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

niwrap_afni/afni/v__is_oblique.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__IS_OBLIQUE_METADATA = Metadata(
-    id="26f04b5daa7f9df4c6266d840714d074632c8670.boutiques",
+    id="1db61c294d0093711594ad61dae63fc37edee3bb.boutiques",
     name="@isOblique",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ V__IS_OBLIQUE_METADATA = Metadata(
 
 
 VIsObliqueParameters = typing.TypedDict('VIsObliqueParameters', {
-    "__STYXTYPE__": typing.Literal["@isOblique"],
+    "@type": typing.NotRequired[typing.Literal["afni/@isOblique"]],
+    "infile": InputPathType,
+})
+VIsObliqueParametersTagged = typing.TypedDict('VIsObliqueParametersTagged', {
+    "@type": typing.Literal["afni/@isOblique"],
     "infile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@isOblique": v__is_oblique_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 {
-        "@isOblique": v__is_oblique_outputs,
-    }.get(t)
 
 
 class VIsObliqueOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__is_oblique(...)`.
+    Output object returned when calling `VIsObliqueParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class VIsObliqueOutputs(typing.NamedTuple):
 
 def v__is_oblique_params(
     infile: InputPathType,
-) -> VIsObliqueParameters:
+) -> VIsObliqueParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def v__is_oblique_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@isOblique",
+        "@type": "afni/@isOblique",
         "infile": infile,
     }
     return params
@@ -94,7 +66,7 @@ def v__is_oblique_cargs(
     """
     cargs = []
     cargs.append("@isOblique")
-    cargs.append(execution.input_file(params.get("infile")))
+    cargs.append(execution.input_file(params.get("infile", None)))
     return cargs
 
 
@@ -120,9 +92,11 @@ def v__is_oblique_outputs(
 
 def v__is_oblique_execute(
     params: VIsObliqueParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VIsObliqueOutputs:
     """
+    @isOblique
+    
     Determine if a file is oblique or plumb.
     
     Author: AFNI Developers
@@ -131,10 +105,12 @@ def v__is_oblique_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VIsObliqueOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__IS_OBLIQUE_METADATA)
     params = execution.params(params)
     cargs = v__is_oblique_cargs(params, execution)
     ret = v__is_oblique_outputs(params, execution)
@@ -147,6 +123,8 @@ def v__is_oblique(
     runner: Runner | None = None,
 ) -> VIsObliqueOutputs:
     """
+    @isOblique
+    
     Determine if a file is oblique or plumb.
     
     Author: AFNI Developers
@@ -159,18 +137,16 @@ def v__is_oblique(
     Returns:
         NamedTuple of outputs (described in `VIsObliqueOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__IS_OBLIQUE_METADATA)
     params = v__is_oblique_params(
         infile=infile,
     )
-    return v__is_oblique_execute(params, execution)
+    return v__is_oblique_execute(params, runner)
 
 
 __all__ = [
     "VIsObliqueOutputs",
-    "VIsObliqueParameters",
     "V__IS_OBLIQUE_METADATA",
     "v__is_oblique",
+    "v__is_oblique_execute",
     "v__is_oblique_params",
 ]

niwrap_afni/afni/v__iso_masks.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ISO_MASKS_METADATA = Metadata(
-    id="efb13b19016645aff7a7273058c6f68edcfc682d.boutiques",
+    id="9aefd10622f856917f37760a8b99e0cabbede244.boutiques",
     name="@IsoMasks",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ V__ISO_MASKS_METADATA = Metadata(
 
