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

niwrap_freesurfer/freesurfer/mris_fix_topology.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_FIX_TOPOLOGY_METADATA = Metadata(
-    id="64e2b9290f868ea668dfb0ff3a646a7a893619d6.boutiques",
+    id="9185f4b3273f3ff9bfae47dd5bb8426cf75e0cfb.boutiques",
     name="mris_fix_topology",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,36 @@ MRIS_FIX_TOPOLOGY_METADATA = Metadata(
 
 
 MrisFixTopologyParameters = typing.TypedDict('MrisFixTopologyParameters', {
-    "__STYXTYPE__": typing.Literal["mris_fix_topology"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_fix_topology"]],
+    "subject_name": str,
+    "hemisphere": str,
+    "orig_name": typing.NotRequired[str | None],
+    "sphere_name": typing.NotRequired[str | None],
+    "inflated_name": typing.NotRequired[str | None],
+    "output_name": typing.NotRequired[str | None],
+    "defect_base_name": typing.NotRequired[str | None],
+    "write_fixed_inflated": bool,
+    "verbose": bool,
+    "verbose_low": bool,
+    "warnings": bool,
+    "errors": bool,
+    "movies": bool,
+    "intersect": bool,
+    "mappings": bool,
+    "correct_defect": typing.NotRequired[float | None],
+    "niters": typing.NotRequired[float | None],
+    "genetic": bool,
+    "optimize": bool,
+    "random": typing.NotRequired[float | None],
+    "seed": typing.NotRequired[float | None],
+    "diag": bool,
+    "mgz": bool,
+    "smooth": typing.NotRequired[float | None],
+    "diagnostic_level": typing.NotRequired[float | None],
+    "threads": typing.NotRequired[float | None],
+})
+MrisFixTopologyParametersTagged = typing.TypedDict('MrisFixTopologyParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_fix_topology"],
     "subject_name": str,
     "hemisphere": str,
     "orig_name": typing.NotRequired[str | None],
@@ -42,42 +71,11 @@ MrisFixTopologyParameters = typing.TypedDict('MrisFixTopologyParameters', {
     "diagnostic_level": typing.NotRequired[float | None],
     "threads": 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 {
-        "mris_fix_topology": mris_fix_topology_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 MrisFixTopologyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_fix_topology(...)`.
+    Output object returned when calling `MrisFixTopologyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,11 +84,11 @@ class MrisFixTopologyOutputs(typing.NamedTuple):
 def mris_fix_topology_params(
     subject_name: str,
     hemisphere: str,
-    orig_name: str | None = "orig.nofix",
-    sphere_name: str | None = "qsphere.nofix",
-    inflated_name: str | None = "inflated.nofix",
-    output_name: str | None = "orig",
-    defect_base_name: str | None = "defect",
+    orig_name: str | None = None,
+    sphere_name: str | None = None,
+    inflated_name: str | None = None,
+    output_name: str | None = None,
+    defect_base_name: str | None = None,
     write_fixed_inflated: bool = False,
     verbose: bool = False,
     verbose_low: bool = False,
@@ -110,7 +108,7 @@ def mris_fix_topology_params(
     smooth: float | None = None,
     diagnostic_level: float | None = None,
     threads: float | None = None,
-) -> MrisFixTopologyParameters:
+) -> MrisFixTopologyParametersTagged:
     """
     Build parameters.
     
