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

niwrap_freesurfer/freesurfer/check_recons_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CHECK_RECONS_SH_METADATA = Metadata(
-    id="52142d2a907acd3a0d9631fc56bcb011b2c8e9af.boutiques",
+    id="b6a9d7c947101234227e0b232da4c1e46cbf1198.boutiques",
     name="check_recons.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ CHECK_RECONS_SH_METADATA = Metadata(
 
 
 CheckReconsShParameters = typing.TypedDict('CheckReconsShParameters', {
-    "__STYXTYPE__": typing.Literal["check_recons.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/check_recons.sh"]],
+    "subject_directory": typing.NotRequired[str | None],
+})
+CheckReconsShParametersTagged = typing.TypedDict('CheckReconsShParametersTagged', {
+    "@type": typing.Literal["freesurfer/check_recons.sh"],
     "subject_directory": 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 {
-        "check_recons.sh": check_recons_sh_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 CheckReconsShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `check_recons_sh(...)`.
+    Output object returned when calling `CheckReconsShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class CheckReconsShOutputs(typing.NamedTuple):
 
 def check_recons_sh_params(
     subject_directory: str | None = None,
-) -> CheckReconsShParameters:
+) -> CheckReconsShParametersTagged:
     """
     Build parameters.
     
@@ -71,7 +44,7 @@ def check_recons_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "check_recons.sh",
+        "@type": "freesurfer/check_recons.sh",
     }
     if subject_directory is not None:
         params["subject_directory"] = subject_directory
@@ -93,8 +66,8 @@ def check_recons_sh_cargs(
     """
     cargs = []
     cargs.append("check_recons.sh")
-    if params.get("subject_directory") is not None:
-        cargs.append(params.get("subject_directory"))
+    if params.get("subject_directory", None) is not None:
+        cargs.append(params.get("subject_directory", None))
     return cargs
 
 
@@ -119,11 +92,13 @@ def check_recons_sh_outputs(
 
 def check_recons_sh_execute(
     params: CheckReconsShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CheckReconsShOutputs:
     """
-    Checks the status of subjects being processed by recon-all in the SUBJECTS_DIR
-    or a specified directory.
+    check_recons.sh
+    
+    Checks the status of subjects being processed by recon-all in the
+    SUBJECTS_DIR or a specified directory.
     
     Author: FreeSurfer Developers
     
@@ -131,10 +106,12 @@ def check_recons_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CheckReconsShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CHECK_RECONS_SH_METADATA)
     params = execution.params(params)
     cargs = check_recons_sh_cargs(params, execution)
     ret = check_recons_sh_outputs(params, execution)
@@ -147,8 +124,10 @@ def check_recons_sh(
     runner: Runner | None = None,
 ) -> CheckReconsShOutputs:
     """
-    Checks the status of subjects being processed by recon-all in the SUBJECTS_DIR
-    or a specified directory.
+    check_recons.sh
+    
+    Checks the status of subjects being processed by recon-all in the
+    SUBJECTS_DIR or a specified directory.
     
     Author: FreeSurfer Developers
     
@@ -161,18 +140,16 @@ def check_recons_sh(
     Returns:
         NamedTuple of outputs (described in `CheckReconsShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CHECK_RECONS_SH_METADATA)
     params = check_recons_sh_params(
         subject_directory=subject_directory,
     )
-    return check_recons_sh_execute(params, execution)
+    return check_recons_sh_execute(params, runner)
 
 
 __all__ = [
     "CHECK_RECONS_SH_METADATA",
     "CheckReconsShOutputs",
-    "CheckReconsShParameters",
     "check_recons_sh",
+    "check_recons_sh_execute",
     "check_recons_sh_params",
 ]

niwrap_freesurfer/freesurfer/check_subject.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CHECK_SUBJECT_METADATA = Metadata(
-    id="a469eabd7979354cb8f4da4909edfba7eca4707c.boutiques",
+    id="b4df2e6bdb47d7da74832b18728ab9312cd83cc9.boutiques",
     name="check_subject",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,45 +14,18 @@ CHECK_SUBJECT_METADATA = Metadata(
 
