niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v__animal_warper.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ANIMAL_WARPER_METADATA = Metadata(
-    id="d18a46908cadbc841d2123e4a66cc4c7fc5756d3.boutiques",
+    id="0c1bdd2a3404fa7897ef96606ac79c836123d8fe.boutiques",
     name="@animal_warper",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,44 @@ V__ANIMAL_WARPER_METADATA = Metadata(
 
 
 VAnimalWarperParameters = typing.TypedDict('VAnimalWarperParameters', {
-    "__STYXTYPE__": typing.Literal["@animal_warper"],
+    "@type": typing.NotRequired[typing.Literal["afni/@animal_warper"]],
+    "input_file": InputPathType,
+    "base_template": InputPathType,
+    "output_dir": str,
+    "brainmask": typing.NotRequired[InputPathType | None],
+    "atlases": typing.NotRequired[list[InputPathType] | None],
+    "atlas_followers": typing.NotRequired[list[InputPathType] | None],
+    "seg_followers": typing.NotRequired[list[InputPathType] | None],
+    "template_followers": typing.NotRequired[list[InputPathType] | None],
+    "dset_followers": typing.NotRequired[list[InputPathType] | None],
+    "roidset_followers": typing.NotRequired[list[InputPathType] | None],
+    "input_abbrev": typing.NotRequired[str | None],
+    "base_abbrev": typing.NotRequired[str | None],
+    "atlas_abbrevs": typing.NotRequired[list[str] | None],
+    "template_abbrevs": typing.NotRequired[list[str] | None],
+    "seg_abbrevs": typing.NotRequired[list[str] | None],
+    "dset_abbrevs": typing.NotRequired[list[str] | None],
+    "roidset_abbrevs": typing.NotRequired[list[str] | None],
+    "align_centers_meth": typing.NotRequired[str | None],
+    "aff_move_opt": typing.NotRequired[str | None],
+    "cost": typing.NotRequired[str | None],
+    "maxlev": typing.NotRequired[float | None],
+    "no_surfaces": bool,
+    "feature_size": typing.NotRequired[float | None],
+    "supersize": bool,
+    "init_scale": typing.NotRequired[float | None],
+    "mode_smooth_size": typing.NotRequired[float | None],
+    "mode_smooth_replacement_off": bool,
+    "center_out": typing.NotRequired[str | None],
+    "align_type": typing.NotRequired[str | None],
+    "extra_qw_opts": typing.NotRequired[str | None],
+    "keep_temp": bool,
+    "version": bool,
+    "ok_to_exist": bool,
+    "echo": bool,
+})
+VAnimalWarperParametersTagged = typing.TypedDict('VAnimalWarperParametersTagged', {
+    "@type": typing.Literal["afni/@animal_warper"],
     "input_file": InputPathType,
     "base_template": InputPathType,
     "output_dir": str,
@@ -50,43 +87,11 @@ VAnimalWarperParameters = typing.TypedDict('VAnimalWarperParameters', {
     "ok_to_exist": bool,
     "echo": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@animal_warper": v__animal_warper_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 {
-        "@animal_warper": v__animal_warper_outputs,
-    }.get(t)
 
 
 class VAnimalWarperOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__animal_warper(...)`.
+    Output object returned when calling `VAnimalWarperParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -140,7 +145,7 @@ def v__animal_warper_params(
     version: bool = False,
     ok_to_exist: bool = False,
     echo: bool = False,
-) -> VAnimalWarperParameters:
+) -> VAnimalWarperParametersTagged:
     """
     Build parameters.
     
