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

niwrap_afni/afni/v_3d_vol2_surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_VOL2_SURF_METADATA = Metadata(
-    id="22298e050bc0d8df23c0654204a19a2ced97ccfa.boutiques",
+    id="e1918dddf9096bb5617b30dfc1231e1b05b02173.boutiques",
     name="3dVol2Surf",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,52 @@ V_3D_VOL2_SURF_METADATA = Metadata(
 
 
 V3dVol2SurfParameters = typing.TypedDict('V3dVol2SurfParameters', {
-    "__STYXTYPE__": typing.Literal["3dVol2Surf"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dVol2Surf"]],
+    "spec_file": InputPathType,
+    "sv": InputPathType,
+    "grid_parent": InputPathType,
+    "map_func": str,
+    "surf_A": str,
+    "surf_B": typing.NotRequired[str | None],
+    "out_1D": typing.NotRequired[str | None],
+    "out_niml": typing.NotRequired[str | None],
+    "use_norms": bool,
+    "norm_len": typing.NotRequired[float | None],
+    "first_node": typing.NotRequired[float | None],
+    "last_node": typing.NotRequired[float | None],
+    "debug_level": typing.NotRequired[float | None],
+    "dnode": typing.NotRequired[float | None],
+    "f_steps": typing.NotRequired[float | None],
+    "f_index": typing.NotRequired[str | None],
+    "f_p1_mm": typing.NotRequired[float | None],
+    "f_pn_mm": typing.NotRequired[float | None],
+    "f_p1_fr": typing.NotRequired[float | None],
+    "f_pn_fr": typing.NotRequired[float | None],
+    "skip_col_nodes": bool,
+    "skip_col_1dindex": bool,
+    "skip_col_i": bool,
+    "skip_col_j": bool,
+    "skip_col_k": bool,
+    "skip_col_vals": bool,
+    "no_headers": bool,
+    "save_seg_coords": typing.NotRequired[str | None],
+    "cmask": typing.NotRequired[str | None],
+    "gp_index": typing.NotRequired[float | None],
+    "oob_index": typing.NotRequired[float | None],
+    "oob_value": typing.NotRequired[float | None],
+    "oom_value": typing.NotRequired[float | None],
+    "outcols_afni_nsd": bool,
+    "outcols_1_result": bool,
+    "outcols_results": bool,
+    "outcols_nsd_format": bool,
+    "help": bool,
+    "hist": bool,
+    "version": bool,
+    "keep_norm_dir": bool,
+    "reverse_norm_dir": bool,
+})
+V3dVol2SurfParametersTagged = typing.TypedDict('V3dVol2SurfParametersTagged', {
+    "@type": typing.Literal["afni/3dVol2Surf"],
     "spec_file": InputPathType,
     "sv": InputPathType,
     "grid_parent": InputPathType,
@@ -58,43 +103,11 @@ V3dVol2SurfParameters = typing.TypedDict('V3dVol2SurfParameters', {
     "keep_norm_dir": bool,
     "reverse_norm_dir": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dVol2Surf": v_3d_vol2_surf_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 {
-        "3dVol2Surf": v_3d_vol2_surf_outputs,
-    }.get(t)
 
 
 class V3dVol2SurfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_vol2_surf(...)`.
+    Output object returned when calling `V3dVol2SurfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -149,7 +162,7 @@ def v_3d_vol2_surf_params(
     version: bool = False,
     keep_norm_dir: bool = False,
     reverse_norm_dir: bool = False,
-) -> V3dVol2SurfParameters:
+) -> V3dVol2SurfParametersTagged:
     """
     Build parameters.
     
