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

niwrap_freesurfer/freesurfer/mris_expand.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_EXPAND_METADATA = Metadata(
-    id="fc34a7ed0b782432dc57d2892c5163e693efa169.boutiques",
+    id="bda23155268275073fa8f9779a6369552009862e.boutiques",
     name="mris_expand",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRIS_EXPAND_METADATA = Metadata(
 
 
 MrisExpandParameters = typing.TypedDict('MrisExpandParameters', {
-    "__STYXTYPE__": typing.Literal["mris_expand"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_expand"]],
+    "input_surface": InputPathType,
+    "expansion_distance": float,
+    "output_surface": str,
+    "thickness": bool,
+    "label": typing.NotRequired[str | None],
+    "tmap": typing.NotRequired[str | None],
+    "tmap_random": typing.NotRequired[str | None],
+})
+MrisExpandParametersTagged = typing.TypedDict('MrisExpandParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_expand"],
     "input_surface": InputPathType,
     "expansion_distance": float,
     "output_surface": str,
@@ -23,43 +33,11 @@ MrisExpandParameters = typing.TypedDict('MrisExpandParameters', {
     "tmap": typing.NotRequired[str | None],
     "tmap_random": 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 {
-        "mris_expand": mris_expand_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 {
-        "mris_expand": mris_expand_outputs,
-    }.get(t)
 
 
 class MrisExpandOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_expand(...)`.
+    Output object returned when calling `MrisExpandParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mris_expand_params(
     label: str | None = None,
     tmap: str | None = None,
     tmap_random: str | None = None,
-) -> MrisExpandParameters:
+) -> MrisExpandParametersTagged:
     """
     Build parameters.
     
@@ -93,7 +71,7 @@ def mris_expand_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_expand",
+        "@type": "freesurfer/mris_expand",
         "input_surface": input_surface,
         "expansion_distance": expansion_distance,
         "output_surface": output_surface,
@@ -123,25 +101,25 @@ def mris_expand_cargs(
     """
     cargs = []
     cargs.append("mris_expand")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(str(params.get("expansion_distance")))
-    cargs.append(params.get("output_surface"))
-    if params.get("thickness"):
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(str(params.get("expansion_distance", None)))
+    cargs.append(params.get("output_surface", None))
+    if params.get("thickness", False):
         cargs.append("-thickness")
-    if params.get("label") is not None:
+    if params.get("label", None) is not None:
         cargs.extend([
             "-label",
-            params.get("label")
+            params.get("label", None)
         ])
-    if params.get("tmap") is not None:
+    if params.get("tmap", None) is not None:
         cargs.extend([
             "-tmap",
-            params.get("tmap")
+            params.get("tmap", None)
         ])
-    if params.get("tmap_random") is not None:
+    if params.get("tmap_random", None) is not None:
         cargs.extend([
             "-tmap random",
-            params.get("tmap_random")
+            params.get("tmap_random", None)
         ])
     return cargs
 
@@ -161,16 +139,18 @@ def mris_expand_outputs(
     """
     ret = MrisExpandOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surface")),
+        output_surface_file=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_expand_execute(
     params: MrisExpandParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisExpandOutputs:
     """
+    mris_expand
+    
     Expand a given surface by a specified distance.
     
     Author: FreeSurfer Developers
@@ -179,10 +159,12 @@ def mris_expand_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisExpandOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_EXPAND_METADATA)
     params = execution.params(params)
     cargs = mris_expand_cargs(params, execution)
     ret = mris_expand_outputs(params, execution)
@@ -201,6 +183,8 @@ def mris_expand(
     runner: Runner | None = None,
 ) -> MrisExpandOutputs:
     """
+    mris_expand
+    
     Expand a given surface by a specified distance.
     
