niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_polyfit.py

@@ -0,0 +1,357 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_POLYFIT_METADATA = Metadata(
+    id="71d806c929428c9ef4f179dbd4ad3511aa5ac59a.boutiques",
+    name="3dPolyfit",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dPolyfitParameters = typing.TypedDict('V3dPolyfitParameters', {
+    "__STYX_TYPE__": typing.Literal["3dPolyfit"],
+    "input_dataset": InputPathType,
+    "poly_order": typing.NotRequired[int | None],
+    "blur": typing.NotRequired[float | None],
+    "median_radius": typing.NotRequired[float | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "resid_prefix": typing.NotRequired[str | None],
+    "coeff_output": typing.NotRequired[str | None],
+    "automask": bool,
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "mean_scale": bool,
+    "clip_box": bool,
+    "fit_method": typing.NotRequired[int | None],
+    "base_dataset": typing.NotRequired[InputPathType | None],
+    "verbose": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dPolyfit": v_3d_polyfit_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 {
+        "3dPolyfit": v_3d_polyfit_outputs,
+    }.get(t)
+
+
+class V3dPolyfitOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_polyfit(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Fitted output dataset"""
+    resid_file: OutputPathType | None
+    """Residual dataset"""
+    coeff_file: OutputPathType | None
+    """Coefficient output file"""
+
+
+def v_3d_polyfit_params(
+    input_dataset: InputPathType,
+    poly_order: int | None = None,
+    blur: float | None = None,
+    median_radius: float | None = None,
+    output_prefix: str | None = None,
+    resid_prefix: str | None = None,
+    coeff_output: str | None = None,
+    automask: bool = False,
+    mask_dataset: InputPathType | None = None,
+    mean_scale: bool = False,
+    clip_box: bool = False,
+    fit_method: int | None = None,
+    base_dataset: InputPathType | None = None,
+    verbose: bool = False,
+) -> V3dPolyfitParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g., data.nii.gz).
+        poly_order: Maximum polynomial order (0..9); [default=3]; [n=0 is the\
+            constant 1]; [n=-1 means only use volumes from '-base'].
+        blur: Gaussian blur input dataset (inside mask) with FWHM='f' (mm).
+        median_radius: Radius (voxels) of preliminary median filter of input;\
+            default is no blurring.
+        output_prefix: Use 'pp' for prefix of output dataset (the fit); default\
+            prefix is 'Polyfit'; use NULL to skip this output.
+        resid_prefix: Use 'rr' for the prefix of the residual dataset; default\
+            is not to output residuals.
+        coeff_output: Save coefficients of fit into text file cc.1D; default is\
+            not to save these coefficients.
+        automask: Create a mask (a la 3dAutomask).
+        mask_dataset: Create a mask from nonzero voxels in 'mset'; default is\
+            not to use a mask.
+        mean_scale: Scale the mean value of the fit (inside the mask) to 1;\
+            probably this option is not useful for anything.
+        clip_box: Clip fit values outside the rectilinear box containing the\
+            mask to the edge of that box, to avoid weird artifacts.
+        fit_method: Set 'mm' to 2 for least squares fit; set it to 1 for L1 fit\
+            [default method=2]; [Note that L1 fitting is slower than L2 fitting].
+        base_dataset: In addition to the polynomial fit, also use the volumes\
+            in dataset 'bb' as extra basis functions.
