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

niwrap_freesurfer/freesurfer/rbbr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RBBR_METADATA = Metadata(
-    id="83d2a121d87ec0c6e66a4604bc69ecd4e43a3343.boutiques",
+    id="5e0ee9517ee4fe28c65009a4f647776480e43eb8.boutiques",
     name="rbbr",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,32 @@ RBBR_METADATA = Metadata(
 
 
 RbbrParameters = typing.TypedDict('RbbrParameters', {
-    "__STYXTYPE__": typing.Literal["rbbr"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rbbr"]],
+    "subject": typing.NotRequired[str | None],
+    "moving_image": str,
+    "t1_contrast": bool,
+    "t2_contrast": bool,
+    "init_reg": bool,
+    "init_spm": bool,
+    "init_fsl": bool,
+    "init_header": bool,
+    "cost_threshold": typing.NotRequired[float | None],
+    "gtm_synthesize": typing.NotRequired[str | None],
+    "tt_reduce": bool,
+    "iterations": typing.NotRequired[float | None],
+    "output_reg": typing.NotRequired[str | None],
+    "output_lta": typing.NotRequired[str | None],
+    "left_hemi": bool,
+    "right_hemi": bool,
+    "gm_proj_frac": typing.NotRequired[float | None],
+    "gm_proj_abs": typing.NotRequired[float | None],
+    "wm_proj_abs": typing.NotRequired[float | None],
+    "frame_no": typing.NotRequired[float | None],
+    "output_template": typing.NotRequired[str | None],
+    "no_merge": bool,
+})
+RbbrParametersTagged = typing.TypedDict('RbbrParametersTagged', {
+    "@type": typing.Literal["freesurfer/rbbr"],
     "subject": typing.NotRequired[str | None],
     "moving_image": str,
     "t1_contrast": bool,
@@ -38,43 +63,11 @@ RbbrParameters = typing.TypedDict('RbbrParameters', {
     "output_template": typing.NotRequired[str | None],
     "no_merge": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "rbbr": rbbr_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 {
-        "rbbr": rbbr_outputs,
-    }.get(t)
 
 
 class RbbrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rbbr(...)`.
+    Output object returned when calling `RbbrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -109,7 +102,7 @@ def rbbr_params(
     frame_no: float | None = None,
     output_template: str | None = None,
     no_merge: bool = False,
-) -> RbbrParameters:
+) -> RbbrParametersTagged:
     """
     Build parameters.
     
