niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/compare_surfaces.py

@@ -0,0 +1,344 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+COMPARE_SURFACES_METADATA = Metadata(
+    id="fae97b4935dc6acada057829467fb30bd5e3f339.boutiques",
+    name="CompareSurfaces",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+CompareSurfacesParameters = typing.TypedDict('CompareSurfacesParameters', {
+    "__STYX_TYPE__": typing.Literal["CompareSurfaces"],
+    "spec_file": InputPathType,
+    "hemisphere": typing.Literal["L", "R"],
+    "volume_parent_1": InputPathType,
+    "volume_parent_2": InputPathType,
+    "file_prefix": typing.NotRequired[str | None],
+    "one_node": typing.NotRequired[float | None],
+    "node_range": typing.NotRequired[list[float] | None],
+    "no_consistency_check": bool,
+    "no_volreg": bool,
+    "no_transform": bool,
+    "set_environment_variable": typing.NotRequired[str | None],
+    "trace": bool,
+    "extreme_trace": bool,
+    "no_memory_trace": bool,
+    "yes_memory_trace": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "CompareSurfaces": compare_surfaces_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 {
+        "CompareSurfaces": compare_surfaces_outputs,
+    }.get(t)
+
+
+class CompareSurfacesOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `compare_surfaces(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    distance_output_file: OutputPathType | None
+    """Distance output file."""
+    color_output_file: OutputPathType | None
+    """Node color output file."""
+
+
+def compare_surfaces_params(
+    spec_file: InputPathType,
+    hemisphere: typing.Literal["L", "R"],
+    volume_parent_1: InputPathType,
+    volume_parent_2: InputPathType,
+    file_prefix: str | None = None,
+    one_node: float | None = None,
+    node_range: list[float] | None = None,
+    no_consistency_check: bool = False,
+    no_volreg: bool = False,
+    no_transform: bool = False,
+    set_environment_variable: str | None = None,
+    trace_: bool = False,
+    extreme_trace: bool = False,
+    no_memory_trace: bool = False,
+    yes_memory_trace: bool = False,
+) -> CompareSurfacesParameters:
+    """
+    Build parameters.
+    
+    Args:
+        spec_file: File containing surface specification.
+        hemisphere: Specify the hemisphere being processed (left or right).
+        volume_parent_1: Volume parent BRIK for first surface.
+        volume_parent_2: Volume parent BRIK for second surface.
+        file_prefix: Prefix for distance and node color output files. Existing\
+            file will not be overwritten.
+        one_node: Output results for node index only. This option is for\
+            debugging.
+        node_range: Output results from node istart to node istop only. This\
+            option is for debugging.
+        no_consistency_check: Skip mesh orientation consistency check. This\
+            speeds up the start time so it is useful for debugging runs.
+        no_volreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        no_transform: Same as -novolreg.
+        set_environment_variable: 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.
+        no_memory_trace: Turn off memory tracing.
+        yes_memory_trace: Turn on memory tracing (default).
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "CompareSurfaces",
+        "spec_file": spec_file,
+        "hemisphere": hemisphere,
+        "volume_parent_1": volume_parent_1,
+        "volume_parent_2": volume_parent_2,
+        "no_consistency_check": no_consistency_check,
+        "no_volreg": no_volreg,
+        "no_transform": no_transform,
+        "trace": trace_,
+        "extreme_trace": extreme_trace,
+        "no_memory_trace": no_memory_trace,
+        "yes_memory_trace": yes_memory_trace,
+    }
+    if file_prefix is not None:
+        params["file_prefix"] = file_prefix
+    if one_node is not None:
+        params["one_node"] = one_node
+    if node_range is not None:
+        params["node_range"] = node_range
+    if set_environment_variable is not None:
+        params["set_environment_variable"] = set_environment_variable
+    return params
+
+
+def compare_surfaces_cargs(
+    params: CompareSurfacesParameters,
+    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("CompareSurfaces")
+    cargs.extend([
+        "-spec",
+        execution.input_file(params.get("spec_file"))
+    ])
+    cargs.extend([
+        "-hemi",
+        params.get("hemisphere")
+    ])
+    cargs.extend([
+        "-sv1",
+        execution.input_file(params.get("volume_parent_1"))
+    ])
+    cargs.extend([
+        "-sv2",
+        execution.input_file(params.get("volume_parent_2"))
+    ])
+    if params.get("file_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("file_prefix")
+        ])
+    if params.get("one_node") is not None:
+        cargs.extend([
+            "-onenode",
+            str(params.get("one_node"))
+        ])
+    if params.get("node_range") is not None:
+        cargs.extend([
+            "-noderange",
+            *map(str, params.get("node_range"))
+        ])
+    if params.get("no_consistency_check"):
+        cargs.append("-nocons")
+    if params.get("no_volreg"):
+        cargs.append("-novolreg")
+    if params.get("no_transform"):
+        cargs.append("-noxform")
+    if params.get("set_environment_variable") is not None:
+        cargs.extend([
+            "-setenv",
+            params.get("set_environment_variable")
+        ])
+    if params.get("trace"):
+        cargs.append("-trace")
+    if params.get("extreme_trace"):
+        cargs.append("-TRACE")
+    if params.get("no_memory_trace"):
+        cargs.append("-nomall")
+    if params.get("yes_memory_trace"):
+        cargs.append("-yesmall")
+    return cargs
+
+
+def compare_surfaces_outputs(
+    params: CompareSurfacesParameters,
+    execution: Execution,
+) -> CompareSurfacesOutputs:
+    """
+    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 = CompareSurfacesOutputs(
+        root=execution.output_file("."),
+        distance_output_file=execution.output_file(params.get("file_prefix") + "_distance.txt") if (params.get("file_prefix") is not None) else None,
+        color_output_file=execution.output_file(params.get("file_prefix") + "_color.txt") if (params.get("file_prefix") is not None) else None,
+    )
+    return ret
+
+
+def compare_surfaces_execute(
+    params: CompareSurfacesParameters,
+    execution: Execution,
+) -> CompareSurfacesOutputs:
+    """
+    Calculates distance at each node in Surface 1 (S1) to Surface 2 (S2) along the
+    local surface normal at each node in S1. Superseded by SurfToSurf.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `CompareSurfacesOutputs`).
