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

niwrap_freesurfer/freesurfer/mri_dct_align_binary.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DCT_ALIGN_BINARY_METADATA = Metadata(
-    id="e05c8e053f59a6f74a1ef04223f889b8dedd61aa.boutiques",
+    id="5d00a7e5d9989ba125502e8b585672188a2afedb.boutiques",
     name="mri_dct_align_binary",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_DCT_ALIGN_BINARY_METADATA = Metadata(
 
 
 MriDctAlignBinaryParameters = typing.TypedDict('MriDctAlignBinaryParameters', {
-    "__STYXTYPE__": typing.Literal["mri_dct_align_binary"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_dct_align_binary"]],
+    "source_image": InputPathType,
+    "destination_image": InputPathType,
+    "output_transformation": str,
+})
+MriDctAlignBinaryParametersTagged = typing.TypedDict('MriDctAlignBinaryParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_dct_align_binary"],
     "source_image": InputPathType,
     "destination_image": InputPathType,
     "output_transformation": 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_dct_align_binary": mri_dct_align_binary_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_dct_align_binary": mri_dct_align_binary_outputs,
-    }.get(t)
 
 
 class MriDctAlignBinaryOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_dct_align_binary(...)`.
+    Output object returned when calling `MriDctAlignBinaryParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_dct_align_binary_params(
     source_image: InputPathType,
     destination_image: InputPathType,
     output_transformation: str,
-) -> MriDctAlignBinaryParameters:
+) -> MriDctAlignBinaryParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_dct_align_binary_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_dct_align_binary",
+        "@type": "freesurfer/mri_dct_align_binary",
         "source_image": source_image,
         "destination_image": destination_image,
         "output_transformation": output_transformation,
@@ -102,9 +76,9 @@ def mri_dct_align_binary_cargs(
     """
     cargs = []
     cargs.append("mri_dct_align_binary")
-    cargs.append(execution.input_file(params.get("source_image")))
-    cargs.append(execution.input_file(params.get("destination_image")))
-    cargs.append(params.get("output_transformation"))
+    cargs.append(execution.input_file(params.get("source_image", None)))
+    cargs.append(execution.input_file(params.get("destination_image", None)))
+    cargs.append(params.get("output_transformation", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_dct_align_binary_outputs(
     """
     ret = MriDctAlignBinaryOutputs(
         root=execution.output_file("."),
-        output_transformation_file=execution.output_file(params.get("output_transformation")),
+        output_transformation_file=execution.output_file(params.get("output_transformation", None)),
     )
     return ret
 
 
 def mri_dct_align_binary_execute(
     params: MriDctAlignBinaryParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDctAlignBinaryOutputs:
     """
+    mri_dct_align_binary
+    
     A binary tool for aligning MRI images using DCT.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mri_dct_align_binary_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDctAlignBinaryOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DCT_ALIGN_BINARY_METADATA)
     params = execution.params(params)
     cargs = mri_dct_align_binary_cargs(params, execution)
     ret = mri_dct_align_binary_outputs(params, execution)
@@ -159,6 +137,8 @@ def mri_dct_align_binary(
     runner: Runner | None = None,
 ) -> MriDctAlignBinaryOutputs:
     """
+    mri_dct_align_binary
+    
     A binary tool for aligning MRI images using DCT.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mri_dct_align_binary(
     Returns:
         NamedTuple of outputs (described in `MriDctAlignBinaryOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DCT_ALIGN_BINARY_METADATA)
     params = mri_dct_align_binary_params(
         source_image=source_image,
         destination_image=destination_image,
         output_transformation=output_transformation,
     )
-    return mri_dct_align_binary_execute(params, execution)
+    return mri_dct_align_binary_execute(params, runner)
 
 
 __all__ = [
     "MRI_DCT_ALIGN_BINARY_METADATA",
     "MriDctAlignBinaryOutputs",
-    "MriDctAlignBinaryParameters",
     "mri_dct_align_binary",
+    "mri_dct_align_binary_execute",
     "mri_dct_align_binary_params",
 ]

niwrap_freesurfer/freesurfer/mri_deface.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DEFACE_METADATA = Metadata(
-    id="71c89563a45aef942fd31396ef879363ac766810.boutiques",
+    id="193371472d0b78279f02c9a40121ebd60bf4ef93.boutiques",
     name="mri_deface",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_DEFACE_METADATA = Metadata(
 
