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

niwrap_freesurfer/freesurfer/hiam_register.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HIAM_REGISTER_METADATA = Metadata(
-    id="f991b3b9d61600e2eb491ce23d796663df3a627a.boutiques",
+    id="c0d9976db59a72d53136e5152d99ba64d191cfdf.boutiques",
     name="hiam_register",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ HIAM_REGISTER_METADATA = Metadata(
 
 
 HiamRegisterParameters = typing.TypedDict('HiamRegisterParameters', {
-    "__STYXTYPE__": typing.Literal["hiam_register"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/hiam_register"]],
+    "input_surface": InputPathType,
+    "average_surface": InputPathType,
+    "output_surface": str,
+})
+HiamRegisterParametersTagged = typing.TypedDict('HiamRegisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/hiam_register"],
     "input_surface": InputPathType,
     "average_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 {
-        "hiam_register": hiam_register_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 {
-        "hiam_register": hiam_register_outputs,
-    }.get(t)
 
 
 class HiamRegisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `hiam_register(...)`.
+    Output object returned when calling `HiamRegisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def hiam_register_params(
     input_surface: InputPathType,
     average_surface: InputPathType,
     output_surface: str,
-) -> HiamRegisterParameters:
+) -> HiamRegisterParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def hiam_register_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "hiam_register",
+        "@type": "freesurfer/hiam_register",
         "input_surface": input_surface,
         "average_surface": average_surface,
         "output_surface": output_surface,
@@ -103,9 +77,9 @@ def hiam_register_cargs(
     """
     cargs = []
     cargs.append("hiam_register")
-    cargs.append(execution.input_file(params.get("input_surface")))
-    cargs.append(execution.input_file(params.get("average_surface")))
-    cargs.append(params.get("output_surface"))
+    cargs.append(execution.input_file(params.get("input_surface", None)))
+    cargs.append(execution.input_file(params.get("average_surface", None)))
+    cargs.append(params.get("output_surface", None))
     return cargs
 
 
@@ -124,16 +98,18 @@ def hiam_register_outputs(
     """
     ret = HiamRegisterOutputs(
         root=execution.output_file("."),
-        registered_surface=execution.output_file(params.get("output_surface")),
+        registered_surface=execution.output_file(params.get("output_surface", None)),
     )
     return ret
 
 
 def hiam_register_execute(
     params: HiamRegisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> HiamRegisterOutputs:
     """
+    hiam_register
+    
     This program registers a surface with an average surface.
     
     Author: FreeSurfer Developers
@@ -142,10 +118,12 @@ def hiam_register_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `HiamRegisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HIAM_REGISTER_METADATA)
     params = execution.params(params)
     cargs = hiam_register_cargs(params, execution)
     ret = hiam_register_outputs(params, execution)
@@ -160,6 +138,8 @@ def hiam_register(
     runner: Runner | None = None,
 ) -> HiamRegisterOutputs:
     """
+    hiam_register
+    
     This program registers a surface with an average surface.
     
     Author: FreeSurfer Developers
@@ -175,20 +155,18 @@ def hiam_register(
     Returns:
         NamedTuple of outputs (described in `HiamRegisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(HIAM_REGISTER_METADATA)
     params = hiam_register_params(
         input_surface=input_surface,
         average_surface=average_surface,
         output_surface=output_surface,
     )
-    return hiam_register_execute(params, execution)
+    return hiam_register_execute(params, runner)
 
 
 __all__ = [
     "HIAM_REGISTER_METADATA",
     "HiamRegisterOutputs",
-    "HiamRegisterParameters",
     "hiam_register",
+    "hiam_register_execute",
     "hiam_register_params",
 ]

niwrap_freesurfer/freesurfer/histo_compute_joint_density.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HISTO_COMPUTE_JOINT_DENSITY_METADATA = Metadata(
-    id="3a36a770d00bbd1f28b86ef82a2c5b6f1aaee144.boutiques",
+    id="9857329ef1b21eee18875ab3ee1f848987d7ec86.boutiques",
     name="histo_compute_joint_density",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ HISTO_COMPUTE_JOINT_DENSITY_METADATA = Metadata(
 
