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

niwrap_freesurfer/freesurfer/mri_exvivo_norm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EXVIVO_NORM_METADATA = Metadata(
-    id="6c5391f769dffd8415570862d131e1708d93a905.boutiques",
+    id="b28d114a15a0409cf167af6596002e62ad8ed825.boutiques",
     name="mri_exvivo_norm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,25 @@ MRI_EXVIVO_NORM_METADATA = Metadata(
 
 
 MriExvivoNormParameters = typing.TypedDict('MriExvivoNormParameters', {
-    "__STYXTYPE__": typing.Literal["mri_exvivo_norm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_exvivo_norm"]],
+    "input_volume": InputPathType,
+    "output_volume": str,
+    "hemi": str,
+    "prediction_volume": typing.NotRequired[str | None],
+    "normalized_volume": typing.NotRequired[str | None],
+    "freeview": bool,
+    "normalize_output_mean": bool,
+    "write_normalization_rounds": bool,
+    "upper_threshold": typing.NotRequired[float | None],
+    "bias_field_sigma": typing.NotRequired[float | None],
+    "normalization_rounds": typing.NotRequired[float | None],
+    "multichannel": bool,
+    "model_file": typing.NotRequired[InputPathType | None],
+    "weights_file": typing.NotRequired[InputPathType | None],
+    "gpu_number": typing.NotRequired[float | None],
+})
+MriExvivoNormParametersTagged = typing.TypedDict('MriExvivoNormParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_exvivo_norm"],
     "input_volume": InputPathType,
     "output_volume": str,
     "hemi": str,
@@ -31,43 +49,11 @@ MriExvivoNormParameters = typing.TypedDict('MriExvivoNormParameters', {
     "weights_file": typing.NotRequired[InputPathType | None],
     "gpu_number": 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_exvivo_norm": mri_exvivo_norm_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_exvivo_norm": mri_exvivo_norm_outputs,
-    }.get(t)
 
 
 class MriExvivoNormOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_exvivo_norm(...)`.
+    Output object returned when calling `MriExvivoNormParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +77,7 @@ def mri_exvivo_norm_params(
     model_file: InputPathType | None = None,
     weights_file: InputPathType | None = None,
     gpu_number: float | None = None,
-) -> MriExvivoNormParameters:
+) -> MriExvivoNormParametersTagged:
     """
     Build parameters.
     
@@ -117,7 +103,7 @@ def mri_exvivo_norm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_exvivo_norm",
+        "@type": "freesurfer/mri_exvivo_norm",
         "input_volume": input_volume,
         "output_volume": output_volume,
         "hemi": hemi,
@@ -162,63 +148,63 @@ def mri_exvivo_norm_cargs(
     cargs.append("mri_exvivo_norm")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "-o",
-        params.get("output_volume")
+        params.get("output_volume", None)
     ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
-    if params.get("prediction_volume") is not None:
+    if params.get("prediction_volume", None) is not None:
         cargs.extend([
             "--pred",
-            params.get("prediction_volume")
+            params.get("prediction_volume", None)
         ])
-    if params.get("normalized_volume") is not None:
+    if params.get("normalized_volume", None) is not None:
         cargs.extend([
             "--norm",
-            params.get("normalized_volume")
+            params.get("normalized_volume", None)
         ])
-    if params.get("freeview"):
+    if params.get("freeview", False):
         cargs.append("--fv")
-    if params.get("normalize_output_mean"):
+    if params.get("normalize_output_mean", False):
         cargs.append("--norm_mean")
-    if params.get("write_normalization_rounds"):
+    if params.get("write_normalization_rounds", False):
         cargs.append("--write_rounds")
-    if params.get("upper_threshold") is not None:
+    if params.get("upper_threshold", None) is not None:
         cargs.extend([
             "--uthresh",
-            str(params.get("upper_threshold"))
+            str(params.get("upper_threshold", None))
         ])
-    if params.get("bias_field_sigma") is not None:
+    if params.get("bias_field_sigma", None) is not None:
         cargs.extend([
             "--sigma",
-            str(params.get("bias_field_sigma"))
+            str(params.get("bias_field_sigma", None))
         ])
-    if params.get("normalization_rounds") is not None:
+    if params.get("normalization_rounds", None) is not None:
         cargs.extend([
             "--nrounds",
-            str(params.get("normalization_rounds"))
+            str(params.get("normalization_rounds", None))
         ])
-    if params.get("multichannel"):
+    if params.get("multichannel", False):
         cargs.append("--multichannel")
-    if params.get("model_file") is not None:
+    if params.get("model_file", None) is not None:
         cargs.extend([
             "--model",
-            execution.input_file(params.get("model_file"))
+            execution.input_file(params.get("model_file", None))
         ])
-    if params.get("weights_file") is not None:
+    if params.get("weights_file", None) is not None:
         cargs.extend([
             "--wts",
-            execution.input_file(params.get("weights_file"))
+            execution.input_file(params.get("weights_file", None))
         ])
-    if params.get("gpu_number") is not None:
+    if params.get("gpu_number", None) is not None:
         cargs.extend([
             "--gpu",
-            str(params.get("gpu_number"))
+            str(params.get("gpu_number", None))
         ])
     return cargs
 
