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

niwrap_freesurfer/freesurfer/morph_subject_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_SUBJECT_LH_METADATA = Metadata(
-    id="50281e785fbd08bfa132876681fac0d45cfa2be9.boutiques",
+    id="16ebb2dc0b8ef734809af9e28ddb9b7d8a465100.boutiques",
     name="morph_subject-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_SUBJECT_LH_METADATA = Metadata(
 
 
 MorphSubjectLhParameters = typing.TypedDict('MorphSubjectLhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_subject-lh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_subject-lh"]],
+    "subject_id": str,
+})
+MorphSubjectLhParametersTagged = typing.TypedDict('MorphSubjectLhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_subject-lh"],
     "subject_id": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "morph_subject-lh": morph_subject_lh_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 MorphSubjectLhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_subject_lh(...)`.
+    Output object returned when calling `MorphSubjectLhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphSubjectLhOutputs(typing.NamedTuple):
 
 def morph_subject_lh_params(
     subject_id: str,
-) -> MorphSubjectLhParameters:
+) -> MorphSubjectLhParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def morph_subject_lh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_subject-lh",
+        "@type": "freesurfer/morph_subject-lh",
         "subject_id": subject_id,
     }
     return params
@@ -93,7 +66,7 @@ def morph_subject_lh_cargs(
     cargs.append("morph_subject-lh")
     cargs.extend([
         "-lh",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     return cargs
 
@@ -119,9 +92,11 @@ def morph_subject_lh_outputs(
 
 def morph_subject_lh_execute(
     params: MorphSubjectLhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphSubjectLhOutputs:
     """
+    morph_subject-lh
+    
     A tool for morphing subject's left hemisphere.
     
     Author: FreeSurfer Developers
@@ -130,10 +105,12 @@ def morph_subject_lh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphSubjectLhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_SUBJECT_LH_METADATA)
     params = execution.params(params)
     cargs = morph_subject_lh_cargs(params, execution)
     ret = morph_subject_lh_outputs(params, execution)
@@ -146,6 +123,8 @@ def morph_subject_lh(
     runner: Runner | None = None,
 ) -> MorphSubjectLhOutputs:
     """
+    morph_subject-lh
+    
     A tool for morphing subject's left hemisphere.
     
     Author: FreeSurfer Developers
@@ -158,18 +137,16 @@ def morph_subject_lh(
     Returns:
         NamedTuple of outputs (described in `MorphSubjectLhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_SUBJECT_LH_METADATA)
     params = morph_subject_lh_params(
         subject_id=subject_id,
     )
-    return morph_subject_lh_execute(params, execution)
+    return morph_subject_lh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_SUBJECT_LH_METADATA",
     "MorphSubjectLhOutputs",
-    "MorphSubjectLhParameters",
     "morph_subject_lh",
+    "morph_subject_lh_execute",
     "morph_subject_lh_params",
 ]

niwrap_freesurfer/freesurfer/morph_subject_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_SUBJECT_RH_METADATA = Metadata(
-    id="3bc20c9a814d4ed47946818ef81d8f65039baeee.boutiques",
+    id="3a2680e6a4464cd0284fbcf5ee8d77bdf45b6062.boutiques",
     name="morph_subject-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_SUBJECT_RH_METADATA = Metadata(
 
 
 MorphSubjectRhParameters = typing.TypedDict('MorphSubjectRhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_subject-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_subject-rh"]],
+    "subject_id": str,
+})
+MorphSubjectRhParametersTagged = typing.TypedDict('MorphSubjectRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_subject-rh"],
     "subject_id": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "morph_subject-rh": morph_subject_rh_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 MorphSubjectRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_subject_rh(...)`.
+    Output object returned when calling `MorphSubjectRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphSubjectRhOutputs(typing.NamedTuple):
 
 def morph_subject_rh_params(
     subject_id: str,
-) -> MorphSubjectRhParameters:
+) -> MorphSubjectRhParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def morph_subject_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_subject-rh",
+        "@type": "freesurfer/morph_subject-rh",
         "subject_id": subject_id,
     }
     return params
@@ -93,7 +66,7 @@ def morph_subject_rh_cargs(
     cargs.append("morph_subject-rh")
     cargs.extend([
         "-rh",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     return cargs
 
