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

niwrap_afni/afni/v_3d_roistats.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ROISTATS_METADATA = Metadata(
-    id="61e00f88ea8f22144368d1110fd8be64f08617a3.boutiques",
+    id="6b928f199c7d06b0d4cf5b6c9c3a9eda49b5549e.boutiques",
     name="3dROIstats",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_ROISTATS_METADATA = Metadata(
 
 
 V3dRoistatsParameters = typing.TypedDict('V3dRoistatsParameters', {
-    "__STYXTYPE__": typing.Literal["3dROIstats"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dROIstats"]],
+    "in_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "debug": bool,
+    "format1D": bool,
+    "format1DR": bool,
+    "mask_f2short": bool,
+    "mask_file": typing.NotRequired[InputPathType | None],
+    "nobriklab": bool,
+    "nomeanout": bool,
+    "num_roi": typing.NotRequired[int | None],
+    "quiet": bool,
+    "roisel": typing.NotRequired[InputPathType | None],
+    "stat": typing.NotRequired[list[InputPathType] | None],
+    "zerofill": typing.NotRequired[str | None],
+})
+V3dRoistatsParametersTagged = typing.TypedDict('V3dRoistatsParametersTagged', {
+    "@type": typing.Literal["afni/3dROIstats"],
     "in_file": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "debug": bool,
@@ -30,42 +47,11 @@ V3dRoistatsParameters = typing.TypedDict('V3dRoistatsParameters', {
     "stat": typing.NotRequired[list[InputPathType] | None],
     "zerofill": 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 {
-        "3dROIstats": v_3d_roistats_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 V3dRoistatsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_roistats(...)`.
+    Output object returned when calling `V3dRoistatsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -93,7 +79,7 @@ def v_3d_roistats_params(
     roisel: InputPathType | None = None,
     stat_: list[InputPathType] | None = None,
     zerofill: str | None = None,
-) -> V3dRoistatsParameters:
+) -> V3dRoistatsParametersTagged:
     """
     Build parameters.
     
@@ -146,7 +132,7 @@ def v_3d_roistats_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dROIstats",
+        "@type": "afni/3dROIstats",
         "in_file": in_file,
         "debug": debug,
         "format1D": format1_d,
@@ -186,47 +172,47 @@ def v_3d_roistats_cargs(
     """
     cargs = []
     cargs.append("3dROIstats")
-    cargs.append(execution.input_file(params.get("in_file")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("in_file", None)))
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("format1D"):
+    if params.get("format1D", False):
         cargs.append("-1Dformat")
-    if params.get("format1DR"):
+    if params.get("format1DR", False):
         cargs.append("-1DRformat")
-    if params.get("mask_f2short"):
+    if params.get("mask_f2short", False):
         cargs.append("-mask_f2short")
-    if params.get("mask_file") is not None:
+    if params.get("mask_file", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask_file"))
+            execution.input_file(params.get("mask_file", None))
         ])
-    if params.get("nobriklab"):
+    if params.get("nobriklab", False):
         cargs.append("-nobriklab")
-    if params.get("nomeanout"):
+    if params.get("nomeanout", False):
         cargs.append("-nomeanout")
-    if params.get("num_roi") is not None:
+    if params.get("num_roi", None) is not None:
         cargs.extend([
             "-numroi",
-            str(params.get("num_roi"))
+            str(params.get("num_roi", None))
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("roisel") is not None:
+    if params.get("roisel", None) is not None:
         cargs.extend([
             "-roisel",
-            execution.input_file(params.get("roisel"))
+            execution.input_file(params.get("roisel", None))
         ])
-    if params.get("stat") is not None:
-        cargs.extend([execution.input_file(f) for f in params.get("stat")])
-    if params.get("zerofill") is not None:
+    if params.get("stat", None) is not None:
+        cargs.extend([execution.input_file(f) for f in params.get("stat", None)])
+    if params.get("zerofill", None) is not None:
         cargs.extend([
             "-zerofill",
-            params.get("zerofill")
+            params.get("zerofill", None)
         ])
     return cargs
 
@@ -253,9 +239,11 @@ def v_3d_roistats_outputs(
 
 def v_3d_roistats_execute(
     params: V3dRoistatsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRoistatsOutputs:
     """
+    3dROIstats
+    
     Display statistics over masked regions.
     