+    """
+    params = execution.params(params)
+    cargs = compare_surfaces_cargs(params, execution)
+    ret = compare_surfaces_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def compare_surfaces(
+    spec_file: InputPathType,
+    hemisphere: typing.Literal["L", "R"],
+    volume_parent_1: InputPathType,
+    volume_parent_2: InputPathType,
+    file_prefix: str | None = None,
+    one_node: float | None = None,
+    node_range: list[float] | None = None,
+    no_consistency_check: bool = False,
+    no_volreg: bool = False,
+    no_transform: bool = False,
+    set_environment_variable: str | None = None,
+    trace_: bool = False,
+    extreme_trace: bool = False,
+    no_memory_trace: bool = False,
+    yes_memory_trace: bool = False,
+    runner: Runner | None = None,
+) -> CompareSurfacesOutputs:
+    """
+    Calculates distance at each node in Surface 1 (S1) to Surface 2 (S2) along the
+    local surface normal at each node in S1. Superseded by SurfToSurf.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        spec_file: File containing surface specification.
+        hemisphere: Specify the hemisphere being processed (left or right).
+        volume_parent_1: Volume parent BRIK for first surface.
+        volume_parent_2: Volume parent BRIK for second surface.
+        file_prefix: Prefix for distance and node color output files. Existing\
+            file will not be overwritten.
+        one_node: Output results for node index only. This option is for\
+            debugging.
+        node_range: Output results from node istart to node istop only. This\
+            option is for debugging.
+        no_consistency_check: Skip mesh orientation consistency check. This\
+            speeds up the start time so it is useful for debugging runs.
+        no_volreg: Ignore any Rotate, Volreg, Tagalign, or WarpDrive\
+            transformations present in the Surface Volume.
+        no_transform: Same as -novolreg.
+        set_environment_variable: 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.
+        no_memory_trace: Turn off memory tracing.
+        yes_memory_trace: Turn on memory tracing (default).
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `CompareSurfacesOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COMPARE_SURFACES_METADATA)
+    params = compare_surfaces_params(
+        spec_file=spec_file,
+        hemisphere=hemisphere,
+        volume_parent_1=volume_parent_1,
+        volume_parent_2=volume_parent_2,
+        file_prefix=file_prefix,
+        one_node=one_node,
+        node_range=node_range,
+        no_consistency_check=no_consistency_check,
+        no_volreg=no_volreg,
+        no_transform=no_transform,
+        set_environment_variable=set_environment_variable,
+        trace_=trace_,
+        extreme_trace=extreme_trace,
+        no_memory_trace=no_memory_trace,
+        yes_memory_trace=yes_memory_trace,
+    )
+    return compare_surfaces_execute(params, execution)
+
+
+__all__ = [
+    "COMPARE_SURFACES_METADATA",
+    "CompareSurfacesOutputs",
+    "CompareSurfacesParameters",
+    "compare_surfaces",
+    "compare_surfaces_params",
+]

niwrap_afni/afni/convert_cdiflist_to_grads.py

@@ -0,0 +1,251 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+CONVERT_CDIFLIST_TO_GRADS_METADATA = Metadata(
+    id="881be0d2d254f2047a6c704bea01fe398f0290f3.boutiques",
+    name="convert_cdiflist_to_grads",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+ConvertCdiflistToGradsParameters = typing.TypedDict('ConvertCdiflistToGradsParameters', {
+    "__STYX_TYPE__": typing.Literal["convert_cdiflist_to_grads"],
+    "cdiflist": InputPathType,
+    "bval_max": float,
+    "prefix": str,
+    "ver": bool,
+    "date": bool,
+    "help": bool,
+    "hview": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "convert_cdiflist_to_grads": convert_cdiflist_to_grads_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 {
+        "convert_cdiflist_to_grads": convert_cdiflist_to_grads_outputs,
+    }.get(t)
+
+
+class ConvertCdiflistToGradsOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `convert_cdiflist_to_grads(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_rvec: OutputPathType
+    """Row-format of gradients (unit magnitude)."""