     Author: FreeSurfer Developers
@@ -221,8 +205,6 @@ def mris_expand(
     Returns:
         NamedTuple of outputs (described in `MrisExpandOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_EXPAND_METADATA)
     params = mris_expand_params(
         input_surface=input_surface,
         expansion_distance=expansion_distance,
@@ -232,13 +214,13 @@ def mris_expand(
         tmap=tmap,
         tmap_random=tmap_random,
     )
-    return mris_expand_execute(params, execution)
+    return mris_expand_execute(params, runner)
 
 
 __all__ = [
     "MRIS_EXPAND_METADATA",
     "MrisExpandOutputs",
-    "MrisExpandParameters",
     "mris_expand",
+    "mris_expand_execute",
     "mris_expand_params",
 ]

niwrap_freesurfer/freesurfer/mris_extract_main_component.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_EXTRACT_MAIN_COMPONENT_METADATA = Metadata(
-    id="d38be2e5a815a2d5da3fba89e218dbc97c4dd64d.boutiques",
+    id="b66191d81b627d97335610b72f8d5de6a80fdaca.boutiques",
     name="mris_extract_main_component",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ MRIS_EXTRACT_MAIN_COMPONENT_METADATA = Metadata(
 
 
 MrisExtractMainComponentParameters = typing.TypedDict('MrisExtractMainComponentParameters', {
-    "__STYXTYPE__": typing.Literal["mris_extract_main_component"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_extract_main_component"]],
+    "input_surface": InputPathType,
+    "output_surface": str,
+})
+MrisExtractMainComponentParametersTagged = typing.TypedDict('MrisExtractMainComponentParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_extract_main_component"],
     "input_surface": InputPathType,
     "output_surface": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_extract_main_component": mris_extract_main_component_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 {
-        "mris_extract_main_component": mris_extract_main_component_outputs,
-    }.get(t)
 
 
 class MrisExtractMainComponentOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_extract_main_component(...)`.
+    Output object returned when calling `MrisExtractMainComponentParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class MrisExtractMainComponentOutputs(typing.NamedTuple):
 def mris_extract_main_component_params(
     input_surface: InputPathType,
     output_surface: str,
-) -> MrisExtractMainComponentParameters:
+) -> MrisExtractMainComponentParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def mris_extract_main_component_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_extract_main_component",
+        "@type": "freesurfer/mris_extract_main_component",
         "input_surface": input_surface,
         "output_surface": output_surface,
     }
@@ -98,8 +71,8 @@ def mris_extract_main_component_cargs(
     """
     cargs = []
     cargs.append("mris_extract_main_component")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def mris_extract_main_component_outputs(
     """
     ret = MrisExtractMainComponentOutputs(
         root=execution.output_file("."),
-        output_surface_file=execution.output_file(params.get("output_surface")),
+        output_surface_file=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def mris_extract_main_component_execute(
     params: MrisExtractMainComponentParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisExtractMainComponentOutputs:
     """
+    mris_extract_main_component
+    
     Tool for extracting the main component from a surface input.
     
     Author: FreeSurfer Developers
@@ -136,10 +111,12 @@ def mris_extract_main_component_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisExtractMainComponentOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_EXTRACT_MAIN_COMPONENT_METADATA)
     params = execution.params(params)
     cargs = mris_extract_main_component_cargs(params, execution)
     ret = mris_extract_main_component_outputs(params, execution)
@@ -153,6 +130,8 @@ def mris_extract_main_component(
     runner: Runner | None = None,
 ) -> MrisExtractMainComponentOutputs:
     """
+    mris_extract_main_component
+    
     Tool for extracting the main component from a surface input.
     
     Author: FreeSurfer Developers
@@ -166,19 +145,17 @@ def mris_extract_main_component(
     Returns:
         NamedTuple of outputs (described in `MrisExtractMainComponentOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_EXTRACT_MAIN_COMPONENT_METADATA)
     params = mris_extract_main_component_params(
         input_surface=input_surface,
         output_surface=output_surface,
     )
-    return mris_extract_main_component_execute(params, execution)
+    return mris_extract_main_component_execute(params, runner)
 
 
 __all__ = [
     "MRIS_EXTRACT_MAIN_COMPONENT_METADATA",
     "MrisExtractMainComponentOutputs",
-    "MrisExtractMainComponentParameters",
     "mris_extract_main_component",
+    "mris_extract_main_component_execute",
     "mris_extract_main_component_params",
 ]

niwrap_freesurfer/freesurfer/mris_extract_patches.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_EXTRACT_PATCHES_METADATA = Metadata(
-    id="4b1b272c0e5d898fdbf11dee43aa5f15d5fc44a4.boutiques",
+    id="2c86c30a429cc2d390ece2cd6a53437150c9c54c.boutiques",
     name="mris_extract_patches",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ MRIS_EXTRACT_PATCHES_METADATA = Metadata(
 
