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

niwrap_afni/afni/surf_patch.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_PATCH_METADATA = Metadata(
-    id="93b33e70e7fed9975e51874f8d35a6d0153496f3.boutiques",
+    id="08104785816f45db8ccb07c9651feda313b200a8.boutiques",
     name="SurfPatch",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,31 @@ SURF_PATCH_METADATA = Metadata(
 
 
 SurfPatchParameters = typing.TypedDict('SurfPatchParameters', {
-    "__STYXTYPE__": typing.Literal["SurfPatch"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfPatch"]],
+    "spec_file": InputPathType,
+    "surf_A": InputPathType,
+    "surf_B": InputPathType,
+    "nodefile": InputPathType,
+    "inode": float,
+    "ilabel": float,
+    "prefix": str,
+    "hits": typing.NotRequired[float | None],
+    "masklabel": typing.NotRequired[str | None],
+    "vol": bool,
+    "vol_only": bool,
+    "patch2surf": bool,
+    "coord_gain": typing.NotRequired[float | None],
+    "check_bowtie": bool,
+    "fix_bowtie": bool,
+    "ok_bowtie": bool,
+    "adjust_contour": bool,
+    "do_not_adjust_contour": bool,
+    "stitched_surface": typing.NotRequired[InputPathType | None],
+    "flip_orientation": bool,
+    "verbosity": typing.NotRequired[float | None],
+})
+SurfPatchParametersTagged = typing.TypedDict('SurfPatchParametersTagged', {
+    "@type": typing.Literal["afni/SurfPatch"],
     "spec_file": InputPathType,
     "surf_A": InputPathType,
     "surf_B": InputPathType,
@@ -37,43 +61,11 @@ SurfPatchParameters = typing.TypedDict('SurfPatchParameters', {
     "flip_orientation": bool,
     "verbosity": 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 {
-        "SurfPatch": surf_patch_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 {
-        "SurfPatch": surf_patch_outputs,
-    }.get(t)
 
 
 class SurfPatchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_patch(...)`.
+    Output object returned when calling `SurfPatchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +99,7 @@ def surf_patch_params(
     stitched_surface: InputPathType | None = None,
     flip_orientation: bool = False,
     verbosity: float | None = None,
-) -> SurfPatchParameters:
+) -> SurfPatchParametersTagged:
     """
     Build parameters.
     
@@ -148,7 +140,7 @@ def surf_patch_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfPatch",
+        "@type": "afni/SurfPatch",
         "spec_file": spec_file,
         "surf_A": surf_a,
         "surf_B": surf_b,
@@ -194,67 +186,67 @@ def surf_patch_cargs(
     """
     cargs = []
     cargs.append("SurfPatch")
-    cargs.append(execution.input_file(params.get("spec_file")))
+    cargs.append(execution.input_file(params.get("spec_file", None)))
     cargs.extend([
         "-surf_A",
-        execution.input_file(params.get("surf_A"))
+        execution.input_file(params.get("surf_A", None))
     ])
     cargs.extend([
         "-surf_B",
-        execution.input_file(params.get("surf_B"))
+        execution.input_file(params.get("surf_B", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("nodefile"))
+        execution.input_file(params.get("nodefile", None))
     ])
-    cargs.append(str(params.get("inode")))
-    cargs.append(str(params.get("ilabel")))
+    cargs.append(str(params.get("inode", None)))
+    cargs.append(str(params.get("ilabel", None)))
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("hits") is not None:
+    if params.get("hits", None) is not None:
         cargs.extend([
             "-hits",
-            str(params.get("hits"))
+            str(params.get("hits", None))
         ])
-    if params.get("masklabel") is not None:
+    if params.get("masklabel", None) is not None:
         cargs.extend([
             "-masklabel",
-            params.get("masklabel")
+            params.get("masklabel", None)
         ])
-    if params.get("vol"):
+    if params.get("vol", False):
         cargs.append("-vol")
-    if params.get("vol_only"):
+    if params.get("vol_only", False):
         cargs.append("-vol_only")
-    if params.get("patch2surf"):
+    if params.get("patch2surf", False):
         cargs.append("-patch2surf")
-    if params.get("coord_gain") is not None:
+    if params.get("coord_gain", None) is not None:
         cargs.extend([
             "-coord_gain",
-            str(params.get("coord_gain"))
+            str(params.get("coord_gain", None))
         ])
-    if params.get("check_bowtie"):
+    if params.get("check_bowtie", False):
         cargs.append("-check_bowtie")
-    if params.get("fix_bowtie"):
+    if params.get("fix_bowtie", False):
         cargs.append("-fix_bowtie")
-    if params.get("ok_bowtie"):
+    if params.get("ok_bowtie", False):
         cargs.append("-ok_bowtie")
-    if params.get("adjust_contour"):
+    if params.get("adjust_contour", False):
         cargs.append("-adjust_contour")
-    if params.get("do_not_adjust_contour"):
+    if params.get("do_not_adjust_contour", False):
         cargs.append("-do-not-adjust_contour")
-    if params.get("stitched_surface") is not None:
+    if params.get("stitched_surface", None) is not None:
         cargs.extend([
             "-stitched_surface",
-            execution.input_file(params.get("stitched_surface"))
+            execution.input_file(params.get("stitched_surface", None))
         ])
-    if params.get("flip_orientation"):
+    if params.get("flip_orientation", False):
         cargs.append("-flip_orientation")
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
     return cargs
 