 
 VIsoMasksParameters = typing.TypedDict('VIsoMasksParameters', {
-    "__STYXTYPE__": typing.Literal["@IsoMasks"],
+    "@type": typing.NotRequired[typing.Literal["afni/@IsoMasks"]],
+    "input_dataset": InputPathType,
+    "isovals": typing.NotRequired[list[float] | None],
+})
+VIsoMasksParametersTagged = typing.TypedDict('VIsoMasksParametersTagged', {
+    "@type": typing.Literal["afni/@IsoMasks"],
     "input_dataset": InputPathType,
     "isovals": typing.NotRequired[list[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 {
-        "@IsoMasks": v__iso_masks_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 VIsoMasksOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__iso_masks(...)`.
+    Output object returned when calling `VIsoMasksParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class VIsoMasksOutputs(typing.NamedTuple):
 def v__iso_masks_params(
     input_dataset: InputPathType,
     isovals: list[float] | None = None,
-) -> VIsoMasksParameters:
+) -> VIsoMasksParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def v__iso_masks_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@IsoMasks",
+        "@type": "afni/@IsoMasks",
         "input_dataset": input_dataset,
     }
     if isovals is not None:
@@ -98,10 +72,10 @@ def v__iso_masks_cargs(
     cargs.append("@IsoMasks")
     cargs.extend([
         "-mask",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
-    if params.get("isovals") is not None:
-        cargs.extend(map(str, params.get("isovals")))
+    if params.get("isovals", None) is not None:
+        cargs.extend(map(str, params.get("isovals", None)))
     return cargs
 
 
@@ -126,9 +100,11 @@ def v__iso_masks_outputs(
 
 def v__iso_masks_execute(
     params: VIsoMasksParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VIsoMasksOutputs:
     """
+    @IsoMasks
+    
     Creates isosurfaces from isovolume envelopes.
     
     Author: AFNI Developers
@@ -137,10 +113,12 @@ def v__iso_masks_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VIsoMasksOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ISO_MASKS_METADATA)
     params = execution.params(params)
     cargs = v__iso_masks_cargs(params, execution)
     ret = v__iso_masks_outputs(params, execution)
@@ -154,6 +132,8 @@ def v__iso_masks(
     runner: Runner | None = None,
 ) -> VIsoMasksOutputs:
     """
+    @IsoMasks
+    
     Creates isosurfaces from isovolume envelopes.
     
     Author: AFNI Developers
@@ -167,19 +147,17 @@ def v__iso_masks(
     Returns:
         NamedTuple of outputs (described in `VIsoMasksOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ISO_MASKS_METADATA)
     params = v__iso_masks_params(
         input_dataset=input_dataset,
         isovals=isovals,
     )
-    return v__iso_masks_execute(params, execution)
+    return v__iso_masks_execute(params, runner)
 
 
 __all__ = [
     "VIsoMasksOutputs",
-    "VIsoMasksParameters",
     "V__ISO_MASKS_METADATA",
     "v__iso_masks",
+    "v__iso_masks_execute",
     "v__iso_masks_params",
 ]

niwrap_afni/afni/v__make_label_table.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MAKE_LABEL_TABLE_METADATA = Metadata(
-    id="bdce4ed3d1cd67a4fbdd4b4b532313914142c2a4.boutiques",
+    id="1b8c5ced10c5b83d8027942844ff657599aa8b4c.boutiques",
     name="@MakeLabelTable",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,45 @@ V__MAKE_LABEL_TABLE_METADATA = Metadata(
 