     Author: AFNI Developers
@@ -264,10 +252,12 @@ def v_3d_roistats_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRoistatsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ROISTATS_METADATA)
     params = execution.params(params)
     cargs = v_3d_roistats_cargs(params, execution)
     ret = v_3d_roistats_outputs(params, execution)
@@ -293,6 +283,8 @@ def v_3d_roistats(
     runner: Runner | None = None,
 ) -> V3dRoistatsOutputs:
     """
+    3dROIstats
+    
     Display statistics over masked regions.
     
     Author: AFNI Developers
@@ -348,8 +340,6 @@ def v_3d_roistats(
     Returns:
         NamedTuple of outputs (described in `V3dRoistatsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ROISTATS_METADATA)
     params = v_3d_roistats_params(
         in_file=in_file,
         mask=mask,
@@ -366,13 +356,13 @@ def v_3d_roistats(
         stat_=stat_,
         zerofill=zerofill,
     )
-    return v_3d_roistats_execute(params, execution)
+    return v_3d_roistats_execute(params, runner)
 
 
 __all__ = [
     "V3dRoistatsOutputs",
-    "V3dRoistatsParameters",
     "V_3D_ROISTATS_METADATA",
     "v_3d_roistats",
+    "v_3d_roistats_execute",
     "v_3d_roistats_params",
 ]

niwrap_afni/afni/v_3d_row_fillin.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_ROW_FILLIN_METADATA = Metadata(
-    id="c2d3b84eb8f4551bbe08b67a7a01425fc630db1c.boutiques",
+    id="78c7480c862459ac4050af05db9b294a5c7bc0e1.boutiques",
     name="3dRowFillin",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,50 +14,26 @@ V_3D_ROW_FILLIN_METADATA = Metadata(
 
 
 V3dRowFillinParameters = typing.TypedDict('V3dRowFillinParameters', {
-    "__STYXTYPE__": typing.Literal["3dRowFillin"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRowFillin"]],
+    "maxgap": typing.NotRequired[float | None],
+    "dir": typing.NotRequired[str | None],
+    "binary": bool,
+    "prefix": typing.NotRequired[str | None],
+    "input_dataset": InputPathType,
+})
+V3dRowFillinParametersTagged = typing.TypedDict('V3dRowFillinParametersTagged', {
+    "@type": typing.Literal["afni/3dRowFillin"],
     "maxgap": typing.NotRequired[float | None],
     "dir": typing.NotRequired[str | None],
     "binary": bool,
     "prefix": typing.NotRequired[str | None],
     "input_dataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dRowFillin": v_3d_row_fillin_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 {
-        "3dRowFillin": v_3d_row_fillin_outputs,
-    }.get(t)
 
 
 class V3dRowFillinOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_row_fillin(...)`.
+    Output object returned when calling `V3dRowFillinParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +49,7 @@ def v_3d_row_fillin_params(
     dir_: str | None = None,
     binary: bool = False,
     prefix: str | None = None,
-) -> V3dRowFillinParameters:
+) -> V3dRowFillinParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +65,7 @@ def v_3d_row_fillin_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRowFillin",
+        "@type": "afni/3dRowFillin",
         "binary": binary,
         "input_dataset": input_dataset,
     }
@@ -117,24 +93,24 @@ def v_3d_row_fillin_cargs(
     """
     cargs = []
     cargs.append("3dRowFillin")
-    if params.get("maxgap") is not None:
+    if params.get("maxgap", None) is not None:
         cargs.extend([
             "-maxgap",
-            str(params.get("maxgap"))
+            str(params.get("maxgap", None))
         ])
-    if params.get("dir") is not None:
+    if params.get("dir", None) is not None:
         cargs.extend([
             "-dir",
-            params.get("dir")
+            params.get("dir", None)
         ])
-    if params.get("binary"):
+    if params.get("binary", False):
         cargs.append("-binary")
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", None)
         ])
-    cargs.append(execution.input_file(params.get("input_dataset")))
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
     return cargs
 
