niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/waver.py

@@ -0,0 +1,458 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+WAVER_METADATA = Metadata(
+    id="853f5c7b1276e654db54518623370e48705e17ef.boutiques",
+    name="waver",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+WaverParameters = typing.TypedDict('WaverParameters', {
+    "__STYX_TYPE__": typing.Literal["waver"],
+    "wav": bool,
+    "gam": bool,
+    "expr": typing.NotRequired[str | None],
+    "file_opt": typing.NotRequired[str | None],
+    "delay_time": typing.NotRequired[float | None],
+    "rise_time": typing.NotRequired[float | None],
+    "fall_time": typing.NotRequired[float | None],
+    "undershoot": typing.NotRequired[float | None],
+    "restore_time": typing.NotRequired[float | None],
+    "gamb": typing.NotRequired[float | None],
+    "gamc": typing.NotRequired[float | None],
+    "gamd": typing.NotRequired[float | None],
+    "peak": typing.NotRequired[float | None],
+    "dt": typing.NotRequired[float | None],
+    "tr": typing.NotRequired[float | None],
+    "xyout": bool,
+    "input_file": typing.NotRequired[InputPathType | None],
+    "inline_data": typing.NotRequired[str | None],
+    "tstim_data": typing.NotRequired[str | None],
+    "when_data": typing.NotRequired[str | None],
+    "numout": typing.NotRequired[int | None],
+    "ver_flag": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "waver": waver_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 {
+        "waver": waver_outputs,
+    }.get(t)
+
+
+class WaverOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `waver(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_filename: OutputPathType
+    """The output filename for the result of the waveform."""
+
+
+def waver_params(
+    wav: bool = False,
+    gam: bool = False,
+    expr: str | None = None,
+    file_opt: str | None = None,
+    delay_time: float | None = None,
+    rise_time: float | None = None,
+    fall_time: float | None = None,
+    undershoot: float | None = None,
+    restore_time: float | None = None,
+    gamb: float | None = None,
+    gamc: float | None = None,
+    gamd: float | None = None,
+    peak: float | None = None,
+    dt: float | None = None,
+    tr: float | None = None,
+    xyout: bool = False,
+    input_file: InputPathType | None = None,
+    inline_data: str | None = None,
+    tstim_data: str | None = None,
+    when_data: str | None = None,
+    numout: int | None = None,
+    ver_flag: bool = False,
+) -> WaverParameters:
+    """
+    Build parameters.
+    
+    Args:
+        wav: Sets waveform to Cox special [default].
+        gam: Sets waveform to form t^b * exp(-t/c) (cf. Mark Cohen).
+        expr: Sets waveform to the expression given, which should depend on the\
+            variable 't'.
+        file_opt: Sets waveform to the values read from the file wname, which\
+            should be a single column .1D file. The dt value is the time step (in\
+            seconds) between lines in wname.
+        delay_time: Sets delay time to # seconds [2].
+        rise_time: Sets rise time to # seconds [4].
+        fall_time: Sets fall time to # seconds [6].
+        undershoot: Sets undershoot to # times the peak [0.2].
+        restore_time: Sets time to restore from undershoot [2].
+        gamb: Sets the parameter 'b' to # [8.6].
+        gamc: Sets the parameter 'c' to # [0.547].
+        gamd: Sets the delay time to # seconds [0.0].
+        peak: Sets peak value to # [100].
+        dt: Sets time step of output AND input [0.1].
+        tr: '-TR' is equivalent to '-dt'.
+        xyout: Output data in 2 columns: 1=time 2=waveform (useful for\
+            graphing) [default is 1 column=waveform].
+        input_file: Read timeseries from *.1D formatted 'infile'; convolve with\
+            waveform to produce output.
+        inline_data: Read timeseries from command line DATA; convolve with\
+            waveform to produce output.
+        tstim_data: Read discrete stimulation times from the command line and\
+            convolve the waveform with delta-functions at those times.
+        when_data: Read time blocks when stimulus is 'on' (=1) from the command\
+            line and convolve the waveform with with a zero-one input.
+        numout: Output a timeseries with NN points; if this option is not\
+            given, then enough points are output to let the result tail back down\
+            to zero.