@@ -193,7 +198,7 @@ def v__animal_warper_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@animal_warper",
+        "@type": "afni/@animal_warper",
         "input_file": input_file,
         "base_template": base_template,
         "output_dir": output_dir,
@@ -271,139 +276,139 @@ def v__animal_warper_cargs(
     """
     cargs = []
     cargs.append("@animal_warper")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(execution.input_file(params.get("base_template")))
-    cargs.append(params.get("output_dir"))
-    if params.get("brainmask") is not None:
-        cargs.append(execution.input_file(params.get("brainmask")))
-    if params.get("atlases") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(execution.input_file(params.get("base_template", None)))
+    cargs.append(params.get("output_dir", None))
+    if params.get("brainmask", None) is not None:
+        cargs.append(execution.input_file(params.get("brainmask", None)))
+    if params.get("atlases", None) is not None:
         cargs.extend([
             "-atlas",
-            *[execution.input_file(f) for f in params.get("atlases")]
+            *[execution.input_file(f) for f in params.get("atlases", None)]
         ])
-    if params.get("atlas_followers") is not None:
+    if params.get("atlas_followers", None) is not None:
         cargs.extend([
             "-atlas_followers",
-            *[execution.input_file(f) for f in params.get("atlas_followers")]
+            *[execution.input_file(f) for f in params.get("atlas_followers", None)]
         ])
-    if params.get("seg_followers") is not None:
+    if params.get("seg_followers", None) is not None:
         cargs.extend([
             "-seg_followers",
-            *[execution.input_file(f) for f in params.get("seg_followers")]
+            *[execution.input_file(f) for f in params.get("seg_followers", None)]
         ])
-    if params.get("template_followers") is not None:
+    if params.get("template_followers", None) is not None:
         cargs.extend([
             "-template_followers",
-            *[execution.input_file(f) for f in params.get("template_followers")]
+            *[execution.input_file(f) for f in params.get("template_followers", None)]
         ])
-    if params.get("dset_followers") is not None:
+    if params.get("dset_followers", None) is not None:
         cargs.extend([
             "-dset_followers",
-            *[execution.input_file(f) for f in params.get("dset_followers")]
+            *[execution.input_file(f) for f in params.get("dset_followers", None)]
         ])
-    if params.get("roidset_followers") is not None:
+    if params.get("roidset_followers", None) is not None:
         cargs.extend([
             "-roidset_followers",
-            *[execution.input_file(f) for f in params.get("roidset_followers")]
+            *[execution.input_file(f) for f in params.get("roidset_followers", None)]
         ])
-    if params.get("input_abbrev") is not None:
+    if params.get("input_abbrev", None) is not None:
         cargs.extend([
             "-input_abbrev",
-            params.get("input_abbrev")
+            params.get("input_abbrev", None)
         ])
-    if params.get("base_abbrev") is not None:
+    if params.get("base_abbrev", None) is not None:
         cargs.extend([
             "-base_abbrev",
-            params.get("base_abbrev")
+            params.get("base_abbrev", None)
         ])
-    if params.get("atlas_abbrevs") is not None:
+    if params.get("atlas_abbrevs", None) is not None:
         cargs.extend([
             "-atlas_abbrevs",
-            *params.get("atlas_abbrevs")
+            *params.get("atlas_abbrevs", None)
         ])
-    if params.get("template_abbrevs") is not None:
+    if params.get("template_abbrevs", None) is not None:
         cargs.extend([
             "-template_abbrevs",
-            *params.get("template_abbrevs")
+            *params.get("template_abbrevs", None)
         ])
-    if params.get("seg_abbrevs") is not None:
+    if params.get("seg_abbrevs", None) is not None:
         cargs.extend([
             "-seg_abbrevs",
-            *params.get("seg_abbrevs")
+            *params.get("seg_abbrevs", None)
         ])
-    if params.get("dset_abbrevs") is not None:
+    if params.get("dset_abbrevs", None) is not None:
         cargs.extend([
             "-dset_abbrevs",
-            *params.get("dset_abbrevs")
+            *params.get("dset_abbrevs", None)
         ])
-    if params.get("roidset_abbrevs") is not None:
+    if params.get("roidset_abbrevs", None) is not None:
         cargs.extend([
             "-roidset_abbrevs",
-            *params.get("roidset_abbrevs")
+            *params.get("roidset_abbrevs", None)
         ])
-    if params.get("align_centers_meth") is not None:
+    if params.get("align_centers_meth", None) is not None:
         cargs.extend([
             "-align_centers_meth",
-            params.get("align_centers_meth")
+            params.get("align_centers_meth", None)
         ])
-    if params.get("aff_move_opt") is not None:
+    if params.get("aff_move_opt", None) is not None:
         cargs.extend([
             "-aff_move_opt",
-            params.get("aff_move_opt")
+            params.get("aff_move_opt", None)
         ])
-    if params.get("cost") is not None:
+    if params.get("cost", None) is not None:
         cargs.extend([
             "-cost",
-            params.get("cost")
+            params.get("cost", None)
         ])
-    if params.get("maxlev") is not None:
+    if params.get("maxlev", None) is not None:
         cargs.extend([
             "-maxlev",
-            str(params.get("maxlev"))
+            str(params.get("maxlev", None))
         ])
-    if params.get("no_surfaces"):
+    if params.get("no_surfaces", False):
         cargs.append("-no_surfaces")
-    if params.get("feature_size") is not None:
+    if params.get("feature_size", None) is not None:
         cargs.extend([
             "-feature_size",
-            str(params.get("feature_size"))
+            str(params.get("feature_size", None))
         ])
-    if params.get("supersize"):
+    if params.get("supersize", False):
         cargs.append("-supersize")
-    if params.get("init_scale") is not None:
+    if params.get("init_scale", None) is not None:
         cargs.extend([
             "-init_scale",
-            str(params.get("init_scale"))
+            str(params.get("init_scale", None))
         ])
-    if params.get("mode_smooth_size") is not None:
+    if params.get("mode_smooth_size", None) is not None:
         cargs.extend([
             "-mode_smooth_size",
-            str(params.get("mode_smooth_size"))
+            str(params.get("mode_smooth_size", None))
         ])
-    if params.get("mode_smooth_replacement_off"):
+    if params.get("mode_smooth_replacement_off", False):
         cargs.append("-mode_smooth_replacement_off")
-    if params.get("center_out") is not None:
+    if params.get("center_out", None) is not None:
         cargs.extend([
             "-center_out",
-            params.get("center_out")
+            params.get("center_out", None)
         ])
-    if params.get("align_type") is not None:
+    if params.get("align_type", None) is not None:
         cargs.extend([
             "-align_type",
-            params.get("align_type")
+            params.get("align_type", None)
         ])
-    if params.get("extra_qw_opts") is not None:
+    if params.get("extra_qw_opts", None) is not None:
         cargs.extend([
             "-extra_qw_opts",
-            params.get("extra_qw_opts")
+            params.get("extra_qw_opts", None)
         ])
-    if params.get("keep_temp"):
+    if params.get("keep_temp", False):
         cargs.append("-keep_temp")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
-    if params.get("ok_to_exist"):
+    if params.get("ok_to_exist", False):
         cargs.append("-ok_to_exist")
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
     return cargs
 
