niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_reg_ana.py

@@ -0,0 +1,377 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_REG_ANA_METADATA = Metadata(
+    id="1631118904756d1061212c150565890bf979dbc0.boutiques",
+    name="3dRegAna",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRegAnaParameters = typing.TypedDict('V3dRegAnaParameters', {
+    "__STYX_TYPE__": typing.Literal["3dRegAna"],
+    "rows": float,
+    "cols": float,
+    "xydata": list[str],
+    "model": str,
+    "diskspace": bool,
+    "workmem": typing.NotRequired[float | None],
+    "rmsmin": typing.NotRequired[float | None],
+    "fdisp": typing.NotRequired[float | None],
+    "flof": typing.NotRequired[float | None],
+    "fcoef": typing.NotRequired[list[str] | None],
+    "rcoef": typing.NotRequired[list[str] | None],
+    "tcoef": typing.NotRequired[list[str] | None],
+    "bucket": typing.NotRequired[str | None],
+    "brick": typing.NotRequired[list[str] | None],
+    "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 {
+        "3dRegAna": v_3d_reg_ana_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 {
+        "3dRegAna": v_3d_reg_ana_outputs,
+    }.get(t)
+
+
+class V3dRegAnaOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_reg_ana(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_fift: OutputPathType
+    """Output fift dataset"""
+    output_fith: OutputPathType
+    """Output fith dataset"""
+    output_fitt: OutputPathType
+    """Output fitt dataset"""
+    output_bucket: OutputPathType
+    """Output bucket dataset"""
+    output_bucket_brik: OutputPathType
+    """Output bucket BRIK file"""
+
+
+def v_3d_reg_ana_params(
+    rows: float,
+    cols: float,
+    xydata: list[str],
+    model: str,
+    diskspace: bool = False,
+    workmem: float | None = None,
+    rmsmin: float | None = None,
+    fdisp: float | None = None,
+    flof: float | None = None,
+    fcoef: list[str] | None = None,
+    rcoef: list[str] | None = None,
+    tcoef: list[str] | None = None,
+    bucket: str | None = None,
+    brick: list[str] | None = None,
+    datum: str | None = None,
+) -> V3dRegAnaParameters:
+    """
+    Build parameters.
+    
+    Args:
+        rows: Number of input datasets.
+        cols: Number of X variables.
+        xydata: X variables and Y observations.
+        model: Definition of linear regression model: reduced model (Y =\
+            f(Xj1,...,Xjr)) and full model (Y = f(Xj1,...,Xjr,Xi1,...,Xiq)).
+        diskspace: Print out disk space required for program execution.
+        workmem: Number of megabytes of RAM to use for statistical workspace\
+            (default = 750).
+        rmsmin: Minimum rms error to reject constant model.
+        fdisp: Display results for voxels whose F-statistic is > fval.
+        flof: Minimum p value for F due to lack of fit.
+        fcoef: Estimate of kth regression coefficient along with F-test for the\
+            regression is written to AFNI `fift` dataset.
+        rcoef: Estimate of kth regression coefficient along with coef. of mult.\
+            deter. R^2 is written to AFNI `fith` dataset.
+        tcoef: Estimate of kth regression coefficient along with t-test for the\
+            coefficient is written to AFNI `fitt` dataset.
+        bucket: Create one AFNI 'bucket' dataset having n sub-bricks; n=0\
+            creates default output.
+        brick: Specify the contents of the mth sub-brick in the bucket dataset.
