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

niwrap_freesurfer/freesurfer/t4img_4dfp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 T4IMG_4DFP_METADATA = Metadata(
-    id="0bed5ef447fb42522806c2679d89e36a77afd790.boutiques",
+    id="d122e00ed8f4305d0e57922fe6e2373707275da9.boutiques",
     name="t4img_4dfp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ T4IMG_4DFP_METADATA = Metadata(
 
 
 T4img4dfpParameters = typing.TypedDict('T4img4dfpParameters', {
-    "__STYXTYPE__": typing.Literal["t4img_4dfp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/t4img_4dfp"]],
+    "t4file": InputPathType,
+    "imgfile": InputPathType,
+    "outfile": typing.NotRequired[str | None],
+})
+T4img4dfpParametersTagged = typing.TypedDict('T4img4dfpParametersTagged', {
+    "@type": typing.Literal["freesurfer/t4img_4dfp"],
     "t4file": InputPathType,
     "imgfile": InputPathType,
     "outfile": 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 {
-        "t4img_4dfp": t4img_4dfp_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 {
-        "t4img_4dfp": t4img_4dfp_outputs,
-    }.get(t)
 
 
 class T4img4dfpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `t4img_4dfp(...)`.
+    Output object returned when calling `T4img4dfpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def t4img_4dfp_params(
     t4file: InputPathType,
     imgfile: InputPathType,
     outfile: str | None = None,
-) -> T4img4dfpParameters:
+) -> T4img4dfpParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def t4img_4dfp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "t4img_4dfp",
+        "@type": "freesurfer/t4img_4dfp",
         "t4file": t4file,
         "imgfile": imgfile,
     }
@@ -104,10 +78,10 @@ def t4img_4dfp_cargs(
     """
     cargs = []
     cargs.append("t4img_4dfp")
-    cargs.append(execution.input_file(params.get("t4file")))
-    cargs.append(execution.input_file(params.get("imgfile")))
-    if params.get("outfile") is not None:
-        cargs.append(params.get("outfile"))
+    cargs.append(execution.input_file(params.get("t4file", None)))
+    cargs.append(execution.input_file(params.get("imgfile", None)))
+    if params.get("outfile", None) is not None:
+        cargs.append(params.get("outfile", None))
     return cargs
 
 
@@ -126,16 +100,18 @@ def t4img_4dfp_outputs(
     """
     ret = T4img4dfpOutputs(
         root=execution.output_file("."),
-        transformed_image=execution.output_file(params.get("outfile") + ".4dfp.img") if (params.get("outfile") is not None) else None,
+        transformed_image=execution.output_file(params.get("outfile", None) + ".4dfp.img") if (params.get("outfile") is not None) else None,
     )
     return ret
 
 
 def t4img_4dfp_execute(
     params: T4img4dfpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> T4img4dfpOutputs:
     """
+    t4img_4dfp
+    
     Transforms a 4dfp image using a specified t4 file.
     
     Author: FreeSurfer Developers
@@ -144,10 +120,12 @@ def t4img_4dfp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `T4img4dfpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(T4IMG_4DFP_METADATA)
     params = execution.params(params)
     cargs = t4img_4dfp_cargs(params, execution)
     ret = t4img_4dfp_outputs(params, execution)
@@ -162,6 +140,8 @@ def t4img_4dfp(
     runner: Runner | None = None,
 ) -> T4img4dfpOutputs:
     """
+    t4img_4dfp
+    
     Transforms a 4dfp image using a specified t4 file.
     
     Author: FreeSurfer Developers
@@ -177,20 +157,18 @@ def t4img_4dfp(
     Returns:
         NamedTuple of outputs (described in `T4img4dfpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(T4IMG_4DFP_METADATA)
     params = t4img_4dfp_params(
         t4file=t4file,
         imgfile=imgfile,
         outfile=outfile,
     )
-    return t4img_4dfp_execute(params, execution)
+    return t4img_4dfp_execute(params, runner)
 
 
 __all__ = [
     "T4IMG_4DFP_METADATA",
     "T4img4dfpOutputs",
-    "T4img4dfpParameters",
     "t4img_4dfp",
+    "t4img_4dfp_execute",
     "t4img_4dfp_params",
 ]

niwrap_freesurfer/freesurfer/t4imgs_4dfp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 T4IMGS_4DFP_METADATA = Metadata(
-    id="f59930980573ba4f92691ede7675eb588b9ae991.boutiques",
+    id="fa7048ce1e8228df24d2eca1d22d12ad55ecd2d5.boutiques",
     name="t4imgs_4dfp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ T4IMGS_4DFP_METADATA = Metadata(
 
