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

niwrap_afni/afni/bayes_view.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BAYES_VIEW_METADATA = Metadata(
-    id="21ede4a2b31dfb05d448cf196912dc72f15188bb.boutiques",
+    id="9505bae1fe22a390a7c949d3eee05a64bdd40fb6.boutiques",
     name="bayes_view",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,22 @@ BAYES_VIEW_METADATA = Metadata(
 
 
 BayesViewParameters = typing.TypedDict('BayesViewParameters', {
-    "__STYXTYPE__": typing.Literal["bayes_view"],
+    "@type": typing.NotRequired[typing.Literal["afni/bayes_view"]],
+    "input_folder": str,
+    "help": bool,
+    "shiny_folder": typing.NotRequired[str | None],
+})
+BayesViewParametersTagged = typing.TypedDict('BayesViewParametersTagged', {
+    "@type": typing.Literal["afni/bayes_view"],
     "input_folder": str,
     "help": bool,
     "shiny_folder": 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 {
-        "bayes_view": bayes_view_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 BayesViewOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bayes_view(...)`.
+    Output object returned when calling `BayesViewParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def bayes_view_params(
     input_folder: str,
     help_: bool = False,
     shiny_folder: str | None = None,
-) -> BayesViewParameters:
+) -> BayesViewParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def bayes_view_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "bayes_view",
+        "@type": "afni/bayes_view",
         "input_folder": input_folder,
         "help": help_,
     }
@@ -100,13 +75,13 @@ def bayes_view_cargs(
     """
     cargs = []
     cargs.append("bayes_view")
-    cargs.append(params.get("input_folder"))
-    if params.get("help"):
+    cargs.append(params.get("input_folder", None))
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("shiny_folder") is not None:
+    if params.get("shiny_folder", None) is not None:
         cargs.extend([
             "-ShinyFolder",
-            params.get("shiny_folder")
+            params.get("shiny_folder", None)
         ])
     return cargs
 
@@ -132,11 +107,13 @@ def bayes_view_outputs(
 
 def bayes_view_execute(
     params: BayesViewParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BayesViewOutputs:
     """
-    Launch a shiny app to visualize RBA output files. The files must have the .RData
-    extension.
+    bayes_view
+    
+    Launch a shiny app to visualize RBA output files. The files must have the
+    .RData extension.
     
     Author: AFNI Developers
     
@@ -144,10 +121,12 @@ def bayes_view_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BayesViewOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BAYES_VIEW_METADATA)
     params = execution.params(params)
     cargs = bayes_view_cargs(params, execution)
     ret = bayes_view_outputs(params, execution)
@@ -162,8 +141,10 @@ def bayes_view(
     runner: Runner | None = None,
 ) -> BayesViewOutputs:
     """
-    Launch a shiny app to visualize RBA output files. The files must have the .RData
-    extension.
+    bayes_view
+    
+    Launch a shiny app to visualize RBA output files. The files must have the
+    .RData extension.
     
     Author: AFNI Developers
     
@@ -177,20 +158,18 @@ def bayes_view(
     Returns:
         NamedTuple of outputs (described in `BayesViewOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BAYES_VIEW_METADATA)
     params = bayes_view_params(
         input_folder=input_folder,
         help_=help_,
         shiny_folder=shiny_folder,
     )
-    return bayes_view_execute(params, execution)
+    return bayes_view_execute(params, runner)
 
 
 __all__ = [
     "BAYES_VIEW_METADATA",
     "BayesViewOutputs",
-    "BayesViewParameters",
     "bayes_view",
+    "bayes_view_execute",
     "bayes_view_params",
 ]

niwrap_afni/afni/bayesian_group_ana_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BAYESIAN_GROUP_ANA_PY_METADATA = Metadata(
-    id="16a41e07083d349e8b592010dd1d0f643a97bab3.boutiques",
+    id="bfff44a85f87d9a3928e423c75c60997d4309948.boutiques",
     name="BayesianGroupAna.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ BAYESIAN_GROUP_ANA_PY_METADATA = Metadata(
 