+        datum: Write the output in DATUM format. Choose from short (default) or\
+            float.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dRegAna",
+        "rows": rows,
+        "cols": cols,
+        "xydata": xydata,
+        "model": model,
+        "diskspace": diskspace,
+    }
+    if workmem is not None:
+        params["workmem"] = workmem
+    if rmsmin is not None:
+        params["rmsmin"] = rmsmin
+    if fdisp is not None:
+        params["fdisp"] = fdisp
+    if flof is not None:
+        params["flof"] = flof
+    if fcoef is not None:
+        params["fcoef"] = fcoef
+    if rcoef is not None:
+        params["rcoef"] = rcoef
+    if tcoef is not None:
+        params["tcoef"] = tcoef
+    if bucket is not None:
+        params["bucket"] = bucket
+    if brick is not None:
+        params["brick"] = brick
+    if datum is not None:
+        params["datum"] = datum
+    return params
+
+
+def v_3d_reg_ana_cargs(
+    params: V3dRegAnaParameters,
+    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("3dRegAna")
+    cargs.extend([
+        "-rows",
+        str(params.get("rows"))
+    ])
+    cargs.extend([
+        "-cols",
+        str(params.get("cols"))
+    ])
+    cargs.extend([
+        "-xydata",
+        *params.get("xydata")
+    ])
+    cargs.extend([
+        "-model",
+        params.get("model")
+    ])
+    if params.get("diskspace"):
+        cargs.append("-diskspace")
+    if params.get("workmem") is not None:
+        cargs.extend([
+            "-workmem",
+            str(params.get("workmem"))
+        ])
+    if params.get("rmsmin") is not None:
+        cargs.extend([
+            "-rmsmin",
+            str(params.get("rmsmin"))
+        ])
+    if params.get("fdisp") is not None:
+        cargs.extend([
+            "-fdisp",
+            str(params.get("fdisp"))
+        ])
+    if params.get("flof") is not None:
+        cargs.extend([
+            "-flof",
+            str(params.get("flof"))
+        ])
+    if params.get("fcoef") is not None:
+        cargs.extend([
+            "-fcoef",
+            *params.get("fcoef")
+        ])
+    if params.get("rcoef") is not None:
+        cargs.extend([
+            "-rcoef",
+            *params.get("rcoef")
+        ])
+    if params.get("tcoef") is not None:
+        cargs.extend([
+            "-tcoef",
+            *params.get("tcoef")
+        ])
+    if params.get("bucket") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("bucket")
+        ])
+    if params.get("brick") is not None:
+        cargs.extend([
+            "-brick",
+            *params.get("brick")
+        ])
+    if params.get("datum") is not None:
+        cargs.extend([
+            "-datum",
+            params.get("datum")
+        ])
+    return cargs
+
+
+def v_3d_reg_ana_outputs(
+    params: V3dRegAnaParameters,
+    execution: Execution,
+) -> V3dRegAnaOutputs:
+    """
+    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 = V3dRegAnaOutputs(
+        root=execution.output_file("."),
+        output_fift=execution.output_file("[PREFIX].fift+orig.HEAD"),
+        output_fith=execution.output_file("[PREFIX].fith+orig.HEAD"),
+        output_fitt=execution.output_file("[PREFIX].fitt+orig.HEAD"),
+        output_bucket=execution.output_file("[PREFIX].bucket+orig.HEAD"),
+        output_bucket_brik=execution.output_file("[PREFIX].bucket+orig.BRIK"),
+    )
+    return ret
+
+
+def v_3d_reg_ana_execute(
+    params: V3dRegAnaParameters,
+    execution: Execution,
+) -> V3dRegAnaOutputs:
+    """
+    Multiple linear regression analysis for AFNI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRegAnaOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_reg_ana_cargs(params, execution)
+    ret = v_3d_reg_ana_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_reg_ana(
+    rows: float,
+    cols: float,
+    xydata: list[str],
+    model: str,
+    diskspace: bool = False,
+    workmem: float | None = None,
+    rmsmin: float | None = None,
+    fdisp: float | None = None,
+    flof: float | None = None,
+    fcoef: list[str] | None = None,
+    rcoef: list[str] | None = None,
+    tcoef: list[str] | None = None,
+    bucket: str | None = None,
+    brick: list[str] | None = None,
+    datum: str | None = None,
+    runner: Runner | None = None,
+) -> V3dRegAnaOutputs:
+    """
+    Multiple linear regression analysis for AFNI datasets.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        rows: Number of input datasets.
+        cols: Number of X variables.
+        xydata: X variables and Y observations.
+        model: Definition of linear regression model: reduced model (Y =\
+            f(Xj1,...,Xjr)) and full model (Y = f(Xj1,...,Xjr,Xi1,...,Xiq)).
+        diskspace: Print out disk space required for program execution.
+        workmem: Number of megabytes of RAM to use for statistical workspace\
+            (default = 750).
+        rmsmin: Minimum rms error to reject constant model.
+        fdisp: Display results for voxels whose F-statistic is > fval.
+        flof: Minimum p value for F due to lack of fit.
+        fcoef: Estimate of kth regression coefficient along with F-test for the\
+            regression is written to AFNI `fift` dataset.
+        rcoef: Estimate of kth regression coefficient along with coef. of mult.\
+            deter. R^2 is written to AFNI `fith` dataset.
+        tcoef: Estimate of kth regression coefficient along with t-test for the\
+            coefficient is written to AFNI `fitt` dataset.
+        bucket: Create one AFNI 'bucket' dataset having n sub-bricks; n=0\
+            creates default output.