 
 T4imgs4dfpParameters = typing.TypedDict('T4imgs4dfpParameters', {
-    "__STYXTYPE__": typing.Literal["t4imgs_4dfp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/t4imgs_4dfp"]],
+    "sqrt_normalize": bool,
+    "cubic_spline": bool,
+    "output_nan": bool,
+    "convert_t4": bool,
+    "nearest_neighbor": bool,
+    "output_111_space": bool,
+    "output_222_space": bool,
+    "output_333n_space": typing.NotRequired[str | None],
+    "duplicate_dimensions": typing.NotRequired[str | None],
+    "big_endian": bool,
+    "little_endian": bool,
+    "input_images": list[InputPathType],
+    "output_image": str,
+})
+T4imgs4dfpParametersTagged = typing.TypedDict('T4imgs4dfpParametersTagged', {
+    "@type": typing.Literal["freesurfer/t4imgs_4dfp"],
     "sqrt_normalize": bool,
     "cubic_spline": bool,
     "output_nan": bool,
@@ -29,43 +45,11 @@ T4imgs4dfpParameters = typing.TypedDict('T4imgs4dfpParameters', {
     "input_images": list[InputPathType],
     "output_image": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "t4imgs_4dfp": t4imgs_4dfp_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 {
-        "t4imgs_4dfp": t4imgs_4dfp_outputs,
-    }.get(t)
 
 
 class T4imgs4dfpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `t4imgs_4dfp(...)`.
+    Output object returned when calling `T4imgs4dfpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -87,7 +71,7 @@ def t4imgs_4dfp_params(
     duplicate_dimensions: str | None = None,
     big_endian: bool = False,
     little_endian: bool = False,
-) -> T4imgs4dfpParameters:
+) -> T4imgs4dfpParametersTagged:
     """
     Build parameters.
     
@@ -109,7 +93,7 @@ def t4imgs_4dfp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "t4imgs_4dfp",
+        "@type": "freesurfer/t4imgs_4dfp",
         "sqrt_normalize": sqrt_normalize,
         "cubic_spline": cubic_spline,
         "output_nan": output_nan,
@@ -144,36 +128,36 @@ def t4imgs_4dfp_cargs(
     """
     cargs = []
     cargs.append("t4imgs_4dfp")
-    if params.get("sqrt_normalize"):
+    if params.get("sqrt_normalize", False):
         cargs.append("-z")
-    if params.get("cubic_spline"):
+    if params.get("cubic_spline", False):
         cargs.append("-s")
-    if params.get("output_nan"):
+    if params.get("output_nan", False):
         cargs.append("-N")
-    if params.get("convert_t4"):
+    if params.get("convert_t4", False):
         cargs.append("-B")
-    if params.get("nearest_neighbor"):
+    if params.get("nearest_neighbor", False):
         cargs.append("-n")
-    if params.get("output_111_space"):
+    if params.get("output_111_space", False):
         cargs.append("-O111")
-    if params.get("output_222_space"):
+    if params.get("output_222_space", False):
         cargs.append("-O222")
-    if params.get("output_333n_space") is not None:
+    if params.get("output_333n_space", None) is not None:
         cargs.extend([
             "-O333.n",
-            params.get("output_333n_space")
+            params.get("output_333n_space", None)
         ])
-    if params.get("duplicate_dimensions") is not None:
+    if params.get("duplicate_dimensions", None) is not None:
         cargs.extend([
             "-O",
-            params.get("duplicate_dimensions")
+            params.get("duplicate_dimensions", None)
         ])
-    if params.get("big_endian"):
+    if params.get("big_endian", False):
         cargs.append("-@b")
-    if params.get("little_endian"):
+    if params.get("little_endian", False):
         cargs.append("-@l")
-    cargs.extend([execution.input_file(f) for f in params.get("input_images")])
-    cargs.append(params.get("output_image"))
+    cargs.extend([execution.input_file(f) for f in params.get("input_images", None)])
+    cargs.append(params.get("output_image", None))
     return cargs
 
 
@@ -192,16 +176,18 @@ def t4imgs_4dfp_outputs(
     """
     ret = T4imgs4dfpOutputs(
         root=execution.output_file("."),
-        transformed_image=execution.output_file(params.get("output_image") + ".4dfp.img"),
+        transformed_image=execution.output_file(params.get("output_image", None) + ".4dfp.img"),
     )
     return ret
 
 
 def t4imgs_4dfp_execute(
     params: T4imgs4dfpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> T4imgs4dfpOutputs:
     """
+    t4imgs_4dfp
+    
     Freesurfer tool for transforming images according to a specified T4 file.
     
     Author: FreeSurfer Developers
@@ -210,10 +196,12 @@ def t4imgs_4dfp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `T4imgs4dfpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(T4IMGS_4DFP_METADATA)
     params = execution.params(params)
     cargs = t4imgs_4dfp_cargs(params, execution)
     ret = t4imgs_4dfp_outputs(params, execution)
@@ -238,6 +226,8 @@ def t4imgs_4dfp(
     runner: Runner | None = None,
 ) -> T4imgs4dfpOutputs:
     """
+    t4imgs_4dfp
+    
     Freesurfer tool for transforming images according to a specified T4 file.
     
