niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_cruiseto_afni.py

@@ -0,0 +1,264 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_CRUISETO_AFNI_METADATA = Metadata(
+    id="4b72eb1971f7fa8dc1755dacfa39929795432071.boutiques",
+    name="3dCRUISEtoAFNI",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dCruisetoAfniParameters = typing.TypedDict('V3dCruisetoAfniParameters', {
+    "__STYX_TYPE__": typing.Literal["3dCRUISEtoAFNI"],
+    "input": InputPathType,
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "TRACE": bool,
+    "TRACE_1": bool,
+    "nomall": bool,
+    "yesmall": bool,
+    "help": bool,
+    "h": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dCRUISEtoAFNI": v_3d_cruiseto_afni_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 {
+    }.get(t)
+
+
+class V3dCruisetoAfniOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_cruiseto_afni(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_cruiseto_afni_params(
+    input_: InputPathType,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    trace_1: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+    help_: bool = False,
+    h: bool = False,
+) -> V3dCruisetoAfniParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_: Input CRUISE header file in OpenDX format.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable ENVname to be ENVvalue. Quotes are\
+            necessary. Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'".
+        trace_: Turns on extreme tracing.
+        trace_1: Turns on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+        help_: The entire help output.
+        h: Displays mini help; in many cases, it's the same as -help.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dCRUISEtoAFNI",
+        "input": input_,
+        "novolreg": novolreg,
+        "noxform": noxform,
+        "TRACE": trace_,
+        "TRACE_1": trace_1,
+        "nomall": nomall,
+        "yesmall": yesmall,
+        "help": help_,
+        "h": h,
+    }
+    if setenv is not None:
+        params["setenv"] = setenv
+    return params
+
+
+def v_3d_cruiseto_afni_cargs(
+    params: V3dCruisetoAfniParameters,
+    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("3dCRUISEtoAFNI")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input"))
+    ])
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("noxform"):
+        cargs.append("-noxform")
+    if params.get("setenv") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("setenv")
+        ])
+    if params.get("TRACE"):
+        cargs.append("-TRACE")
+    if params.get("TRACE_1"):
+        cargs.append("-TRACE")
+    if params.get("nomall"):
+        cargs.append("-nomall")
+    if params.get("yesmall"):
+        cargs.append("-yesmall")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("h"):
+        cargs.append("-h")
+    return cargs
+
+
+def v_3d_cruiseto_afni_outputs(
+    params: V3dCruisetoAfniParameters,
+    execution: Execution,
+) -> V3dCruisetoAfniOutputs:
+    """
+    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 = V3dCruisetoAfniOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_cruiseto_afni_execute(
+    params: V3dCruisetoAfniParameters,
+    execution: Execution,
+) -> V3dCruisetoAfniOutputs:
+    """
+    Converts a CRUISE dataset defined by a header in OpenDX format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dCruisetoAfniOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_cruiseto_afni_cargs(params, execution)
+    ret = v_3d_cruiseto_afni_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_cruiseto_afni(
+    input_: InputPathType,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    trace_1: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+    help_: bool = False,
+    h: bool = False,
+    runner: Runner | None = None,
+) -> V3dCruisetoAfniOutputs:
+    """
+    Converts a CRUISE dataset defined by a header in OpenDX format.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_: Input CRUISE header file in OpenDX format.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable ENVname to be ENVvalue. Quotes are\
+            necessary. Example: suma -setenv "'SUMA_BackgroundColor = 1 0 1'".
+        trace_: Turns on extreme tracing.
+        trace_1: Turns on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+        help_: The entire help output.
+        h: Displays mini help; in many cases, it's the same as -help.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dCruisetoAfniOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_CRUISETO_AFNI_METADATA)
+    params = v_3d_cruiseto_afni_params(
+        input_=input_,
+        novolreg=novolreg,
+        noxform=noxform,
+        setenv=setenv,
+        trace_=trace_,
+        trace_1=trace_1,
+        nomall=nomall,
+        yesmall=yesmall,
+        help_=help_,
+        h=h,
+    )
+    return v_3d_cruiseto_afni_execute(params, execution)
+
+
+__all__ = [
+    "V3dCruisetoAfniOutputs",
+    "V3dCruisetoAfniParameters",
+    "V_3D_CRUISETO_AFNI_METADATA",
+    "v_3d_cruiseto_afni",
+    "v_3d_cruiseto_afni_params",
+]

niwrap_afni/afni/v_3d_deconvolve.py

@@ -0,0 +1,371 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_DECONVOLVE_METADATA = Metadata(
+    id="3c5bd8bab8c9c3f4b4586c2e6fc553ef1b03f1e4.boutiques",
+    name="3dDeconvolve",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dDeconvolveParameters = typing.TypedDict('V3dDeconvolveParameters', {
+    "__STYX_TYPE__": typing.Literal["3dDeconvolve"],
+    "input_dataset": InputPathType,
+    "mask_dataset": typing.NotRequired[InputPathType | None],
+    "num_stimts": typing.NotRequired[int | None],
+    "stim_file": typing.NotRequired[str | None],
+    "stim_label": typing.NotRequired[str | None],
+    "stim_base": bool,
+    "stim_times": typing.NotRequired[str | None],
+    "iresp": typing.NotRequired[str | None],
+    "fitts": typing.NotRequired[str | None],
+    "fout": bool,
+    "tout": bool,
+    "bucket": typing.NotRequired[str | None],
+    "cbucket": typing.NotRequired[str | None],
+    "x1D": typing.NotRequired[str | None],
+    "jobs": 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 {
+        "3dDeconvolve": v_3d_deconvolve_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 {
+        "3dDeconvolve": v_3d_deconvolve_outputs,
+    }.get(t)
+
+
+class V3dDeconvolveOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_deconvolve(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    bucket_output: OutputPathType | None
+    """Main output bucket dataset in AFNI format."""
