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

niwrap_freesurfer/freesurfer/mris_average_curvature.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_AVERAGE_CURVATURE_METADATA = Metadata(
-    id="7bf37b20bf1ca60685f16918f26ebdbff5c07b09.boutiques",
+    id="3655395907a83c7871c6765bc6caba944ea08664.boutiques",
     name="mris_average_curvature",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_AVERAGE_CURVATURE_METADATA = Metadata(
 
 
 MrisAverageCurvatureParameters = typing.TypedDict('MrisAverageCurvatureParameters', {
-    "__STYXTYPE__": typing.Literal["mris_average_curvature"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_average_curvature"]],
+    "input_curvature_file": InputPathType,
+    "hemi": str,
+    "surface": str,
+    "subjects": list[str],
+    "output_curvature_file": str,
+    "summary_stats_flag": bool,
+    "output_surface_flag": bool,
+})
+MrisAverageCurvatureParametersTagged = typing.TypedDict('MrisAverageCurvatureParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_average_curvature"],
     "input_curvature_file": InputPathType,
     "hemi": str,
     "surface": str,
@@ -23,42 +33,11 @@ MrisAverageCurvatureParameters = typing.TypedDict('MrisAverageCurvatureParameter
     "summary_stats_flag": bool,
     "output_surface_flag": 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_average_curvature": mris_average_curvature_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 MrisAverageCurvatureOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_average_curvature(...)`.
+    Output object returned when calling `MrisAverageCurvatureParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def mris_average_curvature_params(
     output_curvature_file: str,
     summary_stats_flag: bool = False,
     output_surface_flag: bool = False,
-) -> MrisAverageCurvatureParameters:
+) -> MrisAverageCurvatureParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +69,7 @@ def mris_average_curvature_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_average_curvature",
+        "@type": "freesurfer/mris_average_curvature",
         "input_curvature_file": input_curvature_file,
         "hemi": hemi,
         "surface": surface,
@@ -117,14 +96,14 @@ def mris_average_curvature_cargs(
     """
     cargs = []
     cargs.append("mris_average_curvature")
-    cargs.append(execution.input_file(params.get("input_curvature_file")))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface"))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_curvature_file"))
-    if params.get("summary_stats_flag"):
+    cargs.append(execution.input_file(params.get("input_curvature_file", None)))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface", None))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_curvature_file", None))
+    if params.get("summary_stats_flag", False):
         cargs.append("-s")
-    if params.get("output_surface_flag"):
+    if params.get("output_surface_flag", False):
         cargs.append("-o")
     return cargs
 
@@ -150,9 +129,11 @@ def mris_average_curvature_outputs(
 
 def mris_average_curvature_execute(
     params: MrisAverageCurvatureParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisAverageCurvatureOutputs:
     """
+    mris_average_curvature
+    
     This tool averages curvature data across multiple subjects and generates an
     output curvature file painted onto the last subject specified. It can also
     generate summary statistics if requested.
@@ -163,10 +144,12 @@ def mris_average_curvature_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisAverageCurvatureOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_AVERAGE_CURVATURE_METADATA)
     params = execution.params(params)
     cargs = mris_average_curvature_cargs(params, execution)
     ret = mris_average_curvature_outputs(params, execution)
@@ -185,6 +168,8 @@ def mris_average_curvature(
     runner: Runner | None = None,
 ) -> MrisAverageCurvatureOutputs:
     """
+    mris_average_curvature
+    
     This tool averages curvature data across multiple subjects and generates an
     output curvature file painted onto the last subject specified. It can also
     generate summary statistics if requested.
@@ -207,8 +192,6 @@ def mris_average_curvature(
     Returns:
         NamedTuple of outputs (described in `MrisAverageCurvatureOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_AVERAGE_CURVATURE_METADATA)
     params = mris_average_curvature_params(
         input_curvature_file=input_curvature_file,
         hemi=hemi,
@@ -218,13 +201,13 @@ def mris_average_curvature(
         summary_stats_flag=summary_stats_flag,
         output_surface_flag=output_surface_flag,
     )
-    return mris_average_curvature_execute(params, execution)
+    return mris_average_curvature_execute(params, runner)
 
