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

niwrap_freesurfer/freesurfer/mri_cvs_data_copy.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CVS_DATA_COPY_METADATA = Metadata(
-    id="36b6c616d7e017b4e640b713764835b6cd0c3d09.boutiques",
+    id="d8deb3fb7cffe550ef0b8e7af287a572a9fad494.boutiques",
     name="mri_cvs_data_copy",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,49 +14,26 @@ MRI_CVS_DATA_COPY_METADATA = Metadata(
 
 
 MriCvsDataCopyParameters = typing.TypedDict('MriCvsDataCopyParameters', {
-    "__STYXTYPE__": typing.Literal["mri_cvs_data_copy"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_cvs_data_copy"]],
+    "subjid": str,
+    "olddir": str,
+    "newdir": str,
+    "version": bool,
+    "help": bool,
+})
+MriCvsDataCopyParametersTagged = typing.TypedDict('MriCvsDataCopyParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_cvs_data_copy"],
     "subjid": str,
     "olddir": str,
     "newdir": str,
     "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_cvs_data_copy": mri_cvs_data_copy_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 MriCvsDataCopyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_cvs_data_copy(...)`.
+    Output object returned when calling `MriCvsDataCopyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def mri_cvs_data_copy_params(
     newdir: str,
     version: bool = False,
     help_: bool = False,
-) -> MriCvsDataCopyParameters:
+) -> MriCvsDataCopyParametersTagged:
     """
     Build parameters.
     
@@ -84,7 +61,7 @@ def mri_cvs_data_copy_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_cvs_data_copy",
+        "@type": "freesurfer/mri_cvs_data_copy",
         "subjid": subjid,
         "olddir": olddir,
         "newdir": newdir,
@@ -111,19 +88,19 @@ def mri_cvs_data_copy_cargs(
     cargs.append("mri_cvs_data_copy")
     cargs.extend([
         "--subjid",
-        params.get("subjid")
+        params.get("subjid", None)
     ])
     cargs.extend([
         "--olddir",
-        params.get("olddir")
+        params.get("olddir", None)
     ])
     cargs.extend([
         "--newdir",
-        params.get("newdir")
+        params.get("newdir", None)
     ])
-    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
 
@@ -149,9 +126,11 @@ def mri_cvs_data_copy_outputs(
 
 def mri_cvs_data_copy_execute(
     params: MriCvsDataCopyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCvsDataCopyOutputs:
     """
+    mri_cvs_data_copy
+    
     Packs and copies files that are required for mri_cvs_register.
     
     Author: FreeSurfer Developers
@@ -160,10 +139,12 @@ def mri_cvs_data_copy_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCvsDataCopyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CVS_DATA_COPY_METADATA)
     params = execution.params(params)
     cargs = mri_cvs_data_copy_cargs(params, execution)
     ret = mri_cvs_data_copy_outputs(params, execution)
@@ -180,6 +161,8 @@ def mri_cvs_data_copy(
     runner: Runner | None = None,
 ) -> MriCvsDataCopyOutputs:
     """
+    mri_cvs_data_copy
+    
     Packs and copies files that are required for mri_cvs_register.
     
     Author: FreeSurfer Developers
@@ -198,8 +181,6 @@ def mri_cvs_data_copy(
     Returns:
         NamedTuple of outputs (described in `MriCvsDataCopyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CVS_DATA_COPY_METADATA)
     params = mri_cvs_data_copy_params(
         subjid=subjid,
         olddir=olddir,
@@ -207,13 +188,13 @@ def mri_cvs_data_copy(
         version=version,
         help_=help_,
     )
-    return mri_cvs_data_copy_execute(params, execution)
+    return mri_cvs_data_copy_execute(params, runner)
 
 
 __all__ = [
     "MRI_CVS_DATA_COPY_METADATA",
     "MriCvsDataCopyOutputs",
-    "MriCvsDataCopyParameters",
     "mri_cvs_data_copy",
+    "mri_cvs_data_copy_execute",
     "mri_cvs_data_copy_params",
 ]

niwrap_freesurfer/freesurfer/mri_cvs_register.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_CVS_REGISTER_METADATA = Metadata(
-    id="3bb422fbeb829e6f72b0b527bc53abe39a30f29d.boutiques",
+    id="3bcacd58a1c587ed63709bef81d5c23ed19ba677.boutiques",
     name="mri_cvs_register",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,37 @@ MRI_CVS_REGISTER_METADATA = Metadata(
 
