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

niwrap_afni/afni/surf_fwhm.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_FWHM_METADATA = Metadata(
-    id="5f3d67852b7237a8609f944b36387016b6ab2c24.boutiques",
+    id="507940e5e4dbb09e2303be71339d44cbb0abc244.boutiques",
     name="SurfFWHM",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ SURF_FWHM_METADATA = Metadata(
 
 
 SurfFwhmParameters = typing.TypedDict('SurfFwhmParameters', {
-    "__STYXTYPE__": typing.Literal["SurfFWHM"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfFWHM"]],
+    "input_file": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "surf_1": typing.NotRequired[str | None],
+    "surf_sphere": typing.NotRequired[str | None],
+    "clean": bool,
+    "detrend": typing.NotRequired[float | None],
+    "detpoly": typing.NotRequired[float | None],
+    "detprefix": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "vox_size": typing.NotRequired[float | None],
+    "neighborhood": typing.NotRequired[float | None],
+    "ok_warn": bool,
+    "examples": bool,
+    "slice": bool,
+})
+SurfFwhmParametersTagged = typing.TypedDict('SurfFwhmParametersTagged', {
+    "@type": typing.Literal["afni/SurfFWHM"],
     "input_file": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "surf_1": typing.NotRequired[str | None],
@@ -30,43 +47,11 @@ SurfFwhmParameters = typing.TypedDict('SurfFwhmParameters', {
     "examples": bool,
     "slice": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SurfFWHM": surf_fwhm_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 {
-        "SurfFWHM": surf_fwhm_outputs,
-    }.get(t)
 
 
 class SurfFwhmOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_fwhm(...)`.
+    Output object returned when calling `SurfFwhmParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -95,7 +80,7 @@ def surf_fwhm_params(
     ok_warn: bool = False,
     examples: bool = False,
     slice_: bool = False,
-) -> SurfFwhmParameters:
+) -> SurfFwhmParametersTagged:
     """
     Build parameters.
     
@@ -122,7 +107,7 @@ def surf_fwhm_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfFWHM",
+        "@type": "afni/SurfFWHM",
         "input_file": input_file,
         "clean": clean,
         "ok_warn": ok_warn,
@@ -165,59 +150,59 @@ def surf_fwhm_cargs(
     """
     cargs = []
     cargs.append("SurfFWHM")
-    cargs.append(execution.input_file(params.get("input_file")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("input_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("surf_1") is not None:
+    if params.get("surf_1", None) is not None:
         cargs.extend([
             "-SURF_1",
-            params.get("surf_1")
+            params.get("surf_1", None)
         ])
-    if params.get("surf_sphere") is not None:
+    if params.get("surf_sphere", None) is not None:
         cargs.extend([
             "-SURF_SPHERE",
-            params.get("surf_sphere")
+            params.get("surf_sphere", None)
         ])
-    if params.get("clean"):
+    if params.get("clean", False):
         cargs.append("-clean")
-    if params.get("detrend") is not None:
+    if params.get("detrend", None) is not None:
         cargs.extend([
             "-detrend",
-            str(params.get("detrend"))
+            str(params.get("detrend", None))
         ])
-    if params.get("detpoly") is not None:
+    if params.get("detpoly", None) is not None:
         cargs.extend([
             "-detpoly",
-            str(params.get("detpoly"))
+            str(params.get("detpoly", None))
         ])
-    if params.get("detprefix") is not None:
+    if params.get("detprefix", None) is not None:
         cargs.extend([
             "-detprefix",
-            params.get("detprefix")
+            params.get("detprefix", None)
         ])
-    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)
         ])
-    if params.get("vox_size") is not None:
+    if params.get("vox_size", None) is not None:
         cargs.extend([
             "-vox_size",
-            str(params.get("vox_size"))
+            str(params.get("vox_size", None))
         ])
-    if params.get("neighborhood") is not None:
+    if params.get("neighborhood", None) is not None:
         cargs.extend([
             "-hood",
-            str(params.get("neighborhood"))
+            str(params.get("neighborhood", None))
         ])
-    if params.get("ok_warn"):
+    if params.get("ok_warn", False):
         cargs.append("-ok_warn")
-    if params.get("examples"):
+    if params.get("examples", False):
         cargs.append("-examples")
-    if params.get("slice"):
+    if params.get("slice", False):
         cargs.append("-slice")
     return cargs
 