@@ -423,9 +428,9 @@ def v__animal_warper_outputs(
     """
     ret = VAnimalWarperOutputs(
         root=execution.output_file("."),
-        warp2std=execution.output_file("aw_results/" + pathlib.Path(params.get("input_file")).name + "_warp2std.nii.gz"),
-        qc_image_initial=execution.output_file("aw_results/init_qc_00.input+base*.jpg"),
-        qc_image_initial_sh=execution.output_file("aw_results/init_qc_01.input_sh+base*.jpg"),
+        warp2std=execution.output_file("aw_results/" + pathlib.Path(params.get("input_file", None)).name + "_warp2std.nii.gz"),
+        qc_image_initial=execution.output_file("aw_results/init_qc_00.input+base.jpg"),
+        qc_image_initial_sh=execution.output_file("aw_results/init_qc_01.input_sh+base.jpg"),
         dset_followers_out=execution.output_file("aw_results/DSET_FOLL.nii.gz"),
         roidset_followers_out=execution.output_file("aw_results/ROIDSET_FOLL.nii.gz"),
         animal_outs_guide=execution.output_file("aw_results/animal_outs.txt"),
@@ -435,9 +440,11 @@ def v__animal_warper_outputs(
 
 def v__animal_warper_execute(
     params: VAnimalWarperParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAnimalWarperOutputs:
     """
+    @animal_warper
+    
     Align a subject structural dataset to a template and perform several
     post-alignment operations.
     
@@ -447,10 +454,12 @@ def v__animal_warper_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAnimalWarperOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ANIMAL_WARPER_METADATA)
     params = execution.params(params)
     cargs = v__animal_warper_cargs(params, execution)
     ret = v__animal_warper_outputs(params, execution)
@@ -496,6 +505,8 @@ def v__animal_warper(
     runner: Runner | None = None,
 ) -> VAnimalWarperOutputs:
     """
+    @animal_warper
+    
     Align a subject structural dataset to a template and perform several
     post-alignment operations.
     
@@ -552,8 +563,6 @@ def v__animal_warper(
     Returns:
         NamedTuple of outputs (described in `VAnimalWarperOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ANIMAL_WARPER_METADATA)
     params = v__animal_warper_params(
         input_file=input_file,
         base_template=base_template,
@@ -590,13 +599,13 @@ def v__animal_warper(
         ok_to_exist=ok_to_exist,
         echo=echo,
     )
-    return v__animal_warper_execute(params, execution)
+    return v__animal_warper_execute(params, runner)
 
 
 __all__ = [
     "VAnimalWarperOutputs",
-    "VAnimalWarperParameters",
     "V__ANIMAL_WARPER_METADATA",
     "v__animal_warper",
+    "v__animal_warper_execute",
     "v__animal_warper_params",
 ]

niwrap_afni/afni/v__atlasize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__ATLASIZE_METADATA = Metadata(
-    id="80ebbb960ab74a3ff7041f59da156e4bd3623503.boutiques",
+    id="6cb4f8454789dddf2e4b221ca560c4b58fa3abfe.boutiques",
     name="@Atlasize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ V__ATLASIZE_METADATA = Metadata(
 