+        ver_flag: Output version information and exit.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "waver",
+        "wav": wav,
+        "gam": gam,
+        "xyout": xyout,
+        "ver_flag": ver_flag,
+    }
+    if expr is not None:
+        params["expr"] = expr
+    if file_opt is not None:
+        params["file_opt"] = file_opt
+    if delay_time is not None:
+        params["delay_time"] = delay_time
+    if rise_time is not None:
+        params["rise_time"] = rise_time
+    if fall_time is not None:
+        params["fall_time"] = fall_time
+    if undershoot is not None:
+        params["undershoot"] = undershoot
+    if restore_time is not None:
+        params["restore_time"] = restore_time
+    if gamb is not None:
+        params["gamb"] = gamb
+    if gamc is not None:
+        params["gamc"] = gamc
+    if gamd is not None:
+        params["gamd"] = gamd
+    if peak is not None:
+        params["peak"] = peak
+    if dt is not None:
+        params["dt"] = dt
+    if tr is not None:
+        params["tr"] = tr
+    if input_file is not None:
+        params["input_file"] = input_file
+    if inline_data is not None:
+        params["inline_data"] = inline_data
+    if tstim_data is not None:
+        params["tstim_data"] = tstim_data
+    if when_data is not None:
+        params["when_data"] = when_data
+    if numout is not None:
+        params["numout"] = numout
+    return params
+
+
+def waver_cargs(
+    params: WaverParameters,
+    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("waver")
+    if params.get("wav"):
+        cargs.append("-WAV")
+    if params.get("gam"):
+        cargs.append("-GAM")
+    if params.get("expr") is not None:
+        cargs.extend([
+            "-EXPR",
+            params.get("expr")
+        ])
+    if params.get("file_opt") is not None:
+        cargs.extend([
+            "-FILE",
+            params.get("file_opt")
+        ])
+    if params.get("delay_time") is not None:
+        cargs.extend([
+            "-delaytime",
+            str(params.get("delay_time"))
+        ])
+    if params.get("rise_time") is not None:
+        cargs.extend([
+            "-risetime",
+            str(params.get("rise_time"))
+        ])
+    if params.get("fall_time") is not None:
+        cargs.extend([
+            "-falltime",
+            str(params.get("fall_time"))
+        ])
+    if params.get("undershoot") is not None:
+        cargs.extend([
+            "-undershoot",
+            str(params.get("undershoot"))
+        ])
+    if params.get("restore_time") is not None:
+        cargs.extend([
+            "-restoretime",
+            str(params.get("restore_time"))
+        ])
+    if params.get("gamb") is not None:
+        cargs.extend([
+            "-gamb",
+            str(params.get("gamb"))
+        ])
+    if params.get("gamc") is not None:
+        cargs.extend([
+            "-gamc",
+            str(params.get("gamc"))
+        ])
+    if params.get("gamd") is not None:
+        cargs.extend([
+            "-gamd",
+            str(params.get("gamd"))
+        ])
+    if params.get("peak") is not None:
+        cargs.extend([
+            "-peak",
+            str(params.get("peak"))
+        ])
+    if params.get("dt") is not None:
+        cargs.extend([
+            "-dt",
+            str(params.get("dt"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("tr"))
+        ])
+    if params.get("xyout"):
+        cargs.append("-xyout")
+    if params.get("input_file") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input_file"))
+        ])
+    if params.get("inline_data") is not None:
+        cargs.extend([
+            "-inline",
+            params.get("inline_data")
+        ])
+    if params.get("tstim_data") is not None:
+        cargs.extend([
+            "-tstim",
+            params.get("tstim_data")
+        ])
+    if params.get("when_data") is not None:
+        cargs.extend([
+            "-when",
+            params.get("when_data")
+        ])
+    if params.get("numout") is not None:
+        cargs.extend([
+            "-numout",
+            str(params.get("numout"))
+        ])
+    if params.get("ver_flag"):
+        cargs.append("-ver")
+    return cargs
+
+
+def waver_outputs(
+    params: WaverParameters,
+    execution: Execution,
+) -> WaverOutputs:
+    """
+    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 = WaverOutputs(
+        root=execution.output_file("."),
+        output_filename=execution.output_file("output_filename"),
+    )
+    return ret
+
+
+def waver_execute(
+    params: WaverParameters,
+    execution: Execution,
+) -> WaverOutputs:
+    """
+    Creates an ideal waveform timeseries file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `WaverOutputs`).