 
@@ -153,17 +129,19 @@ def v_3d_row_fillin_outputs(
     """
     ret = V3dRowFillinOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file(params.get("prefix") + "+orig.BRIK") if (params.get("prefix") is not None) else None,
-        output_head=execution.output_file(params.get("prefix") + "+orig.HEAD") if (params.get("prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("prefix", None) + "+orig.BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix", None) + "+orig.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_row_fillin_execute(
     params: V3dRowFillinParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRowFillinOutputs:
     """
+    3dRowFillin
+    
     Fills in blank regions in 1D rows extracted from a 3D dataset.
     
     Author: AFNI Developers
@@ -172,10 +150,12 @@ def v_3d_row_fillin_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRowFillinOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_ROW_FILLIN_METADATA)
     params = execution.params(params)
     cargs = v_3d_row_fillin_cargs(params, execution)
     ret = v_3d_row_fillin_outputs(params, execution)
@@ -192,6 +172,8 @@ def v_3d_row_fillin(
     runner: Runner | None = None,
 ) -> V3dRowFillinOutputs:
     """
+    3dRowFillin
+    
     Fills in blank regions in 1D rows extracted from a 3D dataset.
     
     Author: AFNI Developers
@@ -210,8 +192,6 @@ def v_3d_row_fillin(
     Returns:
         NamedTuple of outputs (described in `V3dRowFillinOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_ROW_FILLIN_METADATA)
     params = v_3d_row_fillin_params(
         maxgap=maxgap,
         dir_=dir_,
@@ -219,13 +199,13 @@ def v_3d_row_fillin(
         prefix=prefix,
         input_dataset=input_dataset,
     )
-    return v_3d_row_fillin_execute(params, execution)
+    return v_3d_row_fillin_execute(params, runner)
 
 
 __all__ = [
     "V3dRowFillinOutputs",
-    "V3dRowFillinParameters",
     "V_3D_ROW_FILLIN_METADATA",
     "v_3d_row_fillin",
+    "v_3d_row_fillin_execute",
     "v_3d_row_fillin_params",
 ]

niwrap_afni/afni/v_3d_rprog_demo.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_RPROG_DEMO_METADATA = Metadata(
-    id="965f67d5db8cb1e43735f15c15add07116ce526d.boutiques",
+    id="ec4899bd50fc86fb3f445d32de40142f3e9600ce.boutiques",
     name="3dRprogDemo",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ V_3D_RPROG_DEMO_METADATA = Metadata(
 
 
 V3dRprogDemoParameters = typing.TypedDict('V3dRprogDemoParameters', {
-    "__STYXTYPE__": typing.Literal["3dRprogDemo"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRprogDemo"]],
+    "input_dsets": list[InputPathType],
+    "mask": typing.NotRequired[InputPathType | None],
+    "scale": float,
+    "prefix": str,
+    "help_aspx": bool,
+    "help_raw": bool,
+    "help_spx": bool,
+    "help_txt": bool,
+    "help": bool,
+    "show_allowed_options": bool,
+    "verbosity_level": typing.NotRequired[float | None],
+})
+V3dRprogDemoParametersTagged = typing.TypedDict('V3dRprogDemoParametersTagged', {
+    "@type": typing.Literal["afni/3dRprogDemo"],
     "input_dsets": list[InputPathType],
     "mask": typing.NotRequired[InputPathType | None],
     "scale": float,
@@ -27,43 +41,11 @@ V3dRprogDemoParameters = typing.TypedDict('V3dRprogDemoParameters', {
     "show_allowed_options": bool,
     "verbosity_level": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dRprogDemo": v_3d_rprog_demo_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 {
-        "3dRprogDemo": v_3d_rprog_demo_outputs,
-    }.get(t)
 
