niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1d_flag_motion.py

@@ -0,0 +1,212 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_FLAG_MOTION_METADATA = Metadata(
+    id="efc64bd39dbf6f50e88a48eb1a0be3834e4162f6.boutiques",
+    name="1dFlagMotion",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dFlagMotionParameters = typing.TypedDict('V1dFlagMotionParameters', {
+    "__STYX_TYPE__": typing.Literal["1dFlagMotion"],
+    "input_motion_file": InputPathType,
+    "max_translation": typing.NotRequired[float | None],
+    "max_rotation": 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 {
+        "1dFlagMotion": v_1d_flag_motion_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 {
+        "1dFlagMotion": v_1d_flag_motion_outputs,
+    }.get(t)
+
+
+class V1dFlagMotionOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_flag_motion(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_points: OutputPathType
+    """List of points exceeding the motion bounds in 1D format"""
+
+
+def v_1d_flag_motion_params(
+    input_motion_file: InputPathType,
+    max_translation: float | None = None,
+    max_rotation: float | None = None,
+) -> V1dFlagMotionParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_motion_file: Input file with EXACTLY 6 columns: roll pitch yaw\
+            delta-SI delta-LR delta-AP (angles in degrees followed by translations\
+            in mm).
+        max_translation: Maximum translation allowed in any direction (defaults\
+            to 1.5mm).
+        max_rotation: Maximum rotation allowed in any direction (defaults to\
+            1.25 degrees).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dFlagMotion",
+        "input_motion_file": input_motion_file,
+    }
+    if max_translation is not None:
+        params["max_translation"] = max_translation
+    if max_rotation is not None:
+        params["max_rotation"] = max_rotation
+    return params
+
+
+def v_1d_flag_motion_cargs(
+    params: V1dFlagMotionParameters,
+    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("1dFlagMotion")
+    cargs.append(execution.input_file(params.get("input_motion_file")))
+    if params.get("max_translation") is not None:
+        cargs.extend([
+            "-MaxTrans",
+            str(params.get("max_translation"))
+        ])
+    if params.get("max_rotation") is not None:
+        cargs.extend([
+            "-MaxRot",
+            str(params.get("max_rotation"))
+        ])
+    return cargs
+
+
+def v_1d_flag_motion_outputs(
+    params: V1dFlagMotionParameters,
+    execution: Execution,
+) -> V1dFlagMotionOutputs:
+    """
+    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 = V1dFlagMotionOutputs(
+        root=execution.output_file("."),
+        output_points=execution.output_file("output_motion_points.1D"),
+    )
+    return ret
+
+
+def v_1d_flag_motion_execute(
+    params: V1dFlagMotionParameters,
+    execution: Execution,
+) -> V1dFlagMotionOutputs:
+    """
+    Produces a list of time points with excessive motion relative to the previous
+    time point.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dFlagMotionOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_flag_motion_cargs(params, execution)
+    ret = v_1d_flag_motion_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_flag_motion(
+    input_motion_file: InputPathType,
+    max_translation: float | None = None,
+    max_rotation: float | None = None,
+    runner: Runner | None = None,
+) -> V1dFlagMotionOutputs:
+    """
+    Produces a list of time points with excessive motion relative to the previous
+    time point.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_motion_file: Input file with EXACTLY 6 columns: roll pitch yaw\
+            delta-SI delta-LR delta-AP (angles in degrees followed by translations\
+            in mm).
+        max_translation: Maximum translation allowed in any direction (defaults\
+            to 1.5mm).
+        max_rotation: Maximum rotation allowed in any direction (defaults to\
+            1.25 degrees).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dFlagMotionOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_FLAG_MOTION_METADATA)
+    params = v_1d_flag_motion_params(
+        input_motion_file=input_motion_file,
+        max_translation=max_translation,
+        max_rotation=max_rotation,
+    )
+    return v_1d_flag_motion_execute(params, execution)
+
+
+__all__ = [
+    "V1dFlagMotionOutputs",
+    "V1dFlagMotionParameters",
+    "V_1D_FLAG_MOTION_METADATA",
+    "v_1d_flag_motion",
+    "v_1d_flag_motion_params",
+]