@@ -237,19 +222,21 @@ def surf_fwhm_outputs(
     """
     ret = SurfFwhmOutputs(
         root=execution.output_file("."),
-        detrended_output=execution.output_file(params.get("prefix") + ".1D.dset") if (params.get("prefix") is not None) else None,
-        main_output=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        histogram_output=execution.output_file(params.get("prefix") + "_histog.1D") if (params.get("prefix") is not None) else None,
-        mask_output=execution.output_file(params.get("prefix") + "_mask.nii.gz") if (params.get("prefix") is not None) else None,
+        detrended_output=execution.output_file(params.get("prefix", None) + ".1D.dset") if (params.get("prefix") is not None) else None,
+        main_output=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        histogram_output=execution.output_file(params.get("prefix", None) + "_histog.1D") if (params.get("prefix") is not None) else None,
+        mask_output=execution.output_file(params.get("prefix", None) + "_mask.nii.gz") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def surf_fwhm_execute(
     params: SurfFwhmParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfFwhmOutputs:
     """
+    SurfFWHM
+    
     A program for calculating local and global FWHM.
     
     Author: AFNI Developers
@@ -258,10 +245,12 @@ def surf_fwhm_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfFwhmOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_FWHM_METADATA)
     params = execution.params(params)
     cargs = surf_fwhm_cargs(params, execution)
     ret = surf_fwhm_outputs(params, execution)
@@ -287,6 +276,8 @@ def surf_fwhm(
     runner: Runner | None = None,
 ) -> SurfFwhmOutputs:
     """
+    SurfFWHM
+    
     A program for calculating local and global FWHM.
     
     Author: AFNI Developers
@@ -316,8 +307,6 @@ def surf_fwhm(
     Returns:
         NamedTuple of outputs (described in `SurfFwhmOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_FWHM_METADATA)
     params = surf_fwhm_params(
         input_file=input_file,
         mask=mask,
@@ -334,13 +323,13 @@ def surf_fwhm(
         examples=examples,
         slice_=slice_,
     )
-    return surf_fwhm_execute(params, execution)
+    return surf_fwhm_execute(params, runner)
 
 
 __all__ = [
     "SURF_FWHM_METADATA",
     "SurfFwhmOutputs",
-    "SurfFwhmParameters",
     "surf_fwhm",
+    "surf_fwhm_execute",
     "surf_fwhm_params",
 ]

niwrap_afni/afni/surf_info.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 SURF_INFO_METADATA = Metadata(
-    id="da9fc16e9b8222d19dae2ab29da591e8a5f4a0cf.boutiques",
+    id="56af722d55dc6d5f432c8465801c64246f4b10d3.boutiques",
     name="SurfInfo",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ SURF_INFO_METADATA = Metadata(
 
 
 SurfInfoParameters = typing.TypedDict('SurfInfoParameters', {
-    "__STYXTYPE__": typing.Literal["SurfInfo"],
+    "@type": typing.NotRequired[typing.Literal["afni/SurfInfo"]],
+    "surface": InputPathType,
+    "com": bool,
+    "debug_level": typing.NotRequired[float | None],
+    "detail_level": typing.NotRequired[float | None],
+    "n_node": bool,
+    "n_faceset": bool,
+    "n_tri": bool,
+    "quiet": bool,
+    "separator": typing.NotRequired[str | None],
+    "input_surface": typing.NotRequired[str | None],
+    "surface_state": typing.NotRequired[str | None],
+    "surface_volume": typing.NotRequired[InputPathType | None],
+    "spec_file": typing.NotRequired[InputPathType | None],
+    "novolreg": bool,
+    "noxform": bool,
+    "setenv": typing.NotRequired[str | None],
+    "trace": bool,
+    "extreme_trace": bool,
+    "nomall": bool,
+    "yesmall": bool,
+})
+SurfInfoParametersTagged = typing.TypedDict('SurfInfoParametersTagged', {
+    "@type": typing.Literal["afni/SurfInfo"],
     "surface": InputPathType,
     "com": bool,
     "debug_level": typing.NotRequired[float | None],
@@ -36,43 +59,11 @@ SurfInfoParameters = typing.TypedDict('SurfInfoParameters', {
     "nomall": bool,
     "yesmall": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "SurfInfo": surf_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 {
-        "SurfInfo": surf_info_outputs,
-    }.get(t)
 
