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

niwrap_afni/afni/v_3d_spat_norm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_SPAT_NORM_METADATA = Metadata(
-    id="5e25808dc97cedae2e2d6f6da2b00952c1719962.boutiques",
+    id="a7e3b0ea983f6153df299b1f17211df205465114.boutiques",
     name="3dSpatNorm",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_SPAT_NORM_METADATA = Metadata(
 
 
 V3dSpatNormParameters = typing.TypedDict('V3dSpatNormParameters', {
-    "__STYXTYPE__": typing.Literal["3dSpatNorm"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dSpatNorm"]],
+    "dataset": InputPathType,
+    "prefix": typing.NotRequired[str | None],
+    "orig_space": bool,
+    "verbose": bool,
+    "monkey": bool,
+    "marmot": bool,
+    "rat": bool,
+    "human": bool,
+    "bottom_cuts": typing.NotRequired[str | None],
+})
+V3dSpatNormParametersTagged = typing.TypedDict('V3dSpatNormParametersTagged', {
+    "@type": typing.Literal["afni/3dSpatNorm"],
     "dataset": InputPathType,
     "prefix": typing.NotRequired[str | None],
     "orig_space": bool,
@@ -25,43 +37,11 @@ V3dSpatNormParameters = typing.TypedDict('V3dSpatNormParameters', {
     "human": bool,
     "bottom_cuts": 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 {
-        "3dSpatNorm": v_3d_spat_norm_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 {
-        "3dSpatNorm": v_3d_spat_norm_outputs,
-    }.get(t)
 
 
 class V3dSpatNormOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_spat_norm(...)`.
+    Output object returned when calling `V3dSpatNormParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_spat_norm_params(
     rat: bool = False,
     human: bool = False,
     bottom_cuts: str | None = None,
-) -> V3dSpatNormParameters:
+) -> V3dSpatNormParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +82,7 @@ def v_3d_spat_norm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dSpatNorm",
+        "@type": "afni/3dSpatNorm",
         "dataset": dataset,
         "orig_space": orig_space,
         "verbose": verbose,
@@ -133,28 +113,28 @@ def v_3d_spat_norm_cargs(
     """
     cargs = []
     cargs.append("3dSpatNorm")
-    cargs.append(execution.input_file(params.get("dataset")))
-    if params.get("prefix") is not None:
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("orig_space"):
+    if params.get("orig_space", False):
         cargs.append("-orig_space")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("monkey"):
+    if params.get("monkey", False):
         cargs.append("-monkey")
-    if params.get("marmot"):
+    if params.get("marmot", False):
         cargs.append("-marmost")
-    if params.get("rat"):
+    if params.get("rat", False):
         cargs.append("-rat")
-    if params.get("human"):
+    if params.get("human", False):
         cargs.append("-human")
-    if params.get("bottom_cuts") is not None:
+    if params.get("bottom_cuts", None) is not None:
         cargs.extend([
             "-bottom_cuts",
-            params.get("bottom_cuts")
+            params.get("bottom_cuts", None)
         ])
     return cargs
 
@@ -174,17 +154,19 @@ def v_3d_spat_norm_outputs(
     """
     ret = V3dSpatNormOutputs(
         root=execution.output_file("."),
-        out_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        out_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        out_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        out_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_spat_norm_execute(
     params: V3dSpatNormParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dSpatNormOutputs:
     """
+    3dSpatNorm
+    
     An obsolete tool for spatial normalization.
     
     Author: AFNI Developers
@@ -193,10 +175,12 @@ def v_3d_spat_norm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dSpatNormOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_SPAT_NORM_METADATA)
     params = execution.params(params)
     cargs = v_3d_spat_norm_cargs(params, execution)
     ret = v_3d_spat_norm_outputs(params, execution)
@@ -217,6 +201,8 @@ def v_3d_spat_norm(
     runner: Runner | None = None,
 ) -> V3dSpatNormOutputs:
     """
+    3dSpatNorm
+    
     An obsolete tool for spatial normalization.
     
     Author: AFNI Developers
@@ -240,8 +226,6 @@ def v_3d_spat_norm(
     Returns:
         NamedTuple of outputs (described in `V3dSpatNormOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_SPAT_NORM_METADATA)
     params = v_3d_spat_norm_params(
         dataset=dataset,
         prefix=prefix,
@@ -253,13 +237,13 @@ def v_3d_spat_norm(
         human=human,
         bottom_cuts=bottom_cuts,
     )
-    return v_3d_spat_norm_execute(params, execution)
+    return v_3d_spat_norm_execute(params, runner)
 
 
 __all__ = [
     "V3dSpatNormOutputs",
-    "V3dSpatNormParameters",
     "V_3D_SPAT_NORM_METADATA",
     "v_3d_spat_norm",
+    "v_3d_spat_norm_execute",
     "v_3d_spat_norm_params",
 ]

niwrap_afni/afni/v_3d_stat_clust.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_STAT_CLUST_METADATA = Metadata(
-    id="7fb8fe15f4d0d6befb2add54e75d6a7f19f2cc0b.boutiques",
+    id="9100741a27f3cd6f781d10672b602ed37c190d2f.boutiques",
     name="3dStatClust",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,19 @@ V_3D_STAT_CLUST_METADATA = Metadata(
 
