niwrap-freesurfer 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mris_deform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DEFORM_METADATA = Metadata(
-    id="15a9bfc466b885fe98e4cf144f78c4307c6c746c.boutiques",
+    id="1099d393ed8dc1cfcb98f2c4259490fe6ccf228b.boutiques",
     name="mris_deform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_DEFORM_METADATA = Metadata(
 
 
 MrisDeformParameters = typing.TypedDict('MrisDeformParameters', {
-    "__STYXTYPE__": typing.Literal["mris_deform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_deform"]],
+    "input_surface": InputPathType,
+    "input_volume": InputPathType,
+    "xform": InputPathType,
+    "output_surface": str,
+})
+MrisDeformParametersTagged = typing.TypedDict('MrisDeformParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_deform"],
     "input_surface": InputPathType,
     "input_volume": InputPathType,
     "xform": InputPathType,
     "output_surface": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_deform": mris_deform_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_deform": mris_deform_outputs,
-    }.get(t)
 
 
 class MrisDeformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_deform(...)`.
+    Output object returned when calling `MrisDeformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_deform_params(
     input_volume: InputPathType,
     xform: InputPathType,
     output_surface: str,
-) -> MrisDeformParameters:
+) -> MrisDeformParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mris_deform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_deform",
+        "@type": "freesurfer/mris_deform",
         "input_surface": input_surface,
         "input_volume": input_volume,
         "xform": xform,
@@ -106,10 +81,10 @@ def mris_deform_cargs(
     """
     cargs = []
     cargs.append("mris_deform")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("xform")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("xform", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def mris_deform_outputs(
     """
     ret = MrisDeformOutputs(
         root=execution.output_file("."),
-        deformed_surface=execution.output_file(params.get("output_surface")),
+        deformed_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_deform_execute(
     params: MrisDeformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisDeformOutputs:
     """
+    mris_deform
+    
     A tool for deforming surface meshes using volumetric information from an
     auxiliary volume.
     
@@ -147,10 +124,12 @@ def mris_deform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDeformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_DEFORM_METADATA)
     params = execution.params(params)
     cargs = mris_deform_cargs(params, execution)
     ret = mris_deform_outputs(params, execution)
@@ -166,6 +145,8 @@ def mris_deform(
     runner: Runner | None = None,
 ) -> MrisDeformOutputs:
     """
+    mris_deform
+    
     A tool for deforming surface meshes using volumetric information from an
     auxiliary volume.
     
@@ -182,21 +163,19 @@ def mris_deform(
     Returns:
         NamedTuple of outputs (described in `MrisDeformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_DEFORM_METADATA)
     params = mris_deform_params(
         input_surface=input_surface,
         input_volume=input_volume,
         xform=xform,
         output_surface=output_surface,
     )
-    return mris_deform_execute(params, execution)
+    return mris_deform_execute(params, runner)
 
 
 __all__ = [
     "MRIS_DEFORM_METADATA",
     "MrisDeformOutputs",
-    "MrisDeformParameters",
     "mris_deform",
+    "mris_deform_execute",
     "mris_deform_params",
 ]

niwrap_freesurfer/freesurfer/mris_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DIFF_METADATA = Metadata(
-    id="b75e9135951f27be6bd2952dbbcb87b5a6184000.boutiques",
+    id="ea56ba0cce9d9257f1266cde92de0744bd3d23a5.boutiques",
     name="mris_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,39 @@ MRIS_DIFF_METADATA = Metadata(
 
 
 MrisDiffParameters = typing.TypedDict('MrisDiffParameters', {
-    "__STYXTYPE__": typing.Literal["mris_diff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_diff"]],
+    "surface1": InputPathType,
+    "surface2": InputPathType,
+    "subject1": str,
+    "subject2": str,
+    "subj_dir1": typing.NotRequired[str | None],
+    "subj_dir2": typing.NotRequired[str | None],
+    "hemisphere": str,
+    "surf": typing.NotRequired[str | None],
+    "curv": typing.NotRequired[str | None],
+    "aparc": typing.NotRequired[str | None],
+    "aparc2": typing.NotRequired[str | None],
+    "simple": bool,
+    "simple_patch": bool,
+    "thresh": typing.NotRequired[float | None],
+    "maxerrs": typing.NotRequired[float | None],
+    "renumbered": bool,
+    "worst_bucket": typing.NotRequired[str | None],
+    "grid": typing.NotRequired[str | None],
+    "no_check_xyz": bool,
+    "no_check_nxyz": bool,
+    "xyz_rms": typing.NotRequired[str | None],
+    "angle_rms": typing.NotRequired[str | None],
+    "seed": typing.NotRequired[float | None],
+    "min_dist": typing.NotRequired[str | None],
+    "debug": bool,
+    "gdiag_no": typing.NotRequired[float | None],
+    "check_opts": bool,
+    "help": bool,
+    "version": bool,
+})
+MrisDiffParametersTagged = typing.TypedDict('MrisDiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_diff"],
     "surface1": InputPathType,
     "surface2": InputPathType,
     "subject1": str,
@@ -45,42 +77,11 @@ MrisDiffParameters = typing.TypedDict('MrisDiffParameters', {
     "help": bool,
     "version": 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_diff": mris_diff_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 MrisDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_diff(...)`.
+    Output object returned when calling `MrisDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -116,7 +117,7 @@ def mris_diff_params(
     check_opts: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> MrisDiffParameters:
+) -> MrisDiffParametersTagged:
     """
     Build parameters.
     