 
 CheckSubjectParameters = typing.TypedDict('CheckSubjectParameters', {
-    "__STYXTYPE__": typing.Literal["check_subject"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/check_subject"]],
+    "subject_dir": str,
+})
+CheckSubjectParametersTagged = typing.TypedDict('CheckSubjectParametersTagged', {
+    "@type": typing.Literal["freesurfer/check_subject"],
     "subject_dir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "check_subject": check_subject_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 CheckSubjectOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `check_subject(...)`.
+    Output object returned when calling `CheckSubjectParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class CheckSubjectOutputs(typing.NamedTuple):
 
 def check_subject_params(
     subject_dir: str,
-) -> CheckSubjectParameters:
+) -> CheckSubjectParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def check_subject_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "check_subject",
+        "@type": "freesurfer/check_subject",
         "subject_dir": subject_dir,
     }
     return params
@@ -91,7 +64,7 @@ def check_subject_cargs(
     """
     cargs = []
     cargs.append("check_subject")
-    cargs.append(params.get("subject_dir"))
+    cargs.append(params.get("subject_dir", None))
     return cargs
 
 
@@ -116,9 +89,11 @@ def check_subject_outputs(
 
 def check_subject_execute(
     params: CheckSubjectParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> CheckSubjectOutputs:
     """
+    check_subject
+    
     Checks a subject directory for the existence of a surf directory.
     
     Author: FreeSurfer Developers
@@ -127,10 +102,12 @@ def check_subject_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `CheckSubjectOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CHECK_SUBJECT_METADATA)
     params = execution.params(params)
     cargs = check_subject_cargs(params, execution)
     ret = check_subject_outputs(params, execution)
@@ -143,6 +120,8 @@ def check_subject(
     runner: Runner | None = None,
 ) -> CheckSubjectOutputs:
     """
+    check_subject
+    
     Checks a subject directory for the existence of a surf directory.
     
     Author: FreeSurfer Developers
@@ -155,18 +134,16 @@ def check_subject(
     Returns:
         NamedTuple of outputs (described in `CheckSubjectOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CHECK_SUBJECT_METADATA)
     params = check_subject_params(
         subject_dir=subject_dir,
     )
-    return check_subject_execute(params, execution)
+    return check_subject_execute(params, runner)
 
 
 __all__ = [
     "CHECK_SUBJECT_METADATA",
     "CheckSubjectOutputs",
-    "CheckSubjectParameters",
     "check_subject",
+    "check_subject_execute",
     "check_subject_params",
 ]

niwrap_freesurfer/freesurfer/compute_interrater_variability_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 COMPUTE_INTERRATER_VARIABILITY_CSH_METADATA = Metadata(
-    id="7c673e67884e719ac415c4fda5f5ca418d13773d.boutiques",
+    id="b1bd7765a3167287e9c0a0d21996c106d1bcb6dd.boutiques",
     name="compute_interrater_variability.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ COMPUTE_INTERRATER_VARIABILITY_CSH_METADATA = Metadata(
 
 
 ComputeInterraterVariabilityCshParameters = typing.TypedDict('ComputeInterraterVariabilityCshParameters', {
-    "__STYXTYPE__": typing.Literal["compute_interrater_variability.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/compute_interrater_variability.csh"]],
+    "label_vol1": InputPathType,
+    "label_vol2": InputPathType,
+    "output_prefix": str,
+    "version": bool,
+    "help": bool,
+})
+ComputeInterraterVariabilityCshParametersTagged = typing.TypedDict('ComputeInterraterVariabilityCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/compute_interrater_variability.csh"],
     "label_vol1": InputPathType,
     "label_vol2": InputPathType,
     "output_prefix": 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 {
-        "compute_interrater_variability.csh": compute_interrater_variability_csh_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 {
-        "compute_interrater_variability.csh": compute_interrater_variability_csh_outputs,
-    }.get(t)
 
