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

niwrap_freesurfer/freesurfer/test_tutorials_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TEST_TUTORIALS_SH_METADATA = Metadata(
-    id="9883254460c717895085469ee6ef3030faa9e4a9.boutiques",
+    id="8600c995e41717949562ed2ff10d2bfc56126013.boutiques",
     name="test_tutorials.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ TEST_TUTORIALS_SH_METADATA = Metadata(
 
 
 TestTutorialsShParameters = typing.TypedDict('TestTutorialsShParameters', {
-    "__STYXTYPE__": typing.Literal["test_tutorials.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/test_tutorials.sh"]],
+    "all_tutorials": bool,
+    "quick_test": bool,
+    "auto_quit_freeview": bool,
+    "skip_all_guis": bool,
+    "skip_tk_guis": bool,
+    "skip_qdec_guis": bool,
+    "individual_subject": bool,
+    "troubleshooting": bool,
+    "group_analysis": bool,
+    "qdec": bool,
+    "longitudinal": bool,
+    "roi_analysis": bool,
+    "diffusion": bool,
+    "tracula": bool,
+    "fsfast": bool,
+    "multimodal": bool,
+})
+TestTutorialsShParametersTagged = typing.TypedDict('TestTutorialsShParametersTagged', {
+    "@type": typing.Literal["freesurfer/test_tutorials.sh"],
     "all_tutorials": bool,
     "quick_test": bool,
     "auto_quit_freeview": bool,
@@ -32,42 +51,11 @@ TestTutorialsShParameters = typing.TypedDict('TestTutorialsShParameters', {
     "fsfast": bool,
     "multimodal": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "test_tutorials.sh": test_tutorials_sh_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 TestTutorialsShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `test_tutorials_sh(...)`.
+    Output object returned when calling `TestTutorialsShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -90,7 +78,7 @@ def test_tutorials_sh_params(
     tracula: bool = False,
     fsfast: bool = False,
     multimodal: bool = False,
-) -> TestTutorialsShParameters:
+) -> TestTutorialsShParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +105,7 @@ def test_tutorials_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "test_tutorials.sh",
+        "@type": "freesurfer/test_tutorials.sh",
         "all_tutorials": all_tutorials,
         "quick_test": quick_test,
         "auto_quit_freeview": auto_quit_freeview,
@@ -153,37 +141,37 @@ def test_tutorials_sh_cargs(
     """
     cargs = []
     cargs.append("test_tutorials.sh")
-    if params.get("all_tutorials"):
+    if params.get("all_tutorials", False):
         cargs.append("-all")
-    if params.get("quick_test"):
+    if params.get("quick_test", False):
         cargs.append("-quick")
-    if params.get("auto_quit_freeview"):
+    if params.get("auto_quit_freeview", False):
         cargs.append("-auto_quit_freeview")
-    if params.get("skip_all_guis"):
+    if params.get("skip_all_guis", False):
         cargs.append("-skip_all_guis")
-    if params.get("skip_tk_guis"):
+    if params.get("skip_tk_guis", False):
         cargs.append("-skip_tk_guis")
-    if params.get("skip_qdec_guis"):
+    if params.get("skip_qdec_guis", False):
         cargs.append("-skip_qdec_guis")
-    if params.get("individual_subject"):
+    if params.get("individual_subject", False):
         cargs.append("-individual_subject")
-    if params.get("troubleshooting"):
+    if params.get("troubleshooting", False):
         cargs.append("-troubleshooting")
-    if params.get("group_analysis"):
+    if params.get("group_analysis", False):
         cargs.append("-group_analysis")
-    if params.get("qdec"):
+    if params.get("qdec", False):
         cargs.append("-qdec")
-    if params.get("longitudinal"):
+    if params.get("longitudinal", False):
         cargs.append("-longitudinal")
-    if params.get("roi_analysis"):
+    if params.get("roi_analysis", False):
         cargs.append("-roi_analysis")
-    if params.get("diffusion"):
+    if params.get("diffusion", False):
         cargs.append("-diffusion")
-    if params.get("tracula"):
+    if params.get("tracula", False):
         cargs.append("-tracula")
-    if params.get("fsfast"):
+    if params.get("fsfast", False):
         cargs.append("-fsfast")
-    if params.get("multimodal"):
+    if params.get("multimodal", False):
         cargs.append("-multimodal")
     return cargs
 
@@ -209,9 +197,11 @@ def test_tutorials_sh_outputs(
 
 def test_tutorials_sh_execute(
     params: TestTutorialsShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TestTutorialsShOutputs:
     """
+    test_tutorials.sh
+    
     A script to run various tutorial commands, with options for skipping GUI
     components and focusing on specific tutorials.
     