@@ -156,7 +157,7 @@ def mris_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_diff",
+        "@type": "freesurfer/mris_diff",
         "surface1": surface1,
         "surface2": surface2,
         "subject1": subject1,
@@ -220,112 +221,112 @@ def mris_diff_cargs(
     """
     cargs = []
     cargs.append("mris_diff")
-    cargs.append(execution.input_file(params.get("surface1")))
-    cargs.append(execution.input_file(params.get("surface2")))
+    cargs.append(execution.input_file(params.get("surface1", None)))
+    cargs.append(execution.input_file(params.get("surface2", None)))
     cargs.extend([
         "--s1",
-        params.get("subject1")
+        params.get("subject1", None)
     ])
     cargs.extend([
         "--s2",
-        params.get("subject2")
+        params.get("subject2", None)
     ])
-    if params.get("subj_dir1") is not None:
+    if params.get("subj_dir1", None) is not None:
         cargs.extend([
             "--sd1",
-            params.get("subj_dir1")
+            params.get("subj_dir1", None)
         ])
-    if params.get("subj_dir2") is not None:
+    if params.get("subj_dir2", None) is not None:
         cargs.extend([
             "--sd2",
-            params.get("subj_dir2")
+            params.get("subj_dir2", None)
         ])
     cargs.extend([
         "--hemi",
-        params.get("hemisphere")
+        params.get("hemisphere", None)
     ])
-    if params.get("surf") is not None:
+    if params.get("surf", None) is not None:
         cargs.extend([
             "--surf",
-            params.get("surf")
+            params.get("surf", None)
         ])
-    if params.get("curv") is not None:
+    if params.get("curv", None) is not None:
         cargs.extend([
             "--curv",
-            params.get("curv")
+            params.get("curv", None)
         ])
-    if params.get("aparc") is not None:
+    if params.get("aparc", None) is not None:
         cargs.extend([
             "--aparc",
-            params.get("aparc")
+            params.get("aparc", None)
         ])
-    if params.get("aparc2") is not None:
+    if params.get("aparc2", None) is not None:
         cargs.extend([
             "--aparc2",
-            params.get("aparc2")
+            params.get("aparc2", None)
         ])
-    if params.get("simple"):
+    if params.get("simple", False):
         cargs.append("--simple")
-    if params.get("simple_patch"):
+    if params.get("simple_patch", False):
         cargs.append("--simple-patch")
-    if params.get("thresh") is not None:
+    if params.get("thresh", None) is not None:
         cargs.extend([
             "--thresh",
-            str(params.get("thresh"))
+            str(params.get("thresh", None))
         ])
-    if params.get("maxerrs") is not None:
+    if params.get("maxerrs", None) is not None:
         cargs.extend([
             "--maxerrs",
-            str(params.get("maxerrs"))
+            str(params.get("maxerrs", None))
         ])
-    if params.get("renumbered"):
+    if params.get("renumbered", False):
         cargs.append("--renumbered")
-    if params.get("worst_bucket") is not None:
+    if params.get("worst_bucket", None) is not None:
         cargs.extend([
             "--worst-bucket",
-            params.get("worst_bucket")
+            params.get("worst_bucket", None)
         ])
-    if params.get("grid") is not None:
+    if params.get("grid", None) is not None:
         cargs.extend([
             "--grid",
-            params.get("grid")
+            params.get("grid", None)
         ])
-    if params.get("no_check_xyz"):
+    if params.get("no_check_xyz", False):
         cargs.append("--no-check-xyz")
-    if params.get("no_check_nxyz"):
+    if params.get("no_check_nxyz", False):
         cargs.append("--no-check-nxyz")
-    if params.get("xyz_rms") is not None:
+    if params.get("xyz_rms", None) is not None:
         cargs.extend([
             "--xyz-rms",
-            params.get("xyz_rms")
+            params.get("xyz_rms", None)
         ])
-    if params.get("angle_rms") is not None:
+    if params.get("angle_rms", None) is not None:
         cargs.extend([
             "--angle-rms",
-            params.get("angle_rms")
+            params.get("angle_rms", 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("min_dist") is not None:
+    if params.get("min_dist", None) is not None:
         cargs.extend([
             "--min-dist",
-            params.get("min_dist")
+            params.get("min_dist", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("gdiag_no") is not None:
+    if params.get("gdiag_no", None) is not None:
         cargs.extend([
             "--gdiag_no",
-            str(params.get("gdiag_no"))
+            str(params.get("gdiag_no", None))
         ])
-    if params.get("check_opts"):
+    if params.get("check_opts", False):
         cargs.append("--checkopts")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -351,9 +352,11 @@ def mris_diff_outputs(
 