 
 __all__ = [
     "MRIS_AVERAGE_CURVATURE_METADATA",
     "MrisAverageCurvatureOutputs",
-    "MrisAverageCurvatureParameters",
     "mris_average_curvature",
+    "mris_average_curvature_execute",
     "mris_average_curvature_params",
 ]

niwrap_freesurfer/freesurfer/mris_ba_segment.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_BA_SEGMENT_METADATA = Metadata(
-    id="e0fadf7acd0d12f0486a76ae95700c41ad05ab2c.boutiques",
+    id="6c6e8c27ad4e0b5534ce3ada029b6907bf9589b3.boutiques",
     name="mris_BA_segment",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_BA_SEGMENT_METADATA = Metadata(
 
 
 MrisBaSegmentParameters = typing.TypedDict('MrisBaSegmentParameters', {
-    "__STYXTYPE__": typing.Literal["mris_BA_segment"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_BA_segment"]],
+    "surface": InputPathType,
+    "profiles": InputPathType,
+    "prior_label": InputPathType,
+    "output_label": str,
+})
+MrisBaSegmentParametersTagged = typing.TypedDict('MrisBaSegmentParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_BA_segment"],
     "surface": InputPathType,
     "profiles": InputPathType,
     "prior_label": InputPathType,
     "output_label": 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_BA_segment": mris_ba_segment_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_BA_segment": mris_ba_segment_outputs,
-    }.get(t)
 
 
 class MrisBaSegmentOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_ba_segment(...)`.
+    Output object returned when calling `MrisBaSegmentParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_ba_segment_params(
     profiles: InputPathType,
     prior_label: InputPathType,
     output_label: str,
-) -> MrisBaSegmentParameters:
+) -> MrisBaSegmentParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mris_ba_segment_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_BA_segment",
+        "@type": "freesurfer/mris_BA_segment",
         "surface": surface,
         "profiles": profiles,
         "prior_label": prior_label,
@@ -106,10 +81,10 @@ def mris_ba_segment_cargs(
     """
     cargs = []
     cargs.append("mris_BA_segment")
-    cargs.append(execution.input_file(params.get("surface")))
-    cargs.append(execution.input_file(params.get("profiles")))
-    cargs.append(execution.input_file(params.get("prior_label")))
-    cargs.append(params.get("output_label"))
+    cargs.append(execution.input_file(params.get("surface", None)))
+    cargs.append(execution.input_file(params.get("profiles", None)))
+    cargs.append(execution.input_file(params.get("prior_label", None)))
+    cargs.append(params.get("output_label", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def mris_ba_segment_outputs(
     """
     ret = MrisBaSegmentOutputs(
         root=execution.output_file("."),
-        output_label_file=execution.output_file(params.get("output_label")),
+        output_label_file=execution.output_file(params.get("output_label", None)),
     )
     return ret
 
 
 def mris_ba_segment_execute(
     params: MrisBaSegmentParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisBaSegmentOutputs:
     """
+    mris_BA_segment
+    
     Segments a Brodmann area (MT currently) from a laminar intensity profile
     overlay.
     
@@ -147,10 +124,12 @@ def mris_ba_segment_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisBaSegmentOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_BA_SEGMENT_METADATA)
     params = execution.params(params)
     cargs = mris_ba_segment_cargs(params, execution)
     ret = mris_ba_segment_outputs(params, execution)
@@ -166,6 +145,8 @@ def mris_ba_segment(
     runner: Runner | None = None,
 ) -> MrisBaSegmentOutputs:
     """
+    mris_BA_segment
+    
     Segments a Brodmann area (MT currently) from a laminar intensity profile
     overlay.
     
