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

niwrap_freesurfer/freesurfer/mri_ca_train.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CA_TRAIN_METADATA = Metadata(
-    id="3dbdf0aa633756ed33c361f4c0f3860b2e8de014.boutiques",
+    id="5159ad2b2c35b0a95761ed86cb83c9e1c6ccb58c.boutiques",
     name="mri_ca_train",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,24 @@ MRI_CA_TRAIN_METADATA = Metadata(
 
 
 MriCaTrainParameters = typing.TypedDict('MriCaTrainParameters', {
-    "__STYXTYPE__": typing.Literal["mri_ca_train"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_ca_train"]],
+    "subjects": list[str],
+    "output_gca": str,
+    "segmentation": str,
+    "transform": typing.NotRequired[str | None],
+    "mask_volume": typing.NotRequired[str | None],
+    "node_spacing": typing.NotRequired[str | None],
+    "prior_spacing": typing.NotRequired[str | None],
+    "input_training": typing.NotRequired[list[str] | None],
+    "symmetrize": bool,
+    "makesym": typing.NotRequired[list[str] | None],
+    "check_symmetry": typing.NotRequired[list[str] | None],
+    "sanity_check": bool,
+    "threads": typing.NotRequired[int | None],
+    "done_file": typing.NotRequired[str | None],
+})
+MriCaTrainParametersTagged = typing.TypedDict('MriCaTrainParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_ca_train"],
     "subjects": list[str],
     "output_gca": str,
     "segmentation": str,
@@ -30,42 +47,11 @@ MriCaTrainParameters = typing.TypedDict('MriCaTrainParameters', {
     "threads": typing.NotRequired[int | None],
     "done_file": 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 {
-        "mri_ca_train": mri_ca_train_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 MriCaTrainOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_ca_train(...)`.
+    Output object returned when calling `MriCaTrainParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +72,7 @@ def mri_ca_train_params(
     sanity_check: bool = False,
     threads: int | None = None,
     done_file: str | None = None,
-) -> MriCaTrainParameters:
+) -> MriCaTrainParametersTagged:
     """
     Build parameters.
     
@@ -116,7 +102,7 @@ def mri_ca_train_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_ca_train",
+        "@type": "freesurfer/mri_ca_train",
         "subjects": subjects,
         "output_gca": output_gca,
         "segmentation": segmentation,
@@ -159,60 +145,60 @@ def mri_ca_train_cargs(
     """
     cargs = []
     cargs.append("mri_ca_train")
-    cargs.extend(params.get("subjects"))
-    cargs.append(params.get("output_gca"))
+    cargs.extend(params.get("subjects", None))
+    cargs.append(params.get("output_gca", None))
     cargs.extend([
         "-seg",
-        params.get("segmentation")
+        params.get("segmentation", None)
     ])
-    if params.get("transform") is not None:
+    if params.get("transform", None) is not None:
         cargs.extend([
             "-xform",
-            params.get("transform")
+            params.get("transform", None)
         ])
-    if params.get("mask_volume") is not None:
+    if params.get("mask_volume", None) is not None:
         cargs.extend([
             "-mask",
-            params.get("mask_volume")
+            params.get("mask_volume", None)
         ])
-    if params.get("node_spacing") is not None:
+    if params.get("node_spacing", None) is not None:
         cargs.extend([
             "-node_spacing",
-            params.get("node_spacing")
+            params.get("node_spacing", None)
         ])
-    if params.get("prior_spacing") is not None:
+    if params.get("prior_spacing", None) is not None:
         cargs.extend([
             "-prior_spacing",
-            params.get("prior_spacing")
+            params.get("prior_spacing", None)
         ])
-    if params.get("input_training") is not None:
+    if params.get("input_training", None) is not None:
         cargs.extend([
             "-input",
-            *params.get("input_training")
+            *params.get("input_training", None)
         ])
-    if params.get("symmetrize"):
+    if params.get("symmetrize", False):
         cargs.append("-sym")
-    if params.get("makesym") is not None:
+    if params.get("makesym", None) is not None:
         cargs.extend([
             "-makesym",
-            *params.get("makesym")
+            *params.get("makesym", None)
         ])
-    if params.get("check_symmetry") is not None:
+    if params.get("check_symmetry", None) is not None:
         cargs.extend([
             "-checksym",
-            *params.get("check_symmetry")
+            *params.get("check_symmetry", None)
         ])
-    if params.get("sanity_check"):
+    if params.get("sanity_check", False):
         cargs.append("-check")
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "-threads",
-            str(params.get("threads"))
+            str(params.get("threads", None))
         ])
-    if params.get("done_file") is not None:
+    if params.get("done_file", None) is not None:
         cargs.extend([
             "-done",
-            params.get("done_file")
+            params.get("done_file", None)
         ])
     return cargs
 
@@ -238,11 +224,13 @@ def mri_ca_train_outputs(
 
 def mri_ca_train_execute(
     params: MriCaTrainParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCaTrainOutputs:
     """
-    Trains GCA data with multiple subjects using provided segmentation volumes and
-    other configuration.
+    mri_ca_train
+    
+    Trains GCA data with multiple subjects using provided segmentation volumes
+    and other configuration.
     
