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

niwrap_afni/afni/v__spharm_examples.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SPHARM_EXAMPLES_METADATA = Metadata(
-    id="4b0f2ed5a72a84bddb5e61fd3628bb505b66adab.boutiques",
+    id="5cd459e94bc6d1e20183d3aa7e19374116713404.boutiques",
     name="@Spharm.examples",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__SPHARM_EXAMPLES_METADATA = Metadata(
 
 
 VSpharmExamplesParameters = typing.TypedDict('VSpharmExamplesParameters', {
-    "__STYXTYPE__": typing.Literal["@Spharm.examples"],
+    "@type": typing.NotRequired[typing.Literal["afni/@Spharm.examples"]],
+    "help_web": bool,
+    "help_web_alias": bool,
+    "help_view": bool,
+    "help_view_alias": bool,
+    "all_opts": bool,
+    "help_find": typing.NotRequired[str | None],
+})
+VSpharmExamplesParametersTagged = typing.TypedDict('VSpharmExamplesParametersTagged', {
+    "@type": typing.Literal["afni/@Spharm.examples"],
     "help_web": bool,
     "help_web_alias": bool,
     "help_view": bool,
@@ -22,42 +31,11 @@ VSpharmExamplesParameters = typing.TypedDict('VSpharmExamplesParameters', {
     "all_opts": bool,
     "help_find": 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 {
-        "@Spharm.examples": v__spharm_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 VSpharmExamplesOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__spharm_examples(...)`.
+    Output object returned when calling `VSpharmExamplesParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -70,7 +48,7 @@ def v__spharm_examples_params(
     help_view_alias: bool = False,
     all_opts: bool = False,
     help_find: str | None = None,
-) -> VSpharmExamplesParameters:
+) -> VSpharmExamplesParametersTagged:
     """
     Build parameters.
     
@@ -86,7 +64,7 @@ def v__spharm_examples_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@Spharm.examples",
+        "@type": "afni/@Spharm.examples",
         "help_web": help_web,
         "help_web_alias": help_web_alias,
         "help_view": help_view,
@@ -113,20 +91,20 @@ def v__spharm_examples_cargs(
     """
     cargs = []
     cargs.append("@Spharm.examples")
-    if params.get("help_web"):
+    if params.get("help_web", False):
         cargs.append("-h_web")
-    if params.get("help_web_alias"):
+    if params.get("help_web_alias", False):
         cargs.append("-hweb")
-    if params.get("help_view"):
+    if params.get("help_view", False):
         cargs.append("-h_view")
-    if params.get("help_view_alias"):
+    if params.get("help_view_alias", False):
         cargs.append("-hview")
-    if params.get("all_opts"):
+    if params.get("all_opts", False):
         cargs.append("-all_opts")
-    if params.get("help_find") is not None:
+    if params.get("help_find", None) is not None:
         cargs.extend([
             "-h_find",
-            params.get("help_find")
+            params.get("help_find", None)
         ])
     return cargs
 
@@ -152,9 +130,11 @@ def v__spharm_examples_outputs(
 
 def v__spharm_examples_execute(
     params: VSpharmExamplesParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSpharmExamplesOutputs:
     """
+    @Spharm.examples
+    
     A script to demonstrate the usage of spherical harmonics decomposition with
     SUMA.
     
@@ -164,10 +144,12 @@ def v__spharm_examples_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSpharmExamplesOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SPHARM_EXAMPLES_METADATA)
     params = execution.params(params)
     cargs = v__spharm_examples_cargs(params, execution)
     ret = v__spharm_examples_outputs(params, execution)
@@ -185,6 +167,8 @@ def v__spharm_examples(
     runner: Runner | None = None,
 ) -> VSpharmExamplesOutputs:
     """
+    @Spharm.examples
+    
     A script to demonstrate the usage of spherical harmonics decomposition with
     SUMA.
     
@@ -204,8 +188,6 @@ def v__spharm_examples(
     Returns:
         NamedTuple of outputs (described in `VSpharmExamplesOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SPHARM_EXAMPLES_METADATA)
     params = v__spharm_examples_params(
         help_web=help_web,
         help_web_alias=help_web_alias,
@@ -214,13 +196,13 @@ def v__spharm_examples(
         all_opts=all_opts,
         help_find=help_find,
     )
-    return v__spharm_examples_execute(params, execution)
+    return v__spharm_examples_execute(params, runner)
 