     Author: FreeSurfer Developers
@@ -262,8 +252,6 @@ def t4imgs_4dfp(
     Returns:
         NamedTuple of outputs (described in `T4imgs4dfpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(T4IMGS_4DFP_METADATA)
     params = t4imgs_4dfp_params(
         sqrt_normalize=sqrt_normalize,
         cubic_spline=cubic_spline,
@@ -279,13 +267,13 @@ def t4imgs_4dfp(
         input_images=input_images,
         output_image=output_image,
     )
-    return t4imgs_4dfp_execute(params, execution)
+    return t4imgs_4dfp_execute(params, runner)
 
 
 __all__ = [
     "T4IMGS_4DFP_METADATA",
     "T4imgs4dfpOutputs",
-    "T4imgs4dfpParameters",
     "t4imgs_4dfp",
+    "t4imgs_4dfp_execute",
     "t4imgs_4dfp_params",
 ]

niwrap_freesurfer/freesurfer/table2map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TABLE2MAP_METADATA = Metadata(
-    id="a1a6b6fb84c32df9b568c86f461d163ba6cbfca6.boutiques",
+    id="375fcb71ecdd3f7b02dfe12003321f048a22ccc7.boutiques",
     name="table2map",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ TABLE2MAP_METADATA = Metadata(
 
 
 Table2mapParameters = typing.TypedDict('Table2mapParameters', {
-    "__STYXTYPE__": typing.Literal["table2map"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/table2map"]],
+    "input_table": InputPathType,
+    "output_map": str,
+    "segmentation": typing.NotRequired[InputPathType | None],
+    "parcellation": typing.NotRequired[InputPathType | None],
+    "columns": typing.NotRequired[list[str] | None],
+    "lookup_table": typing.NotRequired[InputPathType | None],
+})
+Table2mapParametersTagged = typing.TypedDict('Table2mapParametersTagged', {
+    "@type": typing.Literal["freesurfer/table2map"],
     "input_table": InputPathType,
     "output_map": str,
     "segmentation": typing.NotRequired[InputPathType | None],
@@ -22,42 +31,11 @@ Table2mapParameters = typing.TypedDict('Table2mapParameters', {
     "columns": typing.NotRequired[list[str] | None],
     "lookup_table": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "table2map": table2map_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 Table2mapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `table2map(...)`.
+    Output object returned when calling `Table2mapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def table2map_params(
     parcellation: InputPathType | None = None,
     columns: list[str] | None = None,
     lookup_table: InputPathType | None = None,
-) -> Table2mapParameters:
+) -> Table2mapParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def table2map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "table2map",
+        "@type": "freesurfer/table2map",
         "input_table": input_table,
         "output_map": output_map,
     }
@@ -117,31 +95,31 @@ def table2map_cargs(
     cargs.append("table2map")
     cargs.extend([
         "-t",
-        execution.input_file(params.get("input_table"))
+        execution.input_file(params.get("input_table", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_map")
+        params.get("output_map", None)
     ])
-    if params.get("segmentation") is not None:
+    if params.get("segmentation", None) is not None:
         cargs.extend([
             "-s",
-            execution.input_file(params.get("segmentation"))
+            execution.input_file(params.get("segmentation", None))
         ])
-    if params.get("parcellation") is not None:
+    if params.get("parcellation", None) is not None:
         cargs.extend([
             "-p",
-            execution.input_file(params.get("parcellation"))
+            execution.input_file(params.get("parcellation", None))
         ])
-    if params.get("columns") is not None:
+    if params.get("columns", None) is not None:
         cargs.extend([
             "-c",
-            *params.get("columns")
+            *params.get("columns", None)
         ])
-    if params.get("lookup_table") is not None:
+    if params.get("lookup_table", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("lookup_table"))
+            execution.input_file(params.get("lookup_table", None))
         ])
     return cargs
 
@@ -167,9 +145,11 @@ def table2map_outputs(
 
 def table2map_execute(
     params: Table2mapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Table2mapOutputs:
     """
+    table2map
+    
     A tool to map data from a table onto an output map, optionally using
     segmentation or parcellation files.
     
@@ -179,10 +159,12 @@ def table2map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Table2mapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TABLE2MAP_METADATA)
     params = execution.params(params)
     cargs = table2map_cargs(params, execution)
     ret = table2map_outputs(params, execution)
@@ -200,6 +182,8 @@ def table2map(
     runner: Runner | None = None,
 ) -> Table2mapOutputs:
     """
+    table2map
+    
     A tool to map data from a table onto an output map, optionally using
     segmentation or parcellation files.
     
@@ -218,8 +202,6 @@ def table2map(
     Returns:
         NamedTuple of outputs (described in `Table2mapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TABLE2MAP_METADATA)
     params = table2map_params(
         input_table=input_table,
         output_map=output_map,
@@ -228,13 +210,13 @@ def table2map(
         columns=columns,
         lookup_table=lookup_table,
     )
-    return table2map_execute(params, execution)
+    return table2map_execute(params, runner)
 
 
 __all__ = [
     "TABLE2MAP_METADATA",
     "Table2mapOutputs",
-    "Table2mapParameters",
     "table2map",
+    "table2map_execute",
     "table2map_params",
 ]