niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1d_rplot.py

@@ -0,0 +1,180 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_RPLOT_METADATA = Metadata(
+    id="97370e286ceee3c0b1e0eb62c1b51f85396f905d.boutiques",
+    name="1dRplot",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dRplotParameters = typing.TypedDict('V1dRplotParameters', {
+    "__STYX_TYPE__": typing.Literal["1dRplot"],
+    "input_file": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dRplot": v_1d_rplot_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 {
+        "1dRplot": v_1d_rplot_outputs,
+    }.get(t)
+
+
+class V1dRplotOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_rplot(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_plot: OutputPathType
+    """Output plot file"""
+
+
+def v_1d_rplot_params(
+    input_file: InputPathType,
+) -> V1dRplotParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Input 1D file to plot.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dRplot",
+        "input_file": input_file,
+    }
+    return params
+
+
+def v_1d_rplot_cargs(
+    params: V1dRplotParameters,
+    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("1dRplot")
+    cargs.extend([
+        "-input",
+        execution.input_file(params.get("input_file"))
+    ])
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v_1d_rplot_outputs(
+    params: V1dRplotParameters,
+    execution: Execution,
+) -> V1dRplotOutputs:
+    """
+    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 = V1dRplotOutputs(
+        root=execution.output_file("."),
+        output_plot=execution.output_file("[OUTPUT_PREFIX]*.jpg"),
+    )
+    return ret
+
+
+def v_1d_rplot_execute(
+    params: V1dRplotParameters,
+    execution: Execution,
+) -> V1dRplotOutputs:
+    """
+    Program for plotting a 1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dRplotOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_rplot_cargs(params, execution)
+    ret = v_1d_rplot_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_rplot(
+    input_file: InputPathType,
+    runner: Runner | None = None,
+) -> V1dRplotOutputs:
+    """
+    Program for plotting a 1D file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Input 1D file to plot.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dRplotOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_RPLOT_METADATA)
+    params = v_1d_rplot_params(
+        input_file=input_file,
+    )
+    return v_1d_rplot_execute(params, execution)
+
+
+__all__ = [
+    "V1dRplotOutputs",
+    "V1dRplotParameters",
+    "V_1D_RPLOT_METADATA",
+    "v_1d_rplot",
+    "v_1d_rplot_params",
+]

niwrap_afni/afni/v_1d_sem.py

@@ -0,0 +1,215 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1D_SEM_METADATA = Metadata(
+    id="22951ac5931e28304cde031a44c651e57c4e4a1e.boutiques",
+    name="1dSEM",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dSemParameters = typing.TypedDict('V1dSemParameters', {
+    "__STYX_TYPE__": typing.Literal["1dSEM"],
+    "theta": InputPathType,
+    "correlation_matrix": InputPathType,
+    "residual_variance": InputPathType,
+    "degrees_of_freedom": float,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1dSEM": v_1d_sem_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 {
+        "1dSEM": v_1d_sem_outputs,
+    }.get(t)
+
+
+class V1dSemOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_sem(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType
+    """Output printed to the terminal. This file may be redirected."""
+
+
+def v_1d_sem_params(
+    theta: InputPathType,
+    correlation_matrix: InputPathType,
+    residual_variance: InputPathType,
+    degrees_of_freedom: float,
+) -> V1dSemParameters:
+    """
+    Build parameters.
+    
+    Args:
+        theta: Connection matrix 1D file with initial representation.
+        correlation_matrix: Correlation matrix 1D file.
+        residual_variance: Residual variance vector 1D file.
+        degrees_of_freedom: Degrees of freedom.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dSEM",
+        "theta": theta,
+        "correlation_matrix": correlation_matrix,
+        "residual_variance": residual_variance,
+        "degrees_of_freedom": degrees_of_freedom,
+    }
+    return params
+
+
+def v_1d_sem_cargs(
+    params: V1dSemParameters,
+    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("1dSEM")
+    cargs.extend([
+        "-theta",
+        execution.input_file(params.get("theta"))
+    ])
+    cargs.extend([
+        "-C",
+        execution.input_file(params.get("correlation_matrix"))
+    ])
+    cargs.extend([
+        "-psi",
+        execution.input_file(params.get("residual_variance"))
+    ])
+    cargs.extend([
+        "-DF",
+        str(params.get("degrees_of_freedom"))
+    ])
+    cargs.append("[OPTIONS]")
+    return cargs
+
+
+def v_1d_sem_outputs(
+    params: V1dSemParameters,
+    execution: Execution,
+) -> V1dSemOutputs:
+    """
+    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 = V1dSemOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file("output.txt"),
+    )
+    return ret
+
+
+def v_1d_sem_execute(
+    params: V1dSemParameters,
+    execution: Execution,
+) -> V1dSemOutputs:
+    """
+    Computes path coefficients for connection matrix in Structural Equation Modeling
+    (SEM).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dSemOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_sem_cargs(params, execution)
+    ret = v_1d_sem_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_sem(
+    theta: InputPathType,
+    correlation_matrix: InputPathType,
+    residual_variance: InputPathType,
+    degrees_of_freedom: float,
+    runner: Runner | None = None,
+) -> V1dSemOutputs:
+    """
+    Computes path coefficients for connection matrix in Structural Equation Modeling
+    (SEM).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        theta: Connection matrix 1D file with initial representation.