 
 class ComputeInterraterVariabilityCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `compute_interrater_variability_csh(...)`.
+    Output object returned when calling `ComputeInterraterVariabilityCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -76,7 +52,7 @@ def compute_interrater_variability_csh_params(
     output_prefix: str,
     version: bool = False,
     help_: bool = False,
-) -> ComputeInterraterVariabilityCshParameters:
+) -> ComputeInterraterVariabilityCshParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +67,7 @@ def compute_interrater_variability_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "compute_interrater_variability.csh",
+        "@type": "freesurfer/compute_interrater_variability.csh",
         "label_vol1": label_vol1,
         "label_vol2": label_vol2,
         "output_prefix": output_prefix,
@@ -118,19 +94,19 @@ def compute_interrater_variability_csh_cargs(
     cargs.append("compute_interrater_variability.csh")
     cargs.extend([
         "--vol1",
-        execution.input_file(params.get("label_vol1"))
+        execution.input_file(params.get("label_vol1", None))
     ])
     cargs.extend([
         "--vol2",
-        execution.input_file(params.get("label_vol2"))
+        execution.input_file(params.get("label_vol2", None))
     ])
     cargs.extend([
         "--out",
-        params.get("output_prefix")
+        params.get("output_prefix", 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
 
@@ -150,20 +126,22 @@ def compute_interrater_variability_csh_outputs(
     """
     ret = ComputeInterraterVariabilityCshOutputs(
         root=execution.output_file("."),
-        output_file_1=execution.output_file(params.get("output_prefix") + "_file1.txt"),
-        output_file_2=execution.output_file(params.get("output_prefix") + "_file2.txt"),
-        output_file_3=execution.output_file(params.get("output_prefix") + "_file3.txt"),
+        output_file_1=execution.output_file(params.get("output_prefix", None) + "_file1.txt"),
+        output_file_2=execution.output_file(params.get("output_prefix", None) + "_file2.txt"),
+        output_file_3=execution.output_file(params.get("output_prefix", None) + "_file3.txt"),
     )
     return ret
 
 
 def compute_interrater_variability_csh_execute(
     params: ComputeInterraterVariabilityCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ComputeInterraterVariabilityCshOutputs:
     """
-    Computes the interrater variability between label volumes from different raters
-    or time points using several metrics.
+    compute_interrater_variability.csh
+    
+    Computes the interrater variability between label volumes from different
+    raters or time points using several metrics.
     
     Author: FreeSurfer Developers
     
@@ -171,10 +149,12 @@ def compute_interrater_variability_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ComputeInterraterVariabilityCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(COMPUTE_INTERRATER_VARIABILITY_CSH_METADATA)
     params = execution.params(params)
     cargs = compute_interrater_variability_csh_cargs(params, execution)
     ret = compute_interrater_variability_csh_outputs(params, execution)
@@ -191,8 +171,10 @@ def compute_interrater_variability_csh(
     runner: Runner | None = None,
 ) -> ComputeInterraterVariabilityCshOutputs:
     """
-    Computes the interrater variability between label volumes from different raters
-    or time points using several metrics.
+    compute_interrater_variability.csh
+    
+    Computes the interrater variability between label volumes from different
+    raters or time points using several metrics.
     
     Author: FreeSurfer Developers
     
@@ -209,8 +191,6 @@ def compute_interrater_variability_csh(
     Returns:
         NamedTuple of outputs (described in `ComputeInterraterVariabilityCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(COMPUTE_INTERRATER_VARIABILITY_CSH_METADATA)
     params = compute_interrater_variability_csh_params(
         label_vol1=label_vol1,
         label_vol2=label_vol2,
@@ -218,13 +198,13 @@ def compute_interrater_variability_csh(
         version=version,
         help_=help_,
     )
-    return compute_interrater_variability_csh_execute(params, execution)
+    return compute_interrater_variability_csh_execute(params, runner)
 
 
 __all__ = [
     "COMPUTE_INTERRATER_VARIABILITY_CSH_METADATA",
     "ComputeInterraterVariabilityCshOutputs",
-    "ComputeInterraterVariabilityCshParameters",
     "compute_interrater_variability_csh",
+    "compute_interrater_variability_csh_execute",
     "compute_interrater_variability_csh_params",
 ]