niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/retro_ts_py.py

@@ -0,0 +1,477 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RETRO_TS_PY_METADATA = Metadata(
+    id="cc5cade6ed0e2d569151f1194c507bd0b645c37b.boutiques",
+    name="RetroTS.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RetroTsPyParameters = typing.TypedDict('RetroTsPyParameters', {
+    "__STYX_TYPE__": typing.Literal["RetroTS.py"],
+    "resp_file": typing.NotRequired[InputPathType | None],
+    "card_file": typing.NotRequired[InputPathType | None],
+    "phys_fs": typing.NotRequired[float | None],
+    "num_slices": float,
+    "volume_tr": float,
+    "phys_file": typing.NotRequired[InputPathType | None],
+    "phys_json": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "rvt_shifts": typing.NotRequired[str | None],
+    "rvt_out": bool,
+    "resp_cutoff_freq": typing.NotRequired[float | None],
+    "cardiac_cutoff_freq": typing.NotRequired[float | None],
+    "cardiac_out": bool,
+    "respiration_out": bool,
+    "interp_style": typing.NotRequired[str | None],
+    "fir_order": typing.NotRequired[float | None],
+    "quiet": bool,
+    "demo": bool,
+    "show_graphs": bool,
+    "debug": bool,
+    "slice_offset": typing.NotRequired[str | None],
+    "slice_major": typing.NotRequired[float | None],
+    "slice_order": typing.NotRequired[str | None],
+    "zero_phase_offset": bool,
+    "legacy_transform": 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 {
+        "RetroTS.py": retro_ts_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 {
+        "RetroTS.py": retro_ts_py_outputs,
+    }.get(t)
+
+
+class RetroTsPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `retro_ts_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_file: OutputPathType | None
+    """Output file containing respiratory and cardiac regressors"""
+
+
+def retro_ts_py_params(
+    num_slices: float,
+    volume_tr: float,
+    resp_file: InputPathType | None = None,
+    card_file: InputPathType | None = None,
+    phys_fs: float | None = None,
+    phys_file: InputPathType | None = None,
+    phys_json: InputPathType | None = None,
+    prefix: str | None = None,
+    rvt_shifts: str | None = None,
+    rvt_out: bool = False,
+    resp_cutoff_freq: float | None = None,
+    cardiac_cutoff_freq: float | None = None,
+    cardiac_out: bool = False,
+    respiration_out: bool = False,
+    interp_style: str | None = None,
+    fir_order: float | None = None,
+    quiet: bool = False,
+    demo: bool = False,
+    show_graphs: bool = False,
+    debug: bool = False,
+    slice_offset: str | None = None,
+    slice_major: float | None = None,
+    slice_order: str | None = None,
+    zero_phase_offset: bool = False,
+    legacy_transform: float | None = None,
+) -> RetroTsPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        num_slices: Number of slices.
+        volume_tr: Volume TR in seconds.
+        resp_file: Respiration data file.
+        card_file: Cardiac data file.
+        phys_fs: Physiological signal sampling frequency in Hz.
+        phys_file: BIDS formatted physio file in tab-separated format, can be\
+            gzipped.
+        phys_json: BIDS formatted physio metadata json file. If not specified,\
+            the json corresponding to the phys_file will be loaded.
+        prefix: Prefix of output file.
+        rvt_shifts: Vector of shifts in seconds of RVT signal. (default is\
+            [0:5:20]).
+        rvt_out: Flag for writing RVT regressors (default is 1).
+        resp_cutoff_freq: Cut-off frequency in Hz for respiratory lowpass\
+            filter (default 3 Hz).
+        cardiac_cutoff_freq: Cut-off frequency in Hz for cardiac lowpass filter\
+            (default 3 Hz).
+        cardiac_out: Flag for writing Cardiac regressors (default is 1).
+        respiration_out: Flag for writing Respiratory regressors (default is 1).
+        interp_style: Resampling kernel (default is 'linear').
+        fir_order: Order of FIR filter (default is 40).
+        quiet: Show talkative progress as the program runs (default is 1).
+        demo: Run demonstration of RetroTS (default is 0).
+        show_graphs: Show graphs (default is unset; set with any parameter to\
+            view).
+        debug: Drop into pdb upon an exception (default is False).
+        slice_offset: Vector of slice acquisition time offsets in seconds\
+            (default is equivalent of alt+z).
