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

niwrap_freesurfer/freesurfer/jkgcatrain.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 JKGCATRAIN_METADATA = Metadata(
-    id="f73394990345946d6f0f0547594b7d0a8c67904f.boutiques",
+    id="2fc935b295a01c3e8c5075c012db63cd4ba471d7.boutiques",
     name="jkgcatrain",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ JKGCATRAIN_METADATA = Metadata(
 
 
 JkgcatrainParameters = typing.TypedDict('JkgcatrainParameters', {
-    "__STYXTYPE__": typing.Literal["jkgcatrain"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/jkgcatrain"]],
+    "gca_directory": str,
+    "iteration_number": typing.NotRequired[float | None],
+    "num_threads": typing.NotRequired[float | None],
+    "no_submit": bool,
+    "mail_flag": bool,
+})
+JkgcatrainParametersTagged = typing.TypedDict('JkgcatrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/jkgcatrain"],
     "gca_directory": str,
     "iteration_number": typing.NotRequired[float | None],
     "num_threads": typing.NotRequired[float | None],
     "no_submit": bool,
     "mail_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 {
-        "jkgcatrain": jkgcatrain_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 JkgcatrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `jkgcatrain(...)`.
+    Output object returned when calling `JkgcatrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,11 +41,11 @@ class JkgcatrainOutputs(typing.NamedTuple):
 
 def jkgcatrain_params(
     gca_directory: str,
-    iteration_number: float | None = 2,
+    iteration_number: float | None = None,
     num_threads: float | None = None,
     no_submit: bool = False,
     mail_flag: bool = False,
-) -> JkgcatrainParameters:
+) -> JkgcatrainParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +59,7 @@ def jkgcatrain_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "jkgcatrain",
+        "@type": "freesurfer/jkgcatrain",
         "gca_directory": gca_directory,
         "no_submit": no_submit,
         "mail_flag": mail_flag,
@@ -111,21 +88,21 @@ def jkgcatrain_cargs(
     cargs.append("jkgcatrain")
     cargs.extend([
         "--g",
-        params.get("gca_directory")
+        params.get("gca_directory", None)
     ])
-    if params.get("iteration_number") is not None:
+    if params.get("iteration_number", None) is not None:
         cargs.extend([
             "--iter",
-            str(params.get("iteration_number"))
+            str(params.get("iteration_number", None))
         ])
-    if params.get("num_threads") is not None:
+    if params.get("num_threads", None) is not None:
         cargs.extend([
             "--nthreads",
-            str(params.get("num_threads"))
+            str(params.get("num_threads", None))
         ])
-    if params.get("no_submit"):
+    if params.get("no_submit", False):
         cargs.append("--no-submit")
-    if params.get("mail_flag"):
+    if params.get("mail_flag", False):
         cargs.append("--pb-m")
     return cargs
 
@@ -151,9 +128,11 @@ def jkgcatrain_outputs(
 
 def jkgcatrain_execute(
     params: JkgcatrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> JkgcatrainOutputs:
     """
+    jkgcatrain
+    
     Jackknife training of GCA using existing output from gcatrain.
     
     Author: FreeSurfer Developers
@@ -162,10 +141,12 @@ def jkgcatrain_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `JkgcatrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(JKGCATRAIN_METADATA)
     params = execution.params(params)
     cargs = jkgcatrain_cargs(params, execution)
     ret = jkgcatrain_outputs(params, execution)
@@ -175,13 +156,15 @@ def jkgcatrain_execute(
 
 def jkgcatrain(
     gca_directory: str,
-    iteration_number: float | None = 2,
+    iteration_number: float | None = None,
     num_threads: float | None = None,
     no_submit: bool = False,
     mail_flag: bool = False,
     runner: Runner | None = None,
 ) -> JkgcatrainOutputs:
     """
+    jkgcatrain
+    
     Jackknife training of GCA using existing output from gcatrain.
     
