niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v__fix_fssphere.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FIX_FSSPHERE_METADATA = Metadata(
-    id="f74e39104dce4bf48131b40121e83b0669d1fac9.boutiques",
+    id="57a2fc2c6540525c0a354779c65d7c1d7921414a.boutiques",
     name="@fix_FSsphere",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__FIX_FSSPHERE_METADATA = Metadata(
 
 
 VFixFssphereParameters = typing.TypedDict('VFixFssphereParameters', {
-    "__STYXTYPE__": typing.Literal["@fix_FSsphere"],
+    "@type": typing.NotRequired[typing.Literal["afni/@fix_FSsphere"]],
+    "spec_file": InputPathType,
+    "sphere_file": InputPathType,
+    "num_iterations": typing.NotRequired[int | None],
+    "extent_lim": typing.NotRequired[float | None],
+    "project_first": bool,
+    "keep_temp": bool,
+})
+VFixFssphereParametersTagged = typing.TypedDict('VFixFssphereParametersTagged', {
+    "@type": typing.Literal["afni/@fix_FSsphere"],
     "spec_file": InputPathType,
     "sphere_file": InputPathType,
     "num_iterations": typing.NotRequired[int | None],
@@ -22,43 +31,11 @@ VFixFssphereParameters = typing.TypedDict('VFixFssphereParameters', {
     "project_first": bool,
     "keep_temp": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@fix_FSsphere": v__fix_fssphere_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 {
-        "@fix_FSsphere": v__fix_fssphere_outputs,
-    }.get(t)
 
 
 class VFixFssphereOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__fix_fssphere(...)`.
+    Output object returned when calling `VFixFssphereParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def v__fix_fssphere_params(
     extent_lim: float | None = None,
     project_first: bool = False,
     keep_temp: bool = False,
-) -> VFixFssphereParameters:
+) -> VFixFssphereParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +66,7 @@ def v__fix_fssphere_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@fix_FSsphere",
+        "@type": "afni/@fix_FSsphere",
         "spec_file": spec_file,
         "sphere_file": sphere_file,
         "project_first": project_first,
@@ -119,25 +96,25 @@ def v__fix_fssphere_cargs(
     cargs.append("@fix_FSsphere")
     cargs.extend([
         "-spec",
-        execution.input_file(params.get("spec_file"))
+        execution.input_file(params.get("spec_file", None))
     ])
     cargs.extend([
         "-sphere",
-        execution.input_file(params.get("sphere_file"))
+        execution.input_file(params.get("sphere_file", None))
     ])
-    if params.get("num_iterations") is not None:
+    if params.get("num_iterations", None) is not None:
         cargs.extend([
             "-niter",
-            str(params.get("num_iterations"))
+            str(params.get("num_iterations", None))
         ])
-    if params.get("extent_lim") is not None:
+    if params.get("extent_lim", None) is not None:
         cargs.extend([
             "-lim",
-            str(params.get("extent_lim"))
+            str(params.get("extent_lim", None))
         ])
-    if params.get("project_first"):
+    if params.get("project_first", False):
         cargs.append("-project_first")
-    if params.get("keep_temp"):
+    if params.get("keep_temp", False):
         cargs.append("-keep_temp")
     return cargs
 
@@ -164,9 +141,11 @@ def v__fix_fssphere_outputs(
 
 def v__fix_fssphere_execute(
     params: VFixFssphereParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFixFssphereOutputs:
     """
+    @fix_FSsphere
+    
     Tool for fixing errors in FreeSurfer spherical surfaces.
     
     Author: AFNI Developers
@@ -175,10 +154,12 @@ def v__fix_fssphere_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFixFssphereOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FIX_FSSPHERE_METADATA)
     params = execution.params(params)
     cargs = v__fix_fssphere_cargs(params, execution)
     ret = v__fix_fssphere_outputs(params, execution)
@@ -196,6 +177,8 @@ def v__fix_fssphere(
     runner: Runner | None = None,
 ) -> VFixFssphereOutputs:
     """
+    @fix_FSsphere
+    
     Tool for fixing errors in FreeSurfer spherical surfaces.
     
