niwrap-freesurfer 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_freesurfer/freesurfer/mri_polv.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_POLV_METADATA = Metadata(
-    id="ee8644189f031978bc3740be0222cfee554fee9b.boutiques",
+    id="2855dc9247e5d6b55040855e461f290bb6be8b8e.boutiques",
     name="mri_polv",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ MRI_POLV_METADATA = Metadata(
 
 
 MriPolvParameters = typing.TypedDict('MriPolvParameters', {
-    "__STYXTYPE__": typing.Literal["mri_polv"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_polv"]],
+    "window_size": typing.NotRequired[float | None],
+    "input_image": InputPathType,
+    "output_image": InputPathType,
+})
+MriPolvParametersTagged = typing.TypedDict('MriPolvParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_polv"],
     "window_size": typing.NotRequired[float | None],
     "input_image": InputPathType,
     "output_image": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "mri_polv": mri_polv_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 MriPolvOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_polv(...)`.
+    Output object returned when calling `MriPolvParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def mri_polv_params(
     input_image: InputPathType,
     output_image: InputPathType,
     window_size: float | None = None,
-) -> MriPolvParameters:
+) -> MriPolvParametersTagged:
     """
     Build parameters.
     
@@ -78,7 +53,7 @@ def mri_polv_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_polv",
+        "@type": "freesurfer/mri_polv",
         "input_image": input_image,
         "output_image": output_image,
     }
@@ -102,13 +77,13 @@ def mri_polv_cargs(
     """
     cargs = []
     cargs.append("mri_polv")
-    if params.get("window_size") is not None:
+    if params.get("window_size", None) is not None:
         cargs.extend([
             "-w",
-            str(params.get("window_size"))
+            str(params.get("window_size", None))
         ])
-    cargs.append(execution.input_file(params.get("input_image")))
-    cargs.append(execution.input_file(params.get("output_image")))
+    cargs.append(execution.input_file(params.get("input_image", None)))
+    cargs.append(execution.input_file(params.get("output_image", None)))
     return cargs
 
 
@@ -133,11 +108,13 @@ def mri_polv_outputs(
 
 def mri_polv_execute(
     params: MriPolvParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriPolvOutputs:
     """
-    Calculate an image specifying the plane of least variance at each point in the
-    input image.
+    mri_polv
+    
+    Calculate an image specifying the plane of least variance at each point in
+    the input image.
     
     Author: FreeSurfer Developers
     
@@ -145,10 +122,12 @@ def mri_polv_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriPolvOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_POLV_METADATA)
     params = execution.params(params)
     cargs = mri_polv_cargs(params, execution)
     ret = mri_polv_outputs(params, execution)
@@ -163,8 +142,10 @@ def mri_polv(
     runner: Runner | None = None,
 ) -> MriPolvOutputs:
     """
-    Calculate an image specifying the plane of least variance at each point in the
-    input image.
+    mri_polv
+    
+    Calculate an image specifying the plane of least variance at each point in
+    the input image.
     
     Author: FreeSurfer Developers
     
@@ -180,20 +161,18 @@ def mri_polv(
     Returns:
         NamedTuple of outputs (described in `MriPolvOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_POLV_METADATA)
     params = mri_polv_params(
         window_size=window_size,
         input_image=input_image,
         output_image=output_image,
     )
-    return mri_polv_execute(params, execution)
+    return mri_polv_execute(params, runner)
 
 
 __all__ = [
     "MRI_POLV_METADATA",
     "MriPolvOutputs",
-    "MriPolvParameters",
     "mri_polv",
+    "mri_polv_execute",
     "mri_polv_params",
 ]

niwrap_freesurfer/freesurfer/mri_pretess.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_PRETESS_METADATA = Metadata(
-    id="641c8ed7465afbc036c806429e570f67468946a0.boutiques",
+    id="c68ce0cb43441ea076cb58f756a347937fe174be.boutiques",
     name="mri_pretess",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRI_PRETESS_METADATA = Metadata(
 
