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

niwrap_freesurfer/freesurfer/mri_seg_diff.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SEG_DIFF_METADATA = Metadata(
-    id="78f61554c72a9c79a5a960acc4e0438704b93d91.boutiques",
+    id="6008110879226277aaf1fbd6a697cbdc19b49716.boutiques",
     name="mri_seg_diff",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRI_SEG_DIFF_METADATA = Metadata(
 
 
 MriSegDiffParameters = typing.TypedDict('MriSegDiffParameters', {
-    "__STYXTYPE__": typing.Literal["mri_seg_diff"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_seg_diff"]],
+    "seg1": typing.NotRequired[InputPathType | None],
+    "seg2": typing.NotRequired[InputPathType | None],
+    "seg": typing.NotRequired[InputPathType | None],
+    "diff": str,
+    "diff_in": typing.NotRequired[InputPathType | None],
+    "merged": typing.NotRequired[str | None],
+    "diff_force": bool,
+    "debug": bool,
+    "checkopts": bool,
+    "version": bool,
+})
+MriSegDiffParametersTagged = typing.TypedDict('MriSegDiffParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_seg_diff"],
     "seg1": typing.NotRequired[InputPathType | None],
     "seg2": typing.NotRequired[InputPathType | None],
     "seg": typing.NotRequired[InputPathType | None],
@@ -26,43 +39,11 @@ MriSegDiffParameters = typing.TypedDict('MriSegDiffParameters', {
     "checkopts": 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 {
-        "mri_seg_diff": mri_seg_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 {
-        "mri_seg_diff": mri_seg_diff_outputs,
-    }.get(t)
 
 
 class MriSegDiffOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_seg_diff(...)`.
+    Output object returned when calling `MriSegDiffParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +64,7 @@ def mri_seg_diff_params(
     debug: bool = False,
     checkopts: bool = False,
     version: bool = False,
-) -> MriSegDiffParameters:
+) -> MriSegDiffParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +83,7 @@ def mri_seg_diff_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_seg_diff",
+        "@type": "freesurfer/mri_seg_diff",
         "diff": diff,
         "diff_force": diff_force,
         "debug": debug,
@@ -137,42 +118,42 @@ def mri_seg_diff_cargs(
     """
     cargs = []
     cargs.append("mri_seg_diff")
-    if params.get("seg1") is not None:
+    if params.get("seg1", None) is not None:
         cargs.extend([
             "--seg1",
-            execution.input_file(params.get("seg1"))
+            execution.input_file(params.get("seg1", None))
         ])
-    if params.get("seg2") is not None:
+    if params.get("seg2", None) is not None:
         cargs.extend([
             "--seg2",
-            execution.input_file(params.get("seg2"))
+            execution.input_file(params.get("seg2", None))
         ])
-    if params.get("seg") is not None:
+    if params.get("seg", None) is not None:
         cargs.extend([
             "--seg",
-            execution.input_file(params.get("seg"))
+            execution.input_file(params.get("seg", None))
         ])
     cargs.extend([
         "--diff",
-        params.get("diff")
+        params.get("diff", None)
     ])
-    if params.get("diff_in") is not None:
+    if params.get("diff_in", None) is not None:
         cargs.extend([
             "--diff-in",
-            execution.input_file(params.get("diff_in"))
+            execution.input_file(params.get("diff_in", None))
         ])
-    if params.get("merged") is not None:
+    if params.get("merged", None) is not None:
         cargs.extend([
             "--merged",
-            params.get("merged")
+            params.get("merged", None)
         ])
-    if params.get("diff_force"):
+    if params.get("diff_force", False):
         cargs.append("--diff-force")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -192,19 +173,21 @@ def mri_seg_diff_outputs(
     """
     ret = MriSegDiffOutputs(
         root=execution.output_file("."),
-        diff_output=execution.output_file(params.get("diff")),
-        merged_output=execution.output_file(params.get("merged")) if (params.get("merged") is not None) else None,
+        diff_output=execution.output_file(params.get("diff", None)),
+        merged_output=execution.output_file(params.get("merged", None)) if (params.get("merged") is not None) else None,
     )
     return ret
 
 
 def mri_seg_diff_execute(
     params: MriSegDiffParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSegDiffOutputs:
     """
-    This program computes and merges differences in segmentation volumes, primarily
-    for managing manual edits in FreeSurfer's aseg.mgz.
+    mri_seg_diff
+    
+    This program computes and merges differences in segmentation volumes,
+    primarily for managing manual edits in FreeSurfer's aseg.mgz.
     
