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

niwrap_freesurfer/freesurfer/mris_segment.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SEGMENT_METADATA = Metadata(
-    id="b4b82ace2b5925b14cab9688a638c640dfa792a2.boutiques",
+    id="979f25c32508a2ccbda06c306be8702b17a08e1f.boutiques",
     name="mris_segment",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_SEGMENT_METADATA = Metadata(
 
 
 MrisSegmentParameters = typing.TypedDict('MrisSegmentParameters', {
-    "__STYXTYPE__": typing.Literal["mris_segment"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_segment"]],
+    "subjects": list[str],
+    "output_subject": str,
+    "output_file": str,
+})
+MrisSegmentParametersTagged = typing.TypedDict('MrisSegmentParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_segment"],
     "subjects": list[str],
     "output_subject": str,
     "output_file": 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_segment": mris_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_segment": mris_segment_outputs,
-    }.get(t)
 
 
 class MrisSegmentOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_segment(...)`.
+    Output object returned when calling `MrisSegmentParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mris_segment_params(
     subjects: list[str],
     output_subject: str,
     output_file: str,
-) -> MrisSegmentParameters:
+) -> MrisSegmentParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mris_segment_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_segment",
+        "@type": "freesurfer/mris_segment",
         "subjects": subjects,
         "output_subject": output_subject,
         "output_file": output_file,
@@ -102,9 +76,9 @@ def mris_segment_cargs(
     """
     cargs = []
     cargs.append("mris_segment")
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_subject"))
-    cargs.append(params.get("output_file"))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_subject", None))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mris_segment_outputs(
     """
     ret = MrisSegmentOutputs(
         root=execution.output_file("."),
-        segmented_output=execution.output_file(params.get("output_file")),
+        segmented_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def mris_segment_execute(
     params: MrisSegmentParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSegmentOutputs:
     """
+    mris_segment
+    
     A command-line tool for segmenting surfaces in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mris_segment_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSegmentOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SEGMENT_METADATA)
     params = execution.params(params)
     cargs = mris_segment_cargs(params, execution)
     ret = mris_segment_outputs(params, execution)
@@ -159,6 +137,8 @@ def mris_segment(
     runner: Runner | None = None,
 ) -> MrisSegmentOutputs:
     """
+    mris_segment
+    
     A command-line tool for segmenting surfaces in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mris_segment(
     Returns:
         NamedTuple of outputs (described in `MrisSegmentOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SEGMENT_METADATA)
     params = mris_segment_params(
         subjects=subjects,
         output_subject=output_subject,
         output_file=output_file,
     )
-    return mris_segment_execute(params, execution)
+    return mris_segment_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SEGMENT_METADATA",
     "MrisSegmentOutputs",
-    "MrisSegmentParameters",
     "mris_segment",
+    "mris_segment_execute",
     "mris_segment_params",
 ]

niwrap_freesurfer/freesurfer/mris_segment_vals.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SEGMENT_VALS_METADATA = Metadata(
-    id="70aa435644cb650e288a80d19e31ace5baaed792.boutiques",
+    id="61a9f35935a5a99144fdebb71accfc5f1beaece1.boutiques",
     name="mris_segment_vals",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRIS_SEGMENT_VALS_METADATA = Metadata(
 
 
 MrisSegmentValsParameters = typing.TypedDict('MrisSegmentValsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_segment_vals"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_segment_vals"]],
+    "input_surface": InputPathType,
+    "input_curv_file": InputPathType,
+    "output_curv_file": str,
+    "threshold": typing.NotRequired[float | None],
+    "area_thresh": typing.NotRequired[float | None],
+})
+MrisSegmentValsParametersTagged = typing.TypedDict('MrisSegmentValsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_segment_vals"],
     "input_surface": InputPathType,
     "input_curv_file": InputPathType,
     "output_curv_file": str,
     "threshold": typing.NotRequired[float | None],
     "area_thresh": 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_segment_vals": mris_segment_vals_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_segment_vals": mris_segment_vals_outputs,
-    }.get(t)
 
 
 class MrisSegmentValsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_segment_vals(...)`.
+    Output object returned when calling `MrisSegmentValsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mris_segment_vals_params(
     output_curv_file: str,
     threshold: float | None = None,
     area_thresh: float | None = None,
-) -> MrisSegmentValsParameters:
+) -> MrisSegmentValsParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mris_segment_vals_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_segment_vals",
+        "@type": "freesurfer/mris_segment_vals",
         "input_surface": input_surface,
         "input_curv_file": input_curv_file,
         "output_curv_file": output_curv_file,
@@ -112,18 +88,18 @@ def mris_segment_vals_cargs(
     """
     cargs = []
     cargs.append("mris_segment_vals")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("input_curv_file")))
-    cargs.append(params.get("output_curv_file"))
-    if params.get("threshold") is not None:
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("input_curv_file", None)))
+    cargs.append(params.get("output_curv_file", None))
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
-    if params.get("area_thresh") is not None:
+    if params.get("area_thresh", None) is not None:
         cargs.extend([
             "-A",
-            str(params.get("area_thresh"))
+            str(params.get("area_thresh", None))
         ])
     return cargs
 
@@ -143,16 +119,18 @@ def mris_segment_vals_outputs(
     """
     ret = MrisSegmentValsOutputs(
         root=execution.output_file("."),
-        output_curv=execution.output_file(params.get("output_curv_file")),
+        output_curv=execution.output_file(params.get("output_curv_file", None)),
     )
     return ret
 
 
 def mris_segment_vals_execute(
     params: MrisSegmentValsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSegmentValsOutputs:
     """
+    mris_segment_vals
+    
     This program segments an input val file into connected components.
     