@@ -238,16 +224,18 @@ def mri_exvivo_norm_outputs(
     """
     ret = MriExvivoNormOutputs(
         root=execution.output_file("."),
-        output_volume=execution.output_file(params.get("output_volume")),
+        output_volume=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_exvivo_norm_execute(
     params: MriExvivoNormParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriExvivoNormOutputs:
     """
+    mri_exvivo_norm
+    
     MRI Ex Vivo Normalization Tool.
     
     Author: FreeSurfer Developers
@@ -256,10 +244,12 @@ def mri_exvivo_norm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriExvivoNormOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXVIVO_NORM_METADATA)
     params = execution.params(params)
     cargs = mri_exvivo_norm_cargs(params, execution)
     ret = mri_exvivo_norm_outputs(params, execution)
@@ -286,6 +276,8 @@ def mri_exvivo_norm(
     runner: Runner | None = None,
 ) -> MriExvivoNormOutputs:
     """
+    mri_exvivo_norm
+    
     MRI Ex Vivo Normalization Tool.
     
     Author: FreeSurfer Developers
@@ -314,8 +306,6 @@ def mri_exvivo_norm(
     Returns:
         NamedTuple of outputs (described in `MriExvivoNormOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EXVIVO_NORM_METADATA)
     params = mri_exvivo_norm_params(
         input_volume=input_volume,
         output_volume=output_volume,
@@ -333,13 +323,13 @@ def mri_exvivo_norm(
         weights_file=weights_file,
         gpu_number=gpu_number,
     )
-    return mri_exvivo_norm_execute(params, execution)
+    return mri_exvivo_norm_execute(params, runner)
 
 
 __all__ = [
     "MRI_EXVIVO_NORM_METADATA",
     "MriExvivoNormOutputs",
-    "MriExvivoNormParameters",
     "mri_exvivo_norm",
+    "mri_exvivo_norm_execute",
     "mri_exvivo_norm_params",
 ]

niwrap_freesurfer/freesurfer/mri_exvivo_strip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_EXVIVO_STRIP_METADATA = Metadata(
-    id="1f399e1586b99cedbde972e5d1a2f5e566e10bfb.boutiques",
+    id="136244badbffd0277cca64ac11751e5d28bf543d.boutiques",
     name="mri_exvivo_strip",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,22 @@ MRI_EXVIVO_STRIP_METADATA = Metadata(
 
 
 MriExvivoStripParameters = typing.TypedDict('MriExvivoStripParameters', {
-    "__STYXTYPE__": typing.Literal["mri_exvivo_strip"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_exvivo_strip"]],
+    "invol": InputPathType,
+    "outvol": str,
+    "hemi": str,
+    "pred": typing.NotRequired[InputPathType | None],
+    "norm": typing.NotRequired[InputPathType | None],
+    "fv": bool,
+    "uthresh": typing.NotRequired[float | None],
+    "border": typing.NotRequired[float | None],
+    "multichannel": bool,
+    "model": typing.NotRequired[InputPathType | None],
+    "wts": typing.NotRequired[InputPathType | None],
+    "gpu": typing.NotRequired[float | None],
+})
+MriExvivoStripParametersTagged = typing.TypedDict('MriExvivoStripParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_exvivo_strip"],
     "invol": InputPathType,
     "outvol": str,
     "hemi": str,
@@ -28,43 +43,11 @@ MriExvivoStripParameters = typing.TypedDict('MriExvivoStripParameters', {
     "wts": typing.NotRequired[InputPathType | None],
     "gpu": 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_exvivo_strip": mri_exvivo_strip_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_exvivo_strip": mri_exvivo_strip_outputs,
-    }.get(t)
 
