niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_3d_trfix.py

@@ -0,0 +1,234 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TRFIX_METADATA = Metadata(
+    id="a34882bc067ee157a81c8d48c065fa3edac1cdc8.boutiques",
+    name="3dTRfix",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTrfixParameters = typing.TypedDict('V3dTrfixParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTRfix"],
+    "input_file": InputPathType,
+    "tr_list": typing.NotRequired[InputPathType | None],
+    "time_list": typing.NotRequired[InputPathType | None],
+    "prefix": str,
+    "output_tr": typing.NotRequired[float | None],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "3dTRfix": v_3d_trfix_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 {
+        "3dTRfix": v_3d_trfix_outputs,
+    }.get(t)
+
+
+class V3dTrfixOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_trfix(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file_head: OutputPathType
+    """Output dataset header file"""
+    output_file_brik: OutputPathType
+    """Output dataset brik file"""
+
+
+def v_3d_trfix_params(
+    input_file: InputPathType,
+    prefix: str,
+    tr_list: InputPathType | None = None,
+    time_list: InputPathType | None = None,
+    output_tr: float | None = None,
+) -> V3dTrfixParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input dataset.
+        prefix: Prefix name for output dataset.
+        tr_list: File of time gaps between sub-bricks in input dataset.
+        time_list: File with times at each sub-brick in the input dataset.
+        output_tr: TR value for output dataset (in seconds).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTRfix",
+        "input_file": input_file,
+        "prefix": prefix,
+    }
+    if tr_list is not None:
+        params["tr_list"] = tr_list
+    if time_list is not None:
+        params["time_list"] = time_list
+    if output_tr is not None:
+        params["output_tr"] = output_tr
+    return params
+
+
+def v_3d_trfix_cargs(
+    params: V3dTrfixParameters,
+    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("3dTRfix")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    if params.get("tr_list") is not None:
+        cargs.extend([
+            "-TRlist",
+            execution.input_file(params.get("tr_list"))
+        ])
+    if params.get("time_list") is not None:
+        cargs.extend([
+            "-TIMElist",
+            execution.input_file(params.get("time_list"))
+        ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("output_tr") is not None:
+        cargs.extend([
+            "-TRout",
+            str(params.get("output_tr"))
+        ])
+    return cargs
+
+
+def v_3d_trfix_outputs(
+    params: V3dTrfixParameters,
+    execution: Execution,
+) -> V3dTrfixOutputs:
+    """
+    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 = V3dTrfixOutputs(
+        root=execution.output_file("."),
+        output_file_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        output_file_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+    )
+    return ret
+
+
+def v_3d_trfix_execute(
+    params: V3dTrfixParameters,
+    execution: Execution,
+) -> V3dTrfixOutputs:
+    """
+    Re-sample dataset with irregular time grid to regular time grid via linear
+    interpolation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTrfixOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_trfix_cargs(params, execution)
+    ret = v_3d_trfix_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_trfix(
+    input_file: InputPathType,
+    prefix: str,
+    tr_list: InputPathType | None = None,
+    time_list: InputPathType | None = None,
+    output_tr: float | None = None,
+    runner: Runner | None = None,
+) -> V3dTrfixOutputs:
+    """
+    Re-sample dataset with irregular time grid to regular time grid via linear
+    interpolation.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input dataset.
+        prefix: Prefix name for output dataset.
+        tr_list: File of time gaps between sub-bricks in input dataset.
+        time_list: File with times at each sub-brick in the input dataset.
