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

niwrap_freesurfer/freesurfer/mksubjdirs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MKSUBJDIRS_METADATA = Metadata(
-    id="72f40759596bf85f3287dd70895a2c0cec8c9366.boutiques",
+    id="5a4b4fa4ad4e76639de872219fc283fdb7e306a6.boutiques",
     name="mksubjdirs",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ MKSUBJDIRS_METADATA = Metadata(
 
 
 MksubjdirsParameters = typing.TypedDict('MksubjdirsParameters', {
-    "__STYXTYPE__": typing.Literal["mksubjdirs"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mksubjdirs"]],
+    "subj_name": str,
+    "mode": typing.NotRequired[str | None],
+    "parents": bool,
+    "verbose": bool,
+    "selinux_context": bool,
+    "help": bool,
+    "version": bool,
+})
+MksubjdirsParametersTagged = typing.TypedDict('MksubjdirsParametersTagged', {
+    "@type": typing.Literal["freesurfer/mksubjdirs"],
     "subj_name": str,
     "mode": typing.NotRequired[str | None],
     "parents": bool,
@@ -23,42 +33,11 @@ MksubjdirsParameters = typing.TypedDict('MksubjdirsParameters', {
     "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 {
-        "mksubjdirs": mksubjdirs_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 MksubjdirsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mksubjdirs(...)`.
+    Output object returned when calling `MksubjdirsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def mksubjdirs_params(
     selinux_context: bool = False,
     help_: bool = False,
     version: bool = False,
-) -> MksubjdirsParameters:
+) -> MksubjdirsParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +68,7 @@ def mksubjdirs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mksubjdirs",
+        "@type": "freesurfer/mksubjdirs",
         "subj_name": subj_name,
         "parents": parents,
         "verbose": verbose,
@@ -117,21 +96,21 @@ def mksubjdirs_cargs(
     """
     cargs = []
     cargs.append("mksubjdirs")
-    cargs.append(params.get("subj_name"))
-    if params.get("mode") is not None:
+    cargs.append(params.get("subj_name", None))
+    if params.get("mode", None) is not None:
         cargs.extend([
             "-m",
-            params.get("mode")
+            params.get("mode", None)
         ])
-    if params.get("parents"):
+    if params.get("parents", False):
         cargs.append("-p")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-v")
-    if params.get("selinux_context"):
+    if params.get("selinux_context", False):
         cargs.append("-Z")
-    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
 
@@ -157,9 +136,11 @@ def mksubjdirs_outputs(
 
 def mksubjdirs_execute(
     params: MksubjdirsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MksubjdirsOutputs:
     """
+    mksubjdirs
+    
     A command-line tool to create subject directories.
     
     Author: FreeSurfer Developers
@@ -168,10 +149,12 @@ def mksubjdirs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MksubjdirsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MKSUBJDIRS_METADATA)
     params = execution.params(params)
     cargs = mksubjdirs_cargs(params, execution)
     ret = mksubjdirs_outputs(params, execution)
@@ -190,6 +173,8 @@ def mksubjdirs(
     runner: Runner | None = None,
 ) -> MksubjdirsOutputs:
     """
+    mksubjdirs
+    
     A command-line tool to create subject directories.
     
     Author: FreeSurfer Developers
@@ -209,8 +194,6 @@ def mksubjdirs(
     Returns:
         NamedTuple of outputs (described in `MksubjdirsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MKSUBJDIRS_METADATA)
     params = mksubjdirs_params(
         subj_name=subj_name,
         mode=mode,
@@ -220,13 +203,13 @@ def mksubjdirs(
         help_=help_,
         version=version,
     )
-    return mksubjdirs_execute(params, execution)
+    return mksubjdirs_execute(params, runner)
 
 
 __all__ = [
     "MKSUBJDIRS_METADATA",
     "MksubjdirsOutputs",
-    "MksubjdirsParameters",
     "mksubjdirs",
+    "mksubjdirs_execute",
     "mksubjdirs_params",
 ]

niwrap_freesurfer/freesurfer/mksurfatlas.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MKSURFATLAS_METADATA = Metadata(
-    id="d79ac3c3008bc4ea34030be87ef82c18eea6b065.boutiques",
+    id="e10d98c6c732c2691141d0c7ae1e1069fa4646aa.boutiques",
     name="mksurfatlas",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ MKSURFATLAS_METADATA = Metadata(
 