 
 HistoComputeJointDensityParameters = typing.TypedDict('HistoComputeJointDensityParameters', {
-    "__STYXTYPE__": typing.Literal["histo_compute_joint_density"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/histo_compute_joint_density"]],
+    "volume1": InputPathType,
+    "volume2": InputPathType,
+    "joint_density_file": str,
+})
+HistoComputeJointDensityParametersTagged = typing.TypedDict('HistoComputeJointDensityParametersTagged', {
+    "@type": typing.Literal["freesurfer/histo_compute_joint_density"],
     "volume1": InputPathType,
     "volume2": InputPathType,
     "joint_density_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 {
-        "histo_compute_joint_density": histo_compute_joint_density_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 {
-        "histo_compute_joint_density": histo_compute_joint_density_outputs,
-    }.get(t)
 
 
 class HistoComputeJointDensityOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `histo_compute_joint_density(...)`.
+    Output object returned when calling `HistoComputeJointDensityParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def histo_compute_joint_density_params(
     volume1: InputPathType,
     volume2: InputPathType,
     joint_density_file: str,
-) -> HistoComputeJointDensityParameters:
+) -> HistoComputeJointDensityParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def histo_compute_joint_density_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "histo_compute_joint_density",
+        "@type": "freesurfer/histo_compute_joint_density",
         "volume1": volume1,
         "volume2": volume2,
         "joint_density_file": joint_density_file,
@@ -102,9 +76,9 @@ def histo_compute_joint_density_cargs(
     """
     cargs = []
     cargs.append("histo_compute_joint_density")
-    cargs.append(execution.input_file(params.get("volume1")))
-    cargs.append(execution.input_file(params.get("volume2")))
-    cargs.append(params.get("joint_density_file"))
+    cargs.append(execution.input_file(params.get("volume1", None)))
+    cargs.append(execution.input_file(params.get("volume2", None)))
+    cargs.append(params.get("joint_density_file", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def histo_compute_joint_density_outputs(
     """
     ret = HistoComputeJointDensityOutputs(
         root=execution.output_file("."),
-        output_joint_density=execution.output_file(params.get("joint_density_file")),
+        output_joint_density=execution.output_file(params.get("joint_density_file", None)),
     )
     return ret
 
 
 def histo_compute_joint_density_execute(
     params: HistoComputeJointDensityParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> HistoComputeJointDensityOutputs:
     """
+    histo_compute_joint_density
+    
     A tool to compute the joint density of two volumes.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def histo_compute_joint_density_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `HistoComputeJointDensityOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HISTO_COMPUTE_JOINT_DENSITY_METADATA)
     params = execution.params(params)
     cargs = histo_compute_joint_density_cargs(params, execution)
     ret = histo_compute_joint_density_outputs(params, execution)
@@ -159,6 +137,8 @@ def histo_compute_joint_density(
     runner: Runner | None = None,
 ) -> HistoComputeJointDensityOutputs:
     """
+    histo_compute_joint_density
+    
     A tool to compute the joint density of two volumes.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def histo_compute_joint_density(
     Returns:
         NamedTuple of outputs (described in `HistoComputeJointDensityOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(HISTO_COMPUTE_JOINT_DENSITY_METADATA)
     params = histo_compute_joint_density_params(
         volume1=volume1,
         volume2=volume2,
         joint_density_file=joint_density_file,
     )
-    return histo_compute_joint_density_execute(params, execution)
+    return histo_compute_joint_density_execute(params, runner)
 
 
 __all__ = [
     "HISTO_COMPUTE_JOINT_DENSITY_METADATA",
     "HistoComputeJointDensityOutputs",
-    "HistoComputeJointDensityParameters",
     "histo_compute_joint_density",
+    "histo_compute_joint_density_execute",
     "histo_compute_joint_density_params",
 ]

niwrap_freesurfer/freesurfer/histo_register_block.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HISTO_REGISTER_BLOCK_METADATA = Metadata(
-    id="1572900c1097b5f831c522fde78dfc03b4370b94.boutiques",
+    id="76fb5f1c5ea02886af54d968d979687c9896e8c2.boutiques",
     name="histo_register_block",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ HISTO_REGISTER_BLOCK_METADATA = Metadata(
 