@@ -274,18 +266,20 @@ def surf_patch_outputs(
     """
     ret = SurfPatchOutputs(
         root=execution.output_file("."),
-        outpatch_a=execution.output_file(params.get("prefix") + "_A"),
-        outpatch_b=execution.output_file(params.get("prefix") + "_B"),
-        out_stitched_surface=execution.output_file(params.get("prefix") + "_stitched"),
+        outpatch_a=execution.output_file(params.get("prefix", None) + "_A"),
+        outpatch_b=execution.output_file(params.get("prefix", None) + "_B"),
+        out_stitched_surface=execution.output_file(params.get("prefix", None) + "_stitched"),
     )
     return ret
 
 
 def surf_patch_execute(
     params: SurfPatchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfPatchOutputs:
     """
+    SurfPatch
+    
     Creates a patch of surface formed by nodes in a nodefile and optionally
     calculates the volume between the same patch on two isotopic surfaces.
     
@@ -295,10 +289,12 @@ def surf_patch_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfPatchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_PATCH_METADATA)
     params = execution.params(params)
     cargs = surf_patch_cargs(params, execution)
     ret = surf_patch_outputs(params, execution)
@@ -331,6 +327,8 @@ def surf_patch(
     runner: Runner | None = None,
 ) -> SurfPatchOutputs:
     """
+    SurfPatch
+    
     Creates a patch of surface formed by nodes in a nodefile and optionally
     calculates the volume between the same patch on two isotopic surfaces.
     
@@ -375,8 +373,6 @@ def surf_patch(
     Returns:
         NamedTuple of outputs (described in `SurfPatchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_PATCH_METADATA)
     params = surf_patch_params(
         spec_file=spec_file,
         surf_a=surf_a,
@@ -400,13 +396,13 @@ def surf_patch(
         flip_orientation=flip_orientation,
         verbosity=verbosity,
     )
-    return surf_patch_execute(params, execution)
+    return surf_patch_execute(params, runner)
 
 
 __all__ = [
     "SURF_PATCH_METADATA",
     "SurfPatchOutputs",
-    "SurfPatchParameters",
     "surf_patch",
+    "surf_patch_execute",
     "surf_patch_params",
 ]

niwrap_afni/afni/surf_qual.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_QUAL_METADATA = Metadata(
-    id="dfb574190dfe225eb71023ac6f70ac221b310d08.boutiques",
+    id="ca9fbbde93da6b6ba30bd230838b95dce4404bf8.boutiques",
     name="SurfQual",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ SURF_QUAL_METADATA = Metadata(
 
 
 SurfQualParameters = typing.TypedDict('SurfQualParameters', {
-    "__STYXTYPE__": typing.Literal["SurfQual"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfQual"]],
+    "spec_file": InputPathType,
+    "surface_a": list[InputPathType],
+    "sphere_flag": bool,
+    "summary_flag": bool,
+    "self_intersect_flag": bool,
+    "output_prefix": typing.NotRequired[str | None],
+})
+SurfQualParametersTagged = typing.TypedDict('SurfQualParametersTagged', {
+    "@type": typing.Literal["afni/SurfQual"],
     "spec_file": InputPathType,
     "surface_a": list[InputPathType],
     "sphere_flag": bool,
@@ -22,43 +31,11 @@ SurfQualParameters = typing.TypedDict('SurfQualParameters', {
     "self_intersect_flag": bool,
     "output_prefix": 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 {
-        "SurfQual": surf_qual_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 {
-        "SurfQual": surf_qual_outputs,
-    }.get(t)
 
