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

niwrap_freesurfer/freesurfer/xhemi_tal.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 XHEMI_TAL_METADATA = Metadata(
-    id="75297464bbd5b47449915f4f1464c80da7860766.boutiques",
+    id="79cc5e58c638bd8ad97c8290e29d9c646128e5ba.boutiques",
     name="xhemi-tal",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ XHEMI_TAL_METADATA = Metadata(
 
 
 XhemiTalParameters = typing.TypedDict('XhemiTalParameters', {
-    "__STYXTYPE__": typing.Literal["xhemi-tal"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/xhemi-tal"]],
+    "subject": str,
+})
+XhemiTalParametersTagged = typing.TypedDict('XhemiTalParametersTagged', {
+    "@type": typing.Literal["freesurfer/xhemi-tal"],
     "subject": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "xhemi-tal": xhemi_tal_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 XhemiTalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `xhemi_tal(...)`.
+    Output object returned when calling `XhemiTalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class XhemiTalOutputs(typing.NamedTuple):
 
 def xhemi_tal_params(
     subject: str,
-) -> XhemiTalParameters:
+) -> XhemiTalParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def xhemi_tal_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "xhemi-tal",
+        "@type": "freesurfer/xhemi-tal",
         "subject": subject,
     }
     return params
@@ -93,7 +66,7 @@ def xhemi_tal_cargs(
     cargs.append("xhemi-tal")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
     return cargs
 
@@ -119,9 +92,11 @@ def xhemi_tal_outputs(
 
 def xhemi_tal_execute(
     params: XhemiTalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> XhemiTalOutputs:
     """
+    xhemi-tal
+    
     Computes the talairach.xfm for xhemi based on the original (unflipped)
     talairach.xfm.
     
@@ -131,10 +106,12 @@ def xhemi_tal_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `XhemiTalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XHEMI_TAL_METADATA)
     params = execution.params(params)
     cargs = xhemi_tal_cargs(params, execution)
     ret = xhemi_tal_outputs(params, execution)
@@ -147,6 +124,8 @@ def xhemi_tal(
     runner: Runner | None = None,
 ) -> XhemiTalOutputs:
     """
+    xhemi-tal
+    
     Computes the talairach.xfm for xhemi based on the original (unflipped)
     talairach.xfm.
     
@@ -160,18 +139,16 @@ def xhemi_tal(
     Returns:
         NamedTuple of outputs (described in `XhemiTalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(XHEMI_TAL_METADATA)
     params = xhemi_tal_params(
         subject=subject,
     )
-    return xhemi_tal_execute(params, execution)
+    return xhemi_tal_execute(params, runner)
 
 
 __all__ = [
     "XHEMI_TAL_METADATA",
     "XhemiTalOutputs",
-    "XhemiTalParameters",
     "xhemi_tal",
+    "xhemi_tal_execute",
     "xhemi_tal_params",
 ]

niwrap_freesurfer/freesurfer/xhemireg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 XHEMIREG_METADATA = Metadata(
-    id="261a80c05a860c7fffc88a2e8009768ff040fc71.boutiques",
+    id="017ee566ff5f9f666189c049c2c6a8988842f2cd.boutiques",
     name="xhemireg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,23 @@ XHEMIREG_METADATA = Metadata(
 
 
 XhemiregParameters = typing.TypedDict('XhemiregParameters', {
-    "__STYXTYPE__": typing.Literal["xhemireg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/xhemireg"]],
+    "subject": str,
+    "output_dir": typing.NotRequired[str | None],
+    "map_lh": bool,
+    "map_rh": bool,
+    "perform_reg": bool,
+    "tal_compute": bool,
+    "no_tal_compute": bool,
+    "tal_estimate": bool,
+    "no_tal_estimate": bool,
+    "gcaprep": typing.NotRequired[str | None],
+    "threads": typing.NotRequired[float | None],
+    "version": bool,
+    "help": bool,
+})
+XhemiregParametersTagged = typing.TypedDict('XhemiregParametersTagged', {
+    "@type": typing.Literal["freesurfer/xhemireg"],
     "subject": str,
     "output_dir": typing.NotRequired[str | None],
     "map_lh": bool,
@@ -29,42 +45,11 @@ XhemiregParameters = typing.TypedDict('XhemiregParameters', {
     "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 {
-        "xhemireg": xhemireg_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 XhemiregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `xhemireg(...)`.
+    Output object returned when calling `XhemiregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def xhemireg_params(
     threads: float | None = None,
     version: bool = False,
     help_: bool = False,
-) -> XhemiregParameters:
+) -> XhemiregParametersTagged:
     """
     Build parameters.
     
