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

niwrap_freesurfer/freesurfer/mris2rgb.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS2RGB_METADATA = Metadata(
-    id="4fdbc16148efe88b6fd4eb9b58594698623eae7f.boutiques",
+    id="6726da6230a587382e8e51784edbe8796e30303b.boutiques",
     name="mris2rgb",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MRIS2RGB_METADATA = Metadata(
 
 
 Mris2rgbParameters = typing.TypedDict('Mris2rgbParameters', {
-    "__STYXTYPE__": typing.Literal["mris2rgb"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris2rgb"]],
+    "library_path": str,
+})
+Mris2rgbParametersTagged = typing.TypedDict('Mris2rgbParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris2rgb"],
     "library_path": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris2rgb": mris2rgb_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 Mris2rgbOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris2rgb(...)`.
+    Output object returned when calling `Mris2rgbParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class Mris2rgbOutputs(typing.NamedTuple):
 
 def mris2rgb_params(
     library_path: str,
-) -> Mris2rgbParameters:
+) -> Mris2rgbParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def mris2rgb_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris2rgb",
+        "@type": "freesurfer/mris2rgb",
         "library_path": library_path,
     }
     return params
@@ -94,7 +67,7 @@ def mris2rgb_cargs(
     cargs.append("mris2rgb")
     cargs.extend([
         "export LD_LIBRARY_PATH=",
-        params.get("library_path")
+        params.get("library_path", None)
     ])
     return cargs
 
@@ -120,9 +93,11 @@ def mris2rgb_outputs(
 
 def mris2rgb_execute(
     params: Mris2rgbParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Mris2rgbOutputs:
     """
+    mris2rgb
+    
     A tool from FreeSurfer for converting MRI surface files to RGB images.
     
     Author: FreeSurfer Developers
@@ -131,10 +106,12 @@ def mris2rgb_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Mris2rgbOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS2RGB_METADATA)
     params = execution.params(params)
     cargs = mris2rgb_cargs(params, execution)
     ret = mris2rgb_outputs(params, execution)
@@ -147,6 +124,8 @@ def mris2rgb(
     runner: Runner | None = None,
 ) -> Mris2rgbOutputs:
     """
+    mris2rgb
+    
     A tool from FreeSurfer for converting MRI surface files to RGB images.
     
     Author: FreeSurfer Developers
@@ -160,18 +139,16 @@ def mris2rgb(
     Returns:
         NamedTuple of outputs (described in `Mris2rgbOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS2RGB_METADATA)
     params = mris2rgb_params(
         library_path=library_path,
     )
-    return mris2rgb_execute(params, execution)
+    return mris2rgb_execute(params, runner)
 
 
 __all__ = [
     "MRIS2RGB_METADATA",
     "Mris2rgbOutputs",
-    "Mris2rgbParameters",
     "mris2rgb",
+    "mris2rgb_execute",
     "mris2rgb_params",
 ]

niwrap_freesurfer/freesurfer/mris_aa_shrinkwrap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_AA_SHRINKWRAP_METADATA = Metadata(
-    id="f1b620c2d26413faf9fc31bd238562722d3919d1.boutiques",
+    id="972abb5cda35bd8c389155629780dfed5a0cde84.boutiques",
     name="mris_AA_shrinkwrap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_AA_SHRINKWRAP_METADATA = Metadata(
 
