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

niwrap_freesurfer/freesurfer/reg_feat2anat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REG_FEAT2ANAT_METADATA = Metadata(
-    id="90cae5222fb5bffe4289efcaf84a56fc3ceb6ff5.boutiques",
+    id="2c62c70fcd28e7e86048c180248305074930e5e6.boutiques",
     name="reg-feat2anat",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,26 @@ REG_FEAT2ANAT_METADATA = Metadata(
 
 
 RegFeat2anatParameters = typing.TypedDict('RegFeat2anatParameters', {
-    "__STYXTYPE__": typing.Literal["reg-feat2anat"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reg-feat2anat"]],
+    "feat_dir": str,
+    "subject_id": str,
+    "overwrite_exf2std": bool,
+    "manual": bool,
+    "manxfm_type": typing.NotRequired[str | None],
+    "dof": typing.NotRequired[int | None],
+    "bins": typing.NotRequired[int | None],
+    "cost": typing.NotRequired[str | None],
+    "max_angle": typing.NotRequired[float | None],
+    "bet": bool,
+    "title": typing.NotRequired[str | None],
+    "no_bbr": bool,
+    "spm": bool,
+    "no_inorm": bool,
+    "fmov": typing.NotRequired[str | None],
+    "debug": bool,
+})
+RegFeat2anatParametersTagged = typing.TypedDict('RegFeat2anatParametersTagged', {
+    "@type": typing.Literal["freesurfer/reg-feat2anat"],
     "feat_dir": str,
     "subject_id": str,
     "overwrite_exf2std": bool,
@@ -32,43 +51,11 @@ RegFeat2anatParameters = typing.TypedDict('RegFeat2anatParameters', {
     "fmov": typing.NotRequired[str | None],
     "debug": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reg-feat2anat": reg_feat2anat_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 {
-        "reg-feat2anat": reg_feat2anat_outputs,
-    }.get(t)
 
 
 class RegFeat2anatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reg_feat2anat(...)`.
+    Output object returned when calling `RegFeat2anatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +94,7 @@ def reg_feat2anat_params(
     no_inorm: bool = False,
     fmov: str | None = None,
     debug: bool = False,
-) -> RegFeat2anatParameters:
+) -> RegFeat2anatParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +120,7 @@ def reg_feat2anat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reg-feat2anat",
+        "@type": "freesurfer/reg-feat2anat",
         "feat_dir": feat_dir,
         "subject_id": subject_id,
         "overwrite_exf2std": overwrite_exf2std,
@@ -178,60 +165,60 @@ def reg_feat2anat_cargs(
     cargs.append("reg-feat2anat")
     cargs.extend([
         "--feat",
-        params.get("feat_dir")
+        params.get("feat_dir", None)
     ])
     cargs.extend([
         "--subject",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
-    if params.get("overwrite_exf2std"):
+    if params.get("overwrite_exf2std", False):
         cargs.append("--overwrite-exf2std")
-    if params.get("manual"):
+    if params.get("manual", False):
         cargs.append("--manual")
-    if params.get("manxfm_type") is not None:
+    if params.get("manxfm_type", None) is not None:
         cargs.extend([
             "--manxfm",
-            params.get("manxfm_type")
+            params.get("manxfm_type", None)
         ])
-    if params.get("dof") is not None:
+    if params.get("dof", None) is not None:
         cargs.extend([
             "--dof",
-            str(params.get("dof"))
+            str(params.get("dof", None))
         ])
-    if params.get("bins") is not None:
+    if params.get("bins", None) is not None:
         cargs.extend([
             "--bins",
-            str(params.get("bins"))
+            str(params.get("bins", None))
         ])
-    if params.get("cost") is not None:
+    if params.get("cost", None) is not None:
         cargs.extend([
             "--cost",
-            params.get("cost")
+            params.get("cost", None)
         ])
-    if params.get("max_angle") is not None:
+    if params.get("max_angle", None) is not None:
         cargs.extend([
             "--maxangle",
-            str(params.get("max_angle"))
+            str(params.get("max_angle", None))
         ])
-    if params.get("bet"):
+    if params.get("bet", False):
         cargs.append("--bet")
-    if params.get("title") is not None:
+    if params.get("title", None) is not None:
         cargs.extend([
             "--title",
-            params.get("title")
+            params.get("title", None)
         ])
-    if params.get("no_bbr"):
+    if params.get("no_bbr", False):
         cargs.append("--no-bbr")
-    if params.get("spm"):
+    if params.get("spm", False):
         cargs.append("--spm")
-    if params.get("no_inorm"):
+    if params.get("no_inorm", False):
         cargs.append("--no-inorm")
-    if params.get("fmov") is not None:
+    if params.get("fmov", None) is not None:
         cargs.extend([
             "--fmov",
-            params.get("fmov")
+            params.get("fmov", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
     return cargs
 
@@ -265,9 +252,11 @@ def reg_feat2anat_outputs(
 
 def reg_feat2anat_execute(
     params: RegFeat2anatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RegFeat2anatOutputs:
     """
+    reg-feat2anat
+    
     Registers FSL-Feat example_func to FreeSurfer anatomical data.
     