 
 __all__ = [
     "VSpharmExamplesOutputs",
-    "VSpharmExamplesParameters",
     "V__SPHARM_EXAMPLES_METADATA",
     "v__spharm_examples",
+    "v__spharm_examples_execute",
     "v__spharm_examples_params",
 ]

niwrap_afni/afni/v__sswarper.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SSWARPER_METADATA = Metadata(
-    id="55de91c2c71be7a93c0be727ede67f8d0b90d4a4.boutiques",
+    id="d4ebdeaeea809f80db5dae831f358eb95225158b.boutiques",
     name="@SSwarper",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,33 @@ V__SSWARPER_METADATA = Metadata(
 
 
 VSswarperParameters = typing.TypedDict('VSswarperParameters', {
-    "__STYXTYPE__": typing.Literal["@SSwarper"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SSwarper"]],
+    "input_file": InputPathType,
+    "base_template": InputPathType,
+    "subject_id": str,
+    "output_dir": typing.NotRequired[str | None],
+    "min_patch_size": typing.NotRequired[float | None],
+    "no_lite": bool,
+    "skip_warp": bool,
+    "unifize_off": bool,
+    "init_skullstr_off": bool,
+    "extra_qc_off": bool,
+    "jump_to_extra_qc": bool,
+    "cost_nl_init": typing.NotRequired[str | None],
+    "cost_nl_final": typing.NotRequired[str | None],
+    "deoblique": bool,
+    "deoblique_refitly": bool,
+    "warp_scale": typing.NotRequired[float | None],
+    "ssopt_flag": typing.NotRequired[str | None],
+    "aniso_off": bool,
+    "ceil_off": bool,
+    "tmp_name_nice": bool,
+    "echo": bool,
+    "verbose": bool,
+    "noclean": bool,
+})
+VSswarperParametersTagged = typing.TypedDict('VSswarperParametersTagged', {
+    "@type": typing.Literal["afni/@SSwarper"],
     "input_file": InputPathType,
     "base_template": InputPathType,
     "subject_id": str,
@@ -39,43 +65,11 @@ VSswarperParameters = typing.TypedDict('VSswarperParameters', {
     "verbose": bool,
     "noclean": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@SSwarper": v__sswarper_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 {
-        "@SSwarper": v__sswarper_outputs,
-    }.get(t)
 
 
 class VSswarperOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__sswarper(...)`.
+    Output object returned when calling `VSswarperParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -136,7 +130,7 @@ def v__sswarper_params(
     echo: bool = False,
     verbose: bool = False,
     noclean: bool = False,
-) -> VSswarperParameters:
+) -> VSswarperParametersTagged:
     """
     Build parameters.
     
@@ -176,7 +170,7 @@ def v__sswarper_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SSwarper",
+        "@type": "afni/@SSwarper",
         "input_file": input_file,
         "base_template": base_template,
         "subject_id": subject_id,
@@ -227,73 +221,73 @@ def v__sswarper_cargs(
     cargs.append("@SSwarper")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-base",
-        execution.input_file(params.get("base_template"))
+        execution.input_file(params.get("base_template", None))
     ])
     cargs.extend([
         "-subid",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
-    if params.get("output_dir") is not None:
+    if params.get("output_dir", None) is not None:
         cargs.extend([
             "-odir",
-            params.get("output_dir")
+            params.get("output_dir", None)
         ])
-    if params.get("min_patch_size") is not None:
+    if params.get("min_patch_size", None) is not None:
         cargs.extend([
             "-minp",
-            str(params.get("min_patch_size"))
+            str(params.get("min_patch_size", None))
         ])
-    if params.get("no_lite"):
+    if params.get("no_lite", False):
         cargs.append("-nolite")
-    if params.get("skip_warp"):
+    if params.get("skip_warp", False):
         cargs.append("-skipwarp")
-    if params.get("unifize_off"):
+    if params.get("unifize_off", False):
         cargs.append("-unifize_off")
-    if params.get("init_skullstr_off"):
+    if params.get("init_skullstr_off", False):
         cargs.append("-init_skullstr_off")
-    if params.get("extra_qc_off"):
+    if params.get("extra_qc_off", False):
         cargs.append("-extra_qc_off")
-    if params.get("jump_to_extra_qc"):
+    if params.get("jump_to_extra_qc", False):
         cargs.append("-jump_to_extra_qc")
-    if params.get("cost_nl_init") is not None:
+    if params.get("cost_nl_init", None) is not None:
         cargs.extend([
             "-cost_nl_init",
-            params.get("cost_nl_init")
+            params.get("cost_nl_init", None)
         ])
-    if params.get("cost_nl_final") is not None:
+    if params.get("cost_nl_final", None) is not None:
         cargs.extend([
             "-cost_nl_final",
-            params.get("cost_nl_final")
+            params.get("cost_nl_final", None)
         ])
-    if params.get("deoblique"):
+    if params.get("deoblique", False):
         cargs.append("-deoblique")
-    if params.get("deoblique_refitly"):
+    if params.get("deoblique_refitly", False):
         cargs.append("-deoblique_refitly")
-    if params.get("warp_scale") is not None:
+    if params.get("warp_scale", None) is not None:
         cargs.extend([
             "-warpscale",
-            str(params.get("warp_scale"))
+            str(params.get("warp_scale", None))
         ])
-    if params.get("ssopt_flag") is not None:
+    if params.get("ssopt_flag", None) is not None:
         cargs.extend([
             "-SSopt",
-            params.get("ssopt_flag")
+            params.get("ssopt_flag", None)
         ])
-    if params.get("aniso_off"):
+    if params.get("aniso_off", False):
         cargs.append("-aniso_off")
-    if params.get("ceil_off"):
+    if params.get("ceil_off", False):
         cargs.append("-ceil_off")
-    if params.get("tmp_name_nice"):
+    if params.get("tmp_name_nice", False):
         cargs.append("-tmp_name_nice")
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("noclean"):
+    if params.get("noclean", False):
         cargs.append("-noclean")
     return cargs
 