 
 MriCvsRegisterParameters = typing.TypedDict('MriCvsRegisterParameters', {
-    "__STYXTYPE__": typing.Literal["mri_cvs_register"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_cvs_register"]],
+    "mov_subjid": str,
+    "template_subjid": typing.NotRequired[str | None],
+    "templatedir": typing.NotRequired[str | None],
+    "mni_flag": bool,
+    "outdir": typing.NotRequired[str | None],
+    "asegfname": typing.NotRequired[str | None],
+    "voltype": typing.NotRequired[str | None],
+    "step1_flag": bool,
+    "step2_flag": bool,
+    "step3_flag": bool,
+    "noaseg_flag": bool,
+    "nointensity_flag": bool,
+    "hemi_flag": bool,
+    "masktargethemi_flag": bool,
+    "maskmovinghemi_flag": bool,
+    "nocleanup_flag": bool,
+    "keepelreg_flag": bool,
+    "keepallm3z_flag": bool,
+    "cleanall_flag": bool,
+    "cleansurfreg_flag": bool,
+    "cleanelreg_flag": bool,
+    "cleanvolreg_flag": bool,
+    "m3d_flag": bool,
+    "openmp": typing.NotRequired[int | None],
+    "nolog_flag": bool,
+    "version_flag": bool,
+    "help_flag": bool,
+})
+MriCvsRegisterParametersTagged = typing.TypedDict('MriCvsRegisterParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_cvs_register"],
     "mov_subjid": str,
     "template_subjid": typing.NotRequired[str | None],
     "templatedir": typing.NotRequired[str | None],
@@ -43,43 +73,11 @@ MriCvsRegisterParameters = typing.TypedDict('MriCvsRegisterParameters', {
     "version_flag": bool,
     "help_flag": 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_cvs_register": mri_cvs_register_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_cvs_register": mri_cvs_register_outputs,
-    }.get(t)
 
 
 class MriCvsRegisterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_cvs_register(...)`.
+    Output object returned when calling `MriCvsRegisterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -128,7 +126,7 @@ def mri_cvs_register_params(
     nolog_flag: bool = False,
     version_flag: bool = False,
     help_flag: bool = False,
-) -> MriCvsRegisterParameters:
+) -> MriCvsRegisterParametersTagged:
     """
     Build parameters.
     
@@ -177,7 +175,7 @@ def mri_cvs_register_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_cvs_register",
+        "@type": "freesurfer/mri_cvs_register",
         "mov_subjid": mov_subjid,
         "mni_flag": mni_flag,
         "step1_flag": step1_flag,
@@ -232,77 +230,77 @@ def mri_cvs_register_cargs(
     cargs.append("mri_cvs_register")
     cargs.extend([
         "--mov",
-        params.get("mov_subjid")
+        params.get("mov_subjid", None)
     ])
-    if params.get("template_subjid") is not None:
+    if params.get("template_subjid", None) is not None:
         cargs.extend([
             "--template",
-            params.get("template_subjid")
+            params.get("template_subjid", None)
         ])
-    if params.get("templatedir") is not None:
+    if params.get("templatedir", None) is not None:
         cargs.extend([
             "--templatedir",
-            params.get("templatedir")
+            params.get("templatedir", None)
         ])
-    if params.get("mni_flag"):
+    if params.get("mni_flag", False):
         cargs.append("--mni")
-    if params.get("outdir") is not None:
+    if params.get("outdir", None) is not None:
         cargs.extend([
             "--outdir",
-            params.get("outdir")
+            params.get("outdir", None)
         ])
-    if params.get("asegfname") is not None:
+    if params.get("asegfname", None) is not None:
         cargs.extend([
             "--asegfname",
-            params.get("asegfname")
+            params.get("asegfname", None)
         ])
-    if params.get("voltype") is not None:
+    if params.get("voltype", None) is not None:
         cargs.extend([
             "--voltype",
-            params.get("voltype")
+            params.get("voltype", None)
         ])
-    if params.get("step1_flag"):
+    if params.get("step1_flag", False):
         cargs.append("--step1")
-    if params.get("step2_flag"):
+    if params.get("step2_flag", False):
         cargs.append("--step2")
-    if params.get("step3_flag"):
+    if params.get("step3_flag", False):
         cargs.append("--step3")
-    if params.get("noaseg_flag"):
+    if params.get("noaseg_flag", False):
         cargs.append("--noaseg")
-    if params.get("nointensity_flag"):
+    if params.get("nointensity_flag", False):
         cargs.append("--nointensity")
-    if params.get("hemi_flag"):
+    if params.get("hemi_flag", False):
         cargs.append("--hemi")
-    if params.get("masktargethemi_flag"):
+    if params.get("masktargethemi_flag", False):
         cargs.append("--masktargethemi")
-    if params.get("maskmovinghemi_flag"):
+    if params.get("maskmovinghemi_flag", False):
         cargs.append("--maskmovinghemi")
-    if params.get("nocleanup_flag"):
+    if params.get("nocleanup_flag", False):
         cargs.append("--nocleanup")
-    if params.get("keepelreg_flag"):
+    if params.get("keepelreg_flag", False):
         cargs.append("--keepelreg")
-    if params.get("keepallm3z_flag"):
+    if params.get("keepallm3z_flag", False):
         cargs.append("--keepallm3z")
-    if params.get("cleanall_flag"):
+    if params.get("cleanall_flag", False):
         cargs.append("--cleanall")
-    if params.get("cleansurfreg_flag"):
+    if params.get("cleansurfreg_flag", False):
         cargs.append("--cleansurfreg")
-    if params.get("cleanelreg_flag"):
+    if params.get("cleanelreg_flag", False):
         cargs.append("--cleanelreg")
-    if params.get("cleanvolreg_flag"):
+    if params.get("cleanvolreg_flag", False):
         cargs.append("--cleanvolreg")
-    if params.get("m3d_flag"):
+    if params.get("m3d_flag", False):
         cargs.append("--m3d")
-    if params.get("openmp") is not None:
+    if params.get("openmp", None) is not None:
         cargs.extend([
             "--openmp",
-            str(params.get("openmp"))
+            str(params.get("openmp", None))
         ])
-    if params.get("nolog_flag"):
+    if params.get("nolog_flag", False):
         cargs.append("--nolog")
-    if params.get("version_flag"):
+    if params.get("version_flag", False):
         cargs.append("--version")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("--help")
     return cargs
 