 
 V3dStatClustParameters = typing.TypedDict('V3dStatClustParameters', {
-    "__STYXTYPE__": typing.Literal["3dStatClust"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dStatClust"]],
+    "prefix": typing.NotRequired[str | None],
+    "session_dir": typing.NotRequired[str | None],
+    "verbose": bool,
+    "dist_euc": bool,
+    "dist_ind": bool,
+    "dist_cor": bool,
+    "thresh": str,
+    "nclust": float,
+    "datasets": list[str],
+})
+V3dStatClustParametersTagged = typing.TypedDict('V3dStatClustParametersTagged', {
+    "@type": typing.Literal["afni/3dStatClust"],
     "prefix": typing.NotRequired[str | None],
     "session_dir": typing.NotRequired[str | None],
     "verbose": bool,
@@ -25,43 +37,11 @@ V3dStatClustParameters = typing.TypedDict('V3dStatClustParameters', {
     "nclust": float,
     "datasets": list[str],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dStatClust": v_3d_stat_clust_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 {
-        "3dStatClust": v_3d_stat_clust_outputs,
-    }.get(t)
 
 
 class V3dStatClustOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_stat_clust(...)`.
+    Output object returned when calling `V3dStatClustParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +61,7 @@ def v_3d_stat_clust_params(
     dist_euc: bool = False,
     dist_ind: bool = False,
     dist_cor: bool = False,
-) -> V3dStatClustParameters:
+) -> V3dStatClustParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +83,7 @@ def v_3d_stat_clust_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dStatClust",
+        "@type": "afni/3dStatClust",
         "verbose": verbose,
         "dist_euc": dist_euc,
         "dist_ind": dist_ind,
@@ -134,33 +114,33 @@ def v_3d_stat_clust_cargs(
     """
     cargs = []
     cargs.append("3dStatClust")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("session_dir") is not None:
+    if params.get("session_dir", None) is not None:
         cargs.extend([
             "-session",
-            params.get("session_dir")
+            params.get("session_dir", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("dist_euc"):
+    if params.get("dist_euc", False):
         cargs.append("-dist_euc")
-    if params.get("dist_ind"):
+    if params.get("dist_ind", False):
         cargs.append("-dist_ind")
-    if params.get("dist_cor"):
+    if params.get("dist_cor", False):
         cargs.append("-dist_cor")
     cargs.extend([
         "-thresh",
-        params.get("thresh")
+        params.get("thresh", None)
     ])
     cargs.extend([
         "-nclust",
-        str(params.get("nclust"))
+        str(params.get("nclust", None))
     ])
-    cargs.extend(params.get("datasets"))
+    cargs.extend(params.get("datasets", None))
     return cargs
 
 
@@ -179,20 +159,22 @@ def v_3d_stat_clust_outputs(
     """
     ret = V3dStatClustOutputs(
         root=execution.output_file("."),
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
-        output_brick=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_brick=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_stat_clust_execute(
     params: V3dStatClustParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dStatClustOutputs:
     """
+    3dStatClust
+    
     Perform agglomerative hierarchical clustering for user specified parameter
-    sub-bricks, for all voxels whose threshold statistic is above a user specified
-    value.
+    sub-bricks, for all voxels whose threshold statistic is above a user
+    specified value.
     
     Author: AFNI Developers
     
@@ -200,10 +182,12 @@ def v_3d_stat_clust_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dStatClustOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_STAT_CLUST_METADATA)
     params = execution.params(params)
     cargs = v_3d_stat_clust_cargs(params, execution)
     ret = v_3d_stat_clust_outputs(params, execution)
@@ -224,9 +208,11 @@ def v_3d_stat_clust(
     runner: Runner | None = None,
 ) -> V3dStatClustOutputs:
     """
+    3dStatClust
+    
     Perform agglomerative hierarchical clustering for user specified parameter
-    sub-bricks, for all voxels whose threshold statistic is above a user specified
-    value.
+    sub-bricks, for all voxels whose threshold statistic is above a user
+    specified value.
     
     Author: AFNI Developers
     
@@ -250,8 +236,6 @@ def v_3d_stat_clust(
     Returns:
         NamedTuple of outputs (described in `V3dStatClustOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_STAT_CLUST_METADATA)
     params = v_3d_stat_clust_params(
         prefix=prefix,
         session_dir=session_dir,
@@ -263,13 +247,13 @@ def v_3d_stat_clust(
         nclust=nclust,
         datasets=datasets,
     )
-    return v_3d_stat_clust_execute(params, execution)
+    return v_3d_stat_clust_execute(params, runner)
 
 
 __all__ = [
     "V3dStatClustOutputs",
-    "V3dStatClustParameters",
     "V_3D_STAT_CLUST_METADATA",
     "v_3d_stat_clust",
+    "v_3d_stat_clust_execute",
     "v_3d_stat_clust_params",
 ]