     Author: FreeSurfer Developers
     
@@ -212,10 +195,12 @@ def mri_seg_diff_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSegDiffOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SEG_DIFF_METADATA)
     params = execution.params(params)
     cargs = mri_seg_diff_cargs(params, execution)
     ret = mri_seg_diff_outputs(params, execution)
@@ -237,8 +222,10 @@ def mri_seg_diff(
     runner: Runner | None = None,
 ) -> MriSegDiffOutputs:
     """
-    This program computes and merges differences in segmentation volumes, primarily
-    for managing manual edits in FreeSurfer's aseg.mgz.
+    mri_seg_diff
+    
+    This program computes and merges differences in segmentation volumes,
+    primarily for managing manual edits in FreeSurfer's aseg.mgz.
     
     Author: FreeSurfer Developers
     
@@ -259,8 +246,6 @@ def mri_seg_diff(
     Returns:
         NamedTuple of outputs (described in `MriSegDiffOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SEG_DIFF_METADATA)
     params = mri_seg_diff_params(
         seg1=seg1,
         seg2=seg2,
@@ -273,13 +258,13 @@ def mri_seg_diff(
         checkopts=checkopts,
         version=version,
     )
-    return mri_seg_diff_execute(params, execution)
+    return mri_seg_diff_execute(params, runner)
 
 
 __all__ = [
     "MRI_SEG_DIFF_METADATA",
     "MriSegDiffOutputs",
-    "MriSegDiffParameters",
     "mri_seg_diff",
+    "mri_seg_diff_execute",
     "mri_seg_diff_params",
 ]

niwrap_freesurfer/freesurfer/mri_seg_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SEG_OVERLAP_METADATA = Metadata(
-    id="a985ae1a5c011e1b7cb1fbb3dea706e5e5d7e35b.boutiques",
+    id="f3b538b50d90585bf0105d4b48845c49b1607b96.boutiques",
     name="mri_seg_overlap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ MRI_SEG_OVERLAP_METADATA = Metadata(
 
 
 MriSegOverlapParameters = typing.TypedDict('MriSegOverlapParameters', {
-    "__STYXTYPE__": typing.Literal["mri_seg_overlap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_seg_overlap"]],
+    "vol1": InputPathType,
+    "vol2": InputPathType,
+    "out_file": typing.NotRequired[str | None],
+    "measures": typing.NotRequired[list[str] | None],
+    "labels": typing.NotRequired[list[str] | None],
+    "label_names": typing.NotRequired[list[str] | None],
+    "label_file": typing.NotRequired[InputPathType | None],
+    "no_names_flag": bool,
+    "seg_flag": bool,
+    "quiet_flag": bool,
+})
+MriSegOverlapParametersTagged = typing.TypedDict('MriSegOverlapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_seg_overlap"],
     "vol1": InputPathType,
     "vol2": InputPathType,
     "out_file": typing.NotRequired[str | None],
@@ -26,43 +39,11 @@ MriSegOverlapParameters = typing.TypedDict('MriSegOverlapParameters', {
     "seg_flag": bool,
     "quiet_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 {
-        "mri_seg_overlap": mri_seg_overlap_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 {
-        "mri_seg_overlap": mri_seg_overlap_outputs,
-    }.get(t)
 
 
 class MriSegOverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_seg_overlap(...)`.
+    Output object returned when calling `MriSegOverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -81,7 +62,7 @@ def mri_seg_overlap_params(
     no_names_flag: bool = False,
     seg_flag: bool = False,
     quiet_flag: bool = False,
-) -> MriSegOverlapParameters:
+) -> MriSegOverlapParametersTagged:
     """
     Build parameters.
     