 
 MksurfatlasParameters = typing.TypedDict('MksurfatlasParameters', {
-    "__STYXTYPE__": typing.Literal["mksurfatlas"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mksurfatlas"]],
+    "atlas": str,
+    "hemi": str,
+    "subjects": list[str],
+    "surfval": str,
+    "surfvaldir": typing.NotRequired[str | None],
+    "regsurf": typing.NotRequired[str | None],
+    "debug": bool,
+    "version": bool,
+    "help": bool,
+})
+MksurfatlasParametersTagged = typing.TypedDict('MksurfatlasParametersTagged', {
+    "@type": typing.Literal["freesurfer/mksurfatlas"],
     "atlas": str,
     "hemi": str,
     "subjects": list[str],
@@ -25,43 +37,11 @@ MksurfatlasParameters = typing.TypedDict('MksurfatlasParameters', {
     "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 {
-        "mksurfatlas": mksurfatlas_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 {
-        "mksurfatlas": mksurfatlas_outputs,
-    }.get(t)
 
 
 class MksurfatlasOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mksurfatlas(...)`.
+    Output object returned when calling `MksurfatlasParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,12 +54,12 @@ def mksurfatlas_params(
     hemi: str,
     subjects: list[str],
     surfval: str,
-    surfvaldir: str | None = "label",
-    regsurf: str | None = "sphere",
+    surfvaldir: str | None = None,
+    regsurf: str | None = None,
     debug: bool = False,
     version: bool = False,
     help_: bool = False,
-) -> MksurfatlasParameters:
+) -> MksurfatlasParametersTagged:
     """
     Build parameters.
     
@@ -99,7 +79,7 @@ def mksurfatlas_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mksurfatlas",
+        "@type": "freesurfer/mksurfatlas",
         "atlas": atlas,
         "hemi": hemi,
         "subjects": subjects,
@@ -132,35 +112,35 @@ def mksurfatlas_cargs(
     cargs.append("mksurfatlas")
     cargs.extend([
         "--a",
-        params.get("atlas")
+        params.get("atlas", None)
     ])
     cargs.extend([
         "--h",
-        params.get("hemi")
+        params.get("hemi", None)
     ])
     cargs.extend([
         "--s",
-        *params.get("subjects")
+        *params.get("subjects", None)
     ])
     cargs.extend([
         "--v",
-        params.get("surfval")
+        params.get("surfval", None)
     ])
-    if params.get("surfvaldir") is not None:
+    if params.get("surfvaldir", None) is not None:
         cargs.extend([
             "--d",
-            params.get("surfvaldir")
+            params.get("surfvaldir", None)
         ])
-    if params.get("regsurf") is not None:
+    if params.get("regsurf", None) is not None:
         cargs.extend([
             "--r",
-            params.get("regsurf")
+            params.get("regsurf", None)
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("--debug")
-    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
 
@@ -180,18 +160,20 @@ def mksurfatlas_outputs(
     """
     ret = MksurfatlasOutputs(
         root=execution.output_file("."),
-        output_atlas=execution.output_file(params.get("atlas")),
+        output_atlas=execution.output_file(params.get("atlas", None)),
     )
     return ret
 
 
 def mksurfatlas_execute(
     params: MksurfatlasParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MksurfatlasOutputs:
     """
-    Creates an atlas using mris_make_template. The atlas can then be used to create
-    the surface registration for each subject based on this atlas.
+    mksurfatlas
+    
+    Creates an atlas using mris_make_template. The atlas can then be used to
+    create the surface registration for each subject based on this atlas.
     
     Author: FreeSurfer Developers
     
@@ -199,10 +181,12 @@ def mksurfatlas_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MksurfatlasOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MKSURFATLAS_METADATA)
     params = execution.params(params)
     cargs = mksurfatlas_cargs(params, execution)
     ret = mksurfatlas_outputs(params, execution)
@@ -215,16 +199,18 @@ def mksurfatlas(
     hemi: str,
     subjects: list[str],
     surfval: str,
-    surfvaldir: str | None = "label",
-    regsurf: str | None = "sphere",
+    surfvaldir: str | None = None,
+    regsurf: str | None = None,
     debug: bool = False,
     version: bool = False,
     help_: bool = False,
     runner: Runner | None = None,
 ) -> MksurfatlasOutputs:
     """
-    Creates an atlas using mris_make_template. The atlas can then be used to create
-    the surface registration for each subject based on this atlas.
+    mksurfatlas
+    
+    Creates an atlas using mris_make_template. The atlas can then be used to
+    create the surface registration for each subject based on this atlas.
     
     Author: FreeSurfer Developers
     
@@ -246,8 +232,6 @@ def mksurfatlas(
     Returns:
         NamedTuple of outputs (described in `MksurfatlasOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MKSURFATLAS_METADATA)
     params = mksurfatlas_params(
         atlas=atlas,
         hemi=hemi,
@@ -259,13 +243,13 @@ def mksurfatlas(
         version=version,
         help_=help_,
     )
-    return mksurfatlas_execute(params, execution)
+    return mksurfatlas_execute(params, runner)
 
 
 __all__ = [
     "MKSURFATLAS_METADATA",
     "MksurfatlasOutputs",
-    "MksurfatlasParameters",
     "mksurfatlas",
+    "mksurfatlas_execute",
     "mksurfatlas_params",
 ]

niwrap_freesurfer/freesurfer/mkxsubjreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MKXSUBJREG_METADATA = Metadata(
-    id="2a99c16d9dcf305f5f8757bb3fb394dc61f08290.boutiques",
+    id="bfc691a659657a1a0a2502dff6f140048c147a07.boutiques",
     name="mkxsubjreg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,18 @@ MKXSUBJREG_METADATA = Metadata(
 
