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

niwrap_afni/afni/map_icosahedron.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAP_ICOSAHEDRON_METADATA = Metadata(
-    id="31da18a41b9bc68bbb0a25dfccfcb3c8f8fcc2a0.boutiques",
+    id="a3138b4aa327170500cbb35df97389a3aea3f40c.boutiques",
     name="MapIcosahedron",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ MAP_ICOSAHEDRON_METADATA = Metadata(
 
 
 MapIcosahedronParameters = typing.TypedDict('MapIcosahedronParameters', {
-    "__STYXTYPE__": typing.Literal["MapIcosahedron"],
+    "@type": typing.NotRequired[typing.Literal["afni/MapIcosahedron"]],
+    "spec_file": InputPathType,
+    "rec_depth": typing.NotRequired[float | None],
+    "lin_depth": typing.NotRequired[float | None],
+    "morph_surf": typing.NotRequired[str | None],
+    "num_it": typing.NotRequired[float | None],
+    "prefix": typing.NotRequired[str | None],
+    "nn_dset": typing.NotRequired[str | None],
+    "dset": typing.NotRequired[str | None],
+    "fix_cut_surfaces": bool,
+    "verbosity": bool,
+    "help": bool,
+})
+MapIcosahedronParametersTagged = typing.TypedDict('MapIcosahedronParametersTagged', {
+    "@type": typing.Literal["afni/MapIcosahedron"],
     "spec_file": InputPathType,
     "rec_depth": typing.NotRequired[float | None],
     "lin_depth": typing.NotRequired[float | None],
@@ -27,42 +41,11 @@ MapIcosahedronParameters = typing.TypedDict('MapIcosahedronParameters', {
     "verbosity": 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 {
-        "MapIcosahedron": map_icosahedron_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 MapIcosahedronOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `map_icosahedron(...)`.
+    Output object returned when calling `MapIcosahedronParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -80,7 +63,7 @@ def map_icosahedron_params(
     fix_cut_surfaces: bool = False,
     verbosity: bool = False,
     help_: bool = False,
-) -> MapIcosahedronParameters:
+) -> MapIcosahedronParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +86,7 @@ def map_icosahedron_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "MapIcosahedron",
+        "@type": "afni/MapIcosahedron",
         "spec_file": spec_file,
         "fix_cut_surfaces": fix_cut_surfaces,
         "verbosity": verbosity,
@@ -141,47 +124,47 @@ def map_icosahedron_cargs(
     """
     cargs = []
     cargs.append("MapIcosahedron")
-    cargs.append(execution.input_file(params.get("spec_file")))
-    if params.get("rec_depth") is not None:
+    cargs.append(execution.input_file(params.get("spec_file", None)))
+    if params.get("rec_depth", None) is not None:
         cargs.extend([
             "-rd",
-            str(params.get("rec_depth"))
+            str(params.get("rec_depth", None))
         ])
-    if params.get("lin_depth") is not None:
+    if params.get("lin_depth", None) is not None:
         cargs.extend([
             "-ld",
-            str(params.get("lin_depth"))
+            str(params.get("lin_depth", None))
         ])
-    if params.get("morph_surf") is not None:
+    if params.get("morph_surf", None) is not None:
         cargs.extend([
             "-morph",
-            params.get("morph_surf")
+            params.get("morph_surf", None)
         ])
-    if params.get("num_it") is not None:
+    if params.get("num_it", None) is not None:
         cargs.extend([
             "-it",
-            str(params.get("num_it"))
+            str(params.get("num_it", None))
         ])
-    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("nn_dset") is not None:
+    if params.get("nn_dset", None) is not None:
         cargs.extend([
             "-NN_dset_map",
-            params.get("nn_dset")
+            params.get("nn_dset", None)
         ])
-    if params.get("dset") is not None:
+    if params.get("dset", None) is not None:
         cargs.extend([
             "-dset_map",
-            params.get("dset")
+            params.get("dset", None)
         ])
-    if params.get("fix_cut_surfaces"):
+    if params.get("fix_cut_surfaces", False):
         cargs.append("-fix_cut_surfaces")
-    if params.get("verbosity"):
+    if params.get("verbosity", False):
         cargs.append("-verb")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -207,10 +190,13 @@ def map_icosahedron_outputs(
 
 def map_icosahedron_execute(
     params: MapIcosahedronParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MapIcosahedronOutputs:
     """
-    Creates new versions of original-mesh surfaces using the mesh of an icosahedron.
+    MapIcosahedron
+    
+    Creates new versions of original-mesh surfaces using the mesh of an
+    icosahedron.
     