     Author: AFNI Developers
@@ -214,8 +197,6 @@ def v__fix_fssphere(
     Returns:
         NamedTuple of outputs (described in `VFixFssphereOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FIX_FSSPHERE_METADATA)
     params = v__fix_fssphere_params(
         spec_file=spec_file,
         sphere_file=sphere_file,
@@ -224,13 +205,13 @@ def v__fix_fssphere(
         project_first=project_first,
         keep_temp=keep_temp,
     )
-    return v__fix_fssphere_execute(params, execution)
+    return v__fix_fssphere_execute(params, runner)
 
 
 __all__ = [
     "VFixFssphereOutputs",
-    "VFixFssphereParameters",
     "V__FIX_FSSPHERE_METADATA",
     "v__fix_fssphere",
+    "v__fix_fssphere_execute",
     "v__fix_fssphere_params",
 ]

niwrap_afni/afni/v__float_fix.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FLOAT_FIX_METADATA = Metadata(
-    id="69c8566d3c52dcfb93a135adaaa38398077c4bc6.boutiques",
+    id="767e876d3f0cfcc45088815cd58010847e88edb7.boutiques",
     name="@float_fix",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,45 +14,18 @@ V__FLOAT_FIX_METADATA = Metadata(
 
 
 VFloatFixParameters = typing.TypedDict('VFloatFixParameters', {
-    "__STYXTYPE__": typing.Literal["@float_fix"],
+    "@type": typing.NotRequired[typing.Literal["afni/@float_fix"]],
+    "input_files": list[InputPathType],
+})
+VFloatFixParametersTagged = typing.TypedDict('VFloatFixParametersTagged', {
+    "@type": typing.Literal["afni/@float_fix"],
     "input_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 {
-        "@float_fix": v__float_fix_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 VFloatFixOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__float_fix(...)`.
+    Output object returned when calling `VFloatFixParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class VFloatFixOutputs(typing.NamedTuple):
 
 def v__float_fix_params(
     input_files: list[InputPathType],
-) -> VFloatFixParameters:
+) -> VFloatFixParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def v__float_fix_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@float_fix",
+        "@type": "afni/@float_fix",
         "input_files": input_files,
     }
     return params
@@ -92,7 +65,7 @@ def v__float_fix_cargs(
     """
     cargs = []
     cargs.append("@float_fix")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
     return cargs
 
 
@@ -117,11 +90,13 @@ def v__float_fix_outputs(
 
 def v__float_fix_execute(
     params: VFloatFixParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFloatFixOutputs:
     """
-    Check whether the input files have any IEEE floating point numbers for illegal
-    values: infinities and not-a-number (NaN) values.
+    @float_fix
+    
+    Check whether the input files have any IEEE floating point numbers for
+    illegal values: infinities and not-a-number (NaN) values.
     
     Author: AFNI Developers
     
@@ -129,10 +104,12 @@ def v__float_fix_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFloatFixOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FLOAT_FIX_METADATA)
     params = execution.params(params)
     cargs = v__float_fix_cargs(params, execution)
     ret = v__float_fix_outputs(params, execution)
@@ -145,8 +122,10 @@ def v__float_fix(
     runner: Runner | None = None,
 ) -> VFloatFixOutputs:
     """
-    Check whether the input files have any IEEE floating point numbers for illegal
-    values: infinities and not-a-number (NaN) values.
+    @float_fix
+    
+    Check whether the input files have any IEEE floating point numbers for
+    illegal values: infinities and not-a-number (NaN) values.
     
     Author: AFNI Developers
     
@@ -159,18 +138,16 @@ def v__float_fix(
     Returns:
         NamedTuple of outputs (described in `VFloatFixOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FLOAT_FIX_METADATA)
     params = v__float_fix_params(
         input_files=input_files,
     )
-    return v__float_fix_execute(params, execution)
+    return v__float_fix_execute(params, runner)
 
 
 __all__ = [
     "VFloatFixOutputs",
-    "VFloatFixParameters",
     "V__FLOAT_FIX_METADATA",
     "v__float_fix",
+    "v__float_fix_execute",
     "v__float_fix_params",
 ]

niwrap_afni/afni/v__from_rai.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FROM_RAI_METADATA = Metadata(
-    id="34d0b2acd8f2be090b2dfad6b13f248d55bc3857.boutiques",
+    id="606aa9259f1b8916cc82e8ce0bda762e7da64528.boutiques",
     name="@FromRAI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ V__FROM_RAI_METADATA = Metadata(
 
