niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/tfim.py

@@ -0,0 +1,267 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TFIM_METADATA = Metadata(
+    id="e112b845a4c25dd82a06881f7a7a51dae6274c19.boutiques",
+    name="tfim",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+TfimParameters = typing.TypedDict('TfimParameters', {
+    "__STYX_TYPE__": typing.Literal["tfim"],
+    "prefix": typing.NotRequired[str | None],
+    "pthresh": typing.NotRequired[float | None],
+    "eqcorr": typing.NotRequired[float | None],
+    "paired": bool,
+    "set1_images": list[InputPathType],
+    "set2_images": list[InputPathType],
+    "base1_value": 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 {
+        "tfim": tfim_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 {
+        "tfim": tfim_outputs,
+    }.get(t)
+
+
+class TfimOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `tfim(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    diff_output: OutputPathType | None
+    """Difference image output. Default prefix is 'tfim'."""
+    tspm_output: OutputPathType | None
+    """T-statistic of difference. Default prefix is 'tfim'."""
+    corr_output: OutputPathType | None
+    """Equivalent correlation statistic output. Written if -eqcorr is used."""
+
+
+def tfim_params(
+    set1_images: list[InputPathType],
+    set2_images: list[InputPathType],
+    prefix: str | None = None,
+    pthresh: float | None = None,
+    eqcorr: float | None = None,
+    paired: bool = False,
+    base1_value: float | None = None,
+) -> TfimParameters:
+    """
+    Build parameters.
+    
+    Args:
+        set1_images: First set of image files.
+        set2_images: Second set of image files.
+        prefix: Prefix for output filenames. Default is 'tfim'.
+        pthresh: Significance level (per voxel) to threshold the output with.\
+            Voxels with t-statistic less significant than this will have their diff\
+            output zeroed. Default is no threshold.
+        eqcorr: Write out the equivalent correlation statistic. The number\
+            'dval' is the value to use for 'dof'. Default is not to write this\
+            file.
+        paired: Compare -set1 and -set2 using a paired sample t-test. Illegal\
+            with the -base1 option.
+        base1_value: Base value for the first set of images. Used for Usage 2.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "tfim",
+        "paired": paired,
+        "set1_images": set1_images,
+        "set2_images": set2_images,
+    }
+    if prefix is not None:
+        params["prefix"] = prefix
+    if pthresh is not None:
+        params["pthresh"] = pthresh
+    if eqcorr is not None:
+        params["eqcorr"] = eqcorr
+    if base1_value is not None:
+        params["base1_value"] = base1_value
+    return params
+
+
+def tfim_cargs(
+    params: TfimParameters,
+    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("tfim")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("pthresh") is not None:
+        cargs.extend([
+            "-pthresh",
+            str(params.get("pthresh"))
+        ])
+    if params.get("eqcorr") is not None:
+        cargs.extend([
+            "-eqcorr",
+            str(params.get("eqcorr"))
+        ])
+    if params.get("paired"):
+        cargs.append("-paired")
+    cargs.extend([
+        "-set1",
+        *[execution.input_file(f) for f in params.get("set1_images")]
+    ])
+    cargs.extend([
+        "-set2",
+        *[execution.input_file(f) for f in params.get("set2_images")]
+    ])
+    if params.get("base1_value") is not None:
+        cargs.extend([
+            "-base1",
+            str(params.get("base1_value"))
+        ])
+    return cargs
+
+
+def tfim_outputs(
+    params: TfimParameters,
+    execution: Execution,
+) -> TfimOutputs:
+    """
+    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 = TfimOutputs(
+        root=execution.output_file("."),
+        diff_output=execution.output_file(params.get("prefix") + ".diff") if (params.get("prefix") is not None) else None,
+        tspm_output=execution.output_file(params.get("prefix") + ".tspm") if (params.get("prefix") is not None) else None,
+        corr_output=execution.output_file(params.get("prefix") + ".corr") if (params.get("prefix") is not None) else None,
+    )
+    return ret
+
+
+def tfim_execute(
+    params: TfimParameters,
+    execution: Execution,
+) -> TfimOutputs:
+    """
+    MCW TFIM: t-tests on sets of functional images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TfimOutputs`).
+    """
+    params = execution.params(params)
+    cargs = tfim_cargs(params, execution)
+    ret = tfim_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def tfim(
+    set1_images: list[InputPathType],
+    set2_images: list[InputPathType],
+    prefix: str | None = None,
+    pthresh: float | None = None,
+    eqcorr: float | None = None,
+    paired: bool = False,
+    base1_value: float | None = None,
+    runner: Runner | None = None,
+) -> TfimOutputs:
+    """
+    MCW TFIM: t-tests on sets of functional images.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        set1_images: First set of image files.
