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

niwrap_freesurfer/freesurfer/fname2ext.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FNAME2EXT_METADATA = Metadata(
-    id="cdbc3b779525039eaecbc00609f9a994c8dfa840.boutiques",
+    id="39a88dee540ee5afde8c4b7b82afdc6f01ed6a37.boutiques",
     name="fname2ext",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,18 @@ FNAME2EXT_METADATA = Metadata(
 
 
 Fname2extParameters = typing.TypedDict('Fname2extParameters', {
-    "__STYXTYPE__": typing.Literal["fname2ext"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fname2ext"]],
+    "filename": str,
+})
+Fname2extParametersTagged = typing.TypedDict('Fname2extParametersTagged', {
+    "@type": typing.Literal["freesurfer/fname2ext"],
     "filename": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fname2ext": fname2ext_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 {
-        "fname2ext": fname2ext_outputs,
-    }.get(t)
 
 
 class Fname2extOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fname2ext(...)`.
+    Output object returned when calling `Fname2extParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class Fname2extOutputs(typing.NamedTuple):
 
 def fname2ext_params(
     filename: str,
-) -> Fname2extParameters:
+) -> Fname2extParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +46,7 @@ def fname2ext_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fname2ext",
+        "@type": "freesurfer/fname2ext",
         "filename": filename,
     }
     return params
@@ -95,7 +67,7 @@ def fname2ext_cargs(
     """
     cargs = []
     cargs.append("fname2ext")
-    cargs.append(params.get("filename"))
+    cargs.append(params.get("filename", None))
     return cargs
 
 
@@ -121,9 +93,11 @@ def fname2ext_outputs(
 
 def fname2ext_execute(
     params: Fname2extParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fname2extOutputs:
     """
+    fname2ext
+    
     Converts the name of a file to its extension.
     
     Author: FreeSurfer Developers
@@ -132,10 +106,12 @@ def fname2ext_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fname2extOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FNAME2EXT_METADATA)
     params = execution.params(params)
     cargs = fname2ext_cargs(params, execution)
     ret = fname2ext_outputs(params, execution)
@@ -148,6 +124,8 @@ def fname2ext(
     runner: Runner | None = None,
 ) -> Fname2extOutputs:
     """
+    fname2ext
+    
     Converts the name of a file to its extension.
     
     Author: FreeSurfer Developers
@@ -161,18 +139,16 @@ def fname2ext(
     Returns:
         NamedTuple of outputs (described in `Fname2extOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FNAME2EXT_METADATA)
     params = fname2ext_params(
         filename=filename,
     )
-    return fname2ext_execute(params, execution)
+    return fname2ext_execute(params, runner)
 
 
 __all__ = [
     "FNAME2EXT_METADATA",
     "Fname2extOutputs",
-    "Fname2extParameters",
     "fname2ext",
+    "fname2ext_execute",
     "fname2ext_params",
 ]

niwrap_freesurfer/freesurfer/fname2stem.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FNAME2STEM_METADATA = Metadata(
-    id="94f87797696ba85f60d558b2cd4d3fefe8915133.boutiques",
+    id="618f3f567ece6c5824fca1deb74adb629723f532.boutiques",
     name="fname2stem",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ FNAME2STEM_METADATA = Metadata(
 
 
 Fname2stemParameters = typing.TypedDict('Fname2stemParameters', {
-    "__STYXTYPE__": typing.Literal["fname2stem"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fname2stem"]],
+    "filename": str,
+})
+Fname2stemParametersTagged = typing.TypedDict('Fname2stemParametersTagged', {
+    "@type": typing.Literal["freesurfer/fname2stem"],
     "filename": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fname2stem": fname2stem_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 Fname2stemOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fname2stem(...)`.
+    Output object returned when calling `Fname2stemParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class Fname2stemOutputs(typing.NamedTuple):
 
 def fname2stem_params(
     filename: str,
-) -> Fname2stemParameters:
+) -> Fname2stemParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def fname2stem_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fname2stem",
+        "@type": "freesurfer/fname2stem",
         "filename": filename,
     }
     return params
@@ -92,7 +65,7 @@ def fname2stem_cargs(
     """
     cargs = []
     cargs.append("fname2stem")
-    cargs.append(params.get("filename"))
+    cargs.append(params.get("filename", None))
     return cargs
 
 
@@ -117,9 +90,11 @@ def fname2stem_outputs(
 
 def fname2stem_execute(
     params: Fname2stemParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Fname2stemOutputs:
     """
+    fname2stem
+    
     Converts the name of a file to a stem. Example: f.mgh, f.nii, f.nii.gz would
     return f.
     