 
 class SurfInfoOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `surf_info(...)`.
+    Output object returned when calling `SurfInfoParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +92,7 @@ def surf_info_params(
     extreme_trace: bool = False,
     nomall: bool = False,
     yesmall: bool = False,
-) -> SurfInfoParameters:
+) -> SurfInfoParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +124,7 @@ def surf_info_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "SurfInfo",
+        "@type": "afni/SurfInfo",
         "surface": surface,
         "com": com,
         "n_node": n_node,
@@ -181,68 +172,68 @@ def surf_info_cargs(
     """
     cargs = []
     cargs.append("SurfInfo")
-    cargs.append(execution.input_file(params.get("surface")))
-    if params.get("com"):
+    cargs.append(execution.input_file(params.get("surface", None)))
+    if params.get("com", False):
         cargs.append("-COM")
-    if params.get("debug_level") is not None:
+    if params.get("debug_level", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug_level"))
+            str(params.get("debug_level", None))
         ])
-    if params.get("detail_level") is not None:
+    if params.get("detail_level", None) is not None:
         cargs.extend([
             "-detail",
-            str(params.get("detail_level"))
+            str(params.get("detail_level", None))
         ])
-    if params.get("n_node"):
+    if params.get("n_node", False):
         cargs.append("-N_Node")
-    if params.get("n_faceset"):
+    if params.get("n_faceset", False):
         cargs.append("-N_FaceSet")
-    if params.get("n_tri"):
+    if params.get("n_tri", False):
         cargs.append("-N_Tri")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("separator") is not None:
+    if params.get("separator", None) is not None:
         cargs.extend([
             "-sep",
-            params.get("separator")
+            params.get("separator", None)
         ])
-    if params.get("input_surface") is not None:
+    if params.get("input_surface", None) is not None:
         cargs.extend([
             "-i_TYPE",
-            params.get("input_surface")
+            params.get("input_surface", None)
         ])
-    if params.get("surface_state") is not None:
+    if params.get("surface_state", None) is not None:
         cargs.extend([
             "-tsn",
-            params.get("surface_state")
+            params.get("surface_state", None)
         ])
-    if params.get("surface_volume") is not None:
+    if params.get("surface_volume", None) is not None:
         cargs.extend([
             "-sv",
-            execution.input_file(params.get("surface_volume"))
+            execution.input_file(params.get("surface_volume", None))
         ])
-    if params.get("spec_file") is not None:
+    if params.get("spec_file", None) is not None:
         cargs.extend([
             "-spec",
-            execution.input_file(params.get("spec_file"))
+            execution.input_file(params.get("spec_file", None))
         ])
-    if params.get("novolreg"):
+    if params.get("novolreg", False):
         cargs.append("-novolreg")
-    if params.get("noxform"):
+    if params.get("noxform", False):
         cargs.append("-noxform")
-    if params.get("setenv") is not None:
+    if params.get("setenv", None) is not None:
         cargs.extend([
             "-setenv",
-            params.get("setenv")
+            params.get("setenv", None)
         ])
-    if params.get("trace"):
+    if params.get("trace", False):
         cargs.append("-trace")
-    if params.get("extreme_trace"):
+    if params.get("extreme_trace", False):
         cargs.append("-TRACE")
-    if params.get("nomall"):
+    if params.get("nomall", False):
         cargs.append("-nomall")
-    if params.get("yesmall"):
+    if params.get("yesmall", False):
         cargs.append("-yesmall")
     return cargs
 
@@ -262,16 +253,18 @@ def surf_info_outputs(
     """
     ret = SurfInfoOutputs(
         root=execution.output_file("."),
-        metrics_output=execution.output_file(pathlib.Path(params.get("surface")).name + "_metrics.txt"),
+        metrics_output=execution.output_file(pathlib.Path(params.get("surface", None)).name + "_metrics.txt"),
     )
     return ret
 
 
 def surf_info_execute(
     params: SurfInfoParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> SurfInfoOutputs:
     """
+    SurfInfo
+    
     Tool to gather information about surface files.
     
     Author: AFNI Developers
@@ -280,10 +273,12 @@ def surf_info_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `SurfInfoOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(SURF_INFO_METADATA)
     params = execution.params(params)
     cargs = surf_info_cargs(params, execution)
     ret = surf_info_outputs(params, execution)
@@ -315,6 +310,8 @@ def surf_info(
     runner: Runner | None = None,
 ) -> SurfInfoOutputs:
     """
+    SurfInfo
+    
     Tool to gather information about surface files.
     
     Author: AFNI Developers
@@ -349,8 +346,6 @@ def surf_info(
     Returns:
         NamedTuple of outputs (described in `SurfInfoOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(SURF_INFO_METADATA)
     params = surf_info_params(
         surface=surface,
         com=com,
@@ -373,13 +368,13 @@ def surf_info(
         nomall=nomall,
         yesmall=yesmall,
     )
-    return surf_info_execute(params, execution)
+    return surf_info_execute(params, runner)
 
 
 __all__ = [
     "SURF_INFO_METADATA",
     "SurfInfoOutputs",
-    "SurfInfoParameters",
     "surf_info",
+    "surf_info_execute",
     "surf_info_params",
 ]