@@ -140,7 +133,7 @@ def rbbr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rbbr",
+        "@type": "freesurfer/rbbr",
         "moving_image": moving_image,
         "t1_contrast": t1_contrast,
         "t2_contrast": t2_contrast,
@@ -193,84 +186,84 @@ def rbbr_cargs(
     """
     cargs = []
     cargs.append("rbbr")
-    if params.get("subject") is not None:
+    if params.get("subject", None) is not None:
         cargs.extend([
             "--s",
-            params.get("subject")
+            params.get("subject", None)
         ])
     cargs.extend([
         "--mov",
-        params.get("moving_image")
+        params.get("moving_image", None)
     ])
-    if params.get("t1_contrast"):
+    if params.get("t1_contrast", False):
         cargs.append("--t1")
-    if params.get("t2_contrast"):
+    if params.get("t2_contrast", False):
         cargs.append("--t2")
-    if params.get("init_reg"):
+    if params.get("init_reg", False):
         cargs.append("--init-reg")
-    if params.get("init_spm"):
+    if params.get("init_spm", False):
         cargs.append("--init-spm")
-    if params.get("init_fsl"):
+    if params.get("init_fsl", False):
         cargs.append("--init-fsl")
-    if params.get("init_header"):
+    if params.get("init_header", False):
         cargs.append("--init-header")
-    if params.get("cost_threshold") is not None:
+    if params.get("cost_threshold", None) is not None:
         cargs.extend([
             "--cthresh",
-            str(params.get("cost_threshold"))
+            str(params.get("cost_threshold", None))
         ])
-    if params.get("gtm_synthesize") is not None:
+    if params.get("gtm_synthesize", None) is not None:
         cargs.extend([
             "--gtm",
-            params.get("gtm_synthesize")
+            params.get("gtm_synthesize", None)
         ])
-    if params.get("tt_reduce"):
+    if params.get("tt_reduce", False):
         cargs.append("--tt-reduce")
-    if params.get("iterations") is not None:
+    if params.get("iterations", None) is not None:
         cargs.extend([
             "--iters",
-            str(params.get("iterations"))
+            str(params.get("iterations", None))
         ])
-    if params.get("output_reg") is not None:
+    if params.get("output_reg", None) is not None:
         cargs.extend([
             "--reg",
-            params.get("output_reg")
+            params.get("output_reg", None)
         ])
-    if params.get("output_lta") is not None:
+    if params.get("output_lta", None) is not None:
         cargs.extend([
             "--lta",
-            params.get("output_lta")
+            params.get("output_lta", None)
         ])
-    if params.get("left_hemi"):
+    if params.get("left_hemi", False):
         cargs.append("--lh-only")
-    if params.get("right_hemi"):
+    if params.get("right_hemi", False):
         cargs.append("--rh-only")
-    if params.get("gm_proj_frac") is not None:
+    if params.get("gm_proj_frac", None) is not None:
         cargs.extend([
             "--gm-proj-frac",
-            str(params.get("gm_proj_frac"))
+            str(params.get("gm_proj_frac", None))
         ])
-    if params.get("gm_proj_abs") is not None:
+    if params.get("gm_proj_abs", None) is not None:
         cargs.extend([
             "--gm-proj-abs",
-            str(params.get("gm_proj_abs"))
+            str(params.get("gm_proj_abs", None))
         ])
-    if params.get("wm_proj_abs") is not None:
+    if params.get("wm_proj_abs", None) is not None:
         cargs.extend([
             "--wm-proj-abs",
-            str(params.get("wm_proj_abs"))
+            str(params.get("wm_proj_abs", None))
         ])
-    if params.get("frame_no") is not None:
+    if params.get("frame_no", None) is not None:
         cargs.extend([
             "--frame",
-            str(params.get("frame_no"))
+            str(params.get("frame_no", None))
         ])
-    if params.get("output_template") is not None:
+    if params.get("output_template", None) is not None:
         cargs.extend([
             "--template",
-            params.get("output_template")
+            params.get("output_template", None)
         ])
-    if params.get("no_merge"):
+    if params.get("no_merge", False):
         cargs.append("--no-merge")
     return cargs
 
@@ -290,18 +283,20 @@ def rbbr_outputs(
     """
     ret = RbbrOutputs(
         root=execution.output_file("."),
-        output_reg_file=execution.output_file(params.get("output_reg")) if (params.get("output_reg") is not None) else None,
-        output_lta_file=execution.output_file(params.get("output_lta")) if (params.get("output_lta") is not None) else None,
-        output_template_file=execution.output_file(params.get("output_template")) if (params.get("output_template") is not None) else None,
+        output_reg_file=execution.output_file(params.get("output_reg", None)) if (params.get("output_reg") is not None) else None,
+        output_lta_file=execution.output_file(params.get("output_lta", None)) if (params.get("output_lta") is not None) else None,
+        output_template_file=execution.output_file(params.get("output_template", None)) if (params.get("output_template") is not None) else None,
     )
     return ret
 
 
 def rbbr_execute(
     params: RbbrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RbbrOutputs:
     """
+    rbbr
+    
     Robust version of bbregister.
     
     Author: FreeSurfer Developers
@@ -310,10 +305,12 @@ def rbbr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RbbrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RBBR_METADATA)
     params = execution.params(params)
     cargs = rbbr_cargs(params, execution)
     ret = rbbr_outputs(params, execution)
@@ -347,6 +344,8 @@ def rbbr(
     runner: Runner | None = None,
 ) -> RbbrOutputs:
     """
+    rbbr
+    
     Robust version of bbregister.
     
