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

niwrap_freesurfer/freesurfer/rca_config2csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RCA_CONFIG2CSH_METADATA = Metadata(
-    id="7da3f443ce243dae4e35d8db7f6e15691dc59ca6.boutiques",
+    id="14b4009919a087ddbdec70bbbbc62ee544d46b4c.boutiques",
     name="rca-config2csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ RCA_CONFIG2CSH_METADATA = Metadata(
 
 
 RcaConfig2cshParameters = typing.TypedDict('RcaConfig2cshParameters', {
-    "__STYXTYPE__": typing.Literal["rca-config2csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rca-config2csh"]],
+    "configfile": InputPathType,
+})
+RcaConfig2cshParametersTagged = typing.TypedDict('RcaConfig2cshParametersTagged', {
+    "@type": typing.Literal["freesurfer/rca-config2csh"],
     "configfile": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "rca-config2csh": rca_config2csh_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 RcaConfig2cshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rca_config2csh(...)`.
+    Output object returned when calling `RcaConfig2cshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class RcaConfig2cshOutputs(typing.NamedTuple):
 
 def rca_config2csh_params(
     configfile: InputPathType,
-) -> RcaConfig2cshParameters:
+) -> RcaConfig2cshParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def rca_config2csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rca-config2csh",
+        "@type": "freesurfer/rca-config2csh",
         "configfile": configfile,
     }
     return params
@@ -93,7 +66,7 @@ def rca_config2csh_cargs(
     cargs.append("rca-config2csh")
     cargs.extend([
         "-config2csh",
-        execution.input_file(params.get("configfile"))
+        execution.input_file(params.get("configfile", None))
     ])
     return cargs
 
@@ -119,10 +92,13 @@ def rca_config2csh_outputs(
 
 def rca_config2csh_execute(
     params: RcaConfig2cshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RcaConfig2cshOutputs:
     """
-    rca-config2csh is a utility to convert configuration files into C-shell syntax.
+    rca-config2csh
+    
+    rca-config2csh is a utility to convert configuration files into C-shell
+    syntax.
     
     Author: FreeSurfer Developers
     
@@ -130,10 +106,12 @@ def rca_config2csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RcaConfig2cshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RCA_CONFIG2CSH_METADATA)
     params = execution.params(params)
     cargs = rca_config2csh_cargs(params, execution)
     ret = rca_config2csh_outputs(params, execution)
@@ -146,7 +124,10 @@ def rca_config2csh(
     runner: Runner | None = None,
 ) -> RcaConfig2cshOutputs:
     """
-    rca-config2csh is a utility to convert configuration files into C-shell syntax.
+    rca-config2csh
+    
+    rca-config2csh is a utility to convert configuration files into C-shell
+    syntax.
     
     Author: FreeSurfer Developers
     
@@ -158,18 +139,16 @@ def rca_config2csh(
     Returns:
         NamedTuple of outputs (described in `RcaConfig2cshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RCA_CONFIG2CSH_METADATA)
     params = rca_config2csh_params(
         configfile=configfile,
     )
-    return rca_config2csh_execute(params, execution)
+    return rca_config2csh_execute(params, runner)
 
 
 __all__ = [
     "RCA_CONFIG2CSH_METADATA",
     "RcaConfig2cshOutputs",
-    "RcaConfig2cshParameters",
     "rca_config2csh",
+    "rca_config2csh_execute",
     "rca_config2csh_params",
 ]

niwrap_freesurfer/freesurfer/rca_fix_ento.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RCA_FIX_ENTO_METADATA = Metadata(
-    id="64436bb8ee2aa1d776ae3cc1b1413d243ffaba24.boutiques",
+    id="cabeb6e1416dbf7346f03da383beb1c3461b4ee2.boutiques",
     name="rca-fix-ento",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ RCA_FIX_ENTO_METADATA = Metadata(
 
 
 RcaFixEntoParameters = typing.TypedDict('RcaFixEntoParameters', {
-    "__STYXTYPE__": typing.Literal["rca-fix-ento"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rca-fix-ento"]],
+    "subject": str,
+    "threads": typing.NotRequired[float | None],
+    "submit": bool,
+    "account": typing.NotRequired[str | None],
+    "brain_mask": bool,
+})
+RcaFixEntoParametersTagged = typing.TypedDict('RcaFixEntoParametersTagged', {
+    "@type": typing.Literal["freesurfer/rca-fix-ento"],
     "subject": str,
     "threads": typing.NotRequired[float | None],
     "submit": bool,
     "account": typing.NotRequired[str | None],
     "brain_mask": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "rca-fix-ento": rca_fix_ento_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 {
-        "rca-fix-ento": rca_fix_ento_outputs,
-    }.get(t)
 