+        brick: Specify the contents of the mth sub-brick in the bucket dataset.
+        datum: Write the output in DATUM format. Choose from short (default) or\
+            float.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRegAnaOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_REG_ANA_METADATA)
+    params = v_3d_reg_ana_params(
+        rows=rows,
+        cols=cols,
+        xydata=xydata,
+        model=model,
+        diskspace=diskspace,
+        workmem=workmem,
+        rmsmin=rmsmin,
+        fdisp=fdisp,
+        flof=flof,
+        fcoef=fcoef,
+        rcoef=rcoef,
+        tcoef=tcoef,
+        bucket=bucket,
+        brick=brick,
+        datum=datum,
+    )
+    return v_3d_reg_ana_execute(params, execution)
+
+
+__all__ = [
+    "V3dRegAnaOutputs",
+    "V3dRegAnaParameters",
+    "V_3D_REG_ANA_METADATA",
+    "v_3d_reg_ana",
+    "v_3d_reg_ana_params",
+]

niwrap_afni/afni/v_3d_remlfit.py

@@ -0,0 +1,322 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_REMLFIT_METADATA = Metadata(
+    id="847ea79f5b61b9773e10438597e56d4e78c62c2e.boutiques",
+    name="3dREMLfit",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dRemlfitParameters = typing.TypedDict('V3dRemlfitParameters', {
+    "__STYX_TYPE__": typing.Literal["3dREMLfit"],
+    "input_file": InputPathType,
+    "regression_matrix": InputPathType,
+    "baseline_files": typing.NotRequired[list[str] | None],
+    "sort_nods": bool,
+    "temp_storage": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "go_for_it": bool,
+    "max_b_param": typing.NotRequired[float | None],
+    "grid_param": typing.NotRequired[float | None],
+    "negative_corr": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dREMLfit": v_3d_remlfit_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 {
+        "3dREMLfit": v_3d_remlfit_outputs,
+    }.get(t)
+
+
+class V3dRemlfitOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_remlfit(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """Main default output of 3dREMLfit"""
+    rvar_file: OutputPathType | None
+    """REML variance parameters"""
+    rbeta_file: OutputPathType | None
+    """REML beta weights"""
+    rbuck_file: OutputPathType | None
+    """REML estimates and statistics"""
+    rfitts_file: OutputPathType | None
+    """REML fitted model"""
+    rerrts_file: OutputPathType | None
+    """REML residuals"""
+
+
+def v_3d_remlfit_params(
+    input_file: InputPathType,
+    regression_matrix: InputPathType,
+    baseline_files: list[str] | None = None,
+    sort_nods: bool = False,
+    temp_storage: bool = False,
+    mask: InputPathType | None = None,
+    output_prefix: str | None = None,
+    go_for_it: bool = False,
+    max_b_param: float | None = None,
+    grid_param: float | None = None,
+    negative_corr: bool = False,
+) -> V3dRemlfitParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Read time series dataset.
+        regression_matrix: Read the regression matrix, which should have been\
+            output from 3dDeconvolve via the '-x1D' option.
+        baseline_files: Add baseline model columns to the matrix. Each column\
+            in the specified .1D file will be appended to the matrix.
+        sort_nods: If '-dsort' is used, the output datasets reflect the impact\
+            of the voxel-wise regressor(s). If you want to compare those results to\
+            the case where you did NOT give the '-dsort' option, then also use\
+            '-dsort_nods'.
+        temp_storage: Write intermediate output to disk, to economize on RAM.
+        mask: Read dataset as a mask for the input; voxels outside the mask\
+            will not be fit by the regression model.
+        output_prefix: Dataset prefix for saving REML variance parameters.
+        go_for_it: Force the program to continue past a failed collinearity\
+            check.
+        max_b_param: Set max allowed MA b parameter.
+        grid_param: Set the number of grid divisions in the (a,b) grid.
