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

niwrap_freesurfer/freesurfer/talairach_afd.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALAIRACH_AFD_METADATA = Metadata(
-    id="77c3251247380212cdbe7973621a64bff1fd5736.boutiques",
+    id="e308ee40df66730e1c82a9701897a920e168ea5e.boutiques",
     name="talairach_afd",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ TALAIRACH_AFD_METADATA = Metadata(
 
 
 TalairachAfdParameters = typing.TypedDict('TalairachAfdParameters', {
-    "__STYXTYPE__": typing.Literal["talairach_afd"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/talairach_afd"]],
+    "subject_name": typing.NotRequired[str | None],
+    "xfm_file": typing.NotRequired[InputPathType | None],
+    "p_value_threshold": typing.NotRequired[float | None],
+    "afd_directory": typing.NotRequired[str | None],
+    "verbose": bool,
+})
+TalairachAfdParametersTagged = typing.TypedDict('TalairachAfdParametersTagged', {
+    "@type": typing.Literal["freesurfer/talairach_afd"],
     "subject_name": typing.NotRequired[str | None],
     "xfm_file": typing.NotRequired[InputPathType | None],
     "p_value_threshold": typing.NotRequired[float | None],
     "afd_directory": typing.NotRequired[str | None],
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "talairach_afd": talairach_afd_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 TalairachAfdOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `talairach_afd(...)`.
+    Output object returned when calling `TalairachAfdParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,10 +42,10 @@ class TalairachAfdOutputs(typing.NamedTuple):
 def talairach_afd_params(
     subject_name: str | None = None,
     xfm_file: InputPathType | None = None,
-    p_value_threshold: float | None = 0.01,
+    p_value_threshold: float | None = None,
     afd_directory: str | None = None,
     verbose: bool = False,
-) -> TalairachAfdParameters:
+) -> TalairachAfdParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +60,7 @@ def talairach_afd_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "talairach_afd",
+        "@type": "freesurfer/talairach_afd",
         "verbose": verbose,
     }
     if subject_name is not None:
@@ -112,27 +89,27 @@ def talairach_afd_cargs(
     """
     cargs = []
     cargs.append("talairach_afd")
-    if params.get("subject_name") is not None:
+    if params.get("subject_name", None) is not None:
         cargs.extend([
             "-subj",
-            params.get("subject_name")
+            params.get("subject_name", None)
         ])
-    if params.get("xfm_file") is not None:
+    if params.get("xfm_file", None) is not None:
         cargs.extend([
             "-xfm",
-            execution.input_file(params.get("xfm_file"))
+            execution.input_file(params.get("xfm_file", None))
         ])
-    if params.get("p_value_threshold") is not None:
+    if params.get("p_value_threshold", None) is not None:
         cargs.extend([
             "-T",
-            str(params.get("p_value_threshold"))
+            str(params.get("p_value_threshold", None))
         ])
-    if params.get("afd_directory") is not None:
+    if params.get("afd_directory", None) is not None:
         cargs.extend([
             "-afd",
-            params.get("afd_directory")
+            params.get("afd_directory", None)
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-V")
     return cargs
 
@@ -158,9 +135,11 @@ def talairach_afd_outputs(
 
 def talairach_afd_execute(
     params: TalairachAfdParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalairachAfdOutputs:
     """
+    talairach_afd
+    
     Detects Talairach alignment failures.
     
     Author: FreeSurfer Developers
@@ -169,10 +148,12 @@ def talairach_afd_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalairachAfdOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TALAIRACH_AFD_METADATA)
     params = execution.params(params)
     cargs = talairach_afd_cargs(params, execution)
     ret = talairach_afd_outputs(params, execution)
@@ -183,12 +164,14 @@ def talairach_afd_execute(
 def talairach_afd(
     subject_name: str | None = None,
     xfm_file: InputPathType | None = None,
-    p_value_threshold: float | None = 0.01,
+    p_value_threshold: float | None = None,
     afd_directory: str | None = None,
     verbose: bool = False,
     runner: Runner | None = None,
 ) -> TalairachAfdOutputs:
     """
+    talairach_afd
+    
     Detects Talairach alignment failures.
     