@@ -322,20 +320,22 @@ def mri_cvs_register_outputs(
     """
     ret = MriCvsRegisterOutputs(
         root=execution.output_file("."),
-        final_cvs_morph=execution.output_file(params.get("outdir") + "/final_CVSmorph_toTEMPLATE.m3z") if (params.get("outdir") is not None) else None,
-        final_cvs_morphed_norm=execution.output_file(params.get("outdir") + "/final_CVSmorphed_toTEMPLATE_norm.mgz") if (params.get("outdir") is not None) else None,
-        final_cvs_morphed_aseg=execution.output_file(params.get("outdir") + "/final_CVSmorphed_toTEMPLATE_aseg.mgz") if (params.get("outdir") is not None) else None,
-        step1_morphed_aseg=execution.output_file(params.get("outdir") + "/step1_CVSmorphed_toTEMPLATE_aseg.mgz") if (params.get("outdir") is not None) else None,
-        step1_morphed_norm=execution.output_file(params.get("outdir") + "/step1_CVSmorphed_toTEMPLATE_norm.mgz") if (params.get("outdir") is not None) else None,
+        final_cvs_morph=execution.output_file(params.get("outdir", None) + "/final_CVSmorph_toTEMPLATE.m3z") if (params.get("outdir") is not None) else None,
+        final_cvs_morphed_norm=execution.output_file(params.get("outdir", None) + "/final_CVSmorphed_toTEMPLATE_norm.mgz") if (params.get("outdir") is not None) else None,
+        final_cvs_morphed_aseg=execution.output_file(params.get("outdir", None) + "/final_CVSmorphed_toTEMPLATE_aseg.mgz") if (params.get("outdir") is not None) else None,
+        step1_morphed_aseg=execution.output_file(params.get("outdir", None) + "/step1_CVSmorphed_toTEMPLATE_aseg.mgz") if (params.get("outdir") is not None) else None,
+        step1_morphed_norm=execution.output_file(params.get("outdir", None) + "/step1_CVSmorphed_toTEMPLATE_norm.mgz") if (params.get("outdir") is not None) else None,
     )
     return ret
 
 
 def mri_cvs_register_execute(
     params: MriCvsRegisterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriCvsRegisterOutputs:
     """
+    mri_cvs_register
+    
     Combined Volume and Surface Registration.
     
     Author: FreeSurfer Developers
@@ -344,10 +344,12 @@ def mri_cvs_register_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriCvsRegisterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_CVS_REGISTER_METADATA)
     params = execution.params(params)
     cargs = mri_cvs_register_cargs(params, execution)
     ret = mri_cvs_register_outputs(params, execution)
@@ -386,6 +388,8 @@ def mri_cvs_register(
     runner: Runner | None = None,
 ) -> MriCvsRegisterOutputs:
     """
+    mri_cvs_register
+    
     Combined Volume and Surface Registration.
     