     Author: FreeSurfer Developers
@@ -198,8 +181,6 @@ def jkgcatrain(
     Returns:
         NamedTuple of outputs (described in `JkgcatrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(JKGCATRAIN_METADATA)
     params = jkgcatrain_params(
         gca_directory=gca_directory,
         iteration_number=iteration_number,
@@ -207,13 +188,13 @@ def jkgcatrain(
         no_submit=no_submit,
         mail_flag=mail_flag,
     )
-    return jkgcatrain_execute(params, execution)
+    return jkgcatrain_execute(params, runner)
 
 
 __all__ = [
     "JKGCATRAIN_METADATA",
     "JkgcatrainOutputs",
-    "JkgcatrainParameters",
     "jkgcatrain",
+    "jkgcatrain_execute",
     "jkgcatrain_params",
 ]

niwrap_freesurfer/freesurfer/label2flat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL2FLAT_METADATA = Metadata(
-    id="90c34f8dd4c3992195ca9cfd336c415fc13321a8.boutiques",
+    id="7e626df817b368b3af64b2bf3dcc5e4844fd6510.boutiques",
     name="label2flat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ LABEL2FLAT_METADATA = Metadata(
 
 
 Label2flatParameters = typing.TypedDict('Label2flatParameters', {
-    "__STYXTYPE__": typing.Literal["label2flat"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/label2flat"]],
+    "subject_name": str,
+    "label_file": InputPathType,
+    "patch_file": InputPathType,
+    "output_file": str,
+})
+Label2flatParametersTagged = typing.TypedDict('Label2flatParametersTagged', {
+    "@type": typing.Literal["freesurfer/label2flat"],
     "subject_name": str,
     "label_file": InputPathType,
     "patch_file": InputPathType,
     "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 {
-        "label2flat": label2flat_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 {
-        "label2flat": label2flat_outputs,
-    }.get(t)
 
 
 class Label2flatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label2flat(...)`.
+    Output object returned when calling `Label2flatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def label2flat_params(
     label_file: InputPathType,
     patch_file: InputPathType,
     output_file: str,
-) -> Label2flatParameters:
+) -> Label2flatParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def label2flat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label2flat",
+        "@type": "freesurfer/label2flat",
         "subject_name": subject_name,
         "label_file": label_file,
         "patch_file": patch_file,
@@ -106,10 +81,10 @@ def label2flat_cargs(
     """
     cargs = []
     cargs.append("label2flat")
-    cargs.append(params.get("subject_name"))
-    cargs.append(execution.input_file(params.get("label_file")))
-    cargs.append(execution.input_file(params.get("patch_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(params.get("subject_name", None))
+    cargs.append(execution.input_file(params.get("label_file", None)))
+    cargs.append(execution.input_file(params.get("patch_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def label2flat_outputs(
     """
     ret = Label2flatOutputs(
         root=execution.output_file("."),
-        result_file=execution.output_file(params.get("output_file")),
+        result_file=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def label2flat_execute(
     params: Label2flatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Label2flatOutputs:
     """
+    label2flat
+    
     A tool used in FreeSurfer to process labeling and patch files.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def label2flat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Label2flatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL2FLAT_METADATA)
     params = execution.params(params)
     cargs = label2flat_cargs(params, execution)
     ret = label2flat_outputs(params, execution)
@@ -165,6 +144,8 @@ def label2flat(
     runner: Runner | None = None,
 ) -> Label2flatOutputs:
     """
+    label2flat
+    
     A tool used in FreeSurfer to process labeling and patch files.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def label2flat(
     Returns:
         NamedTuple of outputs (described in `Label2flatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL2FLAT_METADATA)
     params = label2flat_params(
         subject_name=subject_name,
         label_file=label_file,
         patch_file=patch_file,
         output_file=output_file,
     )
-    return label2flat_execute(params, execution)
+    return label2flat_execute(params, runner)
 
 
 __all__ = [
     "LABEL2FLAT_METADATA",
     "Label2flatOutputs",
-    "Label2flatParameters",
     "label2flat",
+    "label2flat_execute",
     "label2flat_params",
 ]

niwrap_freesurfer/freesurfer/label2patch.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 LABEL2PATCH_METADATA = Metadata(
-    id="1c4c1eb31d054d348645153cd56891912e1a70b1.boutiques",
+    id="209d95f6b0fb2b1a5399b2c8f80440646f5bda81.boutiques",
     name="label2patch",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,20 @@ LABEL2PATCH_METADATA = Metadata(
 