     Author: FreeSurfer Developers
@@ -276,10 +265,12 @@ def reg_feat2anat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RegFeat2anatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REG_FEAT2ANAT_METADATA)
     params = execution.params(params)
     cargs = reg_feat2anat_cargs(params, execution)
     ret = reg_feat2anat_outputs(params, execution)
@@ -307,6 +298,8 @@ def reg_feat2anat(
     runner: Runner | None = None,
 ) -> RegFeat2anatOutputs:
     """
+    reg-feat2anat
+    
     Registers FSL-Feat example_func to FreeSurfer anatomical data.
     
     Author: FreeSurfer Developers
@@ -335,8 +328,6 @@ def reg_feat2anat(
     Returns:
         NamedTuple of outputs (described in `RegFeat2anatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REG_FEAT2ANAT_METADATA)
     params = reg_feat2anat_params(
         feat_dir=feat_dir,
         subject_id=subject_id,
@@ -355,13 +346,13 @@ def reg_feat2anat(
         fmov=fmov,
         debug=debug,
     )
-    return reg_feat2anat_execute(params, execution)
+    return reg_feat2anat_execute(params, runner)
 
 
 __all__ = [
     "REG_FEAT2ANAT_METADATA",
     "RegFeat2anatOutputs",
-    "RegFeat2anatParameters",
     "reg_feat2anat",
+    "reg_feat2anat_execute",
     "reg_feat2anat_params",
 ]

niwrap_freesurfer/freesurfer/reg_mni305_2mm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REG_MNI305_2MM_METADATA = Metadata(
-    id="64e1604135d19d48b71f85d6fedba8ada9ab603b.boutiques",
+    id="82c545be6984da6f8a807d110c3a763f0645c18a.boutiques",
     name="reg-mni305.2mm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,20 @@ REG_MNI305_2MM_METADATA = Metadata(
 
 
 RegMni3052mmParameters = typing.TypedDict('RegMni3052mmParameters', {
-    "__STYXTYPE__": typing.Literal["reg-mni305.2mm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/reg-mni305.2mm"]],
+    "subject_id": str,
+    "regfile": InputPathType,
+})
+RegMni3052mmParametersTagged = typing.TypedDict('RegMni3052mmParametersTagged', {
+    "@type": typing.Literal["freesurfer/reg-mni305.2mm"],
     "subject_id": str,
     "regfile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "reg-mni305.2mm": reg_mni305_2mm_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 {
-        "reg-mni305.2mm": reg_mni305_2mm_outputs,
-    }.get(t)
 
 
 class RegMni3052mmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `reg_mni305_2mm(...)`.
+    Output object returned when calling `RegMni3052mmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class RegMni3052mmOutputs(typing.NamedTuple):
 def reg_mni305_2mm_params(
     subject_id: str,
     regfile: InputPathType,
-) -> RegMni3052mmParameters:
+) -> RegMni3052mmParametersTagged:
     """
     Build parameters.
     
@@ -77,7 +50,7 @@ def reg_mni305_2mm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "reg-mni305.2mm",
+        "@type": "freesurfer/reg-mni305.2mm",
         "subject_id": subject_id,
         "regfile": regfile,
     }
@@ -101,11 +74,11 @@ def reg_mni305_2mm_cargs(
     cargs.append("reg-mni305.2mm")
     cargs.extend([
         "--s",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     cargs.extend([
         "--reg",
-        execution.input_file(params.get("regfile"))
+        execution.input_file(params.get("regfile", None))
     ])
     return cargs
 
@@ -125,16 +98,18 @@ def reg_mni305_2mm_outputs(
     """
     ret = RegMni3052mmOutputs(
         root=execution.output_file("."),
-        output_regfile=execution.output_file(pathlib.Path(params.get("regfile")).name),
+        output_regfile=execution.output_file(pathlib.Path(params.get("regfile", None)).name),
     )
     return ret
 
 
 def reg_mni305_2mm_execute(
     params: RegMni3052mmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RegMni3052mmOutputs:
     """
+    reg-mni305.2mm
+    
     Computes the registration between the FreeSurfer MNI305 2mm space and a
     subject's FreeSurfer anatomical space.
     
