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

niwrap_freesurfer/freesurfer/mri_relabel_nonwm_hypos.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_RELABEL_NONWM_HYPOS_METADATA = Metadata(
-    id="1c205a744ee3062f4f4c5f23e5931460720a20c9.boutiques",
+    id="19db68adb409161945a2632065dac7657655dfc6.boutiques",
     name="mri_relabel_nonwm_hypos",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ MRI_RELABEL_NONWM_HYPOS_METADATA = Metadata(
 
 
 MriRelabelNonwmHyposParameters = typing.TypedDict('MriRelabelNonwmHyposParameters', {
-    "__STYXTYPE__": typing.Literal["mri_relabel_nonwm_hypos"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_relabel_nonwm_hypos"]],
+    "inputseg": InputPathType,
+    "outputseg": str,
+    "segments": typing.NotRequired[list[str] | None],
+    "seg_default": bool,
+    "debug": bool,
+    "checkopts": bool,
+})
+MriRelabelNonwmHyposParametersTagged = typing.TypedDict('MriRelabelNonwmHyposParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_relabel_nonwm_hypos"],
     "inputseg": InputPathType,
     "outputseg": str,
     "segments": typing.NotRequired[list[str] | None],
@@ -22,43 +31,11 @@ MriRelabelNonwmHyposParameters = typing.TypedDict('MriRelabelNonwmHyposParameter
     "debug": bool,
     "checkopts": 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_relabel_nonwm_hypos": mri_relabel_nonwm_hypos_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_relabel_nonwm_hypos": mri_relabel_nonwm_hypos_outputs,
-    }.get(t)
 
 
 class MriRelabelNonwmHyposOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_relabel_nonwm_hypos(...)`.
+    Output object returned when calling `MriRelabelNonwmHyposParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def mri_relabel_nonwm_hypos_params(
     seg_default: bool = False,
     debug: bool = False,
     checkopts: bool = False,
-) -> MriRelabelNonwmHyposParameters:
+) -> MriRelabelNonwmHyposParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def mri_relabel_nonwm_hypos_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_relabel_nonwm_hypos",
+        "@type": "freesurfer/mri_relabel_nonwm_hypos",
         "inputseg": inputseg,
         "outputseg": outputseg,
         "seg_default": seg_default,
@@ -119,22 +96,22 @@ def mri_relabel_nonwm_hypos_cargs(
     cargs.append("mri_relabel_nonwm_hypos")
     cargs.extend([
         "-i",
-        execution.input_file(params.get("inputseg"))
+        execution.input_file(params.get("inputseg", None))
     ])
     cargs.extend([
         "-o",
-        params.get("outputseg")
+        params.get("outputseg", None)
     ])
-    if params.get("segments") is not None:
+    if params.get("segments", None) is not None:
         cargs.extend([
             "--seg",
-            *params.get("segments")
+            *params.get("segments", None)
         ])
-    if params.get("seg_default"):
+    if params.get("seg_default", False):
         cargs.append("--seg-default")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    if params.get("checkopts"):
+    if params.get("checkopts", False):
         cargs.append("--checkopts")
     return cargs
 
@@ -154,16 +131,18 @@ def mri_relabel_nonwm_hypos_outputs(
     """
     ret = MriRelabelNonwmHyposOutputs(
         root=execution.output_file("."),
-        out_segmentation=execution.output_file(params.get("outputseg")),
+        out_segmentation=execution.output_file(params.get("outputseg", None)),
     )
     return ret
 
 
 def mri_relabel_nonwm_hypos_execute(
     params: MriRelabelNonwmHyposParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRelabelNonwmHyposOutputs:
     """
+    mri_relabel_nonwm_hypos
+    
     Relabels non-WM hypointensities based on proximity to a nearby label.
     
     Author: FreeSurfer Developers
@@ -172,10 +151,12 @@ def mri_relabel_nonwm_hypos_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRelabelNonwmHyposOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_RELABEL_NONWM_HYPOS_METADATA)
     params = execution.params(params)
     cargs = mri_relabel_nonwm_hypos_cargs(params, execution)
     ret = mri_relabel_nonwm_hypos_outputs(params, execution)
@@ -193,6 +174,8 @@ def mri_relabel_nonwm_hypos(
     runner: Runner | None = None,
 ) -> MriRelabelNonwmHyposOutputs:
     """
+    mri_relabel_nonwm_hypos
+    
     Relabels non-WM hypointensities based on proximity to a nearby label.
     