 
 HistoRegisterBlockParameters = typing.TypedDict('HistoRegisterBlockParameters', {
-    "__STYXTYPE__": typing.Literal["histo_register_block"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/histo_register_block"]],
+    "seg_time1": InputPathType,
+    "seg_time2": InputPathType,
+    "transform1": InputPathType,
+    "transform2": InputPathType,
+    "output_file": str,
+    "out_like": typing.NotRequired[InputPathType | None],
+    "invert_transform": bool,
+})
+HistoRegisterBlockParametersTagged = typing.TypedDict('HistoRegisterBlockParametersTagged', {
+    "@type": typing.Literal["freesurfer/histo_register_block"],
     "seg_time1": InputPathType,
     "seg_time2": InputPathType,
     "transform1": InputPathType,
@@ -23,43 +33,11 @@ HistoRegisterBlockParameters = typing.TypedDict('HistoRegisterBlockParameters',
     "out_like": typing.NotRequired[InputPathType | None],
     "invert_transform": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "histo_register_block": histo_register_block_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 {
-        "histo_register_block": histo_register_block_outputs,
-    }.get(t)
 
 
 class HistoRegisterBlockOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `histo_register_block(...)`.
+    Output object returned when calling `HistoRegisterBlockParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def histo_register_block_params(
     output_file: str,
     out_like: InputPathType | None = None,
     invert_transform: bool = False,
-) -> HistoRegisterBlockParameters:
+) -> HistoRegisterBlockParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def histo_register_block_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "histo_register_block",
+        "@type": "freesurfer/histo_register_block",
         "seg_time1": seg_time1,
         "seg_time2": seg_time2,
         "transform1": transform1,
@@ -119,17 +97,17 @@ def histo_register_block_cargs(
     """
     cargs = []
     cargs.append("histo_register_block")
-    cargs.append(execution.input_file(params.get("seg_time1")))
-    cargs.append(execution.input_file(params.get("seg_time2")))
-    cargs.append(execution.input_file(params.get("transform1")))
-    cargs.append(execution.input_file(params.get("transform2")))
-    cargs.append(params.get("output_file"))
-    if params.get("out_like") is not None:
+    cargs.append(execution.input_file(params.get("seg_time1", None)))
+    cargs.append(execution.input_file(params.get("seg_time2", None)))
+    cargs.append(execution.input_file(params.get("transform1", None)))
+    cargs.append(execution.input_file(params.get("transform2", None)))
+    cargs.append(params.get("output_file", None))
+    if params.get("out_like", None) is not None:
         cargs.extend([
             "-out_like",
-            execution.input_file(params.get("out_like"))
+            execution.input_file(params.get("out_like", None))
         ])
-    if params.get("invert_transform"):
+    if params.get("invert_transform", False):
         cargs.append("-I")
     return cargs
 
@@ -149,16 +127,18 @@ def histo_register_block_outputs(
     """
     ret = HistoRegisterBlockOutputs(
         root=execution.output_file("."),
-        aligned_output=execution.output_file(params.get("output_file")),
+        aligned_output=execution.output_file(params.get("output_file", None)),
     )
     return ret
 
 
 def histo_register_block_execute(
     params: HistoRegisterBlockParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> HistoRegisterBlockOutputs:
     """
+    histo_register_block
+    
     A tool to align a histological slice with a block face image.
     
     Author: FreeSurfer Developers
@@ -167,10 +147,12 @@ def histo_register_block_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `HistoRegisterBlockOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HISTO_REGISTER_BLOCK_METADATA)
     params = execution.params(params)
     cargs = histo_register_block_cargs(params, execution)
     ret = histo_register_block_outputs(params, execution)
@@ -189,6 +171,8 @@ def histo_register_block(
     runner: Runner | None = None,
 ) -> HistoRegisterBlockOutputs:
     """
+    histo_register_block
+    
     A tool to align a histological slice with a block face image.
     