 
 VAtlasizeParameters = typing.TypedDict('VAtlasizeParameters', {
-    "__STYXTYPE__": typing.Literal["@Atlasize"],
+    "@type": typing.NotRequired[typing.Literal["afni/@Atlasize"]],
+    "dset": typing.NotRequired[InputPathType | None],
+    "space": typing.NotRequired[str | None],
+    "lab_file": typing.NotRequired[list[str] | None],
+    "lab_file_delim": typing.NotRequired[str | None],
+    "longnames": typing.NotRequired[float | None],
+    "last_longname_col": typing.NotRequired[float | None],
+    "atlas_type": typing.NotRequired[str | None],
+    "atlas_description": typing.NotRequired[str | None],
+    "atlas_name": typing.NotRequired[str | None],
+    "auto_backup": bool,
+    "centers": bool,
+    "centertype": typing.NotRequired[str | None],
+    "centermask": typing.NotRequired[InputPathType | None],
+    "skip_novoxels": bool,
+    "h_web": bool,
+    "h_view": bool,
+    "all_opts": bool,
+    "h_find": typing.NotRequired[str | None],
+})
+VAtlasizeParametersTagged = typing.TypedDict('VAtlasizeParametersTagged', {
+    "@type": typing.Literal["afni/@Atlasize"],
     "dset": typing.NotRequired[InputPathType | None],
     "space": typing.NotRequired[str | None],
     "lab_file": typing.NotRequired[list[str] | None],
@@ -34,43 +55,11 @@ VAtlasizeParameters = typing.TypedDict('VAtlasizeParameters', {
     "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 {
-        "@Atlasize": v__atlasize_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 {
-        "@Atlasize": v__atlasize_outputs,
-    }.get(t)
 
 
 class VAtlasizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__atlasize(...)`.
+    Output object returned when calling `VAtlasizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -97,7 +86,7 @@ def v__atlasize_params(
     h_view: bool = False,
     all_opts: bool = False,
     h_find: str | None = None,
-) -> VAtlasizeParameters:
+) -> VAtlasizeParametersTagged:
     """
     Build parameters.
     
@@ -136,7 +125,7 @@ def v__atlasize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@Atlasize",
+        "@type": "afni/@Atlasize",
         "auto_backup": auto_backup,
         "centers": centers,
         "skip_novoxels": skip_novoxels,
@@ -186,77 +175,77 @@ def v__atlasize_cargs(
     """
     cargs = []
     cargs.append("@Atlasize")
-    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("space") is not None:
+    if params.get("space", None) is not None:
         cargs.extend([
             "-space",
-            params.get("space")
+            params.get("space", 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("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("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("atlas_type") is not None:
+    if params.get("atlas_type", None) is not None:
         cargs.extend([
             "-atlas_type",
-            params.get("atlas_type")
+            params.get("atlas_type", 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("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("auto_backup"):
+    if params.get("auto_backup", False):
         cargs.append("-auto_backup")
-    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",
-            execution.input_file(params.get("centermask"))
+            execution.input_file(params.get("centermask", None))
         ])
-    if params.get("skip_novoxels"):
+    if params.get("skip_novoxels", False):
         cargs.append("-skip_novoxels")
-    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
 
@@ -276,16 +265,18 @@ def v__atlasize_outputs(
     """
     ret = VAtlasizeOutputs(
         root=execution.output_file("."),
-        niml_file=execution.output_file(pathlib.Path(params.get("dset")).name + ".niml") if (params.get("dset") is not None) else None,
+        niml_file=execution.output_file(pathlib.Path(params.get("dset", None)).name + ".niml") if (params.get("dset") is not None) else None,
     )
     return ret
 
 
 def v__atlasize_execute(
     params: VAtlasizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VAtlasizeOutputs:
     """
+    @Atlasize
+    
     Script to turn a volumetric dataset into an AFNI atlas.
     
     Author: AFNI Developers
@@ -294,10 +285,12 @@ def v__atlasize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VAtlasizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__ATLASIZE_METADATA)
     params = execution.params(params)
     cargs = v__atlasize_cargs(params, execution)
     ret = v__atlasize_outputs(params, execution)
@@ -327,6 +320,8 @@ def v__atlasize(
     runner: Runner | None = None,
 ) -> VAtlasizeOutputs:
     """
+    @Atlasize
+    
     Script to turn a volumetric dataset into an AFNI atlas.
     
     Author: AFNI Developers
@@ -368,8 +363,6 @@ def v__atlasize(
     Returns:
         NamedTuple of outputs (described in `VAtlasizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__ATLASIZE_METADATA)
     params = v__atlasize_params(
         dset=dset,
         space=space,
@@ -390,13 +383,13 @@ def v__atlasize(
         all_opts=all_opts,
         h_find=h_find,
     )
-    return v__atlasize_execute(params, execution)
+    return v__atlasize_execute(params, runner)
 
 
 __all__ = [
     "VAtlasizeOutputs",
-    "VAtlasizeParameters",
     "V__ATLASIZE_METADATA",
     "v__atlasize",
+    "v__atlasize_execute",
     "v__atlasize_params",
 ]