 
 MriDefaceParameters = typing.TypedDict('MriDefaceParameters', {
-    "__STYXTYPE__": typing.Literal["mri_deface"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_deface"]],
+    "input_volume": InputPathType,
+    "brain_template": InputPathType,
+    "face_template": InputPathType,
+    "output_volume": str,
+})
+MriDefaceParametersTagged = typing.TypedDict('MriDefaceParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_deface"],
     "input_volume": InputPathType,
     "brain_template": InputPathType,
     "face_template": InputPathType,
     "output_volume": 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_deface": mri_deface_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_deface": mri_deface_outputs,
-    }.get(t)
 
 
 class MriDefaceOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_deface(...)`.
+    Output object returned when calling `MriDefaceParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_deface_params(
     brain_template: InputPathType,
     face_template: InputPathType,
     output_volume: str,
-) -> MriDefaceParameters:
+) -> MriDefaceParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +58,7 @@ def mri_deface_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_deface",
+        "@type": "freesurfer/mri_deface",
         "input_volume": input_volume,
         "brain_template": brain_template,
         "face_template": face_template,
@@ -107,10 +82,10 @@ def mri_deface_cargs(
     """
     cargs = []
     cargs.append("mri_deface")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("brain_template")))
-    cargs.append(execution.input_file(params.get("face_template")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("brain_template", None)))
+    cargs.append(execution.input_file(params.get("face_template", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -129,16 +104,18 @@ def mri_deface_outputs(
     """
     ret = MriDefaceOutputs(
         root=execution.output_file("."),
-        defaced_output_file=execution.output_file(params.get("output_volume")),
+        defaced_output_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_deface_execute(
     params: MriDefaceParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDefaceOutputs:
     """
+    mri_deface
+    
     MRI Deface utility for removing facial features from MRI images.
     
     Author: FreeSurfer Developers
@@ -147,10 +124,12 @@ def mri_deface_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDefaceOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DEFACE_METADATA)
     params = execution.params(params)
     cargs = mri_deface_cargs(params, execution)
     ret = mri_deface_outputs(params, execution)
@@ -166,6 +145,8 @@ def mri_deface(
     runner: Runner | None = None,
 ) -> MriDefaceOutputs:
     """
+    mri_deface
+    
     MRI Deface utility for removing facial features from MRI images.
     
     Author: FreeSurfer Developers
@@ -182,21 +163,19 @@ def mri_deface(
     Returns:
         NamedTuple of outputs (described in `MriDefaceOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DEFACE_METADATA)
     params = mri_deface_params(
         input_volume=input_volume,
         brain_template=brain_template,
         face_template=face_template,
         output_volume=output_volume,
     )
-    return mri_deface_execute(params, execution)
+    return mri_deface_execute(params, runner)
 
 
 __all__ = [
     "MRI_DEFACE_METADATA",
     "MriDefaceOutputs",
-    "MriDefaceParameters",
     "mri_deface",
+    "mri_deface_execute",
     "mri_deface_params",
 ]

niwrap_freesurfer/freesurfer/mri_defacer.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DEFACER_METADATA = Metadata(
-    id="b4d85cb79ec645b7e7786f442b944bd6515cb968.boutiques",
+    id="9a76bd7cdcb71bdf4008e0ef5d9f6b52b2c77e7e.boutiques",
     name="mri_defacer",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,34 @@ MRI_DEFACER_METADATA = Metadata(
 
