niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/align_epi_anat.py

@@ -0,0 +1,356 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ALIGN_EPI_ANAT_METADATA = Metadata(
+    id="8b0229305647603bf69640345954c0975124bb02.boutiques",
+    name="align_epi_anat",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AlignEpiAnatParameters = typing.TypedDict('AlignEpiAnatParameters', {
+    "__STYX_TYPE__": typing.Literal["align_epi_anat"],
+    "epi": InputPathType,
+    "anat": InputPathType,
+    "epi_base": str,
+    "anat2epi": bool,
+    "epi2anat": bool,
+    "suffix": typing.NotRequired[str | None],
+    "AddEdge": bool,
+    "big_move": bool,
+    "giant_move": bool,
+    "ginormous_move": bool,
+    "keep_rm_files": bool,
+    "prep_only": bool,
+    "ana_has_skull": typing.NotRequired[typing.Literal["yes", "no"] | None],
+    "epi_strip": typing.NotRequired[typing.Literal["3dSkullStrip", "3dAutomask", "None"] | None],
+    "volreg_method": typing.NotRequired[typing.Literal["3dvolreg", "3dWarpDrive", "3dAllineate"] | None],
+    "ex_mode": typing.NotRequired[typing.Literal["quiet", "echo", "dry_run", "script"] | None],
+    "overwrite": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "align_epi_anat": align_epi_anat_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 {
+        "align_epi_anat": align_epi_anat_outputs,
+    }.get(t)
+
+
+class AlignEpiAnatOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `align_epi_anat(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    anat_aligned: OutputPathType
+    """A version of the anatomy that is aligned to the EPI"""
+    epi_aligned: OutputPathType
+    """A version of the EPI dataset aligned to the Anatomy"""
+
+
+def align_epi_anat_params(
+    epi: InputPathType,
+    anat: InputPathType,
+    epi_base: str,
+    anat2epi: bool = False,
+    epi2anat: bool = False,
+    suffix: str | None = None,
+    add_edge: bool = False,
+    big_move: bool = False,
+    giant_move: bool = False,
+    ginormous_move: bool = False,
+    keep_rm_files: bool = False,
+    prep_only: bool = False,
+    ana_has_skull: typing.Literal["yes", "no"] | None = None,
+    epi_strip: typing.Literal["3dSkullStrip", "3dAutomask", "None"] | None = None,
+    volreg_method: typing.Literal["3dvolreg", "3dWarpDrive", "3dAllineate"] | None = None,
+    ex_mode: typing.Literal["quiet", "echo", "dry_run", "script"] | None = None,
+    overwrite: bool = False,
+) -> AlignEpiAnatParameters:
+    """
+    Build parameters.
+    
+    Args:
+        epi: EPI dataset to align or to which to align.
+        anat: Anatomical dataset to align or to which to align.
+        epi_base: Base sub-brick to use for alignment\
+            (0/mean/median/max/subbrick#).
+        anat2epi: Align anatomical to EPI dataset (default).
+        epi2anat: Align EPI to anatomical dataset.
+        suffix: Append suffix to the original anat/epi dataset to use in the\
+            resulting dataset names.
+        add_edge: Run @AddEdge script to create composite edge images.
+        big_move: Large displacement is needed to align the two volumes.
+        giant_move: Even larger movement required, uses cmass, two passes and\
+            very large angles and shifts.
+        ginormous_move: Adds align_centers to giant_move.
+        keep_rm_files: Don't delete any of the temporary files created.
+        prep_only: Do preprocessing steps only without alignment.
+        ana_has_skull: Do not skullstrip anat dataset.
+        epi_strip: Method to remove skull for EPI data.
+        volreg_method: Time series volume registration method.
+        ex_mode: Command execution mode.