 
 VMakeLabelTableParameters = typing.TypedDict('VMakeLabelTableParameters', {
-    "__STYXTYPE__": typing.Literal["@MakeLabelTable"],
+    "@type": typing.NotRequired[typing.Literal["afni/@MakeLabelTable"]],
+    "labeltable": str,
+    "atlas_pointlist": typing.NotRequired[str | None],
+    "lab_r": typing.NotRequired[list[str] | None],
+    "lab_v": typing.NotRequired[list[str] | None],
+    "lab_file_delim": typing.NotRequired[str | None],
+    "lab_file": typing.NotRequired[list[str] | None],
+    "dset": typing.NotRequired[InputPathType | None],
+    "longnames": typing.NotRequired[float | None],
+    "last_longname_col": typing.NotRequired[float | None],
+    "centers": bool,
+    "centertype": typing.NotRequired[str | None],
+    "centermask": typing.NotRequired[str | None],
+    "skip_novoxels": bool,
+    "all_labels": bool,
+    "all_keys": bool,
+    "lkeys": typing.NotRequired[str | None],
+    "rkeys": typing.NotRequired[str | None],
+    "klabel": typing.NotRequired[str | None],
+    "match_label": typing.NotRequired[str | None],
+    "labeltable_of_dset": typing.NotRequired[InputPathType | None],
+    "word_label_match": bool,
+    "quiet_death": bool,
+    "lt_to_atlas_pl": typing.NotRequired[str | None],
+    "dset_lt_to_atlas_pl": typing.NotRequired[list[InputPathType] | None],
+    "lt_to_csv": typing.NotRequired[InputPathType | None],
+    "atlasize_labeled_dset": typing.NotRequired[InputPathType | None],
+    "atlas_file": typing.NotRequired[str | None],
+    "atlas_name": typing.NotRequired[str | None],
+    "atlas_description": typing.NotRequired[str | None],
+    "replace": bool,
+    "add_atlas_dset": typing.NotRequired[InputPathType | None],
+    "h_web": bool,
+    "h_view": bool,
+    "all_opts": bool,
+    "h_find": typing.NotRequired[str | None],
+})
+VMakeLabelTableParametersTagged = typing.TypedDict('VMakeLabelTableParametersTagged', {
+    "@type": typing.Literal["afni/@MakeLabelTable"],
     "labeltable": str,
     "atlas_pointlist": typing.NotRequired[str | None],
     "lab_r": typing.NotRequired[list[str] | None],
@@ -51,43 +89,11 @@ VMakeLabelTableParameters = typing.TypedDict('VMakeLabelTableParameters', {
     "all_opts": bool,
     "h_find": 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 {
-        "@MakeLabelTable": v__make_label_table_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 {
-        "@MakeLabelTable": v__make_label_table_outputs,
-    }.get(t)
 
 
 class VMakeLabelTableOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__make_label_table(...)`.
+    Output object returned when calling `VMakeLabelTableParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -137,7 +143,7 @@ def v__make_label_table_params(
     h_view: bool = False,
     all_opts: bool = False,
     h_find: str | None = None,
-) -> VMakeLabelTableParameters:
+) -> VMakeLabelTableParametersTagged:
     """
     Build parameters.
     
