niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/neuro_deconvolve_py.py

@@ -0,0 +1,291 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+NEURO_DECONVOLVE_PY_METADATA = Metadata(
+    id="429ca6dc167dde226c463210fc24287862627189.boutiques",
+    name="neuro_deconvolve.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+NeuroDeconvolvePyParameters = typing.TypedDict('NeuroDeconvolvePyParameters', {
+    "__STYX_TYPE__": typing.Literal["neuro_deconvolve.py"],
+    "input_file": InputPathType,
+    "prefix": str,
+    "script": str,
+    "kernel": typing.NotRequired[str | None],
+    "kernel_file": typing.NotRequired[str | None],
+    "mask_dset": typing.NotRequired[InputPathType | None],
+    "old_style": bool,
+    "tr": typing.NotRequired[float | None],
+    "tr_nup": typing.NotRequired[float | None],
+    "verbosity": 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 {
+        "neuro_deconvolve.py": neuro_deconvolve_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 {
+        "neuro_deconvolve.py": neuro_deconvolve_py_outputs,
+    }.get(t)
+
+
+class NeuroDeconvolvePyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `neuro_deconvolve_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_head: OutputPathType
+    """Main default output head file"""
+    output_brik: OutputPathType
+    """Main default output BRIK file"""
+    kernel_file_out: OutputPathType | None
+    """File storing the response kernel"""
+
+
+def neuro_deconvolve_py_params(
+    input_file: InputPathType,
+    prefix: str,
+    script: str,
+    kernel: str | None = None,
+    kernel_file: str | None = None,
+    mask_dset: InputPathType | None = None,
+    old_style: bool = False,
+    tr: float | None = None,
+    tr_nup: float | None = None,
+    verbosity: float | None = None,
+) -> NeuroDeconvolvePyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_file: Set the data to deconvolve.
+        prefix: Set the prefix for output filenames.
+        script: Specify the name of the output script.
+        kernel: Set the response kernel.
+        kernel_file: Set the filename to store the kernel in; should be at the\
+            upsampled TR.
+        mask_dset: Set a mask dataset for 3dTfitter to use.
+        old_style: Make old-style script (pre-2015.02.24) for 1D case.
+        tr: Set the scanner TR; needed for 1D formatted input files.
+        tr_nup: Upsample factor for TR; number of pieces each original TR is\
+            divided into.
+        verbosity: Set the verbose level.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "neuro_deconvolve.py",
+        "input_file": input_file,
+        "prefix": prefix,
+        "script": script,
+        "old_style": old_style,
+    }
+    if kernel is not None:
+        params["kernel"] = kernel
+    if kernel_file is not None:
+        params["kernel_file"] = kernel_file
+    if mask_dset is not None:
+        params["mask_dset"] = mask_dset
+    if tr is not None:
+        params["tr"] = tr
+    if tr_nup is not None:
+        params["tr_nup"] = tr_nup
+    if verbosity is not None:
+        params["verbosity"] = verbosity
+    return params
+
+
+def neuro_deconvolve_py_cargs(
+    params: NeuroDeconvolvePyParameters,
+    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("neuro_deconvolve.py")
+    cargs.append(execution.input_file(params.get("input_file")))
+    cargs.append(params.get("prefix"))
+    cargs.append(params.get("script"))
+    if params.get("kernel") is not None:
+        cargs.extend([
+            "-kernel",
+            params.get("kernel")
+        ])
+    if params.get("kernel_file") is not None:
+        cargs.extend([
+            "-kernel_file",
+            params.get("kernel_file")
+        ])
+    if params.get("mask_dset") is not None:
+        cargs.extend([
+            "-mask_dset",
+            execution.input_file(params.get("mask_dset"))
+        ])
+    if params.get("old_style"):
+        cargs.append("-old")
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-tr",
+            str(params.get("tr"))
+        ])
+    if params.get("tr_nup") is not None:
+        cargs.extend([
+            "-tr_nup",
+            str(params.get("tr_nup"))
+        ])
+    if params.get("verbosity") is not None:
+        cargs.extend([
+            "-verb",
+            str(params.get("verbosity"))
+        ])
+    return cargs
+
+
+def neuro_deconvolve_py_outputs(
+    params: NeuroDeconvolvePyParameters,
+    execution: Execution,
+) -> NeuroDeconvolvePyOutputs:
+    """
+    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 = NeuroDeconvolvePyOutputs(
+        root=execution.output_file("."),
+        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD"),
+        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK"),
+        kernel_file_out=execution.output_file(params.get("kernel_file")) if (params.get("kernel_file") is not None) else None,
+    )
+    return ret
+
+
+def neuro_deconvolve_py_execute(
+    params: NeuroDeconvolvePyParameters,
+    execution: Execution,
+) -> NeuroDeconvolvePyOutputs:
+    """
+    Generate a script to apply 3dTfitter to deconvolve an MRI signal (BOLD response
+    curve) into a neuro response curve.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `NeuroDeconvolvePyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = neuro_deconvolve_py_cargs(params, execution)
+    ret = neuro_deconvolve_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def neuro_deconvolve_py(
+    input_file: InputPathType,
+    prefix: str,
+    script: str,
+    kernel: str | None = None,
+    kernel_file: str | None = None,
+    mask_dset: InputPathType | None = None,
+    old_style: bool = False,
+    tr: float | None = None,
+    tr_nup: float | None = None,
+    verbosity: float | None = None,
+    runner: Runner | None = None,
+) -> NeuroDeconvolvePyOutputs:
+    """
+    Generate a script to apply 3dTfitter to deconvolve an MRI signal (BOLD response
+    curve) into a neuro response curve.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_file: Set the data to deconvolve.
+        prefix: Set the prefix for output filenames.
+        script: Specify the name of the output script.
+        kernel: Set the response kernel.
+        kernel_file: Set the filename to store the kernel in; should be at the\
+            upsampled TR.
+        mask_dset: Set a mask dataset for 3dTfitter to use.
+        old_style: Make old-style script (pre-2015.02.24) for 1D case.
+        tr: Set the scanner TR; needed for 1D formatted input files.
+        tr_nup: Upsample factor for TR; number of pieces each original TR is\
+            divided into.
+        verbosity: Set the verbose level.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `NeuroDeconvolvePyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NEURO_DECONVOLVE_PY_METADATA)
+    params = neuro_deconvolve_py_params(
+        input_file=input_file,
+        prefix=prefix,
+        script=script,
+        kernel=kernel,
+        kernel_file=kernel_file,
+        mask_dset=mask_dset,
+        old_style=old_style,
+        tr=tr,
+        tr_nup=tr_nup,
+        verbosity=verbosity,
+    )
+    return neuro_deconvolve_py_execute(params, execution)
+
+
+__all__ = [
+    "NEURO_DECONVOLVE_PY_METADATA",
+    "NeuroDeconvolvePyOutputs",
+    "NeuroDeconvolvePyParameters",
+    "neuro_deconvolve_py",
+    "neuro_deconvolve_py_params",
+]