     Author: FreeSurfer Developers
@@ -207,8 +191,6 @@ def histo_register_block(
     Returns:
         NamedTuple of outputs (described in `HistoRegisterBlockOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(HISTO_REGISTER_BLOCK_METADATA)
     params = histo_register_block_params(
         seg_time1=seg_time1,
         seg_time2=seg_time2,
@@ -218,13 +200,13 @@ def histo_register_block(
         out_like=out_like,
         invert_transform=invert_transform,
     )
-    return histo_register_block_execute(params, execution)
+    return histo_register_block_execute(params, runner)
 
 
 __all__ = [
     "HISTO_REGISTER_BLOCK_METADATA",
     "HistoRegisterBlockOutputs",
-    "HistoRegisterBlockParameters",
     "histo_register_block",
+    "histo_register_block_execute",
     "histo_register_block_params",
 ]

niwrap_freesurfer/freesurfer/histo_synthesize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 HISTO_SYNTHESIZE_METADATA = Metadata(
-    id="946fc632c928dd4853d72358819684fced1a0ab5.boutiques",
+    id="22328b0a53f00b2d16b4d4c6b5dab0dfb12a1d70.boutiques",
     name="histo_synthesize",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ HISTO_SYNTHESIZE_METADATA = Metadata(
 
 
 HistoSynthesizeParameters = typing.TypedDict('HistoSynthesizeParameters', {
-    "__STYXTYPE__": typing.Literal["histo_synthesize"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/histo_synthesize"]],
+    "mri_volume": InputPathType,
+    "histo_volume": InputPathType,
+    "synthetic_histo": str,
+})
+HistoSynthesizeParametersTagged = typing.TypedDict('HistoSynthesizeParametersTagged', {
+    "@type": typing.Literal["freesurfer/histo_synthesize"],
     "mri_volume": InputPathType,
     "histo_volume": InputPathType,
     "synthetic_histo": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "histo_synthesize": histo_synthesize_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 {
-        "histo_synthesize": histo_synthesize_outputs,
-    }.get(t)
 
 
 class HistoSynthesizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `histo_synthesize(...)`.
+    Output object returned when calling `HistoSynthesizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def histo_synthesize_params(
     mri_volume: InputPathType,
     histo_volume: InputPathType,
     synthetic_histo: str,
-) -> HistoSynthesizeParameters:
+) -> HistoSynthesizeParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def histo_synthesize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "histo_synthesize",
+        "@type": "freesurfer/histo_synthesize",
         "mri_volume": mri_volume,
         "histo_volume": histo_volume,
         "synthetic_histo": synthetic_histo,
@@ -102,9 +76,9 @@ def histo_synthesize_cargs(
     """
     cargs = []
     cargs.append("histo_synthesize")
-    cargs.append(execution.input_file(params.get("mri_volume")))
-    cargs.append(execution.input_file(params.get("histo_volume")))
-    cargs.append(params.get("synthetic_histo"))
+    cargs.append(execution.input_file(params.get("mri_volume", None)))
+    cargs.append(execution.input_file(params.get("histo_volume", None)))
+    cargs.append(params.get("synthetic_histo", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def histo_synthesize_outputs(
     """
     ret = HistoSynthesizeOutputs(
         root=execution.output_file("."),
-        output_synthetic_histo=execution.output_file(params.get("synthetic_histo")),
+        output_synthetic_histo=execution.output_file(params.get("synthetic_histo", None)),
     )
     return ret
 
 
 def histo_synthesize_execute(
     params: HistoSynthesizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> HistoSynthesizeOutputs:
     """
+    histo_synthesize
+    
     Tool for synthesizing histology-like volumes from MRI data.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def histo_synthesize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `HistoSynthesizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(HISTO_SYNTHESIZE_METADATA)
     params = execution.params(params)
     cargs = histo_synthesize_cargs(params, execution)
     ret = histo_synthesize_outputs(params, execution)
@@ -159,6 +137,8 @@ def histo_synthesize(
     runner: Runner | None = None,
 ) -> HistoSynthesizeOutputs:
     """
+    histo_synthesize
+    
     Tool for synthesizing histology-like volumes from MRI data.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def histo_synthesize(
     Returns:
         NamedTuple of outputs (described in `HistoSynthesizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(HISTO_SYNTHESIZE_METADATA)
     params = histo_synthesize_params(
         mri_volume=mri_volume,
         histo_volume=histo_volume,
         synthetic_histo=synthetic_histo,
     )
-    return histo_synthesize_execute(params, execution)
+    return histo_synthesize_execute(params, runner)
 
 
 __all__ = [
     "HISTO_SYNTHESIZE_METADATA",
     "HistoSynthesizeOutputs",
-    "HistoSynthesizeParameters",
     "histo_synthesize",
+    "histo_synthesize_execute",
     "histo_synthesize_params",
 ]