 
 class RcaFixEntoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rca_fix_ento(...)`.
+    Output object returned when calling `RcaFixEntoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +51,7 @@ def rca_fix_ento_params(
     submit: bool = False,
     account: str | None = None,
     brain_mask: bool = False,
-) -> RcaFixEntoParameters:
+) -> RcaFixEntoParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +67,7 @@ def rca_fix_ento_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rca-fix-ento",
+        "@type": "freesurfer/rca-fix-ento",
         "subject": subject,
         "submit": submit,
         "brain_mask": brain_mask,
@@ -120,21 +96,21 @@ def rca_fix_ento_cargs(
     cargs.append("rca-fix-ento")
     cargs.extend([
         "-s",
-        params.get("subject")
+        params.get("subject", 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("submit"):
+    if params.get("submit", False):
         cargs.append("--submit")
-    if params.get("account") is not None:
+    if params.get("account", None) is not None:
         cargs.extend([
             "--account",
-            params.get("account")
+            params.get("account", None)
         ])
-    if params.get("brain_mask"):
+    if params.get("brain_mask", False):
         cargs.append("--brain-mask")
     return cargs
 
@@ -154,20 +130,22 @@ def rca_fix_ento_outputs(
     """
     ret = RcaFixEntoOutputs(
         root=execution.output_file("."),
-        entowm_output=execution.output_file(params.get("subject") + "/mri/entowm.mgz"),
-        finalsurfs_output=execution.output_file(params.get("subject") + "/mri/brain.finalsurfs.manedit.mgz"),
-        backup_finalsufs_output=execution.output_file(params.get("subject") + "/mri/backup.brain.finalsurfs.manedit.mgz"),
+        entowm_output=execution.output_file(params.get("subject", None) + "/mri/entowm.mgz"),
+        finalsurfs_output=execution.output_file(params.get("subject", None) + "/mri/brain.finalsurfs.manedit.mgz"),
+        backup_finalsufs_output=execution.output_file(params.get("subject", None) + "/mri/backup.brain.finalsurfs.manedit.mgz"),
     )
     return ret
 
 
 def rca_fix_ento_execute(
     params: RcaFixEntoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RcaFixEntoOutputs:
     """
-    A tool to fix the entorhinal white matter in FreeSurfer using a deep learning
-    network.
+    rca-fix-ento
+    
+    A tool to fix the entorhinal white matter in FreeSurfer using a deep
+    learning network.
     
     Author: FreeSurfer Developers
     
@@ -175,10 +153,12 @@ def rca_fix_ento_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RcaFixEntoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RCA_FIX_ENTO_METADATA)
     params = execution.params(params)
     cargs = rca_fix_ento_cargs(params, execution)
     ret = rca_fix_ento_outputs(params, execution)
@@ -195,8 +175,10 @@ def rca_fix_ento(
     runner: Runner | None = None,
 ) -> RcaFixEntoOutputs:
     """
-    A tool to fix the entorhinal white matter in FreeSurfer using a deep learning
-    network.
+    rca-fix-ento
+    
+    A tool to fix the entorhinal white matter in FreeSurfer using a deep
+    learning network.
     
     Author: FreeSurfer Developers
     
@@ -214,8 +196,6 @@ def rca_fix_ento(
     Returns:
         NamedTuple of outputs (described in `RcaFixEntoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RCA_FIX_ENTO_METADATA)
     params = rca_fix_ento_params(
         subject=subject,
         threads=threads,
@@ -223,13 +203,13 @@ def rca_fix_ento(
         account=account,
         brain_mask=brain_mask,
     )
-    return rca_fix_ento_execute(params, execution)
+    return rca_fix_ento_execute(params, runner)
 
 
 __all__ = [
     "RCA_FIX_ENTO_METADATA",
     "RcaFixEntoOutputs",
-    "RcaFixEntoParameters",
     "rca_fix_ento",
+    "rca_fix_ento_execute",
     "rca_fix_ento_params",
 ]

niwrap_freesurfer/freesurfer/rca_long_tp_init.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RCA_LONG_TP_INIT_METADATA = Metadata(
-    id="1ba25741004958df03ca6fd11c8637b4fcf2ca35.boutiques",
+    id="d4bcfb42f971e1967e6f26ab2697ec78299fa783.boutiques",
     name="rca-long-tp-init",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ RCA_LONG_TP_INIT_METADATA = Metadata(
 