niwrap_afni/afni/v_1d_marry.py

@@ -0,0 +1,214 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_MARRY_METADATA = Metadata(
+    id="bf4086d827742de99647b8c529893b01461d76ef.boutiques",
+    name="1dMarry",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dMarryParameters = typing.TypedDict('V1dMarryParameters', {
+    "__STYX_TYPE__": typing.Literal["1dMarry"],
+    "sep": typing.NotRequired[str | None],
+    "divorce": bool,
+    "files": list[InputPathType],
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dMarry": v_1d_marry_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 {
+        "1dMarry": v_1d_marry_outputs,
+    }.get(t)
+
+
+class V1dMarryOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_marry(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType
+    """Output file when marrying files. This file should be captured using a
+    redirection such as '>'."""
+    divorcee_a: OutputPathType
+    """First output file when divorcing."""
+    divorcee_b: OutputPathType
+    """Second output file when divorcing."""
+
+
+def v_1d_marry_params(
+    files: list[InputPathType],
+    sep: str | None = None,
+    divorce: bool = False,
+) -> V1dMarryParameters:
+    """
+    Build parameters.
+    
+    Args:
+        files: Input file(s) to be married or divorced.
+        sep: Separator(s) for marrying files. The first character is used as\
+            the separator between values 1 and 2, the second character between\
+            values 2 and 3, etc.
+        divorce: Divorce mode: splits married file into separate files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dMarry",
+        "divorce": divorce,
+        "files": files,
+    }
+    if sep is not None:
+        params["sep"] = sep
+    return params
+
+
+def v_1d_marry_cargs(
+    params: V1dMarryParameters,
+    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("1dMarry")
+    if params.get("sep") is not None:
+        cargs.extend([
+            "-sep",
+            params.get("sep")
+        ])
+    if params.get("divorce"):
+        cargs.append("-divorce")
+    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    cargs.append("[FILE2]")
+    return cargs
+
+
+def v_1d_marry_outputs(
+    params: V1dMarryParameters,
+    execution: Execution,
+) -> V1dMarryOutputs:
+    """
+    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 = V1dMarryOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file("stdout"),
+        divorcee_a=execution.output_file("[FILE2]_A.1D"),
+        divorcee_b=execution.output_file("[FILE2]_B.1D"),
+    )
+    return ret
+
+
+def v_1d_marry_execute(
+    params: V1dMarryParameters,
+    execution: Execution,
+) -> V1dMarryOutputs:
+    """
+    Joins together 2 (or more) ragged-right .1D files, for use with 3dDeconvolve
+    -stim_times_AM2, or breaks up 1 married file into 2 (or more) single-valued
+    files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dMarryOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_marry_cargs(params, execution)
+    ret = v_1d_marry_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_marry(
+    files: list[InputPathType],
+    sep: str | None = None,
+    divorce: bool = False,
+    runner: Runner | None = None,
+) -> V1dMarryOutputs:
+    """
+    Joins together 2 (or more) ragged-right .1D files, for use with 3dDeconvolve
+    -stim_times_AM2, or breaks up 1 married file into 2 (or more) single-valued
+    files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        files: Input file(s) to be married or divorced.
+        sep: Separator(s) for marrying files. The first character is used as\
+            the separator between values 1 and 2, the second character between\
+            values 2 and 3, etc.
+        divorce: Divorce mode: splits married file into separate files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dMarryOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_MARRY_METADATA)
+    params = v_1d_marry_params(
+        sep=sep,
+        divorce=divorce,
+        files=files,
+    )
+    return v_1d_marry_execute(params, execution)
+
+
+__all__ = [
+    "V1dMarryOutputs",
+    "V1dMarryParameters",
+    "V_1D_MARRY_METADATA",
+    "v_1d_marry",
+    "v_1d_marry_params",
+]

