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

niwrap_freesurfer/freesurfer/predict_v1_sh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PREDICT_V1_SH_METADATA = Metadata(
-    id="a2a49b8ffc476b3fa2e75490295c5f01b94168c0.boutiques",
+    id="a30a6b09004e916461882f1652d289e2a24e590a.boutiques",
     name="predict_v1.sh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,16 @@ PREDICT_V1_SH_METADATA = Metadata(
 
 
 PredictV1ShParameters = typing.TypedDict('PredictV1ShParameters', {
-    "__STYXTYPE__": typing.Literal["predict_v1.sh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/predict_v1.sh"]],
+    "template": typing.NotRequired[str | None],
+    "inflated_surface_flag": bool,
+    "hemisphere": typing.NotRequired[str | None],
+    "print_mode_flag": bool,
+    "subjects": list[str],
+    "usage_flag": bool,
+})
+PredictV1ShParametersTagged = typing.TypedDict('PredictV1ShParametersTagged', {
+    "@type": typing.Literal["freesurfer/predict_v1.sh"],
     "template": typing.NotRequired[str | None],
     "inflated_surface_flag": bool,
     "hemisphere": typing.NotRequired[str | None],
@@ -22,42 +31,11 @@ PredictV1ShParameters = typing.TypedDict('PredictV1ShParameters', {
     "subjects": list[str],
     "usage_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "predict_v1.sh": predict_v1_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 PredictV1ShOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `predict_v1_sh(...)`.
+    Output object returned when calling `PredictV1ShParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def predict_v1_sh_params(
     hemisphere: str | None = None,
     print_mode_flag: bool = False,
     usage_flag: bool = False,
-) -> PredictV1ShParameters:
+) -> PredictV1ShParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +64,7 @@ def predict_v1_sh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "predict_v1.sh",
+        "@type": "freesurfer/predict_v1.sh",
         "inflated_surface_flag": inflated_surface_flag,
         "print_mode_flag": print_mode_flag,
         "subjects": subjects,
@@ -114,22 +92,22 @@ def predict_v1_sh_cargs(
     """
     cargs = []
     cargs.append("predict_v1.sh")
-    if params.get("template") is not None:
+    if params.get("template", None) is not None:
         cargs.extend([
             "-t",
-            params.get("template")
+            params.get("template", None)
         ])
-    if params.get("inflated_surface_flag"):
+    if params.get("inflated_surface_flag", False):
         cargs.append("-i")
-    if params.get("hemisphere") is not None:
+    if params.get("hemisphere", None) is not None:
         cargs.extend([
             "-h",
-            params.get("hemisphere")
+            params.get("hemisphere", None)
         ])
-    if params.get("print_mode_flag"):
+    if params.get("print_mode_flag", False):
         cargs.append("-p")
-    cargs.extend(params.get("subjects"))
-    if params.get("usage_flag"):
+    cargs.extend(params.get("subjects", None))
+    if params.get("usage_flag", False):
         cargs.append("-u")
     return cargs
 
@@ -155,9 +133,11 @@ def predict_v1_sh_outputs(
 
 def predict_v1_sh_execute(
     params: PredictV1ShParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PredictV1ShOutputs:
     """
+    predict_v1.sh
+    
     A script for predicting brain images using registration.
     
     Author: FreeSurfer Developers
@@ -166,10 +146,12 @@ def predict_v1_sh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PredictV1ShOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PREDICT_V1_SH_METADATA)
     params = execution.params(params)
     cargs = predict_v1_sh_cargs(params, execution)
     ret = predict_v1_sh_outputs(params, execution)
@@ -187,6 +169,8 @@ def predict_v1_sh(
     runner: Runner | None = None,
 ) -> PredictV1ShOutputs:
     """
+    predict_v1.sh
+    
     A script for predicting brain images using registration.
     
     Author: FreeSurfer Developers
@@ -205,8 +189,6 @@ def predict_v1_sh(
     Returns:
         NamedTuple of outputs (described in `PredictV1ShOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PREDICT_V1_SH_METADATA)
     params = predict_v1_sh_params(
         template=template,
         inflated_surface_flag=inflated_surface_flag,
@@ -215,13 +197,13 @@ def predict_v1_sh(
         subjects=subjects,
         usage_flag=usage_flag,
     )
-    return predict_v1_sh_execute(params, execution)
+    return predict_v1_sh_execute(params, runner)
 
 
 __all__ = [
     "PREDICT_V1_SH_METADATA",
     "PredictV1ShOutputs",
-    "PredictV1ShParameters",
     "predict_v1_sh",
+    "predict_v1_sh_execute",
     "predict_v1_sh_params",
 ]

niwrap_freesurfer/freesurfer/print_unique_labels_csh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PRINT_UNIQUE_LABELS_CSH_METADATA = Metadata(
-    id="5dca4f4c348d9237bae9336374cad3ee2174c9c8.boutiques",
+    id="48fe28c3cd4e1b6bc6c3d6a4373c5b626603010e.boutiques",
     name="print_unique_labels.csh",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,50 +14,26 @@ PRINT_UNIQUE_LABELS_CSH_METADATA = Metadata(
 
