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

niwrap_afni/afni/{adjunct_simplify_cost.py → adjunct_simplify_cost_py.py}

@@ -5,62 +5,35 @@ import typing
 import pathlib
 from styxdefs import *
 
-ADJUNCT_SIMPLIFY_COST_METADATA = Metadata(
-    id="0291c293f6b2eaf6626f15fdc0c7c7079ef500e7.boutiques",
-    name="adjunct_simplify_cost",
+ADJUNCT_SIMPLIFY_COST_PY_METADATA = Metadata(
+    id="829e8e6deae200b0466a903fca638f1647be7707.boutiques",
+    name="adjunct_simplify_cost.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-AdjunctSimplifyCostParameters = typing.TypedDict('AdjunctSimplifyCostParameters', {
-    "__STYXTYPE__": typing.Literal["adjunct_simplify_cost"],
+AdjunctSimplifyCostPyParameters = typing.TypedDict('AdjunctSimplifyCostPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/adjunct_simplify_cost.py"]],
+    "cost_function": str,
+})
+AdjunctSimplifyCostPyParametersTagged = typing.TypedDict('AdjunctSimplifyCostPyParametersTagged', {
+    "@type": typing.Literal["afni/adjunct_simplify_cost.py"],
     "cost_function": str,
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "adjunct_simplify_cost": adjunct_simplify_cost_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 AdjunctSimplifyCostOutputs(typing.NamedTuple):
+class AdjunctSimplifyCostPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `adjunct_simplify_cost(...)`.
+    Output object returned when calling `AdjunctSimplifyCostPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
 
 
-def adjunct_simplify_cost_params(
+def adjunct_simplify_cost_py_params(
     cost_function: str,
-) -> AdjunctSimplifyCostParameters:
+) -> AdjunctSimplifyCostPyParametersTagged:
     """
     Build parameters.
     
@@ -70,14 +43,14 @@ def adjunct_simplify_cost_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "adjunct_simplify_cost",
+        "@type": "afni/adjunct_simplify_cost.py",
         "cost_function": cost_function,
     }
     return params
 
 
-def adjunct_simplify_cost_cargs(
-    params: AdjunctSimplifyCostParameters,
+def adjunct_simplify_cost_py_cargs(
+    params: AdjunctSimplifyCostPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -91,14 +64,14 @@ def adjunct_simplify_cost_cargs(
     """
     cargs = []
     cargs.append("adjunct_simplify_cost.py")
-    cargs.append(params.get("cost_function"))
+    cargs.append(params.get("cost_function", None))
     return cargs
 
 
-def adjunct_simplify_cost_outputs(
-    params: AdjunctSimplifyCostParameters,
+def adjunct_simplify_cost_py_outputs(
+    params: AdjunctSimplifyCostPyParameters,
     execution: Execution,
-) -> AdjunctSimplifyCostOutputs:
+) -> AdjunctSimplifyCostPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -108,18 +81,21 @@ def adjunct_simplify_cost_outputs(
     Returns:
         Outputs object.
     """
-    ret = AdjunctSimplifyCostOutputs(
+    ret = AdjunctSimplifyCostPyOutputs(
         root=execution.output_file("."),
     )
     return ret
 
 
-def adjunct_simplify_cost_execute(
-    params: AdjunctSimplifyCostParameters,
-    execution: Execution,
-) -> AdjunctSimplifyCostOutputs:
+def adjunct_simplify_cost_py_execute(
+    params: AdjunctSimplifyCostPyParameters,
+    runner: Runner | None = None,
+) -> AdjunctSimplifyCostPyOutputs:
     """
-    Simplifies a cost function name by removing the '+' and anything following it.
+    adjunct_simplify_cost.py
+    
+    Simplifies a cost function name by removing the '+' and anything following
+    it.
     
     Author: AFNI Developers
     
@@ -127,23 +103,28 @@ def adjunct_simplify_cost_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `AdjunctSimplifyCostOutputs`).
+        NamedTuple of outputs (described in `AdjunctSimplifyCostPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SIMPLIFY_COST_PY_METADATA)
     params = execution.params(params)
-    cargs = adjunct_simplify_cost_cargs(params, execution)
-    ret = adjunct_simplify_cost_outputs(params, execution)
+    cargs = adjunct_simplify_cost_py_cargs(params, execution)
+    ret = adjunct_simplify_cost_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def adjunct_simplify_cost(
+def adjunct_simplify_cost_py(
     cost_function: str,
     runner: Runner | None = None,
-) -> AdjunctSimplifyCostOutputs:
+) -> AdjunctSimplifyCostPyOutputs:
     """
-    Simplifies a cost function name by removing the '+' and anything following it.
+    adjunct_simplify_cost.py
+    
+    Simplifies a cost function name by removing the '+' and anything following
+    it.
     
