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

niwrap_freesurfer/freesurfer/samseg_long.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SAMSEG_LONG_METADATA = Metadata(
-    id="765b3bcdab2d7c42a40957c0344f10707c49df51.boutiques",
+    id="d33d740bdb8772937d1e2f0bc11ecb17fca74eda.boutiques",
     name="samseg-long",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ SAMSEG_LONG_METADATA = Metadata(
 
 
 SamsegLongParameters = typing.TypedDict('SamsegLongParameters', {
-    "__STYXTYPE__": typing.Literal["samseg-long"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/samseg-long"]],
+    "output_dir": str,
+    "input_files": list[InputPathType],
+    "align_mc": bool,
+    "align_no_mc": bool,
+    "threads": typing.NotRequired[float | None],
+    "save_posteriors": bool,
+    "force_update": bool,
+})
+SamsegLongParametersTagged = typing.TypedDict('SamsegLongParametersTagged', {
+    "@type": typing.Literal["freesurfer/samseg-long"],
     "output_dir": str,
     "input_files": list[InputPathType],
     "align_mc": bool,
@@ -23,43 +33,11 @@ SamsegLongParameters = typing.TypedDict('SamsegLongParameters', {
     "save_posteriors": bool,
     "force_update": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "samseg-long": samseg_long_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 {
-        "samseg-long": samseg_long_outputs,
-    }.get(t)
 
 
 class SamsegLongOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `samseg_long(...)`.
+    Output object returned when calling `SamsegLongParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +57,7 @@ def samseg_long_params(
     threads: float | None = None,
     save_posteriors: bool = False,
     force_update: bool = False,
-) -> SamsegLongParameters:
+) -> SamsegLongParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +73,7 @@ def samseg_long_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "samseg-long",
+        "@type": "freesurfer/samseg-long",
         "output_dir": output_dir,
         "input_files": input_files,
         "align_mc": align_mc,
@@ -125,24 +103,24 @@ def samseg_long_cargs(
     cargs.append("samseg-long")
     cargs.extend([
         "--o",
-        params.get("output_dir")
+        params.get("output_dir", None)
     ])
     cargs.extend([
         "--i",
-        *[execution.input_file(f) for f in params.get("input_files")]
+        *[execution.input_file(f) for f in params.get("input_files", None)]
     ])
-    if params.get("align_mc"):
+    if params.get("align_mc", False):
         cargs.append("--mc")
-    if params.get("align_no_mc"):
+    if params.get("align_no_mc", False):
         cargs.append("--no-mc")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("save_posteriors"):
+    if params.get("save_posteriors", False):
         cargs.append("--save-posteriors")
-    if params.get("force_update"):
+    if params.get("force_update", False):
         cargs.append("--force-update")
     return cargs
 
@@ -162,18 +140,20 @@ def samseg_long_outputs(
     """
     ret = SamsegLongOutputs(
         root=execution.output_file("."),
-        tp001_output=execution.output_file(params.get("output_dir") + "/tp001"),
-        tp002_output=execution.output_file(params.get("output_dir") + "/tp002"),
-        base_output=execution.output_file(params.get("output_dir") + "/base"),
+        tp001_output=execution.output_file(params.get("output_dir", None) + "/tp001"),
+        tp002_output=execution.output_file(params.get("output_dir", None) + "/tp002"),
+        base_output=execution.output_file(params.get("output_dir", None) + "/base"),
     )
     return ret
 
 
 def samseg_long_execute(
     params: SamsegLongParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SamsegLongOutputs:
     """
+    samseg-long
+    
     Longitudinal analysis tool using SAMSEG in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -182,10 +162,12 @@ def samseg_long_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SamsegLongOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SAMSEG_LONG_METADATA)
     params = execution.params(params)
     cargs = samseg_long_cargs(params, execution)
     ret = samseg_long_outputs(params, execution)
@@ -204,6 +186,8 @@ def samseg_long(
     runner: Runner | None = None,
 ) -> SamsegLongOutputs:
     """
+    samseg-long
+    
     Longitudinal analysis tool using SAMSEG in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -222,8 +206,6 @@ def samseg_long(
     Returns:
         NamedTuple of outputs (described in `SamsegLongOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SAMSEG_LONG_METADATA)
     params = samseg_long_params(
         output_dir=output_dir,
         input_files=input_files,
@@ -233,13 +215,13 @@ def samseg_long(
         save_posteriors=save_posteriors,
         force_update=force_update,
     )
-    return samseg_long_execute(params, execution)
+    return samseg_long_execute(params, runner)
 