 
 MrisExtractPatchesParameters = typing.TypedDict('MrisExtractPatchesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_extract_patches"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_extract_patches"]],
+    "subject": str,
+    "output_dir": str,
+})
+MrisExtractPatchesParametersTagged = typing.TypedDict('MrisExtractPatchesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_extract_patches"],
     "subject": str,
     "output_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_extract_patches": mris_extract_patches_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 MrisExtractPatchesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_extract_patches(...)`.
+    Output object returned when calling `MrisExtractPatchesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class MrisExtractPatchesOutputs(typing.NamedTuple):
 def mris_extract_patches_params(
     subject: str,
     output_dir: str,
-) -> MrisExtractPatchesParameters:
+) -> MrisExtractPatchesParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def mris_extract_patches_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_extract_patches",
+        "@type": "freesurfer/mris_extract_patches",
         "subject": subject,
         "output_dir": output_dir,
     }
@@ -95,8 +69,8 @@ def mris_extract_patches_cargs(
     """
     cargs = []
     cargs.append("mris_extract_patches")
-    cargs.append(params.get("subject"))
-    cargs.append(params.get("output_dir"))
+    cargs.append(params.get("subject", None))
+    cargs.append(params.get("output_dir", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def mris_extract_patches_outputs(
 
 def mris_extract_patches_execute(
     params: MrisExtractPatchesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisExtractPatchesOutputs:
     """
+    mris_extract_patches
+    
     A tool for extracting patches from brain surfaces.
     
     Author: FreeSurfer Developers
@@ -132,10 +108,12 @@ def mris_extract_patches_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisExtractPatchesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_EXTRACT_PATCHES_METADATA)
     params = execution.params(params)
     cargs = mris_extract_patches_cargs(params, execution)
     ret = mris_extract_patches_outputs(params, execution)
@@ -149,6 +127,8 @@ def mris_extract_patches(
     runner: Runner | None = None,
 ) -> MrisExtractPatchesOutputs:
     """
+    mris_extract_patches
+    
     A tool for extracting patches from brain surfaces.
     
     Author: FreeSurfer Developers
@@ -162,19 +142,17 @@ def mris_extract_patches(
     Returns:
         NamedTuple of outputs (described in `MrisExtractPatchesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_EXTRACT_PATCHES_METADATA)
     params = mris_extract_patches_params(
         subject=subject,
         output_dir=output_dir,
     )
-    return mris_extract_patches_execute(params, execution)
+    return mris_extract_patches_execute(params, runner)
 
 
 __all__ = [
     "MRIS_EXTRACT_PATCHES_METADATA",
     "MrisExtractPatchesOutputs",
-    "MrisExtractPatchesParameters",
     "mris_extract_patches",
+    "mris_extract_patches_execute",
     "mris_extract_patches_params",
 ]

niwrap_freesurfer/freesurfer/mris_extract_values.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRIS_EXTRACT_VALUES_METADATA = Metadata(
-    id="7070abfad47a418df612126e2e44d16aaeb6ccdc.boutiques",
+    id="2367e47189e1fa3c5c889bbaca46aee7e7120936.boutiques",
     name="mris_extract_values",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRIS_EXTRACT_VALUES_METADATA = Metadata(
 