+        set2_images: Second set of image files.
+        prefix: Prefix for output filenames. Default is 'tfim'.
+        pthresh: Significance level (per voxel) to threshold the output with.\
+            Voxels with t-statistic less significant than this will have their diff\
+            output zeroed. Default is no threshold.
+        eqcorr: Write out the equivalent correlation statistic. The number\
+            'dval' is the value to use for 'dof'. Default is not to write this\
+            file.
+        paired: Compare -set1 and -set2 using a paired sample t-test. Illegal\
+            with the -base1 option.
+        base1_value: Base value for the first set of images. Used for Usage 2.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TfimOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TFIM_METADATA)
+    params = tfim_params(
+        prefix=prefix,
+        pthresh=pthresh,
+        eqcorr=eqcorr,
+        paired=paired,
+        set1_images=set1_images,
+        set2_images=set2_images,
+        base1_value=base1_value,
+    )
+    return tfim_execute(params, execution)
+
+
+__all__ = [
+    "TFIM_METADATA",
+    "TfimOutputs",
+    "TfimParameters",
+    "tfim",
+    "tfim_params",
+]

niwrap_afni/afni/timing_tool_py.py

@@ -0,0 +1,406 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+TIMING_TOOL_PY_METADATA = Metadata(
+    id="e72448a163610156059a44280593b8076536b24a.boutiques",
+    name="timing_tool.py",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+TimingToolPyParameters = typing.TypedDict('TimingToolPyParameters', {
+    "__STYX_TYPE__": typing.Literal["timing_tool.py"],
+    "timing_file": typing.NotRequired[InputPathType | None],
+    "output_file": typing.NotRequired[str | None],
+    "run_length": typing.NotRequired[list[float] | None],
+    "tr": typing.NotRequired[float | None],
+    "offset": typing.NotRequired[float | None],
+    "extend_file": typing.NotRequired[InputPathType | None],
+    "sort": bool,
+    "scale_data": typing.NotRequired[float | None],
+    "shift_to_run_offset": typing.NotRequired[float | None],
+    "timing_to_1D_file": typing.NotRequired[str | None],
+    "stim_duration": typing.NotRequired[float | None],
+    "multi_timing_files": typing.NotRequired[list[InputPathType] | None],
+    "multi_show_isi_stats": bool,
+    "multi_show_timing": bool,
+    "show_timing": bool,
+    "multi_stim_duration": typing.NotRequired[list[float] | None],
+    "round_times_frac": typing.NotRequired[float | None],
+    "truncate_times": bool,
+    "multi_timing_event_list": 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 {
+        "timing_tool.py": timing_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 {
+        "timing_tool.py": timing_tool_py_outputs,
+    }.get(t)
+
+
+class TimingToolPyOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `timing_tool_py(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_timing_file: OutputPathType | None
+    """Output timing file as specified"""
+    timing_to_1_d_output: OutputPathType | None
+    """Output 1D formatted stimulus data"""
+
+
+def timing_tool_py_params(
+    timing_file: InputPathType | None = None,
+    output_file: str | None = None,
+    run_length: list[float] | None = None,
+    tr: float | None = None,
+    offset: float | None = None,
+    extend_file: InputPathType | None = None,
+    sort: bool = False,
+    scale_data: float | None = None,
+    shift_to_run_offset: float | None = None,
+    timing_to_1_d_file: str | None = None,
+    stim_duration: float | None = None,
+    multi_timing_files: list[InputPathType] | None = None,
+    multi_show_isi_stats: bool = False,
+    multi_show_timing: bool = False,
+    show_timing: bool = False,
+    multi_stim_duration: list[float] | None = None,
+    round_times_frac: float | None = None,
+    truncate_times: bool = False,
+    multi_timing_event_list: str | None = None,
+) -> TimingToolPyParameters:
+    """
+    Build parameters.
+    
+    Args:
+        timing_file: Specify a stimulus timing file to load.
+        output_file: Specify the output timing file.
+        run_length: Specify the run duration(s), in seconds.
+        tr: Specify the time resolution in 1D output (in seconds).
+        offset: Add OFFSET to every time in the main element.
+        extend_file: Extend timing rows with those in NEW_FILE.
+        sort: Sort the times, per row (run).
+        scale_data: Multiply every stim time by SCALAR.
+        shift_to_run_offset: Shift times so first event is at start of run.