@@ -119,9 +92,11 @@ def morph_subject_rh_outputs(
 
 def morph_subject_rh_execute(
     params: MorphSubjectRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphSubjectRhOutputs:
     """
+    morph_subject-rh
+    
     A tool for morphing the right hemisphere of subject data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -130,10 +105,12 @@ def morph_subject_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphSubjectRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_SUBJECT_RH_METADATA)
     params = execution.params(params)
     cargs = morph_subject_rh_cargs(params, execution)
     ret = morph_subject_rh_outputs(params, execution)
@@ -146,6 +123,8 @@ def morph_subject_rh(
     runner: Runner | None = None,
 ) -> MorphSubjectRhOutputs:
     """
+    morph_subject-rh
+    
     A tool for morphing the right hemisphere of subject data in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -158,18 +137,16 @@ def morph_subject_rh(
     Returns:
         NamedTuple of outputs (described in `MorphSubjectRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_SUBJECT_RH_METADATA)
     params = morph_subject_rh_params(
         subject_id=subject_id,
     )
-    return morph_subject_rh_execute(params, execution)
+    return morph_subject_rh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_SUBJECT_RH_METADATA",
     "MorphSubjectRhOutputs",
-    "MorphSubjectRhParameters",
     "morph_subject_rh",
+    "morph_subject_rh_execute",
     "morph_subject_rh_params",
 ]

niwrap_freesurfer/freesurfer/morph_tables_lh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_TABLES_LH_METADATA = Metadata(
-    id="866a14f40d53d744f21eba0c69ccf4cecb15c51c.boutiques",
+    id="2822ee9534bad8b98be9bcfe634df7548fd6891c.boutiques",
     name="morph_tables-lh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MORPH_TABLES_LH_METADATA = Metadata(
 
 
 MorphTablesLhParameters = typing.TypedDict('MorphTablesLhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_tables-lh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_tables-lh"]],
+    "input_file": InputPathType,
+    "some_flag": bool,
+})
+MorphTablesLhParametersTagged = typing.TypedDict('MorphTablesLhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_tables-lh"],
     "input_file": InputPathType,
     "some_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 {
-        "morph_tables-lh": morph_tables_lh_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 {
-        "morph_tables-lh": morph_tables_lh_outputs,
-    }.get(t)
 
 
 class MorphTablesLhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_tables_lh(...)`.
+    Output object returned when calling `MorphTablesLhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MorphTablesLhOutputs(typing.NamedTuple):
 def morph_tables_lh_params(
     input_file: InputPathType,
     some_flag: bool = False,
-) -> MorphTablesLhParameters:
+) -> MorphTablesLhParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def morph_tables_lh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_tables-lh",
+        "@type": "freesurfer/morph_tables-lh",
         "input_file": input_file,
         "some_flag": some_flag,
     }
@@ -101,9 +74,9 @@ def morph_tables_lh_cargs(
     cargs.append("morph_tables-lh")
     cargs.extend([
         "-lh",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("some_flag"):
+    if params.get("some_flag", False):
         cargs.append("--some-flag")
     return cargs
 
@@ -123,16 +96,18 @@ def morph_tables_lh_outputs(
     """
     ret = MorphTablesLhOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(pathlib.Path(params.get("input_file")).name + "_output.txt"),
+        output_file=execution.output_file(pathlib.Path(params.get("input_file", None)).name + "_output.txt"),
     )
     return ret
 
 
 def morph_tables_lh_execute(
     params: MorphTablesLhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphTablesLhOutputs:
     """
+    morph_tables-lh
+    
     Morphological analysis tool for left hemisphere in Freesurfer.
     
     Author: FreeSurfer Developers
@@ -141,10 +116,12 @@ def morph_tables_lh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphTablesLhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_TABLES_LH_METADATA)
     params = execution.params(params)
     cargs = morph_tables_lh_cargs(params, execution)
     ret = morph_tables_lh_outputs(params, execution)
@@ -158,6 +135,8 @@ def morph_tables_lh(
     runner: Runner | None = None,
 ) -> MorphTablesLhOutputs:
     """
+    morph_tables-lh
+    
     Morphological analysis tool for left hemisphere in Freesurfer.
     