+        overwrite: Overwrite existing files.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "align_epi_anat",
+        "epi": epi,
+        "anat": anat,
+        "epi_base": epi_base,
+        "anat2epi": anat2epi,
+        "epi2anat": epi2anat,
+        "AddEdge": add_edge,
+        "big_move": big_move,
+        "giant_move": giant_move,
+        "ginormous_move": ginormous_move,
+        "keep_rm_files": keep_rm_files,
+        "prep_only": prep_only,
+        "overwrite": overwrite,
+    }
+    if suffix is not None:
+        params["suffix"] = suffix
+    if ana_has_skull is not None:
+        params["ana_has_skull"] = ana_has_skull
+    if epi_strip is not None:
+        params["epi_strip"] = epi_strip
+    if volreg_method is not None:
+        params["volreg_method"] = volreg_method
+    if ex_mode is not None:
+        params["ex_mode"] = ex_mode
+    return params
+
+
+def align_epi_anat_cargs(
+    params: AlignEpiAnatParameters,
+    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("align_epi_anat.py")
+    cargs.extend([
+        "-epi",
+        execution.input_file(params.get("epi"))
+    ])
+    cargs.extend([
+        "-anat",
+        execution.input_file(params.get("anat"))
+    ])
+    cargs.extend([
+        "-epi_base",
+        params.get("epi_base")
+    ])
+    if params.get("anat2epi"):
+        cargs.append("-anat2epi")
+    if params.get("epi2anat"):
+        cargs.append("-epi2anat")
+    if params.get("suffix") is not None:
+        cargs.extend([
+            "-suffix",
+            params.get("suffix")
+        ])
+    if params.get("AddEdge"):
+        cargs.append("-AddEdge")
+    if params.get("big_move"):
+        cargs.append("-big_move")
+    if params.get("giant_move"):
+        cargs.append("-giant_move")
+    if params.get("ginormous_move"):
+        cargs.append("-ginormous_move")
+    if params.get("keep_rm_files"):
+        cargs.append("-keep_rm_files")
+    if params.get("prep_only"):
+        cargs.append("-prep_only")
+    if params.get("ana_has_skull") is not None:
+        cargs.extend([
+            "-anat_has_skull",
+            params.get("ana_has_skull")
+        ])
+    if params.get("epi_strip") is not None:
+        cargs.extend([
+            "-epi_strip",
+            params.get("epi_strip")
+        ])
+    if params.get("volreg_method") is not None:
+        cargs.extend([
+            "-volreg_method",
+            params.get("volreg_method")
+        ])
+    if params.get("ex_mode") is not None:
+        cargs.extend([
+            "-ex_mode",
+            params.get("ex_mode")
+        ])
+    if params.get("overwrite"):
+        cargs.append("-overwrite")
+    return cargs
+
+
+def align_epi_anat_outputs(
+    params: AlignEpiAnatParameters,
+    execution: Execution,
+) -> AlignEpiAnatOutputs:
+    """
+    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 = AlignEpiAnatOutputs(
+        root=execution.output_file("."),
+        anat_aligned=execution.output_file(pathlib.Path(params.get("anat")).name + "+orig"),
+        epi_aligned=execution.output_file(pathlib.Path(params.get("epi")).name + "+orig"),
+    )
+    return ret
+
+
+def align_epi_anat_execute(
+    params: AlignEpiAnatParameters,
+    execution: Execution,
+) -> AlignEpiAnatOutputs:
+    """
+    Align EPI to anatomical datasets or vice versa.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AlignEpiAnatOutputs`).
+    """
+    params = execution.params(params)
+    cargs = align_epi_anat_cargs(params, execution)
+    ret = align_epi_anat_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def align_epi_anat(
+    epi: InputPathType,
+    anat: InputPathType,
+    epi_base: str,
+    anat2epi: bool = False,
+    epi2anat: bool = False,
+    suffix: str | None = None,
+    add_edge: bool = False,
+    big_move: bool = False,
+    giant_move: bool = False,
+    ginormous_move: bool = False,
+    keep_rm_files: bool = False,
+    prep_only: bool = False,
+    ana_has_skull: typing.Literal["yes", "no"] | None = None,
+    epi_strip: typing.Literal["3dSkullStrip", "3dAutomask", "None"] | None = None,
+    volreg_method: typing.Literal["3dvolreg", "3dWarpDrive", "3dAllineate"] | None = None,
+    ex_mode: typing.Literal["quiet", "echo", "dry_run", "script"] | None = None,
+    overwrite: bool = False,
+    runner: Runner | None = None,
+) -> AlignEpiAnatOutputs:
+    """
+    Align EPI to anatomical datasets or vice versa.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        epi: EPI dataset to align or to which to align.
