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

niwrap_freesurfer/freesurfer/connected_components.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONNECTED_COMPONENTS_METADATA = Metadata(
-    id="b9d479aaa7ac641f9959d97c1f7c18cc18043629.boutiques",
+    id="7f90eb6d5a07cc028a8f6217054ba32de106f4c7.boutiques",
     name="connected_components",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ CONNECTED_COMPONENTS_METADATA = Metadata(
 
 
 ConnectedComponentsParameters = typing.TypedDict('ConnectedComponentsParameters', {
-    "__STYXTYPE__": typing.Literal["connected_components"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/connected_components"]],
+    "input_image": InputPathType,
+    "output_image": str,
+    "threshold": typing.NotRequired[float | None],
+})
+ConnectedComponentsParametersTagged = typing.TypedDict('ConnectedComponentsParametersTagged', {
+    "@type": typing.Literal["freesurfer/connected_components"],
     "input_image": InputPathType,
     "output_image": str,
     "threshold": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "connected_components": connected_components_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 {
-        "connected_components": connected_components_outputs,
-    }.get(t)
 
 
 class ConnectedComponentsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `connected_components(...)`.
+    Output object returned when calling `ConnectedComponentsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def connected_components_params(
     input_image: InputPathType,
     output_image: str = "output_labelled_image",
     threshold: float | None = None,
-) -> ConnectedComponentsParameters:
+) -> ConnectedComponentsParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def connected_components_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "connected_components",
+        "@type": "freesurfer/connected_components",
         "input_image": input_image,
         "output_image": output_image,
     }
@@ -103,15 +77,15 @@ def connected_components_cargs(
     """
     cargs = []
     cargs.append("connected_components")
-    cargs.append(execution.input_file(params.get("input_image")))
+    cargs.append(execution.input_file(params.get("input_image", None)))
     cargs.extend([
         "-o",
-        params.get("output_image")
+        params.get("output_image", "output_labelled_image")
     ])
-    if params.get("threshold") is not None:
+    if params.get("threshold", None) is not None:
         cargs.extend([
             "-t",
-            str(params.get("threshold"))
+            str(params.get("threshold", None))
         ])
     return cargs
 
@@ -131,16 +105,18 @@ def connected_components_outputs(
     """
     ret = ConnectedComponentsOutputs(
         root=execution.output_file("."),
-        output_labelled_image_file=execution.output_file(params.get("output_image") + ".nii.gz"),
+        output_labelled_image_file=execution.output_file(params.get("output_image", "output_labelled_image") + ".nii.gz"),
     )
     return ret
 
 
 def connected_components_execute(
     params: ConnectedComponentsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ConnectedComponentsOutputs:
     """
+    connected_components
+    
     A tool for identifying connected components in an image.
     
     Author: FreeSurfer Developers
@@ -149,10 +125,12 @@ def connected_components_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ConnectedComponentsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONNECTED_COMPONENTS_METADATA)
     params = execution.params(params)
     cargs = connected_components_cargs(params, execution)
     ret = connected_components_outputs(params, execution)
@@ -167,6 +145,8 @@ def connected_components(
     runner: Runner | None = None,
 ) -> ConnectedComponentsOutputs:
     """
+    connected_components
+    
     A tool for identifying connected components in an image.
     
     Author: FreeSurfer Developers
@@ -181,20 +161,18 @@ def connected_components(
     Returns:
         NamedTuple of outputs (described in `ConnectedComponentsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONNECTED_COMPONENTS_METADATA)
     params = connected_components_params(
         input_image=input_image,
         output_image=output_image,
         threshold=threshold,
     )
-    return connected_components_execute(params, execution)
+    return connected_components_execute(params, runner)
 
 
 __all__ = [
     "CONNECTED_COMPONENTS_METADATA",
     "ConnectedComponentsOutputs",
-    "ConnectedComponentsParameters",
     "connected_components",
+    "connected_components_execute",
     "connected_components_params",
 ]

niwrap_freesurfer/freesurfer/cor_to_minc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 COR_TO_MINC_METADATA = Metadata(
-    id="15dda396a0f22d201e6574171b77090fc72b06a2.boutiques",
+    id="8adb4d1ee02a3fae783d528e0102da2cb37144ee.boutiques",
     name="cor_to_minc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ COR_TO_MINC_METADATA = Metadata(
 
