niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/v_1dsvd.py

@@ -0,0 +1,272 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DSVD_METADATA = Metadata(
+    id="c137a2a26ce0b2c14b24befee7a12ab31db435c8.boutiques",
+    name="1dsvd",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dsvdParameters = typing.TypedDict('V1dsvdParameters', {
+    "__STYX_TYPE__": typing.Literal["1dsvd"],
+    "one": bool,
+    "vmean": bool,
+    "vnorm": bool,
+    "cond": bool,
+    "sing": bool,
+    "sort": bool,
+    "nosort": bool,
+    "asort": bool,
+    "left_eigenvectors": bool,
+    "num_eigenvectors": typing.NotRequired[str | None],
+    "input_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 {
+        "1dsvd": v_1dsvd_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 {
+        "1dsvd": v_1dsvd_outputs,
+    }.get(t)
+
+
+class V1dsvdOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1dsvd(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    stdout: OutputPathType
+    """Output of the SVD computation"""
+
+
+def v_1dsvd_params(
+    input_files: list[InputPathType],
+    one: bool = False,
+    vmean: bool = False,
+    vnorm: bool = False,
+    cond: bool = False,
+    sing: bool = False,
+    sort: bool = False,
+    nosort: bool = False,
+    asort: bool = False,
+    left_eigenvectors: bool = False,
+    num_eigenvectors: str | None = None,
+) -> V1dsvdParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input 1D file(s) for SVD computation.
+        one: Make 1st vector be all 1's.
+        vmean: Remove mean from each vector (cannot be used with -one).
+        vnorm: Make L2-norm of each vector = 1 before SVD.
+        cond: Only print condition number (ratio of extremes).
+        sing: Only print singular values.
+        sort: Sort singular values in descending order (default).
+        nosort: Don't sort singular values.
+        asort: Sort singular values in ascending order.
+        left_eigenvectors: Only output left eigenvectors in .1D format.
+        num_eigenvectors: Specify number of left eigenvectors to output.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dsvd",
+        "one": one,
+        "vmean": vmean,
+        "vnorm": vnorm,
+        "cond": cond,
+        "sing": sing,
+        "sort": sort,
+        "nosort": nosort,
+        "asort": asort,
+        "left_eigenvectors": left_eigenvectors,
+        "input_files": input_files,
+    }
+    if num_eigenvectors is not None:
+        params["num_eigenvectors"] = num_eigenvectors
+    return params
+
+
+def v_1dsvd_cargs(
+    params: V1dsvdParameters,
+    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("1dsvd")
+    if params.get("one"):
+        cargs.append("-one")
+    if params.get("vmean"):
+        cargs.append("-vmean")
+    if params.get("vnorm"):
+        cargs.append("-vnorm")
+    if params.get("cond"):
+        cargs.append("-cond")
+    if params.get("sing"):
+        cargs.append("-sing")
+    if params.get("sort"):
+        cargs.append("-sort")
+    if params.get("nosort"):
+        cargs.append("-nosort")
+    if params.get("asort"):
+        cargs.append("-asort")
+    if params.get("left_eigenvectors"):
+        cargs.append("-1Dleft")
+    if params.get("num_eigenvectors") is not None:
+        cargs.extend([
+            "-nev",
+            params.get("num_eigenvectors")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def v_1dsvd_outputs(
+    params: V1dsvdParameters,
+    execution: Execution,
+) -> V1dsvdOutputs:
+    """
+    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 = V1dsvdOutputs(
+        root=execution.output_file("."),
+        stdout=execution.output_file("stdout"),
+    )
+    return ret
+
+
+def v_1dsvd_execute(
+    params: V1dsvdParameters,
+    execution: Execution,
+) -> V1dsvdOutputs:
+    """
+    Computes SVD of the matrix formed by the 1D file(s) and outputs the result on
+    stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dsvdOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1dsvd_cargs(params, execution)
+    ret = v_1dsvd_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1dsvd(
+    input_files: list[InputPathType],
+    one: bool = False,
+    vmean: bool = False,
+    vnorm: bool = False,
+    cond: bool = False,
+    sing: bool = False,
+    sort: bool = False,
+    nosort: bool = False,
+    asort: bool = False,
+    left_eigenvectors: bool = False,
+    num_eigenvectors: str | None = None,
+    runner: Runner | None = None,
+) -> V1dsvdOutputs:
+    """
+    Computes SVD of the matrix formed by the 1D file(s) and outputs the result on
+    stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input 1D file(s) for SVD computation.
+        one: Make 1st vector be all 1's.
+        vmean: Remove mean from each vector (cannot be used with -one).
+        vnorm: Make L2-norm of each vector = 1 before SVD.
+        cond: Only print condition number (ratio of extremes).
+        sing: Only print singular values.
+        sort: Sort singular values in descending order (default).
+        nosort: Don't sort singular values.
+        asort: Sort singular values in ascending order.
+        left_eigenvectors: Only output left eigenvectors in .1D format.
+        num_eigenvectors: Specify number of left eigenvectors to output.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dsvdOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DSVD_METADATA)
+    params = v_1dsvd_params(
+        one=one,
+        vmean=vmean,
+        vnorm=vnorm,
+        cond=cond,
+        sing=sing,
+        sort=sort,
+        nosort=nosort,
+        asort=asort,
+        left_eigenvectors=left_eigenvectors,
+        num_eigenvectors=num_eigenvectors,
+        input_files=input_files,
+    )
+    return v_1dsvd_execute(params, execution)
+
+
+__all__ = [
+    "V1dsvdOutputs",
+    "V1dsvdParameters",
+    "V_1DSVD_METADATA",
+    "v_1dsvd",
+    "v_1dsvd_params",
+]