     Author: FreeSurfer Developers
@@ -380,8 +379,6 @@ def rbbr(
     Returns:
         NamedTuple of outputs (described in `RbbrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RBBR_METADATA)
     params = rbbr_params(
         subject=subject,
         moving_image=moving_image,
@@ -406,13 +403,13 @@ def rbbr(
         output_template=output_template,
         no_merge=no_merge,
     )
-    return rbbr_execute(params, execution)
+    return rbbr_execute(params, runner)
 
 
 __all__ = [
     "RBBR_METADATA",
     "RbbrOutputs",
-    "RbbrParameters",
     "rbbr",
+    "rbbr_execute",
     "rbbr_params",
 ]

niwrap_freesurfer/freesurfer/rca_base_init.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RCA_BASE_INIT_METADATA = Metadata(
-    id="3c8d3ad6bcb4fc42684b1829ed14e08e22b13cd8.boutiques",
+    id="c55fc947d11178c3dfdddb94eba9f0a50fdf398f.boutiques",
     name="rca-base-init",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,47 +14,22 @@ RCA_BASE_INIT_METADATA = Metadata(
 
 
 RcaBaseInitParameters = typing.TypedDict('RcaBaseInitParameters', {
-    "__STYXTYPE__": typing.Literal["rca-base-init"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rca-base-init"]],
+    "log_file": typing.NotRequired[str | None],
+    "status_file": typing.NotRequired[str | None],
+    "cmd_file": typing.NotRequired[str | None],
+})
+RcaBaseInitParametersTagged = typing.TypedDict('RcaBaseInitParametersTagged', {
+    "@type": typing.Literal["freesurfer/rca-base-init"],
     "log_file": typing.NotRequired[str | None],
     "status_file": typing.NotRequired[str | None],
     "cmd_file": 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 {
-        "rca-base-init": rca_base_init_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 RcaBaseInitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rca_base_init(...)`.
+    Output object returned when calling `RcaBaseInitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,7 +39,7 @@ def rca_base_init_params(
     log_file: str | None = None,
     status_file: str | None = None,
     cmd_file: str | None = None,
-) -> RcaBaseInitParameters:
+) -> RcaBaseInitParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +51,7 @@ def rca_base_init_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rca-base-init",
+        "@type": "freesurfer/rca-base-init",
     }
     if log_file is not None:
         params["log_file"] = log_file
@@ -102,15 +77,15 @@ def rca_base_init_cargs(
     """
     cargs = []
     cargs.append("rca-base-init")
-    if params.get("log_file") is not None:
+    if params.get("log_file", None) is not None:
         cargs.extend([
             "-init",
-            params.get("log_file")
+            params.get("log_file", None)
         ])
-    if params.get("status_file") is not None:
-        cargs.append(params.get("status_file"))
-    if params.get("cmd_file") is not None:
-        cargs.append(params.get("cmd_file"))
+    if params.get("status_file", None) is not None:
+        cargs.append(params.get("status_file", None))
+    if params.get("cmd_file", None) is not None:
+        cargs.append(params.get("cmd_file", None))
     return cargs
 
 
@@ -135,9 +110,11 @@ def rca_base_init_outputs(
 
 def rca_base_init_execute(
     params: RcaBaseInitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RcaBaseInitOutputs:
     """
+    rca-base-init
+    
     Initialize base subject for recon-all processing.
     
     Author: FreeSurfer Developers
@@ -146,10 +123,12 @@ def rca_base_init_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RcaBaseInitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RCA_BASE_INIT_METADATA)
     params = execution.params(params)
     cargs = rca_base_init_cargs(params, execution)
     ret = rca_base_init_outputs(params, execution)
@@ -164,6 +143,8 @@ def rca_base_init(
     runner: Runner | None = None,
 ) -> RcaBaseInitOutputs:
     """
+    rca-base-init
+    
     Initialize base subject for recon-all processing.
     