niwrap_afni/afni/nicat.py

@@ -0,0 +1,207 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+NICAT_METADATA = Metadata(
+    id="150f64c79ef2ef5b2c3f9c0b00bdeb1447c981cd.boutiques",
+    name="nicat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+NicatParameters = typing.TypedDict('NicatParameters', {
+    "__STYX_TYPE__": typing.Literal["nicat"],
+    "stream_spec": str,
+    "reopen": typing.NotRequired[str | None],
+    "copy_stream": bool,
+    "read_only": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "nicat": nicat_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 NicatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `nicat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def nicat_params(
+    stream_spec: str,
+    reopen: str | None = None,
+    copy_stream: bool = False,
+    read_only: bool = False,
+) -> NicatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        stream_spec: Stream specification (e.g., tcp:localhost:4444).
+        reopen: Reopen the stream after connection to the stream specified by\
+            the given value.
+        copy_stream: Copy the stream to stdout instead; the 'streamspec' will\
+            be opened for reading.
+        read_only: Read the stream but don't copy to stdout.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "nicat",
+        "stream_spec": stream_spec,
+        "copy_stream": copy_stream,
+        "read_only": read_only,
+    }
+    if reopen is not None:
+        params["reopen"] = reopen
+    return params
+
+
+def nicat_cargs(
+    params: NicatParameters,
+    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("nicat")
+    cargs.append(params.get("stream_spec"))
+    if params.get("reopen") is not None:
+        cargs.extend([
+            "-reopen",
+            params.get("reopen")
+        ])
+    if params.get("copy_stream"):
+        cargs.append("-r")
+    if params.get("read_only"):
+        cargs.append("-R")
+    return cargs
+
+
+def nicat_outputs(
+    params: NicatParameters,
+    execution: Execution,
+) -> NicatOutputs:
+    """
+    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 = NicatOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def nicat_execute(
+    params: NicatParameters,
+    execution: Execution,
+) -> NicatOutputs:
+    """
+    Copies stdin to the NIML stream, which will be opened for writing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `NicatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = nicat_cargs(params, execution)
+    ret = nicat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def nicat(
+    stream_spec: str,
+    reopen: str | None = None,
+    copy_stream: bool = False,
+    read_only: bool = False,
+    runner: Runner | None = None,
+) -> NicatOutputs:
+    """
+    Copies stdin to the NIML stream, which will be opened for writing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        stream_spec: Stream specification (e.g., tcp:localhost:4444).
+        reopen: Reopen the stream after connection to the stream specified by\
+            the given value.
+        copy_stream: Copy the stream to stdout instead; the 'streamspec' will\
+            be opened for reading.
+        read_only: Read the stream but don't copy to stdout.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `NicatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NICAT_METADATA)
+    params = nicat_params(
+        stream_spec=stream_spec,
+        reopen=reopen,
+        copy_stream=copy_stream,
+        read_only=read_only,
+    )
+    return nicat_execute(params, execution)
+
+
+__all__ = [
+    "NICAT_METADATA",
+    "NicatOutputs",
+    "NicatParameters",
+    "nicat",
+    "nicat_params",
+]