 
 class V3dRprogDemoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_rprog_demo(...)`.
+    Output object returned when calling `V3dRprogDemoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +65,7 @@ def v_3d_rprog_demo_params(
     help_: bool = False,
     show_allowed_options: bool = False,
     verbosity_level: float | None = None,
-) -> V3dRprogDemoParameters:
+) -> V3dRprogDemoParametersTagged:
     """
     Build parameters.
     
@@ -104,7 +86,7 @@ def v_3d_rprog_demo_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRprogDemo",
+        "@type": "afni/3dRprogDemo",
         "input_dsets": input_dsets,
         "scale": scale,
         "prefix": prefix,
@@ -137,36 +119,36 @@ def v_3d_rprog_demo_cargs(
     """
     cargs = []
     cargs.append("3dRprogDemo")
-    cargs.extend([execution.input_file(f) for f in params.get("input_dsets")])
-    if params.get("mask") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("input_dsets", None)])
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
     cargs.extend([
         "-scale",
-        str(params.get("scale"))
+        str(params.get("scale", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("help_aspx"):
+    if params.get("help_aspx", False):
         cargs.append("-h_aspx")
-    if params.get("help_raw"):
+    if params.get("help_raw", False):
         cargs.append("-h_raw")
-    if params.get("help_spx"):
+    if params.get("help_spx", False):
         cargs.append("-h_spx")
-    if params.get("help_txt"):
+    if params.get("help_txt", False):
         cargs.append("-h_txt")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("show_allowed_options"):
+    if params.get("show_allowed_options", False):
         cargs.append("-show_allowed_options")
-    if params.get("verbosity_level") is not None:
+    if params.get("verbosity_level", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity_level"))
+            str(params.get("verbosity_level", None))
         ])
     return cargs
 
@@ -186,16 +168,18 @@ def v_3d_rprog_demo_outputs(
     """
     ret = V3dRprogDemoOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii"),
+        output_file=execution.output_file(params.get("prefix", None) + ".nii"),
     )
     return ret
 
 
 def v_3d_rprog_demo_execute(
     params: V3dRprogDemoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRprogDemoOutputs:
     """
+    3dRprogDemo
+    
     Template program to help users write their own R processing routines on MRI
     volumes.
     
@@ -205,10 +189,12 @@ def v_3d_rprog_demo_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRprogDemoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_RPROG_DEMO_METADATA)
     params = execution.params(params)
     cargs = v_3d_rprog_demo_cargs(params, execution)
     ret = v_3d_rprog_demo_outputs(params, execution)
@@ -231,6 +217,8 @@ def v_3d_rprog_demo(
     runner: Runner | None = None,
 ) -> V3dRprogDemoOutputs:
     """
+    3dRprogDemo
+    
     Template program to help users write their own R processing routines on MRI
     volumes.
     
@@ -255,8 +243,6 @@ def v_3d_rprog_demo(
     Returns:
         NamedTuple of outputs (described in `V3dRprogDemoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_RPROG_DEMO_METADATA)
     params = v_3d_rprog_demo_params(
         input_dsets=input_dsets,
         mask=mask,
@@ -270,13 +256,13 @@ def v_3d_rprog_demo(
         show_allowed_options=show_allowed_options,
         verbosity_level=verbosity_level,
     )
-    return v_3d_rprog_demo_execute(params, execution)
+    return v_3d_rprog_demo_execute(params, runner)
 
 
 __all__ = [
     "V3dRprogDemoOutputs",
-    "V3dRprogDemoParameters",
     "V_3D_RPROG_DEMO_METADATA",
     "v_3d_rprog_demo",
+    "v_3d_rprog_demo_execute",
     "v_3d_rprog_demo_params",
 ]