     Author: FreeSurfer Developers
@@ -178,20 +159,18 @@ def rca_base_init(
     Returns:
         NamedTuple of outputs (described in `RcaBaseInitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RCA_BASE_INIT_METADATA)
     params = rca_base_init_params(
         log_file=log_file,
         status_file=status_file,
         cmd_file=cmd_file,
     )
-    return rca_base_init_execute(params, execution)
+    return rca_base_init_execute(params, runner)
 
 
 __all__ = [
     "RCA_BASE_INIT_METADATA",
     "RcaBaseInitOutputs",
-    "RcaBaseInitParameters",
     "rca_base_init",
+    "rca_base_init_execute",
     "rca_base_init_params",
 ]

niwrap_freesurfer/freesurfer/rca_config.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RCA_CONFIG_METADATA = Metadata(
-    id="46eae30104e8ee7e67f818e2a5df2c8456668ef9.boutiques",
+    id="160467e3c542343d523fa8c1f55238fb2e457b06.boutiques",
     name="rca-config",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,48 +14,24 @@ RCA_CONFIG_METADATA = Metadata(
 
 
 RcaConfigParameters = typing.TypedDict('RcaConfigParameters', {
-    "__STYXTYPE__": typing.Literal["rca-config"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rca-config"]],
+    "source_config": InputPathType,
+    "updated_config": InputPathType,
+    "unknown_args_file": InputPathType,
+    "args": typing.NotRequired[list[str] | None],
+})
+RcaConfigParametersTagged = typing.TypedDict('RcaConfigParametersTagged', {
+    "@type": typing.Literal["freesurfer/rca-config"],
     "source_config": InputPathType,
     "updated_config": InputPathType,
     "unknown_args_file": InputPathType,
     "args": typing.NotRequired[list[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 {
-        "rca-config": rca_config_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 RcaConfigOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rca_config(...)`.
+    Output object returned when calling `RcaConfigParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def rca_config_params(
     updated_config: InputPathType,
     unknown_args_file: InputPathType,
     args: list[str] | None = None,
-) -> RcaConfigParameters:
+) -> RcaConfigParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +56,7 @@ def rca_config_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rca-config",
+        "@type": "freesurfer/rca-config",
         "source_config": source_config,
         "updated_config": updated_config,
         "unknown_args_file": unknown_args_file,
@@ -107,12 +83,12 @@ def rca_config_cargs(
     cargs.append("rca-config")
     cargs.extend([
         "-config",
-        execution.input_file(params.get("source_config"))
+        execution.input_file(params.get("source_config", None))
     ])
-    cargs.append(execution.input_file(params.get("updated_config")))
-    cargs.append(execution.input_file(params.get("unknown_args_file")))
-    if params.get("args") is not None:
-        cargs.extend(params.get("args"))
+    cargs.append(execution.input_file(params.get("updated_config", None)))
+    cargs.append(execution.input_file(params.get("unknown_args_file", None)))
+    if params.get("args", None) is not None:
+        cargs.extend(params.get("args", None))
     return cargs
 
 
@@ -137,9 +113,11 @@ def rca_config_outputs(
 
 def rca_config_execute(
     params: RcaConfigParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RcaConfigOutputs:
     """
+    rca-config
+    
     A command-line tool that processes configuration files and arguments.
     
     Author: FreeSurfer Developers
@@ -148,10 +126,12 @@ def rca_config_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RcaConfigOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RCA_CONFIG_METADATA)
     params = execution.params(params)
     cargs = rca_config_cargs(params, execution)
     ret = rca_config_outputs(params, execution)
@@ -167,6 +147,8 @@ def rca_config(
     runner: Runner | None = None,
 ) -> RcaConfigOutputs:
     """
+    rca-config
+    
     A command-line tool that processes configuration files and arguments.
     
     Author: FreeSurfer Developers
@@ -183,21 +165,19 @@ def rca_config(
     Returns:
         NamedTuple of outputs (described in `RcaConfigOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RCA_CONFIG_METADATA)
     params = rca_config_params(
         source_config=source_config,
         updated_config=updated_config,
         unknown_args_file=unknown_args_file,
         args=args,
     )
-    return rca_config_execute(params, execution)
+    return rca_config_execute(params, runner)
 
 
 __all__ = [
     "RCA_CONFIG_METADATA",
     "RcaConfigOutputs",
-    "RcaConfigParameters",
     "rca_config",
+    "rca_config_execute",
     "rca_config_params",
 ]