@@ -186,7 +192,7 @@ def v__make_label_table_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@MakeLabelTable",
+        "@type": "afni/@MakeLabelTable",
         "labeltable": labeltable,
         "centers": centers,
         "skip_novoxels": skip_novoxels,
@@ -267,147 +273,147 @@ def v__make_label_table_cargs(
     cargs.append("@MakeLabelTable")
     cargs.extend([
         "-labeltable",
-        params.get("labeltable")
+        params.get("labeltable", None)
     ])
-    if params.get("atlas_pointlist") is not None:
+    if params.get("atlas_pointlist", None) is not None:
         cargs.extend([
             "-atlas_pointlist",
-            params.get("atlas_pointlist")
+            params.get("atlas_pointlist", None)
         ])
-    if params.get("lab_r") is not None:
+    if params.get("lab_r", None) is not None:
         cargs.extend([
             "-lab_r",
-            *params.get("lab_r")
+            *params.get("lab_r", None)
         ])
-    if params.get("lab_v") is not None:
+    if params.get("lab_v", None) is not None:
         cargs.extend([
             "-lab_v",
-            *params.get("lab_v")
+            *params.get("lab_v", None)
         ])
-    if params.get("lab_file_delim") is not None:
+    if params.get("lab_file_delim", None) is not None:
         cargs.extend([
             "-lab_file_delim",
-            params.get("lab_file_delim")
+            params.get("lab_file_delim", None)
         ])
-    if params.get("lab_file") is not None:
+    if params.get("lab_file", None) is not None:
         cargs.extend([
             "-lab_file",
-            *params.get("lab_file")
+            *params.get("lab_file", None)
         ])
-    if params.get("dset") is not None:
+    if params.get("dset", None) is not None:
         cargs.extend([
             "-dset",
-            execution.input_file(params.get("dset"))
+            execution.input_file(params.get("dset", None))
         ])
-    if params.get("longnames") is not None:
+    if params.get("longnames", None) is not None:
         cargs.extend([
             "-longnames",
-            str(params.get("longnames"))
+            str(params.get("longnames", None))
         ])
-    if params.get("last_longname_col") is not None:
+    if params.get("last_longname_col", None) is not None:
         cargs.extend([
             "-last_longname_col",
-            str(params.get("last_longname_col"))
+            str(params.get("last_longname_col", None))
         ])
-    if params.get("centers"):
+    if params.get("centers", False):
         cargs.append("-centers")
-    if params.get("centertype") is not None:
+    if params.get("centertype", None) is not None:
         cargs.extend([
             "-centertype",
-            params.get("centertype")
+            params.get("centertype", None)
         ])
-    if params.get("centermask") is not None:
+    if params.get("centermask", None) is not None:
         cargs.extend([
             "-centermask",
-            params.get("centermask")
+            params.get("centermask", None)
         ])
-    if params.get("skip_novoxels"):
+    if params.get("skip_novoxels", False):
         cargs.append("-skip_novoxels")
-    if params.get("all_labels"):
+    if params.get("all_labels", False):
         cargs.append("-all_labels")
-    if params.get("all_keys"):
+    if params.get("all_keys", False):
         cargs.append("-all_keys")
-    if params.get("lkeys") is not None:
+    if params.get("lkeys", None) is not None:
         cargs.extend([
             "-lkeys",
-            params.get("lkeys")
+            params.get("lkeys", None)
         ])
-    if params.get("rkeys") is not None:
+    if params.get("rkeys", None) is not None:
         cargs.extend([
             "-rkeys",
-            params.get("rkeys")
+            params.get("rkeys", None)
         ])
-    if params.get("klabel") is not None:
+    if params.get("klabel", None) is not None:
         cargs.extend([
             "-klabel",
-            params.get("klabel")
+            params.get("klabel", None)
         ])
-    if params.get("match_label") is not None:
+    if params.get("match_label", None) is not None:
         cargs.extend([
             "-match_label",
-            params.get("match_label")
+            params.get("match_label", None)
         ])
-    if params.get("labeltable_of_dset") is not None:
+    if params.get("labeltable_of_dset", None) is not None:
         cargs.extend([
             "-labeltable_of_dset",
-            execution.input_file(params.get("labeltable_of_dset"))
+            execution.input_file(params.get("labeltable_of_dset", None))
         ])
-    if params.get("word_label_match"):
+    if params.get("word_label_match", False):
         cargs.append("-word_label_match")
-    if params.get("quiet_death"):
+    if params.get("quiet_death", False):
         cargs.append("-quiet_death")
-    if params.get("lt_to_atlas_pl") is not None:
+    if params.get("lt_to_atlas_pl", None) is not None:
         cargs.extend([
             "-LT_to_atlas_PL",
-            params.get("lt_to_atlas_pl")
+            params.get("lt_to_atlas_pl", None)
         ])
-    if params.get("dset_lt_to_atlas_pl") is not None:
+    if params.get("dset_lt_to_atlas_pl", None) is not None:
         cargs.extend([
             "-dset_LT_to_atlas_PL",
-            *[execution.input_file(f) for f in params.get("dset_lt_to_atlas_pl")]
+            *[execution.input_file(f) for f in params.get("dset_lt_to_atlas_pl", None)]
         ])
-    if params.get("lt_to_csv") is not None:
+    if params.get("lt_to_csv", None) is not None:
         cargs.extend([
             "-LT_to_CSV",
-            execution.input_file(params.get("lt_to_csv"))
+            execution.input_file(params.get("lt_to_csv", None))
         ])
-    if params.get("atlasize_labeled_dset") is not None:
+    if params.get("atlasize_labeled_dset", None) is not None:
         cargs.extend([
             "-atlasize_labeled_dset",
-            execution.input_file(params.get("atlasize_labeled_dset"))
+            execution.input_file(params.get("atlasize_labeled_dset", None))
         ])
-    if params.get("atlas_file") is not None:
+    if params.get("atlas_file", None) is not None:
         cargs.extend([
             "-atlas_file",
-            params.get("atlas_file")
+            params.get("atlas_file", None)
         ])
-    if params.get("atlas_name") is not None:
+    if params.get("atlas_name", None) is not None:
         cargs.extend([
             "-atlas_name",
-            params.get("atlas_name")
+            params.get("atlas_name", None)
         ])
-    if params.get("atlas_description") is not None:
+    if params.get("atlas_description", None) is not None:
         cargs.extend([
             "-atlas_description",
-            params.get("atlas_description")
+            params.get("atlas_description", None)
         ])
-    if params.get("replace"):
+    if params.get("replace", False):
         cargs.append("-replace")
-    if params.get("add_atlas_dset") is not None:
+    if params.get("add_atlas_dset", None) is not None:
         cargs.extend([
             "-add_atlas_dset",
-            execution.input_file(params.get("add_atlas_dset"))
+            execution.input_file(params.get("add_atlas_dset", None))
         ])
-    if params.get("h_web"):
+    if params.get("h_web", False):
         cargs.append("-h_web")
-    if params.get("h_view"):
+    if params.get("h_view", False):
         cargs.append("-h_view")
-    if params.get("all_opts"):
+    if params.get("all_opts", False):
         cargs.append("-all_opts")
-    if params.get("h_find") is not None:
+    if params.get("h_find", None) is not None:
         cargs.extend([
             "-h_find",
-            params.get("h_find")
+            params.get("h_find", None)
         ])
     return cargs
 