 
 BayesianGroupAnaPyParameters = typing.TypedDict('BayesianGroupAnaPyParameters', {
-    "__STYXTYPE__": typing.Literal["BayesianGroupAna.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/BayesianGroupAna.py"]],
+    "dataTable": InputPathType,
+    "y_variable": str,
+    "prefix": typing.NotRequired[str | None],
+    "x_variables": typing.NotRequired[list[str] | None],
+    "no_center": bool,
+    "iterations": typing.NotRequired[float | None],
+    "chains": typing.NotRequired[float | None],
+    "control_list": typing.NotRequired[str | None],
+    "plot": bool,
+    "more_plots": typing.NotRequired[list[str] | None],
+    "RData": bool,
+    "seed": typing.NotRequired[float | None],
+    "overwrite": bool,
+    "help": bool,
+})
+BayesianGroupAnaPyParametersTagged = typing.TypedDict('BayesianGroupAnaPyParametersTagged', {
+    "@type": typing.Literal["afni/BayesianGroupAna.py"],
     "dataTable": InputPathType,
     "y_variable": str,
     "prefix": typing.NotRequired[str | None],
@@ -30,43 +47,11 @@ BayesianGroupAnaPyParameters = typing.TypedDict('BayesianGroupAnaPyParameters',
     "overwrite": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "BayesianGroupAna.py": bayesian_group_ana_py_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 {
-        "BayesianGroupAna.py": bayesian_group_ana_py_outputs,
-    }.get(t)
 
 
 class BayesianGroupAnaPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `bayesian_group_ana_py(...)`.
+    Output object returned when calling `BayesianGroupAnaPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -96,7 +81,7 @@ def bayesian_group_ana_py_params(
     seed: float | None = None,
     overwrite: bool = False,
     help_: bool = False,
-) -> BayesianGroupAnaPyParameters:
+) -> BayesianGroupAnaPyParametersTagged:
     """
     Build parameters.
     
