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

niwrap_freesurfer/freesurfer/mpr2mni305.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MPR2MNI305_METADATA = Metadata(
-    id="43f9475eba43e43bb6641a614ad0e97898040bbb.boutiques",
+    id="06578c48b79fc7cf0a25d7f90572e339f54dc80e.boutiques",
     name="mpr2mni305",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ MPR2MNI305_METADATA = Metadata(
 
 
 Mpr2mni305Parameters = typing.TypedDict('Mpr2mni305Parameters', {
-    "__STYXTYPE__": typing.Literal["mpr2mni305"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mpr2mni305"]],
+    "mpr_anat": str,
+})
+Mpr2mni305ParametersTagged = typing.TypedDict('Mpr2mni305ParametersTagged', {
+    "@type": typing.Literal["freesurfer/mpr2mni305"],
     "mpr_anat": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mpr2mni305": mpr2mni305_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 Mpr2mni305Outputs(typing.NamedTuple):
     """
-    Output object returned when calling `mpr2mni305(...)`.
+    Output object returned when calling `Mpr2mni305Parameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class Mpr2mni305Outputs(typing.NamedTuple):
 
 def mpr2mni305_params(
     mpr_anat: str,
-) -> Mpr2mni305Parameters:
+) -> Mpr2mni305ParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def mpr2mni305_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mpr2mni305",
+        "@type": "freesurfer/mpr2mni305",
         "mpr_anat": mpr_anat,
     }
     return params
@@ -91,7 +64,7 @@ def mpr2mni305_cargs(
     """
     cargs = []
     cargs.append("mpr2mni305")
-    cargs.append(params.get("mpr_anat"))
+    cargs.append(params.get("mpr_anat", None))
     return cargs
 
 
@@ -116,9 +89,11 @@ def mpr2mni305_outputs(
 
 def mpr2mni305_execute(
     params: Mpr2mni305Parameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Mpr2mni305Outputs:
     """
+    mpr2mni305
+    
     Tool for transforming MPRAGE dataset to MNI305 coordinate space.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def mpr2mni305_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Mpr2mni305Outputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MPR2MNI305_METADATA)
     params = execution.params(params)
     cargs = mpr2mni305_cargs(params, execution)
     ret = mpr2mni305_outputs(params, execution)
@@ -143,6 +120,8 @@ def mpr2mni305(
     runner: Runner | None = None,
 ) -> Mpr2mni305Outputs:
     """
+    mpr2mni305
+    
     Tool for transforming MPRAGE dataset to MNI305 coordinate space.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def mpr2mni305(
     Returns:
         NamedTuple of outputs (described in `Mpr2mni305Outputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MPR2MNI305_METADATA)
     params = mpr2mni305_params(
         mpr_anat=mpr_anat,
     )
-    return mpr2mni305_execute(params, execution)
+    return mpr2mni305_execute(params, runner)
 
 
 __all__ = [
     "MPR2MNI305_METADATA",
     "Mpr2mni305Outputs",
-    "Mpr2mni305Parameters",
     "mpr2mni305",
+    "mpr2mni305_execute",
     "mpr2mni305_params",
 ]

niwrap_freesurfer/freesurfer/mri_3d_photo_recon.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_3D_PHOTO_RECON_METADATA = Metadata(
-    id="1da2f095a43ac3c7dfc286883ae9220b1018660e.boutiques",
+    id="4cb1261f10c23cef2b43151076bcd523107af056.boutiques",
     name="mri_3d_photo_recon",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRI_3D_PHOTO_RECON_METADATA = Metadata(
 
 
 Mri3dPhotoReconParameters = typing.TypedDict('Mri3dPhotoReconParameters', {
-    "__STYXTYPE__": typing.Literal["mri_3d_photo_recon"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_3d_photo_recon"]],
+    "input_photo_dir": list[InputPathType],
+    "input_segmentation_dir": list[InputPathType],
+    "slice_thickness": float,
+    "photo_resolution": float,
+    "output_directory": str,
+    "ref_mask": typing.NotRequired[InputPathType | None],
+    "ref_surface": typing.NotRequired[InputPathType | None],
+    "ref_soft_mask": typing.NotRequired[InputPathType | None],
+    "mesh_reorient_with_indices": typing.NotRequired[str | None],
+    "photos_posterior_side": bool,
+    "order_posterior_to_anterior": bool,
+    "allow_z_stretch": bool,
+    "rigid_only_for_photos": bool,
+    "gpu_index": typing.NotRequired[float | None],
+})
+Mri3dPhotoReconParametersTagged = typing.TypedDict('Mri3dPhotoReconParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_3d_photo_recon"],
     "input_photo_dir": list[InputPathType],
     "input_segmentation_dir": list[InputPathType],
     "slice_thickness": float,
@@ -30,43 +47,11 @@ Mri3dPhotoReconParameters = typing.TypedDict('Mri3dPhotoReconParameters', {
     "rigid_only_for_photos": bool,
     "gpu_index": 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 {
-        "mri_3d_photo_recon": mri_3d_photo_recon_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 {
-        "mri_3d_photo_recon": mri_3d_photo_recon_outputs,
-    }.get(t)
 
 
 class Mri3dPhotoReconOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_3d_photo_recon(...)`.
+    Output object returned when calling `Mri3dPhotoReconParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def mri_3d_photo_recon_params(
     allow_z_stretch: bool = False,
     rigid_only_for_photos: bool = False,
     gpu_index: float | None = None,
-) -> Mri3dPhotoReconParameters:
+) -> Mri3dPhotoReconParametersTagged:
     """
     Build parameters.
     