 
 class MriExvivoStripOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_exvivo_strip(...)`.
+    Output object returned when calling `MriExvivoStripParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +72,7 @@ def mri_exvivo_strip_params(
     model: InputPathType | None = None,
     wts: InputPathType | None = None,
     gpu: float | None = None,
-) -> MriExvivoStripParameters:
+) -> MriExvivoStripParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +93,7 @@ def mri_exvivo_strip_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_exvivo_strip",
+        "@type": "freesurfer/mri_exvivo_strip",
         "invol": invol,
         "outvol": outvol,
         "hemi": hemi,
@@ -151,54 +134,54 @@ def mri_exvivo_strip_cargs(
     cargs.append("mri_exvivo_strip")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("invol"))
+        execution.input_file(params.get("invol", None))
     ])
     cargs.extend([
         "-o",
-        params.get("outvol")
+        params.get("outvol", None)
     ])
     cargs.extend([
         "--hemi",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
-    if params.get("pred") is not None:
+    if params.get("pred", None) is not None:
         cargs.extend([
             "--pred",
-            execution.input_file(params.get("pred"))
+            execution.input_file(params.get("pred", None))
         ])
-    if params.get("norm") is not None:
+    if params.get("norm", None) is not None:
         cargs.extend([
             "--norm",
-            execution.input_file(params.get("norm"))
+            execution.input_file(params.get("norm", None))
         ])
-    if params.get("fv"):
+    if params.get("fv", False):
         cargs.append("--fv")
-    if params.get("uthresh") is not None:
+    if params.get("uthresh", None) is not None:
         cargs.extend([
             "--uthresh",
-            str(params.get("uthresh"))
+            str(params.get("uthresh", None))
         ])
-    if params.get("border") is not None:
+    if params.get("border", None) is not None:
         cargs.extend([
             "--border",
-            str(params.get("border"))
+            str(params.get("border", None))
         ])
-    if params.get("multichannel"):
+    if params.get("multichannel", False):
         cargs.append("--multichannel")
-    if params.get("model") is not None:
+    if params.get("model", None) is not None:
         cargs.extend([
             "--model",
-            execution.input_file(params.get("model"))
+            execution.input_file(params.get("model", None))
         ])
-    if params.get("wts") is not None:
+    if params.get("wts", None) is not None:
         cargs.extend([
             "--wts",
-            execution.input_file(params.get("wts"))
+            execution.input_file(params.get("wts", None))
         ])
-    if params.get("gpu") is not None:
+    if params.get("gpu", None) is not None:
         cargs.extend([
             "--gpu",
-            str(params.get("gpu"))
+            str(params.get("gpu", None))
         ])
     return cargs
 
@@ -218,18 +201,20 @@ def mri_exvivo_strip_outputs(
     """
     ret = MriExvivoStripOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("outvol")),
-        prediction_output=execution.output_file(pathlib.Path(params.get("pred")).name) if (params.get("pred") is not None) else None,
-        normalized_output=execution.output_file(pathlib.Path(params.get("norm")).name) if (params.get("norm") is not None) else None,
+        output_file=execution.output_file(params.get("outvol", None)),
+        prediction_output=execution.output_file(pathlib.Path(params.get("pred", None)).name) if (params.get("pred") is not None) else None,
+        normalized_output=execution.output_file(pathlib.Path(params.get("norm", None)).name) if (params.get("norm") is not None) else None,
     )
     return ret
 
 
 def mri_exvivo_strip_execute(
     params: MriExvivoStripParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriExvivoStripOutputs:
     """
+    mri_exvivo_strip
+    
     Tool for processing MRI volumes for ex vivo data.
     
     Author: FreeSurfer Developers
@@ -238,10 +223,12 @@ def mri_exvivo_strip_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriExvivoStripOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_EXVIVO_STRIP_METADATA)
     params = execution.params(params)
     cargs = mri_exvivo_strip_cargs(params, execution)
     ret = mri_exvivo_strip_outputs(params, execution)
@@ -265,6 +252,8 @@ def mri_exvivo_strip(
     runner: Runner | None = None,
 ) -> MriExvivoStripOutputs:
     """
+    mri_exvivo_strip
+    
     Tool for processing MRI volumes for ex vivo data.
     
     Author: FreeSurfer Developers
@@ -288,8 +277,6 @@ def mri_exvivo_strip(
     Returns:
         NamedTuple of outputs (described in `MriExvivoStripOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_EXVIVO_STRIP_METADATA)
     params = mri_exvivo_strip_params(
         invol=invol,
         outvol=outvol,
@@ -304,13 +291,13 @@ def mri_exvivo_strip(
         wts=wts,
         gpu=gpu,
     )
-    return mri_exvivo_strip_execute(params, execution)
+    return mri_exvivo_strip_execute(params, runner)
 
 
 __all__ = [
     "MRI_EXVIVO_STRIP_METADATA",
     "MriExvivoStripOutputs",
-    "MriExvivoStripParameters",
     "mri_exvivo_strip",
+    "mri_exvivo_strip_execute",
     "mri_exvivo_strip_params",
 ]