     Author: AFNI Developers
     
@@ -153,20 +134,18 @@ def adjunct_simplify_cost(
         cost_function: The cost function name to be simplified.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `AdjunctSimplifyCostOutputs`).
+        NamedTuple of outputs (described in `AdjunctSimplifyCostPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ADJUNCT_SIMPLIFY_COST_METADATA)
-    params = adjunct_simplify_cost_params(
+    params = adjunct_simplify_cost_py_params(
         cost_function=cost_function,
     )
-    return adjunct_simplify_cost_execute(params, execution)
+    return adjunct_simplify_cost_py_execute(params, runner)
 
 
 __all__ = [
-    "ADJUNCT_SIMPLIFY_COST_METADATA",
-    "AdjunctSimplifyCostOutputs",
-    "AdjunctSimplifyCostParameters",
-    "adjunct_simplify_cost",
-    "adjunct_simplify_cost_params",
+    "ADJUNCT_SIMPLIFY_COST_PY_METADATA",
+    "AdjunctSimplifyCostPyOutputs",
+    "adjunct_simplify_cost_py",
+    "adjunct_simplify_cost_py_execute",
+    "adjunct_simplify_cost_py_params",
 ]

niwrap_afni/afni/adjunct_suma_fs_mask_and_qc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA = Metadata(
-    id="a5fd3e30999988458acf431df9f21ab685cbbe45.boutiques",
+    id="0b8258892cbf5ad4aa648c0f8ea129aed0f967cd.boutiques",
     name="adjunct_suma_fs_mask_and_qc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA = Metadata(
 
 
 AdjunctSumaFsMaskAndQcParameters = typing.TypedDict('AdjunctSumaFsMaskAndQcParameters', {
-    "__STYXTYPE__": typing.Literal["adjunct_suma_fs_mask_and_qc"],
+    "@type": typing.NotRequired[typing.Literal["afni/adjunct_suma_fs_mask_and_qc"]],
+    "subj_id": str,
+    "suma_dir": str,
+    "no_clean": bool,
+    "help": bool,
+    "hview": bool,
+    "version": bool,
+})
+AdjunctSumaFsMaskAndQcParametersTagged = typing.TypedDict('AdjunctSumaFsMaskAndQcParametersTagged', {
+    "@type": typing.Literal["afni/adjunct_suma_fs_mask_and_qc"],
     "subj_id": str,
     "suma_dir": str,
     "no_clean": bool,
@@ -22,43 +31,11 @@ AdjunctSumaFsMaskAndQcParameters = typing.TypedDict('AdjunctSumaFsMaskAndQcParam
     "hview": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "adjunct_suma_fs_mask_and_qc": adjunct_suma_fs_mask_and_qc_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 {
-        "adjunct_suma_fs_mask_and_qc": adjunct_suma_fs_mask_and_qc_outputs,
-    }.get(t)
 
 
 class AdjunctSumaFsMaskAndQcOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `adjunct_suma_fs_mask_and_qc(...)`.
+    Output object returned when calling `AdjunctSumaFsMaskAndQcParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -86,7 +63,7 @@ def adjunct_suma_fs_mask_and_qc_params(
     help_: bool = False,
     hview: bool = False,
     version: bool = False,
-) -> AdjunctSumaFsMaskAndQcParameters:
+) -> AdjunctSumaFsMaskAndQcParametersTagged:
     """
     Build parameters.
     