+        timing_to_1_d_file: Convert stim_times format to stim_file.
+        stim_duration: Specify the stimulus duration, in seconds.
+        multi_timing_files: Specify multiple timing files to load.
+        multi_show_isi_stats: Display timing and ISI statistics for the\
+            multiple timing files.
+        multi_show_timing: Display info on multiple timing elements.
+        show_timing: Display info on the main timing element.
+        multi_stim_duration: Specify stimulus duration(s), in seconds, for\
+            multiple timing elements.
+        round_times_frac: Round times to multiples of the TR (0.0 <= FRAC <=\
+            1.0).
+        truncate_times: Truncate times to multiples of the TR.
+        multi_timing_event_list: Create an event list file from multiple timing\
+            files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "timing_tool.py",
+        "sort": sort,
+        "multi_show_isi_stats": multi_show_isi_stats,
+        "multi_show_timing": multi_show_timing,
+        "show_timing": show_timing,
+        "truncate_times": truncate_times,
+    }
+    if timing_file is not None:
+        params["timing_file"] = timing_file
+    if output_file is not None:
+        params["output_file"] = output_file
+    if run_length is not None:
+        params["run_length"] = run_length
+    if tr is not None:
+        params["tr"] = tr
+    if offset is not None:
+        params["offset"] = offset
+    if extend_file is not None:
+        params["extend_file"] = extend_file
+    if scale_data is not None:
+        params["scale_data"] = scale_data
+    if shift_to_run_offset is not None:
+        params["shift_to_run_offset"] = shift_to_run_offset
+    if timing_to_1_d_file is not None:
+        params["timing_to_1D_file"] = timing_to_1_d_file
+    if stim_duration is not None:
+        params["stim_duration"] = stim_duration
+    if multi_timing_files is not None:
+        params["multi_timing_files"] = multi_timing_files
+    if multi_stim_duration is not None:
+        params["multi_stim_duration"] = multi_stim_duration
+    if round_times_frac is not None:
+        params["round_times_frac"] = round_times_frac
+    if multi_timing_event_list is not None:
+        params["multi_timing_event_list"] = multi_timing_event_list
+    return params
+
+
+def timing_tool_py_cargs(
+    params: TimingToolPyParameters,
+    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("timing_tool.py")
+    if params.get("timing_file") is not None:
+        cargs.extend([
+            "-timing",
+            execution.input_file(params.get("timing_file"))
+        ])
+    if params.get("output_file") is not None:
+        cargs.extend([
+            "-write_timing",
+            params.get("output_file")
+        ])
+    if params.get("run_length") is not None:
+        cargs.extend([
+            "-run_len",
+            *map(str, params.get("run_length"))
+        ])
+    if params.get("tr") is not None:
+        cargs.extend([
+            "-tr",
+            str(params.get("tr"))
+        ])
+    if params.get("offset") is not None:
+        cargs.extend([
+            "-add_offset",
+            str(params.get("offset"))
+        ])
+    if params.get("extend_file") is not None:
+        cargs.extend([
+            "-extend",
+            execution.input_file(params.get("extend_file"))
+        ])
+    if params.get("sort"):
+        cargs.append("-sort")
+    if params.get("scale_data") is not None:
+        cargs.extend([
+            "-scale_data",
+            str(params.get("scale_data"))
+        ])
+    if params.get("shift_to_run_offset") is not None:
+        cargs.extend([
+            "-shift_to_run_offset",
+            str(params.get("shift_to_run_offset"))
+        ])
+    if params.get("timing_to_1D_file") is not None:
+        cargs.extend([
+            "-timing_to_1D",
+            params.get("timing_to_1D_file")
+        ])
+    if params.get("stim_duration") is not None:
+        cargs.extend([
+            "-stim_dur",
+            str(params.get("stim_duration"))
+        ])
+    if params.get("multi_timing_files") is not None:
+        cargs.extend([
+            "-multi_timing",
+            *[execution.input_file(f) for f in params.get("multi_timing_files")]
+        ])
+    if params.get("multi_show_isi_stats"):
+        cargs.append("-multi_show_isi_stats")
+    if params.get("multi_show_timing"):
+        cargs.append("-multi_show_timing_ele")
+    if params.get("show_timing"):
+        cargs.append("-show_timing_ele")
+    if params.get("multi_stim_duration") is not None:
+        cargs.extend([
+            "-multi_stim_dur",
+            *map(str, params.get("multi_stim_duration"))
+        ])
+    if params.get("round_times_frac") is not None:
+        cargs.extend([
+            "-round_times",
+            str(params.get("round_times_frac"))
+        ])
+    if params.get("truncate_times"):
+        cargs.append("-truncate_times")
+    if params.get("multi_timing_event_list") is not None:
+        cargs.extend([
+            "-multi_timing_to_event_list",
+            params.get("multi_timing_event_list")
+        ])
+    return cargs
+
+
+def timing_tool_py_outputs(
+    params: TimingToolPyParameters,
+    execution: Execution,
+) -> TimingToolPyOutputs:
+    """
+    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 = TimingToolPyOutputs(
+        root=execution.output_file("."),
+        output_timing_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        timing_to_1_d_output=execution.output_file(params.get("timing_to_1D_file")) if (params.get("timing_to_1D_file") is not None) else None,
+    )
+    return ret
+
+
+def timing_tool_py_execute(
+    params: TimingToolPyParameters,
+    execution: Execution,
+) -> TimingToolPyOutputs:
+    """
+    Tool for manipulating and evaluating stimulus timing files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `TimingToolPyOutputs`).