+    cbucket_output: OutputPathType | None
+    """Regression coefficients stored in a dataset."""
+    iresp_output: OutputPathType | None
+    """Estimated Impulse Response dataset."""
+    fitts_output: OutputPathType | None
+    """Fitted Time Series dataset in AFNI format."""
+    x1d_file: OutputPathType | None
+    """X-matrix output file in .1D format."""
+
+
+def v_3d_deconvolve_params(
+    input_dataset: InputPathType,
+    mask_dataset: InputPathType | None = None,
+    num_stimts: int | None = None,
+    stim_file: str | None = None,
+    stim_label: str | None = None,
+    stim_base: bool = False,
+    stim_times: str | None = None,
+    iresp: str | None = None,
+    fitts: str | None = None,
+    fout: bool = False,
+    tout: bool = False,
+    bucket: str | None = None,
+    cbucket: str | None = None,
+    x1_d: str | None = None,
+    jobs: int | None = None,
+) -> V3dDeconvolveParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dataset: Filename of 3D+time input dataset.
+        mask_dataset: Filename of 3D mask dataset.
+        num_stimts: Number of input stimulus time series.
+        stim_file: Filename of kth time series input stimulus.
+        stim_label: Label for kth input stimulus.
+        stim_base: Kth input stimulus is part of the baseline model.
+        stim_times: Deconvolution response model for kth stimulus.
+        iresp: Prefix for 3D+time output dataset which will contain the kth\
+            estimated impulse response.
+        fitts: Prefix for 3D+time output dataset which will contain the (full\
+            model) time series fit to the input data.
+        fout: Flag to output the F-statistics for each stimulus.
+        tout: Flag to output the t-statistics.
+        bucket: Create one AFNI 'bucket' dataset containing various parameters\
+            of interest.
+        cbucket: Save the regression coefficients (no statistics) into a\
+            dataset.
+        x1_d: Save X matrix to a .xmat.1D (ASCII) file.
+        jobs: Run the program with multiple jobs (sub-processes).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dDeconvolve",
+        "input_dataset": input_dataset,
+        "stim_base": stim_base,
+        "fout": fout,
+        "tout": tout,
+    }
+    if mask_dataset is not None:
+        params["mask_dataset"] = mask_dataset
+    if num_stimts is not None:
+        params["num_stimts"] = num_stimts
+    if stim_file is not None:
+        params["stim_file"] = stim_file
+    if stim_label is not None:
+        params["stim_label"] = stim_label
+    if stim_times is not None:
+        params["stim_times"] = stim_times
+    if iresp is not None:
+        params["iresp"] = iresp
+    if fitts is not None:
+        params["fitts"] = fitts
+    if bucket is not None:
+        params["bucket"] = bucket
+    if cbucket is not None:
+        params["cbucket"] = cbucket
+    if x1_d is not None:
+        params["x1D"] = x1_d
+    if jobs is not None:
+        params["jobs"] = jobs
+    return params
+
+
+def v_3d_deconvolve_cargs(
+    params: V3dDeconvolveParameters,
+    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("3dDeconvolve")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_dataset"))
+    ])
+    if params.get("mask_dataset") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask_dataset"))
+        ])
+    if params.get("num_stimts") is not None:
+        cargs.extend([
+            "-num_stimts",
+            str(params.get("num_stimts"))
+        ])
+    if params.get("stim_file") is not None:
+        cargs.extend([
+            "-stim_file",
+            params.get("stim_file")
+        ])
+    if params.get("stim_label") is not None:
+        cargs.extend([
+            "-stim_label",
+            params.get("stim_label")
+        ])
+    if params.get("stim_base"):
+        cargs.append("-stim_base")
+    if params.get("stim_times") is not None:
+        cargs.extend([
+            "-stim_times",
+            params.get("stim_times")
+        ])
+    if params.get("iresp") is not None:
+        cargs.extend([
+            "-iresp",
+            params.get("iresp")
+        ])
+    if params.get("fitts") is not None:
+        cargs.extend([
+            "-fitts",
+            params.get("fitts")
+        ])
+    if params.get("fout"):
+        cargs.append("-fout")
+    if params.get("tout"):
+        cargs.append("-tout")
+    if params.get("bucket") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("bucket")