+        output_tr: TR value for output dataset (in seconds).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTrfixOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TRFIX_METADATA)
+    params = v_3d_trfix_params(
+        input_file=input_file,
+        tr_list=tr_list,
+        time_list=time_list,
+        prefix=prefix,
+        output_tr=output_tr,
+    )
+    return v_3d_trfix_execute(params, execution)
+
+
+__all__ = [
+    "V3dTrfixOutputs",
+    "V3dTrfixParameters",
+    "V_3D_TRFIX_METADATA",
+    "v_3d_trfix",
+    "v_3d_trfix_params",
+]

niwrap_afni/afni/v_3d_tsgen.py

@@ -0,0 +1,319 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_3D_TSGEN_METADATA = Metadata(
+    id="99758b64781663ffd508cccdf61b5f963c784b4a.boutiques",
+    name="3dTSgen",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V3dTsgenParameters = typing.TypedDict('V3dTsgenParameters', {
+    "__STYX_TYPE__": typing.Literal["3dTSgen"],
+    "input_file": InputPathType,
+    "in_tr_flag": bool,
+    "signal_label": str,
+    "noise_label": str,
+    "signal_constr": typing.NotRequired[str | None],
+    "noise_constr": typing.NotRequired[str | None],
+    "sigma_value": float,
+    "voxel_number": typing.NotRequired[float | None],
+    "output_file": str,
+    "signal_coef": typing.NotRequired[str | None],
+    "noise_coef": typing.NotRequired[str | None],
+    "bucket_config": 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 {
+        "3dTSgen": v_3d_tsgen_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 V3dTsgenOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_3d_tsgen(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_3d_tsgen_params(
+    input_file: InputPathType,
+    signal_label: str,
+    noise_label: str,
+    sigma_value: float,
+    output_file: str,
+    in_tr_flag: bool = False,
+    signal_constr: str | None = None,
+    noise_constr: str | None = None,
+    voxel_number: float | None = None,
+    signal_coef: str | None = None,
+    noise_coef: str | None = None,
+    bucket_config: str | None = None,
+) -> V3dTsgenParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Filename of prototype 3d + time data file.
+        signal_label: Name of the (non-linear) signal model.
+        noise_label: Name of the (linear) noise model.
+        sigma_value: Standard deviation of additive Gaussian noise.
+        output_file: Filename of output 3d + time data file.
+        in_tr_flag: Set the TR of the created timeseries to be the TR of the\
+            prototype dataset. The default is TR = 1.
+        signal_constr: Constraints for kth signal parameter. Format: k c d\
+            where c <= gs[k] <= d.
+        noise_constr: Constraints for kth noise parameter. Format: k c d where\
+            c+b[k] <= gn[k] <= d+b[k].
+        voxel_number: Screen output for voxel number.
+        signal_coef: Write kth signal parameter gs[k]. Output 'fim' is written\
+            to prefix filename.
+        noise_coef: Write kth noise parameter gn[k]. Output 'fim' is written to\
+            prefix filename.
+        bucket_config: Create one AFNI 'bucket' dataset containing n\
+            sub-bricks. n=0 creates the default output. Output 'bucket' is written\
+            to prefixname.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "3dTSgen",
+        "input_file": input_file,
+        "in_tr_flag": in_tr_flag,
+        "signal_label": signal_label,
+        "noise_label": noise_label,
+        "sigma_value": sigma_value,
+        "output_file": output_file,
+    }
+    if signal_constr is not None:
+        params["signal_constr"] = signal_constr
+    if noise_constr is not None:
+        params["noise_constr"] = noise_constr
+    if voxel_number is not None:
+        params["voxel_number"] = voxel_number
+    if signal_coef is not None:
+        params["signal_coef"] = signal_coef
+    if noise_coef is not None:
+        params["noise_coef"] = noise_coef
+    if bucket_config is not None:
+        params["bucket_config"] = bucket_config
+    return params
+
+
+def v_3d_tsgen_cargs(
+    params: V3dTsgenParameters,
+    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("3dTSgen")
+    cargs.append(execution.input_file(params.get("input_file")))
+    if params.get("in_tr_flag"):
+        cargs.append("-inTR")
+    cargs.extend([
+        "-signal",
+        params.get("signal_label")
+    ])