+    """
+    params = execution.params(params)
+    cargs = timing_tool_py_cargs(params, execution)
+    ret = timing_tool_py_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def timing_tool_py(
+    timing_file: InputPathType | None = None,
+    output_file: str | None = None,
+    run_length: list[float] | None = None,
+    tr: float | None = None,
+    offset: float | None = None,
+    extend_file: InputPathType | None = None,
+    sort: bool = False,
+    scale_data: float | None = None,
+    shift_to_run_offset: float | None = None,
+    timing_to_1_d_file: str | None = None,
+    stim_duration: float | None = None,
+    multi_timing_files: list[InputPathType] | None = None,
+    multi_show_isi_stats: bool = False,
+    multi_show_timing: bool = False,
+    show_timing: bool = False,
+    multi_stim_duration: list[float] | None = None,
+    round_times_frac: float | None = None,
+    truncate_times: bool = False,
+    multi_timing_event_list: str | None = None,
+    runner: Runner | None = None,
+) -> TimingToolPyOutputs:
+    """
+    Tool for manipulating and evaluating stimulus timing files.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        timing_file: Specify a stimulus timing file to load.
+        output_file: Specify the output timing file.
+        run_length: Specify the run duration(s), in seconds.
+        tr: Specify the time resolution in 1D output (in seconds).
+        offset: Add OFFSET to every time in the main element.
+        extend_file: Extend timing rows with those in NEW_FILE.
+        sort: Sort the times, per row (run).
+        scale_data: Multiply every stim time by SCALAR.
+        shift_to_run_offset: Shift times so first event is at start of run.
+        timing_to_1_d_file: Convert stim_times format to stim_file.
+        stim_duration: Specify the stimulus duration, in seconds.
+        multi_timing_files: Specify multiple timing files to load.
+        multi_show_isi_stats: Display timing and ISI statistics for the\
+            multiple timing files.
+        multi_show_timing: Display info on multiple timing elements.
+        show_timing: Display info on the main timing element.
+        multi_stim_duration: Specify stimulus duration(s), in seconds, for\
+            multiple timing elements.
+        round_times_frac: Round times to multiples of the TR (0.0 <= FRAC <=\
+            1.0).
+        truncate_times: Truncate times to multiples of the TR.
+        multi_timing_event_list: Create an event list file from multiple timing\
+            files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `TimingToolPyOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TIMING_TOOL_PY_METADATA)
+    params = timing_tool_py_params(
+        timing_file=timing_file,
+        output_file=output_file,
+        run_length=run_length,
+        tr=tr,
+        offset=offset,
+        extend_file=extend_file,
+        sort=sort,
+        scale_data=scale_data,
+        shift_to_run_offset=shift_to_run_offset,
+        timing_to_1_d_file=timing_to_1_d_file,
+        stim_duration=stim_duration,
+        multi_timing_files=multi_timing_files,
+        multi_show_isi_stats=multi_show_isi_stats,
+        multi_show_timing=multi_show_timing,
+        show_timing=show_timing,
+        multi_stim_duration=multi_stim_duration,
+        round_times_frac=round_times_frac,
+        truncate_times=truncate_times,
+        multi_timing_event_list=multi_timing_event_list,
+    )
+    return timing_tool_py_execute(params, execution)
+
+
+__all__ = [
+    "TIMING_TOOL_PY_METADATA",
+    "TimingToolPyOutputs",
+    "TimingToolPyParameters",
+    "timing_tool_py",
+    "timing_tool_py_params",
+]