+        ])
+    if params.get("cbucket") is not None:
+        cargs.extend([
+            "-cbucket",
+            params.get("cbucket")
+        ])
+    if params.get("x1D") is not None:
+        cargs.extend([
+            "-x1D",
+            params.get("x1D")
+        ])
+    if params.get("jobs") is not None:
+        cargs.extend([
+            "-jobs",
+            str(params.get("jobs"))
+        ])
+    return cargs
+
+
+def v_3d_deconvolve_outputs(
+    params: V3dDeconvolveParameters,
+    execution: Execution,
+) -> V3dDeconvolveOutputs:
+    """
+    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 = V3dDeconvolveOutputs(
+        root=execution.output_file("."),
+        bucket_output=execution.output_file(params.get("bucket") + ".HEAD") if (params.get("bucket") is not None) else None,
+        cbucket_output=execution.output_file(params.get("cbucket") + ".HEAD") if (params.get("cbucket") is not None) else None,
+        iresp_output=execution.output_file(params.get("iresp") + ".HEAD") if (params.get("iresp") is not None) else None,
+        fitts_output=execution.output_file(params.get("fitts") + ".HEAD") if (params.get("fitts") is not None) else None,
+        x1d_file=execution.output_file(params.get("x1D") + ".1D") if (params.get("x1D") is not None) else None,
+    )
+    return ret
+
+
+def v_3d_deconvolve_execute(
+    params: V3dDeconvolveParameters,
+    execution: Execution,
+) -> V3dDeconvolveOutputs:
+    """
+    Program to calculate the deconvolution of a measurement 3D+time dataset with a
+    specified input stimulus 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 `V3dDeconvolveOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_deconvolve_cargs(params, execution)
+    ret = v_3d_deconvolve_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_deconvolve(
+    input_dataset: InputPathType,
+    mask_dataset: InputPathType | None = None,
+    num_stimts: int | None = None,
+    stim_file: str | None = None,
+    stim_label: str | None = None,
+    stim_base: bool = False,
+    stim_times: str | None = None,
+    iresp: str | None = None,
+    fitts: str | None = None,
+    fout: bool = False,
+    tout: bool = False,
+    bucket: str | None = None,
+    cbucket: str | None = None,
+    x1_d: str | None = None,
+    jobs: int | None = None,
+    runner: Runner | None = None,
+) -> V3dDeconvolveOutputs:
+    """
+    Program to calculate the deconvolution of a measurement 3D+time dataset with a
+    specified input stimulus time series.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dataset: Filename of 3D+time input dataset.
+        mask_dataset: Filename of 3D mask dataset.
+        num_stimts: Number of input stimulus time series.
+        stim_file: Filename of kth time series input stimulus.
+        stim_label: Label for kth input stimulus.
+        stim_base: Kth input stimulus is part of the baseline model.
+        stim_times: Deconvolution response model for kth stimulus.
+        iresp: Prefix for 3D+time output dataset which will contain the kth\
+            estimated impulse response.
+        fitts: Prefix for 3D+time output dataset which will contain the (full\
+            model) time series fit to the input data.
+        fout: Flag to output the F-statistics for each stimulus.
+        tout: Flag to output the t-statistics.
+        bucket: Create one AFNI 'bucket' dataset containing various parameters\
+            of interest.
+        cbucket: Save the regression coefficients (no statistics) into a\
+            dataset.
+        x1_d: Save X matrix to a .xmat.1D (ASCII) file.
+        jobs: Run the program with multiple jobs (sub-processes).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dDeconvolveOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_DECONVOLVE_METADATA)
+    params = v_3d_deconvolve_params(
+        input_dataset=input_dataset,
+        mask_dataset=mask_dataset,
+        num_stimts=num_stimts,
+        stim_file=stim_file,
+        stim_label=stim_label,
+        stim_base=stim_base,
+        stim_times=stim_times,
+        iresp=iresp,
+        fitts=fitts,
+        fout=fout,
+        tout=tout,
+        bucket=bucket,
+        cbucket=cbucket,
+        x1_d=x1_d,
+        jobs=jobs,
+    )
+    return v_3d_deconvolve_execute(params, execution)
+
+
+__all__ = [
+    "V3dDeconvolveOutputs",
+    "V3dDeconvolveParameters",
+    "V_3D_DECONVOLVE_METADATA",
+    "v_3d_deconvolve",
+    "v_3d_deconvolve_params",
+]