     Author: AFNI Developers
     
@@ -218,10 +204,12 @@ def map_icosahedron_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MapIcosahedronOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAP_ICOSAHEDRON_METADATA)
     params = execution.params(params)
     cargs = map_icosahedron_cargs(params, execution)
     ret = map_icosahedron_outputs(params, execution)
@@ -244,7 +232,10 @@ def map_icosahedron(
     runner: Runner | None = None,
 ) -> MapIcosahedronOutputs:
     """
-    Creates new versions of original-mesh surfaces using the mesh of an icosahedron.
+    MapIcosahedron
+    
+    Creates new versions of original-mesh surfaces using the mesh of an
+    icosahedron.
     
     Author: AFNI Developers
     
@@ -269,8 +260,6 @@ def map_icosahedron(
     Returns:
         NamedTuple of outputs (described in `MapIcosahedronOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAP_ICOSAHEDRON_METADATA)
     params = map_icosahedron_params(
         spec_file=spec_file,
         rec_depth=rec_depth,
@@ -284,13 +273,13 @@ def map_icosahedron(
         verbosity=verbosity,
         help_=help_,
     )
-    return map_icosahedron_execute(params, execution)
+    return map_icosahedron_execute(params, runner)
 
 
 __all__ = [
     "MAP_ICOSAHEDRON_METADATA",
     "MapIcosahedronOutputs",
-    "MapIcosahedronParameters",
     "map_icosahedron",
+    "map_icosahedron_execute",
     "map_icosahedron_params",
 ]

niwrap_afni/afni/map_track_id.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAP_TRACK_ID_METADATA = Metadata(
-    id="202a6fa3ea0cff136f48e1fd155d368bc1c373ce.boutiques",
+    id="4ee10f84c4d6677586bf4ac90f7a7517bc13dbea.boutiques",
     name="map_TrackID",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ MAP_TRACK_ID_METADATA = Metadata(
 
 
 MapTrackIdParameters = typing.TypedDict('MapTrackIdParameters', {
-    "__STYXTYPE__": typing.Literal["map_TrackID"],
+    "@type": typing.NotRequired[typing.Literal["afni/map_TrackID"]],
+    "prefix": str,
+    "in_trk": InputPathType,
+    "in_map": InputPathType,
+    "reference": InputPathType,
+    "verbose": bool,
+    "orig_zero": bool,
+    "line_only_num": bool,
+    "already_inv": bool,
+})
+MapTrackIdParametersTagged = typing.TypedDict('MapTrackIdParametersTagged', {
+    "@type": typing.Literal["afni/map_TrackID"],
     "prefix": str,
     "in_trk": InputPathType,
     "in_map": InputPathType,
@@ -24,43 +35,11 @@ MapTrackIdParameters = typing.TypedDict('MapTrackIdParameters', {
     "line_only_num": bool,
     "already_inv": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "map_TrackID": map_track_id_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 {
-        "map_TrackID": map_track_id_outputs,
-    }.get(t)
 
 
 class MapTrackIdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `map_track_id(...)`.
+    Output object returned when calling `MapTrackIdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def map_track_id_params(
     orig_zero: bool = False,
     line_only_num: bool = False,
     already_inv: bool = False,
-) -> MapTrackIdParameters:
+) -> MapTrackIdParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +75,7 @@ def map_track_id_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "map_TrackID",
+        "@type": "afni/map_TrackID",
         "prefix": prefix,
         "in_trk": in_trk,
         "in_map": in_map,
@@ -126,27 +105,27 @@ def map_track_id_cargs(
     cargs.append("map_TrackID")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-in_trk",
-        execution.input_file(params.get("in_trk"))
+        execution.input_file(params.get("in_trk", None))
     ])
     cargs.extend([
         "-in_map",
-        execution.input_file(params.get("in_map"))
+        execution.input_file(params.get("in_map", None))
     ])
     cargs.extend([
         "-ref",
-        execution.input_file(params.get("reference"))
+        execution.input_file(params.get("reference", None))
     ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("orig_zero"):
+    if params.get("orig_zero", False):
         cargs.append("-orig_zero")
-    if params.get("line_only_num"):
+    if params.get("line_only_num", False):
         cargs.append("-line_only_num")
-    if params.get("already_inv"):
+    if params.get("already_inv", False):
         cargs.append("-already_inv")
     return cargs
 