 
 PrintUniqueLabelsCshParameters = typing.TypedDict('PrintUniqueLabelsCshParameters', {
-    "__STYXTYPE__": typing.Literal["print_unique_labels.csh"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/print_unique_labels.csh"]],
+    "label_volume": InputPathType,
+    "output_file": typing.NotRequired[str | None],
+    "list_only": bool,
+    "version": bool,
+    "help": bool,
+})
+PrintUniqueLabelsCshParametersTagged = typing.TypedDict('PrintUniqueLabelsCshParametersTagged', {
+    "@type": typing.Literal["freesurfer/print_unique_labels.csh"],
     "label_volume": InputPathType,
     "output_file": typing.NotRequired[str | None],
     "list_only": bool,
     "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 {
-        "print_unique_labels.csh": print_unique_labels_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 {
-        "print_unique_labels.csh": print_unique_labels_csh_outputs,
-    }.get(t)
 
 
 class PrintUniqueLabelsCshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `print_unique_labels_csh(...)`.
+    Output object returned when calling `PrintUniqueLabelsCshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +47,7 @@ def print_unique_labels_csh_params(
     list_only: bool = False,
     version: bool = False,
     help_: bool = False,
-) -> PrintUniqueLabelsCshParameters:
+) -> PrintUniqueLabelsCshParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +61,7 @@ def print_unique_labels_csh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "print_unique_labels.csh",
+        "@type": "freesurfer/print_unique_labels.csh",
         "label_volume": label_volume,
         "list_only": list_only,
         "version": version,
@@ -113,18 +89,18 @@ def print_unique_labels_csh_cargs(
     cargs.append("print_unique_labels.csh")
     cargs.extend([
         "--vol",
-        execution.input_file(params.get("label_volume"))
+        execution.input_file(params.get("label_volume", None))
     ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "--out",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("list_only"):
+    if params.get("list_only", False):
         cargs.append("--list")
-    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
 
@@ -144,16 +120,18 @@ def print_unique_labels_csh_outputs(
     """
     ret = PrintUniqueLabelsCshOutputs(
         root=execution.output_file("."),
-        results_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
+        results_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
     )
     return ret
 
 
 def print_unique_labels_csh_execute(
     params: PrintUniqueLabelsCshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> PrintUniqueLabelsCshOutputs:
     """
+    print_unique_labels.csh
+    
     Prints the list of unique labels (with structure name) in the input volume.
     
     Author: FreeSurfer Developers
@@ -162,10 +140,12 @@ def print_unique_labels_csh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `PrintUniqueLabelsCshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PRINT_UNIQUE_LABELS_CSH_METADATA)
     params = execution.params(params)
     cargs = print_unique_labels_csh_cargs(params, execution)
     ret = print_unique_labels_csh_outputs(params, execution)
@@ -182,6 +162,8 @@ def print_unique_labels_csh(
     runner: Runner | None = None,
 ) -> PrintUniqueLabelsCshOutputs:
     """
+    print_unique_labels.csh
+    
     Prints the list of unique labels (with structure name) in the input volume.
     
     Author: FreeSurfer Developers
@@ -198,8 +180,6 @@ def print_unique_labels_csh(
     Returns:
         NamedTuple of outputs (described in `PrintUniqueLabelsCshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PRINT_UNIQUE_LABELS_CSH_METADATA)
     params = print_unique_labels_csh_params(
         label_volume=label_volume,
         output_file=output_file,
@@ -207,13 +187,13 @@ def print_unique_labels_csh(
         version=version,
         help_=help_,
     )
-    return print_unique_labels_csh_execute(params, execution)
+    return print_unique_labels_csh_execute(params, runner)
 
 
 __all__ = [
     "PRINT_UNIQUE_LABELS_CSH_METADATA",
     "PrintUniqueLabelsCshOutputs",
-    "PrintUniqueLabelsCshParameters",
     "print_unique_labels_csh",
+    "print_unique_labels_csh_execute",
     "print_unique_labels_csh_params",
 ]

niwrap_freesurfer/freesurfer/qatools_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 QATOOLS_PY_METADATA = Metadata(
-    id="6830cf95e0c05f1ec7fd4998d49b50f118ce2b30.boutiques",
+    id="be8bffcb0766232f6ad42ad88f6d89654a43fdb4.boutiques",
     name="qatools.py",
     package="freesurfer",
     container_image_tag="freesurfer/freesurfer:7.4.1",
@@ -14,7 +14,17 @@ QATOOLS_PY_METADATA = Metadata(
 