 
 MkxsubjregParameters = typing.TypedDict('MkxsubjregParameters', {
-    "__STYXTYPE__": typing.Literal["mkxsubjreg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/mkxsubjreg"]],
+    "srcreg": InputPathType,
+    "targreg": InputPathType,
+    "targsubj": typing.NotRequired[str | None],
+    "xfm": typing.NotRequired[str | None],
+    "sd": typing.NotRequired[str | None],
+    "fvol": typing.NotRequired[InputPathType | None],
+    "help": bool,
+    "version": bool,
+})
+MkxsubjregParametersTagged = typing.TypedDict('MkxsubjregParametersTagged', {
+    "@type": typing.Literal["freesurfer/mkxsubjreg"],
     "srcreg": InputPathType,
     "targreg": InputPathType,
     "targsubj": typing.NotRequired[str | None],
@@ -24,42 +35,11 @@ MkxsubjregParameters = typing.TypedDict('MkxsubjregParameters', {
     "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 {
-        "mkxsubjreg": mkxsubjreg_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 MkxsubjregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `mkxsubjreg(...)`.
+    Output object returned when calling `MkxsubjregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def mkxsubjreg_params(
     fvol: InputPathType | None = None,
     help_: bool = False,
     version: bool = False,
-) -> MkxsubjregParameters:
+) -> MkxsubjregParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +71,7 @@ def mkxsubjreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "mkxsubjreg",
+        "@type": "freesurfer/mkxsubjreg",
         "srcreg": srcreg,
         "targreg": targreg,
         "help": help_,
@@ -125,35 +105,35 @@ def mkxsubjreg_cargs(
     cargs.append("mkxsubjreg")
     cargs.extend([
         "--srcreg",
-        execution.input_file(params.get("srcreg"))
+        execution.input_file(params.get("srcreg", None))
     ])
     cargs.extend([
         "--targreg",
-        execution.input_file(params.get("targreg"))
+        execution.input_file(params.get("targreg", None))
     ])
-    if params.get("targsubj") is not None:
+    if params.get("targsubj", None) is not None:
         cargs.extend([
             "--targsubj",
-            params.get("targsubj")
+            params.get("targsubj", None)
         ])
-    if params.get("xfm") is not None:
+    if params.get("xfm", None) is not None:
         cargs.extend([
             "--xfm",
-            params.get("xfm")
+            params.get("xfm", None)
         ])
-    if params.get("sd") is not None:
+    if params.get("sd", None) is not None:
         cargs.extend([
             "--sd",
-            params.get("sd")
+            params.get("sd", None)
         ])
-    if params.get("fvol") is not None:
+    if params.get("fvol", None) is not None:
         cargs.extend([
             "--fvol",
-            execution.input_file(params.get("fvol"))
+            execution.input_file(params.get("fvol", 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
 
@@ -179,11 +159,13 @@ def mkxsubjreg_outputs(
 
 def mkxsubjreg_execute(
     params: MkxsubjregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MkxsubjregOutputs:
     """
-    Creates a new registration matrix that maps from the functional volume of the
-    source subject to the orig of the target subject through the talairach
+    mkxsubjreg
+    
+    Creates a new registration matrix that maps from the functional volume of
+    the source subject to the orig of the target subject through the talairach
     transform.
     
     Author: FreeSurfer Developers
@@ -192,10 +174,12 @@ def mkxsubjreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MkxsubjregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MKXSUBJREG_METADATA)
     params = execution.params(params)
     cargs = mkxsubjreg_cargs(params, execution)
     ret = mkxsubjreg_outputs(params, execution)
@@ -215,8 +199,10 @@ def mkxsubjreg(
     runner: Runner | None = None,
 ) -> MkxsubjregOutputs:
     """
-    Creates a new registration matrix that maps from the functional volume of the
-    source subject to the orig of the target subject through the talairach
+    mkxsubjreg
+    
+    Creates a new registration matrix that maps from the functional volume of
+    the source subject to the orig of the target subject through the talairach
     transform.
     
     Author: FreeSurfer Developers
@@ -236,8 +222,6 @@ def mkxsubjreg(
     Returns:
         NamedTuple of outputs (described in `MkxsubjregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MKXSUBJREG_METADATA)
     params = mkxsubjreg_params(
         srcreg=srcreg,
         targreg=targreg,
@@ -248,13 +232,13 @@ def mkxsubjreg(
         help_=help_,
         version=version,
     )
-    return mkxsubjreg_execute(params, execution)
+    return mkxsubjreg_execute(params, runner)
 
 
 __all__ = [
     "MKXSUBJREG_METADATA",
     "MkxsubjregOutputs",
-    "MkxsubjregParameters",
     "mkxsubjreg",
+    "mkxsubjreg_execute",
     "mkxsubjreg_params",
 ]