+        verbose: Print fun and useful progress reports.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dPolyfit",
+        "input_dataset": input_dataset,
+        "automask": automask,
+        "mean_scale": mean_scale,
+        "clip_box": clip_box,
+        "verbose": verbose,
+    }
+    if poly_order is not None:
+        params["poly_order"] = poly_order
+    if blur is not None:
+        params["blur"] = blur
+    if median_radius is not None:
+        params["median_radius"] = median_radius
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if resid_prefix is not None:
+        params["resid_prefix"] = resid_prefix
+    if coeff_output is not None:
+        params["coeff_output"] = coeff_output
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if fit_method is not None:
+        params["fit_method"] = fit_method
+    if base_dataset is not None:
+        params["base_dataset"] = base_dataset
+    return params
+
+
+def v_3d_polyfit_cargs(
+    params: V3dPolyfitParameters,
+    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("3dPolyfit")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("poly_order") is not None:
+        cargs.extend([
+            "-nord",
+            str(params.get("poly_order"))
+        ])
+    if params.get("blur") is not None:
+        cargs.extend([
+            "-blur",
+            str(params.get("blur"))
+        ])
+    if params.get("median_radius") is not None:
+        cargs.extend([
+            "-mrad",
+            str(params.get("median_radius"))
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("resid_prefix") is not None:
+        cargs.extend([
+            "-resid",
+            params.get("resid_prefix")
+        ])
+    if params.get("coeff_output") is not None:
+        cargs.extend([
+            "-1Dcoef",
+            params.get("coeff_output")
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    if params.get("mean_scale"):
+        cargs.append("-mone")
+    if params.get("clip_box"):
+        cargs.append("-mclip")
+    if params.get("fit_method") is not None:
+        cargs.extend([
+            "-meth",
+            str(params.get("fit_method"))
+        ])
+    if params.get("base_dataset") is not None:
+        cargs.extend([
+            "-base",
+            execution.input_file(params.get("base_dataset"))
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
+    return cargs
+
+
+def v_3d_polyfit_outputs(
+    params: V3dPolyfitParameters,
+    execution: Execution,
+) -> V3dPolyfitOutputs:
+    """
+    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 = V3dPolyfitOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("output_prefix") + ".nii.gz") if (params.get("output_prefix") is not None) else None,
+        resid_file=execution.output_file(params.get("resid_prefix") + ".nii.gz") if (params.get("resid_prefix") is not None) else None,
+        coeff_file=execution.output_file(params.get("coeff_output") + ".1D") if (params.get("coeff_output") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_polyfit_execute(
+    params: V3dPolyfitParameters,
+    execution: Execution,
+) -> V3dPolyfitOutputs:
+    """
+    Fits a polynomial in space to the input dataset and outputs that fitted dataset.
+    You can also add your own basis datasets to the fitting mix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dPolyfitOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_polyfit_cargs(params, execution)
+    ret = v_3d_polyfit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_polyfit(
+    input_dataset: InputPathType,
+    poly_order: int | None = None,
+    blur: float | None = None,
+    median_radius: float | None = None,
+    output_prefix: str | None = None,
+    resid_prefix: str | None = None,
+    coeff_output: str | None = None,
+    automask: bool = False,
+    mask_dataset: InputPathType | None = None,
+    mean_scale: bool = False,
+    clip_box: bool = False,
+    fit_method: int | None = None,
+    base_dataset: InputPathType | None = None,
+    verbose: bool = False,
+    runner: Runner | None = None,
+) -> V3dPolyfitOutputs:
+    """
+    Fits a polynomial in space to the input dataset and outputs that fitted dataset.
+    You can also add your own basis datasets to the fitting mix.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g., data.nii.gz).
+        poly_order: Maximum polynomial order (0..9); [default=3]; [n=0 is the\
+            constant 1]; [n=-1 means only use volumes from '-base'].
+        blur: Gaussian blur input dataset (inside mask) with FWHM='f' (mm).
+        median_radius: Radius (voxels) of preliminary median filter of input;\
+            default is no blurring.
+        output_prefix: Use 'pp' for prefix of output dataset (the fit); default\
+            prefix is 'Polyfit'; use NULL to skip this output.
+        resid_prefix: Use 'rr' for the prefix of the residual dataset; default\
+            is not to output residuals.
+        coeff_output: Save coefficients of fit into text file cc.1D; default is\
+            not to save these coefficients.
+        automask: Create a mask (a la 3dAutomask).
+        mask_dataset: Create a mask from nonzero voxels in 'mset'; default is\
+            not to use a mask.
+        mean_scale: Scale the mean value of the fit (inside the mask) to 1;\
+            probably this option is not useful for anything.
+        clip_box: Clip fit values outside the rectilinear box containing the\
+            mask to the edge of that box, to avoid weird artifacts.
+        fit_method: Set 'mm' to 2 for least squares fit; set it to 1 for L1 fit\
+            [default method=2]; [Note that L1 fitting is slower than L2 fitting].
+        base_dataset: In addition to the polynomial fit, also use the volumes\
+            in dataset 'bb' as extra basis functions.