niwrap_afni/afni/v_1dtranspose.py

@@ -0,0 +1,188 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_1DTRANSPOSE_METADATA = Metadata(
+    id="8aeb8ffe1bc2def81876ed4d22208279a8077957.boutiques",
+    name="1dtranspose",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V1dtransposeParameters = typing.TypedDict('V1dtransposeParameters', {
+    "__STYX_TYPE__": typing.Literal["1dtranspose"],
+    "infile": InputPathType,
+    "outfile": 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 {
+        "1dtranspose": v_1dtranspose_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 {
+        "1dtranspose": v_1dtranspose_outputs,
+    }.get(t)
+
+
+class V1dtransposeOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_1dtranspose(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    outfile: OutputPathType | None
+    """Transposed output file"""
+
+
+def v_1dtranspose_params(
+    infile: InputPathType,
+    outfile: str | None = None,
+) -> V1dtransposeParameters:
+    """
+    Build parameters.
+    
+    Args:
+        infile: Input file (e.g. data.1D).
+        outfile: Output file (e.g. transposed_data.1D), or '-' to write to\
+            stdout.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "1dtranspose",
+        "infile": infile,
+    }
+    if outfile is not None:
+        params["outfile"] = outfile
+    return params
+
+
+def v_1dtranspose_cargs(
+    params: V1dtransposeParameters,
+    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("1dtranspose")
+    cargs.append(execution.input_file(params.get("infile")))
+    if params.get("outfile") is not None:
+        cargs.append(params.get("outfile"))
+    return cargs
+
+
+def v_1dtranspose_outputs(
+    params: V1dtransposeParameters,
+    execution: Execution,
+) -> V1dtransposeOutputs:
+    """
+    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 = V1dtransposeOutputs(
+        root=execution.output_file("."),
+        outfile=execution.output_file(params.get("outfile")) if (params.get("outfile") is not None) else None,
+    )
+    return ret
+
+
+def v_1dtranspose_execute(
+    params: V1dtransposeParameters,
+    execution: Execution,
+) -> V1dtransposeOutputs:
+    """
+    Transpose an AFNI *.1D file (ASCII list of numbers arranged in columns).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V1dtransposeOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_1dtranspose_cargs(params, execution)
+    ret = v_1dtranspose_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_1dtranspose(
+    infile: InputPathType,
+    outfile: str | None = None,
+    runner: Runner | None = None,
+) -> V1dtransposeOutputs:
+    """
+    Transpose an AFNI *.1D file (ASCII list of numbers arranged in columns).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        infile: Input file (e.g. data.1D).
+        outfile: Output file (e.g. transposed_data.1D), or '-' to write to\
+            stdout.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V1dtransposeOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_1DTRANSPOSE_METADATA)
+    params = v_1dtranspose_params(
+        infile=infile,
+        outfile=outfile,
+    )
+    return v_1dtranspose_execute(params, execution)
+
+
+__all__ = [
+    "V1dtransposeOutputs",
+    "V1dtransposeParameters",
+    "V_1DTRANSPOSE_METADATA",
+    "v_1dtranspose",
+    "v_1dtranspose_params",
+]

niwrap_afni/afni/v_24swap.py

@@ -0,0 +1,194 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+V_24SWAP_METADATA = Metadata(
+    id="bf5fd18b81c5c9e1a6698d3e136d7e97296fa6fb.boutiques",
+    name="24swap",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+V24swapParameters = typing.TypedDict('V24swapParameters', {
+    "__STYX_TYPE__": typing.Literal["24swap"],
+    "quiet": bool,
+    "pattern": typing.NotRequired[str | None],
+    "input_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 {
+        "24swap": v_24swap_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 V24swapOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `v_24swap(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def v_24swap_params(
+    input_files: list[InputPathType],
+    quiet: bool = False,
+    pattern: str | None = None,
+) -> V24swapParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_files: Input file(s) to swap bytes.
+        quiet: Operate quietly.
+        pattern: Pattern that determines the pattern of 2 and 4 byte swaps.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "24swap",
+        "quiet": quiet,
+        "input_files": input_files,
+    }
+    if pattern is not None:
+        params["pattern"] = pattern
+    return params
+
+
+def v_24swap_cargs(
+    params: V24swapParameters,
+    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("24swap")
+    if params.get("quiet"):
+        cargs.append("-q")
+    if params.get("pattern") is not None:
+        cargs.extend([
+            "-pattern",
+            params.get("pattern")
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    return cargs
+
+
+def v_24swap_outputs(
+    params: V24swapParameters,
+    execution: Execution,
+) -> V24swapOutputs:
+    """
+    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 = V24swapOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def v_24swap_execute(
+    params: V24swapParameters,
+    execution: Execution,
+) -> V24swapOutputs:
+    """
+    Swaps bytes pairs and/or quadruples on the files listed.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `V24swapOutputs`).
+    """
+    params = execution.params(params)
+    cargs = v_24swap_cargs(params, execution)
+    ret = v_24swap_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def v_24swap(
+    input_files: list[InputPathType],
+    quiet: bool = False,
+    pattern: str | None = None,
+    runner: Runner | None = None,
+) -> V24swapOutputs:
+    """
+    Swaps bytes pairs and/or quadruples on the files listed.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_files: Input file(s) to swap bytes.
+        quiet: Operate quietly.
+        pattern: Pattern that determines the pattern of 2 and 4 byte swaps.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `V24swapOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_24SWAP_METADATA)
+    params = v_24swap_params(
+        quiet=quiet,
+        pattern=pattern,
+        input_files=input_files,
+    )
+    return v_24swap_execute(params, execution)
+
+
+__all__ = [
+    "V24swapOutputs",
+    "V24swapParameters",
+    "V_24SWAP_METADATA",
+    "v_24swap",
+    "v_24swap_params",
+]