     Author: FreeSurfer Developers
     
@@ -250,10 +238,12 @@ def mri_ca_train_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCaTrainOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CA_TRAIN_METADATA)
     params = execution.params(params)
     cargs = mri_ca_train_cargs(params, execution)
     ret = mri_ca_train_outputs(params, execution)
@@ -279,8 +269,10 @@ def mri_ca_train(
     runner: Runner | None = None,
 ) -> MriCaTrainOutputs:
     """
-    Trains GCA data with multiple subjects using provided segmentation volumes and
-    other configuration.
+    mri_ca_train
+    
+    Trains GCA data with multiple subjects using provided segmentation volumes
+    and other configuration.
     
     Author: FreeSurfer Developers
     
@@ -312,8 +304,6 @@ def mri_ca_train(
     Returns:
         NamedTuple of outputs (described in `MriCaTrainOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CA_TRAIN_METADATA)
     params = mri_ca_train_params(
         subjects=subjects,
         output_gca=output_gca,
@@ -330,13 +320,13 @@ def mri_ca_train(
         threads=threads,
         done_file=done_file,
     )
-    return mri_ca_train_execute(params, execution)
+    return mri_ca_train_execute(params, runner)
 
 
 __all__ = [
     "MRI_CA_TRAIN_METADATA",
     "MriCaTrainOutputs",
-    "MriCaTrainParameters",
     "mri_ca_train",
+    "mri_ca_train_execute",
     "mri_ca_train_params",
 ]

niwrap_freesurfer/freesurfer/mri_cal_renormalize_gca.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CAL_RENORMALIZE_GCA_METADATA = Metadata(
-    id="14248dd0e801de44865ab35dbf488e7e2c657ff0.boutiques",
+    id="3427802787eacffbf4678b2765d22730cfcc5c16.boutiques",
     name="mri_cal_renormalize_gca",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ MRI_CAL_RENORMALIZE_GCA_METADATA = Metadata(
 
 
 MriCalRenormalizeGcaParameters = typing.TypedDict('MriCalRenormalizeGcaParameters', {
-    "__STYXTYPE__": typing.Literal["mri_cal_renormalize_gca"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_cal_renormalize_gca"]],
+    "timepoint_file": InputPathType,
+    "in_vol": InputPathType,
+    "input_atlas": InputPathType,
+    "transform_file": InputPathType,
+    "output_atlas": str,
+})
+MriCalRenormalizeGcaParametersTagged = typing.TypedDict('MriCalRenormalizeGcaParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_cal_renormalize_gca"],
     "timepoint_file": InputPathType,
     "in_vol": InputPathType,
     "input_atlas": InputPathType,
     "transform_file": InputPathType,
     "output_atlas": 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_cal_renormalize_gca": mri_cal_renormalize_gca_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_cal_renormalize_gca": mri_cal_renormalize_gca_outputs,
-    }.get(t)
 
 
 class MriCalRenormalizeGcaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_cal_renormalize_gca(...)`.
+    Output object returned when calling `MriCalRenormalizeGcaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def mri_cal_renormalize_gca_params(
     input_atlas: InputPathType,
     transform_file: InputPathType,
     output_atlas: str,
-) -> MriCalRenormalizeGcaParameters:
+) -> MriCalRenormalizeGcaParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def mri_cal_renormalize_gca_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_cal_renormalize_gca",
+        "@type": "freesurfer/mri_cal_renormalize_gca",
         "timepoint_file": timepoint_file,
         "in_vol": in_vol,
         "input_atlas": input_atlas,
@@ -110,11 +86,11 @@ def mri_cal_renormalize_gca_cargs(
     """
     cargs = []
     cargs.append("mri_cal_renormalize_gca")
-    cargs.append(execution.input_file(params.get("timepoint_file")))
-    cargs.append(execution.input_file(params.get("in_vol")))
-    cargs.append(execution.input_file(params.get("input_atlas")))
-    cargs.append(execution.input_file(params.get("transform_file")))
-    cargs.append(params.get("output_atlas"))
+    cargs.append(execution.input_file(params.get("timepoint_file", None)))
+    cargs.append(execution.input_file(params.get("in_vol", None)))
+    cargs.append(execution.input_file(params.get("input_atlas", None)))
+    cargs.append(execution.input_file(params.get("transform_file", None)))
+    cargs.append(params.get("output_atlas", None))
     return cargs
 