 
 MrisExtractValuesParameters = typing.TypedDict('MrisExtractValuesParameters', {
-    "__STYXTYPE__": typing.Literal["mris_extract_values"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mris_extract_values"]],
+    "surface": InputPathType,
+    "overlay": InputPathType,
+    "annotation": InputPathType,
+    "csvfile": str,
+    "num_images": float,
+    "image_files": list[InputPathType],
+})
+MrisExtractValuesParametersTagged = typing.TypedDict('MrisExtractValuesParametersTagged', {
+    "@type": typing.Literal["freesurfer/mris_extract_values"],
     "surface": InputPathType,
     "overlay": InputPathType,
     "annotation": InputPathType,
@@ -22,43 +31,11 @@ MrisExtractValuesParameters = typing.TypedDict('MrisExtractValuesParameters', {
     "num_images": float,
     "image_files": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mris_extract_values": mris_extract_values_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 {
-        "mris_extract_values": mris_extract_values_outputs,
-    }.get(t)
 
 
 class MrisExtractValuesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mris_extract_values(...)`.
+    Output object returned when calling `MrisExtractValuesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mris_extract_values_params(
     csvfile: str,
     num_images: float,
     image_files: list[InputPathType],
-) -> MrisExtractValuesParameters:
+) -> MrisExtractValuesParametersTagged:
     """
     Build parameters.
     
@@ -88,7 +65,7 @@ def mris_extract_values_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mris_extract_values",
+        "@type": "freesurfer/mris_extract_values",
         "surface": surface,
         "overlay": overlay,
         "annotation": annotation,
@@ -116,27 +93,27 @@ def mris_extract_values_cargs(
     cargs.append("mris_extract_values")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("surface"))
+        execution.input_file(params.get("surface", None))
     ])
     cargs.extend([
         "-v",
-        execution.input_file(params.get("overlay"))
+        execution.input_file(params.get("overlay", None))
     ])
     cargs.extend([
         "-a",
-        execution.input_file(params.get("annotation"))
+        execution.input_file(params.get("annotation", None))
     ])
     cargs.extend([
         "-o",
-        params.get("csvfile")
+        params.get("csvfile", None)
     ])
     cargs.extend([
         "-m",
-        str(params.get("num_images"))
+        str(params.get("num_images", None))
     ])
     cargs.extend([
         "--images",
-        *[execution.input_file(f) for f in params.get("image_files")]
+        *[execution.input_file(f) for f in params.get("image_files", None)]
     ])
     return cargs
 
@@ -156,18 +133,20 @@ def mris_extract_values_outputs(
     """
     ret = MrisExtractValuesOutputs(
         root=execution.output_file("."),
-        output_csv=execution.output_file(params.get("csvfile")),
+        output_csv=execution.output_file(params.get("csvfile", None)),
     )
     return ret
 
 
 def mris_extract_values_execute(
     params: MrisExtractValuesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MrisExtractValuesOutputs:
     """
-    Extracts values from surface, overlay, and annotation files and outputs them to
-    a CSV file.
+    mris_extract_values
+    
+    Extracts values from surface, overlay, and annotation files and outputs them
+    to a CSV file.
     
     Author: FreeSurfer Developers
     
@@ -175,10 +154,12 @@ def mris_extract_values_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MrisExtractValuesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRIS_EXTRACT_VALUES_METADATA)
     params = execution.params(params)
     cargs = mris_extract_values_cargs(params, execution)
     ret = mris_extract_values_outputs(params, execution)
@@ -196,8 +177,10 @@ def mris_extract_values(
     runner: Runner | None = None,
 ) -> MrisExtractValuesOutputs:
     """
-    Extracts values from surface, overlay, and annotation files and outputs them to
-    a CSV file.
+    mris_extract_values
+    
+    Extracts values from surface, overlay, and annotation files and outputs them
+    to a CSV file.
     
     Author: FreeSurfer Developers
     
@@ -214,8 +197,6 @@ def mris_extract_values(
     Returns:
         NamedTuple of outputs (described in `MrisExtractValuesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRIS_EXTRACT_VALUES_METADATA)
     params = mris_extract_values_params(
         surface=surface,
         overlay=overlay,
@@ -224,13 +205,13 @@ def mris_extract_values(
         num_images=num_images,
         image_files=image_files,
     )
-    return mris_extract_values_execute(params, execution)
+    return mris_extract_values_execute(params, runner)
 
 
 __all__ = [
     "MRIS_EXTRACT_VALUES_METADATA",
     "MrisExtractValuesOutputs",
-    "MrisExtractValuesParameters",
     "mris_extract_values",
+    "mris_extract_values_execute",
     "mris_extract_values_params",
 ]