 
 MrisAaShrinkwrapParameters = typing.TypedDict('MrisAaShrinkwrapParameters', {
-    "__STYXTYPE__": typing.Literal["mris_AA_shrinkwrap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_AA_shrinkwrap"]],
+    "t1_vol": InputPathType,
+    "pd_vol": InputPathType,
+    "output_dir": str,
+    "omit_self_intersection": bool,
+    "create_curvature_area": bool,
+    "average_curvature": typing.NotRequired[float | None],
+    "white_only": bool,
+})
+MrisAaShrinkwrapParametersTagged = typing.TypedDict('MrisAaShrinkwrapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_AA_shrinkwrap"],
     "t1_vol": InputPathType,
     "pd_vol": InputPathType,
     "output_dir": str,
@@ -23,42 +33,11 @@ MrisAaShrinkwrapParameters = typing.TypedDict('MrisAaShrinkwrapParameters', {
     "average_curvature": typing.NotRequired[float | None],
     "white_only": 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_AA_shrinkwrap": mris_aa_shrinkwrap_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 MrisAaShrinkwrapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_aa_shrinkwrap(...)`.
+    Output object returned when calling `MrisAaShrinkwrapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,9 +49,9 @@ def mris_aa_shrinkwrap_params(
     output_dir: str,
     omit_self_intersection: bool = False,
     create_curvature_area: bool = False,
-    average_curvature: float | None = 10,
+    average_curvature: float | None = None,
     white_only: bool = False,
-) -> MrisAaShrinkwrapParameters:
+) -> MrisAaShrinkwrapParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +70,7 @@ def mris_aa_shrinkwrap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_AA_shrinkwrap",
+        "@type": "freesurfer/mris_AA_shrinkwrap",
         "t1_vol": t1_vol,
         "pd_vol": pd_vol,
         "output_dir": output_dir,
@@ -119,19 +98,19 @@ def mris_aa_shrinkwrap_cargs(
     """
     cargs = []
     cargs.append("mris_AA_shrinkwrap")
-    cargs.append(execution.input_file(params.get("t1_vol")))
-    cargs.append(execution.input_file(params.get("pd_vol")))
-    cargs.append(params.get("output_dir"))
-    if params.get("omit_self_intersection"):
+    cargs.append(execution.input_file(params.get("t1_vol", None)))
+    cargs.append(execution.input_file(params.get("pd_vol", None)))
+    cargs.append(params.get("output_dir", None))
+    if params.get("omit_self_intersection", False):
         cargs.append("-q")
-    if params.get("create_curvature_area"):
+    if params.get("create_curvature_area", False):
         cargs.append("-c")
-    if params.get("average_curvature") is not None:
+    if params.get("average_curvature", None) is not None:
         cargs.extend([
             "-a",
-            str(params.get("average_curvature"))
+            str(params.get("average_curvature", None))
         ])
-    if params.get("white_only"):
+    if params.get("white_only", False):
         cargs.append("-whiteonly")
     return cargs
 
@@ -157,13 +136,15 @@ def mris_aa_shrinkwrap_outputs(
 
 def mris_aa_shrinkwrap_execute(
     params: MrisAaShrinkwrapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAaShrinkwrapOutputs:
     """
+    mris_AA_shrinkwrap
+    
     This program positions the tessellation of the cortical surface at the white
     matter surface, then the gray matter surface and generates surface files for
-    these surfaces as well as a 'curvature' file for the cortical thickness, and a
-    surface file which approximates layer IV of the cortical sheet.
+    these surfaces as well as a 'curvature' file for the cortical thickness, and
+    a surface file which approximates layer IV of the cortical sheet.
     
     Author: FreeSurfer Developers
     
@@ -171,10 +152,12 @@ def mris_aa_shrinkwrap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAaShrinkwrapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_AA_SHRINKWRAP_METADATA)
     params = execution.params(params)
     cargs = mris_aa_shrinkwrap_cargs(params, execution)
     ret = mris_aa_shrinkwrap_outputs(params, execution)
@@ -188,15 +171,17 @@ def mris_aa_shrinkwrap(
     output_dir: str,
     omit_self_intersection: bool = False,
     create_curvature_area: bool = False,
-    average_curvature: float | None = 10,
+    average_curvature: float | None = None,
     white_only: bool = False,
     runner: Runner | None = None,
 ) -> MrisAaShrinkwrapOutputs:
     """
+    mris_AA_shrinkwrap
+    
     This program positions the tessellation of the cortical surface at the white
     matter surface, then the gray matter surface and generates surface files for
-    these surfaces as well as a 'curvature' file for the cortical thickness, and a
-    surface file which approximates layer IV of the cortical sheet.
+    these surfaces as well as a 'curvature' file for the cortical thickness, and
+    a surface file which approximates layer IV of the cortical sheet.
     