@@ -207,7 +220,7 @@ def v_3d_vol2_surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dVol2Surf",
+        "@type": "afni/3dVol2Surf",
         "spec_file": spec_file,
         "sv": sv,
         "grid_parent": grid_parent,
@@ -289,156 +302,156 @@ def v_3d_vol2_surf_cargs(
     """
     cargs = []
     cargs.append("3dVol2Surf")
-    cargs.append(execution.input_file(params.get("spec_file")))
+    cargs.append(execution.input_file(params.get("spec_file", None)))
     cargs.extend([
         "-sv",
-        execution.input_file(params.get("sv"))
+        execution.input_file(params.get("sv", None))
     ])
     cargs.extend([
         "-grid_parent",
-        execution.input_file(params.get("grid_parent"))
+        execution.input_file(params.get("grid_parent", None))
     ])
     cargs.extend([
         "-map_func",
-        params.get("map_func")
+        params.get("map_func", None)
     ])
     cargs.extend([
         "-surf_A",
-        params.get("surf_A")
+        params.get("surf_A", None)
     ])
-    if params.get("surf_B") is not None:
+    if params.get("surf_B", None) is not None:
         cargs.extend([
             "-surf_B",
-            params.get("surf_B")
+            params.get("surf_B", None)
         ])
-    if params.get("out_1D") is not None:
+    if params.get("out_1D", None) is not None:
         cargs.extend([
             "-out_1D",
-            params.get("out_1D")
+            params.get("out_1D", None)
         ])
-    if params.get("out_niml") is not None:
+    if params.get("out_niml", None) is not None:
         cargs.extend([
             "-out_niml",
-            params.get("out_niml")
+            params.get("out_niml", None)
         ])
-    if params.get("use_norms"):
+    if params.get("use_norms", False):
         cargs.append("-use_norms")
-    if params.get("norm_len") is not None:
+    if params.get("norm_len", None) is not None:
         cargs.extend([
             "-norm_len",
-            str(params.get("norm_len"))
+            str(params.get("norm_len", None))
         ])
-    if params.get("first_node") is not None:
+    if params.get("first_node", None) is not None:
         cargs.extend([
             "-first_node",
-            str(params.get("first_node"))
+            str(params.get("first_node", None))
         ])
-    if params.get("last_node") is not None:
+    if params.get("last_node", None) is not None:
         cargs.extend([
             "-last_node",
-            str(params.get("last_node"))
+            str(params.get("last_node", None))
         ])
-    if params.get("debug_level") is not None:
+    if params.get("debug_level", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug_level"))
+            str(params.get("debug_level", None))
         ])
-    if params.get("dnode") is not None:
+    if params.get("dnode", None) is not None:
         cargs.extend([
             "-dnode",
-            str(params.get("dnode"))
+            str(params.get("dnode", None))
         ])
-    if params.get("f_steps") is not None:
+    if params.get("f_steps", None) is not None:
         cargs.extend([
             "-f_steps",
-            str(params.get("f_steps"))
+            str(params.get("f_steps", None))
         ])
-    if params.get("f_index") is not None:
+    if params.get("f_index", None) is not None:
         cargs.extend([
             "-f_index",
-            params.get("f_index")
+            params.get("f_index", None)
         ])
-    if params.get("f_p1_mm") is not None:
+    if params.get("f_p1_mm", None) is not None:
         cargs.extend([
             "-f_p1_mm",
-            str(params.get("f_p1_mm"))
+            str(params.get("f_p1_mm", None))
         ])
-    if params.get("f_pn_mm") is not None:
+    if params.get("f_pn_mm", None) is not None:
         cargs.extend([
             "-f_pn_mm",
-            str(params.get("f_pn_mm"))
+            str(params.get("f_pn_mm", None))
         ])
-    if params.get("f_p1_fr") is not None:
+    if params.get("f_p1_fr", None) is not None:
         cargs.extend([
             "-f_p1_fr",
-            str(params.get("f_p1_fr"))
+            str(params.get("f_p1_fr", None))
         ])
-    if params.get("f_pn_fr") is not None:
+    if params.get("f_pn_fr", None) is not None:
         cargs.extend([
             "-f_pn_fr",
-            str(params.get("f_pn_fr"))
+            str(params.get("f_pn_fr", None))
         ])
-    if params.get("skip_col_nodes"):
+    if params.get("skip_col_nodes", False):
         cargs.append("-skip_col_nodes")
-    if params.get("skip_col_1dindex"):
+    if params.get("skip_col_1dindex", False):
         cargs.append("-skip_col_1dindex")
-    if params.get("skip_col_i"):
+    if params.get("skip_col_i", False):
         cargs.append("-skip_col_i")
-    if params.get("skip_col_j"):
+    if params.get("skip_col_j", False):
         cargs.append("-skip_col_j")
-    if params.get("skip_col_k"):
+    if params.get("skip_col_k", False):
         cargs.append("-skip_col_k")
-    if params.get("skip_col_vals"):
+    if params.get("skip_col_vals", False):
         cargs.append("-skip_col_vals")
-    if params.get("no_headers"):
+    if params.get("no_headers", False):
         cargs.append("-no_headers")
-    if params.get("save_seg_coords") is not None:
+    if params.get("save_seg_coords", None) is not None:
         cargs.extend([
             "-save_seg_coords",
-            params.get("save_seg_coords")
+            params.get("save_seg_coords", None)
         ])
-    if params.get("cmask") is not None:
+    if params.get("cmask", None) is not None:
         cargs.extend([
             "-cmask",
-            params.get("cmask")
+            params.get("cmask", None)
         ])
-    if params.get("gp_index") is not None:
+    if params.get("gp_index", None) is not None:
         cargs.extend([
             "-gp_index",
-            str(params.get("gp_index"))
+            str(params.get("gp_index", None))
         ])
-    if params.get("oob_index") is not None:
+    if params.get("oob_index", None) is not None:
         cargs.extend([
             "-oob_index",
-            str(params.get("oob_index"))
+            str(params.get("oob_index", None))
         ])
-    if params.get("oob_value") is not None:
+    if params.get("oob_value", None) is not None:
         cargs.extend([
             "-oob_value",
-            str(params.get("oob_value"))
+            str(params.get("oob_value", None))
         ])
-    if params.get("oom_value") is not None:
+    if params.get("oom_value", None) is not None:
         cargs.extend([
             "-oom_value",
-            str(params.get("oom_value"))
+            str(params.get("oom_value", None))
         ])
-    if params.get("outcols_afni_nsd"):
+    if params.get("outcols_afni_nsd", False):
         cargs.append("-outcols_afni_NSD")
-    if params.get("outcols_1_result"):
+    if params.get("outcols_1_result", False):
         cargs.append("-outcols_1_result")
-    if params.get("outcols_results"):
+    if params.get("outcols_results", False):
         cargs.append("-outcols_results")
-    if params.get("outcols_nsd_format"):
+    if params.get("outcols_nsd_format", False):
         cargs.append("-outcols_NSD_format")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hist"):
+    if params.get("hist", False):
         cargs.append("-hist")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    if params.get("keep_norm_dir"):
+    if params.get("keep_norm_dir", False):
         cargs.append("-keep_norm_dir")
-    if params.get("reverse_norm_dir"):
+    if params.get("reverse_norm_dir", False):
         cargs.append("-reverse_norm_dir")
     return cargs
 