@@ -123,7 +108,7 @@ def mri_3d_photo_recon_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_3d_photo_recon",
+        "@type": "freesurfer/mri_3d_photo_recon",
         "input_photo_dir": input_photo_dir,
         "input_segmentation_dir": input_segmentation_dir,
         "slice_thickness": slice_thickness,
@@ -164,56 +149,56 @@ def mri_3d_photo_recon_cargs(
     cargs.append("mri_3d_photo_recon")
     cargs.extend([
         "--input_photo_dir",
-        *[execution.input_file(f) for f in params.get("input_photo_dir")]
+        *[execution.input_file(f) for f in params.get("input_photo_dir", None)]
     ])
     cargs.extend([
         "--input_segmentation_dir",
-        *[execution.input_file(f) for f in params.get("input_segmentation_dir")]
+        *[execution.input_file(f) for f in params.get("input_segmentation_dir", None)]
     ])
     cargs.extend([
         "--slice_thickness",
-        str(params.get("slice_thickness"))
+        str(params.get("slice_thickness", None))
     ])
     cargs.extend([
         "--photo_resolution",
-        str(params.get("photo_resolution"))
+        str(params.get("photo_resolution", None))
     ])
     cargs.extend([
         "--output_directory",
-        params.get("output_directory")
+        params.get("output_directory", None)
     ])
-    if params.get("ref_mask") is not None:
+    if params.get("ref_mask", None) is not None:
         cargs.extend([
             "--ref_mask",
-            execution.input_file(params.get("ref_mask"))
+            execution.input_file(params.get("ref_mask", None))
         ])
-    if params.get("ref_surface") is not None:
+    if params.get("ref_surface", None) is not None:
         cargs.extend([
             "--ref_surface",
-            execution.input_file(params.get("ref_surface"))
+            execution.input_file(params.get("ref_surface", None))
         ])
-    if params.get("ref_soft_mask") is not None:
+    if params.get("ref_soft_mask", None) is not None:
         cargs.extend([
             "--ref_soft_mask",
-            execution.input_file(params.get("ref_soft_mask"))
+            execution.input_file(params.get("ref_soft_mask", None))
         ])
-    if params.get("mesh_reorient_with_indices") is not None:
+    if params.get("mesh_reorient_with_indices", None) is not None:
         cargs.extend([
             "--mesh_reorient_with_indices",
-            params.get("mesh_reorient_with_indices")
+            params.get("mesh_reorient_with_indices", None)
         ])
-    if params.get("photos_posterior_side"):
+    if params.get("photos_posterior_side", False):
         cargs.append("--photos_of_posterior_side")
-    if params.get("order_posterior_to_anterior"):
+    if params.get("order_posterior_to_anterior", False):
         cargs.append("--order_posterior_to_anterior")
-    if params.get("allow_z_stretch"):
+    if params.get("allow_z_stretch", False):
         cargs.append("--allow_z_stretch")
-    if params.get("rigid_only_for_photos"):
+    if params.get("rigid_only_for_photos", False):
         cargs.append("--rigid_only_for_photos")
-    if params.get("gpu_index") is not None:
+    if params.get("gpu_index", None) is not None:
         cargs.extend([
             "--gpu",
-            str(params.get("gpu_index"))
+            str(params.get("gpu_index", None))
         ])
     return cargs
 
@@ -233,17 +218,19 @@ def mri_3d_photo_recon_outputs(
     """
     ret = Mri3dPhotoReconOutputs(
         root=execution.output_file("."),
-        reconstructed_volume=execution.output_file(params.get("output_directory") + "/reconstructed_volume.nii.gz"),
-        reference_data=execution.output_file(params.get("output_directory") + "/reference_data.nii.gz"),
+        reconstructed_volume=execution.output_file(params.get("output_directory", None) + "/reconstructed_volume.nii.gz"),
+        reference_data=execution.output_file(params.get("output_directory", None) + "/reference_data.nii.gz"),
     )
     return ret
 
 
 def mri_3d_photo_recon_execute(
     params: Mri3dPhotoReconParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Mri3dPhotoReconOutputs:
     """
+    mri_3d_photo_recon
+    
     Code for 3D photo reconstruction (Tregidgo, et al., MICCAI 2020).
     
     Author: FreeSurfer Developers
@@ -252,10 +239,12 @@ def mri_3d_photo_recon_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Mri3dPhotoReconOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_3D_PHOTO_RECON_METADATA)
     params = execution.params(params)
     cargs = mri_3d_photo_recon_cargs(params, execution)
     ret = mri_3d_photo_recon_outputs(params, execution)
@@ -281,6 +270,8 @@ def mri_3d_photo_recon(
     runner: Runner | None = None,
 ) -> Mri3dPhotoReconOutputs:
     """
+    mri_3d_photo_recon
+    
     Code for 3D photo reconstruction (Tregidgo, et al., MICCAI 2020).
     