 
 MriDefacerParameters = typing.TypedDict('MriDefacerParameters', {
-    "__STYXTYPE__": typing.Literal["mri_defacer"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_defacer"]],
+    "input_volume": InputPathType,
+    "headmask": InputPathType,
+    "tempsurf": InputPathType,
+    "templabel": typing.NotRequired[list[InputPathType] | None],
+    "watermark": typing.NotRequired[float | None],
+    "defaced_volume": str,
+    "facemask": typing.NotRequired[str | None],
+    "fill_constants": typing.NotRequired[list[float] | None],
+    "exclude_mask": typing.NotRequired[InputPathType | None],
+    "tempreg": typing.NotRequired[InputPathType | None],
+    "minsurfpath": typing.NotRequired[str | None],
+    "maxsurfpath": typing.NotRequired[str | None],
+    "distbounds": typing.NotRequired[InputPathType | None],
+    "distoverlay": typing.NotRequired[InputPathType | None],
+    "distdat": typing.NotRequired[InputPathType | None],
+    "statspath": typing.NotRequired[InputPathType | None],
+    "output_tempsurf": typing.NotRequired[InputPathType | None],
+    "apply_to_volume": typing.NotRequired[list[str] | None],
+    "ripple_center": typing.NotRequired[list[float] | None],
+    "apply_ripple": typing.NotRequired[list[str] | None],
+    "diagnostic_level": typing.NotRequired[float | None],
+    "debug": bool,
+    "checkopts": bool,
+    "version": bool,
+})
+MriDefacerParametersTagged = typing.TypedDict('MriDefacerParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_defacer"],
     "input_volume": InputPathType,
     "headmask": InputPathType,
     "tempsurf": InputPathType,
@@ -40,42 +67,11 @@ MriDefacerParameters = typing.TypedDict('MriDefacerParameters', {
     "checkopts": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_defacer": mri_defacer_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 MriDefacerOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_defacer(...)`.
+    Output object returned when calling `MriDefacerParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -106,7 +102,7 @@ def mri_defacer_params(
     debug: bool = False,
     checkopts: bool = False,
     version: bool = False,
-) -> MriDefacerParameters:
+) -> MriDefacerParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +135,7 @@ def mri_defacer_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_defacer",
+        "@type": "freesurfer/mri_defacer",
         "input_volume": input_volume,
         "headmask": headmask,
         "tempsurf": tempsurf,
@@ -202,110 +198,110 @@ def mri_defacer_cargs(
     cargs.append("mri_defacer")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("input_volume"))
+        execution.input_file(params.get("input_volume", None))
     ])
     cargs.extend([
         "-hm",
-        execution.input_file(params.get("headmask"))
+        execution.input_file(params.get("headmask", None))
     ])
     cargs.extend([
         "-ts",
-        execution.input_file(params.get("tempsurf"))
+        execution.input_file(params.get("tempsurf", None))
     ])
-    if params.get("templabel") is not None:
+    if params.get("templabel", None) is not None:
         cargs.extend([
             "--l",
-            *[execution.input_file(f) for f in params.get("templabel")]
+            *[execution.input_file(f) for f in params.get("templabel", None)]
         ])
-    if params.get("watermark") is not None:
+    if params.get("watermark", None) is not None:
         cargs.extend([
             "--w",
-            str(params.get("watermark"))
+            str(params.get("watermark", None))
         ])
     cargs.extend([
         "-o",
-        params.get("defaced_volume")
+        params.get("defaced_volume", None)
     ])
-    if params.get("facemask") is not None:
+    if params.get("facemask", None) is not None:
         cargs.extend([
             "--m",
-            params.get("facemask")
+            params.get("facemask", None)
         ])
-    if params.get("fill_constants") is not None:
+    if params.get("fill_constants", None) is not None:
         cargs.extend([
             "--fill-const",
-            *map(str, params.get("fill_constants"))
+            *map(str, params.get("fill_constants", None))
         ])
-    if params.get("exclude_mask") is not None:
+    if params.get("exclude_mask", None) is not None:
         cargs.extend([
             "--xmask",
-            execution.input_file(params.get("exclude_mask"))
+            execution.input_file(params.get("exclude_mask", None))
         ])
-    if params.get("tempreg") is not None:
+    if params.get("tempreg", None) is not None:
         cargs.extend([
             "--reg",
-            execution.input_file(params.get("tempreg"))
+            execution.input_file(params.get("tempreg", None))
         ])
-    if params.get("minsurfpath") is not None:
+    if params.get("minsurfpath", None) is not None:
         cargs.extend([
             "--min",
-            params.get("minsurfpath")
+            params.get("minsurfpath", None)
         ])
-    if params.get("maxsurfpath") is not None:
+    if params.get("maxsurfpath", None) is not None:
         cargs.extend([
             "--max",
-            params.get("maxsurfpath")
+            params.get("maxsurfpath", None)
         ])
-    if params.get("distbounds") is not None:
+    if params.get("distbounds", None) is not None:
         cargs.extend([
             "--distbounds",
-            execution.input_file(params.get("distbounds"))
+            execution.input_file(params.get("distbounds", None))
         ])
-    if params.get("distoverlay") is not None:
+    if params.get("distoverlay", None) is not None:
         cargs.extend([
             "--distoverlay",
-            execution.input_file(params.get("distoverlay"))
+            execution.input_file(params.get("distoverlay", None))
         ])
-    if params.get("distdat") is not None:
+    if params.get("distdat", None) is not None:
         cargs.extend([
             "--distdat",
-            execution.input_file(params.get("distdat"))
+            execution.input_file(params.get("distdat", None))
         ])
-    if params.get("statspath") is not None:
+    if params.get("statspath", None) is not None:
         cargs.extend([
             "--stats",
-            execution.input_file(params.get("statspath"))
+            execution.input_file(params.get("statspath", None))
         ])
-    if params.get("output_tempsurf") is not None:
+    if params.get("output_tempsurf", None) is not None:
         cargs.extend([
             "--ots",
-            execution.input_file(params.get("output_tempsurf"))
+            execution.input_file(params.get("output_tempsurf", None))
         ])
-    if params.get("apply_to_volume") is not None:
+    if params.get("apply_to_volume", None) is not None:
         cargs.extend([
             "--apply",
-            *params.get("apply_to_volume")
+            *params.get("apply_to_volume", None)
         ])
-    if params.get("ripple_center") is not None:
+    if params.get("ripple_center", None) is not None:
         cargs.extend([
             "--ripple-center",
-            *map(str, params.get("ripple_center"))
+            *map(str, params.get("ripple_center", None))
         ])
-    if params.get("apply_ripple") is not None:
+    if params.get("apply_ripple", None) is not None:
         cargs.extend([
             "--apply-ripple",
-            *params.get("apply_ripple")
+            *params.get("apply_ripple", None)
         ])
-    if params.get("diagnostic_level") is not None:
+    if params.get("diagnostic_level", None) is not None:
         cargs.extend([
             "--gdiag",
-            str(params.get("diagnostic_level"))
+            str(params.get("diagnostic_level", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -331,9 +327,11 @@ def mri_defacer_outputs(
 