 
 __all__ = [
     "SAMSEG_LONG_METADATA",
     "SamsegLongOutputs",
-    "SamsegLongParameters",
     "samseg_long",
+    "samseg_long_execute",
     "samseg_long_params",
 ]

niwrap_freesurfer/freesurfer/samsegmesh2surf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SAMSEGMESH2SURF_METADATA = Metadata(
-    id="87f0bba3783ef8326dcf1be161656bcc456d2f40.boutiques",
+    id="d3e9c8289d2b6f776a0193c487cb8308e01486dc.boutiques",
     name="samsegmesh2surf",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ SAMSEGMESH2SURF_METADATA = Metadata(
 
 
 Samsegmesh2surfParameters = typing.TypedDict('Samsegmesh2surfParameters', {
-    "__STYXTYPE__": typing.Literal["samsegmesh2surf"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/samsegmesh2surf"]],
+    "atlas_mesh": InputPathType,
+    "template": typing.NotRequired[InputPathType | None],
+    "lta_transform": typing.NotRequired[InputPathType | None],
+    "output_surface": typing.NotRequired[str | None],
+    "output_priors": typing.NotRequired[str | None],
+    "invert_flag": bool,
+})
+Samsegmesh2surfParametersTagged = typing.TypedDict('Samsegmesh2surfParametersTagged', {
+    "@type": typing.Literal["freesurfer/samsegmesh2surf"],
     "atlas_mesh": InputPathType,
     "template": typing.NotRequired[InputPathType | None],
     "lta_transform": typing.NotRequired[InputPathType | None],
@@ -22,43 +31,11 @@ Samsegmesh2surfParameters = typing.TypedDict('Samsegmesh2surfParameters', {
     "output_priors": typing.NotRequired[str | None],
     "invert_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 {
-        "samsegmesh2surf": samsegmesh2surf_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 {
-        "samsegmesh2surf": samsegmesh2surf_outputs,
-    }.get(t)
 
 
 class Samsegmesh2surfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `samsegmesh2surf(...)`.
+    Output object returned when calling `Samsegmesh2surfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def samsegmesh2surf_params(
     output_surface: str | None = None,
     output_priors: str | None = None,
     invert_flag: bool = False,
-) -> Samsegmesh2surfParameters:
+) -> Samsegmesh2surfParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def samsegmesh2surf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "samsegmesh2surf",
+        "@type": "freesurfer/samsegmesh2surf",
         "atlas_mesh": atlas_mesh,
         "invert_flag": invert_flag,
     }
@@ -122,29 +99,29 @@ def samsegmesh2surf_cargs(
     cargs.append("samsegmesh2surf")
     cargs.extend([
         "--atlasmesh",
-        execution.input_file(params.get("atlas_mesh"))
+        execution.input_file(params.get("atlas_mesh", None))
     ])
-    if params.get("template") is not None:
+    if params.get("template", None) is not None:
         cargs.extend([
             "--template",
-            execution.input_file(params.get("template"))
+            execution.input_file(params.get("template", None))
         ])
-    if params.get("lta_transform") is not None:
+    if params.get("lta_transform", None) is not None:
         cargs.extend([
             "--lta",
-            execution.input_file(params.get("lta_transform"))
+            execution.input_file(params.get("lta_transform", None))
         ])
-    if params.get("output_surface") is not None:
+    if params.get("output_surface", None) is not None:
         cargs.extend([
             "--osurf",
-            params.get("output_surface")
+            params.get("output_surface", None)
         ])
-    if params.get("output_priors") is not None:
+    if params.get("output_priors", None) is not None:
         cargs.extend([
             "--opriors",
-            params.get("output_priors")
+            params.get("output_priors", None)
         ])
-    if params.get("invert_flag"):
+    if params.get("invert_flag", False):
         cargs.append("--invert")
     return cargs
 
@@ -164,19 +141,21 @@ def samsegmesh2surf_outputs(
     """
     ret = Samsegmesh2surfOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surface")) if (params.get("output_surface") is not None) else None,
-        output_priors_file=execution.output_file(params.get("output_priors")) if (params.get("output_priors") is not None) else None,
+        output_surface_file=execution.output_file(params.get("output_surface", None)) if (params.get("output_surface") is not None) else None,
+        output_priors_file=execution.output_file(params.get("output_priors", None)) if (params.get("output_priors") is not None) else None,
     )
     return ret
 
 
 def samsegmesh2surf_execute(
     params: Samsegmesh2surfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Samsegmesh2surfOutputs:
     """
-    Generate Freesurfer surface from a SAMSEG atlas mesh file and generate priors at
-    each vertex as overlay MRI volume.
+    samsegmesh2surf
+    
+    Generate Freesurfer surface from a SAMSEG atlas mesh file and generate
+    priors at each vertex as overlay MRI volume.
     