+        correlation_matrix: Correlation matrix 1D file.
+        residual_variance: Residual variance vector 1D file.
+        degrees_of_freedom: Degrees of freedom.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dSemOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_SEM_METADATA)
+    params = v_1d_sem_params(
+        theta=theta,
+        correlation_matrix=correlation_matrix,
+        residual_variance=residual_variance,
+        degrees_of_freedom=degrees_of_freedom,
+    )
+    return v_1d_sem_execute(params, execution)
+
+
+__all__ = [
+    "V1dSemOutputs",
+    "V1dSemParameters",
+    "V_1D_SEM_METADATA",
+    "v_1d_sem",
+    "v_1d_sem_params",
+]

niwrap_afni/afni/v_1d_tool_py.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_1D_TOOL_PY_METADATA = Metadata(
+    id="14f0b3bf351835bacda04353b7e54c019220ebc2.boutiques",
+    name="1d_tool.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dToolPyParameters = typing.TypedDict('V1dToolPyParameters', {
+    "__STYX_TYPE__": typing.Literal["1d_tool.py"],
+    "infile": InputPathType,
+    "write": typing.NotRequired[str | None],
+    "select_cols": typing.NotRequired[str | None],
+    "select_rows": typing.NotRequired[str | None],
+    "select_groups": typing.NotRequired[str | None],
+    "censor_motion": typing.NotRequired[float | None],
+    "pad_into_many_runs": typing.NotRequired[str | None],
+    "set_nruns": typing.NotRequired[float | None],
+    "set_run_lengths": typing.NotRequired[str | None],
+    "show_rows_cols": bool,
+    "transpose": bool,
+    "reverse": bool,
+    "show_max_displace": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "1d_tool.py": v_1d_tool_py_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 {
+        "1d_tool.py": v_1d_tool_py_outputs,
+    }.get(t)
+
+
+class V1dToolPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1d_tool_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """Resulting 1D file"""
+
+
+def v_1d_tool_py_params(
+    infile: InputPathType,
+    write: str | None = None,
+    select_cols: str | None = None,
+    select_rows: str | None = None,
+    select_groups: str | None = None,
+    censor_motion: float | None = None,
+    pad_into_many_runs: str | None = None,
+    set_nruns: float | None = None,
+    set_run_lengths: str | None = None,
+    show_rows_cols: bool = False,
+    transpose: bool = False,
+    reverse: bool = False,
+    show_max_displace: bool = False,
+) -> V1dToolPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input 1D file.
+        write: Output file to write results.
+        select_cols: Select specific columns.
+        select_rows: Select specific rows.
+        select_groups: Select columns by group numbers.
+        censor_motion: Generate a boolean censor file.
+        pad_into_many_runs: Pad a 1D file into many runs.
+        set_nruns: Set number of runs.
+        set_run_lengths: Set run lengths.
+        show_rows_cols: Show the number of rows and columns.
+        transpose: Transpose the input matrix.
+        reverse: Reverse the data over time.