@@ -145,7 +143,7 @@ def mris_fix_topology_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_fix_topology",
+        "@type": "freesurfer/mris_fix_topology",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "write_fixed_inflated": write_fixed_inflated,
@@ -203,91 +201,91 @@ def mris_fix_topology_cargs(
     """
     cargs = []
     cargs.append("mris_fix_topology")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemisphere"))
-    if params.get("orig_name") is not None:
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemisphere", None))
+    if params.get("orig_name", None) is not None:
         cargs.extend([
             "-orig",
-            params.get("orig_name")
+            params.get("orig_name", None)
         ])
-    if params.get("sphere_name") is not None:
+    if params.get("sphere_name", None) is not None:
         cargs.extend([
             "-sphere",
-            params.get("sphere_name")
+            params.get("sphere_name", None)
         ])
-    if params.get("inflated_name") is not None:
+    if params.get("inflated_name", None) is not None:
         cargs.extend([
             "-inflated",
-            params.get("inflated_name")
+            params.get("inflated_name", None)
         ])
-    if params.get("output_name") is not None:
+    if params.get("output_name", None) is not None:
         cargs.extend([
             "-out",
-            params.get("output_name")
+            params.get("output_name", None)
         ])
-    if params.get("defect_base_name") is not None:
+    if params.get("defect_base_name", None) is not None:
         cargs.extend([
             "-defect",
-            params.get("defect_base_name")
+            params.get("defect_base_name", None)
         ])
-    if params.get("write_fixed_inflated"):
+    if params.get("write_fixed_inflated", False):
         cargs.append("-wi")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verbose")
-    if params.get("verbose_low"):
+    if params.get("verbose_low", False):
         cargs.append("-verbose_low")
-    if params.get("warnings"):
+    if params.get("warnings", False):
         cargs.append("-warnings")
-    if params.get("errors"):
+    if params.get("errors", False):
         cargs.append("-errors")
-    if params.get("movies"):
+    if params.get("movies", False):
         cargs.append("-movies")
-    if params.get("intersect"):
+    if params.get("intersect", False):
         cargs.append("-intersect")
-    if params.get("mappings"):
+    if params.get("mappings", False):
         cargs.append("-mappings")
-    if params.get("correct_defect") is not None:
+    if params.get("correct_defect", None) is not None:
         cargs.extend([
             "-correct_defect",
-            str(params.get("correct_defect"))
+            str(params.get("correct_defect", None))
         ])
-    if params.get("niters") is not None:
+    if params.get("niters", None) is not None:
         cargs.extend([
             "-niters",
-            str(params.get("niters"))
+            str(params.get("niters", None))
         ])
-    if params.get("genetic"):
+    if params.get("genetic", False):
         cargs.append("-genetic")
-    if params.get("optimize"):
+    if params.get("optimize", False):
         cargs.append("-optimize")
-    if params.get("random") is not None:
+    if params.get("random", None) is not None:
         cargs.extend([
             "-random",
-            str(params.get("random"))
+            str(params.get("random", None))
         ])
-    if params.get("seed") is not None:
+    if params.get("seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("seed"))
+            str(params.get("seed", None))
         ])
-    if params.get("diag"):
+    if params.get("diag", False):
         cargs.append("-diag")
-    if params.get("mgz"):
+    if params.get("mgz", False):
         cargs.append("-mgz")
-    if params.get("smooth") is not None:
+    if params.get("smooth", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("smooth"))
+            str(params.get("smooth", None))
         ])
-    if params.get("diagnostic_level") is not None:
+    if params.get("diagnostic_level", None) is not None:
         cargs.extend([
             "-v",
-            str(params.get("diagnostic_level"))
+            str(params.get("diagnostic_level", None))
         ])
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "-threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
     return cargs
 
@@ -313,11 +311,13 @@ def mris_fix_topology_outputs(
 
 def mris_fix_topology_execute(
     params: MrisFixTopologyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisFixTopologyOutputs:
     """
-    Computes a mapping from the unit sphere onto the cortical surface, ensuring a
-    topologically correct surface.
+    mris_fix_topology
+    
+    Computes a mapping from the unit sphere onto the cortical surface, ensuring
+    a topologically correct surface.
     
     Author: FreeSurfer Developers
     
@@ -325,10 +325,12 @@ def mris_fix_topology_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisFixTopologyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FIX_TOPOLOGY_METADATA)
     params = execution.params(params)
     cargs = mris_fix_topology_cargs(params, execution)
     ret = mris_fix_topology_outputs(params, execution)
@@ -339,11 +341,11 @@ def mris_fix_topology_execute(
 def mris_fix_topology(
     subject_name: str,
     hemisphere: str,
-    orig_name: str | None = "orig.nofix",
-    sphere_name: str | None = "qsphere.nofix",
-    inflated_name: str | None = "inflated.nofix",
-    output_name: str | None = "orig",
-    defect_base_name: str | None = "defect",
+    orig_name: str | None = None,
+    sphere_name: str | None = None,
+    inflated_name: str | None = None,
+    output_name: str | None = None,
+    defect_base_name: str | None = None,
     write_fixed_inflated: bool = False,
     verbose: bool = False,
     verbose_low: bool = False,
@@ -366,8 +368,10 @@ def mris_fix_topology(
     runner: Runner | None = None,
 ) -> MrisFixTopologyOutputs:
     """
-    Computes a mapping from the unit sphere onto the cortical surface, ensuring a
-    topologically correct surface.
+    mris_fix_topology
+    
+    Computes a mapping from the unit sphere onto the cortical surface, ensuring
+    a topologically correct surface.
     
     Author: FreeSurfer Developers
     
@@ -404,8 +408,6 @@ def mris_fix_topology(
     Returns:
         NamedTuple of outputs (described in `MrisFixTopologyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_FIX_TOPOLOGY_METADATA)
     params = mris_fix_topology_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
@@ -434,13 +436,13 @@ def mris_fix_topology(
         diagnostic_level=diagnostic_level,
         threads=threads,
     )
-    return mris_fix_topology_execute(params, execution)
+    return mris_fix_topology_execute(params, runner)
 
 
 __all__ = [
     "MRIS_FIX_TOPOLOGY_METADATA",
     "MrisFixTopologyOutputs",
-    "MrisFixTopologyParameters",
     "mris_fix_topology",
+    "mris_fix_topology_execute",
     "mris_fix_topology_params",
 ]

niwrap_freesurfer/freesurfer/mris_flatten.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_FLATTEN_METADATA = Metadata(
-    id="725b5eeb8bd019b005552e8b6e644ddc90b3d002.boutiques",
+    id="f2c58fce211d9963524057e5ef67fb2a493e603e.boutiques",
     name="mris_flatten",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRIS_FLATTEN_METADATA = Metadata(
 
