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

niwrap_freesurfer/freesurfer/mris_compute_lgi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_COMPUTE_LGI_METADATA = Metadata(
-    id="54e899bdd2e1bd731402ea4604c71a992774b070.boutiques",
+    id="6f9fee2f3e78ea7ef72ab93a7ead7a3ce713a28d.boutiques",
     name="mris_compute_lgi",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_COMPUTE_LGI_METADATA = Metadata(
 
 
 MrisComputeLgiParameters = typing.TypedDict('MrisComputeLgiParameters', {
-    "__STYXTYPE__": typing.Literal["mris_compute_lgi"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_compute_lgi"]],
+    "input_surface": InputPathType,
+    "close_sphere_size": typing.NotRequired[float | None],
+    "smooth_iters": typing.NotRequired[float | None],
+    "step_size": typing.NotRequired[float | None],
+    "echo": bool,
+    "dontrun": bool,
+})
+MrisComputeLgiParametersTagged = typing.TypedDict('MrisComputeLgiParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_compute_lgi"],
     "input_surface": InputPathType,
     "close_sphere_size": typing.NotRequired[float | None],
     "smooth_iters": typing.NotRequired[float | None],
@@ -22,43 +31,11 @@ MrisComputeLgiParameters = typing.TypedDict('MrisComputeLgiParameters', {
     "echo": bool,
     "dontrun": 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_compute_lgi": mris_compute_lgi_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_compute_lgi": mris_compute_lgi_outputs,
-    }.get(t)
 
 
 class MrisComputeLgiOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_compute_lgi(...)`.
+    Output object returned when calling `MrisComputeLgiParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mris_compute_lgi_params(
     step_size: float | None = None,
     echo: bool = False,
     dontrun: bool = False,
-) -> MrisComputeLgiParameters:
+) -> MrisComputeLgiParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +68,7 @@ def mris_compute_lgi_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_compute_lgi",
+        "@type": "freesurfer/mris_compute_lgi",
         "input_surface": input_surface,
         "echo": echo,
         "dontrun": dontrun,
@@ -122,26 +99,26 @@ def mris_compute_lgi_cargs(
     cargs.append("mris_compute_lgi")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_surface"))
+        execution.input_file(params.get("input_surface", None))
     ])
-    if params.get("close_sphere_size") is not None:
+    if params.get("close_sphere_size", None) is not None:
         cargs.extend([
             "--close_sphere_size",
-            str(params.get("close_sphere_size"))
+            str(params.get("close_sphere_size", None))
         ])
-    if params.get("smooth_iters") is not None:
+    if params.get("smooth_iters", None) is not None:
         cargs.extend([
             "--smooth_iters",
-            str(params.get("smooth_iters"))
+            str(params.get("smooth_iters", None))
         ])
-    if params.get("step_size") is not None:
+    if params.get("step_size", None) is not None:
         cargs.extend([
             "--step_size",
-            str(params.get("step_size"))
+            str(params.get("step_size", None))
         ])
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("--echo")
-    if params.get("dontrun"):
+    if params.get("dontrun", False):
         cargs.append("--dontrun")
     return cargs
 
@@ -161,16 +138,18 @@ def mris_compute_lgi_outputs(
     """
     ret = MrisComputeLgiOutputs(
         root=execution.output_file("."),
-        output_surface_map=execution.output_file(pathlib.Path(params.get("input_surface")).name + "_lgi"),
+        output_surface_map=execution.output_file(pathlib.Path(params.get("input_surface", None)).name + "_lgi"),
     )
     return ret
 
 
 def mris_compute_lgi_execute(
     params: MrisComputeLgiParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisComputeLgiOutputs:
     """
+    mris_compute_lgi
+    
     Computes local measurements of gyrification at thousands of points over the
     entire cortical surface.
     
@@ -180,10 +159,12 @@ def mris_compute_lgi_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisComputeLgiOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_LGI_METADATA)
     params = execution.params(params)
     cargs = mris_compute_lgi_cargs(params, execution)
     ret = mris_compute_lgi_outputs(params, execution)
@@ -201,6 +182,8 @@ def mris_compute_lgi(
     runner: Runner | None = None,
 ) -> MrisComputeLgiOutputs:
     """
+    mris_compute_lgi
+    
     Computes local measurements of gyrification at thousands of points over the
     entire cortical surface.
     