 
 VFromRaiParameters = typing.TypedDict('VFromRaiParameters', {
-    "__STYXTYPE__": typing.Literal["@FromRAI"],
+    "@type": typing.NotRequired[typing.Literal["afni/@FromRAI"]],
+    "rai_coordinates": list[float],
+    "orientation": str,
+})
+VFromRaiParametersTagged = typing.TypedDict('VFromRaiParametersTagged', {
+    "@type": typing.Literal["afni/@FromRAI"],
     "rai_coordinates": list[float],
     "orientation": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@FromRAI": v__from_rai_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 VFromRaiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__from_rai(...)`.
+    Output object returned when calling `VFromRaiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class VFromRaiOutputs(typing.NamedTuple):
 def v__from_rai_params(
     rai_coordinates: list[float],
     orientation: str,
-) -> VFromRaiParameters:
+) -> VFromRaiParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def v__from_rai_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@FromRAI",
+        "@type": "afni/@FromRAI",
         "rai_coordinates": rai_coordinates,
         "orientation": orientation,
     }
@@ -97,11 +71,11 @@ def v__from_rai_cargs(
     cargs.append("@FromRAI")
     cargs.extend([
         "-xyz",
-        *map(str, params.get("rai_coordinates"))
+        *map(str, params.get("rai_coordinates", None))
     ])
     cargs.extend([
         "-or",
-        params.get("orientation")
+        params.get("orientation", None)
     ])
     return cargs
 
@@ -127,9 +101,11 @@ def v__from_rai_outputs(
 
 def v__from_rai_execute(
     params: VFromRaiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFromRaiOutputs:
     """
+    @FromRAI
+    
     Changes the RAI coordinates to the specified orientation.
     
     Author: AFNI Developers
@@ -138,10 +114,12 @@ def v__from_rai_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFromRaiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FROM_RAI_METADATA)
     params = execution.params(params)
     cargs = v__from_rai_cargs(params, execution)
     ret = v__from_rai_outputs(params, execution)
@@ -155,6 +133,8 @@ def v__from_rai(
     runner: Runner | None = None,
 ) -> VFromRaiOutputs:
     """
+    @FromRAI
+    
     Changes the RAI coordinates to the specified orientation.
     
     Author: AFNI Developers
@@ -168,19 +148,17 @@ def v__from_rai(
     Returns:
         NamedTuple of outputs (described in `VFromRaiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FROM_RAI_METADATA)
     params = v__from_rai_params(
         rai_coordinates=rai_coordinates,
         orientation=orientation,
     )
-    return v__from_rai_execute(params, execution)
+    return v__from_rai_execute(params, runner)
 
 
 __all__ = [
     "VFromRaiOutputs",
-    "VFromRaiParameters",
     "V__FROM_RAI_METADATA",
     "v__from_rai",
+    "v__from_rai_execute",
     "v__from_rai_params",
 ]

niwrap_afni/afni/v__fs_roi_label.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__FS_ROI_LABEL_METADATA = Metadata(
-    id="a7302764b06fe1cdcf5b431a5db63243d5a576e3.boutiques",
+    id="8a41a17a9222a2bf21cd7e6c811372972bf44b20.boutiques",
     name="@FS_roi_label",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V__FS_ROI_LABEL_METADATA = Metadata(
 