+        negative_corr: Allows negative correlations to be used.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dREMLfit",
+        "input_file": input_file,
+        "regression_matrix": regression_matrix,
+        "sort_nods": sort_nods,
+        "temp_storage": temp_storage,
+        "go_for_it": go_for_it,
+        "negative_corr": negative_corr,
+    }
+    if baseline_files is not None:
+        params["baseline_files"] = baseline_files
+    if mask is not None:
+        params["mask"] = mask
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if max_b_param is not None:
+        params["max_b_param"] = max_b_param
+    if grid_param is not None:
+        params["grid_param"] = grid_param
+    return params
+
+
+def v_3d_remlfit_cargs(
+    params: V3dRemlfitParameters,
+    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("3dREMLfit")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.extend([
+        "-matrix",
+        execution.input_file(params.get("regression_matrix"))
+    ])
+    if params.get("baseline_files") is not None:
+        cargs.extend([
+            "-addbase",
+            *params.get("baseline_files")
+        ])
+    if params.get("sort_nods"):
+        cargs.append("-dsort_nods")
+    if params.get("temp_storage"):
+        cargs.append("-usetemp")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-Rvar",
+            params.get("output_prefix")
+        ])
+    if params.get("go_for_it"):
+        cargs.append("-GOFORIT")
+    if params.get("max_b_param") is not None:
+        cargs.extend([
+            "-MAXb",
+            str(params.get("max_b_param"))
+        ])
+    if params.get("grid_param") is not None:
+        cargs.extend([
+            "-Grid",
+            str(params.get("grid_param"))
+        ])
+    if params.get("negative_corr"):
+        cargs.append("-NEGcor")
+    return cargs
+
+
+def v_3d_remlfit_outputs(
+    params: V3dRemlfitParameters,
+    execution: Execution,
+) -> V3dRemlfitOutputs:
+    """
+    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 = V3dRemlfitOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("output_prefix") + ".nii.gz") if (params.get("output_prefix") is not None) else None,
+        rvar_file=execution.output_file(params.get("output_prefix") + "_Rvar.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rbeta_file=execution.output_file(params.get("output_prefix") + "_Rbeta.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rbuck_file=execution.output_file(params.get("output_prefix") + "_Rbuck.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rfitts_file=execution.output_file(params.get("output_prefix") + "_Rfitts.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rerrts_file=execution.output_file(params.get("output_prefix") + "_Rerrts.nii.gz") if (params.get("output_prefix") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_remlfit_execute(
+    params: V3dRemlfitParameters,
+    execution: Execution,
+) -> V3dRemlfitOutputs:
+    """
+    Generalized least squares time series fit, with REML estimation of the temporal
+    auto-correlation structure.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dRemlfitOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_remlfit_cargs(params, execution)
+    ret = v_3d_remlfit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_remlfit(
+    input_file: InputPathType,
+    regression_matrix: InputPathType,
+    baseline_files: list[str] | None = None,
+    sort_nods: bool = False,
+    temp_storage: bool = False,
+    mask: InputPathType | None = None,
+    output_prefix: str | None = None,
+    go_for_it: bool = False,
+    max_b_param: float | None = None,
+    grid_param: float | None = None,
+    negative_corr: bool = False,
+    runner: Runner | None = None,
+) -> V3dRemlfitOutputs:
+    """
+    Generalized least squares time series fit, with REML estimation of the temporal
+    auto-correlation structure.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Read time series dataset.
+        regression_matrix: Read the regression matrix, which should have been\
+            output from 3dDeconvolve via the '-x1D' option.
+        baseline_files: Add baseline model columns to the matrix. Each column\
+            in the specified .1D file will be appended to the matrix.
+        sort_nods: If '-dsort' is used, the output datasets reflect the impact\
+            of the voxel-wise regressor(s). If you want to compare those results to\
+            the case where you did NOT give the '-dsort' option, then also use\
+            '-dsort_nods'.
+        temp_storage: Write intermediate output to disk, to economize on RAM.
+        mask: Read dataset as a mask for the input; voxels outside the mask\
+            will not be fit by the regression model.
+        output_prefix: Dataset prefix for saving REML variance parameters.
+        go_for_it: Force the program to continue past a failed collinearity\
+            check.
+        max_b_param: Set max allowed MA b parameter.
+        grid_param: Set the number of grid divisions in the (a,b) grid.
+        negative_corr: Allows negative correlations to be used.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dRemlfitOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_REMLFIT_METADATA)
+    params = v_3d_remlfit_params(
+        input_file=input_file,
+        regression_matrix=regression_matrix,
+        baseline_files=baseline_files,
+        sort_nods=sort_nods,
+        temp_storage=temp_storage,
+        mask=mask,
+        output_prefix=output_prefix,
+        go_for_it=go_for_it,
+        max_b_param=max_b_param,
+        grid_param=grid_param,
+        negative_corr=negative_corr,
+    )
+    return v_3d_remlfit_execute(params, execution)
+
+
+__all__ = [
+    "V3dRemlfitOutputs",
+    "V3dRemlfitParameters",
+    "V_3D_REMLFIT_METADATA",
+    "v_3d_remlfit",
+    "v_3d_remlfit_params",
+]