@@ -222,8 +205,6 @@ def mris_compute_lgi(
     Returns:
         NamedTuple of outputs (described in `MrisComputeLgiOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_COMPUTE_LGI_METADATA)
     params = mris_compute_lgi_params(
         input_surface=input_surface,
         close_sphere_size=close_sphere_size,
@@ -232,13 +213,13 @@ def mris_compute_lgi(
         echo=echo,
         dontrun=dontrun,
     )
-    return mris_compute_lgi_execute(params, execution)
+    return mris_compute_lgi_execute(params, runner)
 
 
 __all__ = [
     "MRIS_COMPUTE_LGI_METADATA",
     "MrisComputeLgiOutputs",
-    "MrisComputeLgiParameters",
     "mris_compute_lgi",
+    "mris_compute_lgi_execute",
     "mris_compute_lgi_params",
 ]

niwrap_freesurfer/freesurfer/mris_compute_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_COMPUTE_OVERLAP_METADATA = Metadata(
-    id="096c1bc6d75f5b86bf00d48b1b16b7c7e55a5520.boutiques",
+    id="fa079c980b384b24f3a9016664533407fcc892fb.boutiques",
     name="mris_compute_overlap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MRIS_COMPUTE_OVERLAP_METADATA = Metadata(
 
 
 MrisComputeOverlapParameters = typing.TypedDict('MrisComputeOverlapParameters', {
-    "__STYXTYPE__": typing.Literal["mris_compute_overlap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_compute_overlap"]],
+    "subject": str,
+    "hemi": str,
+    "surface": str,
+    "annotation": str,
+    "labels": list[str],
+    "percentage": bool,
+    "log_file": typing.NotRequired[str | None],
+    "brain_volume": typing.NotRequired[InputPathType | None],
+})
+MrisComputeOverlapParametersTagged = typing.TypedDict('MrisComputeOverlapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_compute_overlap"],
     "subject": str,
     "hemi": str,
     "surface": str,
@@ -24,42 +35,11 @@ MrisComputeOverlapParameters = typing.TypedDict('MrisComputeOverlapParameters',
     "log_file": typing.NotRequired[str | None],
     "brain_volume": typing.NotRequired[InputPathType | 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_compute_overlap": mris_compute_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 {
-    }.get(t)
 
 
 class MrisComputeOverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_compute_overlap(...)`.
+    Output object returned when calling `MrisComputeOverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def mris_compute_overlap_params(
     percentage: bool = False,
     log_file: str | None = None,
     brain_volume: InputPathType | None = None,
-) -> MrisComputeOverlapParameters:
+) -> MrisComputeOverlapParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def mris_compute_overlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_compute_overlap",
+        "@type": "freesurfer/mris_compute_overlap",
         "subject": subject,
         "hemi": hemi,
         "surface": surface,
@@ -121,22 +101,22 @@ def mris_compute_overlap_cargs(
     """
     cargs = []
     cargs.append("mris_compute_overlap")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("hemi"))
-    cargs.append(params.get("surface"))
-    cargs.append(params.get("annotation"))
-    cargs.extend(params.get("labels"))
-    if params.get("percentage"):
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("hemi", None))
+    cargs.append(params.get("surface", None))
+    cargs.append(params.get("annotation", None))
+    cargs.extend(params.get("labels", None))
+    if params.get("percentage", False):
         cargs.append("-p")
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-l",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("brain_volume") is not None:
+    if params.get("brain_volume", None) is not None:
         cargs.extend([
             "-b",
-            execution.input_file(params.get("brain_volume"))
+            execution.input_file(params.get("brain_volume", None))
         ])
     return cargs
 
@@ -162,10 +142,13 @@ def mris_compute_overlap_outputs(
 
 def mris_compute_overlap_execute(
     params: MrisComputeOverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisComputeOverlapOutputs:
     """
-    Tool to compute the overlap between two or more labels on a cortical surface.
+    mris_compute_overlap
+    
+    Tool to compute the overlap between two or more labels on a cortical
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -173,10 +156,12 @@ def mris_compute_overlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisComputeOverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_OVERLAP_METADATA)
     params = execution.params(params)
     cargs = mris_compute_overlap_cargs(params, execution)
     ret = mris_compute_overlap_outputs(params, execution)
@@ -196,7 +181,10 @@ def mris_compute_overlap(
     runner: Runner | None = None,
 ) -> MrisComputeOverlapOutputs:
     """
-    Tool to compute the overlap between two or more labels on a cortical surface.
+    mris_compute_overlap
+    
+    Tool to compute the overlap between two or more labels on a cortical
+    surface.
     