+        slice_major: Unknown parameter (default is 1).
+        slice_order: Slice timing information in seconds. (default is alt+z).
+        zero_phase_offset: Zero phase offset flag.
+        legacy_transform: Specify the version of the original Matlab code's\
+            transformation (default is 0).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "RetroTS.py",
+        "num_slices": num_slices,
+        "volume_tr": volume_tr,
+        "rvt_out": rvt_out,
+        "cardiac_out": cardiac_out,
+        "respiration_out": respiration_out,
+        "quiet": quiet,
+        "demo": demo,
+        "show_graphs": show_graphs,
+        "debug": debug,
+        "zero_phase_offset": zero_phase_offset,
+    }
+    if resp_file is not None:
+        params["resp_file"] = resp_file
+    if card_file is not None:
+        params["card_file"] = card_file
+    if phys_fs is not None:
+        params["phys_fs"] = phys_fs
+    if phys_file is not None:
+        params["phys_file"] = phys_file
+    if phys_json is not None:
+        params["phys_json"] = phys_json
+    if prefix is not None:
+        params["prefix"] = prefix
+    if rvt_shifts is not None:
+        params["rvt_shifts"] = rvt_shifts
+    if resp_cutoff_freq is not None:
+        params["resp_cutoff_freq"] = resp_cutoff_freq
+    if cardiac_cutoff_freq is not None:
+        params["cardiac_cutoff_freq"] = cardiac_cutoff_freq
+    if interp_style is not None:
+        params["interp_style"] = interp_style
+    if fir_order is not None:
+        params["fir_order"] = fir_order
+    if slice_offset is not None:
+        params["slice_offset"] = slice_offset
+    if slice_major is not None:
+        params["slice_major"] = slice_major
+    if slice_order is not None:
+        params["slice_order"] = slice_order
+    if legacy_transform is not None:
+        params["legacy_transform"] = legacy_transform
+    return params
+
+
+def retro_ts_py_cargs(
+    params: RetroTsPyParameters,
+    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("RetroTS.py")
+    if params.get("resp_file") is not None:
+        cargs.extend([
+            "-r",
+            execution.input_file(params.get("resp_file"))
+        ])
+    if params.get("card_file") is not None:
+        cargs.extend([
+            "-c",
+            execution.input_file(params.get("card_file"))
+        ])
+    if params.get("phys_fs") is not None:
+        cargs.extend([
+            "-p",
+            str(params.get("phys_fs"))
+        ])
+    cargs.extend([
+        "-n",
+        str(params.get("num_slices"))
+    ])
+    cargs.extend([
+        "-v",
+        str(params.get("volume_tr"))
+    ])
+    if params.get("phys_file") is not None:
+        cargs.extend([
+            "-phys_file",
+            execution.input_file(params.get("phys_file"))
+        ])
+    if params.get("phys_json") is not None:
+        cargs.extend([
+            "-phys_json",
+            execution.input_file(params.get("phys_json"))
+        ])
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("rvt_shifts") is not None:
+        cargs.extend([
+            "-rvt_shifts",
+            params.get("rvt_shifts")
+        ])
+    if params.get("rvt_out"):
+        cargs.append("-rvt_out")
+    if params.get("resp_cutoff_freq") is not None:
+        cargs.extend([
+            "-respiration_cutoff_frequency",
+            str(params.get("resp_cutoff_freq"))
+        ])
+    if params.get("cardiac_cutoff_freq") is not None:
+        cargs.extend([
+            "-cardiac_cutoff_frequency",
+            str(params.get("cardiac_cutoff_freq"))
+        ])
+    if params.get("cardiac_out"):
+        cargs.append("-cardiac_out")
+    if params.get("respiration_out"):
+        cargs.append("-respiration_out")
+    if params.get("interp_style") is not None:
+        cargs.extend([
+            "-interpolation_style",
+            params.get("interp_style")
+        ])
+    if params.get("fir_order") is not None:
+        cargs.extend([
+            "-fir_order",
+            str(params.get("fir_order"))
+        ])
+    if params.get("quiet"):
+        cargs.append("-quiet")
+    if params.get("demo"):
+        cargs.append("-demo")
+    if params.get("show_graphs"):
+        cargs.append("-show_graphs")
+    if params.get("debug"):
+        cargs.append("-debug")
+    if params.get("slice_offset") is not None:
+        cargs.extend([
+            "-slice_offset",
+            params.get("slice_offset")
+        ])