@@ -221,10 +211,12 @@ def test_tutorials_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TestTutorialsShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TEST_TUTORIALS_SH_METADATA)
     params = execution.params(params)
     cargs = test_tutorials_sh_cargs(params, execution)
     ret = test_tutorials_sh_outputs(params, execution)
@@ -252,6 +244,8 @@ def test_tutorials_sh(
     runner: Runner | None = None,
 ) -> TestTutorialsShOutputs:
     """
+    test_tutorials.sh
+    
     A script to run various tutorial commands, with options for skipping GUI
     components and focusing on specific tutorials.
     
@@ -282,8 +276,6 @@ def test_tutorials_sh(
     Returns:
         NamedTuple of outputs (described in `TestTutorialsShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TEST_TUTORIALS_SH_METADATA)
     params = test_tutorials_sh_params(
         all_tutorials=all_tutorials,
         quick_test=quick_test,
@@ -302,13 +294,13 @@ def test_tutorials_sh(
         fsfast=fsfast,
         multimodal=multimodal,
     )
-    return test_tutorials_sh_execute(params, execution)
+    return test_tutorials_sh_execute(params, runner)
 
 
 __all__ = [
     "TEST_TUTORIALS_SH_METADATA",
     "TestTutorialsShOutputs",
-    "TestTutorialsShParameters",
     "test_tutorials_sh",
+    "test_tutorials_sh_execute",
     "test_tutorials_sh_params",
 ]

niwrap_freesurfer/freesurfer/thickdiffmap.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 THICKDIFFMAP_METADATA = Metadata(
-    id="386d35dd120f181e0cd722b783b2ab7dab134ec4.boutiques",
+    id="3d6eab27a99149bcf829df0f8a5e86635a6ed4d0.boutiques",
     name="thickdiffmap",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ THICKDIFFMAP_METADATA = Metadata(
 
 
 ThickdiffmapParameters = typing.TypedDict('ThickdiffmapParameters', {
-    "__STYXTYPE__": typing.Literal["thickdiffmap"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/thickdiffmap"]],
+    "subjscan1": InputPathType,
+    "subjscan2": InputPathType,
+    "commonsubj": str,
+    "hemi": str,
+    "steps": typing.NotRequired[list[str] | None],
+})
+ThickdiffmapParametersTagged = typing.TypedDict('ThickdiffmapParametersTagged', {
+    "@type": typing.Literal["freesurfer/thickdiffmap"],
     "subjscan1": InputPathType,
     "subjscan2": InputPathType,
     "commonsubj": str,
     "hemi": str,
     "steps": typing.NotRequired[list[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 {
-        "thickdiffmap": thickdiffmap_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 ThickdiffmapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `thickdiffmap(...)`.
+    Output object returned when calling `ThickdiffmapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def thickdiffmap_params(
     commonsubj: str,
     hemi: str,
     steps: list[str] | None = None,
-) -> ThickdiffmapParameters:
+) -> ThickdiffmapParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +59,7 @@ def thickdiffmap_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "thickdiffmap",
+        "@type": "freesurfer/thickdiffmap",
         "subjscan1": subjscan1,
         "subjscan2": subjscan2,
         "commonsubj": commonsubj,
@@ -108,12 +85,12 @@ def thickdiffmap_cargs(
     """
     cargs = []
     cargs.append("thickdiffmap")
-    cargs.append(execution.input_file(params.get("subjscan1")))
-    cargs.append(execution.input_file(params.get("subjscan2")))
-    cargs.append(params.get("commonsubj"))
-    cargs.append(params.get("hemi"))
-    if params.get("steps") is not None:
-        cargs.extend(params.get("steps"))
+    cargs.append(execution.input_file(params.get("subjscan1", None)))
+    cargs.append(execution.input_file(params.get("subjscan2", None)))
+    cargs.append(params.get("commonsubj", None))
+    cargs.append(params.get("hemi", None))
+    if params.get("steps", None) is not None:
+        cargs.extend(params.get("steps", None))
     return cargs
 
 
@@ -138,9 +115,11 @@ def thickdiffmap_outputs(
 
 def thickdiffmap_execute(
     params: ThickdiffmapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ThickdiffmapOutputs:
     """
+    thickdiffmap
+    
     Compute and analyze cortical thickness difference maps.
     
