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

niwrap_afni/afni/v__suma_renumber_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SUMA_RENUMBER_FS_METADATA = Metadata(
-    id="d6b26ce01bc843b54df7040889d91aaf2856abf4.boutiques",
+    id="0697ae6a2709e6ef926f690c7fcc6f1562f456cd.boutiques",
     name="@SUMA_renumber_FS",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ V__SUMA_RENUMBER_FS_METADATA = Metadata(
 
 
 VSumaRenumberFsParameters = typing.TypedDict('VSumaRenumberFsParameters', {
-    "__STYXTYPE__": typing.Literal["@SUMA_renumber_FS"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SUMA_renumber_FS"]],
+    "sumadir": str,
+})
+VSumaRenumberFsParametersTagged = typing.TypedDict('VSumaRenumberFsParametersTagged', {
+    "@type": typing.Literal["afni/@SUMA_renumber_FS"],
     "sumadir": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@SUMA_renumber_FS": v__suma_renumber_fs_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 {
-        "@SUMA_renumber_FS": v__suma_renumber_fs_outputs,
-    }.get(t)
 
 
 class VSumaRenumberFsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__suma_renumber_fs(...)`.
+    Output object returned when calling `VSumaRenumberFsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +56,7 @@ class VSumaRenumberFsOutputs(typing.NamedTuple):
 
 def v__suma_renumber_fs_params(
     sumadir: str,
-) -> VSumaRenumberFsParameters:
+) -> VSumaRenumberFsParametersTagged:
     """
     Build parameters.
     
@@ -94,7 +66,7 @@ def v__suma_renumber_fs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SUMA_renumber_FS",
+        "@type": "afni/@SUMA_renumber_FS",
         "sumadir": sumadir,
     }
     return params
@@ -115,7 +87,7 @@ def v__suma_renumber_fs_cargs(
     """
     cargs = []
     cargs.append("@SUMA_renumber_FS")
-    cargs.append(params.get("sumadir"))
+    cargs.append(params.get("sumadir", None))
     return cargs
 
 
@@ -134,26 +106,28 @@ def v__suma_renumber_fs_outputs(
     """
     ret = VSumaRenumberFsOutputs(
         root=execution.output_file("."),
-        ren_all=execution.output_file("*_REN_all.nii.gz"),
-        ren_gm=execution.output_file("*_REN_gm.nii.gz"),
-        ren_wmat=execution.output_file("*_REN_wmat.nii.gz"),
-        ren_csf=execution.output_file("*_REN_csf.nii.gz"),
-        ren_vent=execution.output_file("*_REN_vent.nii.gz"),
-        ren_othr=execution.output_file("*_REN_othr.nii.gz"),
-        ren_unkn=execution.output_file("*_REN_unkn.nii.gz"),
-        ren_gmrois=execution.output_file("*_REN_gmrois.nii.gz"),
+        ren_all=execution.output_file("REN_all.nii.gz"),
+        ren_gm=execution.output_file("REN_gm.nii.gz"),
+        ren_wmat=execution.output_file("REN_wmat.nii.gz"),
+        ren_csf=execution.output_file("REN_csf.nii.gz"),
+        ren_vent=execution.output_file("REN_vent.nii.gz"),
+        ren_othr=execution.output_file("REN_othr.nii.gz"),
+        ren_unkn=execution.output_file("REN_unkn.nii.gz"),
+        ren_gmrois=execution.output_file("REN_gmrois.nii.gz"),
         fs_ap_wm=execution.output_file("fs_ap_wm.nii.gz"),
         fs_ap_latvent=execution.output_file("fs_ap_latvent.nii.gz"),
-        ren_lbl_table=execution.output_file("*_REN_all.niml.lt"),
+        ren_lbl_table=execution.output_file("REN_all.niml.lt"),
     )
     return ret
 
 
 def v__suma_renumber_fs_execute(
     params: VSumaRenumberFsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSumaRenumberFsOutputs:
     """
+    @SUMA_renumber_FS
+    
     This script processes FreeSurfer-generated parcellation files and produces
     various derived datasets and segmentation maps.
     
@@ -163,10 +137,12 @@ def v__suma_renumber_fs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSumaRenumberFsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_RENUMBER_FS_METADATA)
     params = execution.params(params)
     cargs = v__suma_renumber_fs_cargs(params, execution)
     ret = v__suma_renumber_fs_outputs(params, execution)
@@ -179,6 +155,8 @@ def v__suma_renumber_fs(
     runner: Runner | None = None,
 ) -> VSumaRenumberFsOutputs:
     """
+    @SUMA_renumber_FS
+    
     This script processes FreeSurfer-generated parcellation files and produces
     various derived datasets and segmentation maps.
     