@@ -103,7 +84,7 @@ def mri_seg_overlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_seg_overlap",
+        "@type": "freesurfer/mri_seg_overlap",
         "vol1": vol1,
         "vol2": vol2,
         "no_names_flag": no_names_flag,
@@ -138,38 +119,38 @@ def mri_seg_overlap_cargs(
     """
     cargs = []
     cargs.append("mri_seg_overlap")
-    cargs.append(execution.input_file(params.get("vol1")))
-    cargs.append(execution.input_file(params.get("vol2")))
-    if params.get("out_file") is not None:
+    cargs.append(execution.input_file(params.get("vol1", None)))
+    cargs.append(execution.input_file(params.get("vol2", None)))
+    if params.get("out_file", None) is not None:
         cargs.extend([
             "-o",
-            params.get("out_file")
+            params.get("out_file", None)
         ])
-    if params.get("measures") is not None:
+    if params.get("measures", None) is not None:
         cargs.extend([
             "-m",
-            *params.get("measures")
+            *params.get("measures", None)
         ])
-    if params.get("labels") is not None:
+    if params.get("labels", None) is not None:
         cargs.extend([
             "-l",
-            *params.get("labels")
+            *params.get("labels", None)
         ])
-    if params.get("label_names") is not None:
+    if params.get("label_names", None) is not None:
         cargs.extend([
             "-n",
-            *params.get("label_names")
+            *params.get("label_names", None)
         ])
-    if params.get("label_file") is not None:
+    if params.get("label_file", None) is not None:
         cargs.extend([
             "-f",
-            execution.input_file(params.get("label_file"))
+            execution.input_file(params.get("label_file", None))
         ])
-    if params.get("no_names_flag"):
+    if params.get("no_names_flag", False):
         cargs.append("-x")
-    if params.get("seg_flag"):
+    if params.get("seg_flag", False):
         cargs.append("-s")
-    if params.get("quiet_flag"):
+    if params.get("quiet_flag", False):
         cargs.append("-q")
     return cargs
 
@@ -189,16 +170,18 @@ def mri_seg_overlap_outputs(
     """
     ret = MriSegOverlapOutputs(
         root=execution.output_file("."),
-        overlap_report=execution.output_file(params.get("out_file")) if (params.get("out_file") is not None) else None,
+        overlap_report=execution.output_file(params.get("out_file", None)) if (params.get("out_file") is not None) else None,
     )
     return ret
 
 
 def mri_seg_overlap_execute(
     params: MriSegOverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSegOverlapOutputs:
     """
+    mri_seg_overlap
+    
     Compute the structural overlap between two segmentation volumes.
     
     Author: FreeSurfer Developers
@@ -207,10 +190,12 @@ def mri_seg_overlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSegOverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SEG_OVERLAP_METADATA)
     params = execution.params(params)
     cargs = mri_seg_overlap_cargs(params, execution)
     ret = mri_seg_overlap_outputs(params, execution)
@@ -232,6 +217,8 @@ def mri_seg_overlap(
     runner: Runner | None = None,
 ) -> MriSegOverlapOutputs:
     """
+    mri_seg_overlap
+    
     Compute the structural overlap between two segmentation volumes.
     
     Author: FreeSurfer Developers
@@ -256,8 +243,6 @@ def mri_seg_overlap(
     Returns:
         NamedTuple of outputs (described in `MriSegOverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SEG_OVERLAP_METADATA)
     params = mri_seg_overlap_params(
         vol1=vol1,
         vol2=vol2,
@@ -270,13 +255,13 @@ def mri_seg_overlap(
         seg_flag=seg_flag,
         quiet_flag=quiet_flag,
     )
-    return mri_seg_overlap_execute(params, execution)
+    return mri_seg_overlap_execute(params, runner)
 
 
 __all__ = [
     "MRI_SEG_OVERLAP_METADATA",
     "MriSegOverlapOutputs",
-    "MriSegOverlapParameters",
     "mri_seg_overlap",
+    "mri_seg_overlap_execute",
     "mri_seg_overlap_params",
 ]

niwrap_freesurfer/freesurfer/mri_segcentroids.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_SEGCENTROIDS_METADATA = Metadata(
-    id="ad1b76368fee88d8cea9119432892c20600ba077.boutiques",
+    id="c75788a84147e37e8f8fa9dc1444d520f1fdb410.boutiques",
     name="mri_segcentroids",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_SEGCENTROIDS_METADATA = Metadata(
 