     Author: FreeSurfer Developers
@@ -172,19 +151,17 @@ def morph_tables_lh(
     Returns:
         NamedTuple of outputs (described in `MorphTablesLhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_TABLES_LH_METADATA)
     params = morph_tables_lh_params(
         input_file=input_file,
         some_flag=some_flag,
     )
-    return morph_tables_lh_execute(params, execution)
+    return morph_tables_lh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_TABLES_LH_METADATA",
     "MorphTablesLhOutputs",
-    "MorphTablesLhParameters",
     "morph_tables_lh",
+    "morph_tables_lh_execute",
     "morph_tables_lh_params",
 ]

niwrap_freesurfer/freesurfer/morph_tables_rh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MORPH_TABLES_RH_METADATA = Metadata(
-    id="0b7bdfd333d1ae3ca12dd01263420412372bb510.boutiques",
+    id="f6fbf33ff571242ee51f5f8e5a73a9abf1d87d0b.boutiques",
     name="morph_tables-rh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MORPH_TABLES_RH_METADATA = Metadata(
 
 
 MorphTablesRhParameters = typing.TypedDict('MorphTablesRhParameters', {
-    "__STYXTYPE__": typing.Literal["morph_tables-rh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/morph_tables-rh"]],
+    "options": typing.NotRequired[str | None],
+})
+MorphTablesRhParametersTagged = typing.TypedDict('MorphTablesRhParametersTagged', {
+    "@type": typing.Literal["freesurfer/morph_tables-rh"],
     "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 {
-        "morph_tables-rh": morph_tables_rh_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 MorphTablesRhOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `morph_tables_rh(...)`.
+    Output object returned when calling `MorphTablesRhParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class MorphTablesRhOutputs(typing.NamedTuple):
 
 def morph_tables_rh_params(
     options: str | None = None,
-) -> MorphTablesRhParameters:
+) -> MorphTablesRhParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def morph_tables_rh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "morph_tables-rh",
+        "@type": "freesurfer/morph_tables-rh",
     }
     if options is not None:
         params["options"] = options
@@ -92,10 +65,10 @@ def morph_tables_rh_cargs(
     """
     cargs = []
     cargs.append("morph_tables-rh")
-    if params.get("options") is not None:
+    if params.get("options", None) is not None:
         cargs.extend([
             "-rh",
-            params.get("options")
+            params.get("options", None)
         ])
     return cargs
 
@@ -121,9 +94,11 @@ def morph_tables_rh_outputs(
 
 def morph_tables_rh_execute(
     params: MorphTablesRhParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MorphTablesRhOutputs:
     """
+    morph_tables-rh
+    
     A tool from Freesurfer associated with morphological tables for the right
     hemisphere.
     
@@ -133,10 +108,12 @@ def morph_tables_rh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MorphTablesRhOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MORPH_TABLES_RH_METADATA)
     params = execution.params(params)
     cargs = morph_tables_rh_cargs(params, execution)
     ret = morph_tables_rh_outputs(params, execution)
@@ -149,6 +126,8 @@ def morph_tables_rh(
     runner: Runner | None = None,
 ) -> MorphTablesRhOutputs:
     """
+    morph_tables-rh
+    
     A tool from Freesurfer associated with morphological tables for the right
     hemisphere.
     
@@ -162,18 +141,16 @@ def morph_tables_rh(
     Returns:
         NamedTuple of outputs (described in `MorphTablesRhOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MORPH_TABLES_RH_METADATA)
     params = morph_tables_rh_params(
         options=options,
     )
-    return morph_tables_rh_execute(params, execution)
+    return morph_tables_rh_execute(params, runner)
 
 
 __all__ = [
     "MORPH_TABLES_RH_METADATA",
     "MorphTablesRhOutputs",
-    "MorphTablesRhParameters",
     "morph_tables_rh",
+    "morph_tables_rh_execute",
     "morph_tables_rh_params",
 ]