@@ -107,7 +92,7 @@ def xhemireg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "xhemireg",
+        "@type": "freesurfer/xhemireg",
         "subject": subject,
         "map_lh": map_lh,
         "map_rh": map_rh,
@@ -145,40 +130,40 @@ def xhemireg_cargs(
     cargs.append("xhemireg")
     cargs.extend([
         "--s",
-        params.get("subject")
+        params.get("subject", None)
     ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "--o",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("map_lh"):
+    if params.get("map_lh", False):
         cargs.append("--lh")
-    if params.get("map_rh"):
+    if params.get("map_rh", False):
         cargs.append("--rh")
-    if params.get("perform_reg"):
+    if params.get("perform_reg", False):
         cargs.append("--reg")
-    if params.get("tal_compute"):
+    if params.get("tal_compute", False):
         cargs.append("--tal-compute")
-    if params.get("no_tal_compute"):
+    if params.get("no_tal_compute", False):
         cargs.append("--no-tal-compute")
-    if params.get("tal_estimate"):
+    if params.get("tal_estimate", False):
         cargs.append("--tal-estimate")
-    if params.get("no_tal_estimate"):
+    if params.get("no_tal_estimate", False):
         cargs.append("--no-tal-estimate")
-    if params.get("gcaprep") is not None:
+    if params.get("gcaprep", None) is not None:
         cargs.extend([
             "--gcaprep",
-            params.get("gcaprep")
+            params.get("gcaprep", None)
         ])
-    if params.get("threads") is not None:
+    if params.get("threads", None) is not None:
         cargs.extend([
             "--threads",
-            str(params.get("threads"))
+            str(params.get("threads", 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
 
@@ -204,9 +189,11 @@ def xhemireg_outputs(
 
 def xhemireg_execute(
     params: XhemiregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> XhemiregOutputs:
     """
+    xhemireg
+    
     Tool for hemisphere registration in neuroimaging.
     
     Author: FreeSurfer Developers
@@ -215,10 +202,12 @@ def xhemireg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `XhemiregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XHEMIREG_METADATA)
     params = execution.params(params)
     cargs = xhemireg_cargs(params, execution)
     ret = xhemireg_outputs(params, execution)
@@ -243,6 +232,8 @@ def xhemireg(
     runner: Runner | None = None,
 ) -> XhemiregOutputs:
     """
+    xhemireg
+    
     Tool for hemisphere registration in neuroimaging.
     
     Author: FreeSurfer Developers
@@ -268,8 +259,6 @@ def xhemireg(
     Returns:
         NamedTuple of outputs (described in `XhemiregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(XHEMIREG_METADATA)
     params = xhemireg_params(
         subject=subject,
         output_dir=output_dir,
@@ -285,13 +274,13 @@ def xhemireg(
         version=version,
         help_=help_,
     )
-    return xhemireg_execute(params, execution)
+    return xhemireg_execute(params, runner)
 
 
 __all__ = [
     "XHEMIREG_METADATA",
     "XhemiregOutputs",
-    "XhemiregParameters",
     "xhemireg",
+    "xhemireg_execute",
     "xhemireg_params",
 ]

niwrap_freesurfer/freesurfer/xsanatreg.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 XSANATREG_METADATA = Metadata(
-    id="92e3106d67a2897fb7d26ce43be63611d67973c8.boutiques",
+    id="6612591f7b571f5c566e4e010ea7b64138eea8d8.boutiques",
     name="xsanatreg",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,19 @@ XSANATREG_METADATA = Metadata(
 