 
 MrisFlattenParameters = typing.TypedDict('MrisFlattenParameters', {
-    "__STYXTYPE__": typing.Literal["mris_flatten"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_flatten"]],
+    "input_patch": InputPathType,
+    "output_patch": str,
+    "iterations": typing.NotRequired[float | None],
+    "distances": typing.NotRequired[list[float] | None],
+    "dilations": typing.NotRequired[float | None],
+    "random_seed": typing.NotRequired[float | None],
+    "copy_coords": typing.NotRequired[str | None],
+    "norand": bool,
+})
+MrisFlattenParametersTagged = typing.TypedDict('MrisFlattenParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_flatten"],
     "input_patch": InputPathType,
     "output_patch": str,
     "iterations": typing.NotRequired[float | None],
@@ -24,43 +35,11 @@ MrisFlattenParameters = typing.TypedDict('MrisFlattenParameters', {
     "copy_coords": typing.NotRequired[str | None],
     "norand": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_flatten": mris_flatten_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 {
-        "mris_flatten": mris_flatten_outputs,
-    }.get(t)
 
 
 class MrisFlattenOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_flatten(...)`.
+    Output object returned when calling `MrisFlattenParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def mris_flatten_params(
     random_seed: float | None = None,
     copy_coords: str | None = None,
     norand: bool = False,
-) -> MrisFlattenParameters:
+) -> MrisFlattenParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +76,7 @@ def mris_flatten_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_flatten",
+        "@type": "freesurfer/mris_flatten",
         "input_patch": input_patch,
         "output_patch": output_patch,
         "norand": norand,
@@ -130,34 +109,34 @@ def mris_flatten_cargs(
     """
     cargs = []
     cargs.append("mris_flatten")
-    cargs.append(execution.input_file(params.get("input_patch")))
-    cargs.append(params.get("output_patch"))
-    if params.get("iterations") is not None:
+    cargs.append(execution.input_file(params.get("input_patch", None)))
+    cargs.append(params.get("output_patch", None))
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
-    if params.get("distances") is not None:
+    if params.get("distances", None) is not None:
         cargs.extend([
             "-distances",
-            *map(str, params.get("distances"))
+            *map(str, params.get("distances", None))
         ])
-    if params.get("dilations") is not None:
+    if params.get("dilations", None) is not None:
         cargs.extend([
             "-dilate",
-            str(params.get("dilations"))
+            str(params.get("dilations", None))
         ])
-    if params.get("random_seed") is not None:
+    if params.get("random_seed", None) is not None:
         cargs.extend([
             "-seed",
-            str(params.get("random_seed"))
+            str(params.get("random_seed", None))
         ])
-    if params.get("copy_coords") is not None:
+    if params.get("copy_coords", None) is not None:
         cargs.extend([
             "-copy-coords",
-            params.get("copy_coords")
+            params.get("copy_coords", None)
         ])
-    if params.get("norand"):
+    if params.get("norand", False):
         cargs.append("-norand")
     return cargs
 
@@ -177,16 +156,18 @@ def mris_flatten_outputs(
     """
     ret = MrisFlattenOutputs(
         root=execution.output_file("."),
-        output_patch_file=execution.output_file(params.get("output_patch")),
+        output_patch_file=execution.output_file(params.get("output_patch", None)),
     )
     return ret
 
 
 def mris_flatten_execute(
     params: MrisFlattenParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisFlattenOutputs:
     """
+    mris_flatten
+    
     This program will flatten a surface patch.
     
     Author: FreeSurfer Developers
@@ -195,10 +176,12 @@ def mris_flatten_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisFlattenOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_FLATTEN_METADATA)
     params = execution.params(params)
     cargs = mris_flatten_cargs(params, execution)
     ret = mris_flatten_outputs(params, execution)
@@ -218,6 +201,8 @@ def mris_flatten(
     runner: Runner | None = None,
 ) -> MrisFlattenOutputs:
     """
+    mris_flatten
+    
     This program will flatten a surface patch.
     
     Author: FreeSurfer Developers
@@ -240,8 +225,6 @@ def mris_flatten(
     Returns:
         NamedTuple of outputs (described in `MrisFlattenOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_FLATTEN_METADATA)
     params = mris_flatten_params(
         input_patch=input_patch,
         output_patch=output_patch,
@@ -252,13 +235,13 @@ def mris_flatten(
         copy_coords=copy_coords,
         norand=norand,
     )
-    return mris_flatten_execute(params, execution)
+    return mris_flatten_execute(params, runner)
 
 
 __all__ = [
     "MRIS_FLATTEN_METADATA",
     "MrisFlattenOutputs",
-    "MrisFlattenParameters",
     "mris_flatten",
+    "mris_flatten_execute",
     "mris_flatten_params",
 ]