     Author: FreeSurfer Developers
@@ -161,10 +139,12 @@ def mris_segment_vals_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSegmentValsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SEGMENT_VALS_METADATA)
     params = execution.params(params)
     cargs = mris_segment_vals_cargs(params, execution)
     ret = mris_segment_vals_outputs(params, execution)
@@ -181,6 +161,8 @@ def mris_segment_vals(
     runner: Runner | None = None,
 ) -> MrisSegmentValsOutputs:
     """
+    mris_segment_vals
+    
     This program segments an input val file into connected components.
     
     Author: FreeSurfer Developers
@@ -197,8 +179,6 @@ def mris_segment_vals(
     Returns:
         NamedTuple of outputs (described in `MrisSegmentValsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SEGMENT_VALS_METADATA)
     params = mris_segment_vals_params(
         input_surface=input_surface,
         input_curv_file=input_curv_file,
@@ -206,13 +186,13 @@ def mris_segment_vals(
         threshold=threshold,
         area_thresh=area_thresh,
     )
-    return mris_segment_vals_execute(params, execution)
+    return mris_segment_vals_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SEGMENT_VALS_METADATA",
     "MrisSegmentValsOutputs",
-    "MrisSegmentValsParameters",
     "mris_segment_vals",
+    "mris_segment_vals_execute",
     "mris_segment_vals_params",
 ]

niwrap_freesurfer/freesurfer/mris_segmentation_stats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SEGMENTATION_STATS_METADATA = Metadata(
-    id="7e3ee3ba2a78febe7620d4f6780e4c14229db52d.boutiques",
+    id="de9849720af633844121d12399c9858bc49fd276.boutiques",
     name="mris_segmentation_stats",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRIS_SEGMENTATION_STATS_METADATA = Metadata(
 
 
 MrisSegmentationStatsParameters = typing.TypedDict('MrisSegmentationStatsParameters', {
-    "__STYXTYPE__": typing.Literal["mris_segmentation_stats"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_segmentation_stats"]],
+    "overlay_name": str,
+    "segmentation_label_name": str,
+    "subjects": list[str],
+    "roc_file": str,
+})
+MrisSegmentationStatsParametersTagged = typing.TypedDict('MrisSegmentationStatsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_segmentation_stats"],
     "overlay_name": str,
     "segmentation_label_name": str,
     "subjects": list[str],
     "roc_file": 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_segmentation_stats": mris_segmentation_stats_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_segmentation_stats": mris_segmentation_stats_outputs,
-    }.get(t)
 
 
 class MrisSegmentationStatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_segmentation_stats(...)`.
+    Output object returned when calling `MrisSegmentationStatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mris_segmentation_stats_params(
     segmentation_label_name: str,
     subjects: list[str],
     roc_file: str,
-) -> MrisSegmentationStatsParameters:
+) -> MrisSegmentationStatsParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mris_segmentation_stats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_segmentation_stats",
+        "@type": "freesurfer/mris_segmentation_stats",
         "overlay_name": overlay_name,
         "segmentation_label_name": segmentation_label_name,
         "subjects": subjects,
@@ -106,10 +81,10 @@ def mris_segmentation_stats_cargs(
     """
     cargs = []
     cargs.append("mris_segmentation_stats")
-    cargs.append(params.get("overlay_name"))
-    cargs.append(params.get("segmentation_label_name"))
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("roc_file"))
+    cargs.append(params.get("overlay_name", None))
+    cargs.append(params.get("segmentation_label_name", None))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("roc_file", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def mris_segmentation_stats_outputs(
     """
     ret = MrisSegmentationStatsOutputs(
         root=execution.output_file("."),
-        roc_output_file=execution.output_file(params.get("roc_file")),
+        roc_output_file=execution.output_file(params.get("roc_file", None)),
     )
     return ret
 
 
 def mris_segmentation_stats_execute(
     params: MrisSegmentationStatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisSegmentationStatsOutputs:
     """
+    mris_segmentation_stats
+    
     Tool for calculating segmentation statistics.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def mris_segmentation_stats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisSegmentationStatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SEGMENTATION_STATS_METADATA)
     params = execution.params(params)
     cargs = mris_segmentation_stats_cargs(params, execution)
     ret = mris_segmentation_stats_outputs(params, execution)
@@ -165,6 +144,8 @@ def mris_segmentation_stats(
     runner: Runner | None = None,
 ) -> MrisSegmentationStatsOutputs:
     """
+    mris_segmentation_stats
+    
     Tool for calculating segmentation statistics.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def mris_segmentation_stats(
     Returns:
         NamedTuple of outputs (described in `MrisSegmentationStatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SEGMENTATION_STATS_METADATA)
     params = mris_segmentation_stats_params(
         overlay_name=overlay_name,
         segmentation_label_name=segmentation_label_name,
         subjects=subjects,
         roc_file=roc_file,
     )
-    return mris_segmentation_stats_execute(params, execution)
+    return mris_segmentation_stats_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SEGMENTATION_STATS_METADATA",
     "MrisSegmentationStatsOutputs",
-    "MrisSegmentationStatsParameters",
     "mris_segmentation_stats",
+    "mris_segmentation_stats_execute",
     "mris_segmentation_stats_params",
 ]