@@ -458,18 +471,20 @@ def v_3d_vol2_surf_outputs(
     """
     ret = V3dVol2SurfOutputs(
         root=execution.output_file("."),
-        out_1d_file=execution.output_file(params.get("out_1D")) if (params.get("out_1D") is not None) else None,
-        out_niml_file=execution.output_file(params.get("out_niml")) if (params.get("out_niml") is not None) else None,
-        seg_coords_file=execution.output_file(params.get("save_seg_coords")) if (params.get("save_seg_coords") is not None) else None,
+        out_1d_file=execution.output_file(params.get("out_1D", None)) if (params.get("out_1D") is not None) else None,
+        out_niml_file=execution.output_file(params.get("out_niml", None)) if (params.get("out_niml") is not None) else None,
+        seg_coords_file=execution.output_file(params.get("save_seg_coords", None)) if (params.get("save_seg_coords") is not None) else None,
     )
     return ret
 
 
 def v_3d_vol2_surf_execute(
     params: V3dVol2SurfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dVol2SurfOutputs:
     """
+    3dVol2Surf
+    
     Map data from a volume domain to a surface domain.
     
     Author: AFNI Developers
@@ -478,10 +493,12 @@ def v_3d_vol2_surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dVol2SurfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_VOL2_SURF_METADATA)
     params = execution.params(params)
     cargs = v_3d_vol2_surf_cargs(params, execution)
     ret = v_3d_vol2_surf_outputs(params, execution)
@@ -535,6 +552,8 @@ def v_3d_vol2_surf(
     runner: Runner | None = None,
 ) -> V3dVol2SurfOutputs:
     """
+    3dVol2Surf
+    
     Map data from a volume domain to a surface domain.
     