 
 VFsRoiLabelParameters = typing.TypedDict('VFsRoiLabelParameters', {
-    "__STYXTYPE__": typing.Literal["@FS_roi_label"],
+    "@type": typing.NotRequired[typing.Literal["afni/@FS_roi_label"]],
+    "label_int": typing.NotRequired[float | None],
+    "lab_flag": typing.NotRequired[float | None],
+    "rank_int": typing.NotRequired[float | None],
+    "rankmap_file": typing.NotRequired[InputPathType | None],
+    "name": typing.NotRequired[str | None],
+    "labeltable_file": typing.NotRequired[InputPathType | None],
+    "surf_annot_cmap": typing.NotRequired[InputPathType | None],
+    "slab_int": typing.NotRequired[float | None],
+    "sname_name": typing.NotRequired[str | None],
+})
+VFsRoiLabelParametersTagged = typing.TypedDict('VFsRoiLabelParametersTagged', {
+    "@type": typing.Literal["afni/@FS_roi_label"],
     "label_int": typing.NotRequired[float | None],
     "lab_flag": typing.NotRequired[float | None],
     "rank_int": typing.NotRequired[float | None],
@@ -25,42 +37,11 @@ VFsRoiLabelParameters = typing.TypedDict('VFsRoiLabelParameters', {
     "slab_int": typing.NotRequired[float | None],
     "sname_name": 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 {
-        "@FS_roi_label": v__fs_roi_label_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 VFsRoiLabelOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__fs_roi_label(...)`.
+    Output object returned when calling `VFsRoiLabelParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def v__fs_roi_label_params(
     surf_annot_cmap: InputPathType | None = None,
     slab_int: float | None = None,
     sname_name: str | None = None,
-) -> VFsRoiLabelParameters:
+) -> VFsRoiLabelParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +80,7 @@ def v__fs_roi_label_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@FS_roi_label",
+        "@type": "afni/@FS_roi_label",
     }
     if label_int is not None:
         params["label_int"] = label_int
@@ -137,47 +118,47 @@ def v__fs_roi_label_cargs(
     """
     cargs = []
     cargs.append("@FS_roi_label")
-    if params.get("label_int") is not None:
-        cargs.append(str(params.get("label_int")))
-    if params.get("lab_flag") is not None:
+    if params.get("label_int", None) is not None:
+        cargs.append(str(params.get("label_int", None)))
+    if params.get("lab_flag", None) is not None:
         cargs.extend([
             "-lab",
-            str(params.get("lab_flag"))
+            str(params.get("lab_flag", None))
         ])
-    if params.get("rank_int") is not None:
+    if params.get("rank_int", None) is not None:
         cargs.extend([
             "-rank",
-            str(params.get("rank_int"))
+            str(params.get("rank_int", None))
         ])
-    if params.get("rankmap_file") is not None:
+    if params.get("rankmap_file", None) is not None:
         cargs.extend([
             "-rankmap",
-            execution.input_file(params.get("rankmap_file"))
+            execution.input_file(params.get("rankmap_file", None))
         ])
-    if params.get("name") is not None:
+    if params.get("name", None) is not None:
         cargs.extend([
             "-name",
-            params.get("name")
+            params.get("name", None)
         ])
-    if params.get("labeltable_file") is not None:
+    if params.get("labeltable_file", None) is not None:
         cargs.extend([
             "-labeltable",
-            execution.input_file(params.get("labeltable_file"))
+            execution.input_file(params.get("labeltable_file", None))
         ])
-    if params.get("surf_annot_cmap") is not None:
+    if params.get("surf_annot_cmap", None) is not None:
         cargs.extend([
             "-surf_annot_cmap",
-            execution.input_file(params.get("surf_annot_cmap"))
+            execution.input_file(params.get("surf_annot_cmap", None))
         ])
-    if params.get("slab_int") is not None:
+    if params.get("slab_int", None) is not None:
         cargs.extend([
             "-slab",
-            str(params.get("slab_int"))
+            str(params.get("slab_int", None))
         ])
-    if params.get("sname_name") is not None:
+    if params.get("sname_name", None) is not None:
         cargs.extend([
             "-sname",
-            params.get("sname_name")
+            params.get("sname_name", None)
         ])
     return cargs
 
@@ -203,9 +184,11 @@ def v__fs_roi_label_outputs(
 
 def v__fs_roi_label_execute(
     params: VFsRoiLabelParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VFsRoiLabelOutputs:
     """
+    @FS_roi_label
+    
     Tool to get labels associated with FreeSurfer's parcellation and annotation
     files.
     
@@ -215,10 +198,12 @@ def v__fs_roi_label_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VFsRoiLabelOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__FS_ROI_LABEL_METADATA)
     params = execution.params(params)
     cargs = v__fs_roi_label_cargs(params, execution)
     ret = v__fs_roi_label_outputs(params, execution)
@@ -239,6 +224,8 @@ def v__fs_roi_label(
     runner: Runner | None = None,
 ) -> VFsRoiLabelOutputs:
     """
+    @FS_roi_label
+    
     Tool to get labels associated with FreeSurfer's parcellation and annotation
     files.
     
@@ -265,8 +252,6 @@ def v__fs_roi_label(
     Returns:
         NamedTuple of outputs (described in `VFsRoiLabelOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__FS_ROI_LABEL_METADATA)
     params = v__fs_roi_label_params(
         label_int=label_int,
         lab_flag=lab_flag,
@@ -278,13 +263,13 @@ def v__fs_roi_label(
         slab_int=slab_int,
         sname_name=sname_name,
     )
-    return v__fs_roi_label_execute(params, execution)
+    return v__fs_roi_label_execute(params, runner)
 
 
 __all__ = [
     "VFsRoiLabelOutputs",
-    "VFsRoiLabelParameters",
     "V__FS_ROI_LABEL_METADATA",
     "v__fs_roi_label",
+    "v__fs_roi_label_execute",
     "v__fs_roi_label_params",
 ]