@@ -144,10 +119,12 @@ def reg_mni305_2mm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RegMni3052mmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REG_MNI305_2MM_METADATA)
     params = execution.params(params)
     cargs = reg_mni305_2mm_cargs(params, execution)
     ret = reg_mni305_2mm_outputs(params, execution)
@@ -161,6 +138,8 @@ def reg_mni305_2mm(
     runner: Runner | None = None,
 ) -> RegMni3052mmOutputs:
     """
+    reg-mni305.2mm
+    
     Computes the registration between the FreeSurfer MNI305 2mm space and a
     subject's FreeSurfer anatomical space.
     
@@ -176,19 +155,17 @@ def reg_mni305_2mm(
     Returns:
         NamedTuple of outputs (described in `RegMni3052mmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REG_MNI305_2MM_METADATA)
     params = reg_mni305_2mm_params(
         subject_id=subject_id,
         regfile=regfile,
     )
-    return reg_mni305_2mm_execute(params, execution)
+    return reg_mni305_2mm_execute(params, runner)
 
 
 __all__ = [
     "REG_MNI305_2MM_METADATA",
     "RegMni3052mmOutputs",
-    "RegMni3052mmParameters",
     "reg_mni305_2mm",
+    "reg_mni305_2mm_execute",
     "reg_mni305_2mm_params",
 ]

niwrap_freesurfer/freesurfer/regdat2xfm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 REGDAT2XFM_METADATA = Metadata(
-    id="b9432995881f050a69f7f6321a3344dd584bf012.boutiques",
+    id="6616f4ea03802055d15b1827ab4098f01d0e1d0d.boutiques",
     name="regdat2xfm",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,46 +14,20 @@ REGDAT2XFM_METADATA = Metadata(
 
 
 Regdat2xfmParameters = typing.TypedDict('Regdat2xfmParameters', {
-    "__STYXTYPE__": typing.Literal["regdat2xfm"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/regdat2xfm"]],
+    "input_file": InputPathType,
+    "output_file": str,
+})
+Regdat2xfmParametersTagged = typing.TypedDict('Regdat2xfmParametersTagged', {
+    "@type": typing.Literal["freesurfer/regdat2xfm"],
     "input_file": InputPathType,
     "output_file": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "regdat2xfm": regdat2xfm_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 Regdat2xfmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `regdat2xfm(...)`.
+    Output object returned when calling `Regdat2xfmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class Regdat2xfmOutputs(typing.NamedTuple):
 def regdat2xfm_params(
     input_file: InputPathType,
     output_file: str,
-) -> Regdat2xfmParameters:
+) -> Regdat2xfmParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def regdat2xfm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "regdat2xfm",
+        "@type": "freesurfer/regdat2xfm",
         "input_file": input_file,
         "output_file": output_file,
     }
@@ -95,8 +69,8 @@ def regdat2xfm_cargs(
     """
     cargs = []
     cargs.append("regdat2xfm")
-    cargs.append(execution.input_file(params.get("input_file")))
-    cargs.append(params.get("output_file"))
+    cargs.append(execution.input_file(params.get("input_file", None)))
+    cargs.append(params.get("output_file", None))
     return cargs
 
 
@@ -121,9 +95,11 @@ def regdat2xfm_outputs(
 
 def regdat2xfm_execute(
     params: Regdat2xfmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> Regdat2xfmOutputs:
     """
+    regdat2xfm
+    
     This tool has been removed from the current version of FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -132,10 +108,12 @@ def regdat2xfm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `Regdat2xfmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(REGDAT2XFM_METADATA)
     params = execution.params(params)
     cargs = regdat2xfm_cargs(params, execution)
     ret = regdat2xfm_outputs(params, execution)
@@ -149,6 +127,8 @@ def regdat2xfm(
     runner: Runner | None = None,
 ) -> Regdat2xfmOutputs:
     """
+    regdat2xfm
+    
     This tool has been removed from the current version of FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -162,19 +142,17 @@ def regdat2xfm(
     Returns:
         NamedTuple of outputs (described in `Regdat2xfmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(REGDAT2XFM_METADATA)
     params = regdat2xfm_params(
         input_file=input_file,
         output_file=output_file,
     )
-    return regdat2xfm_execute(params, execution)
+    return regdat2xfm_execute(params, runner)
 
 
 __all__ = [
     "REGDAT2XFM_METADATA",
     "Regdat2xfmOutputs",
-    "Regdat2xfmParameters",
     "regdat2xfm",
+    "regdat2xfm_execute",
     "regdat2xfm_params",
 ]