 
 XsanatregParameters = typing.TypedDict('XsanatregParameters', {
-    "__STYXTYPE__": typing.Literal["xsanatreg"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/xsanatreg"]],
+    "src_cordir": str,
+    "targ_cordir": str,
+    "transform_file": str,
+    "temp_directory": typing.NotRequired[str | None],
+    "source_minc": typing.NotRequired[str | None],
+    "target_minc": typing.NotRequired[str | None],
+    "no_cleanup": bool,
+    "version": bool,
+    "umask": typing.NotRequired[str | None],
+})
+XsanatregParametersTagged = typing.TypedDict('XsanatregParametersTagged', {
+    "@type": typing.Literal["freesurfer/xsanatreg"],
     "src_cordir": str,
     "targ_cordir": str,
     "transform_file": str,
@@ -25,42 +37,11 @@ XsanatregParameters = typing.TypedDict('XsanatregParameters', {
     "version": bool,
     "umask": typing.NotRequired[str | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "xsanatreg": xsanatreg_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 XsanatregOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `xsanatreg(...)`.
+    Output object returned when calling `XsanatregParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +57,7 @@ def xsanatreg_params(
     no_cleanup: bool = False,
     version: bool = False,
     umask: str | None = None,
-) -> XsanatregParameters:
+) -> XsanatregParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +77,7 @@ def xsanatreg_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "xsanatreg",
+        "@type": "freesurfer/xsanatreg",
         "src_cordir": src_cordir,
         "targ_cordir": targ_cordir,
         "transform_file": transform_file,
@@ -131,39 +112,39 @@ def xsanatreg_cargs(
     cargs.append("xsanatreg")
     cargs.extend([
         "-src",
-        params.get("src_cordir")
+        params.get("src_cordir", None)
     ])
     cargs.extend([
         "-targ",
-        params.get("targ_cordir")
+        params.get("targ_cordir", None)
     ])
     cargs.extend([
         "-xfm",
-        params.get("transform_file")
+        params.get("transform_file", None)
     ])
-    if params.get("temp_directory") is not None:
+    if params.get("temp_directory", None) is not None:
         cargs.extend([
             "-tmpdir",
-            params.get("temp_directory")
+            params.get("temp_directory", None)
         ])
-    if params.get("source_minc") is not None:
+    if params.get("source_minc", None) is not None:
         cargs.extend([
             "-srcminc",
-            params.get("source_minc")
+            params.get("source_minc", None)
         ])
-    if params.get("target_minc") is not None:
+    if params.get("target_minc", None) is not None:
         cargs.extend([
             "-targminc",
-            params.get("target_minc")
+            params.get("target_minc", None)
         ])
-    if params.get("no_cleanup"):
+    if params.get("no_cleanup", False):
         cargs.append("-nocleanup")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-version")
-    if params.get("umask") is not None:
+    if params.get("umask", None) is not None:
         cargs.extend([
             "-umask",
-            params.get("umask")
+            params.get("umask", None)
         ])
     return cargs
 
@@ -189,9 +170,11 @@ def xsanatreg_outputs(
 
 def xsanatreg_execute(
     params: XsanatregParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> XsanatregOutputs:
     """
+    xsanatreg
+    
     A tool for registering source and target COR volumes.
     
     Author: FreeSurfer Developers
@@ -200,10 +183,12 @@ def xsanatreg_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `XsanatregOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(XSANATREG_METADATA)
     params = execution.params(params)
     cargs = xsanatreg_cargs(params, execution)
     ret = xsanatreg_outputs(params, execution)
@@ -224,6 +209,8 @@ def xsanatreg(
     runner: Runner | None = None,
 ) -> XsanatregOutputs:
     """
+    xsanatreg
+    
     A tool for registering source and target COR volumes.
     
     Author: FreeSurfer Developers
@@ -246,8 +233,6 @@ def xsanatreg(
     Returns:
         NamedTuple of outputs (described in `XsanatregOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(XSANATREG_METADATA)
     params = xsanatreg_params(
         src_cordir=src_cordir,
         targ_cordir=targ_cordir,
@@ -259,13 +244,13 @@ def xsanatreg(
         version=version,
         umask=umask,
     )
-    return xsanatreg_execute(params, execution)
+    return xsanatreg_execute(params, runner)
 
 
 __all__ = [
     "XSANATREG_METADATA",
     "XsanatregOutputs",
-    "XsanatregParameters",
     "xsanatreg",
+    "xsanatreg_execute",
     "xsanatreg_params",
 ]