@@ -182,21 +163,19 @@ def mris_ba_segment(
     Returns:
         NamedTuple of outputs (described in `MrisBaSegmentOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_BA_SEGMENT_METADATA)
     params = mris_ba_segment_params(
         surface=surface,
         profiles=profiles,
         prior_label=prior_label,
         output_label=output_label,
     )
-    return mris_ba_segment_execute(params, execution)
+    return mris_ba_segment_execute(params, runner)
 
 
 __all__ = [
     "MRIS_BA_SEGMENT_METADATA",
     "MrisBaSegmentOutputs",
-    "MrisBaSegmentParameters",
     "mris_ba_segment",
+    "mris_ba_segment_execute",
     "mris_ba_segment_params",
 ]

niwrap_freesurfer/freesurfer/mris_ca_deform.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_CA_DEFORM_METADATA = Metadata(
-    id="f7a184212f3f0c6bda47adcf8ca71b73b93d49f3.boutiques",
+    id="c256de885cf0fa05e5677f45b973c6b0e67b7c00.boutiques",
     name="mris_ca_deform",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_CA_DEFORM_METADATA = Metadata(
 
 
 MrisCaDeformParameters = typing.TypedDict('MrisCaDeformParameters', {
-    "__STYXTYPE__": typing.Literal["mris_ca_deform"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_ca_deform"]],
+    "input_surface": InputPathType,
+    "label_vol": InputPathType,
+    "transform": InputPathType,
+    "intensity_vol": InputPathType,
+    "output_surface": str,
+})
+MrisCaDeformParametersTagged = typing.TypedDict('MrisCaDeformParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_ca_deform"],
     "input_surface": InputPathType,
     "label_vol": InputPathType,
     "transform": InputPathType,
     "intensity_vol": 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_ca_deform": mris_ca_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_ca_deform": mris_ca_deform_outputs,
-    }.get(t)
 
 
 class MrisCaDeformOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_ca_deform(...)`.
+    Output object returned when calling `MrisCaDeformParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mris_ca_deform_params(
     transform: InputPathType,
     intensity_vol: InputPathType,
     output_surface: str,
-) -> MrisCaDeformParameters:
+) -> MrisCaDeformParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +63,7 @@ def mris_ca_deform_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_ca_deform",
+        "@type": "freesurfer/mris_ca_deform",
         "input_surface": input_surface,
         "label_vol": label_vol,
         "transform": transform,
@@ -112,11 +88,11 @@ def mris_ca_deform_cargs(
     """
     cargs = []
     cargs.append("mris_ca_deform")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("label_vol")))
-    cargs.append(execution.input_file(params.get("transform")))
-    cargs.append(execution.input_file(params.get("intensity_vol")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("label_vol", None)))
+    cargs.append(execution.input_file(params.get("transform", None)))
+    cargs.append(execution.input_file(params.get("intensity_vol", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -135,16 +111,18 @@ def mris_ca_deform_outputs(
     """
     ret = MrisCaDeformOutputs(
         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_ca_deform_execute(
     params: MrisCaDeformParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisCaDeformOutputs:
     """
+    mris_ca_deform
+    
     Deforms a surface to match it to a volumetric map of cortical labels.
     
     Author: FreeSurfer Developers
@@ -153,10 +131,12 @@ def mris_ca_deform_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisCaDeformOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_CA_DEFORM_METADATA)
     params = execution.params(params)
     cargs = mris_ca_deform_cargs(params, execution)
     ret = mris_ca_deform_outputs(params, execution)
@@ -173,6 +153,8 @@ def mris_ca_deform(
     runner: Runner | None = None,
 ) -> MrisCaDeformOutputs:
     """
+    mris_ca_deform
+    
     Deforms a surface to match it to a volumetric map of cortical labels.
     
     Author: FreeSurfer Developers
@@ -191,8 +173,6 @@ def mris_ca_deform(
     Returns:
         NamedTuple of outputs (described in `MrisCaDeformOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_CA_DEFORM_METADATA)
     params = mris_ca_deform_params(
         input_surface=input_surface,
         label_vol=label_vol,
@@ -200,13 +180,13 @@ def mris_ca_deform(
         intensity_vol=intensity_vol,
         output_surface=output_surface,
     )
-    return mris_ca_deform_execute(params, execution)
+    return mris_ca_deform_execute(params, runner)
 
 
 __all__ = [
     "MRIS_CA_DEFORM_METADATA",
     "MrisCaDeformOutputs",
-    "MrisCaDeformParameters",
     "mris_ca_deform",
+    "mris_ca_deform_execute",
     "mris_ca_deform_params",
 ]