 
 class SurfQualOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_qual(...)`.
+    Output object returned when calling `SurfQualParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +64,7 @@ def surf_qual_params(
     summary_flag: bool = False,
     self_intersect_flag: bool = False,
     output_prefix: str | None = None,
-) -> SurfQualParameters:
+) -> SurfQualParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +79,7 @@ def surf_qual_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfQual",
+        "@type": "afni/SurfQual",
         "spec_file": spec_file,
         "surface_a": surface_a,
         "sphere_flag": sphere_flag,
@@ -131,22 +108,22 @@ def surf_qual_cargs(
     cargs.append("SurfQual")
     cargs.extend([
         "-spec",
-        execution.input_file(params.get("spec_file"))
+        execution.input_file(params.get("spec_file", None))
     ])
     cargs.extend([
         "-surf_A",
-        *[execution.input_file(f) for f in params.get("surface_a")]
+        *[execution.input_file(f) for f in params.get("surface_a", None)]
     ])
-    if params.get("sphere_flag"):
+    if params.get("sphere_flag", False):
         cargs.append("-sphere")
-    if params.get("summary_flag"):
+    if params.get("summary_flag", False):
         cargs.append("-summary")
-    if params.get("self_intersect_flag"):
+    if params.get("self_intersect_flag", False):
         cargs.append("-self_intersect")
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
     return cargs
 
@@ -166,22 +143,24 @@ def surf_qual_outputs(
     """
     ret = SurfQualOutputs(
         root=execution.output_file("."),
-        dist_output=execution.output_file(params.get("output_prefix") + "_Dist.1D.dset") if (params.get("output_prefix") is not None) else None,
-        dist_color_output=execution.output_file(params.get("output_prefix") + "_Dist.1D.col") if (params.get("output_prefix") is not None) else None,
-        bad_nodes_output=execution.output_file(params.get("output_prefix") + "_BadNodes.1D.dset") if (params.get("output_prefix") is not None) else None,
-        bad_nodes_color_output=execution.output_file(params.get("output_prefix") + "_BadNodes.1D.col") if (params.get("output_prefix") is not None) else None,
-        dotprod_output=execution.output_file(params.get("output_prefix") + "_dotprod.1D.dset") if (params.get("output_prefix") is not None) else None,
-        dotprod_color_output=execution.output_file(params.get("output_prefix") + "_dotprod.1D.col") if (params.get("output_prefix") is not None) else None,
-        intersect_nodes_output=execution.output_file(params.get("output_prefix") + "_IntersNodes.1D.dset") if (params.get("output_prefix") is not None) else None,
+        dist_output=execution.output_file(params.get("output_prefix", None) + "_Dist.1D.dset") if (params.get("output_prefix") is not None) else None,
+        dist_color_output=execution.output_file(params.get("output_prefix", None) + "_Dist.1D.col") if (params.get("output_prefix") is not None) else None,
+        bad_nodes_output=execution.output_file(params.get("output_prefix", None) + "_BadNodes.1D.dset") if (params.get("output_prefix") is not None) else None,
+        bad_nodes_color_output=execution.output_file(params.get("output_prefix", None) + "_BadNodes.1D.col") if (params.get("output_prefix") is not None) else None,
+        dotprod_output=execution.output_file(params.get("output_prefix", None) + "_dotprod.1D.dset") if (params.get("output_prefix") is not None) else None,
+        dotprod_color_output=execution.output_file(params.get("output_prefix", None) + "_dotprod.1D.col") if (params.get("output_prefix") is not None) else None,
+        intersect_nodes_output=execution.output_file(params.get("output_prefix", None) + "_IntersNodes.1D.dset") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def surf_qual_execute(
     params: SurfQualParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfQualOutputs:
     """
+    SurfQual
+    
     A program to check the quality of surfaces.
     
     Author: AFNI Developers
@@ -190,10 +169,12 @@ def surf_qual_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfQualOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_QUAL_METADATA)
     params = execution.params(params)
     cargs = surf_qual_cargs(params, execution)
     ret = surf_qual_outputs(params, execution)
@@ -211,6 +192,8 @@ def surf_qual(
     runner: Runner | None = None,
 ) -> SurfQualOutputs:
     """
+    SurfQual
+    
     A program to check the quality of surfaces.
     
     Author: AFNI Developers
@@ -228,8 +211,6 @@ def surf_qual(
     Returns:
         NamedTuple of outputs (described in `SurfQualOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_QUAL_METADATA)
     params = surf_qual_params(
         spec_file=spec_file,
         surface_a=surface_a,
@@ -238,13 +219,13 @@ def surf_qual(
         self_intersect_flag=self_intersect_flag,
         output_prefix=output_prefix,
     )
-    return surf_qual_execute(params, execution)
+    return surf_qual_execute(params, runner)
 