@@ -123,7 +108,7 @@ def bayesian_group_ana_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "BayesianGroupAna.py",
+        "@type": "afni/BayesianGroupAna.py",
         "dataTable": data_table,
         "y_variable": y_variable,
         "no_center": no_center,
@@ -164,52 +149,52 @@ def bayesian_group_ana_py_cargs(
     """
     cargs = []
     cargs.append("BayesianGroupAna.py")
-    cargs.append(execution.input_file(params.get("dataTable")))
-    cargs.append(params.get("y_variable"))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("dataTable", None)))
+    cargs.append(params.get("y_variable", None))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("x_variables") is not None:
+    if params.get("x_variables", None) is not None:
         cargs.extend([
             "-x",
-            *params.get("x_variables")
+            *params.get("x_variables", None)
         ])
-    if params.get("no_center"):
+    if params.get("no_center", False):
         cargs.append("-no_center")
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "-iterations",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
-    if params.get("chains") is not None:
+    if params.get("chains", None) is not None:
         cargs.extend([
             "-chains",
-            str(params.get("chains"))
+            str(params.get("chains", None))
         ])
-    if params.get("control_list") is not None:
+    if params.get("control_list", None) is not None:
         cargs.extend([
             "-control_list",
-            params.get("control_list")
+            params.get("control_list", None)
         ])
-    if params.get("plot"):
+    if params.get("plot", False):
         cargs.append("-plot")
-    if params.get("more_plots") is not None:
+    if params.get("more_plots", None) is not None:
         cargs.extend([
             "-more_plots",
-            *params.get("more_plots")
+            *params.get("more_plots", None)
         ])
-    if params.get("RData"):
+    if params.get("RData", False):
         cargs.append("-RData")
-    if params.get("seed") is not None:
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("seed"))
+            str(params.get("seed", None))
         ])
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -229,19 +214,21 @@ def bayesian_group_ana_py_outputs(
     """
     ret = BayesianGroupAnaPyOutputs(
         root=execution.output_file("."),
-        summary=execution.output_file(params.get("prefix") + "_summary.txt") if (params.get("prefix") is not None) else None,
-        rhats=execution.output_file(params.get("prefix") + "_rhats.csv") if (params.get("prefix") is not None) else None,
-        intercept_table=execution.output_file(params.get("prefix") + "_Intercept_table.csv") if (params.get("prefix") is not None) else None,
-        x_var_table=execution.output_file(params.get("prefix") + "_table.csv") if (params.get("prefix") is not None) else None,
+        summary=execution.output_file(params.get("prefix", None) + "_summary.txt") if (params.get("prefix") is not None) else None,
+        rhats=execution.output_file(params.get("prefix", None) + "_rhats.csv") if (params.get("prefix") is not None) else None,
+        intercept_table=execution.output_file(params.get("prefix", None) + "_Intercept_table.csv") if (params.get("prefix") is not None) else None,
+        x_var_table=execution.output_file(params.get("prefix", None) + "_table.csv") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def bayesian_group_ana_py_execute(
     params: BayesianGroupAnaPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BayesianGroupAnaPyOutputs:
     """
+    BayesianGroupAna.py
+    
     This program conducts Bayesian Group Analysis (BGA) on a list of regions of
     interest (ROIs). Compared to the conventional univariate GLM, BGA pools and
     shares the information across the ROIs in a multilevel system.
@@ -252,10 +239,12 @@ def bayesian_group_ana_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BayesianGroupAnaPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BAYESIAN_GROUP_ANA_PY_METADATA)
     params = execution.params(params)
     cargs = bayesian_group_ana_py_cargs(params, execution)
     ret = bayesian_group_ana_py_outputs(params, execution)
@@ -281,6 +270,8 @@ def bayesian_group_ana_py(
     runner: Runner | None = None,
 ) -> BayesianGroupAnaPyOutputs:
     """
+    BayesianGroupAna.py
+    
     This program conducts Bayesian Group Analysis (BGA) on a list of regions of
     interest (ROIs). Compared to the conventional univariate GLM, BGA pools and
     shares the information across the ROIs in a multilevel system.
@@ -312,8 +303,6 @@ def bayesian_group_ana_py(
     Returns:
         NamedTuple of outputs (described in `BayesianGroupAnaPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BAYESIAN_GROUP_ANA_PY_METADATA)
     params = bayesian_group_ana_py_params(
         data_table=data_table,
         y_variable=y_variable,
@@ -330,13 +319,13 @@ def bayesian_group_ana_py(
         overwrite=overwrite,
         help_=help_,
     )
-    return bayesian_group_ana_py_execute(params, execution)
+    return bayesian_group_ana_py_execute(params, runner)
 
 
 __all__ = [
     "BAYESIAN_GROUP_ANA_PY_METADATA",
     "BayesianGroupAnaPyOutputs",
-    "BayesianGroupAnaPyParameters",
     "bayesian_group_ana_py",
+    "bayesian_group_ana_py_execute",
     "bayesian_group_ana_py_params",
 ]

niwrap_afni/afni/brain_skin.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 BRAIN_SKIN_METADATA = Metadata(
-    id="0d74e03c612b5e5a46624d4adb229be24b424b58.boutiques",
+    id="d0d1c3e3c3e6ac7de4b980399cd1d6fc70595b98.boutiques",
     name="BrainSkin",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ BRAIN_SKIN_METADATA = Metadata(
 