 
@@ -133,16 +109,18 @@ def mri_cal_renormalize_gca_outputs(
     """
     ret = MriCalRenormalizeGcaOutputs(
         root=execution.output_file("."),
-        output_atlas_file=execution.output_file(params.get("output_atlas")),
+        output_atlas_file=execution.output_file(params.get("output_atlas", None)),
     )
     return ret
 
 
 def mri_cal_renormalize_gca_execute(
     params: MriCalRenormalizeGcaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCalRenormalizeGcaOutputs:
     """
+    mri_cal_renormalize_gca
+    
     Tool for atlas renormalization in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -151,10 +129,12 @@ def mri_cal_renormalize_gca_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCalRenormalizeGcaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CAL_RENORMALIZE_GCA_METADATA)
     params = execution.params(params)
     cargs = mri_cal_renormalize_gca_cargs(params, execution)
     ret = mri_cal_renormalize_gca_outputs(params, execution)
@@ -171,6 +151,8 @@ def mri_cal_renormalize_gca(
     runner: Runner | None = None,
 ) -> MriCalRenormalizeGcaOutputs:
     """
+    mri_cal_renormalize_gca
+    
     Tool for atlas renormalization in FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -187,8 +169,6 @@ def mri_cal_renormalize_gca(
     Returns:
         NamedTuple of outputs (described in `MriCalRenormalizeGcaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CAL_RENORMALIZE_GCA_METADATA)
     params = mri_cal_renormalize_gca_params(
         timepoint_file=timepoint_file,
         in_vol=in_vol,
@@ -196,13 +176,13 @@ def mri_cal_renormalize_gca(
         transform_file=transform_file,
         output_atlas=output_atlas,
     )
-    return mri_cal_renormalize_gca_execute(params, execution)
+    return mri_cal_renormalize_gca_execute(params, runner)
 
 
 __all__ = [
     "MRI_CAL_RENORMALIZE_GCA_METADATA",
     "MriCalRenormalizeGcaOutputs",
-    "MriCalRenormalizeGcaParameters",
     "mri_cal_renormalize_gca",
+    "mri_cal_renormalize_gca_execute",
     "mri_cal_renormalize_gca_params",
 ]

niwrap_freesurfer/freesurfer/mri_cc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CC_METADATA = Metadata(
-    id="587b9657e3019c8eef25c4532b4599586af52fc7.boutiques",
+    id="d318bda8342a63ef83b48c3583a7df0c903372c4.boutiques",
     name="mri_cc",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_CC_METADATA = Metadata(
 
 
 MriCcParameters = typing.TypedDict('MriCcParameters', {
-    "__STYXTYPE__": typing.Literal["mri_cc"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_cc"]],
+    "subject_name": str,
+    "output_file": typing.NotRequired[str | None],
+    "aseg_file": typing.NotRequired[InputPathType | None],
+    "norm_file": typing.NotRequired[InputPathType | None],
+    "sdir": typing.NotRequired[str | None],
+    "rotation_lta": typing.NotRequired[InputPathType | None],
+    "force_flag": bool,
+    "include_fornix": bool,
+    "compartments": typing.NotRequired[float | None],
+    "thickness": typing.NotRequired[float | None],
+    "skip_voxels": typing.NotRequired[float | None],
+    "max_rotation": typing.NotRequired[float | None],
+})
+MriCcParametersTagged = typing.TypedDict('MriCcParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_cc"],
     "subject_name": str,
     "output_file": typing.NotRequired[str | None],
     "aseg_file": typing.NotRequired[InputPathType | None],
@@ -28,43 +43,11 @@ MriCcParameters = typing.TypedDict('MriCcParameters', {
     "skip_voxels": typing.NotRequired[float | None],
     "max_rotation": 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_cc": mri_cc_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_cc": mri_cc_outputs,
-    }.get(t)
 