+        anat: Anatomical dataset to align or to which to align.
+        epi_base: Base sub-brick to use for alignment\
+            (0/mean/median/max/subbrick#).
+        anat2epi: Align anatomical to EPI dataset (default).
+        epi2anat: Align EPI to anatomical dataset.
+        suffix: Append suffix to the original anat/epi dataset to use in the\
+            resulting dataset names.
+        add_edge: Run @AddEdge script to create composite edge images.
+        big_move: Large displacement is needed to align the two volumes.
+        giant_move: Even larger movement required, uses cmass, two passes and\
+            very large angles and shifts.
+        ginormous_move: Adds align_centers to giant_move.
+        keep_rm_files: Don't delete any of the temporary files created.
+        prep_only: Do preprocessing steps only without alignment.
+        ana_has_skull: Do not skullstrip anat dataset.
+        epi_strip: Method to remove skull for EPI data.
+        volreg_method: Time series volume registration method.
+        ex_mode: Command execution mode.
+        overwrite: Overwrite existing files.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AlignEpiAnatOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ALIGN_EPI_ANAT_METADATA)
+    params = align_epi_anat_params(
+        epi=epi,
+        anat=anat,
+        epi_base=epi_base,
+        anat2epi=anat2epi,
+        epi2anat=epi2anat,
+        suffix=suffix,
+        add_edge=add_edge,
+        big_move=big_move,
+        giant_move=giant_move,
+        ginormous_move=ginormous_move,
+        keep_rm_files=keep_rm_files,
+        prep_only=prep_only,
+        ana_has_skull=ana_has_skull,
+        epi_strip=epi_strip,
+        volreg_method=volreg_method,
+        ex_mode=ex_mode,
+        overwrite=overwrite,
+    )
+    return align_epi_anat_execute(params, execution)
+
+
+__all__ = [
+    "ALIGN_EPI_ANAT_METADATA",
+    "AlignEpiAnatOutputs",
+    "AlignEpiAnatParameters",
+    "align_epi_anat",
+    "align_epi_anat_params",
+]

niwrap_afni/afni/analyze_trace.py

@@ -0,0 +1,292 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+ANALYZE_TRACE_METADATA = Metadata(
+    id="3d880a6da4a3639545433e9f6739d09c2df6cf76.boutiques",
+    name="AnalyzeTrace",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+AnalyzeTraceParameters = typing.TypedDict('AnalyzeTraceParameters', {
+    "__STYX_TYPE__": typing.Literal["AnalyzeTrace"],
+    "tracefile": InputPathType,
+    "max_func_lines": typing.NotRequired[int | None],
+    "suma_c": typing.NotRequired[InputPathType | None],
+    "max_err": typing.NotRequired[int | None],
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "trace": bool,
+    "extreme_trace": bool,
+    "nomall": bool,
+    "yesmall": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "AnalyzeTrace": analyze_trace_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 AnalyzeTraceOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `analyze_trace(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def analyze_trace_params(
+    tracefile: InputPathType,
+    max_func_lines: int | None = None,
+    suma_c: InputPathType | None = None,
+    max_err: int | None = None,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    extreme_trace: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+) -> AnalyzeTraceParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tracefile: Trace output file obtained by redirecting the program’s\
+            trace output.
+        max_func_lines: Set the maximum number of code lines before a function\
+            returns. Default is no limit.
+        suma_c: FILE is a SUMA_*.c file. It is analyzed for functions that use\
+            SUMA_RETURN without ENTRY.
+        max_err: Stop after encountering MAX_ERR errors reported in log.\
+            Default is 5. Error key terms are: 'Error', 'error', 'corruption'.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable ENVname to be ENVvalue. Quotes are\
+            necessary.
+        trace_: Turns on In/Out debug and Memory tracing.