     Author: FreeSurfer Developers
     
@@ -215,8 +203,6 @@ def mris_compute_overlap(
     Returns:
         NamedTuple of outputs (described in `MrisComputeOverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_COMPUTE_OVERLAP_METADATA)
     params = mris_compute_overlap_params(
         subject=subject,
         hemi=hemi,
@@ -227,13 +213,13 @@ def mris_compute_overlap(
         log_file=log_file,
         brain_volume=brain_volume,
     )
-    return mris_compute_overlap_execute(params, execution)
+    return mris_compute_overlap_execute(params, runner)
 
 
 __all__ = [
     "MRIS_COMPUTE_OVERLAP_METADATA",
     "MrisComputeOverlapOutputs",
-    "MrisComputeOverlapParameters",
     "mris_compute_overlap",
+    "mris_compute_overlap_execute",
     "mris_compute_overlap_params",
 ]

niwrap_freesurfer/freesurfer/mris_compute_parc_overlap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_COMPUTE_PARC_OVERLAP_METADATA = Metadata(
-    id="9b688cf4965e4242fe321ef384e08a9d1310e055.boutiques",
+    id="a65b1a2318c3059189212d91b81528c2ce7eb0b4.boutiques",
     name="mris_compute_parc_overlap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ MRIS_COMPUTE_PARC_OVERLAP_METADATA = Metadata(
 
 
 MrisComputeParcOverlapParameters = typing.TypedDict('MrisComputeParcOverlapParameters', {
-    "__STYXTYPE__": typing.Literal["mris_compute_parc_overlap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_compute_parc_overlap"]],
+    "subject": str,
+    "hemi": str,
+    "annot1": typing.NotRequired[InputPathType | None],
+    "annot2": typing.NotRequired[InputPathType | None],
+    "label1": typing.NotRequired[InputPathType | None],
+    "label2": typing.NotRequired[InputPathType | None],
+    "subj_dir": typing.NotRequired[str | None],
+    "log_file": typing.NotRequired[str | None],
+    "label_list": typing.NotRequired[InputPathType | None],
+    "nocheck_label1_xyz": bool,
+    "nocheck_label2_xyz": bool,
+    "nocheck_label_xyz": bool,
+    "use_label1_xyz": bool,
+    "use_label2_xyz": bool,
+    "use_label_xyz": bool,
+    "debug_overlap": bool,
+})
+MrisComputeParcOverlapParametersTagged = typing.TypedDict('MrisComputeParcOverlapParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_compute_parc_overlap"],
     "subject": str,
     "hemi": str,
     "annot1": typing.NotRequired[InputPathType | None],
@@ -32,42 +51,11 @@ MrisComputeParcOverlapParameters = typing.TypedDict('MrisComputeParcOverlapParam
     "use_label_xyz": bool,
     "debug_overlap": 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_compute_parc_overlap": mris_compute_parc_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 {
-    }.get(t)
 