 
 RcaLongTpInitParameters = typing.TypedDict('RcaLongTpInitParameters', {
-    "__STYXTYPE__": typing.Literal["rca-long-tp-init"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/rca-long-tp-init"]],
+    "timepoint": str,
+    "base": str,
+    "use_long_base_ctrl_vol": bool,
+    "hemisphere": typing.NotRequired[typing.Literal["lh", "rh"] | None],
+    "expert_opts": typing.NotRequired[InputPathType | None],
+    "subject": typing.NotRequired[str | None],
+})
+RcaLongTpInitParametersTagged = typing.TypedDict('RcaLongTpInitParametersTagged', {
+    "@type": typing.Literal["freesurfer/rca-long-tp-init"],
     "timepoint": str,
     "base": str,
     "use_long_base_ctrl_vol": bool,
@@ -22,42 +31,11 @@ RcaLongTpInitParameters = typing.TypedDict('RcaLongTpInitParameters', {
     "expert_opts": typing.NotRequired[InputPathType | None],
     "subject": 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-long-tp-init": rca_long_tp_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 RcaLongTpInitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rca_long_tp_init(...)`.
+    Output object returned when calling `RcaLongTpInitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def rca_long_tp_init_params(
     hemisphere: typing.Literal["lh", "rh"] | None = None,
     expert_opts: InputPathType | None = None,
     subject: str | None = None,
-) -> RcaLongTpInitParameters:
+) -> RcaLongTpInitParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +63,7 @@ def rca_long_tp_init_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rca-long-tp-init",
+        "@type": "freesurfer/rca-long-tp-init",
         "timepoint": timepoint,
         "base": base,
         "use_long_base_ctrl_vol": use_long_base_ctrl_vol,
@@ -116,25 +94,25 @@ def rca_long_tp_init_cargs(
     cargs.append("rca-long-tp-init")
     cargs.extend([
         "-long",
-        params.get("timepoint")
+        params.get("timepoint", None)
     ])
-    cargs.append(params.get("base"))
-    if params.get("use_long_base_ctrl_vol"):
+    cargs.append(params.get("base", None))
+    if params.get("use_long_base_ctrl_vol", False):
         cargs.append("-uselongbasectrlvol")
-    if params.get("hemisphere") is not None:
+    if params.get("hemisphere", None) is not None:
         cargs.extend([
             "-hemi",
-            params.get("hemisphere")
+            params.get("hemisphere", None)
         ])
-    if params.get("expert_opts") is not None:
+    if params.get("expert_opts", None) is not None:
         cargs.extend([
             "-expert",
-            execution.input_file(params.get("expert_opts"))
+            execution.input_file(params.get("expert_opts", None))
         ])
-    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)
         ])
     return cargs
 
@@ -160,9 +138,11 @@ def rca_long_tp_init_outputs(
 
 def rca_long_tp_init_execute(
     params: RcaLongTpInitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RcaLongTpInitOutputs:
     """
+    rca-long-tp-init
+    
     Initialize long timepoint subject for recon-all processing.
     
     Author: FreeSurfer Developers
@@ -171,10 +151,12 @@ def rca_long_tp_init_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RcaLongTpInitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RCA_LONG_TP_INIT_METADATA)
     params = execution.params(params)
     cargs = rca_long_tp_init_cargs(params, execution)
     ret = rca_long_tp_init_outputs(params, execution)
@@ -192,6 +174,8 @@ def rca_long_tp_init(
     runner: Runner | None = None,
 ) -> RcaLongTpInitOutputs:
     """
+    rca-long-tp-init
+    
     Initialize long timepoint subject for recon-all processing.
     
     Author: FreeSurfer Developers
@@ -209,8 +193,6 @@ def rca_long_tp_init(
     Returns:
         NamedTuple of outputs (described in `RcaLongTpInitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RCA_LONG_TP_INIT_METADATA)
     params = rca_long_tp_init_params(
         timepoint=timepoint,
         base=base,
@@ -219,13 +201,13 @@ def rca_long_tp_init(
         expert_opts=expert_opts,
         subject=subject,
     )
-    return rca_long_tp_init_execute(params, execution)
+    return rca_long_tp_init_execute(params, runner)
 
 
 __all__ = [
     "RCA_LONG_TP_INIT_METADATA",
     "RcaLongTpInitOutputs",
-    "RcaLongTpInitParameters",
     "rca_long_tp_init",
+    "rca_long_tp_init_execute",
     "rca_long_tp_init_params",
 ]