+        extreme_trace: Turns on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "AnalyzeTrace",
+        "tracefile": tracefile,
+        "novolreg": novolreg,
+        "noxform": noxform,
+        "trace": trace_,
+        "extreme_trace": extreme_trace,
+        "nomall": nomall,
+        "yesmall": yesmall,
+    }
+    if max_func_lines is not None:
+        params["max_func_lines"] = max_func_lines
+    if suma_c is not None:
+        params["suma_c"] = suma_c
+    if max_err is not None:
+        params["max_err"] = max_err
+    if setenv is not None:
+        params["setenv"] = setenv
+    return params
+
+
+def analyze_trace_cargs(
+    params: AnalyzeTraceParameters,
+    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("AnalyzeTrace")
+    cargs.append(execution.input_file(params.get("tracefile")))
+    if params.get("max_func_lines") is not None:
+        cargs.extend([
+            "-max_func_lines",
+            str(params.get("max_func_lines"))
+        ])
+    if params.get("suma_c") is not None:
+        cargs.extend([
+            "-suma_c",
+            execution.input_file(params.get("suma_c"))
+        ])
+    if params.get("max_err") is not None:
+        cargs.extend([
+            "-max_err",
+            str(params.get("max_err"))
+        ])
+    if params.get("novolreg"):
+        cargs.append("-novolreg")
+    if params.get("noxform"):
+        cargs.append("-noxform")
+    if params.get("setenv") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("setenv")
+        ])
+    if params.get("trace"):
+        cargs.append("-trace")
+    if params.get("extreme_trace"):
+        cargs.append("-TRACE")
+    if params.get("nomall"):
+        cargs.append("-nomall")
+    if params.get("yesmall"):
+        cargs.append("-yesmall")
+    return cargs
+
+
+def analyze_trace_outputs(
+    params: AnalyzeTraceParameters,
+    execution: Execution,
+) -> AnalyzeTraceOutputs:
+    """
+    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 = AnalyzeTraceOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def analyze_trace_execute(
+    params: AnalyzeTraceParameters,
+    execution: Execution,
+) -> AnalyzeTraceOutputs:
+    """
+    A program to analyze SUMA (and AFNI's perhaps) stack output for functions that
+    return with RETURN without bothering to go on the stack.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `AnalyzeTraceOutputs`).
+    """
+    params = execution.params(params)
+    cargs = analyze_trace_cargs(params, execution)
+    ret = analyze_trace_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def analyze_trace(
+    tracefile: InputPathType,
+    max_func_lines: int | None = None,
+    suma_c: InputPathType | None = None,
+    max_err: int | None = None,
+    novolreg: bool = False,
+    noxform: bool = False,
+    setenv: str | None = None,
+    trace_: bool = False,
+    extreme_trace: bool = False,
+    nomall: bool = False,
+    yesmall: bool = False,
+    runner: Runner | None = None,
+) -> AnalyzeTraceOutputs:
+    """
+    A program to analyze SUMA (and AFNI's perhaps) stack output for functions that
+    return with RETURN without bothering to go on the stack.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        tracefile: Trace output file obtained by redirecting the program’s\
+            trace output.
+        max_func_lines: Set the maximum number of code lines before a function\
+            returns. Default is no limit.
+        suma_c: FILE is a SUMA_*.c file. It is analyzed for functions that use\
+            SUMA_RETURN without ENTRY.
+        max_err: Stop after encountering MAX_ERR errors reported in log.\
+            Default is 5. Error key terms are: 'Error', 'error', 'corruption'.
+        novolreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        noxform: Same as -novolreg.
+        setenv: Set environment variable ENVname to be ENVvalue. Quotes are\
+            necessary.
+        trace_: Turns on In/Out debug and Memory tracing.
+        extreme_trace: Turns on extreme tracing.
+        nomall: Turn off memory tracing.
+        yesmall: Turn on memory tracing (default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `AnalyzeTraceOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ANALYZE_TRACE_METADATA)
+    params = analyze_trace_params(
+        tracefile=tracefile,
+        max_func_lines=max_func_lines,
+        suma_c=suma_c,
+        max_err=max_err,
+        novolreg=novolreg,
+        noxform=noxform,
+        setenv=setenv,
+        trace_=trace_,
+        extreme_trace=extreme_trace,
+        nomall=nomall,
+        yesmall=yesmall,
+    )
+    return analyze_trace_execute(params, execution)
+
+
+__all__ = [
+    "ANALYZE_TRACE_METADATA",
+    "AnalyzeTraceOutputs",
+    "AnalyzeTraceParameters",
+    "analyze_trace",
+    "analyze_trace_params",
+]