr"):
+        cargs.append("-ts_wb_corr")
+    if params.get("ts_wb_Z"):
+        cargs.append("-ts_wb_Z")
+    if params.get("weight_ts") is not None:
+        cargs.extend([
+            "-weight_ts",
+            execution.input_file(params.get("weight_ts"))
+        ])
+    if params.get("weight_corr") is not None:
+        cargs.extend([
+            "-weight_corr",
+            execution.input_file(params.get("weight_corr"))
+        ])
+    if params.get("ts_wb_strlabel"):
+        cargs.append("-ts_wb_strlabel")
+    if params.get("nifti"):
+        cargs.append("-nifti")
+    if params.get("output_mask_nonnull"):
+        cargs.append("-output_mask_nonnull")
+    if params.get("push_thru_many_zeros"):
+        cargs.append("-push_thru_many_zeros")
+    if params.get("allow_roi_zeros"):
+        cargs.append("-allow_roi_zeros")
+    if params.get("automask_off"):
+        cargs.append("-automask_off")
+    if params.get("ignore_LT"):
+        cargs.append("-ignore_LT")
+    return cargs
+
+
+def v_3d_net_corr_outputs(
+    params: V3dNetCorrParameters,
+    execution: Execution,
+) -> V3dNetCorrOutputs:
+    """
+    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 = V3dNetCorrOutputs(
+        root=execution.output_file("."),
+        output_netcc=execution.output_file(params.get("prefix") + "_000.netcc"),
+        output_netts=execution.output_file(params.get("prefix") + "_000.netts"),
+        output_niml=execution.output_file(params.get("prefix") + "_000.niml.dset"),
+        output_roidat=execution.output_file(params.get("prefix") + ".roidat"),
+        output_mask_nnull=execution.output_file(params.get("prefix") + "_mask_nnull"),
+        output_indiv=execution.output_file(params.get("prefix") + "_000_INDIV"),
+        output_binary_mask_nnull=execution.output_file("PREFIX_mask_nnull"),
+    )
+    return ret
+
+
+def v_3d_net_corr_execute(
+    params: V3dNetCorrParameters,
+    execution: Execution,
+) -> V3dNetCorrOutputs:
+    """
+    Compute correlation matrix of a set of ROIs based on mean time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNetCorrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_net_corr_cargs(params, execution)
+    ret = v_3d_net_corr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_net_corr(
+    prefix: str,
+    inset: InputPathType,
+    in_rois: InputPathType,
+    mask: InputPathType | None = None,
+    fish_z: bool = False,
+    part_corr: bool = False,
+    ts_out: bool = False,
+    ts_label: bool = False,
+    ts_indiv: bool = False,
+    ts_wb_corr: bool = False,
+    ts_wb_z: bool = False,
+    weight_ts: InputPathType | None = None,
+    weight_corr: InputPathType | None = None,
+    ts_wb_strlabel: bool = False,
+    nifti: bool = False,
+    output_mask_nonnull: bool = False,
+    push_thru_many_zeros: bool = False,
+    allow_roi_zeros: bool = False,
+    automask_off: bool = False,
+    ignore_lt: bool = False,
+    runner: Runner | None = None,
+) -> V3dNetCorrOutputs:
+    """
+    Compute correlation matrix of a set of ROIs based on mean time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        prefix: Output file name prefix.
+        inset: Time series file (4D data set).
+        in_rois: Input a set of ROIs each labelled with distinct integers.\
+            Multiple subbricks can be input, each will be treated as a separate\
+            network.
+        mask: Whole brain mask within which to calculate correlation.
+        fish_z: Output Fisher Z-transform matrix along with correlation matrix.
+        part_corr: Output the partial correlation matrix.
+        ts_out: Output the mean time series of the ROIs.
+        ts_label: Insert the integer ROI label at the start of each line of the\
+            *.netts file created.
+        ts_indiv: Create a directory for each network that contains the average\
+            time series for each ROI in individual files.
+        ts_wb_corr: Perform whole brain correlation for each ROI's average time\
+            series and output as Pearson 'r' values.
+        ts_wb_z: Perform whole brain correlation for each ROI's average time\
+            series and output as Fisher transformed Z-scores.
+        weight_ts: Input a 1D file of weights to be applied multiplicatively to\
+            each ROI's average time series.
+        weight_corr: Input a 1D file of weights to estimate a weighted Pearson\
+            Correlation.
+        ts_wb_strlabel: Apply string labels to the WB correlation/Z-score\
+            output files.
+        nifti: Output any correlation map files as NIFTI files.
+        output_mask_nonnull: Output mask of non-null time series.
+        push_thru_many_zeros: Push through the calculation even if any ROI\
+            contains more than 10 percent of voxels with null time series.
+        allow_roi_zeros: Allow ROIs to have all-zero time series.
+        automask_off: Disable internal automasking of where time series are not\
+            uniformly zero.