niwrap_freesurfer/freesurfer/mris_shrinkwrap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_SHRINKWRAP_METADATA = Metadata(
-    id="96cfd148136c6ebc9a24c2fb8339a045d4233c65.boutiques",
+    id="dad31b4a11b8cec8d42062a2c9ca9f757d582e84.boutiques",
     name="mris_shrinkwrap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRIS_SHRINKWRAP_METADATA = Metadata(
 
 
 MrisShrinkwrapParameters = typing.TypedDict('MrisShrinkwrapParameters', {
-    "__STYXTYPE__": typing.Literal["mris_shrinkwrap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_shrinkwrap"]],
+    "volume": InputPathType,
+    "output_name": str,
+    "threshold": typing.NotRequired[float | None],
+})
+MrisShrinkwrapParametersTagged = typing.TypedDict('MrisShrinkwrapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_shrinkwrap"],
     "volume": InputPathType,
     "output_name": str,
     "threshold": 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_shrinkwrap": mris_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 {
-        "mris_shrinkwrap": mris_shrinkwrap_outputs,
-    }.get(t)
 
 
 class MrisShrinkwrapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_shrinkwrap(...)`.
+    Output object returned when calling `MrisShrinkwrapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +45,7 @@ def mris_shrinkwrap_params(
     volume: InputPathType,
     output_name: str,
     threshold: float | None = None,
-) -> MrisShrinkwrapParameters:
+) -> MrisShrinkwrapParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +58,7 @@ def mris_shrinkwrap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_shrinkwrap",
+        "@type": "freesurfer/mris_shrinkwrap",
         "volume": volume,
         "output_name": output_name,
     }
@@ -108,12 +82,12 @@ def mris_shrinkwrap_cargs(
     """
     cargs = []
     cargs.append("mris_shrinkwrap")
-    cargs.append(execution.input_file(params.get("volume")))
-    cargs.append(params.get("output_name"))
-    if params.get("threshold") is not None:
+    cargs.append(execution.input_file(params.get("volume", None)))
+    cargs.append(params.get("output_name", None))
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-t",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
     return cargs
 
@@ -133,18 +107,20 @@ def mris_shrinkwrap_outputs(
     """
     ret = MrisShrinkwrapOutputs(
         root=execution.output_file("."),
-        inner_skull=execution.output_file(params.get("output_name") + "_inner_skull.tri"),
-        outer_skull=execution.output_file(params.get("output_name") + "_outer_skull.tri"),
-        outer_skin=execution.output_file(params.get("output_name") + "_outer_skin.tri"),
+        inner_skull=execution.output_file(params.get("output_name", None) + "_inner_skull.tri"),
+        outer_skull=execution.output_file(params.get("output_name", None) + "_outer_skull.tri"),
+        outer_skin=execution.output_file(params.get("output_name", None) + "_outer_skin.tri"),
     )
     return ret
 
 
 def mris_shrinkwrap_execute(
     params: MrisShrinkwrapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisShrinkwrapOutputs:
     """
+    mris_shrinkwrap
+    
     Generate shrink-wrapped tessellations of the input volume.
     
     Author: FreeSurfer Developers
@@ -153,10 +129,12 @@ def mris_shrinkwrap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisShrinkwrapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_SHRINKWRAP_METADATA)
     params = execution.params(params)
     cargs = mris_shrinkwrap_cargs(params, execution)
     ret = mris_shrinkwrap_outputs(params, execution)
@@ -171,6 +149,8 @@ def mris_shrinkwrap(
     runner: Runner | None = None,
 ) -> MrisShrinkwrapOutputs:
     """
+    mris_shrinkwrap
+    
     Generate shrink-wrapped tessellations of the input volume.
     
     Author: FreeSurfer Developers
@@ -186,20 +166,18 @@ def mris_shrinkwrap(
     Returns:
         NamedTuple of outputs (described in `MrisShrinkwrapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_SHRINKWRAP_METADATA)
     params = mris_shrinkwrap_params(
         volume=volume,
         output_name=output_name,
         threshold=threshold,
     )
-    return mris_shrinkwrap_execute(params, execution)
+    return mris_shrinkwrap_execute(params, runner)
 
 
 __all__ = [
     "MRIS_SHRINKWRAP_METADATA",
     "MrisShrinkwrapOutputs",
-    "MrisShrinkwrapParameters",
     "mris_shrinkwrap",
+    "mris_shrinkwrap_execute",
     "mris_shrinkwrap_params",
 ]