 
 BrainSkinParameters = typing.TypedDict('BrainSkinParameters', {
-    "__STYXTYPE__": typing.Literal["BrainSkin"],
+    "@type": typing.NotRequired[typing.Literal["afni/BrainSkin"]],
+    "surface": str,
+    "skingrid_volume": InputPathType,
+    "prefix": str,
+    "plimit": typing.NotRequired[float | None],
+    "dlimit": typing.NotRequired[float | None],
+    "segdo": typing.NotRequired[str | None],
+    "voxelize": typing.NotRequired[str | None],
+    "infill": typing.NotRequired[str | None],
+    "out_file": typing.NotRequired[InputPathType | None],
+    "vol_skin": typing.NotRequired[InputPathType | None],
+    "vol_hull": typing.NotRequired[InputPathType | None],
+    "no_zero_attraction": bool,
+    "node_dbg": typing.NotRequired[float | None],
+})
+BrainSkinParametersTagged = typing.TypedDict('BrainSkinParametersTagged', {
+    "@type": typing.Literal["afni/BrainSkin"],
     "surface": str,
     "skingrid_volume": InputPathType,
     "prefix": str,
@@ -29,43 +45,11 @@ BrainSkinParameters = typing.TypedDict('BrainSkinParameters', {
     "no_zero_attraction": bool,
     "node_dbg": typing.NotRequired[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 {
-        "BrainSkin": brain_skin_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 {
-        "BrainSkin": brain_skin_outputs,
-    }.get(t)
 
 
 class BrainSkinOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `brain_skin(...)`.
+    Output object returned when calling `BrainSkinParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -108,7 +92,7 @@ def brain_skin_params(
     vol_hull: InputPathType | None = None,
     no_zero_attraction: bool = False,
     node_dbg: float | None = None,
-) -> BrainSkinParameters:
+) -> BrainSkinParametersTagged:
     """
     Build parameters.
     
@@ -138,7 +122,7 @@ def brain_skin_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "BrainSkin",
+        "@type": "afni/BrainSkin",
         "surface": surface,
         "skingrid_volume": skingrid_volume,
         "prefix": prefix,
@@ -180,61 +164,61 @@ def brain_skin_cargs(
     """
     cargs = []
     cargs.append("BrainSkin")
-    cargs.append(params.get("surface"))
+    cargs.append(params.get("surface", None))
     cargs.extend([
         "-skingrid",
-        execution.input_file(params.get("skingrid_volume"))
+        execution.input_file(params.get("skingrid_volume", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("plimit") is not None:
+    if params.get("plimit", None) is not None:
         cargs.extend([
             "-plimit",
-            str(params.get("plimit"))
+            str(params.get("plimit", None))
         ])
-    if params.get("dlimit") is not None:
+    if params.get("dlimit", None) is not None:
         cargs.extend([
             "-dlimit",
-            str(params.get("dlimit"))
+            str(params.get("dlimit", None))
         ])
-    if params.get("segdo") is not None:
+    if params.get("segdo", None) is not None:
         cargs.extend([
             "-segdo",
-            params.get("segdo")
+            params.get("segdo", None)
         ])
-    if params.get("voxelize") is not None:
+    if params.get("voxelize", None) is not None:
         cargs.extend([
             "-voxelize",
-            params.get("voxelize")
+            params.get("voxelize", None)
         ])
-    if params.get("infill") is not None:
+    if params.get("infill", None) is not None:
         cargs.extend([
             "-infill",
-            params.get("infill")
+            params.get("infill", None)
         ])
-    if params.get("out_file") is not None:
+    if params.get("out_file", None) is not None:
         cargs.extend([
             "-out",
-            execution.input_file(params.get("out_file"))
+            execution.input_file(params.get("out_file", None))
         ])
-    if params.get("vol_skin") is not None:
+    if params.get("vol_skin", None) is not None:
         cargs.extend([
             "-vol_skin",
-            execution.input_file(params.get("vol_skin"))
+            execution.input_file(params.get("vol_skin", None))
         ])
-    if params.get("vol_hull") is not None:
+    if params.get("vol_hull", None) is not None:
         cargs.extend([
             "-vol_hull",
-            execution.input_file(params.get("vol_hull"))
+            execution.input_file(params.get("vol_hull", None))
         ])
-    if params.get("no_zero_attraction"):
+    if params.get("no_zero_attraction", False):
         cargs.append("-no_zero_attraction")
-    if params.get("node_dbg") is not None:
+    if params.get("node_dbg", None) is not None:
         cargs.extend([
             "-node_dbg",
-            str(params.get("node_dbg"))
+            str(params.get("node_dbg", None))
         ])
     return cargs
 
