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

niwrap_freesurfer/freesurfer/ventfix.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VENTFIX_METADATA = Metadata(
-    id="e71901d7b79bb5fd53811d2c81452b885bbecc11.boutiques",
+    id="06158b94512724cbe2e29b5e7e1c80b3bc5380d4.boutiques",
     name="ventfix",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ VENTFIX_METADATA = Metadata(
 
 
 VentfixParameters = typing.TypedDict('VentfixParameters', {
-    "__STYXTYPE__": typing.Literal["ventfix"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/ventfix"]],
+    "subject_dir": str,
+    "option1": typing.NotRequired[str | None],
+})
+VentfixParametersTagged = typing.TypedDict('VentfixParametersTagged', {
+    "@type": typing.Literal["freesurfer/ventfix"],
     "subject_dir": str,
     "option1": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ventfix": ventfix_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 {
-        "ventfix": ventfix_outputs,
-    }.get(t)
 
 
 class VentfixOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `ventfix(...)`.
+    Output object returned when calling `VentfixParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class VentfixOutputs(typing.NamedTuple):
 def ventfix_params(
     subject_dir: str,
     option1: str | None = None,
-) -> VentfixParameters:
+) -> VentfixParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def ventfix_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ventfix",
+        "@type": "freesurfer/ventfix",
         "subject_dir": subject_dir,
     }
     if option1 is not None:
@@ -99,11 +72,11 @@ def ventfix_cargs(
     """
     cargs = []
     cargs.append("ventfix")
-    cargs.append(params.get("subject_dir"))
-    if params.get("option1") is not None:
+    cargs.append(params.get("subject_dir", None))
+    if params.get("option1", None) is not None:
         cargs.extend([
             "--option1",
-            params.get("option1")
+            params.get("option1", None)
         ])
     return cargs
 
@@ -123,16 +96,18 @@ def ventfix_outputs(
     """
     ret = VentfixOutputs(
         root=execution.output_file("."),
-        fixed_ventricles=execution.output_file(params.get("subject_dir") + "/fixed_ventricles.nii.gz"),
+        fixed_ventricles=execution.output_file(params.get("subject_dir", None) + "/fixed_ventricles.nii.gz"),
     )
     return ret
 
 
 def ventfix_execute(
     params: VentfixParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VentfixOutputs:
     """
+    ventfix
+    
     Tool for fixing ventricles in MRI scans.
     
     Author: FreeSurfer Developers
@@ -141,10 +116,12 @@ def ventfix_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VentfixOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VENTFIX_METADATA)
     params = execution.params(params)
     cargs = ventfix_cargs(params, execution)
     ret = ventfix_outputs(params, execution)
@@ -158,6 +135,8 @@ def ventfix(
     runner: Runner | None = None,
 ) -> VentfixOutputs:
     """
+    ventfix
+    
     Tool for fixing ventricles in MRI scans.
     
     Author: FreeSurfer Developers
@@ -171,19 +150,17 @@ def ventfix(
     Returns:
         NamedTuple of outputs (described in `VentfixOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VENTFIX_METADATA)
     params = ventfix_params(
         subject_dir=subject_dir,
         option1=option1,
     )
-    return ventfix_execute(params, execution)
+    return ventfix_execute(params, runner)
 
 
 __all__ = [
     "VENTFIX_METADATA",
     "VentfixOutputs",
-    "VentfixParameters",
     "ventfix",
+    "ventfix_execute",
     "ventfix_params",
 ]

niwrap_freesurfer/freesurfer/vertexvol.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VERTEXVOL_METADATA = Metadata(
-    id="aedf6bfbc68d398b67ba8bf52f969278f2f9468d.boutiques",
+    id="8baaecedc11fde7b13401f036b6eb18a6aa86e88.boutiques",
     name="vertexvol",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ VERTEXVOL_METADATA = Metadata(
 
 
 VertexvolParameters = typing.TypedDict('VertexvolParameters', {
-    "__STYXTYPE__": typing.Literal["vertexvol"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/vertexvol"]],
+    "subject": str,
+    "left_hemisphere": bool,
+    "right_hemisphere": bool,
+    "output_file": typing.NotRequired[str | None],
+    "use_th3": bool,
+    "no_th3": bool,
+})
+VertexvolParametersTagged = typing.TypedDict('VertexvolParametersTagged', {
+    "@type": typing.Literal["freesurfer/vertexvol"],
     "subject": str,
     "left_hemisphere": bool,
     "right_hemisphere": bool,
@@ -22,43 +31,11 @@ VertexvolParameters = typing.TypedDict('VertexvolParameters', {
     "use_th3": bool,
     "no_th3": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "vertexvol": vertexvol_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 {
-        "vertexvol": vertexvol_outputs,
-    }.get(t)
 
 
 class VertexvolOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `vertexvol(...)`.
+    Output object returned when calling `VertexvolParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,10 +47,10 @@ def vertexvol_params(
     subject: str,
     left_hemisphere: bool = False,
     right_hemisphere: bool = False,
-    output_file: str | None = "?h.volume",
+    output_file: str | None = None,
     use_th3: bool = False,
     no_th3: bool = False,
-) -> VertexvolParameters:
+) -> VertexvolParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def vertexvol_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "vertexvol",
+        "@type": "freesurfer/vertexvol",
         "subject": subject,
         "left_hemisphere": left_hemisphere,
         "right_hemisphere": right_hemisphere,
@@ -117,20 +94,20 @@ def vertexvol_cargs(
     cargs.append("vertexvol")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("left_hemisphere"):
+    if params.get("left_hemisphere", False):
         cargs.append("--lh")
-    if params.get("right_hemisphere"):
+    if params.get("right_hemisphere", False):
         cargs.append("--rh")
-    if params.get("output_file") is not 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("use_th3"):
+    if params.get("use_th3", False):
         cargs.append("--th3")
-    if params.get("no_th3"):
+    if params.get("no_th3", False):
         cargs.append("--no-th3")
     return cargs
 
@@ -150,16 +127,18 @@ def vertexvol_outputs(
     """
     ret = VertexvolOutputs(
         root=execution.output_file("."),
-        output_volume_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        output_volume_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def vertexvol_execute(
     params: VertexvolParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VertexvolOutputs:
     """
+    vertexvol
+    
     Computes vertex-wise volume (and mid.area).
     