 
 CorToMincParameters = typing.TypedDict('CorToMincParameters', {
-    "__STYXTYPE__": typing.Literal["cor_to_minc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/cor_to_minc"]],
+    "cor_directory": str,
+    "minc_file": str,
+})
+CorToMincParametersTagged = typing.TypedDict('CorToMincParametersTagged', {
+    "@type": typing.Literal["freesurfer/cor_to_minc"],
     "cor_directory": str,
     "minc_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 {
-        "cor_to_minc": cor_to_minc_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 {
-        "cor_to_minc": cor_to_minc_outputs,
-    }.get(t)
 
 
 class CorToMincOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `cor_to_minc(...)`.
+    Output object returned when calling `CorToMincParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class CorToMincOutputs(typing.NamedTuple):
 def cor_to_minc_params(
     cor_directory: str,
     minc_file: str,
-) -> CorToMincParameters:
+) -> CorToMincParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def cor_to_minc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "cor_to_minc",
+        "@type": "freesurfer/cor_to_minc",
         "cor_directory": cor_directory,
         "minc_file": minc_file,
     }
@@ -98,8 +71,8 @@ def cor_to_minc_cargs(
     """
     cargs = []
     cargs.append("cor_to_minc")
-    cargs.append(params.get("cor_directory"))
-    cargs.append(params.get("minc_file"))
+    cargs.append(params.get("cor_directory", None))
+    cargs.append(params.get("minc_file", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def cor_to_minc_outputs(
     """
     ret = CorToMincOutputs(
         root=execution.output_file("."),
-        output_minc=execution.output_file(params.get("minc_file")),
+        output_minc=execution.output_file(params.get("minc_file", None)),
     )
     return ret
 
 
 def cor_to_minc_execute(
     params: CorToMincParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CorToMincOutputs:
     """
+    cor_to_minc
+    
     Converts a directory of COR files to a MINC file.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def cor_to_minc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CorToMincOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COR_TO_MINC_METADATA)
     params = execution.params(params)
     cargs = cor_to_minc_cargs(params, execution)
     ret = cor_to_minc_outputs(params, execution)
@@ -153,6 +130,8 @@ def cor_to_minc(
     runner: Runner | None = None,
 ) -> CorToMincOutputs:
     """
+    cor_to_minc
+    
     Converts a directory of COR files to a MINC file.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def cor_to_minc(
     Returns:
         NamedTuple of outputs (described in `CorToMincOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(COR_TO_MINC_METADATA)
     params = cor_to_minc_params(
         cor_directory=cor_directory,
         minc_file=minc_file,
     )
-    return cor_to_minc_execute(params, execution)
+    return cor_to_minc_execute(params, runner)
 
 
 __all__ = [
     "COR_TO_MINC_METADATA",
     "CorToMincOutputs",
-    "CorToMincParameters",
     "cor_to_minc",
+    "cor_to_minc_execute",
     "cor_to_minc_params",
 ]

niwrap_freesurfer/freesurfer/cp_dicom.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CP_DICOM_METADATA = Metadata(
-    id="a3b5658a53886c2046aff8ddfa60c01956982a5b.boutiques",
+    id="a61a44a95b9acc4f8c31cd28c22febf9e54641e5.boutiques",
     name="cp-dicom",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ CP_DICOM_METADATA = Metadata(
 
 
 CpDicomParameters = typing.TypedDict('CpDicomParameters', {
-    "__STYXTYPE__": typing.Literal["cp-dicom"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/cp-dicom"]],
+    "dicom_dir": str,
+    "output_dir": str,
+    "debug": bool,
+})
+CpDicomParametersTagged = typing.TypedDict('CpDicomParametersTagged', {
+    "@type": typing.Literal["freesurfer/cp-dicom"],
     "dicom_dir": str,
     "output_dir": str,
     "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 {
-        "cp-dicom": cp_dicom_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 CpDicomOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `cp_dicom(...)`.
+    Output object returned when calling `CpDicomParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def cp_dicom_params(
     dicom_dir: str,
     output_dir: str,
     debug: bool = False,
-) -> CpDicomParameters:
+) -> CpDicomParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def cp_dicom_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "cp-dicom",
+        "@type": "freesurfer/cp-dicom",
         "dicom_dir": dicom_dir,
         "output_dir": output_dir,
         "debug": debug,
@@ -101,13 +76,13 @@ def cp_dicom_cargs(
     cargs.append("cp-dicom")
     cargs.extend([
         "-d",
-        params.get("dicom_dir")
+        params.get("dicom_dir", None)
     ])
     cargs.extend([
         "-o",
-        params.get("output_dir")
+        params.get("output_dir", None)
     ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
     return cargs
 
@@ -133,9 +108,11 @@ def cp_dicom_outputs(
 
 def cp_dicom_execute(
     params: CpDicomParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CpDicomOutputs:
     """
+    cp-dicom
+    
     Copies DICOM files into separate directories for each series based on DICOM
     headers.
     
@@ -145,10 +122,12 @@ def cp_dicom_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CpDicomOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CP_DICOM_METADATA)
     params = execution.params(params)
     cargs = cp_dicom_cargs(params, execution)
     ret = cp_dicom_outputs(params, execution)
@@ -163,6 +142,8 @@ def cp_dicom(
     runner: Runner | None = None,
 ) -> CpDicomOutputs:
     """
+    cp-dicom
+    
     Copies DICOM files into separate directories for each series based on DICOM
     headers.
     