     Author: FreeSurfer Developers
     
@@ -184,10 +163,12 @@ def samsegmesh2surf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Samsegmesh2surfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SAMSEGMESH2SURF_METADATA)
     params = execution.params(params)
     cargs = samsegmesh2surf_cargs(params, execution)
     ret = samsegmesh2surf_outputs(params, execution)
@@ -205,8 +186,10 @@ def samsegmesh2surf(
     runner: Runner | None = None,
 ) -> Samsegmesh2surfOutputs:
     """
-    Generate Freesurfer surface from a SAMSEG atlas mesh file and generate priors at
-    each vertex as overlay MRI volume.
+    samsegmesh2surf
+    
+    Generate Freesurfer surface from a SAMSEG atlas mesh file and generate
+    priors at each vertex as overlay MRI volume.
     
     Author: FreeSurfer Developers
     
@@ -223,8 +206,6 @@ def samsegmesh2surf(
     Returns:
         NamedTuple of outputs (described in `Samsegmesh2surfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SAMSEGMESH2SURF_METADATA)
     params = samsegmesh2surf_params(
         atlas_mesh=atlas_mesh,
         template=template,
@@ -233,13 +214,13 @@ def samsegmesh2surf(
         output_priors=output_priors,
         invert_flag=invert_flag,
     )
-    return samsegmesh2surf_execute(params, execution)
+    return samsegmesh2surf_execute(params, runner)
 
 
 __all__ = [
     "SAMSEGMESH2SURF_METADATA",
     "Samsegmesh2surfOutputs",
-    "Samsegmesh2surfParameters",
     "samsegmesh2surf",
+    "samsegmesh2surf_execute",
     "samsegmesh2surf_params",
 ]

niwrap_freesurfer/freesurfer/sbtiv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SBTIV_METADATA = Metadata(
-    id="48b2c4316f4126f05735de6d4b50fba4dbe07310.boutiques",
+    id="2501dc56ac76a6c528e5cbe82bcd12ab097cecc2.boutiques",
     name="sbtiv",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ SBTIV_METADATA = Metadata(
 
 
 SbtivParameters = typing.TypedDict('SbtivParameters', {
-    "__STYXTYPE__": typing.Literal["sbtiv"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/sbtiv"]],
+    "input_file": InputPathType,
+    "output_file": typing.NotRequired[str | None],
+    "labels_file": typing.NotRequired[InputPathType | None],
+})
+SbtivParametersTagged = typing.TypedDict('SbtivParametersTagged', {
+    "@type": typing.Literal["freesurfer/sbtiv"],
     "input_file": InputPathType,
     "output_file": typing.NotRequired[str | None],
     "labels_file": 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 {
-        "sbtiv": sbtiv_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 {
-        "sbtiv": sbtiv_outputs,
-    }.get(t)
 
 
 class SbtivOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `sbtiv(...)`.
+    Output object returned when calling `SbtivParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def sbtiv_params(
     input_file: InputPathType,
     output_file: str | None = None,
     labels_file: InputPathType | None = None,
-) -> SbtivParameters:
+) -> SbtivParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def sbtiv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "sbtiv",
+        "@type": "freesurfer/sbtiv",
         "input_file": input_file,
     }
     if output_file is not None:
@@ -105,16 +79,16 @@ def sbtiv_cargs(
     """
     cargs = []
     cargs.append("sbtiv")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("output_file") is not None:
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("labels_file") is not None:
+    if params.get("labels_file", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("labels_file"))
+            execution.input_file(params.get("labels_file", None))
         ])
     return cargs
 
@@ -134,16 +108,18 @@ def sbtiv_outputs(
     """
     ret = SbtivOutputs(
         root=execution.output_file("."),
-        out_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        out_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def sbtiv_execute(
     params: SbtivParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SbtivOutputs:
     """
+    sbtiv
+    
     Tool to calculate the total intracranial volume of a subject by summing
     individual volumes computed by samseg.
     
@@ -153,10 +129,12 @@ def sbtiv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SbtivOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SBTIV_METADATA)
     params = execution.params(params)
     cargs = sbtiv_cargs(params, execution)
     ret = sbtiv_outputs(params, execution)
@@ -171,6 +149,8 @@ def sbtiv(
     runner: Runner | None = None,
 ) -> SbtivOutputs:
     """
+    sbtiv
+    
     Tool to calculate the total intracranial volume of a subject by summing
     individual volumes computed by samseg.
     
@@ -187,20 +167,18 @@ def sbtiv(
     Returns:
         NamedTuple of outputs (described in `SbtivOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SBTIV_METADATA)
     params = sbtiv_params(
         input_file=input_file,
         output_file=output_file,
         labels_file=labels_file,
     )
-    return sbtiv_execute(params, execution)
+    return sbtiv_execute(params, runner)
 
 
 __all__ = [
     "SBTIV_METADATA",
     "SbtivOutputs",
-    "SbtivParameters",
     "sbtiv",
+    "sbtiv_execute",
     "sbtiv_params",
 ]