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

niwrap_freesurfer/freesurfer/mri_aparc2wmseg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_APARC2WMSEG_METADATA = Metadata(
-    id="87041c67737f5fcea13d8a9bfb01ff795c1c95a2.boutiques",
+    id="7619486b848b6254295a0d9c8f5041b0df2c66f4.boutiques",
     name="mri_aparc2wmseg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ MRI_APARC2WMSEG_METADATA = Metadata(
 
 
 MriAparc2wmsegParameters = typing.TypedDict('MriAparc2wmsegParameters', {
-    "__STYXTYPE__": typing.Literal["mri_aparc2wmseg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_aparc2wmseg"]],
+    "subject": str,
+    "wmseg_file": str,
+    "help": bool,
+    "version": bool,
+})
+MriAparc2wmsegParametersTagged = typing.TypedDict('MriAparc2wmsegParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_aparc2wmseg"],
     "subject": str,
     "wmseg_file": str,
     "help": 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_aparc2wmseg": mri_aparc2wmseg_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 MriAparc2wmsegOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_aparc2wmseg(...)`.
+    Output object returned when calling `MriAparc2wmsegParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def mri_aparc2wmseg_params(
     wmseg_file: str,
     help_: bool = False,
     version: bool = False,
-) -> MriAparc2wmsegParameters:
+) -> MriAparc2wmsegParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def mri_aparc2wmseg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_aparc2wmseg",
+        "@type": "freesurfer/mri_aparc2wmseg",
         "subject": subject,
         "wmseg_file": wmseg_file,
         "help": help_,
@@ -105,15 +81,15 @@ def mri_aparc2wmseg_cargs(
     cargs.append("mri_aparc2wmseg")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     cargs.extend([
         "--wmseg",
-        params.get("wmseg_file")
+        params.get("wmseg_file", None)
     ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
     return cargs
 
@@ -139,11 +115,13 @@ def mri_aparc2wmseg_outputs(
 
 def mri_aparc2wmseg_execute(
     params: MriAparc2wmsegParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriAparc2wmsegOutputs:
     """
-    A tool to convert aparc+aseg.mgz annotations into a white matter segmentation
-    file.
+    mri_aparc2wmseg
+    
+    A tool to convert aparc+aseg.mgz annotations into a white matter
+    segmentation file.
     
     Author: FreeSurfer Developers
     
@@ -151,10 +129,12 @@ def mri_aparc2wmseg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriAparc2wmsegOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_APARC2WMSEG_METADATA)
     params = execution.params(params)
     cargs = mri_aparc2wmseg_cargs(params, execution)
     ret = mri_aparc2wmseg_outputs(params, execution)
@@ -170,8 +150,10 @@ def mri_aparc2wmseg(
     runner: Runner | None = None,
 ) -> MriAparc2wmsegOutputs:
     """
-    A tool to convert aparc+aseg.mgz annotations into a white matter segmentation
-    file.
+    mri_aparc2wmseg
+    
+    A tool to convert aparc+aseg.mgz annotations into a white matter
+    segmentation file.
     
     Author: FreeSurfer Developers
     
@@ -186,21 +168,19 @@ def mri_aparc2wmseg(
     Returns:
         NamedTuple of outputs (described in `MriAparc2wmsegOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_APARC2WMSEG_METADATA)
     params = mri_aparc2wmseg_params(
         subject=subject,
         wmseg_file=wmseg_file,
         help_=help_,
         version=version,
     )
-    return mri_aparc2wmseg_execute(params, execution)
+    return mri_aparc2wmseg_execute(params, runner)
 
 
 __all__ = [
     "MRI_APARC2WMSEG_METADATA",
     "MriAparc2wmsegOutputs",
-    "MriAparc2wmsegParameters",
     "mri_aparc2wmseg",
+    "mri_aparc2wmseg_execute",
     "mri_aparc2wmseg_params",
 ]

niwrap_freesurfer/freesurfer/mri_apply_bias.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_APPLY_BIAS_METADATA = Metadata(
-    id="8790ac35c67e85f35da9bcad35b81fe9d35d833c.boutiques",
+    id="46b5e2a3948d9f2b59a26ae51155880173698a3f.boutiques",
     name="mri_apply_bias",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_APPLY_BIAS_METADATA = Metadata(
 