+    output_bval: OutputPathType
+    """Row-format of bvals."""
+    output_cvec: OutputPathType
+    """Col-format of gradients (scaled by b-values)."""
+
+
+def convert_cdiflist_to_grads_params(
+    cdiflist: InputPathType,
+    bval_max: float,
+    prefix: str,
+    ver: bool = False,
+    date: bool = False,
+    help_: bool = False,
+    hview: bool = False,
+) -> ConvertCdiflistToGradsParameters:
+    """
+    Build parameters.
+    
+    Args:
+        cdiflist: Name(s) of cdiflist text file output by GE scanners when\
+            acquiring DWIs.
+        bval_max: Max bvalue used, which provides a reference value for scaling\
+            everything else.
+        prefix: Output basename for the subsequent grad and bvalue files\
+            (suffix and extensions will be added).
+        ver: Display current version.
+        date: Display release/editing date of current version.
+        help_: Display help in terminal.
+        hview: Display help in terminal.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "convert_cdiflist_to_grads",
+        "cdiflist": cdiflist,
+        "bval_max": bval_max,
+        "prefix": prefix,
+        "ver": ver,
+        "date": date,
+        "help": help_,
+        "hview": hview,
+    }
+    return params
+
+
+def convert_cdiflist_to_grads_cargs(
+    params: ConvertCdiflistToGradsParameters,
+    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("convert_cdiflist_to_grads.py")
+    cargs.extend([
+        "-cdiflist",
+        execution.input_file(params.get("cdiflist"))
+    ])
+    cargs.extend([
+        "-bval_max",
+        str(params.get("bval_max"))
+    ])
+    cargs.extend([
+        "-prefix",
+        params.get("prefix")
+    ])
+    if params.get("ver"):
+        cargs.append("-ver")
+    if params.get("date"):
+        cargs.append("-date")
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("hview"):
+        cargs.append("-h")
+    return cargs
+
+
+def convert_cdiflist_to_grads_outputs(
+    params: ConvertCdiflistToGradsParameters,
+    execution: Execution,
+) -> ConvertCdiflistToGradsOutputs:
+    """
+    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 = ConvertCdiflistToGradsOutputs(
+        root=execution.output_file("."),
+        output_rvec=execution.output_file(params.get("prefix") + "_rvec.dat"),
+        output_bval=execution.output_file(params.get("prefix") + "_bval.dat"),
+        output_cvec=execution.output_file(params.get("prefix") + "_cvec.dat"),
+    )
+    return ret
+
+
+def convert_cdiflist_to_grads_execute(
+    params: ConvertCdiflistToGradsParameters,
+    execution: Execution,
+) -> ConvertCdiflistToGradsOutputs:
+    """
+    This program reads in a GE cdiflist and outputs gradient file and file of
+    bvalues for subsequent processing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `ConvertCdiflistToGradsOutputs`).
+    """
+    params = execution.params(params)
+    cargs = convert_cdiflist_to_grads_cargs(params, execution)
+    ret = convert_cdiflist_to_grads_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def convert_cdiflist_to_grads(
+    cdiflist: InputPathType,
+    bval_max: float,
+    prefix: str,
+    ver: bool = False,
+    date: bool = False,
+    help_: bool = False,
+    hview: bool = False,
+    runner: Runner | None = None,
+) -> ConvertCdiflistToGradsOutputs:
+    """
+    This program reads in a GE cdiflist and outputs gradient file and file of
+    bvalues for subsequent processing.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        cdiflist: Name(s) of cdiflist text file output by GE scanners when\
+            acquiring DWIs.
+        bval_max: Max bvalue used, which provides a reference value for scaling\
+            everything else.
+        prefix: Output basename for the subsequent grad and bvalue files\
+            (suffix and extensions will be added).
+        ver: Display current version.
+        date: Display release/editing date of current version.
+        help_: Display help in terminal.
+        hview: Display help in terminal.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `ConvertCdiflistToGradsOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVERT_CDIFLIST_TO_GRADS_METADATA)
+    params = convert_cdiflist_to_grads_params(
+        cdiflist=cdiflist,
+        bval_max=bval_max,
+        prefix=prefix,
+        ver=ver,
+        date=date,
+        help_=help_,
+        hview=hview,
+    )
+    return convert_cdiflist_to_grads_execute(params, execution)
+
+
+__all__ = [
+    "CONVERT_CDIFLIST_TO_GRADS_METADATA",
+    "ConvertCdiflistToGradsOutputs",
+    "ConvertCdiflistToGradsParameters",
+    "convert_cdiflist_to_grads",
+    "convert_cdiflist_to_grads_params",
+]