@@ -102,7 +79,7 @@ def adjunct_suma_fs_mask_and_qc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "adjunct_suma_fs_mask_and_qc",
+        "@type": "afni/adjunct_suma_fs_mask_and_qc",
         "subj_id": subj_id,
         "suma_dir": suma_dir,
         "no_clean": no_clean,
@@ -130,19 +107,19 @@ def adjunct_suma_fs_mask_and_qc_cargs(
     cargs.append("adjunct_suma_fs_mask_and_qc")
     cargs.extend([
         "-sid",
-        params.get("subj_id")
+        params.get("subj_id", None)
     ])
     cargs.extend([
         "-suma_dir",
-        params.get("suma_dir")
+        params.get("suma_dir", None)
     ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hview"):
+    if params.get("hview", False):
         cargs.append("-hview")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
     return cargs
 
@@ -163,21 +140,23 @@ def adjunct_suma_fs_mask_and_qc_outputs(
     ret = AdjunctSumaFsMaskAndQcOutputs(
         root=execution.output_file("."),
         fs_parc_wb_mask=execution.output_file("SUMA/fs_parc_wb_mask.nii.gz"),
-        qc_image_00=execution.output_file("SUMA/qc_00*.jpg"),
-        qc_image_01=execution.output_file("SUMA/qc_01*.jpg"),
-        qc_image_02=execution.output_file("SUMA/qc_02*.jpg"),
-        qc_image_03=execution.output_file("SUMA/qc_03*.jpg"),
-        qc_image_04=execution.output_file("SUMA/qc_04*.jpg"),
-        qc_image_05=execution.output_file("SUMA/qc_05*.jpg"),
+        qc_image_00=execution.output_file("SUMA/qc_00.jpg"),
+        qc_image_01=execution.output_file("SUMA/qc_01.jpg"),
+        qc_image_02=execution.output_file("SUMA/qc_02.jpg"),
+        qc_image_03=execution.output_file("SUMA/qc_03.jpg"),
+        qc_image_04=execution.output_file("SUMA/qc_04.jpg"),
+        qc_image_05=execution.output_file("SUMA/qc_05.jpg"),
     )
     return ret
 
 
 def adjunct_suma_fs_mask_and_qc_execute(
     params: AdjunctSumaFsMaskAndQcParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AdjunctSumaFsMaskAndQcOutputs:
     """
+    adjunct_suma_fs_mask_and_qc
+    
     Script for quickly making some QC images for the SUMA/ directory created by
     @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
     
@@ -187,10 +166,12 @@ def adjunct_suma_fs_mask_and_qc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AdjunctSumaFsMaskAndQcOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA)
     params = execution.params(params)
     cargs = adjunct_suma_fs_mask_and_qc_cargs(params, execution)
     ret = adjunct_suma_fs_mask_and_qc_outputs(params, execution)
@@ -208,6 +189,8 @@ def adjunct_suma_fs_mask_and_qc(
     runner: Runner | None = None,
 ) -> AdjunctSumaFsMaskAndQcOutputs:
     """
+    adjunct_suma_fs_mask_and_qc
+    
     Script for quickly making some QC images for the SUMA/ directory created by
     @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
     
@@ -227,8 +210,6 @@ def adjunct_suma_fs_mask_and_qc(
     Returns:
         NamedTuple of outputs (described in `AdjunctSumaFsMaskAndQcOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA)
     params = adjunct_suma_fs_mask_and_qc_params(
         subj_id=subj_id,
         suma_dir=suma_dir,
@@ -237,13 +218,13 @@ def adjunct_suma_fs_mask_and_qc(
         hview=hview,
         version=version,
     )
-    return adjunct_suma_fs_mask_and_qc_execute(params, execution)
+    return adjunct_suma_fs_mask_and_qc_execute(params, runner)
 
 
 __all__ = [
     "ADJUNCT_SUMA_FS_MASK_AND_QC_METADATA",
     "AdjunctSumaFsMaskAndQcOutputs",
-    "AdjunctSumaFsMaskAndQcParameters",
     "adjunct_suma_fs_mask_and_qc",
+    "adjunct_suma_fs_mask_and_qc_execute",
     "adjunct_suma_fs_mask_and_qc_params",
 ]

niwrap_afni/afni/adjunct_suma_fs_roi_info.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ADJUNCT_SUMA_FS_ROI_INFO_METADATA = Metadata(
-    id="174d682bbfbcc03f436d1ab2dd83376c7847145f.boutiques",
+    id="4c3bf5516cdbc83d322f7348efd10351c15c126e.boutiques",
     name="adjunct_suma_fs_roi_info",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ ADJUNCT_SUMA_FS_ROI_INFO_METADATA = Metadata(
 