+    cargs.extend([
+        "-noise",
+        params.get("noise_label")
+    ])
+    if params.get("signal_constr") is not None:
+        cargs.extend([
+            "-sconstr",
+            params.get("signal_constr")
+        ])
+    if params.get("noise_constr") is not None:
+        cargs.extend([
+            "-nconstr",
+            params.get("noise_constr")
+        ])
+    cargs.extend([
+        "-sigma",
+        str(params.get("sigma_value"))
+    ])
+    if params.get("voxel_number") is not None:
+        cargs.extend([
+            "-voxel",
+            str(params.get("voxel_number"))
+        ])
+    cargs.extend([
+        "-output",
+        params.get("output_file")
+    ])
+    if params.get("signal_coef") is not None:
+        cargs.extend([
+            "-scoef",
+            params.get("signal_coef")
+        ])
+    if params.get("noise_coef") is not None:
+        cargs.extend([
+            "-ncoef",
+            params.get("noise_coef")
+        ])
+    if params.get("bucket_config") is not None:
+        cargs.extend([
+            "-bucket",
+            params.get("bucket_config")
+        ])
+    return cargs
+
+
+def v_3d_tsgen_outputs(
+    params: V3dTsgenParameters,
+    execution: Execution,
+) -> V3dTsgenOutputs:
+    """
+    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 = V3dTsgenOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_3d_tsgen_execute(
+    params: V3dTsgenParameters,
+    execution: Execution,
+) -> V3dTsgenOutputs:
+    """
+    This program generates an AFNI 3d+time data set based on user-specified signal
+    and noise models for each voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsgenOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_3d_tsgen_cargs(params, execution)
+    ret = v_3d_tsgen_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_3d_tsgen(
+    input_file: InputPathType,
+    signal_label: str,
+    noise_label: str,
+    sigma_value: float,
+    output_file: str,
+    in_tr_flag: bool = False,
+    signal_constr: str | None = None,
+    noise_constr: str | None = None,
+    voxel_number: float | None = None,
+    signal_coef: str | None = None,
+    noise_coef: str | None = None,
+    bucket_config: str | None = None,
+    runner: Runner | None = None,
+) -> V3dTsgenOutputs:
+    """
+    This program generates an AFNI 3d+time data set based on user-specified signal
+    and noise models for each voxel.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Filename of prototype 3d + time data file.
+        signal_label: Name of the (non-linear) signal model.
+        noise_label: Name of the (linear) noise model.
+        sigma_value: Standard deviation of additive Gaussian noise.
+        output_file: Filename of output 3d + time data file.
+        in_tr_flag: Set the TR of the created timeseries to be the TR of the\
+            prototype dataset. The default is TR = 1.
+        signal_constr: Constraints for kth signal parameter. Format: k c d\
+            where c <= gs[k] <= d.
+        noise_constr: Constraints for kth noise parameter. Format: k c d where\
+            c+b[k] <= gn[k] <= d+b[k].
+        voxel_number: Screen output for voxel number.
+        signal_coef: Write kth signal parameter gs[k]. Output 'fim' is written\
+            to prefix filename.
+        noise_coef: Write kth noise parameter gn[k]. Output 'fim' is written to\
+            prefix filename.
+        bucket_config: Create one AFNI 'bucket' dataset containing n\
+            sub-bricks. n=0 creates the default output. Output 'bucket' is written\
+            to prefixname.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V3dTsgenOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_TSGEN_METADATA)
+    params = v_3d_tsgen_params(
+        input_file=input_file,
+        in_tr_flag=in_tr_flag,
+        signal_label=signal_label,
+        noise_label=noise_label,
+        signal_constr=signal_constr,
+        noise_constr=noise_constr,
+        sigma_value=sigma_value,
+        voxel_number=voxel_number,
+        output_file=output_file,
+        signal_coef=signal_coef,
+        noise_coef=noise_coef,
+        bucket_config=bucket_config,
+    )
+    return v_3d_tsgen_execute(params, execution)
+
+
+__all__ = [
+    "V3dTsgenOutputs",
+    "V3dTsgenParameters",
+    "V_3D_TSGEN_METADATA",
+    "v_3d_tsgen",
+    "v_3d_tsgen_params",
+]