 
 class MriCcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_cc(...)`.
+    Output object returned when calling `MriCcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,8 +67,8 @@ def mri_cc_params(
     compartments: float | None = None,
     thickness: float | None = None,
     skip_voxels: float | None = None,
-    max_rotation: float | None = 7.0,
-) -> MriCcParameters:
+    max_rotation: float | None = None,
+) -> MriCcParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +89,7 @@ def mri_cc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_cc",
+        "@type": "freesurfer/mri_cc",
         "subject_name": subject_name,
         "force_flag": force_flag,
         "include_fornix": include_fornix,
@@ -147,55 +130,55 @@ def mri_cc_cargs(
     """
     cargs = []
     cargs.append("mri_cc")
-    cargs.append(params.get("subject_name"))
-    if params.get("output_file") is not None:
+    cargs.append(params.get("subject_name", None))
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-o",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("aseg_file") is not None:
+    if params.get("aseg_file", None) is not None:
         cargs.extend([
             "-aseg",
-            execution.input_file(params.get("aseg_file"))
+            execution.input_file(params.get("aseg_file", None))
         ])
-    if params.get("norm_file") is not None:
+    if params.get("norm_file", None) is not None:
         cargs.extend([
             "-norm",
-            execution.input_file(params.get("norm_file"))
+            execution.input_file(params.get("norm_file", None))
         ])
-    if params.get("sdir") is not None:
+    if params.get("sdir", None) is not None:
         cargs.extend([
             "-sdir",
-            params.get("sdir")
+            params.get("sdir", None)
         ])
-    if params.get("rotation_lta") is not None:
+    if params.get("rotation_lta", None) is not None:
         cargs.extend([
             "-lta",
-            execution.input_file(params.get("rotation_lta"))
+            execution.input_file(params.get("rotation_lta", None))
         ])
-    if params.get("force_flag"):
+    if params.get("force_flag", False):
         cargs.append("-force")
-    if params.get("include_fornix"):
+    if params.get("include_fornix", False):
         cargs.append("-f")
-    if params.get("compartments") is not None:
+    if params.get("compartments", None) is not None:
         cargs.extend([
             "-d",
-            str(params.get("compartments"))
+            str(params.get("compartments", None))
         ])
-    if params.get("thickness") is not None:
+    if params.get("thickness", None) is not None:
         cargs.extend([
             "-t",
-            str(params.get("thickness"))
+            str(params.get("thickness", None))
         ])
-    if params.get("skip_voxels") is not None:
+    if params.get("skip_voxels", None) is not None:
         cargs.extend([
             "-s",
-            str(params.get("skip_voxels"))
+            str(params.get("skip_voxels", None))
         ])
-    if params.get("max_rotation") is not None:
+    if params.get("max_rotation", None) is not None:
         cargs.extend([
             "-m",
-            str(params.get("max_rotation"))
+            str(params.get("max_rotation", None))
         ])
     return cargs
 
@@ -215,16 +198,18 @@ def mri_cc_outputs(
     """
     ret = MriCcOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file("SDIR/mri/" + params.get("output_file")) if (params.get("output_file") is not None) else None,
+        output_volume=execution.output_file("SDIR/mri/" + params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def mri_cc_execute(
     params: MriCcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCcOutputs:
     """
+    mri_cc
+    
     Segments the corpus callosum into five separate labels in the subcortical
     segmentation volume.
     
@@ -234,10 +219,12 @@ def mri_cc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CC_METADATA)
     params = execution.params(params)
     cargs = mri_cc_cargs(params, execution)
     ret = mri_cc_outputs(params, execution)
@@ -257,10 +244,12 @@ def mri_cc(
     compartments: float | None = None,
     thickness: float | None = None,
     skip_voxels: float | None = None,
-    max_rotation: float | None = 7.0,
+    max_rotation: float | None = None,
     runner: Runner | None = None,
 ) -> MriCcOutputs:
     """
+    mri_cc
+    
     Segments the corpus callosum into five separate labels in the subcortical
     segmentation volume.
     
@@ -285,8 +274,6 @@ def mri_cc(
     Returns:
         NamedTuple of outputs (described in `MriCcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CC_METADATA)
     params = mri_cc_params(
         subject_name=subject_name,
         output_file=output_file,
@@ -301,13 +288,13 @@ def mri_cc(
         skip_voxels=skip_voxels,
         max_rotation=max_rotation,
     )
-    return mri_cc_execute(params, execution)
+    return mri_cc_execute(params, runner)
 
 
 __all__ = [
     "MRI_CC_METADATA",
     "MriCcOutputs",
-    "MriCcParameters",
     "mri_cc",
+    "mri_cc_execute",
     "mri_cc_params",
 ]