     Author: FreeSurfer Developers
@@ -206,8 +189,6 @@ def talairach_afd(
     Returns:
         NamedTuple of outputs (described in `TalairachAfdOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TALAIRACH_AFD_METADATA)
     params = talairach_afd_params(
         subject_name=subject_name,
         xfm_file=xfm_file,
@@ -215,13 +196,13 @@ def talairach_afd(
         afd_directory=afd_directory,
         verbose=verbose,
     )
-    return talairach_afd_execute(params, execution)
+    return talairach_afd_execute(params, runner)
 
 
 __all__ = [
     "TALAIRACH_AFD_METADATA",
     "TalairachAfdOutputs",
-    "TalairachAfdParameters",
     "talairach_afd",
+    "talairach_afd_execute",
     "talairach_afd_params",
 ]

niwrap_freesurfer/freesurfer/talairach_avi.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALAIRACH_AVI_METADATA = Metadata(
-    id="a3baecf55289c2a25f7c0c586907569e12de1415.boutiques",
+    id="62db8e91323313e662697c3e2bf8d5e807bdecce.boutiques",
     name="talairach_avi",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ TALAIRACH_AVI_METADATA = Metadata(
 
 
 TalairachAviParameters = typing.TypedDict('TalairachAviParameters', {
-    "__STYXTYPE__": typing.Literal["talairach_avi"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/talairach_avi"]],
+    "input_file": InputPathType,
+    "output_xfm": str,
+    "atlas": typing.NotRequired[str | None],
+    "log": typing.NotRequired[str | None],
+    "debug": bool,
+})
+TalairachAviParametersTagged = typing.TypedDict('TalairachAviParametersTagged', {
+    "@type": typing.Literal["freesurfer/talairach_avi"],
     "input_file": InputPathType,
     "output_xfm": str,
     "atlas": typing.NotRequired[str | None],
     "log": typing.NotRequired[str | None],
     "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 {
-        "talairach_avi": talairach_avi_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 {
-        "talairach_avi": talairach_avi_outputs,
-    }.get(t)
 
 
 class TalairachAviOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `talairach_avi(...)`.
+    Output object returned when calling `TalairachAviParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def talairach_avi_params(
     atlas: str | None = None,
     log: str | None = None,
     debug: bool = False,
-) -> TalairachAviParameters:
+) -> TalairachAviParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def talairach_avi_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "talairach_avi",
+        "@type": "freesurfer/talairach_avi",
         "input_file": input_file,
         "output_xfm": output_xfm,
         "debug": debug,
@@ -114,23 +90,23 @@ def talairach_avi_cargs(
     cargs.append("talairach_avi")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "--xfm",
-        params.get("output_xfm")
+        params.get("output_xfm", None)
     ])
-    if params.get("atlas") is not None:
+    if params.get("atlas", None) is not None:
         cargs.extend([
             "--atlas",
-            params.get("atlas")
+            params.get("atlas", None)
         ])
-    if params.get("log") is not None:
+    if params.get("log", None) is not None:
         cargs.extend([
             "--log",
-            params.get("log")
+            params.get("log", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -150,16 +126,18 @@ def talairach_avi_outputs(
     """
     ret = TalairachAviOutputs(
         root=execution.output_file("."),
-        output_xfm_file=execution.output_file(params.get("output_xfm")),
+        output_xfm_file=execution.output_file(params.get("output_xfm", None)),
     )
     return ret
 
 
 def talairach_avi_execute(
     params: TalairachAviParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalairachAviOutputs:
     """
+    talairach_avi
+    
     Front-end for Avi Snyder's image registration tool. Computes the Talairach
     transform that maps the input volume to the MNI average_305.
     
@@ -169,10 +147,12 @@ def talairach_avi_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalairachAviOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TALAIRACH_AVI_METADATA)
     params = execution.params(params)
     cargs = talairach_avi_cargs(params, execution)
     ret = talairach_avi_outputs(params, execution)
@@ -189,6 +169,8 @@ def talairach_avi(
     runner: Runner | None = None,
 ) -> TalairachAviOutputs:
     """
+    talairach_avi
+    
     Front-end for Avi Snyder's image registration tool. Computes the Talairach
     transform that maps the input volume to the MNI average_305.
     