+    if params.get("slice_major") is not None:
+        cargs.extend([
+            "-slice_major",
+            str(params.get("slice_major"))
+        ])
+    if params.get("slice_order") is not None:
+        cargs.extend([
+            "-slice_order",
+            params.get("slice_order")
+        ])
+    if params.get("zero_phase_offset"):
+        cargs.append("-zero_phase_offset")
+    if params.get("legacy_transform") is not None:
+        cargs.extend([
+            "-legacy_transform",
+            str(params.get("legacy_transform"))
+        ])
+    return cargs
+
+
+def retro_ts_py_outputs(
+    params: RetroTsPyParameters,
+    execution: Execution,
+) -> RetroTsPyOutputs:
+    """
+    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 = RetroTsPyOutputs(
+        root=execution.output_file("."),
+        output_file=execution.output_file(params.get("prefix") + ".slibase.1D") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def retro_ts_py_execute(
+    params: RetroTsPyParameters,
+    execution: Execution,
+) -> RetroTsPyOutputs:
+    """
+    Creates slice-based regressors for regressing out components of heart rate,
+    respiration, and respiration volume per time using independent data files or
+    BIDS formatted files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RetroTsPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = retro_ts_py_cargs(params, execution)
+    ret = retro_ts_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def retro_ts_py(
+    num_slices: float,
+    volume_tr: float,
+    resp_file: InputPathType | None = None,
+    card_file: InputPathType | None = None,
+    phys_fs: float | None = None,
+    phys_file: InputPathType | None = None,
+    phys_json: InputPathType | None = None,
+    prefix: str | None = None,
+    rvt_shifts: str | None = None,
+    rvt_out: bool = False,
+    resp_cutoff_freq: float | None = None,
+    cardiac_cutoff_freq: float | None = None,
+    cardiac_out: bool = False,
+    respiration_out: bool = False,
+    interp_style: str | None = None,
+    fir_order: float | None = None,
+    quiet: bool = False,
+    demo: bool = False,
+    show_graphs: bool = False,
+    debug: bool = False,
+    slice_offset: str | None = None,
+    slice_major: float | None = None,
+    slice_order: str | None = None,
+    zero_phase_offset: bool = False,
+    legacy_transform: float | None = None,
+    runner: Runner | None = None,
+) -> RetroTsPyOutputs:
+    """
+    Creates slice-based regressors for regressing out components of heart rate,
+    respiration, and respiration volume per time using independent data files or
+    BIDS formatted files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        num_slices: Number of slices.
+        volume_tr: Volume TR in seconds.
+        resp_file: Respiration data file.
+        card_file: Cardiac data file.
+        phys_fs: Physiological signal sampling frequency in Hz.
+        phys_file: BIDS formatted physio file in tab-separated format, can be\
+            gzipped.
+        phys_json: BIDS formatted physio metadata json file. If not specified,\
+            the json corresponding to the phys_file will be loaded.
+        prefix: Prefix of output file.
+        rvt_shifts: Vector of shifts in seconds of RVT signal. (default is\
+            [0:5:20]).
+        rvt_out: Flag for writing RVT regressors (default is 1).
+        resp_cutoff_freq: Cut-off frequency in Hz for respiratory lowpass\
+            filter (default 3 Hz).
+        cardiac_cutoff_freq: Cut-off frequency in Hz for cardiac lowpass filter\
+            (default 3 Hz).
+        cardiac_out: Flag for writing Cardiac regressors (default is 1).
+        respiration_out: Flag for writing Respiratory regressors (default is 1).
+        interp_style: Resampling kernel (default is 'linear').
+        fir_order: Order of FIR filter (default is 40).
+        quiet: Show talkative progress as the program runs (default is 1).
+        demo: Run demonstration of RetroTS (default is 0).
+        show_graphs: Show graphs (default is unset; set with any parameter to\
+            view).
+        debug: Drop into pdb upon an exception (default is False).
+        slice_offset: Vector of slice acquisition time offsets in seconds\
+            (default is equivalent of alt+z).
+        slice_major: Unknown parameter (default is 1).
+        slice_order: Slice timing information in seconds. (default is alt+z).
+        zero_phase_offset: Zero phase offset flag.