@@ -166,16 +145,18 @@ def map_track_id_outputs(
     """
     ret = MapTrackIdOutputs(
         root=execution.output_file("."),
-        output_trk_file=execution.output_file(params.get("prefix") + ".trk"),
+        output_trk_file=execution.output_file(params.get("prefix", None) + ".trk"),
     )
     return ret
 
 
 def map_track_id_execute(
     params: MapTrackIdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MapTrackIdOutputs:
     """
+    map_TrackID
+    
     Maps the track file (*.trk) output of 3dTrackID to another space using the
     1Dmatrix_save info of 3dAllineate.
     
@@ -185,10 +166,12 @@ def map_track_id_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MapTrackIdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAP_TRACK_ID_METADATA)
     params = execution.params(params)
     cargs = map_track_id_cargs(params, execution)
     ret = map_track_id_outputs(params, execution)
@@ -208,6 +191,8 @@ def map_track_id(
     runner: Runner | None = None,
 ) -> MapTrackIdOutputs:
     """
+    map_TrackID
+    
     Maps the track file (*.trk) output of 3dTrackID to another space using the
     1Dmatrix_save info of 3dAllineate.
     
@@ -230,8 +215,6 @@ def map_track_id(
     Returns:
         NamedTuple of outputs (described in `MapTrackIdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAP_TRACK_ID_METADATA)
     params = map_track_id_params(
         prefix=prefix,
         in_trk=in_trk,
@@ -242,13 +225,13 @@ def map_track_id(
         line_only_num=line_only_num,
         already_inv=already_inv,
     )
-    return map_track_id_execute(params, execution)
+    return map_track_id_execute(params, runner)
 
 
 __all__ = [
     "MAP_TRACK_ID_METADATA",
     "MapTrackIdOutputs",
-    "MapTrackIdParameters",
     "map_track_id",
+    "map_track_id_execute",
     "map_track_id_params",
 ]

niwrap_afni/afni/mba.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MBA_METADATA = Metadata(
-    id="f8f6f30c2f9a76d32aa2209cf855c9214666a8bc.boutiques",
+    id="fa3a353d15b81d784871209d7d1f7526f3580483.boutiques",
     name="MBA",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ MBA_METADATA = Metadata(
 
 
 MbaParameters = typing.TypedDict('MbaParameters', {
-    "__STYXTYPE__": typing.Literal["MBA"],
+    "@type": typing.NotRequired[typing.Literal["afni/MBA"]],
+    "prefix": str,
+    "chains": typing.NotRequired[int | None],
+    "iterations": typing.NotRequired[int | None],
+    "model": typing.NotRequired[str | None],
+    "eoi": typing.NotRequired[str | None],
+    "data_table": InputPathType,
+    "cvars": typing.NotRequired[str | None],
+    "qvars": typing.NotRequired[str | None],
+    "qcvar": typing.NotRequired[str | None],
+    "stdz": typing.NotRequired[str | None],
+    "wcp": typing.NotRequired[int | None],
+    "disty": typing.NotRequired[str | None],
+    "se": typing.NotRequired[str | None],
+    "dbgArgs": bool,
+    "help": bool,
+})
+MbaParametersTagged = typing.TypedDict('MbaParametersTagged', {
+    "@type": typing.Literal["afni/MBA"],
     "prefix": str,
     "chains": typing.NotRequired[int | None],
     "iterations": typing.NotRequired[int | None],
@@ -31,43 +49,11 @@ MbaParameters = typing.TypedDict('MbaParameters', {
     "dbgArgs": 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 {
-        "MBA": mba_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 {
-        "MBA": mba_outputs,
-    }.get(t)
 
 
 class MbaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mba(...)`.
+    Output object returned when calling `MbaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +81,7 @@ def mba_params(
     se: str | None = None,
     dbg_args: bool = False,
     help_: bool = False,
-) -> MbaParameters:
+) -> MbaParametersTagged:
     """
     Build parameters.
     