 def mris_diff_execute(
     params: MrisDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisDiffOutputs:
     """
+    mris_diff
+    
     A tool for comparing differences between surface files in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -362,10 +365,12 @@ def mris_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_DIFF_METADATA)
     params = execution.params(params)
     cargs = mris_diff_cargs(params, execution)
     ret = mris_diff_outputs(params, execution)
@@ -406,6 +411,8 @@ def mris_diff(
     runner: Runner | None = None,
 ) -> MrisDiffOutputs:
     """
+    mris_diff
+    
     A tool for comparing differences between surface files in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -448,8 +455,6 @@ def mris_diff(
     Returns:
         NamedTuple of outputs (described in `MrisDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_DIFF_METADATA)
     params = mris_diff_params(
         surface1=surface1,
         surface2=surface2,
@@ -481,13 +486,13 @@ def mris_diff(
         help_=help_,
         version=version,
     )
-    return mris_diff_execute(params, execution)
+    return mris_diff_execute(params, runner)
 
 
 __all__ = [
     "MRIS_DIFF_METADATA",
     "MrisDiffOutputs",
-    "MrisDiffParameters",
     "mris_diff",
+    "mris_diff_execute",
     "mris_diff_params",
 ]

niwrap_freesurfer/freesurfer/mris_distance_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_DISTANCE_MAP_METADATA = Metadata(
-    id="0893c6f050e343dadac472a8f00aeaaaecf0a30c.boutiques",
+    id="22c160b7b3865ec08573b48e335694cf0791593a.boutiques",
     name="mris_distance_map",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_DISTANCE_MAP_METADATA = Metadata(
 
 
 MrisDistanceMapParameters = typing.TypedDict('MrisDistanceMapParameters', {
-    "__STYXTYPE__": typing.Literal["mris_distance_map"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_distance_map"]],
+    "input_surface_file": InputPathType,
+    "output_scalar_field": str,
+})
+MrisDistanceMapParametersTagged = typing.TypedDict('MrisDistanceMapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_distance_map"],
     "input_surface_file": InputPathType,
     "output_scalar_field": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_distance_map": mris_distance_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 {
-        "mris_distance_map": mris_distance_map_outputs,
-    }.get(t)
 
 
 class MrisDistanceMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_distance_map(...)`.
+    Output object returned when calling `MrisDistanceMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisDistanceMapOutputs(typing.NamedTuple):
 def mris_distance_map_params(
     input_surface_file: InputPathType,
     output_scalar_field: str,
-) -> MrisDistanceMapParameters:
+) -> MrisDistanceMapParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_distance_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_distance_map",
+        "@type": "freesurfer/mris_distance_map",
         "input_surface_file": input_surface_file,
         "output_scalar_field": output_scalar_field,
     }
@@ -98,8 +71,8 @@ def mris_distance_map_cargs(
     """
     cargs = []
     cargs.append("mris_distance_map")
-    cargs.append(execution.input_file(params.get("input_surface_file")))
-    cargs.append(params.get("output_scalar_field"))
+    cargs.append(execution.input_file(params.get("input_surface_file", None)))
+    cargs.append(params.get("output_scalar_field", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mris_distance_map_outputs(
     """
     ret = MrisDistanceMapOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_scalar_field") + ".mgz"),
+        output_file=execution.output_file(params.get("output_scalar_field", None) + ".mgz"),
     )
     return ret
 
 
 def mris_distance_map_execute(
     params: MrisDistanceMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisDistanceMapOutputs:
     """
+    mris_distance_map
+    
     Tool to compute a distance map of each point on the surface to a reference
     point.
     
@@ -137,10 +112,12 @@ def mris_distance_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisDistanceMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_DISTANCE_MAP_METADATA)
     params = execution.params(params)
     cargs = mris_distance_map_cargs(params, execution)
     ret = mris_distance_map_outputs(params, execution)
@@ -154,6 +131,8 @@ def mris_distance_map(
     runner: Runner | None = None,
 ) -> MrisDistanceMapOutputs:
     """
+    mris_distance_map
+    
     Tool to compute a distance map of each point on the surface to a reference
     point.
     
@@ -168,19 +147,17 @@ def mris_distance_map(
     Returns:
         NamedTuple of outputs (described in `MrisDistanceMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_DISTANCE_MAP_METADATA)
     params = mris_distance_map_params(
         input_surface_file=input_surface_file,
         output_scalar_field=output_scalar_field,
     )
-    return mris_distance_map_execute(params, execution)
+    return mris_distance_map_execute(params, runner)
 
 
 __all__ = [
     "MRIS_DISTANCE_MAP_METADATA",
     "MrisDistanceMapOutputs",
-    "MrisDistanceMapParameters",
     "mris_distance_map",
+    "mris_distance_map_execute",
     "mris_distance_map_params",
 ]