@@ -129,10 +104,12 @@ def fname2stem_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Fname2stemOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FNAME2STEM_METADATA)
     params = execution.params(params)
     cargs = fname2stem_cargs(params, execution)
     ret = fname2stem_outputs(params, execution)
@@ -145,6 +122,8 @@ def fname2stem(
     runner: Runner | None = None,
 ) -> Fname2stemOutputs:
     """
+    fname2stem
+    
     Converts the name of a file to a stem. Example: f.mgh, f.nii, f.nii.gz would
     return f.
     
@@ -159,18 +138,16 @@ def fname2stem(
     Returns:
         NamedTuple of outputs (described in `Fname2stemOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FNAME2STEM_METADATA)
     params = fname2stem_params(
         filename=filename,
     )
-    return fname2stem_execute(params, execution)
+    return fname2stem_execute(params, runner)
 
 
 __all__ = [
     "FNAME2STEM_METADATA",
     "Fname2stemOutputs",
-    "Fname2stemParameters",
     "fname2stem",
+    "fname2stem_execute",
     "fname2stem_params",
 ]

niwrap_freesurfer/freesurfer/freeview.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FREEVIEW_METADATA = Metadata(
-    id="c7a33420dcdb44d944cc751c512e7e743300b534.boutiques",
+    id="d816f0d3dba7c6ee822421423d6d161df3fed35f.boutiques",
     name="freeview",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ FREEVIEW_METADATA = Metadata(
 
 
 FreeviewParameters = typing.TypedDict('FreeviewParameters', {
-    "__STYXTYPE__": typing.Literal["freeview"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/freeview"]],
+    "args": typing.NotRequired[str | None],
+})
+FreeviewParametersTagged = typing.TypedDict('FreeviewParametersTagged', {
+    "@type": typing.Literal["freesurfer/freeview"],
     "args": 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 {
-        "freeview": freeview_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 FreeviewOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `freeview(...)`.
+    Output object returned when calling `FreeviewParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class FreeviewOutputs(typing.NamedTuple):
 
 def freeview_params(
     args: str | None = None,
-) -> FreeviewParameters:
+) -> FreeviewParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def freeview_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "freeview",
+        "@type": "freesurfer/freeview",
     }
     if args is not None:
         params["args"] = args
@@ -92,8 +65,8 @@ def freeview_cargs(
     """
     cargs = []
     cargs.append("freeview")
-    if params.get("args") is not None:
-        cargs.append(params.get("args"))
+    if params.get("args", None) is not None:
+        cargs.append(params.get("args", None))
     return cargs
 
 
@@ -118,9 +91,11 @@ def freeview_outputs(
 
 def freeview_execute(
     params: FreeviewParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FreeviewOutputs:
     """
+    freeview
+    
     Freeview is a 3D/2D brain visualization tool.
     
     Author: FreeSurfer Developers
@@ -129,10 +104,12 @@ def freeview_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FreeviewOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FREEVIEW_METADATA)
     params = execution.params(params)
     cargs = freeview_cargs(params, execution)
     ret = freeview_outputs(params, execution)
@@ -145,6 +122,8 @@ def freeview(
     runner: Runner | None = None,
 ) -> FreeviewOutputs:
     """
+    freeview
+    
     Freeview is a 3D/2D brain visualization tool.
     
     Author: FreeSurfer Developers
@@ -157,18 +136,16 @@ def freeview(
     Returns:
         NamedTuple of outputs (described in `FreeviewOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FREEVIEW_METADATA)
     params = freeview_params(
         args=args,
     )
-    return freeview_execute(params, execution)
+    return freeview_execute(params, runner)
 
 
 __all__ = [
     "FREEVIEW_METADATA",
     "FreeviewOutputs",
-    "FreeviewParameters",
     "freeview",
+    "freeview_execute",
     "freeview_params",
 ]

niwrap_freesurfer/freesurfer/fs_check_version.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FS_CHECK_VERSION_METADATA = Metadata(
-    id="ac2742ad52c0ec9531a37b18769e9a1969669e97.boutiques",
+    id="64bf79bdbdbb8ec6bf819241f1e5d3ea6e450803.boutiques",
     name="fs-check-version",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ FS_CHECK_VERSION_METADATA = Metadata(
 