     Author: AFNI Developers
@@ -595,8 +614,6 @@ def v_3d_vol2_surf(
     Returns:
         NamedTuple of outputs (described in `V3dVol2SurfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_VOL2_SURF_METADATA)
     params = v_3d_vol2_surf_params(
         spec_file=spec_file,
         sv=sv,
@@ -641,13 +658,13 @@ def v_3d_vol2_surf(
         keep_norm_dir=keep_norm_dir,
         reverse_norm_dir=reverse_norm_dir,
     )
-    return v_3d_vol2_surf_execute(params, execution)
+    return v_3d_vol2_surf_execute(params, runner)
 
 
 __all__ = [
     "V3dVol2SurfOutputs",
-    "V3dVol2SurfParameters",
     "V_3D_VOL2_SURF_METADATA",
     "v_3d_vol2_surf",
+    "v_3d_vol2_surf_execute",
     "v_3d_vol2_surf_params",
 ]

niwrap_afni/afni/v_3d_warp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_WARP_METADATA = Metadata(
-    id="f905d9db7eb4dc5e4bba6d7a453936b46a2e8f24.boutiques",
+    id="3cc4b83e99b0d4bb9865a424333eb9d9321024b5.boutiques",
     name="3dWarp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,32 @@ V_3D_WARP_METADATA = Metadata(
 
 
 V3dWarpParameters = typing.TypedDict('V3dWarpParameters', {
-    "__STYXTYPE__": typing.Literal["3dWarp"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dWarp"]],
+    "matvec_in2out": typing.NotRequired[InputPathType | None],
+    "matvec_out2in": typing.NotRequired[InputPathType | None],
+    "tta2mni": bool,
+    "mni2tta": bool,
+    "matparent": typing.NotRequired[str | None],
+    "card2oblique": typing.NotRequired[str | None],
+    "oblique_parent": typing.NotRequired[str | None],
+    "deoblique": bool,
+    "oblique2card": bool,
+    "disp_obl_xform_only": bool,
+    "linear": bool,
+    "cubic": bool,
+    "NN": bool,
+    "quintic": bool,
+    "wsinc5": bool,
+    "fsl_matvec": bool,
+    "newgrid": typing.NotRequired[float | None],
+    "gridset": typing.NotRequired[str | None],
+    "zpad": typing.NotRequired[float | None],
+    "verb": bool,
+    "prefix": typing.NotRequired[str | None],
+    "dataset": str,
+})
+V3dWarpParametersTagged = typing.TypedDict('V3dWarpParametersTagged', {
+    "@type": typing.Literal["afni/3dWarp"],
     "matvec_in2out": typing.NotRequired[InputPathType | None],
     "matvec_out2in": typing.NotRequired[InputPathType | None],
     "tta2mni": bool,
@@ -38,42 +63,11 @@ V3dWarpParameters = typing.TypedDict('V3dWarpParameters', {
     "prefix": typing.NotRequired[str | None],
     "dataset": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dWarp": v_3d_warp_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 V3dWarpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_warp(...)`.
+    Output object returned when calling `V3dWarpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -102,7 +96,7 @@ def v_3d_warp_params(
     zpad: float | None = None,
     verb: bool = False,
     prefix: str | None = None,
-) -> V3dWarpParameters:
+) -> V3dWarpParametersTagged:
     """
     Build parameters.
     