     Author: FreeSurfer Developers
@@ -212,8 +195,6 @@ def mri_relabel_nonwm_hypos(
     Returns:
         NamedTuple of outputs (described in `MriRelabelNonwmHyposOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_RELABEL_NONWM_HYPOS_METADATA)
     params = mri_relabel_nonwm_hypos_params(
         inputseg=inputseg,
         outputseg=outputseg,
@@ -222,13 +203,13 @@ def mri_relabel_nonwm_hypos(
         debug=debug,
         checkopts=checkopts,
     )
-    return mri_relabel_nonwm_hypos_execute(params, execution)
+    return mri_relabel_nonwm_hypos_execute(params, runner)
 
 
 __all__ = [
     "MRI_RELABEL_NONWM_HYPOS_METADATA",
     "MriRelabelNonwmHyposOutputs",
-    "MriRelabelNonwmHyposParameters",
     "mri_relabel_nonwm_hypos",
+    "mri_relabel_nonwm_hypos_execute",
     "mri_relabel_nonwm_hypos_params",
 ]

niwrap_freesurfer/freesurfer/mri_remove_neck.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_REMOVE_NECK_METADATA = Metadata(
-    id="816c0b5433a26ae4baa8b91d1bbe9f04ac56345b.boutiques",
+    id="3316fffb095cf14ca5773288539b410eaf192d20.boutiques",
     name="mri_remove_neck",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,24 @@ MRI_REMOVE_NECK_METADATA = Metadata(
 
 
 MriRemoveNeckParameters = typing.TypedDict('MriRemoveNeckParameters', {
-    "__STYXTYPE__": typing.Literal["mri_remove_neck"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_remove_neck"]],
+    "input_volume": InputPathType,
+    "transform": InputPathType,
+    "gca": InputPathType,
+    "output_volume": str,
+})
+MriRemoveNeckParametersTagged = typing.TypedDict('MriRemoveNeckParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_remove_neck"],
     "input_volume": InputPathType,
     "transform": InputPathType,
     "gca": 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_remove_neck": mri_remove_neck_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_remove_neck": mri_remove_neck_outputs,
-    }.get(t)
 
 
 class MriRemoveNeckOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_remove_neck(...)`.
+    Output object returned when calling `MriRemoveNeckParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def mri_remove_neck_params(
     transform: InputPathType,
     gca: InputPathType,
     output_volume: str,
-) -> MriRemoveNeckParameters:
+) -> MriRemoveNeckParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def mri_remove_neck_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_remove_neck",
+        "@type": "freesurfer/mri_remove_neck",
         "input_volume": input_volume,
         "transform": transform,
         "gca": gca,
@@ -106,10 +81,10 @@ def mri_remove_neck_cargs(
     """
     cargs = []
     cargs.append("mri_remove_neck")
-    cargs.append(execution.input_file(params.get("input_volume")))
-    cargs.append(execution.input_file(params.get("transform")))
-    cargs.append(execution.input_file(params.get("gca")))
-    cargs.append(params.get("output_volume"))
+    cargs.append(execution.input_file(params.get("input_volume", None)))
+    cargs.append(execution.input_file(params.get("transform", None)))
+    cargs.append(execution.input_file(params.get("gca", None)))
+    cargs.append(params.get("output_volume", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def mri_remove_neck_outputs(
     """
     ret = MriRemoveNeckOutputs(
         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_remove_neck_execute(
     params: MriRemoveNeckParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriRemoveNeckOutputs:
     """
+    mri_remove_neck
+    
     Tool for removing neck from MRI volumes.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def mri_remove_neck_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriRemoveNeckOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_REMOVE_NECK_METADATA)
     params = execution.params(params)
     cargs = mri_remove_neck_cargs(params, execution)
     ret = mri_remove_neck_outputs(params, execution)
@@ -165,6 +144,8 @@ def mri_remove_neck(
     runner: Runner | None = None,
 ) -> MriRemoveNeckOutputs:
     """
+    mri_remove_neck
+    
     Tool for removing neck from MRI volumes.
     
     Author: FreeSurfer Developers
@@ -180,21 +161,19 @@ def mri_remove_neck(
     Returns:
         NamedTuple of outputs (described in `MriRemoveNeckOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_REMOVE_NECK_METADATA)
     params = mri_remove_neck_params(
         input_volume=input_volume,
         transform=transform,
         gca=gca,
         output_volume=output_volume,
     )
-    return mri_remove_neck_execute(params, execution)
+    return mri_remove_neck_execute(params, runner)
 
 
 __all__ = [
     "MRI_REMOVE_NECK_METADATA",
     "MriRemoveNeckOutputs",
-    "MriRemoveNeckParameters",
     "mri_remove_neck",
+    "mri_remove_neck_execute",
     "mri_remove_neck_params",
 ]

niwrap_freesurfer/freesurfer/mri_reorient_lr_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_REORIENT_LR_CSH_METADATA = Metadata(
-    id="05322ddfbba756994657c542f9080b8197d048b6.boutiques",
+    id="6efdc9d1eda19cd4e86c9f20673956a16ac97b79.boutiques",
     name="mri_reorient_LR.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MRI_REORIENT_LR_CSH_METADATA = Metadata(
 