@@ -192,18 +170,16 @@ def v__suma_renumber_fs(
     Returns:
         NamedTuple of outputs (described in `VSumaRenumberFsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SUMA_RENUMBER_FS_METADATA)
     params = v__suma_renumber_fs_params(
         sumadir=sumadir,
     )
-    return v__suma_renumber_fs_execute(params, execution)
+    return v__suma_renumber_fs_execute(params, runner)
 
 
 __all__ = [
     "VSumaRenumberFsOutputs",
-    "VSumaRenumberFsParameters",
     "V__SUMA_RENUMBER_FS_METADATA",
     "v__suma_renumber_fs",
+    "v__suma_renumber_fs_execute",
     "v__suma_renumber_fs_params",
 ]

niwrap_afni/afni/v__suma_reprefixize_spec.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SUMA_REPREFIXIZE_SPEC_METADATA = Metadata(
-    id="a8545098535b72c07ad26ff409d12a14404e4007.boutiques",
+    id="6cfc02f203c0f727d55853e820f666475c263072.boutiques",
     name="@suma_reprefixize_spec",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,55 +14,29 @@ V__SUMA_REPREFIXIZE_SPEC_METADATA = Metadata(
 
 
 VSumaReprefixizeSpecParameters = typing.TypedDict('VSumaReprefixizeSpecParameters', {
-    "__STYXTYPE__": typing.Literal["@suma_reprefixize_spec"],
+    "@type": typing.NotRequired[typing.Literal["afni/@suma_reprefixize_spec"]],
+    "input_file": InputPathType,
+    "prefix": str,
+    "output_dir": str,
+    "work_dir": str,
+    "no_clean": bool,
+})
+VSumaReprefixizeSpecParametersTagged = typing.TypedDict('VSumaReprefixizeSpecParametersTagged', {
+    "@type": typing.Literal["afni/@suma_reprefixize_spec"],
     "input_file": InputPathType,
     "prefix": str,
     "output_dir": str,
     "work_dir": str,
     "no_clean": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@suma_reprefixize_spec": v__suma_reprefixize_spec_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 {
-        "@suma_reprefixize_spec": v__suma_reprefixize_spec_outputs,
-    }.get(t)
 
 
 class VSumaReprefixizeSpecOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__suma_reprefixize_spec(...)`.
+    Output object returned when calling `VSumaReprefixizeSpecParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    prefixed_spec_files: OutputPathType
-    """Prefixed SUMA specification files"""
 
 
 def v__suma_reprefixize_spec_params(
@@ -71,7 +45,7 @@ def v__suma_reprefixize_spec_params(
     output_dir: str,
     work_dir: str,
     no_clean: bool = False,
-) -> VSumaReprefixizeSpecParameters:
+) -> VSumaReprefixizeSpecParametersTagged:
     """
     Build parameters.
     
@@ -85,7 +59,7 @@ def v__suma_reprefixize_spec_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@suma_reprefixize_spec",
+        "@type": "afni/@suma_reprefixize_spec",
         "input_file": input_file,
         "prefix": prefix,
         "output_dir": output_dir,
@@ -112,21 +86,21 @@ def v__suma_reprefixize_spec_cargs(
     cargs.append("@suma_reprefixize_spec")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-preprefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-odir",
-        params.get("output_dir")
+        params.get("output_dir", None)
     ])
     cargs.extend([
         "-workdir",
-        params.get("work_dir")
+        params.get("work_dir", None)
     ])
-    if params.get("no_clean"):
+    if params.get("no_clean", False):
         cargs.append("-no_clean")
     return cargs
 
@@ -146,16 +120,17 @@ def v__suma_reprefixize_spec_outputs(
     """
     ret = VSumaReprefixizeSpecOutputs(
         root=execution.output_file("."),
-        prefixed_spec_files=execution.output_file(params.get("output_dir") + "/*.spec"),
     )
     return ret
 
 
 def v__suma_reprefixize_spec_execute(
     params: VSumaReprefixizeSpecParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSumaReprefixizeSpecOutputs:
     """
+    @suma_reprefixize_spec
+    
     A tool for prefixing and working with SUMA specification files.
     
     Author: AFNI Developers
@@ -164,10 +139,12 @@ def v__suma_reprefixize_spec_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSumaReprefixizeSpecOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_REPREFIXIZE_SPEC_METADATA)
     params = execution.params(params)
     cargs = v__suma_reprefixize_spec_cargs(params, execution)
     ret = v__suma_reprefixize_spec_outputs(params, execution)
@@ -184,6 +161,8 @@ def v__suma_reprefixize_spec(
     runner: Runner | None = None,
 ) -> VSumaReprefixizeSpecOutputs:
     """
+    @suma_reprefixize_spec
+    
     A tool for prefixing and working with SUMA specification files.
     