     Author: FreeSurfer Developers
@@ -149,10 +128,12 @@ def thickdiffmap_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ThickdiffmapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(THICKDIFFMAP_METADATA)
     params = execution.params(params)
     cargs = thickdiffmap_cargs(params, execution)
     ret = thickdiffmap_outputs(params, execution)
@@ -169,6 +150,8 @@ def thickdiffmap(
     runner: Runner | None = None,
 ) -> ThickdiffmapOutputs:
     """
+    thickdiffmap
+    
     Compute and analyze cortical thickness difference maps.
     
     Author: FreeSurfer Developers
@@ -185,8 +168,6 @@ def thickdiffmap(
     Returns:
         NamedTuple of outputs (described in `ThickdiffmapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(THICKDIFFMAP_METADATA)
     params = thickdiffmap_params(
         subjscan1=subjscan1,
         subjscan2=subjscan2,
@@ -194,13 +175,13 @@ def thickdiffmap(
         hemi=hemi,
         steps=steps,
     )
-    return thickdiffmap_execute(params, execution)
+    return thickdiffmap_execute(params, runner)
 
 
 __all__ = [
     "THICKDIFFMAP_METADATA",
     "ThickdiffmapOutputs",
-    "ThickdiffmapParameters",
     "thickdiffmap",
+    "thickdiffmap_execute",
     "thickdiffmap_params",
 ]

niwrap_freesurfer/freesurfer/tkmedit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TKMEDIT_METADATA = Metadata(
-    id="215f4c63f4d1d614a5f6ddc04a121949f2f19d48.boutiques",
+    id="1ef038e572c241b77b39724dc6c02177b89b4cc1.boutiques",
     name="tkmedit",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ TKMEDIT_METADATA = Metadata(
 
 
 TkmeditParameters = typing.TypedDict('TkmeditParameters', {
-    "__STYXTYPE__": typing.Literal["tkmedit"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/tkmedit"]],
+    "input_volume": InputPathType,
+    "options": typing.NotRequired[str | None],
+})
+TkmeditParametersTagged = typing.TypedDict('TkmeditParametersTagged', {
+    "@type": typing.Literal["freesurfer/tkmedit"],
     "input_volume": InputPathType,
     "options": 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 {
-        "tkmedit": tkmedit_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 TkmeditOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tkmedit(...)`.
+    Output object returned when calling `TkmeditParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class TkmeditOutputs(typing.NamedTuple):
 def tkmedit_params(
     input_volume: InputPathType,
     options: str | None = None,
-) -> TkmeditParameters:
+) -> TkmeditParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def tkmedit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tkmedit",
+        "@type": "freesurfer/tkmedit",
         "input_volume": input_volume,
     }
     if options is not None:
@@ -96,9 +70,9 @@ def tkmedit_cargs(
     """
     cargs = []
     cargs.append("tkmedit")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    if params.get("options") is not None:
-        cargs.append(params.get("options"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    if params.get("options", None) is not None:
+        cargs.append(params.get("options", None))
     return cargs
 
 
@@ -123,12 +97,14 @@ def tkmedit_outputs(
 
 def tkmedit_execute(
     params: TkmeditParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TkmeditOutputs:
     """
+    tkmedit
+    
     tkmedit is a multi-functional imaging tool for viewing and editing surface
-    models and volumes in FreeSurfer. It provides a GUI representation of volumetric
-    data and facilitates modifications in the data.
+    models and volumes in FreeSurfer. It provides a GUI representation of
+    volumetric data and facilitates modifications in the data.
     
     Author: FreeSurfer Developers
     
@@ -136,10 +112,12 @@ def tkmedit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TkmeditOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TKMEDIT_METADATA)
     params = execution.params(params)
     cargs = tkmedit_cargs(params, execution)
     ret = tkmedit_outputs(params, execution)
@@ -153,9 +131,11 @@ def tkmedit(
     runner: Runner | None = None,
 ) -> TkmeditOutputs:
     """
+    tkmedit
+    
     tkmedit is a multi-functional imaging tool for viewing and editing surface
-    models and volumes in FreeSurfer. It provides a GUI representation of volumetric
-    data and facilitates modifications in the data.
+    models and volumes in FreeSurfer. It provides a GUI representation of
+    volumetric data and facilitates modifications in the data.
     
     Author: FreeSurfer Developers
     
@@ -168,19 +148,17 @@ def tkmedit(
     Returns:
         NamedTuple of outputs (described in `TkmeditOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TKMEDIT_METADATA)
     params = tkmedit_params(
         input_volume=input_volume,
         options=options,
     )
-    return tkmedit_execute(params, execution)
+    return tkmedit_execute(params, runner)
 
 
 __all__ = [
     "TKMEDIT_METADATA",
     "TkmeditOutputs",
-    "TkmeditParameters",
     "tkmedit",
+    "tkmedit_execute",
     "tkmedit_params",
 ]