     Author: FreeSurfer Developers
@@ -168,10 +147,12 @@ def vertexvol_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VertexvolOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VERTEXVOL_METADATA)
     params = execution.params(params)
     cargs = vertexvol_cargs(params, execution)
     ret = vertexvol_outputs(params, execution)
@@ -183,12 +164,14 @@ def vertexvol(
     subject: str,
     left_hemisphere: bool = False,
     right_hemisphere: bool = False,
-    output_file: str | None = "?h.volume",
+    output_file: str | None = None,
     use_th3: bool = False,
     no_th3: bool = False,
     runner: Runner | None = None,
 ) -> VertexvolOutputs:
     """
+    vertexvol
+    
     Computes vertex-wise volume (and mid.area).
     
     Author: FreeSurfer Developers
@@ -206,8 +189,6 @@ def vertexvol(
     Returns:
         NamedTuple of outputs (described in `VertexvolOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VERTEXVOL_METADATA)
     params = vertexvol_params(
         subject=subject,
         left_hemisphere=left_hemisphere,
@@ -216,13 +197,13 @@ def vertexvol(
         use_th3=use_th3,
         no_th3=no_th3,
     )
-    return vertexvol_execute(params, execution)
+    return vertexvol_execute(params, runner)
 
 
 __all__ = [
     "VERTEXVOL_METADATA",
     "VertexvolOutputs",
-    "VertexvolParameters",
     "vertexvol",
+    "vertexvol_execute",
     "vertexvol_params",
 ]

niwrap_freesurfer/freesurfer/vno_match_check.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 VNO_MATCH_CHECK_METADATA = Metadata(
-    id="f8067972f626da6ba2d1f49f4d099ebfb3bccb87.boutiques",
+    id="9a3a5462fe2518cc3bd6acf304f950d94e93ceac.boutiques",
     name="vno_match_check",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ VNO_MATCH_CHECK_METADATA = Metadata(
 
 
 VnoMatchCheckParameters = typing.TypedDict('VnoMatchCheckParameters', {
-    "__STYXTYPE__": typing.Literal["vno_match_check"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/vno_match_check"]],
+    "subjid": str,
+    "debug": bool,
+    "right_hemi": bool,
+    "left_hemi": bool,
+})
+VnoMatchCheckParametersTagged = typing.TypedDict('VnoMatchCheckParametersTagged', {
+    "@type": typing.Literal["freesurfer/vno_match_check"],
     "subjid": str,
     "debug": bool,
     "right_hemi": bool,
     "left_hemi": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "vno_match_check": vno_match_check_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 VnoMatchCheckOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `vno_match_check(...)`.
+    Output object returned when calling `VnoMatchCheckParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def vno_match_check_params(
     debug: bool = False,
     right_hemi: bool = False,
     left_hemi: bool = False,
-) -> VnoMatchCheckParameters:
+) -> VnoMatchCheckParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def vno_match_check_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "vno_match_check",
+        "@type": "freesurfer/vno_match_check",
         "subjid": subjid,
         "debug": debug,
         "right_hemi": right_hemi,
@@ -103,12 +79,12 @@ def vno_match_check_cargs(
     """
     cargs = []
     cargs.append("vno_match_check")
-    cargs.append(params.get("subjid"))
-    if params.get("debug"):
+    cargs.append(params.get("subjid", None))
+    if params.get("debug", False):
         cargs.append("debug")
-    if params.get("right_hemi"):
+    if params.get("right_hemi", False):
         cargs.append("rh")
-    if params.get("left_hemi"):
+    if params.get("left_hemi", False):
         cargs.append("lh")
     return cargs
 
@@ -134,9 +110,11 @@ def vno_match_check_outputs(
 
 def vno_match_check_execute(
     params: VnoMatchCheckParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VnoMatchCheckOutputs:
     """
+    vno_match_check
+    
     Checks that all surfaces and surface data files for a subject have the same
     number of vertices.
     
@@ -146,10 +124,12 @@ def vno_match_check_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VnoMatchCheckOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(VNO_MATCH_CHECK_METADATA)
     params = execution.params(params)
     cargs = vno_match_check_cargs(params, execution)
     ret = vno_match_check_outputs(params, execution)
@@ -165,6 +145,8 @@ def vno_match_check(
     runner: Runner | None = None,
 ) -> VnoMatchCheckOutputs:
     """
+    vno_match_check
+    
     Checks that all surfaces and surface data files for a subject have the same
     number of vertices.
     
@@ -181,21 +163,19 @@ def vno_match_check(
     Returns:
         NamedTuple of outputs (described in `VnoMatchCheckOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(VNO_MATCH_CHECK_METADATA)
     params = vno_match_check_params(
         subjid=subjid,
         debug=debug,
         right_hemi=right_hemi,
         left_hemi=left_hemi,
     )
-    return vno_match_check_execute(params, execution)
+    return vno_match_check_execute(params, runner)
 
 
 __all__ = [
     "VNO_MATCH_CHECK_METADATA",
     "VnoMatchCheckOutputs",
-    "VnoMatchCheckParameters",
     "vno_match_check",
+    "vno_match_check_execute",
     "vno_match_check_params",
 ]