+        verbose: Print fun and useful progress reports.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dPolyfitOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_POLYFIT_METADATA)
+    params = v_3d_polyfit_params(
+        input_dataset=input_dataset,
+        poly_order=poly_order,
+        blur=blur,
+        median_radius=median_radius,
+        output_prefix=output_prefix,
+        resid_prefix=resid_prefix,
+        coeff_output=coeff_output,
+        automask=automask,
+        mask_dataset=mask_dataset,
+        mean_scale=mean_scale,
+        clip_box=clip_box,
+        fit_method=fit_method,
+        base_dataset=base_dataset,
+        verbose=verbose,
+    )
+    return v_3d_polyfit_execute(params, execution)
+
+
+__all__ = [
+    "V3dPolyfitOutputs",
+    "V3dPolyfitParameters",
+    "V_3D_POLYFIT_METADATA",
+    "v_3d_polyfit",
+    "v_3d_polyfit_params",
+]

niwrap_afni/afni/v_3d_pval.py

@@ -0,0 +1,232 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_PVAL_METADATA = Metadata(
+    id="728ce13fea332a59b9d1741e5383247954eba774.boutiques",
+    name="3dPval",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dPvalParameters = typing.TypedDict('V3dPvalParameters', {
+    "__STYX_TYPE__": typing.Literal["3dPval"],
+    "input_dataset": InputPathType,
+    "zscore": bool,
+    "log2": bool,
+    "log10": bool,
+    "qval": bool,
+    "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 {
+        "3dPval": v_3d_pval_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 {
+        "3dPval": v_3d_pval_outputs,
+    }.get(t)
+
+
+class V3dPvalOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_pval(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output dataset with converted statistical values. Default output filename
+    is 'Pval.nii.gz'."""
+
+
+def v_3d_pval_params(
+    input_dataset: InputPathType,
+    zscore: bool = False,
+    log2: bool = False,
+    log10: bool = False,
+    qval: bool = False,
+    prefix: str | None = None,
+) -> V3dPvalParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Input dataset (e.g., InputDataset.nii).
+        zscore: Convert statistic to a z-score instead, an N(0,1) deviate that\
+            represents the same p-value.
+        log2: Convert statistic to -log2(p).
+        log10: Convert statistic to -log10(p).
+        qval: Convert statistic to a q-value (FDR) instead. This option only\
+            works with datasets that have FDR curves inserted in their headers.
+        prefix: Prefix name for output file (default name is 'Pval').
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dPval",
+        "input_dataset": input_dataset,
+        "zscore": zscore,
+        "log2": log2,
+        "log10": log10,
+        "qval": qval,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    return params
+
+
+def v_3d_pval_cargs(
+    params: V3dPvalParameters,
+    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("3dPval")
+    cargs.append(execution.input_file(params.get("input_dataset")))
+    if params.get("zscore"):
+        cargs.append("-zscore")
+    if params.get("log2"):
+        cargs.append("-log2")
+    if params.get("log10"):
+        cargs.append("-log10")
+    if params.get("qval"):
+        cargs.append("-qval")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    return cargs
+
+
+def v_3d_pval_outputs(
+    params: V3dPvalParameters,
+    execution: Execution,
+) -> V3dPvalOutputs:
+    """
+    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 = V3dPvalOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_pval_execute(
+    params: V3dPvalParameters,
+    execution: Execution,
+) -> V3dPvalOutputs:
+    """
+    Convert a dataset's statistical sub-bricks to p-values or other statistical
+    representations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dPvalOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_pval_cargs(params, execution)
+    ret = v_3d_pval_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_pval(
+    input_dataset: InputPathType,
+    zscore: bool = False,
+    log2: bool = False,
+    log10: bool = False,
+    qval: bool = False,
+    prefix: str | None = None,
+    runner: Runner | None = None,
+) -> V3dPvalOutputs:
+    """
+    Convert a dataset's statistical sub-bricks to p-values or other statistical
+    representations.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Input dataset (e.g., InputDataset.nii).
+        zscore: Convert statistic to a z-score instead, an N(0,1) deviate that\
+            represents the same p-value.
+        log2: Convert statistic to -log2(p).
+        log10: Convert statistic to -log10(p).
+        qval: Convert statistic to a q-value (FDR) instead. This option only\
+            works with datasets that have FDR curves inserted in their headers.
+        prefix: Prefix name for output file (default name is 'Pval').
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dPvalOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_PVAL_METADATA)
+    params = v_3d_pval_params(
+        input_dataset=input_dataset,
+        zscore=zscore,
+        log2=log2,
+        log10=log10,
+        qval=qval,
+        prefix=prefix,
+    )
+    return v_3d_pval_execute(params, execution)
+
+
+__all__ = [
+    "V3dPvalOutputs",
+    "V3dPvalParameters",
+    "V_3D_PVAL_METADATA",
+    "v_3d_pval",
+    "v_3d_pval_params",
+]