@@ -254,26 +238,28 @@ def brain_skin_outputs(
     """
     ret = BrainSkinOutputs(
         root=execution.output_file("."),
-        stitch_surface=execution.output_file(params.get("prefix") + ".stitch.gii"),
-        initial_skin_surface=execution.output_file(params.get("prefix") + ".skin.gii"),
-        reduced_skin_surface=execution.output_file(params.get("prefix") + ".skin_simp.gii"),
-        inflated_skin_surface=execution.output_file(params.get("prefix") + ".skin.isotopic.gii"),
-        patching_voxels=execution.output_file(params.get("prefix") + ".ptchvox+orig"),
-        surf_voxels=execution.output_file(params.get("prefix") + ".surfvox+orig"),
-        skin_voxels=execution.output_file(params.get("prefix") + ".skinvox+orig"),
-        infilled_voxels=execution.output_file(params.get("prefix") + ".infilled+orig"),
-        node_pairs_results=execution.output_file(params.get("prefix") + ".niml.dset"),
-        inflating_surface_results=execution.output_file(params.get("prefix") + ".areas.niml.dset"),
-        segments_display=execution.output_file(params.get("prefix") + ".1D.do"),
+        stitch_surface=execution.output_file(params.get("prefix", None) + ".stitch.gii"),
+        initial_skin_surface=execution.output_file(params.get("prefix", None) + ".skin.gii"),
+        reduced_skin_surface=execution.output_file(params.get("prefix", None) + ".skin_simp.gii"),
+        inflated_skin_surface=execution.output_file(params.get("prefix", None) + ".skin.isotopic.gii"),
+        patching_voxels=execution.output_file(params.get("prefix", None) + ".ptchvox+orig"),
+        surf_voxels=execution.output_file(params.get("prefix", None) + ".surfvox+orig"),
+        skin_voxels=execution.output_file(params.get("prefix", None) + ".skinvox+orig"),
+        infilled_voxels=execution.output_file(params.get("prefix", None) + ".infilled+orig"),
+        node_pairs_results=execution.output_file(params.get("prefix", None) + ".niml.dset"),
+        inflating_surface_results=execution.output_file(params.get("prefix", None) + ".areas.niml.dset"),
+        segments_display=execution.output_file(params.get("prefix", None) + ".1D.do"),
     )
     return ret
 
 
 def brain_skin_execute(
     params: BrainSkinParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> BrainSkinOutputs:
     """
+    BrainSkin
+    
     A program to create an unfolded surface that wraps the brain (skin) and
     Gyrification Indices.
     
@@ -283,10 +269,12 @@ def brain_skin_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `BrainSkinOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(BRAIN_SKIN_METADATA)
     params = execution.params(params)
     cargs = brain_skin_cargs(params, execution)
     ret = brain_skin_outputs(params, execution)
@@ -311,6 +299,8 @@ def brain_skin(
     runner: Runner | None = None,
 ) -> BrainSkinOutputs:
     """
+    BrainSkin
+    
     A program to create an unfolded surface that wraps the brain (skin) and
     Gyrification Indices.
     
@@ -344,8 +334,6 @@ def brain_skin(
     Returns:
         NamedTuple of outputs (described in `BrainSkinOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(BRAIN_SKIN_METADATA)
     params = brain_skin_params(
         surface=surface,
         skingrid_volume=skingrid_volume,
@@ -361,13 +349,13 @@ def brain_skin(
         no_zero_attraction=no_zero_attraction,
         node_dbg=node_dbg,
     )
-    return brain_skin_execute(params, execution)
+    return brain_skin_execute(params, runner)
 
 
 __all__ = [
     "BRAIN_SKIN_METADATA",
     "BrainSkinOutputs",
-    "BrainSkinParameters",
     "brain_skin",
+    "brain_skin_execute",
     "brain_skin_params",
 ]