 
 AdjunctSumaFsRoiInfoParameters = typing.TypedDict('AdjunctSumaFsRoiInfoParameters', {
-    "__STYXTYPE__": typing.Literal["adjunct_suma_fs_roi_info"],
+    "@type": typing.NotRequired[typing.Literal["afni/adjunct_suma_fs_roi_info"]],
+    "subject_id": str,
+    "suma_directory": str,
+    "help": bool,
+    "hview": bool,
+    "version": bool,
+})
+AdjunctSumaFsRoiInfoParametersTagged = typing.TypedDict('AdjunctSumaFsRoiInfoParametersTagged', {
+    "@type": typing.Literal["afni/adjunct_suma_fs_roi_info"],
     "subject_id": str,
     "suma_directory": str,
     "help": bool,
     "hview": bool,
     "version": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "adjunct_suma_fs_roi_info": adjunct_suma_fs_roi_info_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 {
-        "adjunct_suma_fs_roi_info": adjunct_suma_fs_roi_info_outputs,
-    }.get(t)
 
 
 class AdjunctSumaFsRoiInfoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `adjunct_suma_fs_roi_info(...)`.
+    Output object returned when calling `AdjunctSumaFsRoiInfoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +53,7 @@ def adjunct_suma_fs_roi_info_params(
     help_: bool = False,
     hview: bool = False,
     version: bool = False,
-) -> AdjunctSumaFsRoiInfoParameters:
+) -> AdjunctSumaFsRoiInfoParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +67,7 @@ def adjunct_suma_fs_roi_info_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "adjunct_suma_fs_roi_info",
+        "@type": "afni/adjunct_suma_fs_roi_info",
         "subject_id": subject_id,
         "suma_directory": suma_directory,
         "help": help_,
@@ -118,17 +94,17 @@ def adjunct_suma_fs_roi_info_cargs(
     cargs.append("adjunct_suma_fs_roi_info")
     cargs.extend([
         "-sid",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     cargs.extend([
         "-suma_dir",
-        params.get("suma_directory")
+        params.get("suma_directory", None)
     ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hview"):
+    if params.get("hview", False):
         cargs.append("-hview")
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
     return cargs
 
@@ -158,9 +134,11 @@ def adjunct_suma_fs_roi_info_outputs(
 
 def adjunct_suma_fs_roi_info_execute(
     params: AdjunctSumaFsRoiInfoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AdjunctSumaFsRoiInfoOutputs:
     """
+    adjunct_suma_fs_roi_info
+    
     Script for making ROI stats for the SUMA/ directory created by
     @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
     
@@ -170,10 +148,12 @@ def adjunct_suma_fs_roi_info_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AdjunctSumaFsRoiInfoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ADJUNCT_SUMA_FS_ROI_INFO_METADATA)
     params = execution.params(params)
     cargs = adjunct_suma_fs_roi_info_cargs(params, execution)
     ret = adjunct_suma_fs_roi_info_outputs(params, execution)
@@ -190,6 +170,8 @@ def adjunct_suma_fs_roi_info(
     runner: Runner | None = None,
 ) -> AdjunctSumaFsRoiInfoOutputs:
     """
+    adjunct_suma_fs_roi_info
+    
     Script for making ROI stats for the SUMA/ directory created by
     @SUMA_Make_Spec_FS after running FreeSurfer's recon-all.
     
@@ -207,8 +189,6 @@ def adjunct_suma_fs_roi_info(
     Returns:
         NamedTuple of outputs (described in `AdjunctSumaFsRoiInfoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ADJUNCT_SUMA_FS_ROI_INFO_METADATA)
     params = adjunct_suma_fs_roi_info_params(
         subject_id=subject_id,
         suma_directory=suma_directory,
@@ -216,13 +196,13 @@ def adjunct_suma_fs_roi_info(
         hview=hview,
         version=version,
     )
-    return adjunct_suma_fs_roi_info_execute(params, execution)
+    return adjunct_suma_fs_roi_info_execute(params, runner)
 
 
 __all__ = [
     "ADJUNCT_SUMA_FS_ROI_INFO_METADATA",
     "AdjunctSumaFsRoiInfoOutputs",
-    "AdjunctSumaFsRoiInfoParameters",
     "adjunct_suma_fs_roi_info",
+    "adjunct_suma_fs_roi_info_execute",
     "adjunct_suma_fs_roi_info_params",
 ]