 
 MriApplyBiasParameters = typing.TypedDict('MriApplyBiasParameters', {
-    "__STYXTYPE__": typing.Literal["mri_apply_bias"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_apply_bias"]],
+    "input_volume": InputPathType,
+    "bias_volume": InputPathType,
+    "output_volume": str,
+})
+MriApplyBiasParametersTagged = typing.TypedDict('MriApplyBiasParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_apply_bias"],
     "input_volume": InputPathType,
     "bias_volume": 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_apply_bias": mri_apply_bias_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_apply_bias": mri_apply_bias_outputs,
-    }.get(t)
 
 
 class MriApplyBiasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_apply_bias(...)`.
+    Output object returned when calling `MriApplyBiasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_apply_bias_params(
     input_volume: InputPathType,
     bias_volume: InputPathType,
     output_volume: str,
-) -> MriApplyBiasParameters:
+) -> MriApplyBiasParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_apply_bias_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_apply_bias",
+        "@type": "freesurfer/mri_apply_bias",
         "input_volume": input_volume,
         "bias_volume": bias_volume,
         "output_volume": output_volume,
@@ -102,9 +76,9 @@ def mri_apply_bias_cargs(
     """
     cargs = []
     cargs.append("mri_apply_bias")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("bias_volume")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("bias_volume", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_apply_bias_outputs(
     """
     ret = MriApplyBiasOutputs(
         root=execution.output_file("."),
-        output_volume_file=execution.output_file(params.get("output_volume")),
+        output_volume_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_apply_bias_execute(
     params: MriApplyBiasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriApplyBiasOutputs:
     """
+    mri_apply_bias
+    
     A tool for applying a bias volume to an input volume to produce an output
     volume.
     
@@ -142,10 +118,12 @@ def mri_apply_bias_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriApplyBiasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_APPLY_BIAS_METADATA)
     params = execution.params(params)
     cargs = mri_apply_bias_cargs(params, execution)
     ret = mri_apply_bias_outputs(params, execution)
@@ -160,6 +138,8 @@ def mri_apply_bias(
     runner: Runner | None = None,
 ) -> MriApplyBiasOutputs:
     """
+    mri_apply_bias
+    
     A tool for applying a bias volume to an input volume to produce an output
     volume.
     
@@ -175,20 +155,18 @@ def mri_apply_bias(
     Returns:
         NamedTuple of outputs (described in `MriApplyBiasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_APPLY_BIAS_METADATA)
     params = mri_apply_bias_params(
         input_volume=input_volume,
         bias_volume=bias_volume,
         output_volume=output_volume,
     )
-    return mri_apply_bias_execute(params, execution)
+    return mri_apply_bias_execute(params, runner)
 
 
 __all__ = [
     "MRI_APPLY_BIAS_METADATA",
     "MriApplyBiasOutputs",
-    "MriApplyBiasParameters",
     "mri_apply_bias",
+    "mri_apply_bias_execute",
     "mri_apply_bias_params",
 ]

niwrap_freesurfer/freesurfer/mri_average.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_AVERAGE_METADATA = Metadata(
-    id="eb15546d738076b6fe7c57e66238b82613f7eb29.boutiques",
+    id="b3f32f14636c8ffec10c09466e6ffcd8ac3e9675.boutiques",
     name="mri_average",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,31 @@ MRI_AVERAGE_METADATA = Metadata(
 
 
 MriAverageParameters = typing.TypedDict('MriAverageParameters', {
-    "__STYXTYPE__": typing.Literal["mri_average"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_average"]],
+    "input_volumes": list[InputPathType],
+    "output_volume": str,
+    "rigid_alignment": bool,
+    "read_from_file": bool,
+    "dt": typing.NotRequired[float | None],
+    "tol": typing.NotRequired[float | None],
+    "conform": bool,
+    "noconform": bool,
+    "reduce": typing.NotRequired[float | None],
+    "sinc_interpolation": typing.NotRequired[float | None],
+    "trilinear": bool,
+    "window": bool,
+    "snapshots": typing.NotRequired[float | None],
+    "translation": typing.NotRequired[list[float] | None],
+    "rotation": typing.NotRequired[list[float] | None],
+    "momentum": typing.NotRequired[float | None],
+    "rms": bool,
+    "rms_alt": bool,
+    "percent": bool,
+    "binarize": typing.NotRequired[float | None],
+    "absolute": bool,
+})
+MriAverageParametersTagged = typing.TypedDict('MriAverageParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_average"],
     "input_volumes": list[InputPathType],
     "output_volume": str,
     "rigid_alignment": bool,
@@ -37,43 +61,11 @@ MriAverageParameters = typing.TypedDict('MriAverageParameters', {
     "binarize": typing.NotRequired[float | None],
     "absolute": 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_average": mri_average_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_average": mri_average_outputs,
-    }.get(t)
 