+    """
+    params = execution.params(params)
+    cargs = waver_cargs(params, execution)
+    ret = waver_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def waver(
+    wav: bool = False,
+    gam: bool = False,
+    expr: str | None = None,
+    file_opt: str | None = None,
+    delay_time: float | None = None,
+    rise_time: float | None = None,
+    fall_time: float | None = None,
+    undershoot: float | None = None,
+    restore_time: float | None = None,
+    gamb: float | None = None,
+    gamc: float | None = None,
+    gamd: float | None = None,
+    peak: float | None = None,
+    dt: float | None = None,
+    tr: float | None = None,
+    xyout: bool = False,
+    input_file: InputPathType | None = None,
+    inline_data: str | None = None,
+    tstim_data: str | None = None,
+    when_data: str | None = None,
+    numout: int | None = None,
+    ver_flag: bool = False,
+    runner: Runner | None = None,
+) -> WaverOutputs:
+    """
+    Creates an ideal waveform timeseries file.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        wav: Sets waveform to Cox special [default].
+        gam: Sets waveform to form t^b * exp(-t/c) (cf. Mark Cohen).
+        expr: Sets waveform to the expression given, which should depend on the\
+            variable 't'.
+        file_opt: Sets waveform to the values read from the file wname, which\
+            should be a single column .1D file. The dt value is the time step (in\
+            seconds) between lines in wname.
+        delay_time: Sets delay time to # seconds [2].
+        rise_time: Sets rise time to # seconds [4].
+        fall_time: Sets fall time to # seconds [6].
+        undershoot: Sets undershoot to # times the peak [0.2].
+        restore_time: Sets time to restore from undershoot [2].
+        gamb: Sets the parameter 'b' to # [8.6].
+        gamc: Sets the parameter 'c' to # [0.547].
+        gamd: Sets the delay time to # seconds [0.0].
+        peak: Sets peak value to # [100].
+        dt: Sets time step of output AND input [0.1].
+        tr: '-TR' is equivalent to '-dt'.
+        xyout: Output data in 2 columns: 1=time 2=waveform (useful for\
+            graphing) [default is 1 column=waveform].
+        input_file: Read timeseries from *.1D formatted 'infile'; convolve with\
+            waveform to produce output.
+        inline_data: Read timeseries from command line DATA; convolve with\
+            waveform to produce output.
+        tstim_data: Read discrete stimulation times from the command line and\
+            convolve the waveform with delta-functions at those times.
+        when_data: Read time blocks when stimulus is 'on' (=1) from the command\
+            line and convolve the waveform with with a zero-one input.
+        numout: Output a timeseries with NN points; if this option is not\
+            given, then enough points are output to let the result tail back down\
+            to zero.
+        ver_flag: Output version information and exit.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `WaverOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WAVER_METADATA)
+    params = waver_params(
+        wav=wav,
+        gam=gam,
+        expr=expr,
+        file_opt=file_opt,
+        delay_time=delay_time,
+        rise_time=rise_time,
+        fall_time=fall_time,
+        undershoot=undershoot,
+        restore_time=restore_time,
+        gamb=gamb,
+        gamc=gamc,
+        gamd=gamd,
+        peak=peak,
+        dt=dt,
+        tr=tr,
+        xyout=xyout,
+        input_file=input_file,
+        inline_data=inline_data,
+        tstim_data=tstim_data,
+        when_data=when_data,
+        numout=numout,
+        ver_flag=ver_flag,
+    )
+    return waver_execute(params, execution)
+
+
+__all__ = [
+    "WAVER_METADATA",
+    "WaverOutputs",
+    "WaverParameters",
+    "waver",
+    "waver_params",
+]

niwrap_afni/afni/whirlgif.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 *
+
+WHIRLGIF_METADATA = Metadata(
+    id="e4c0871988c7cdc7bddc466fe2124de7c556f8a7.boutiques",
+    name="whirlgif",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+WhirlgifParameters = typing.TypedDict('WhirlgifParameters', {
+    "__STYX_TYPE__": typing.Literal["whirlgif"],
+    "verbose": bool,
+    "loop": typing.NotRequired[str | None],
+    "transparency_index": typing.NotRequired[float | None],
+    "inter_frame_delay": typing.NotRequired[float | None],
+    "outfile": typing.NotRequired[str | None],
+    "infile": typing.NotRequired[InputPathType | None],
+    "gif_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 {
+        "whirlgif": whirlgif_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 {
+        "whirlgif": whirlgif_outputs,
+    }.get(t)
+
+
+class WhirlgifOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `whirlgif(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_gif: OutputPathType | None
+    """The output GIF file"""
+
+
+def whirlgif_params(
+    gif_files: list[InputPathType],
+    verbose: bool = False,
+    loop: str | None = None,
+    transparency_index: float | None = None,
+    inter_frame_delay: float | None = None,
+    outfile: str | None = None,
+    infile: InputPathType | None = None,
+) -> WhirlgifParameters:
+    """
+    Build parameters.