@@ -178,20 +159,18 @@ def cp_dicom(
     Returns:
         NamedTuple of outputs (described in `CpDicomOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CP_DICOM_METADATA)
     params = cp_dicom_params(
         dicom_dir=dicom_dir,
         output_dir=output_dir,
         debug=debug,
     )
-    return cp_dicom_execute(params, execution)
+    return cp_dicom_execute(params, runner)
 
 
 __all__ = [
     "CP_DICOM_METADATA",
     "CpDicomOutputs",
-    "CpDicomParameters",
     "cp_dicom",
+    "cp_dicom_execute",
     "cp_dicom_params",
 ]

niwrap_freesurfer/freesurfer/create_morph.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CREATE_MORPH_METADATA = Metadata(
-    id="d00775e741e3933385d72fe876f856c711446cb8.boutiques",
+    id="0ff99b3441c14b38521318fab3badba78909daaf.boutiques",
     name="createMorph",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ CREATE_MORPH_METADATA = Metadata(
 
 
 CreateMorphParameters = typing.TypedDict('CreateMorphParameters', {
-    "__STYXTYPE__": typing.Literal["createMorph"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/createMorph"]],
+    "input_transforms": list[str],
+    "output_transform": str,
+    "template": typing.NotRequired[InputPathType | None],
+    "subject": typing.NotRequired[InputPathType | None],
+    "debug_coordinates": typing.NotRequired[list[float] | None],
+})
+CreateMorphParametersTagged = typing.TypedDict('CreateMorphParametersTagged', {
+    "@type": typing.Literal["freesurfer/createMorph"],
     "input_transforms": list[str],
     "output_transform": str,
     "template": typing.NotRequired[InputPathType | None],
     "subject": typing.NotRequired[InputPathType | None],
     "debug_coordinates": typing.NotRequired[list[float] | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "createMorph": create_morph_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 {
-        "createMorph": create_morph_outputs,
-    }.get(t)
 
 
 class CreateMorphOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `create_morph(...)`.
+    Output object returned when calling `CreateMorphParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def create_morph_params(
     template: InputPathType | None = None,
     subject: InputPathType | None = None,
     debug_coordinates: list[float] | None = None,
-) -> CreateMorphParameters:
+) -> CreateMorphParametersTagged:
     """
     Build parameters.
     
@@ -87,7 +63,7 @@ def create_morph_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "createMorph",
+        "@type": "freesurfer/createMorph",
         "input_transforms": input_transforms,
         "output_transform": output_transform,
     }
@@ -117,26 +93,26 @@ def create_morph_cargs(
     cargs.append("createMorph")
     cargs.extend([
         "--in",
-        *params.get("input_transforms")
+        *params.get("input_transforms", None)
     ])
     cargs.extend([
         "--out",
-        params.get("output_transform")
+        params.get("output_transform", None)
     ])
-    if params.get("template") is not None:
+    if params.get("template", None) is not None:
         cargs.extend([
             "--template",
-            execution.input_file(params.get("template"))
+            execution.input_file(params.get("template", None))
         ])
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--subject",
-            execution.input_file(params.get("subject"))
+            execution.input_file(params.get("subject", None))
         ])
-    if params.get("debug_coordinates") is not None:
+    if params.get("debug_coordinates", None) is not None:
         cargs.extend([
             "--dbg",
-            *map(str, params.get("debug_coordinates"))
+            *map(str, params.get("debug_coordinates", None))
         ])
     return cargs
 
@@ -156,17 +132,20 @@ def create_morph_outputs(
     """
     ret = CreateMorphOutputs(
         root=execution.output_file("."),
-        output_transform_file=execution.output_file(params.get("output_transform")),
+        output_transform_file=execution.output_file(params.get("output_transform", None)),
     )
     return ret
 
 
 def create_morph_execute(
     params: CreateMorphParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CreateMorphOutputs:
     """
-    Tool to create morphological transformations using specified input transforms.
+    createMorph
+    
+    Tool to create morphological transformations using specified input
+    transforms.
     
     Author: FreeSurfer Developers
     
@@ -174,10 +153,12 @@ def create_morph_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CreateMorphOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CREATE_MORPH_METADATA)
     params = execution.params(params)
     cargs = create_morph_cargs(params, execution)
     ret = create_morph_outputs(params, execution)
@@ -194,7 +175,10 @@ def create_morph(
     runner: Runner | None = None,
 ) -> CreateMorphOutputs:
     """
-    Tool to create morphological transformations using specified input transforms.
+    createMorph
+    
+    Tool to create morphological transformations using specified input
+    transforms.
     
     Author: FreeSurfer Developers
     
@@ -212,8 +196,6 @@ def create_morph(
     Returns:
         NamedTuple of outputs (described in `CreateMorphOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CREATE_MORPH_METADATA)
     params = create_morph_params(
         input_transforms=input_transforms,
         output_transform=output_transform,
@@ -221,13 +203,13 @@ def create_morph(
         subject=subject,
         debug_coordinates=debug_coordinates,
     )
-    return create_morph_execute(params, execution)
+    return create_morph_execute(params, runner)
 
 
 __all__ = [
     "CREATE_MORPH_METADATA",
     "CreateMorphOutputs",
-    "CreateMorphParameters",
     "create_morph",
+    "create_morph_execute",
     "create_morph_params",
 ]