+        ignore_lt: Ignore any label table labels in the '-in_rois' file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNetCorrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NET_CORR_METADATA)
+    params = v_3d_net_corr_params(
+        prefix=prefix,
+        inset=inset,
+        in_rois=in_rois,
+        mask=mask,
+        fish_z=fish_z,
+        part_corr=part_corr,
+        ts_out=ts_out,
+        ts_label=ts_label,
+        ts_indiv=ts_indiv,
+        ts_wb_corr=ts_wb_corr,
+        ts_wb_z=ts_wb_z,
+        weight_ts=weight_ts,
+        weight_corr=weight_corr,
+        ts_wb_strlabel=ts_wb_strlabel,
+        nifti=nifti,
+        output_mask_nonnull=output_mask_nonnull,
+        push_thru_many_zeros=push_thru_many_zeros,
+        allow_roi_zeros=allow_roi_zeros,
+        automask_off=automask_off,
+        ignore_lt=ignore_lt,
+    )
+    return v_3d_net_corr_execute(params, execution)
+
+
+__all__ = [
+    "V3dNetCorrOutputs",
+    "V3dNetCorrParameters",
+    "V_3D_NET_CORR_METADATA",
+    "v_3d_net_corr",
+    "v_3d_net_corr_params",
+]

niwrap_afni/afni/v_3d_nlfim.py

@@ -0,0 +1,241 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_NLFIM_METADATA = Metadata(
+    id="b2553c2bf57346747079630757e1d16620ea8119.boutiques",
+    name="3dNLfim",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dNlfimParameters = typing.TypedDict('V3dNlfimParameters', {
+    "__STYX_TYPE__": typing.Literal["3dNLfim"],
+    "input_file": InputPathType,
+    "signal_model": str,
+    "noise_model": str,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dNLfim": v_3d_nlfim_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 {
+        "3dNLfim": v_3d_nlfim_outputs,
+    }.get(t)
+
+
+class V3dNlfimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_nlfim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    freg_outfile: OutputPathType
+    """F-test for significance of the regression"""
+    frsqr_outfile: OutputPathType
+    """R^2 calculation for regression"""
+    fsmax_outfile: OutputPathType
+    """Signed maximum signal estimate"""
+    ftmax_outfile: OutputPathType
+    """Time of signed maximum estimate"""
+    fpsmax_outfile: OutputPathType
+    """Maximum percentage change estimate"""
+    farea_outfile: OutputPathType
+    """Area between signal and baseline"""
+    fparea_outfile: OutputPathType
+    """Percentage area of signal estimate"""
+    fscoef_outfile: OutputPathType
+    """Signal parameter estimate"""
+    fncoef_outfile: OutputPathType
+    """Noise parameter estimate"""
+    tscoef_outfile: OutputPathType
+    """T-test for significance of signal parameter"""
+    tncoef_outfile: OutputPathType
+    """T-test for significance of noise parameter"""
+    bucket_outfile: OutputPathType
+    """AFNI 'bucket' dataset"""
+    sfit_outfile: OutputPathType
+    """Output 3d+time signal model fit"""
+    snfit_outfile: OutputPathType
+    """Output 3d+time signal+noise fit"""
+
+
+def v_3d_nlfim_params(
+    input_file: InputPathType,
+    signal_model: str,
+    noise_model: str,
+) -> V3dNlfimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Filename of 3d+time data file for input.
+        signal_model: Name of the nonlinear signal model.
+        noise_model: Name of the linear noise model.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dNLfim",
+        "input_file": input_file,
+        "signal_model": signal_model,
+        "noise_model": noise_model,
+    }
+    return params
+
+
+def v_3d_nlfim_cargs(
+    params: V3dNlfimParameters,
+    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("3dNLfim")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-signal",
+        params.get("signal_model")
+    ])
+    cargs.extend([
+        "-noise",
+        params.get("noise_model")
+    ])
+    cargs.append("[ADDITIONAL_OPTIONS]")
+    return cargs
+
+
+def v_3d_nlfim_outputs(
+    params: V3dNlfimParameters,
+    execution: Execution,
+) -> V3dNlfimOutputs:
+    """
+    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 = V3dNlfimOutputs(
+        root=execution.output_file("."),
+        freg_outfile=execution.output_file("[FREG].fift"),
+        frsqr_outfile=execution.output_file("[FRSQR].fift"),
+        fsmax_outfile=execution.output_file("[FSMAX].fift"),
+        ftmax_outfile=execution.output_file("[FTMAX].fift"),
+        fpsmax_outfile=execution.output_file("[FPSMAX].fift"),
+        farea_outfile=execution.output_file("[FAREA].fift"),
+        fparea_outfile=execution.output_file("[FPAREA].fift"),
+        fscoef_outfile=execution.output_file("[FSCOEF].fift"),
+        fncoef_outfile=execution.output_file("[FNCOEF].fift"),
+        tscoef_outfile=execution.output_file("[TSCOEF].fitt"),
+        tncoef_outfile=execution.output_file("[TNCOEF].fitt"),
+        bucket_outfile=execution.output_file("[BUCKET].bucket"),
+        sfit_outfile=execution.output_file("[SFIT].sfit"),
+        snfit_outfile=execution.output_file("[SNFIT].snfit"),
+    )
+    return ret
+
+
+def v_3d_nlfim_execute(
+    params: V3dNlfimParameters,
+    execution: Execution,
+) -> V3dNlfimOutputs:
+    """
+    Nonlinear regression for each voxel of the input AFNI 3d+time data set.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dNlfimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_nlfim_cargs(params, execution)
+    ret = v_3d_nlfim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_nlfim(
+    input_file: InputPathType,
+    signal_model: str,
+    noise_model: str,
+    runner: Runner | None = None,
+) -> V3dNlfimOutputs:
+    """
+    Nonlinear regression for each voxel of the input AFNI 3d+time data set.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Filename of 3d+time data file for input.
+        signal_model: Name of the nonlinear signal model.
+        noise_model: Name of the linear noise model.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dNlfimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_NLFIM_METADATA)
+    params = v_3d_nlfim_params(
+        input_file=input_file,
+        signal_model=signal_model,
+        noise_model=noise_model,
+    )
+    return v_3d_nlfim_execute(params, execution)
+
+
+__all__ = [
+    "V3dNlfimOutputs",
+    "V3dNlfimParameters",
+    "V_3D_NLFIM_METADATA",
+    "v_3d_nlfim",
+    "v_3d_nlfim_params",
+]