 
 class MrisComputeParcOverlapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_compute_parc_overlap(...)`.
+    Output object returned when calling `MrisComputeParcOverlapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -90,7 +78,7 @@ def mris_compute_parc_overlap_params(
     use_label2_xyz: bool = False,
     use_label_xyz: bool = False,
     debug_overlap: bool = False,
-) -> MrisComputeParcOverlapParameters:
+) -> MrisComputeParcOverlapParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +105,7 @@ def mris_compute_parc_overlap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_compute_parc_overlap",
+        "@type": "freesurfer/mris_compute_parc_overlap",
         "subject": subject,
         "hemi": hemi,
         "nocheck_label1_xyz": nocheck_label1_xyz,
@@ -162,60 +150,60 @@ def mris_compute_parc_overlap_cargs(
     cargs.append("mris_compute_parc_overlap")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
-    if params.get("annot1") is not None:
+    if params.get("annot1", None) is not None:
         cargs.extend([
             "--annot1",
-            execution.input_file(params.get("annot1"))
+            execution.input_file(params.get("annot1", None))
         ])
-    if params.get("annot2") is not None:
+    if params.get("annot2", None) is not None:
         cargs.extend([
             "--annot2",
-            execution.input_file(params.get("annot2"))
+            execution.input_file(params.get("annot2", None))
         ])
-    if params.get("label1") is not None:
+    if params.get("label1", None) is not None:
         cargs.extend([
             "--label1",
-            execution.input_file(params.get("label1"))
+            execution.input_file(params.get("label1", None))
         ])
-    if params.get("label2") is not None:
+    if params.get("label2", None) is not None:
         cargs.extend([
             "--label2",
-            execution.input_file(params.get("label2"))
+            execution.input_file(params.get("label2", None))
         ])
-    if params.get("subj_dir") is not None:
+    if params.get("subj_dir", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("subj_dir")
+            params.get("subj_dir", None)
         ])
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("label_list") is not None:
+    if params.get("label_list", None) is not None:
         cargs.extend([
             "--label-list",
-            execution.input_file(params.get("label_list"))
+            execution.input_file(params.get("label_list", None))
         ])
-    if params.get("nocheck_label1_xyz"):
+    if params.get("nocheck_label1_xyz", False):
         cargs.append("--nocheck-label1-xyz")
-    if params.get("nocheck_label2_xyz"):
+    if params.get("nocheck_label2_xyz", False):
         cargs.append("--nocheck-label2-xyz")
-    if params.get("nocheck_label_xyz"):
+    if params.get("nocheck_label_xyz", False):
         cargs.append("--nocheck-label-xyz")
-    if params.get("use_label1_xyz"):
+    if params.get("use_label1_xyz", False):
         cargs.append("--use-label1-xyz")
-    if params.get("use_label2_xyz"):
+    if params.get("use_label2_xyz", False):
         cargs.append("--use-label2-xyz")
-    if params.get("use_label_xyz"):
+    if params.get("use_label_xyz", False):
         cargs.append("--use-label-xyz")
-    if params.get("debug_overlap"):
+    if params.get("debug_overlap", False):
         cargs.append("--debug-overlap")
     return cargs
 
@@ -241,11 +229,13 @@ def mris_compute_parc_overlap_outputs(
 
 def mris_compute_parc_overlap_execute(
     params: MrisComputeParcOverlapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisComputeParcOverlapOutputs:
     """
-    Compares two parcellated (annotated or labeled) surfaces and computes an overall
-    Dice coefficient and mean minimum distances (mm).
+    mris_compute_parc_overlap
+    
+    Compares two parcellated (annotated or labeled) surfaces and computes an
+    overall Dice coefficient and mean minimum distances (mm).
     
     Author: FreeSurfer Developers
     
@@ -253,10 +243,12 @@ def mris_compute_parc_overlap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisComputeParcOverlapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_COMPUTE_PARC_OVERLAP_METADATA)
     params = execution.params(params)
     cargs = mris_compute_parc_overlap_cargs(params, execution)
     ret = mris_compute_parc_overlap_outputs(params, execution)
@@ -284,8 +276,10 @@ def mris_compute_parc_overlap(
     runner: Runner | None = None,
 ) -> MrisComputeParcOverlapOutputs:
     """
-    Compares two parcellated (annotated or labeled) surfaces and computes an overall
-    Dice coefficient and mean minimum distances (mm).
+    mris_compute_parc_overlap
+    
+    Compares two parcellated (annotated or labeled) surfaces and computes an
+    overall Dice coefficient and mean minimum distances (mm).
     
     Author: FreeSurfer Developers
     
@@ -314,8 +308,6 @@ def mris_compute_parc_overlap(
     Returns:
         NamedTuple of outputs (described in `MrisComputeParcOverlapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_COMPUTE_PARC_OVERLAP_METADATA)
     params = mris_compute_parc_overlap_params(
         subject=subject,
         hemi=hemi,
@@ -334,13 +326,13 @@ def mris_compute_parc_overlap(
         use_label_xyz=use_label_xyz,
         debug_overlap=debug_overlap,
     )
-    return mris_compute_parc_overlap_execute(params, execution)
+    return mris_compute_parc_overlap_execute(params, runner)
 
 
 __all__ = [
     "MRIS_COMPUTE_PARC_OVERLAP_METADATA",
     "MrisComputeParcOverlapOutputs",
-    "MrisComputeParcOverlapParameters",
     "mris_compute_parc_overlap",
+    "mris_compute_parc_overlap_execute",
     "mris_compute_parc_overlap_params",
 ]