 def mri_defacer_execute(
     params: MriDefacerParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDefacerOutputs:
     """
+    mri_defacer
+    
     Tool for defacing MRI images to remove facial features.
     
     Author: FreeSurfer Developers
@@ -342,10 +340,12 @@ def mri_defacer_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDefacerOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DEFACER_METADATA)
     params = execution.params(params)
     cargs = mri_defacer_cargs(params, execution)
     ret = mri_defacer_outputs(params, execution)
@@ -381,6 +381,8 @@ def mri_defacer(
     runner: Runner | None = None,
 ) -> MriDefacerOutputs:
     """
+    mri_defacer
+    
     Tool for defacing MRI images to remove facial features.
     
     Author: FreeSurfer Developers
@@ -416,8 +418,6 @@ def mri_defacer(
     Returns:
         NamedTuple of outputs (described in `MriDefacerOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DEFACER_METADATA)
     params = mri_defacer_params(
         input_volume=input_volume,
         headmask=headmask,
@@ -444,13 +444,13 @@ def mri_defacer(
         checkopts=checkopts,
         version=version,
     )
-    return mri_defacer_execute(params, execution)
+    return mri_defacer_execute(params, runner)
 
 
 __all__ = [
     "MRI_DEFACER_METADATA",
     "MriDefacerOutputs",
-    "MriDefacerParameters",
     "mri_defacer",
+    "mri_defacer_execute",
     "mri_defacer_params",
 ]