+    
+    Args:
+        gif_files: Input GIF files to be combined into a single GIF file.
+        verbose: Verbose mode.
+        loop: Add the Netscape 'loop' extension. Optionally specify a loop\
+            count.
+        transparency_index: Set the colormap index 'index' to be transparent.
+        inter_frame_delay: Inter-frame timing delay.
+        outfile: Specify the output file to write the results to.
+        infile: Read a list of filenames from a file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "whirlgif",
+        "verbose": verbose,
+        "gif_files": gif_files,
+    }
+    if loop is not None:
+        params["loop"] = loop
+    if transparency_index is not None:
+        params["transparency_index"] = transparency_index
+    if inter_frame_delay is not None:
+        params["inter_frame_delay"] = inter_frame_delay
+    if outfile is not None:
+        params["outfile"] = outfile
+    if infile is not None:
+        params["infile"] = infile
+    return params
+
+
+def whirlgif_cargs(
+    params: WhirlgifParameters,
+    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("whirlgif")
+    if params.get("verbose"):
+        cargs.append("-v")
+    if params.get("loop") is not None:
+        cargs.extend([
+            "-loop",
+            params.get("loop")
+        ])
+    if params.get("transparency_index") is not None:
+        cargs.extend([
+            "-trans",
+            str(params.get("transparency_index"))
+        ])
+    if params.get("inter_frame_delay") is not None:
+        cargs.extend([
+            "-time",
+            str(params.get("inter_frame_delay"))
+        ])
+    if params.get("outfile") is not None:
+        cargs.extend([
+            "-o",
+            params.get("outfile")
+        ])
+    if params.get("infile") is not None:
+        cargs.extend([
+            "-i",
+            execution.input_file(params.get("infile"))
+        ])
+    cargs.extend([execution.input_file(f) for f in params.get("gif_files")])
+    return cargs
+
+
+def whirlgif_outputs(
+    params: WhirlgifParameters,
+    execution: Execution,
+) -> WhirlgifOutputs:
+    """
+    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 = WhirlgifOutputs(
+        root=execution.output_file("."),
+        output_gif=execution.output_file(params.get("outfile")) if (params.get("outfile") is not None) else None,
+    )
+    return ret
+
+
+def whirlgif_execute(
+    params: WhirlgifParameters,
+    execution: Execution,
+) -> WhirlgifOutputs:
+    """
+    A quick program that reads a series of GIF files and produces a single GIF file
+    composed of those images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `WhirlgifOutputs`).
+    """
+    params = execution.params(params)
+    cargs = whirlgif_cargs(params, execution)
+    ret = whirlgif_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def whirlgif(
+    gif_files: list[InputPathType],
+    verbose: bool = False,
+    loop: str | None = None,
+    transparency_index: float | None = None,
+    inter_frame_delay: float | None = None,
+    outfile: str | None = None,
+    infile: InputPathType | None = None,
+    runner: Runner | None = None,
+) -> WhirlgifOutputs:
+    """
+    A quick program that reads a series of GIF files and produces a single GIF file
+    composed of those images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        gif_files: Input GIF files to be combined into a single GIF file.
+        verbose: Verbose mode.
+        loop: Add the Netscape 'loop' extension. Optionally specify a loop\
+            count.
+        transparency_index: Set the colormap index 'index' to be transparent.
+        inter_frame_delay: Inter-frame timing delay.
+        outfile: Specify the output file to write the results to.
+        infile: Read a list of filenames from a file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `WhirlgifOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(WHIRLGIF_METADATA)
+    params = whirlgif_params(
+        verbose=verbose,
+        loop=loop,
+        transparency_index=transparency_index,
+        inter_frame_delay=inter_frame_delay,
+        outfile=outfile,
+        infile=infile,
+        gif_files=gif_files,
+    )
+    return whirlgif_execute(params, execution)
+
+
+__all__ = [
+    "WHIRLGIF_METADATA",
+    "WhirlgifOutputs",
+    "WhirlgifParameters",
+    "whirlgif",
+    "whirlgif_params",
+]