 
 MriReorientLrCshParameters = typing.TypedDict('MriReorientLrCshParameters', {
-    "__STYXTYPE__": typing.Literal["mri_reorient_LR.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_reorient_LR.csh"]],
+    "input_vol": InputPathType,
+    "output_vol": str,
+    "display_result": bool,
+    "clean_files": bool,
+    "output_registration": bool,
+    "version": bool,
+    "help": bool,
+})
+MriReorientLrCshParametersTagged = typing.TypedDict('MriReorientLrCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_reorient_LR.csh"],
     "input_vol": InputPathType,
     "output_vol": str,
     "display_result": bool,
@@ -23,43 +33,11 @@ MriReorientLrCshParameters = typing.TypedDict('MriReorientLrCshParameters', {
     "version": bool,
     "help": 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_reorient_LR.csh": mri_reorient_lr_csh_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_reorient_LR.csh": mri_reorient_lr_csh_outputs,
-    }.get(t)
 
 
 class MriReorientLrCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_reorient_lr_csh(...)`.
+    Output object returned when calling `MriReorientLrCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def mri_reorient_lr_csh_params(
     output_registration: bool = False,
     version: bool = False,
     help_: bool = False,
-) -> MriReorientLrCshParameters:
+) -> MriReorientLrCshParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +70,7 @@ def mri_reorient_lr_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_reorient_LR.csh",
+        "@type": "freesurfer/mri_reorient_LR.csh",
         "input_vol": input_vol,
         "output_vol": output_vol,
         "display_result": display_result,
@@ -121,21 +99,21 @@ def mri_reorient_lr_csh_cargs(
     cargs.append("mri_reorient_LR.csh")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("input_vol"))
+        execution.input_file(params.get("input_vol", None))
     ])
     cargs.extend([
         "--o",
-        params.get("output_vol")
+        params.get("output_vol", None)
     ])
-    if params.get("display_result"):
+    if params.get("display_result", False):
         cargs.append("--disp")
-    if params.get("clean_files"):
+    if params.get("clean_files", False):
         cargs.append("--clean")
-    if params.get("output_registration"):
+    if params.get("output_registration", False):
         cargs.append("--outreg")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("--version")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("--help")
     return cargs
 
@@ -155,16 +133,18 @@ def mri_reorient_lr_csh_outputs(
     """
     ret = MriReorientLrCshOutputs(
         root=execution.output_file("."),
-        reoriented_vol=execution.output_file(params.get("output_vol")),
+        reoriented_vol=execution.output_file(params.get("output_vol", None)),
     )
     return ret
 
 
 def mri_reorient_lr_csh_execute(
     params: MriReorientLrCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriReorientLrCshOutputs:
     """
+    mri_reorient_LR.csh
+    
     A script to reorient MRI volumes from left-right orientation.
     
     Author: FreeSurfer Developers
@@ -173,10 +153,12 @@ def mri_reorient_lr_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriReorientLrCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_REORIENT_LR_CSH_METADATA)
     params = execution.params(params)
     cargs = mri_reorient_lr_csh_cargs(params, execution)
     ret = mri_reorient_lr_csh_outputs(params, execution)
@@ -195,6 +177,8 @@ def mri_reorient_lr_csh(
     runner: Runner | None = None,
 ) -> MriReorientLrCshOutputs:
     """
+    mri_reorient_LR.csh
+    
     A script to reorient MRI volumes from left-right orientation.
     
     Author: FreeSurfer Developers
@@ -214,8 +198,6 @@ def mri_reorient_lr_csh(
     Returns:
         NamedTuple of outputs (described in `MriReorientLrCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_REORIENT_LR_CSH_METADATA)
     params = mri_reorient_lr_csh_params(
         input_vol=input_vol,
         output_vol=output_vol,
@@ -225,13 +207,13 @@ def mri_reorient_lr_csh(
         version=version,
         help_=help_,
     )
-    return mri_reorient_lr_csh_execute(params, execution)
+    return mri_reorient_lr_csh_execute(params, runner)
 
 
 __all__ = [
     "MRI_REORIENT_LR_CSH_METADATA",
     "MriReorientLrCshOutputs",
-    "MriReorientLrCshParameters",
     "mri_reorient_lr_csh",
+    "mri_reorient_lr_csh_execute",
     "mri_reorient_lr_csh_params",
 ]