 
 Label2patchParameters = typing.TypedDict('Label2patchParameters', {
-    "__STYXTYPE__": typing.Literal["label2patch"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/label2patch"]],
+    "subject_name": str,
+    "hemisphere": str,
+    "label_file": InputPathType,
+    "output_patch": str,
+    "dilate": typing.NotRequired[float | None],
+    "erode": typing.NotRequired[float | None],
+    "close": typing.NotRequired[float | None],
+    "subjects_dir": typing.NotRequired[str | None],
+    "surface_name": typing.NotRequired[str | None],
+    "write_surface": bool,
+})
+Label2patchParametersTagged = typing.TypedDict('Label2patchParametersTagged', {
+    "@type": typing.Literal["freesurfer/label2patch"],
     "subject_name": str,
     "hemisphere": str,
     "label_file": InputPathType,
@@ -26,42 +39,11 @@ Label2patchParameters = typing.TypedDict('Label2patchParameters', {
     "surface_name": typing.NotRequired[str | None],
     "write_surface": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "label2patch": label2patch_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 Label2patchOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `label2patch(...)`.
+    Output object returned when calling `Label2patchParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def label2patch_params(
     subjects_dir: str | None = None,
     surface_name: str | None = None,
     write_surface: bool = False,
-) -> Label2patchParameters:
+) -> Label2patchParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +81,7 @@ def label2patch_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "label2patch",
+        "@type": "freesurfer/label2patch",
         "subject_name": subject_name,
         "hemisphere": hemisphere,
         "label_file": label_file,
@@ -134,36 +116,36 @@ def label2patch_cargs(
     """
     cargs = []
     cargs.append("label2patch")
-    cargs.append(params.get("subject_name"))
-    cargs.append(params.get("hemisphere"))
-    cargs.append(execution.input_file(params.get("label_file")))
-    cargs.append(params.get("output_patch"))
-    if params.get("dilate") is not None:
+    cargs.append(params.get("subject_name", None))
+    cargs.append(params.get("hemisphere", None))
+    cargs.append(execution.input_file(params.get("label_file", None)))
+    cargs.append(params.get("output_patch", None))
+    if params.get("dilate", None) is not None:
         cargs.extend([
             "-dilate",
-            str(params.get("dilate"))
+            str(params.get("dilate", None))
         ])
-    if params.get("erode") is not None:
+    if params.get("erode", None) is not None:
         cargs.extend([
             "-erode",
-            str(params.get("erode"))
+            str(params.get("erode", None))
         ])
-    if params.get("close") is not None:
+    if params.get("close", None) is not None:
         cargs.extend([
             "-close",
-            str(params.get("close"))
+            str(params.get("close", None))
         ])
-    if params.get("subjects_dir") is not None:
+    if params.get("subjects_dir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("subjects_dir")
+            params.get("subjects_dir", None)
         ])
-    if params.get("surface_name") is not None:
+    if params.get("surface_name", None) is not None:
         cargs.extend([
             "-surf",
-            params.get("surface_name")
+            params.get("surface_name", None)
         ])
-    if params.get("write_surface"):
+    if params.get("write_surface", False):
         cargs.append("-writesurf")
     return cargs
 
@@ -189,9 +171,11 @@ def label2patch_outputs(
 
 def label2patch_execute(
     params: Label2patchParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Label2patchOutputs:
     """
+    label2patch
+    
     Utility to create patches from label files in Freesurfer.
     
     Author: FreeSurfer Developers
@@ -200,10 +184,12 @@ def label2patch_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Label2patchOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(LABEL2PATCH_METADATA)
     params = execution.params(params)
     cargs = label2patch_cargs(params, execution)
     ret = label2patch_outputs(params, execution)
@@ -225,6 +211,8 @@ def label2patch(
     runner: Runner | None = None,
 ) -> Label2patchOutputs:
     """
+    label2patch
+    
     Utility to create patches from label files in Freesurfer.
     
     Author: FreeSurfer Developers
@@ -248,8 +236,6 @@ def label2patch(
     Returns:
         NamedTuple of outputs (described in `Label2patchOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(LABEL2PATCH_METADATA)
     params = label2patch_params(
         subject_name=subject_name,
         hemisphere=hemisphere,
@@ -262,13 +248,13 @@ def label2patch(
         surface_name=surface_name,
         write_surface=write_surface,
     )
-    return label2patch_execute(params, execution)
+    return label2patch_execute(params, runner)
 
 
 __all__ = [
     "LABEL2PATCH_METADATA",
     "Label2patchOutputs",
-    "Label2patchParameters",
     "label2patch",
+    "label2patch_execute",
     "label2patch_params",
 ]