@@ -206,8 +188,6 @@ def talairach_avi(
     Returns:
         NamedTuple of outputs (described in `TalairachAviOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TALAIRACH_AVI_METADATA)
     params = talairach_avi_params(
         input_file=input_file,
         output_xfm=output_xfm,
@@ -215,13 +195,13 @@ def talairach_avi(
         log=log,
         debug=debug,
     )
-    return talairach_avi_execute(params, execution)
+    return talairach_avi_execute(params, runner)
 
 
 __all__ = [
     "TALAIRACH_AVI_METADATA",
     "TalairachAviOutputs",
-    "TalairachAviParameters",
     "talairach_avi",
+    "talairach_avi_execute",
     "talairach_avi_params",
 ]

niwrap_freesurfer/freesurfer/talairach_mgh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TALAIRACH_MGH_METADATA = Metadata(
-    id="6b9e2a03c841e63355d5121337160b9481a21d90.boutiques",
+    id="1ec4eaf8700fa11dd94f9b3ca21df6ff98e94a80.boutiques",
     name="talairach_mgh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ TALAIRACH_MGH_METADATA = Metadata(
 
 
 TalairachMghParameters = typing.TypedDict('TalairachMghParameters', {
-    "__STYXTYPE__": typing.Literal["talairach_mgh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/talairach_mgh"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+})
+TalairachMghParametersTagged = typing.TypedDict('TalairachMghParametersTagged', {
+    "@type": typing.Literal["freesurfer/talairach_mgh"],
     "input_volume": InputPathType,
     "output_volume": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "talairach_mgh": talairach_mgh_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 {
-        "talairach_mgh": talairach_mgh_outputs,
-    }.get(t)
 
 
 class TalairachMghOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `talairach_mgh(...)`.
+    Output object returned when calling `TalairachMghParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class TalairachMghOutputs(typing.NamedTuple):
 def talairach_mgh_params(
     input_volume: InputPathType,
     output_volume: str,
-) -> TalairachMghParameters:
+) -> TalairachMghParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def talairach_mgh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "talairach_mgh",
+        "@type": "freesurfer/talairach_mgh",
         "input_volume": input_volume,
         "output_volume": output_volume,
     }
@@ -98,8 +71,8 @@ def talairach_mgh_cargs(
     """
     cargs = []
     cargs.append("talairach_mgh")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def talairach_mgh_outputs(
     """
     ret = TalairachMghOutputs(
         root=execution.output_file("."),
-        transformed_output=execution.output_file(params.get("output_volume")),
+        transformed_output=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def talairach_mgh_execute(
     params: TalairachMghParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TalairachMghOutputs:
     """
+    talairach_mgh
+    
     A tool for aligning brain volume with Talairach reference brain.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def talairach_mgh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TalairachMghOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TALAIRACH_MGH_METADATA)
     params = execution.params(params)
     cargs = talairach_mgh_cargs(params, execution)
     ret = talairach_mgh_outputs(params, execution)
@@ -153,6 +130,8 @@ def talairach_mgh(
     runner: Runner | None = None,
 ) -> TalairachMghOutputs:
     """
+    talairach_mgh
+    
     A tool for aligning brain volume with Talairach reference brain.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def talairach_mgh(
     Returns:
         NamedTuple of outputs (described in `TalairachMghOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TALAIRACH_MGH_METADATA)
     params = talairach_mgh_params(
         input_volume=input_volume,
         output_volume=output_volume,
     )
-    return talairach_mgh_execute(params, execution)
+    return talairach_mgh_execute(params, runner)
 
 
 __all__ = [
     "TALAIRACH_MGH_METADATA",
     "TalairachMghOutputs",
-    "TalairachMghParameters",
     "talairach_mgh",
+    "talairach_mgh_execute",
     "talairach_mgh_params",
 ]