+        legacy_transform: Specify the version of the original Matlab code's\
+            transformation (default is 0).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RetroTsPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RETRO_TS_PY_METADATA)
+    params = retro_ts_py_params(
+        resp_file=resp_file,
+        card_file=card_file,
+        phys_fs=phys_fs,
+        num_slices=num_slices,
+        volume_tr=volume_tr,
+        phys_file=phys_file,
+        phys_json=phys_json,
+        prefix=prefix,
+        rvt_shifts=rvt_shifts,
+        rvt_out=rvt_out,
+        resp_cutoff_freq=resp_cutoff_freq,
+        cardiac_cutoff_freq=cardiac_cutoff_freq,
+        cardiac_out=cardiac_out,
+        respiration_out=respiration_out,
+        interp_style=interp_style,
+        fir_order=fir_order,
+        quiet=quiet,
+        demo=demo,
+        show_graphs=show_graphs,
+        debug=debug,
+        slice_offset=slice_offset,
+        slice_major=slice_major,
+        slice_order=slice_order,
+        zero_phase_offset=zero_phase_offset,
+        legacy_transform=legacy_transform,
+    )
+    return retro_ts_py_execute(params, execution)
+
+
+__all__ = [
+    "RETRO_TS_PY_METADATA",
+    "RetroTsPyOutputs",
+    "RetroTsPyParameters",
+    "retro_ts_py",
+    "retro_ts_py_params",
+]

niwrap_afni/afni/rmz.py

@@ -0,0 +1,203 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+RMZ_METADATA = Metadata(
+    id="22b10eb7b144fa126d7ddab3cdc645947980a96b.boutiques",
+    name="rmz",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+RmzParameters = typing.TypedDict('RmzParameters', {
+    "__STYX_TYPE__": typing.Literal["rmz"],
+    "quiet": bool,
+    "hash_flag": typing.NotRequired[float | None],
+    "keep_flag": bool,
+    "filenames": 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 {
+        "rmz": rmz_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 RmzOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `rmz(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def rmz_params(
+    filenames: list[InputPathType],
+    quiet: bool = False,
+    hash_flag: float | None = None,
+    keep_flag: bool = False,
+) -> RmzParameters:
+    """
+    Build parameters.
+    
+    Args:
+        filenames: Files to zero out and remove.
+        quiet: Quiet mode.
+        hash_flag: Number of times to zero out the files.
+        keep_flag: Keep the files instead of removing them.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "rmz",
+        "quiet": quiet,
+        "keep_flag": keep_flag,
+        "filenames": filenames,
+    }
+    if hash_flag is not None:
+        params["hash_flag"] = hash_flag
+    return params
+
+
+def rmz_cargs(
+    params: RmzParameters,
+    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("rmz")
+    if params.get("quiet"):
+        cargs.append("-q")
+    if params.get("hash_flag") is not None:
+        cargs.extend([
+            "-#",
+            str(params.get("hash_flag"))
+        ])
+    if params.get("keep_flag"):
+        cargs.append("-k")
+    cargs.extend([execution.input_file(f) for f in params.get("filenames")])
+    return cargs
+
+
+def rmz_outputs(
+    params: RmzParameters,
+    execution: Execution,
+) -> RmzOutputs:
+    """
+    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 = RmzOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def rmz_execute(
+    params: RmzParameters,
+    execution: Execution,
+) -> RmzOutputs:
+    """
+    Zeros out files before removing them.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `RmzOutputs`).
+    """
+    params = execution.params(params)
+    cargs = rmz_cargs(params, execution)
+    ret = rmz_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def rmz(
+    filenames: list[InputPathType],
+    quiet: bool = False,
+    hash_flag: float | None = None,
+    keep_flag: bool = False,
+    runner: Runner | None = None,
+) -> RmzOutputs:
+    """
+    Zeros out files before removing them.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        filenames: Files to zero out and remove.
+        quiet: Quiet mode.
+        hash_flag: Number of times to zero out the files.
+        keep_flag: Keep the files instead of removing them.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `RmzOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RMZ_METADATA)
+    params = rmz_params(
+        quiet=quiet,
+        hash_flag=hash_flag,
+        keep_flag=keep_flag,
+        filenames=filenames,
+    )
+    return rmz_execute(params, execution)
+
+
+__all__ = [
+    "RMZ_METADATA",
+    "RmzOutputs",
+    "RmzParameters",
+    "rmz",
+    "rmz_params",
+]