 
 MriSegcentroidsParameters = typing.TypedDict('MriSegcentroidsParameters', {
-    "__STYXTYPE__": typing.Literal["mri_segcentroids"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_segcentroids"]],
+    "input_segmentation": InputPathType,
+    "output_file": str,
+    "pointset_flag": bool,
+    "registration_file": typing.NotRequired[InputPathType | None],
+    "weights_file": typing.NotRequired[InputPathType | None],
+    "lut_file": typing.NotRequired[InputPathType | None],
+    "default_lut_flag": bool,
+})
+MriSegcentroidsParametersTagged = typing.TypedDict('MriSegcentroidsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_segcentroids"],
     "input_segmentation": InputPathType,
     "output_file": str,
     "pointset_flag": bool,
@@ -23,43 +33,11 @@ MriSegcentroidsParameters = typing.TypedDict('MriSegcentroidsParameters', {
     "lut_file": typing.NotRequired[InputPathType | None],
     "default_lut_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 {
-        "mri_segcentroids": mri_segcentroids_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 {
-        "mri_segcentroids": mri_segcentroids_outputs,
-    }.get(t)
 
 
 class MriSegcentroidsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_segcentroids(...)`.
+    Output object returned when calling `MriSegcentroidsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mri_segcentroids_params(
     weights_file: InputPathType | None = None,
     lut_file: InputPathType | None = None,
     default_lut_flag: bool = False,
-) -> MriSegcentroidsParameters:
+) -> MriSegcentroidsParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def mri_segcentroids_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_segcentroids",
+        "@type": "freesurfer/mri_segcentroids",
         "input_segmentation": input_segmentation,
         "output_file": output_file,
         "pointset_flag": pointset_flag,
@@ -123,30 +101,30 @@ def mri_segcentroids_cargs(
     cargs.append("mri_segcentroids")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_segmentation"))
+        execution.input_file(params.get("input_segmentation", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_file")
+        params.get("output_file", None)
     ])
-    if params.get("pointset_flag"):
+    if params.get("pointset_flag", False):
         cargs.append("--p")
-    if params.get("registration_file") is not None:
+    if params.get("registration_file", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("registration_file"))
+            execution.input_file(params.get("registration_file", None))
         ])
-    if params.get("weights_file") is not None:
+    if params.get("weights_file", None) is not None:
         cargs.extend([
             "--weights",
-            execution.input_file(params.get("weights_file"))
+            execution.input_file(params.get("weights_file", None))
         ])
-    if params.get("lut_file") is not None:
+    if params.get("lut_file", None) is not None:
         cargs.extend([
             "--ctab",
-            execution.input_file(params.get("lut_file"))
+            execution.input_file(params.get("lut_file", None))
         ])
-    if params.get("default_lut_flag"):
+    if params.get("default_lut_flag", False):
         cargs.append("--ctab-default")
     return cargs
 
@@ -166,16 +144,18 @@ def mri_segcentroids_outputs(
     """
     ret = MriSegcentroidsOutputs(
         root=execution.output_file("."),
-        output_centroids=execution.output_file(params.get("output_file")),
+        output_centroids=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mri_segcentroids_execute(
     params: MriSegcentroidsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriSegcentroidsOutputs:
     """
+    mri_segcentroids
+    
     Computes the center of mass for individual structures in a segmentation.
     
     Author: FreeSurfer Developers
@@ -184,10 +164,12 @@ def mri_segcentroids_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriSegcentroidsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_SEGCENTROIDS_METADATA)
     params = execution.params(params)
     cargs = mri_segcentroids_cargs(params, execution)
     ret = mri_segcentroids_outputs(params, execution)
@@ -206,6 +188,8 @@ def mri_segcentroids(
     runner: Runner | None = None,
 ) -> MriSegcentroidsOutputs:
     """
+    mri_segcentroids
+    
     Computes the center of mass for individual structures in a segmentation.
     
     Author: FreeSurfer Developers
@@ -224,8 +208,6 @@ def mri_segcentroids(
     Returns:
         NamedTuple of outputs (described in `MriSegcentroidsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_SEGCENTROIDS_METADATA)
     params = mri_segcentroids_params(
         input_segmentation=input_segmentation,
         output_file=output_file,
@@ -235,13 +217,13 @@ def mri_segcentroids(
         lut_file=lut_file,
         default_lut_flag=default_lut_flag,
     )
-    return mri_segcentroids_execute(params, execution)
+    return mri_segcentroids_execute(params, runner)
 
 
 __all__ = [
     "MRI_SEGCENTROIDS_METADATA",
     "MriSegcentroidsOutputs",
-    "MriSegcentroidsParameters",
     "mri_segcentroids",
+    "mri_segcentroids_execute",
     "mri_segcentroids_params",
 ]