 
 FsCheckVersionParameters = typing.TypedDict('FsCheckVersionParameters', {
-    "__STYXTYPE__": typing.Literal["fs-check-version"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/fs-check-version"]],
+    "subjects_dir": str,
+    "outfile": str,
+    "subject": typing.NotRequired[str | None],
+    "require_match": bool,
+    "no_require_match": bool,
+    "test": bool,
+    "test_debug": bool,
+})
+FsCheckVersionParametersTagged = typing.TypedDict('FsCheckVersionParametersTagged', {
+    "@type": typing.Literal["freesurfer/fs-check-version"],
     "subjects_dir": str,
     "outfile": str,
     "subject": typing.NotRequired[str | None],
@@ -23,43 +33,11 @@ FsCheckVersionParameters = typing.TypedDict('FsCheckVersionParameters', {
     "test": bool,
     "test_debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fs-check-version": fs_check_version_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 {
-        "fs-check-version": fs_check_version_outputs,
-    }.get(t)
 
 
 class FsCheckVersionOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fs_check_version(...)`.
+    Output object returned when calling `FsCheckVersionParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def fs_check_version_params(
     no_require_match: bool = False,
     test: bool = False,
     test_debug: bool = False,
-) -> FsCheckVersionParameters:
+) -> FsCheckVersionParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def fs_check_version_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fs-check-version",
+        "@type": "freesurfer/fs-check-version",
         "subjects_dir": subjects_dir,
         "outfile": outfile,
         "require_match": require_match,
@@ -121,24 +99,24 @@ def fs_check_version_cargs(
     cargs.append("fs-check-version")
     cargs.extend([
         "--sd",
-        params.get("subjects_dir")
+        params.get("subjects_dir", None)
     ])
     cargs.extend([
         "--o",
-        params.get("outfile")
+        params.get("outfile", None)
     ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
-    if params.get("require_match"):
+    if params.get("require_match", False):
         cargs.append("--require-match")
-    if params.get("no_require_match"):
+    if params.get("no_require_match", False):
         cargs.append("--no-require-match")
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("--test")
-    if params.get("test_debug"):
+    if params.get("test_debug", False):
         cargs.append("--test-debug")
     return cargs
 
@@ -158,16 +136,18 @@ def fs_check_version_outputs(
     """
     ret = FsCheckVersionOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("outfile")),
+        output_file=execution.output_file(params.get("outfile", None)),
     )
     return ret
 
 
 def fs_check_version_execute(
     params: FsCheckVersionParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsCheckVersionOutputs:
     """
+    fs-check-version
+    
     Script to manage which version of FreeSurfer can be used to analyze data
     ensuring consistency with the desired version.
     
@@ -177,10 +157,12 @@ def fs_check_version_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsCheckVersionOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FS_CHECK_VERSION_METADATA)
     params = execution.params(params)
     cargs = fs_check_version_cargs(params, execution)
     ret = fs_check_version_outputs(params, execution)
@@ -199,6 +181,8 @@ def fs_check_version(
     runner: Runner | None = None,
 ) -> FsCheckVersionOutputs:
     """
+    fs-check-version
+    
     Script to manage which version of FreeSurfer can be used to analyze data
     ensuring consistency with the desired version.
     
@@ -218,8 +202,6 @@ def fs_check_version(
     Returns:
         NamedTuple of outputs (described in `FsCheckVersionOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FS_CHECK_VERSION_METADATA)
     params = fs_check_version_params(
         subjects_dir=subjects_dir,
         outfile=outfile,
@@ -229,13 +211,13 @@ def fs_check_version(
         test=test,
         test_debug=test_debug,
     )
-    return fs_check_version_execute(params, execution)
+    return fs_check_version_execute(params, runner)
 
 
 __all__ = [
     "FS_CHECK_VERSION_METADATA",
     "FsCheckVersionOutputs",
-    "FsCheckVersionParameters",
     "fs_check_version",
+    "fs_check_version_execute",
     "fs_check_version_params",
 ]