     Author: AFNI Developers
@@ -200,8 +179,6 @@ def v__suma_reprefixize_spec(
     Returns:
         NamedTuple of outputs (described in `VSumaReprefixizeSpecOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SUMA_REPREFIXIZE_SPEC_METADATA)
     params = v__suma_reprefixize_spec_params(
         input_file=input_file,
         prefix=prefix,
@@ -209,13 +186,13 @@ def v__suma_reprefixize_spec(
         work_dir=work_dir,
         no_clean=no_clean,
     )
-    return v__suma_reprefixize_spec_execute(params, execution)
+    return v__suma_reprefixize_spec_execute(params, runner)
 
 
 __all__ = [
     "VSumaReprefixizeSpecOutputs",
-    "VSumaReprefixizeSpecParameters",
     "V__SUMA_REPREFIXIZE_SPEC_METADATA",
     "v__suma_reprefixize_spec",
+    "v__suma_reprefixize_spec_execute",
     "v__suma_reprefixize_spec_params",
 ]

niwrap_afni/afni/v__surf_smooth_heat_07_examples.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA = Metadata(
-    id="dc0b150ee17a89e1651ca52dbda01cc2f717b438.boutiques",
+    id="e949214fe8e851ec50f03632f2968ca8d52d6359.boutiques",
     name="@SurfSmooth.HEAT_07.examples",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,45 +14,18 @@ V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA = Metadata(
 
 
 VSurfSmoothHeat07ExamplesParameters = typing.TypedDict('VSurfSmoothHeat07ExamplesParameters', {
-    "__STYXTYPE__": typing.Literal["@SurfSmooth.HEAT_07.examples"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SurfSmooth.HEAT_07.examples"]],
+    "path_to_suma_demo": str,
+})
+VSurfSmoothHeat07ExamplesParametersTagged = typing.TypedDict('VSurfSmoothHeat07ExamplesParametersTagged', {
+    "@type": typing.Literal["afni/@SurfSmooth.HEAT_07.examples"],
     "path_to_suma_demo": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@SurfSmooth.HEAT_07.examples": v__surf_smooth_heat_07_examples_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 VSurfSmoothHeat07ExamplesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__surf_smooth_heat_07_examples(...)`.
+    Output object returned when calling `VSurfSmoothHeat07ExamplesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -60,7 +33,7 @@ class VSurfSmoothHeat07ExamplesOutputs(typing.NamedTuple):
 
 def v__surf_smooth_heat_07_examples_params(
     path_to_suma_demo: str,
-) -> VSurfSmoothHeat07ExamplesParameters:
+) -> VSurfSmoothHeat07ExamplesParametersTagged:
     """
     Build parameters.
     
@@ -70,7 +43,7 @@ def v__surf_smooth_heat_07_examples_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SurfSmooth.HEAT_07.examples",
+        "@type": "afni/@SurfSmooth.HEAT_07.examples",
         "path_to_suma_demo": path_to_suma_demo,
     }
     return params
@@ -91,7 +64,7 @@ def v__surf_smooth_heat_07_examples_cargs(
     """
     cargs = []
     cargs.append("@SurfSmooth.HEAT_07.examples")
-    cargs.append(params.get("path_to_suma_demo"))
+    cargs.append(params.get("path_to_suma_demo", None))
     return cargs
 
 
@@ -116,9 +89,11 @@ def v__surf_smooth_heat_07_examples_outputs(
 
 def v__surf_smooth_heat_07_examples_execute(
     params: VSurfSmoothHeat07ExamplesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSurfSmoothHeat07ExamplesOutputs:
     """
+    @SurfSmooth.HEAT_07.examples
+    
     A script to illustrate controlled blurring of data on the surface.
     
     Author: AFNI Developers
@@ -127,10 +102,12 @@ def v__surf_smooth_heat_07_examples_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSurfSmoothHeat07ExamplesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA)
     params = execution.params(params)
     cargs = v__surf_smooth_heat_07_examples_cargs(params, execution)
     ret = v__surf_smooth_heat_07_examples_outputs(params, execution)
@@ -143,6 +120,8 @@ def v__surf_smooth_heat_07_examples(
     runner: Runner | None = None,
 ) -> VSurfSmoothHeat07ExamplesOutputs:
     """
+    @SurfSmooth.HEAT_07.examples
+    
     A script to illustrate controlled blurring of data on the surface.
     
     Author: AFNI Developers
@@ -155,18 +134,16 @@ def v__surf_smooth_heat_07_examples(
     Returns:
         NamedTuple of outputs (described in `VSurfSmoothHeat07ExamplesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA)
     params = v__surf_smooth_heat_07_examples_params(
         path_to_suma_demo=path_to_suma_demo,
     )
-    return v__surf_smooth_heat_07_examples_execute(params, execution)
+    return v__surf_smooth_heat_07_examples_execute(params, runner)
 
 
 __all__ = [
     "VSurfSmoothHeat07ExamplesOutputs",
-    "VSurfSmoothHeat07ExamplesParameters",
     "V__SURF_SMOOTH_HEAT_07_EXAMPLES_METADATA",
     "v__surf_smooth_heat_07_examples",
+    "v__surf_smooth_heat_07_examples_execute",
     "v__surf_smooth_heat_07_examples_params",
 ]