 
 QatoolsPyParameters = typing.TypedDict('QatoolsPyParameters', {
-    "__STYXTYPE__": typing.Literal["qatools.py"],
+    "@type": typing.NotRequired[typing.Literal["freesurfer/qatools.py"]],
+    "subjects_dir": str,
+    "output_dir": str,
+    "subjects": typing.NotRequired[list[str] | None],
+    "screenshots": bool,
+    "fornix": bool,
+    "outlier": bool,
+    "outlier_table": typing.NotRequired[InputPathType | None],
+})
+QatoolsPyParametersTagged = typing.TypedDict('QatoolsPyParametersTagged', {
+    "@type": typing.Literal["freesurfer/qatools.py"],
     "subjects_dir": str,
     "output_dir": str,
     "subjects": typing.NotRequired[list[str] | None],
@@ -23,43 +33,11 @@ QatoolsPyParameters = typing.TypedDict('QatoolsPyParameters', {
     "outlier": bool,
     "outlier_table": typing.NotRequired[InputPathType | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "qatools.py": qatools_py_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 {
-        "qatools.py": qatools_py_outputs,
-    }.get(t)
 
 
 class QatoolsPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `qatools_py(...)`.
+    Output object returned when calling `QatoolsPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +56,7 @@ def qatools_py_params(
     fornix: bool = False,
     outlier: bool = False,
     outlier_table: InputPathType | None = None,
-) -> QatoolsPyParameters:
+) -> QatoolsPyParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +74,7 @@ def qatools_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "qatools.py",
+        "@type": "freesurfer/qatools.py",
         "subjects_dir": subjects_dir,
         "output_dir": output_dir,
         "screenshots": screenshots,
@@ -127,27 +105,27 @@ def qatools_py_cargs(
     cargs.append("qatools.py")
     cargs.extend([
         "--subjects_dir",
-        params.get("subjects_dir")
+        params.get("subjects_dir", None)
     ])
     cargs.extend([
         "--output_dir",
-        params.get("output_dir")
+        params.get("output_dir", None)
     ])
-    if params.get("subjects") is not None:
+    if params.get("subjects", None) is not None:
         cargs.extend([
             "--subjects",
-            *params.get("subjects")
+            *params.get("subjects", None)
         ])
-    if params.get("screenshots"):
+    if params.get("screenshots", False):
         cargs.append("--screenshots")
-    if params.get("fornix"):
+    if params.get("fornix", False):
         cargs.append("--fornix")
-    if params.get("outlier"):
+    if params.get("outlier", False):
         cargs.append("--outlier")
-    if params.get("outlier_table") is not None:
+    if params.get("outlier_table", None) is not None:
         cargs.extend([
             "--outlier-table",
-            execution.input_file(params.get("outlier_table"))
+            execution.input_file(params.get("outlier_table", None))
         ])
     return cargs
 
@@ -167,17 +145,19 @@ def qatools_py_outputs(
     """
     ret = QatoolsPyOutputs(
         root=execution.output_file("."),
-        summary_csv=execution.output_file(params.get("output_dir") + "/summary.csv"),
-        screenshots_output=execution.output_file(params.get("output_dir") + "/screenshots/"),
+        summary_csv=execution.output_file(params.get("output_dir", None) + "/summary.csv"),
+        screenshots_output=execution.output_file(params.get("output_dir", None) + "/screenshots/"),
     )
     return ret
 
 
 def qatools_py_execute(
     params: QatoolsPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> QatoolsPyOutputs:
     """
+    qatools.py
+    
     A tool to compute quality metrics from Freesurfer 6.0 analysis results.
     
     Author: FreeSurfer Developers
@@ -186,10 +166,12 @@ def qatools_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `QatoolsPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(QATOOLS_PY_METADATA)
     params = execution.params(params)
     cargs = qatools_py_cargs(params, execution)
     ret = qatools_py_outputs(params, execution)
@@ -208,6 +190,8 @@ def qatools_py(
     runner: Runner | None = None,
 ) -> QatoolsPyOutputs:
     """
+    qatools.py
+    
     A tool to compute quality metrics from Freesurfer 6.0 analysis results.
     
     Author: FreeSurfer Developers
@@ -228,8 +212,6 @@ def qatools_py(
     Returns:
         NamedTuple of outputs (described in `QatoolsPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(QATOOLS_PY_METADATA)
     params = qatools_py_params(
         subjects_dir=subjects_dir,
         output_dir=output_dir,
@@ -239,13 +221,13 @@ def qatools_py(
         outlier=outlier,
         outlier_table=outlier_table,
     )
-    return qatools_py_execute(params, execution)
+    return qatools_py_execute(params, runner)
 
 
 __all__ = [
     "QATOOLS_PY_METADATA",
     "QatoolsPyOutputs",
-    "QatoolsPyParameters",
     "qatools_py",
+    "qatools_py_execute",
     "qatools_py_params",
 ]