+        show_max_displace: Show the maximum pairwise displacement.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1d_tool.py",
+        "infile": infile,
+        "show_rows_cols": show_rows_cols,
+        "transpose": transpose,
+        "reverse": reverse,
+        "show_max_displace": show_max_displace,
+    }
+    if write is not None:
+        params["write"] = write
+    if select_cols is not None:
+        params["select_cols"] = select_cols
+    if select_rows is not None:
+        params["select_rows"] = select_rows
+    if select_groups is not None:
+        params["select_groups"] = select_groups
+    if censor_motion is not None:
+        params["censor_motion"] = censor_motion
+    if pad_into_many_runs is not None:
+        params["pad_into_many_runs"] = pad_into_many_runs
+    if set_nruns is not None:
+        params["set_nruns"] = set_nruns
+    if set_run_lengths is not None:
+        params["set_run_lengths"] = set_run_lengths
+    return params
+
+
+def v_1d_tool_py_cargs(
+    params: V1dToolPyParameters,
+    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("1d_tool.py")
+    cargs.extend([
+        "-infile",
+        execution.input_file(params.get("infile"))
+    ])
+    if params.get("write") is not None:
+        cargs.extend([
+            "-write",
+            params.get("write")
+        ])
+    if params.get("select_cols") is not None:
+        cargs.extend([
+            "-select_cols",
+            params.get("select_cols")
+        ])
+    if params.get("select_rows") is not None:
+        cargs.extend([
+            "-select_rows",
+            params.get("select_rows")
+        ])
+    if params.get("select_groups") is not None:
+        cargs.extend([
+            "-select_groups",
+            params.get("select_groups")
+        ])
+    if params.get("censor_motion") is not None:
+        cargs.extend([
+            "-censor_motion",
+            str(params.get("censor_motion"))
+        ])
+    if params.get("pad_into_many_runs") is not None:
+        cargs.extend([
+            "-pad_into_many_runs",
+            params.get("pad_into_many_runs")
+        ])
+    if params.get("set_nruns") is not None:
+        cargs.extend([
+            "-set_nruns",
+            str(params.get("set_nruns"))
+        ])
+    if params.get("set_run_lengths") is not None:
+        cargs.extend([
+            "-set_run_lengths",
+            params.get("set_run_lengths")
+        ])
+    if params.get("show_rows_cols"):
+        cargs.append("-show_rows_cols")
+    if params.get("transpose"):
+        cargs.append("-transpose")
+    if params.get("reverse"):
+        cargs.append("-reverse")
+    if params.get("show_max_displace"):
+        cargs.append("-show_max_displace")
+    return cargs
+
+
+def v_1d_tool_py_outputs(
+    params: V1dToolPyParameters,
+    execution: Execution,
+) -> V1dToolPyOutputs:
+    """
+    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 = V1dToolPyOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("write")) if (params.get("write") is not None) else None,
+    )
+    return ret
+
+
+def v_1d_tool_py_execute(
+    params: V1dToolPyParameters,
+    execution: Execution,
+) -> V1dToolPyOutputs:
+    """
+    A tool for manipulating and evaluating 1D files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dToolPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1d_tool_py_cargs(params, execution)
+    ret = v_1d_tool_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1d_tool_py(
+    infile: InputPathType,
+    write: str | None = None,
+    select_cols: str | None = None,
+    select_rows: str | None = None,
+    select_groups: str | None = None,
+    censor_motion: float | None = None,
+    pad_into_many_runs: str | None = None,
+    set_nruns: float | None = None,
+    set_run_lengths: str | None = None,
+    show_rows_cols: bool = False,
+    transpose: bool = False,
+    reverse: bool = False,
+    show_max_displace: bool = False,
+    runner: Runner | None = None,
+) -> V1dToolPyOutputs:
+    """
+    A tool for manipulating and evaluating 1D files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input 1D file.
+        write: Output file to write results.
+        select_cols: Select specific columns.
+        select_rows: Select specific rows.
+        select_groups: Select columns by group numbers.
+        censor_motion: Generate a boolean censor file.
+        pad_into_many_runs: Pad a 1D file into many runs.
+        set_nruns: Set number of runs.
+        set_run_lengths: Set run lengths.
+        show_rows_cols: Show the number of rows and columns.
+        transpose: Transpose the input matrix.
+        reverse: Reverse the data over time.
+        show_max_displace: Show the maximum pairwise displacement.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dToolPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1D_TOOL_PY_METADATA)
+    params = v_1d_tool_py_params(
+        infile=infile,
+        write=write,
+        select_cols=select_cols,
+        select_rows=select_rows,
+        select_groups=select_groups,
+        censor_motion=censor_motion,
+        pad_into_many_runs=pad_into_many_runs,
+        set_nruns=set_nruns,
+        set_run_lengths=set_run_lengths,
+        show_rows_cols=show_rows_cols,
+        transpose=transpose,
+        reverse=reverse,
+        show_max_displace=show_max_displace,
+    )
+    return v_1d_tool_py_execute(params, execution)
+
+
+__all__ = [
+    "V1dToolPyOutputs",
+    "V1dToolPyParameters",
+    "V_1D_TOOL_PY_METADATA",
+    "v_1d_tool_py",
+    "v_1d_tool_py_params",
+]