niwrap_afni/afni/v_1d_nlfit.py

@@ -0,0 +1,254 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_NLFIT_METADATA = Metadata(
+    id="278b48af705917ecf316b95eb2c3d2075a15c475.boutiques",
+    name="1dNLfit",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dNlfitParameters = typing.TypedDict('V1dNlfitParameters', {
+    "__STYX_TYPE__": typing.Literal["1dNLfit"],
+    "expression": str,
+    "independent_variable": str,
+    "parameters": list[str],
+    "dependent_data": InputPathType,
+    "method": 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 {
+        "1dNLfit": v_1d_nlfit_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 {
+        "1dNLfit": v_1d_nlfit_outputs,
+    }.get(t)
+
+
+class V1dNlfitOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_nlfit(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    fit_results: OutputPathType
+    """Results (fitted time series models) are written to stdout. Should be
+    saved by '>' redirection."""
+
+
+def v_1d_nlfit_params(
+    expression: str,
+    independent_variable: str,
+    parameters: list[str],
+    dependent_data: InputPathType,
+    method: int | None = None,
+) -> V1dNlfitParameters:
+    """
+    Build parameters.
+    
+    Args:
+        expression: The expression for the fit. It must contain one symbol from\
+            'a' to 'z' which is marked as the independent variable by option\
+            '-indvar', and at least one more symbol which is a parameter to be\
+            estimated.
+        independent_variable: Indicates which variable in '-expr' is the\
+            independent variable. All other symbols are parameters, which are\
+            either fixed (constants) or variables to be estimated. Read the values\
+            of the independent variable from 1D file.
+        parameters: Set fixed value or estimating range for a particular\
+            symbol. For a fixed value, it takes the form 'a=3.14'. For an estimated\
+            parameter, it takes the form 'q=-sqrt(2):sqrt(2)'. All symbols in\
+            '-expr' must have a corresponding '-param' option, EXCEPT for the\
+            '-indvar' symbol.
+        dependent_data: Read the values of the dependent variable (to be fitted\
+            to '-expr') from 1D file. The file must have the same number of rows as\
+            the '-indvar' file.
+        method: Set the method for fitting: '1' for L1, '2' for L2 (default is\
+            L2).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dNLfit",
+        "expression": expression,
+        "independent_variable": independent_variable,
+        "parameters": parameters,
+        "dependent_data": dependent_data,
+    }
+    if method is not None:
+        params["method"] = method
+    return params
+
+
+def v_1d_nlfit_cargs(
+    params: V1dNlfitParameters,
+    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("1dNLfit")
+    cargs.extend([
+        "-expr",
+        params.get("expression")
+    ])
+    cargs.extend([
+        "-indvar",
+        params.get("independent_variable")
+    ])
+    cargs.extend([
+        "-param",
+        *params.get("parameters")
+    ])
+    cargs.extend([
+        "-depdata",
+        execution.input_file(params.get("dependent_data"))
+    ])
+    if params.get("method") is not None:
+        cargs.extend([
+            "-meth",
+            str(params.get("method"))
+        ])
+    return cargs
+
+
+def v_1d_nlfit_outputs(
+    params: V1dNlfitParameters,
+    execution: Execution,
+) -> V1dNlfitOutputs:
+    """
+    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 = V1dNlfitOutputs(
+        root=execution.output_file("."),
+        fit_results=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_1d_nlfit_execute(
+    params: V1dNlfitParameters,
+    execution: Execution,
+) -> V1dNlfitOutputs:
+    """
+    Program to fit a model to a vector of data. The model is given by a symbolic
+    expression, with parameters to be estimated.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dNlfitOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_nlfit_cargs(params, execution)
+    ret = v_1d_nlfit_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_nlfit(
+    expression: str,
+    independent_variable: str,
+    parameters: list[str],
+    dependent_data: InputPathType,
+    method: int | None = None,
+    runner: Runner | None = None,
+) -> V1dNlfitOutputs:
+    """
+    Program to fit a model to a vector of data. The model is given by a symbolic
+    expression, with parameters to be estimated.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        expression: The expression for the fit. It must contain one symbol from\
+            'a' to 'z' which is marked as the independent variable by option\
+            '-indvar', and at least one more symbol which is a parameter to be\
+            estimated.
+        independent_variable: Indicates which variable in '-expr' is the\
+            independent variable. All other symbols are parameters, which are\
+            either fixed (constants) or variables to be estimated. Read the values\
+            of the independent variable from 1D file.
+        parameters: Set fixed value or estimating range for a particular\
+            symbol. For a fixed value, it takes the form 'a=3.14'. For an estimated\
+            parameter, it takes the form 'q=-sqrt(2):sqrt(2)'. All symbols in\
+            '-expr' must have a corresponding '-param' option, EXCEPT for the\
+            '-indvar' symbol.
+        dependent_data: Read the values of the dependent variable (to be fitted\
+            to '-expr') from 1D file. The file must have the same number of rows as\
+            the '-indvar' file.
+        method: Set the method for fitting: '1' for L1, '2' for L2 (default is\
+            L2).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dNlfitOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_NLFIT_METADATA)
+    params = v_1d_nlfit_params(
+        expression=expression,
+        independent_variable=independent_variable,
+        parameters=parameters,
+        dependent_data=dependent_data,
+        method=method,
+    )
+    return v_1d_nlfit_execute(params, execution)
+
+
+__all__ = [
+    "V1dNlfitOutputs",
+    "V1dNlfitParameters",
+    "V_1D_NLFIT_METADATA",
+    "v_1d_nlfit",
+    "v_1d_nlfit_params",
+]