 
 MriPretessParameters = typing.TypedDict('MriPretessParameters', {
-    "__STYXTYPE__": typing.Literal["mri_pretess"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_pretess"]],
+    "filledvol": InputPathType,
+    "labelstring": str,
+    "normvol": InputPathType,
+    "newfilledvol": str,
+    "debug_voxel": typing.NotRequired[list[float] | None],
+    "nocorners": bool,
+    "write": bool,
+    "keep": bool,
+    "test": bool,
+})
+MriPretessParametersTagged = typing.TypedDict('MriPretessParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_pretess"],
     "filledvol": InputPathType,
     "labelstring": str,
     "normvol": InputPathType,
@@ -25,43 +37,11 @@ MriPretessParameters = typing.TypedDict('MriPretessParameters', {
     "keep": bool,
     "test": 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_pretess": mri_pretess_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_pretess": mri_pretess_outputs,
-    }.get(t)
 
 
 class MriPretessOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_pretess(...)`.
+    Output object returned when calling `MriPretessParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +59,7 @@ def mri_pretess_params(
     write: bool = False,
     keep: bool = False,
     test: bool = False,
-) -> MriPretessParameters:
+) -> MriPretessParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +78,7 @@ def mri_pretess_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_pretess",
+        "@type": "freesurfer/mri_pretess",
         "filledvol": filledvol,
         "labelstring": labelstring,
         "normvol": normvol,
@@ -128,22 +108,22 @@ def mri_pretess_cargs(
     """
     cargs = []
     cargs.append("mri_pretess")
-    cargs.append(execution.input_file(params.get("filledvol")))
-    cargs.append(params.get("labelstring"))
-    cargs.append(execution.input_file(params.get("normvol")))
-    cargs.append(params.get("newfilledvol"))
-    if params.get("debug_voxel") is not None:
+    cargs.append(execution.input_file(params.get("filledvol", None)))
+    cargs.append(params.get("labelstring", None))
+    cargs.append(execution.input_file(params.get("normvol", None)))
+    cargs.append(params.get("newfilledvol", None))
+    if params.get("debug_voxel", None) is not None:
         cargs.extend([
             "-debug_voxel",
-            *map(str, params.get("debug_voxel"))
+            *map(str, params.get("debug_voxel", None))
         ])
-    if params.get("nocorners"):
+    if params.get("nocorners", False):
         cargs.append("-nocorners")
-    if params.get("write"):
+    if params.get("write", False):
         cargs.append("-w")
-    if params.get("keep"):
+    if params.get("keep", False):
         cargs.append("-keep")
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("-test")
     return cargs
 
@@ -163,18 +143,20 @@ def mri_pretess_outputs(
     """
     ret = MriPretessOutputs(
         root=execution.output_file("."),
-        out_newfilledvol=execution.output_file(params.get("newfilledvol")),
+        out_newfilledvol=execution.output_file(params.get("newfilledvol", None)),
     )
     return ret
 
 
 def mri_pretess_execute(
     params: MriPretessParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriPretessOutputs:
     """
-    Tool to modify WM segmentation so that all neighbors of WM voxels have a common
-    face.
+    mri_pretess
+    
+    Tool to modify WM segmentation so that all neighbors of WM voxels have a
+    common face.
     
     Author: FreeSurfer Developers
     
@@ -182,10 +164,12 @@ def mri_pretess_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriPretessOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_PRETESS_METADATA)
     params = execution.params(params)
     cargs = mri_pretess_cargs(params, execution)
     ret = mri_pretess_outputs(params, execution)
@@ -206,8 +190,10 @@ def mri_pretess(
     runner: Runner | None = None,
 ) -> MriPretessOutputs:
     """
-    Tool to modify WM segmentation so that all neighbors of WM voxels have a common
-    face.
+    mri_pretess
+    
+    Tool to modify WM segmentation so that all neighbors of WM voxels have a
+    common face.
     
     Author: FreeSurfer Developers
     
@@ -228,8 +214,6 @@ def mri_pretess(
     Returns:
         NamedTuple of outputs (described in `MriPretessOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_PRETESS_METADATA)
     params = mri_pretess_params(
         filledvol=filledvol,
         labelstring=labelstring,
@@ -241,13 +225,13 @@ def mri_pretess(
         keep=keep,
         test=test,
     )
-    return mri_pretess_execute(params, execution)
+    return mri_pretess_execute(params, runner)
 
 
 __all__ = [
     "MRI_PRETESS_METADATA",
     "MriPretessOutputs",
-    "MriPretessParameters",
     "mri_pretess",
+    "mri_pretess_execute",
     "mri_pretess_params",
 ]

niwrap_freesurfer/freesurfer/mri_probe_ima.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_PROBE_IMA_METADATA = Metadata(
-    id="b65fa164df8c152f809036a62acf6694a68d33bd.boutiques",
+    id="5fa4fc0601daa1858523f5477b0490cf22997bfc.boutiques",
     name="mri_probe_ima",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MRI_PROBE_IMA_METADATA = Metadata(
 