     Author: FreeSurfer Developers
@@ -437,8 +441,6 @@ def mri_cvs_register(
     Returns:
         NamedTuple of outputs (described in `MriCvsRegisterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_CVS_REGISTER_METADATA)
     params = mri_cvs_register_params(
         mov_subjid=mov_subjid,
         template_subjid=template_subjid,
@@ -468,13 +470,13 @@ def mri_cvs_register(
         version_flag=version_flag,
         help_flag=help_flag,
     )
-    return mri_cvs_register_execute(params, execution)
+    return mri_cvs_register_execute(params, runner)
 
 
 __all__ = [
     "MRI_CVS_REGISTER_METADATA",
     "MriCvsRegisterOutputs",
-    "MriCvsRegisterParameters",
     "mri_cvs_register",
+    "mri_cvs_register_execute",
     "mri_cvs_register_params",
 ]

niwrap_freesurfer/freesurfer/mri_dct_align.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MRI_DCT_ALIGN_METADATA = Metadata(
-    id="41e6e579d5ddb08e54325cc779dff53fb8fda430.boutiques",
+    id="fb4d96e7ddbde097470bc8b0b9668f31e70c7eba.boutiques",
     name="mri_dct_align",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,22 @@ MRI_DCT_ALIGN_METADATA = Metadata(
 
 
 MriDctAlignParameters = typing.TypedDict('MriDctAlignParameters', {
-    "__STYXTYPE__": typing.Literal["mri_dct_align"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mri_dct_align"]],
+    "source": InputPathType,
+    "destination": InputPathType,
+    "output_xform": str,
+})
+MriDctAlignParametersTagged = typing.TypedDict('MriDctAlignParametersTagged', {
+    "@type": typing.Literal["freesurfer/mri_dct_align"],
     "source": InputPathType,
     "destination": InputPathType,
     "output_xform": 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": mri_dct_align_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": mri_dct_align_outputs,
-    }.get(t)
 
 
 class MriDctAlignOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mri_dct_align(...)`.
+    Output object returned when calling `MriDctAlignParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -67,7 +41,7 @@ def mri_dct_align_params(
     source: InputPathType,
     destination: InputPathType,
     output_xform: str,
-) -> MriDctAlignParameters:
+) -> MriDctAlignParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +53,7 @@ def mri_dct_align_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mri_dct_align",
+        "@type": "freesurfer/mri_dct_align",
         "source": source,
         "destination": destination,
         "output_xform": output_xform,
@@ -102,9 +76,9 @@ def mri_dct_align_cargs(
     """
     cargs = []
     cargs.append("mri_dct_align")
-    cargs.append(execution.input_file(params.get("source")))
-    cargs.append(execution.input_file(params.get("destination")))
-    cargs.append(params.get("output_xform"))
+    cargs.append(execution.input_file(params.get("source", None)))
+    cargs.append(execution.input_file(params.get("destination", None)))
+    cargs.append(params.get("output_xform", None))
     return cargs
 
 
@@ -123,16 +97,18 @@ def mri_dct_align_outputs(
     """
     ret = MriDctAlignOutputs(
         root=execution.output_file("."),
-        output_xform_file=execution.output_file(params.get("output_xform")),
+        output_xform_file=execution.output_file(params.get("output_xform", None)),
     )
     return ret
 
 
 def mri_dct_align_execute(
     params: MriDctAlignParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MriDctAlignOutputs:
     """
+    mri_dct_align
+    
     MRI DCT alignment tool from FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -141,10 +117,12 @@ def mri_dct_align_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MriDctAlignOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MRI_DCT_ALIGN_METADATA)
     params = execution.params(params)
     cargs = mri_dct_align_cargs(params, execution)
     ret = mri_dct_align_outputs(params, execution)
@@ -159,6 +137,8 @@ def mri_dct_align(
     runner: Runner | None = None,
 ) -> MriDctAlignOutputs:
     """
+    mri_dct_align
+    
     MRI DCT alignment tool from FreeSurfer.
     
     Author: FreeSurfer Developers
@@ -173,20 +153,18 @@ def mri_dct_align(
     Returns:
         NamedTuple of outputs (described in `MriDctAlignOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MRI_DCT_ALIGN_METADATA)
     params = mri_dct_align_params(
         source=source,
         destination=destination,
         output_xform=output_xform,
     )
-    return mri_dct_align_execute(params, execution)
+    return mri_dct_align_execute(params, runner)
 
 
 __all__ = [
     "MRI_DCT_ALIGN_METADATA",
     "MriDctAlignOutputs",
-    "MriDctAlignParameters",
     "mri_dct_align",
+    "mri_dct_align_execute",
     "mri_dct_align_params",
 ]