@@ -122,7 +108,7 @@ def mba_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "MBA",
+        "@type": "afni/MBA",
         "prefix": prefix,
         "data_table": data_table,
         "dbgArgs": dbg_args,
@@ -168,69 +154,69 @@ def mba_cargs(
     """
     cargs = []
     cargs.append("MBA")
-    cargs.append(params.get("prefix"))
-    if params.get("chains") is not None:
+    cargs.append(params.get("prefix", None))
+    if params.get("chains", None) is not None:
         cargs.extend([
             "-chains",
-            str(params.get("chains"))
+            str(params.get("chains", None))
         ])
-    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("model") is not None:
+    if params.get("model", None) is not None:
         cargs.extend([
             "-model",
-            params.get("model")
+            params.get("model", None)
         ])
-    if params.get("eoi") is not None:
+    if params.get("eoi", None) is not None:
         cargs.extend([
             "-EOI",
-            params.get("eoi")
+            params.get("eoi", None)
         ])
     cargs.extend([
         "-dataTable",
-        execution.input_file(params.get("data_table"))
+        execution.input_file(params.get("data_table", None))
     ])
-    if params.get("cvars") is not None:
+    if params.get("cvars", None) is not None:
         cargs.extend([
             "-cVars",
-            params.get("cvars")
+            params.get("cvars", None)
         ])
-    if params.get("qvars") is not None:
+    if params.get("qvars", None) is not None:
         cargs.extend([
             "-qVars",
-            params.get("qvars")
+            params.get("qvars", None)
         ])
-    if params.get("qcvar") is not None:
+    if params.get("qcvar", None) is not None:
         cargs.extend([
             "-qContr",
-            params.get("qcvar")
+            params.get("qcvar", None)
         ])
-    if params.get("stdz") is not None:
+    if params.get("stdz", None) is not None:
         cargs.extend([
             "-stdz",
-            params.get("stdz")
+            params.get("stdz", None)
         ])
-    if params.get("wcp") is not None:
+    if params.get("wcp", None) is not None:
         cargs.extend([
             "-WCP",
-            str(params.get("wcp"))
+            str(params.get("wcp", None))
         ])
-    if params.get("disty") is not None:
+    if params.get("disty", None) is not None:
         cargs.extend([
             "-distY",
-            params.get("disty")
+            params.get("disty", None)
         ])
-    if params.get("se") is not None:
+    if params.get("se", None) is not None:
         cargs.extend([
             "-se",
-            params.get("se")
+            params.get("se", None)
         ])
-    if params.get("dbgArgs"):
+    if params.get("dbgArgs", False):
         cargs.append("-dbgArgs")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -250,18 +236,20 @@ def mba_outputs(
     """
     ret = MbaOutputs(
         root=execution.output_file("."),
-        output_txt=execution.output_file(params.get("prefix") + ".txt"),
-        output_rdata=execution.output_file(params.get("prefix") + ".RData"),
-        matrix_plot=execution.output_file(params.get("prefix") + "_matrixplot.png"),
+        output_txt=execution.output_file(params.get("prefix", None) + ".txt"),
+        output_rdata=execution.output_file(params.get("prefix", None) + ".RData"),
+        matrix_plot=execution.output_file(params.get("prefix", None) + "_matrixplot.png"),
     )
     return ret
 
 
 def mba_execute(
     params: MbaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MbaOutputs:
     """
+    MBA
+    
     Matrix-Based Analysis Program through Bayesian Multilevel Modeling.
     
     Author: AFNI Developers
@@ -270,10 +258,12 @@ def mba_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MbaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MBA_METADATA)
     params = execution.params(params)
     cargs = mba_cargs(params, execution)
     ret = mba_outputs(params, execution)
@@ -300,6 +290,8 @@ def mba(
     runner: Runner | None = None,
 ) -> MbaOutputs:
     """
+    MBA
+    
     Matrix-Based Analysis Program through Bayesian Multilevel Modeling.
     
     Author: AFNI Developers
@@ -329,8 +321,6 @@ def mba(
     Returns:
         NamedTuple of outputs (described in `MbaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MBA_METADATA)
     params = mba_params(
         prefix=prefix,
         chains=chains,
@@ -348,13 +338,13 @@ def mba(
         dbg_args=dbg_args,
         help_=help_,
     )
-    return mba_execute(params, execution)
+    return mba_execute(params, runner)
 
 
 __all__ = [
     "MBA_METADATA",
     "MbaOutputs",
-    "MbaParameters",
     "mba",
+    "mba_execute",
     "mba_params",
 ]