 
 class MriAverageOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_average(...)`.
+    Output object returned when calling `MriAverageParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +95,7 @@ def mri_average_params(
     percent: bool = False,
     binarize: float | None = None,
     absolute: bool = False,
-) -> MriAverageParameters:
+) -> MriAverageParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +127,7 @@ def mri_average_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_average",
+        "@type": "freesurfer/mri_average",
         "input_volumes": input_volumes,
         "output_volume": output_volume,
         "rigid_alignment": rigid_alignment,
@@ -185,72 +177,72 @@ def mri_average_cargs(
     """
     cargs = []
     cargs.append("mri_average")
-    cargs.extend([execution.input_file(f) for f in params.get("input_volumes")])
-    cargs.append(params.get("output_volume"))
-    if params.get("rigid_alignment"):
+    cargs.extend([execution.input_file(f) for f in params.get("input_volumes", None)])
+    cargs.append(params.get("output_volume", None))
+    if params.get("rigid_alignment", False):
         cargs.append("-a")
-    if params.get("read_from_file"):
+    if params.get("read_from_file", False):
         cargs.append("-F")
-    if params.get("dt") is not None:
+    if params.get("dt", None) is not None:
         cargs.extend([
             "-dt",
-            str(params.get("dt"))
+            str(params.get("dt", None))
         ])
-    if params.get("tol") is not None:
+    if params.get("tol", None) is not None:
         cargs.extend([
             "-tol",
-            str(params.get("tol"))
+            str(params.get("tol", None))
         ])
-    if params.get("conform"):
+    if params.get("conform", False):
         cargs.append("-conform")
-    if params.get("noconform"):
+    if params.get("noconform", False):
         cargs.append("-noconform")
-    if params.get("reduce") is not None:
+    if params.get("reduce", None) is not None:
         cargs.extend([
             "-reduce",
-            str(params.get("reduce"))
+            str(params.get("reduce", None))
         ])
-    if params.get("sinc_interpolation") is not None:
+    if params.get("sinc_interpolation", None) is not None:
         cargs.extend([
             "-sinc",
-            str(params.get("sinc_interpolation"))
+            str(params.get("sinc_interpolation", None))
         ])
-    if params.get("trilinear"):
+    if params.get("trilinear", False):
         cargs.append("-trilinear")
-    if params.get("window"):
+    if params.get("window", False):
         cargs.append("-window")
-    if params.get("snapshots") is not None:
+    if params.get("snapshots", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("snapshots"))
+            str(params.get("snapshots", None))
         ])
-    if params.get("translation") is not None:
+    if params.get("translation", None) is not None:
         cargs.extend([
             "-t",
-            *map(str, params.get("translation"))
+            *map(str, params.get("translation", None))
         ])
-    if params.get("rotation") is not None:
+    if params.get("rotation", None) is not None:
         cargs.extend([
             "-r",
-            *map(str, params.get("rotation"))
+            *map(str, params.get("rotation", None))
         ])
-    if params.get("momentum") is not None:
+    if params.get("momentum", None) is not None:
         cargs.extend([
             "-m",
-            str(params.get("momentum"))
+            str(params.get("momentum", None))
         ])
-    if params.get("rms"):
+    if params.get("rms", False):
         cargs.append("-sqr")
-    if params.get("rms_alt"):
+    if params.get("rms_alt", False):
         cargs.append("-rms")
-    if params.get("percent"):
+    if params.get("percent", False):
         cargs.append("-p")
-    if params.get("binarize") is not None:
+    if params.get("binarize", None) is not None:
         cargs.extend([
             "-b",
-            str(params.get("binarize"))
+            str(params.get("binarize", None))
         ])
-    if params.get("absolute"):
+    if params.get("absolute", False):
         cargs.append("-abs")
     return cargs
 
@@ -270,18 +262,20 @@ def mri_average_outputs(
     """
     ret = MriAverageOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("output_volume")),
+        output_file=execution.output_file(params.get("output_volume", None)),
     )
     return ret
 
 
 def mri_average_execute(
     params: MriAverageParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriAverageOutputs:
     """
-    Averages multiple volumes with various options for alignment, interpolation, and
-    transformations.
+    mri_average
+    
+    Averages multiple volumes with various options for alignment, interpolation,
+    and transformations.
     
     Author: FreeSurfer Developers
     
@@ -289,10 +283,12 @@ def mri_average_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriAverageOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_AVERAGE_METADATA)
     params = execution.params(params)
     cargs = mri_average_cargs(params, execution)
     ret = mri_average_outputs(params, execution)
@@ -325,8 +321,10 @@ def mri_average(
     runner: Runner | None = None,
 ) -> MriAverageOutputs:
     """
-    Averages multiple volumes with various options for alignment, interpolation, and
-    transformations.
+    mri_average
+    
+    Averages multiple volumes with various options for alignment, interpolation,
+    and transformations.
     
     Author: FreeSurfer Developers
     
@@ -360,8 +358,6 @@ def mri_average(
     Returns:
         NamedTuple of outputs (described in `MriAverageOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_AVERAGE_METADATA)
     params = mri_average_params(
         input_volumes=input_volumes,
         output_volume=output_volume,
@@ -385,13 +381,13 @@ def mri_average(
         binarize=binarize,
         absolute=absolute,
     )
-    return mri_average_execute(params, execution)
+    return mri_average_execute(params, runner)
 
 
 __all__ = [
     "MRI_AVERAGE_METADATA",
     "MriAverageOutputs",
-    "MriAverageParameters",
     "mri_average",
+    "mri_average_execute",
     "mri_average_params",
 ]