 
 __all__ = [
     "SURF_QUAL_METADATA",
     "SurfQualOutputs",
-    "SurfQualParameters",
     "surf_qual",
+    "surf_qual_execute",
     "surf_qual_params",
 ]

niwrap_afni/afni/surf_retino_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_RETINO_MAP_METADATA = Metadata(
-    id="fdc8b6d1c56b104c1c85ed05e61553f8ef0d8d73.boutiques",
+    id="759f3f4ec4008d75ee870dbe1ee1e5e8b576e660.boutiques",
     name="SurfRetinoMap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ SURF_RETINO_MAP_METADATA = Metadata(
 
 
 SurfRetinoMapParameters = typing.TypedDict('SurfRetinoMapParameters', {
-    "__STYXTYPE__": typing.Literal["SurfRetinoMap"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfRetinoMap"]],
+    "surface": str,
+    "polar": str,
+    "eccentricity": str,
+    "prefix": typing.NotRequired[str | None],
+    "node_debug": typing.NotRequired[float | None],
+})
+SurfRetinoMapParametersTagged = typing.TypedDict('SurfRetinoMapParametersTagged', {
+    "@type": typing.Literal["afni/SurfRetinoMap"],
     "surface": str,
     "polar": str,
     "eccentricity": str,
     "prefix": typing.NotRequired[str | None],
     "node_debug": 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 {
-        "SurfRetinoMap": surf_retino_map_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 {
-        "SurfRetinoMap": surf_retino_map_outputs,
-    }.get(t)
 
 
 class SurfRetinoMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_retino_map(...)`.
+    Output object returned when calling `SurfRetinoMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def surf_retino_map_params(
     eccentricity: str,
     prefix: str | None = None,
     node_debug: float | None = None,
-) -> SurfRetinoMapParameters:
+) -> SurfRetinoMapParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +65,7 @@ def surf_retino_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfRetinoMap",
+        "@type": "afni/SurfRetinoMap",
         "surface": surface,
         "polar": polar,
         "eccentricity": eccentricity,
@@ -116,18 +92,18 @@ def surf_retino_map_cargs(
     """
     cargs = []
     cargs.append("SurfRetinoMap")
-    cargs.append(params.get("surface"))
-    cargs.append(params.get("polar"))
-    cargs.append(params.get("eccentricity"))
-    if params.get("prefix") is not None:
+    cargs.append(params.get("surface", None))
+    cargs.append(params.get("polar", None))
+    cargs.append(params.get("eccentricity", None))
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "--prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    if params.get("node_debug") is not None:
+    if params.get("node_debug", None) is not None:
         cargs.extend([
             "--node_dbg",
-            str(params.get("node_debug"))
+            str(params.get("node_debug", None))
         ])
     return cargs
 
@@ -147,17 +123,19 @@ def surf_retino_map_outputs(
     """
     ret = SurfRetinoMapOutputs(
         root=execution.output_file("."),
-        vfr_output=execution.output_file(params.get("prefix") + "_VFR.nii.gz") if (params.get("prefix") is not None) else None,
-        threshold_max_output=execution.output_file(params.get("prefix") + "_threshold_max.nii.gz") if (params.get("prefix") is not None) else None,
+        vfr_output=execution.output_file(params.get("prefix", None) + "_VFR.nii.gz") if (params.get("prefix") is not None) else None,
+        threshold_max_output=execution.output_file(params.get("prefix", None) + "_threshold_max.nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def surf_retino_map_execute(
     params: SurfRetinoMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfRetinoMapOutputs:
     """
+    SurfRetinoMap
+    
     Tool for retinotopic mapping on cortical surfaces.
     
     Author: AFNI Developers
@@ -166,10 +144,12 @@ def surf_retino_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfRetinoMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_RETINO_MAP_METADATA)
     params = execution.params(params)
     cargs = surf_retino_map_cargs(params, execution)
     ret = surf_retino_map_outputs(params, execution)
@@ -186,6 +166,8 @@ def surf_retino_map(
     runner: Runner | None = None,
 ) -> SurfRetinoMapOutputs:
     """
+    SurfRetinoMap
+    
     Tool for retinotopic mapping on cortical surfaces.
     
     Author: AFNI Developers
@@ -204,8 +186,6 @@ def surf_retino_map(
     Returns:
         NamedTuple of outputs (described in `SurfRetinoMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_RETINO_MAP_METADATA)
     params = surf_retino_map_params(
         surface=surface,
         polar=polar,
@@ -213,13 +193,13 @@ def surf_retino_map(
         prefix=prefix,
         node_debug=node_debug,
     )
-    return surf_retino_map_execute(params, execution)
+    return surf_retino_map_execute(params, runner)
 
 
 __all__ = [
     "SURF_RETINO_MAP_METADATA",
     "SurfRetinoMapOutputs",
-    "SurfRetinoMapParameters",
     "surf_retino_map",
+    "surf_retino_map_execute",
     "surf_retino_map_params",
 ]