 
 MriProbeImaParameters = typing.TypedDict('MriProbeImaParameters', {
-    "__STYXTYPE__": typing.Literal["mri_probe_ima"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_probe_ima"]],
+    "ima_file": InputPathType,
+    "key_string": typing.NotRequired[str | None],
+    "offset_type_len": typing.NotRequired[str | None],
+    "attribute_name": typing.NotRequired[str | None],
+    "fileinfo": bool,
+    "dictionary": bool,
+    "ob_stem": typing.NotRequired[str | None],
+    "help": bool,
+    "version": bool,
+})
+MriProbeImaParametersTagged = typing.TypedDict('MriProbeImaParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_probe_ima"],
     "ima_file": InputPathType,
     "key_string": typing.NotRequired[str | None],
     "offset_type_len": typing.NotRequired[str | None],
@@ -25,42 +37,11 @@ MriProbeImaParameters = typing.TypedDict('MriProbeImaParameters', {
     "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_probe_ima": mri_probe_ima_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 MriProbeImaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_probe_ima(...)`.
+    Output object returned when calling `MriProbeImaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def mri_probe_ima_params(
     ob_stem: str | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MriProbeImaParameters:
+) -> MriProbeImaParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +76,7 @@ def mri_probe_ima_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_probe_ima",
+        "@type": "freesurfer/mri_probe_ima",
         "ima_file": ima_file,
         "fileinfo": fileinfo,
         "dictionary": dictionary,
@@ -130,35 +111,35 @@ def mri_probe_ima_cargs(
     cargs.append("mri_probe_ima")
     cargs.extend([
         "--i",
-        execution.input_file(params.get("ima_file"))
+        execution.input_file(params.get("ima_file", None))
     ])
-    if params.get("key_string") is not None:
+    if params.get("key_string", None) is not None:
         cargs.extend([
             "--key",
-            params.get("key_string")
+            params.get("key_string", None)
         ])
-    if params.get("offset_type_len") is not None:
+    if params.get("offset_type_len", None) is not None:
         cargs.extend([
             "--o",
-            params.get("offset_type_len")
+            params.get("offset_type_len", None)
         ])
-    if params.get("attribute_name") is not None:
+    if params.get("attribute_name", None) is not None:
         cargs.extend([
             "--attr",
-            params.get("attribute_name")
+            params.get("attribute_name", None)
         ])
-    if params.get("fileinfo"):
+    if params.get("fileinfo", False):
         cargs.append("--fileinfo")
-    if params.get("dictionary"):
+    if params.get("dictionary", False):
         cargs.append("--dictionary")
-    if params.get("ob_stem") is not None:
+    if params.get("ob_stem", None) is not None:
         cargs.extend([
             "--ob",
-            params.get("ob_stem")
+            params.get("ob_stem", 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
 
@@ -184,9 +165,11 @@ def mri_probe_ima_outputs(
 
 def mri_probe_ima_execute(
     params: MriProbeImaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriProbeImaOutputs:
     """
+    mri_probe_ima
+    
     Query Siemens IMA files to extract header information.
     
     Author: FreeSurfer Developers
@@ -195,10 +178,12 @@ def mri_probe_ima_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriProbeImaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_PROBE_IMA_METADATA)
     params = execution.params(params)
     cargs = mri_probe_ima_cargs(params, execution)
     ret = mri_probe_ima_outputs(params, execution)
@@ -219,6 +204,8 @@ def mri_probe_ima(
     runner: Runner | None = None,
 ) -> MriProbeImaOutputs:
     """
+    mri_probe_ima
+    
     Query Siemens IMA files to extract header information.
     
     Author: FreeSurfer Developers
@@ -240,8 +227,6 @@ def mri_probe_ima(
     Returns:
         NamedTuple of outputs (described in `MriProbeImaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_PROBE_IMA_METADATA)
     params = mri_probe_ima_params(
         ima_file=ima_file,
         key_string=key_string,
@@ -253,13 +238,13 @@ def mri_probe_ima(
         help_=help_,
         version=version,
     )
-    return mri_probe_ima_execute(params, execution)
+    return mri_probe_ima_execute(params, runner)
 
 
 __all__ = [
     "MRI_PROBE_IMA_METADATA",
     "MriProbeImaOutputs",
-    "MriProbeImaParameters",
     "mri_probe_ima",
+    "mri_probe_ima_execute",
     "mri_probe_ima_params",
 ]