     Author: FreeSurfer Developers
@@ -315,8 +306,6 @@ def mri_3d_photo_recon(
     Returns:
         NamedTuple of outputs (described in `Mri3dPhotoReconOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_3D_PHOTO_RECON_METADATA)
     params = mri_3d_photo_recon_params(
         input_photo_dir=input_photo_dir,
         input_segmentation_dir=input_segmentation_dir,
@@ -333,13 +322,13 @@ def mri_3d_photo_recon(
         rigid_only_for_photos=rigid_only_for_photos,
         gpu_index=gpu_index,
     )
-    return mri_3d_photo_recon_execute(params, execution)
+    return mri_3d_photo_recon_execute(params, runner)
 
 
 __all__ = [
     "MRI_3D_PHOTO_RECON_METADATA",
     "Mri3dPhotoReconOutputs",
-    "Mri3dPhotoReconParameters",
     "mri_3d_photo_recon",
+    "mri_3d_photo_recon_execute",
     "mri_3d_photo_recon_params",
 ]

niwrap_freesurfer/freesurfer/mri_add_new_tp.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_ADD_NEW_TP_METADATA = Metadata(
-    id="c092850ac196635799818218f41e6c048de46b98.boutiques",
+    id="1cba05d89df7914334369b19d68a4c6b3c2c3c76.boutiques",
     name="mri_add_new_tp",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ MRI_ADD_NEW_TP_METADATA = Metadata(
 
 
 MriAddNewTpParameters = typing.TypedDict('MriAddNewTpParameters', {
-    "__STYXTYPE__": typing.Literal["mri_add_new_tp"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_add_new_tp"]],
+    "base_id": str,
+    "newtp_id": str,
+})
+MriAddNewTpParametersTagged = typing.TypedDict('MriAddNewTpParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_add_new_tp"],
     "base_id": str,
     "newtp_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 {
-        "mri_add_new_tp": mri_add_new_tp_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 MriAddNewTpOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_add_new_tp(...)`.
+    Output object returned when calling `MriAddNewTpParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class MriAddNewTpOutputs(typing.NamedTuple):
 def mri_add_new_tp_params(
     base_id: str,
     newtp_id: str,
-) -> MriAddNewTpParameters:
+) -> MriAddNewTpParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def mri_add_new_tp_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_add_new_tp",
+        "@type": "freesurfer/mri_add_new_tp",
         "base_id": base_id,
         "newtp_id": newtp_id,
     }
@@ -95,8 +69,8 @@ def mri_add_new_tp_cargs(
     """
     cargs = []
     cargs.append("mri_add_new_tp")
-    cargs.append(params.get("base_id"))
-    cargs.append(params.get("newtp_id"))
+    cargs.append(params.get("base_id", None))
+    cargs.append(params.get("newtp_id", None))
     return cargs
 
 
@@ -121,11 +95,13 @@ def mri_add_new_tp_outputs(
 
 def mri_add_new_tp_execute(
     params: MriAddNewTpParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriAddNewTpOutputs:
     """
-    Adds a new time point to the base/template without re-creating the base. Only
-    the new time point needs to be run longitudinally.
+    mri_add_new_tp
+    
+    Adds a new time point to the base/template without re-creating the base.
+    Only the new time point needs to be run longitudinally.
     
     Author: FreeSurfer Developers
     
@@ -133,10 +109,12 @@ def mri_add_new_tp_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriAddNewTpOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_ADD_NEW_TP_METADATA)
     params = execution.params(params)
     cargs = mri_add_new_tp_cargs(params, execution)
     ret = mri_add_new_tp_outputs(params, execution)
@@ -150,8 +128,10 @@ def mri_add_new_tp(
     runner: Runner | None = None,
 ) -> MriAddNewTpOutputs:
     """
-    Adds a new time point to the base/template without re-creating the base. Only
-    the new time point needs to be run longitudinally.
+    mri_add_new_tp
+    
+    Adds a new time point to the base/template without re-creating the base.
+    Only the new time point needs to be run longitudinally.
     
     Author: FreeSurfer Developers
     
@@ -164,19 +144,17 @@ def mri_add_new_tp(
     Returns:
         NamedTuple of outputs (described in `MriAddNewTpOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_ADD_NEW_TP_METADATA)
     params = mri_add_new_tp_params(
         base_id=base_id,
         newtp_id=newtp_id,
     )
-    return mri_add_new_tp_execute(params, execution)
+    return mri_add_new_tp_execute(params, runner)
 
 
 __all__ = [
     "MRI_ADD_NEW_TP_METADATA",
     "MriAddNewTpOutputs",
-    "MriAddNewTpParameters",
     "mri_add_new_tp",
+    "mri_add_new_tp_execute",
     "mri_add_new_tp_params",
 ]