     Author: FreeSurfer Developers
     
@@ -217,8 +202,6 @@ def mris_aa_shrinkwrap(
     Returns:
         NamedTuple of outputs (described in `MrisAaShrinkwrapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_AA_SHRINKWRAP_METADATA)
     params = mris_aa_shrinkwrap_params(
         t1_vol=t1_vol,
         pd_vol=pd_vol,
@@ -228,13 +211,13 @@ def mris_aa_shrinkwrap(
         average_curvature=average_curvature,
         white_only=white_only,
     )
-    return mris_aa_shrinkwrap_execute(params, execution)
+    return mris_aa_shrinkwrap_execute(params, runner)
 
 
 __all__ = [
     "MRIS_AA_SHRINKWRAP_METADATA",
     "MrisAaShrinkwrapOutputs",
-    "MrisAaShrinkwrapParameters",
     "mris_aa_shrinkwrap",
+    "mris_aa_shrinkwrap_execute",
     "mris_aa_shrinkwrap_params",
 ]

niwrap_freesurfer/freesurfer/mris_add_template.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_ADD_TEMPLATE_METADATA = Metadata(
-    id="9a71856917ab14ff8fae69a16dee1fd03c9534e5.boutiques",
+    id="f2ee0984a4f5067041d4565cfaf96e4c1a417eaa.boutiques",
     name="mris_add_template",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ MRIS_ADD_TEMPLATE_METADATA = Metadata(
 
 
 MrisAddTemplateParameters = typing.TypedDict('MrisAddTemplateParameters', {
-    "__STYXTYPE__": typing.Literal["mris_add_template"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_add_template"]],
+    "placeholder_input": typing.NotRequired[str | None],
+})
+MrisAddTemplateParametersTagged = typing.TypedDict('MrisAddTemplateParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_add_template"],
     "placeholder_input": 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 {
-        "mris_add_template": mris_add_template_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_add_template": mris_add_template_outputs,
-    }.get(t)
 
 
 class MrisAddTemplateOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_add_template(...)`.
+    Output object returned when calling `MrisAddTemplateParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class MrisAddTemplateOutputs(typing.NamedTuple):
 
 def mris_add_template_params(
     placeholder_input: str | None = None,
-) -> MrisAddTemplateParameters:
+) -> MrisAddTemplateParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +45,7 @@ def mris_add_template_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_add_template",
+        "@type": "freesurfer/mris_add_template",
     }
     if placeholder_input is not None:
         params["placeholder_input"] = placeholder_input
@@ -95,8 +67,8 @@ def mris_add_template_cargs(
     """
     cargs = []
     cargs.append("mris_add_template")
-    if params.get("placeholder_input") is not None:
-        cargs.append(params.get("placeholder_input"))
+    if params.get("placeholder_input", None) is not None:
+        cargs.append(params.get("placeholder_input", None))
     return cargs
 
 
@@ -122,9 +94,11 @@ def mris_add_template_outputs(
 
 def mris_add_template_execute(
     params: MrisAddTemplateParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAddTemplateOutputs:
     """
+    mris_add_template
+    
     This tool has been removed from the current version of FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -133,10 +107,12 @@ def mris_add_template_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAddTemplateOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_ADD_TEMPLATE_METADATA)
     params = execution.params(params)
     cargs = mris_add_template_cargs(params, execution)
     ret = mris_add_template_outputs(params, execution)
@@ -149,6 +125,8 @@ def mris_add_template(
     runner: Runner | None = None,
 ) -> MrisAddTemplateOutputs:
     """
+    mris_add_template
+    
     This tool has been removed from the current version of FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -161,18 +139,16 @@ def mris_add_template(
     Returns:
         NamedTuple of outputs (described in `MrisAddTemplateOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_ADD_TEMPLATE_METADATA)
     params = mris_add_template_params(
         placeholder_input=placeholder_input,
     )
-    return mris_add_template_execute(params, execution)
+    return mris_add_template_execute(params, runner)
 
 
 __all__ = [
     "MRIS_ADD_TEMPLATE_METADATA",
     "MrisAddTemplateOutputs",
-    "MrisAddTemplateParameters",
     "mris_add_template",
+    "mris_add_template_execute",
     "mris_add_template_params",
 ]