@@ -313,19 +307,19 @@ def v__sswarper_outputs(
     """
     ret = VSswarperOutputs(
         root=execution.output_file("."),
-        anat_do=execution.output_file("anatDO." + params.get("subject_id") + ".nii"),
-        anat_u=execution.output_file("anatU." + params.get("subject_id") + ".nii"),
-        anat_ua=execution.output_file("anatUA." + params.get("subject_id") + ".nii"),
-        anat_uac=execution.output_file("anatUAC." + params.get("subject_id") + ".nii"),
-        anat_s=execution.output_file("anatS." + params.get("subject_id") + ".nii"),
-        anat_ss=execution.output_file("anatSS." + params.get("subject_id") + ".nii"),
-        anat_qq=execution.output_file("anatQQ." + params.get("subject_id") + ".nii"),
-        anat_qq_affine=execution.output_file("anatQQ." + params.get("subject_id") + ".aff12.1D"),
-        anat_qq_warp=execution.output_file("anatQQ." + params.get("subject_id") + "_WARP.nii"),
-        am_snapshot=execution.output_file("AM" + params.get("subject_id") + ".jpg"),
-        ma_snapshot=execution.output_file("MA" + params.get("subject_id") + ".jpg"),
-        qc_anat_qq=execution.output_file("QC_anatQQ." + params.get("subject_id") + ".jpg"),
-        qc_anat_ss=execution.output_file("QC_anatSS." + params.get("subject_id") + ".jpg"),
+        anat_do=execution.output_file("anatDO." + params.get("subject_id", None) + ".nii"),
+        anat_u=execution.output_file("anatU." + params.get("subject_id", None) + ".nii"),
+        anat_ua=execution.output_file("anatUA." + params.get("subject_id", None) + ".nii"),
+        anat_uac=execution.output_file("anatUAC." + params.get("subject_id", None) + ".nii"),
+        anat_s=execution.output_file("anatS." + params.get("subject_id", None) + ".nii"),
+        anat_ss=execution.output_file("anatSS." + params.get("subject_id", None) + ".nii"),
+        anat_qq=execution.output_file("anatQQ." + params.get("subject_id", None) + ".nii"),
+        anat_qq_affine=execution.output_file("anatQQ." + params.get("subject_id", None) + ".aff12.1D"),
+        anat_qq_warp=execution.output_file("anatQQ." + params.get("subject_id", None) + "_WARP.nii"),
+        am_snapshot=execution.output_file("AM" + params.get("subject_id", None) + ".jpg"),
+        ma_snapshot=execution.output_file("MA" + params.get("subject_id", None) + ".jpg"),
+        qc_anat_qq=execution.output_file("QC_anatQQ." + params.get("subject_id", None) + ".jpg"),
+        qc_anat_ss=execution.output_file("QC_anatSS." + params.get("subject_id", None) + ".jpg"),
         init_overlap_qc=execution.output_file("init_qc_00_overlap_uinp_obase.jpg"),
     )
     return ret
@@ -333,11 +327,14 @@ def v__sswarper_outputs(
 
 def v__sswarper_execute(
     params: VSswarperParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSswarperOutputs:
     """
-    Dual purposes for processing a given subject's anatomical volume: skull-strip
-    the brain and calculate the warp to a reference template/standard space.
+    @SSwarper
+    
+    Dual purposes for processing a given subject's anatomical volume:
+    skull-strip the brain and calculate the warp to a reference
+    template/standard space.
     