@@ -427,19 +433,21 @@ def v__make_label_table_outputs(
     """
     ret = VMakeLabelTableOutputs(
         root=execution.output_file("."),
-        output_labeltable=execution.output_file(params.get("labeltable") + ".niml.lt"),
-        output_atlas_pointlist=execution.output_file(params.get("atlas_pointlist") + ".niml.atlas") if (params.get("atlas_pointlist") is not None) else None,
-        output_csv=execution.output_file(pathlib.Path(params.get("lt_to_csv")).name + ".csv") if (params.get("lt_to_csv") is not None) else None,
-        output_niml_atlas=execution.output_file(pathlib.Path(params.get("atlasize_labeled_dset")).name + ".niml") if (params.get("atlasize_labeled_dset") is not None) else None,
+        output_labeltable=execution.output_file(params.get("labeltable", None) + ".niml.lt"),
+        output_atlas_pointlist=execution.output_file(params.get("atlas_pointlist", None) + ".niml.atlas") if (params.get("atlas_pointlist") is not None) else None,
+        output_csv=execution.output_file(pathlib.Path(params.get("lt_to_csv", None)).name + ".csv") if (params.get("lt_to_csv") is not None) else None,
+        output_niml_atlas=execution.output_file(pathlib.Path(params.get("atlasize_labeled_dset", None)).name + ".niml") if (params.get("atlasize_labeled_dset") is not None) else None,
     )
     return ret
 
 
 def v__make_label_table_execute(
     params: VMakeLabelTableParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VMakeLabelTableOutputs:
     """
+    @MakeLabelTable
+    
     Script used to create, modify, and transform label tables.
     
     Author: AFNI Developers
@@ -448,10 +456,12 @@ def v__make_label_table_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VMakeLabelTableOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__MAKE_LABEL_TABLE_METADATA)
     params = execution.params(params)
     cargs = v__make_label_table_cargs(params, execution)
     ret = v__make_label_table_outputs(params, execution)
@@ -498,6 +508,8 @@ def v__make_label_table(
     runner: Runner | None = None,
 ) -> VMakeLabelTableOutputs:
     """
+    @MakeLabelTable
+    
     Script used to create, modify, and transform label tables.
     
     Author: AFNI Developers
@@ -549,8 +561,6 @@ def v__make_label_table(
     Returns:
         NamedTuple of outputs (described in `VMakeLabelTableOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__MAKE_LABEL_TABLE_METADATA)
     params = v__make_label_table_params(
         labeltable=labeltable,
         atlas_pointlist=atlas_pointlist,
@@ -588,13 +598,13 @@ def v__make_label_table(
         all_opts=all_opts,
         h_find=h_find,
     )
-    return v__make_label_table_execute(params, execution)
+    return v__make_label_table_execute(params, runner)
 
 
 __all__ = [
     "VMakeLabelTableOutputs",
-    "VMakeLabelTableParameters",
     "V__MAKE_LABEL_TABLE_METADATA",
     "v__make_label_table",
+    "v__make_label_table_execute",
     "v__make_label_table_params",
 ]