@@ -138,7 +132,7 @@ def v_3d_warp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dWarp",
+        "@type": "afni/3dWarp",
         "tta2mni": tta2mni,
         "mni2tta": mni2tta,
         "deoblique": deoblique,
@@ -189,76 +183,76 @@ def v_3d_warp_cargs(
     """
     cargs = []
     cargs.append("3dWarp")
-    if params.get("matvec_in2out") is not None:
+    if params.get("matvec_in2out", None) is not None:
         cargs.extend([
             "-matvec_in2out",
-            execution.input_file(params.get("matvec_in2out"))
+            execution.input_file(params.get("matvec_in2out", None))
         ])
-    if params.get("matvec_out2in") is not None:
+    if params.get("matvec_out2in", None) is not None:
         cargs.extend([
             "-matvec_out2in",
-            execution.input_file(params.get("matvec_out2in"))
+            execution.input_file(params.get("matvec_out2in", None))
         ])
-    if params.get("tta2mni"):
+    if params.get("tta2mni", False):
         cargs.append("-tta2mni")
-    if params.get("mni2tta"):
+    if params.get("mni2tta", False):
         cargs.append("-mni2tta")
-    if params.get("matparent") is not None:
+    if params.get("matparent", None) is not None:
         cargs.extend([
             "-matparent",
-            params.get("matparent")
+            params.get("matparent", None)
         ])
-    if params.get("card2oblique") is not None:
+    if params.get("card2oblique", None) is not None:
         cargs.extend([
             "-card2oblique",
-            params.get("card2oblique")
+            params.get("card2oblique", None)
         ])
-    if params.get("oblique_parent") is not None:
+    if params.get("oblique_parent", None) is not None:
         cargs.extend([
             "-oblique_parent",
-            params.get("oblique_parent")
+            params.get("oblique_parent", None)
         ])
-    if params.get("deoblique"):
+    if params.get("deoblique", False):
         cargs.append("-deoblique")
-    if params.get("oblique2card"):
+    if params.get("oblique2card", False):
         cargs.append("-oblique2card")
-    if params.get("disp_obl_xform_only"):
+    if params.get("disp_obl_xform_only", False):
         cargs.append("-disp_obl_xform_only")
-    if params.get("linear"):
+    if params.get("linear", False):
         cargs.append("-linear")
-    if params.get("cubic"):
+    if params.get("cubic", False):
         cargs.append("-cubic")
-    if params.get("NN"):
+    if params.get("NN", False):
         cargs.append("-NN")
-    if params.get("quintic"):
+    if params.get("quintic", False):
         cargs.append("-quintic")
-    if params.get("wsinc5"):
+    if params.get("wsinc5", False):
         cargs.append("-wsinc5")
-    if params.get("fsl_matvec"):
+    if params.get("fsl_matvec", False):
         cargs.append("-fsl_matvec")
-    if params.get("newgrid") is not None:
+    if params.get("newgrid", None) is not None:
         cargs.extend([
             "-newgrid",
-            str(params.get("newgrid"))
+            str(params.get("newgrid", None))
         ])
-    if params.get("gridset") is not None:
+    if params.get("gridset", None) is not None:
         cargs.extend([
             "-gridset",
-            params.get("gridset")
+            params.get("gridset", None)
         ])
-    if params.get("zpad") is not None:
+    if params.get("zpad", None) is not None:
         cargs.extend([
             "-zpad",
-            str(params.get("zpad"))
+            str(params.get("zpad", None))
         ])
-    if params.get("verb"):
+    if params.get("verb", False):
         cargs.append("-verb")
-    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)
         ])
-    cargs.append(params.get("dataset"))
+    cargs.append(params.get("dataset", None))
     return cargs
 
 
@@ -283,9 +277,11 @@ def v_3d_warp_outputs(
 
 def v_3d_warp_execute(
     params: V3dWarpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dWarpOutputs:
     """
+    3dWarp
+    
     Warp (spatially transform) one 3D dataset.
     
     Author: AFNI Developers
@@ -294,10 +290,12 @@ def v_3d_warp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dWarpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_WARP_METADATA)
     params = execution.params(params)
     cargs = v_3d_warp_cargs(params, execution)
     ret = v_3d_warp_outputs(params, execution)
@@ -331,6 +329,8 @@ def v_3d_warp(
     runner: Runner | None = None,
 ) -> V3dWarpOutputs:
     """
+    3dWarp
+    
     Warp (spatially transform) one 3D dataset.
     
     Author: AFNI Developers
@@ -369,8 +369,6 @@ def v_3d_warp(
     Returns:
         NamedTuple of outputs (described in `V3dWarpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_WARP_METADATA)
     params = v_3d_warp_params(
         matvec_in2out=matvec_in2out,
         matvec_out2in=matvec_out2in,
@@ -395,13 +393,13 @@ def v_3d_warp(
         prefix=prefix,
         dataset=dataset,
     )
-    return v_3d_warp_execute(params, execution)
+    return v_3d_warp_execute(params, runner)
 
 
 __all__ = [
     "V3dWarpOutputs",
-    "V3dWarpParameters",
     "V_3D_WARP_METADATA",
     "v_3d_warp",
+    "v_3d_warp_execute",
     "v_3d_warp_params",
 ]