     Author: AFNI Developers
     
@@ -345,10 +342,12 @@ def v__sswarper_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSswarperOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SSWARPER_METADATA)
     params = execution.params(params)
     cargs = v__sswarper_cargs(params, execution)
     ret = v__sswarper_outputs(params, execution)
@@ -383,8 +382,11 @@ def v__sswarper(
     runner: Runner | None = None,
 ) -> VSswarperOutputs:
     """
-    Dual purposes for processing a given subject's anatomical volume: skull-strip
-    the brain and calculate the warp to a reference template/standard space.
+    @SSwarper
+    
+    Dual purposes for processing a given subject's anatomical volume:
+    skull-strip the brain and calculate the warp to a reference
+    template/standard space.
     
     Author: AFNI Developers
     
@@ -426,8 +428,6 @@ def v__sswarper(
     Returns:
         NamedTuple of outputs (described in `VSswarperOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SSWARPER_METADATA)
     params = v__sswarper_params(
         input_file=input_file,
         base_template=base_template,
@@ -453,13 +453,13 @@ def v__sswarper(
         verbose=verbose,
         noclean=noclean,
     )
-    return v__sswarper_execute(params, execution)
+    return v__sswarper_execute(params, runner)
 
 
 __all__ = [
     "VSswarperOutputs",
-    "VSswarperParameters",
     "V__SSWARPER_METADATA",
     "v__sswarper",
+    "v__sswarper_execute",
     "v__sswarper_params",
 ]

niwrap_afni/afni/v__statauxcode.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__STATAUXCODE_METADATA = Metadata(
-    id="ef385d8519f887dde3897dff25a19db608549dca.boutiques",
+    id="f249ed207b146f32e78b50fa7123b4ea024d66ee.boutiques",
     name="@statauxcode",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,18 @@ V__STATAUXCODE_METADATA = Metadata(
 
 
 VStatauxcodeParameters = typing.TypedDict('VStatauxcodeParameters', {
-    "__STYXTYPE__": typing.Literal["@statauxcode"],
+    "@type": typing.NotRequired[typing.Literal["afni/@statauxcode"]],
+    "code": str,
+})
+VStatauxcodeParametersTagged = typing.TypedDict('VStatauxcodeParametersTagged', {
+    "@type": typing.Literal["afni/@statauxcode"],
     "code": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@statauxcode": v__statauxcode_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 {
-        "@statauxcode": v__statauxcode_outputs,
-    }.get(t)
 
 
 class VStatauxcodeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__statauxcode(...)`.
+    Output object returned when calling `VStatauxcodeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -63,7 +35,7 @@ class VStatauxcodeOutputs(typing.NamedTuple):
 
 def v__statauxcode_params(
     code_: str,
-) -> VStatauxcodeParameters:
+) -> VStatauxcodeParametersTagged:
     """
     Build parameters.
     
@@ -74,7 +46,7 @@ def v__statauxcode_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@statauxcode",
+        "@type": "afni/@statauxcode",
         "code": code_,
     }
     return params
@@ -95,7 +67,7 @@ def v__statauxcode_cargs(
     """
     cargs = []
     cargs.append("@statauxcode")
-    cargs.append(params.get("code"))
+    cargs.append(params.get("code", None))
     return cargs
 
 
@@ -121,9 +93,11 @@ def v__statauxcode_outputs(
 
 def v__statauxcode_execute(
     params: VStatauxcodeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VStatauxcodeOutputs:
     """
+    @statauxcode
+    
     Returns the name or number of a statistics code based on specified mappings.
     
     Author: AFNI Developers
@@ -132,10 +106,12 @@ def v__statauxcode_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VStatauxcodeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__STATAUXCODE_METADATA)
     params = execution.params(params)
     cargs = v__statauxcode_cargs(params, execution)
     ret = v__statauxcode_outputs(params, execution)
@@ -148,6 +124,8 @@ def v__statauxcode(
     runner: Runner | None = None,
 ) -> VStatauxcodeOutputs:
     """
+    @statauxcode
+    
     Returns the name or number of a statistics code based on specified mappings.
     
     Author: AFNI Developers
@@ -161,18 +139,16 @@ def v__statauxcode(
     Returns:
         NamedTuple of outputs (described in `VStatauxcodeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__STATAUXCODE_METADATA)
     params = v__statauxcode_params(
         code_=code_,
     )
-    return v__statauxcode_execute(params, execution)
+    return v__statauxcode_execute(params, runner)
 
 
 __all__ = [
     "VStatauxcodeOutputs",
-    "VStatauxcodeParameters",
     "V__STATAUXCODE_METADATA",
     "v__statauxcode",
+    "v__statauxcode_execute",
     "v__statauxcode_params",
 ]