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

niwrap_afni/afni/v__suma_make_spec_caret.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SUMA_MAKE_SPEC_CARET_METADATA = Metadata(
-    id="9f583a038a94aad61db75157df703ae8d46fc78e.boutiques",
+    id="feaa100c7c92cb262519c13b181c1cebc4b05816.boutiques",
     name="@SUMA_Make_Spec_Caret",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V__SUMA_MAKE_SPEC_CARET_METADATA = Metadata(
 
 
 VSumaMakeSpecCaretParameters = typing.TypedDict('VSumaMakeSpecCaretParameters', {
-    "__STYXTYPE__": typing.Literal["@SUMA_Make_Spec_Caret"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SUMA_Make_Spec_Caret"]],
+    "subject_id": str,
+    "help": bool,
+    "debug": typing.NotRequired[int | None],
+    "echo": bool,
+    "surface_path": typing.NotRequired[str | None],
+    "side_labels_style": typing.NotRequired[int | None],
+})
+VSumaMakeSpecCaretParametersTagged = typing.TypedDict('VSumaMakeSpecCaretParametersTagged', {
+    "@type": typing.Literal["afni/@SUMA_Make_Spec_Caret"],
     "subject_id": str,
     "help": bool,
     "debug": typing.NotRequired[int | None],
@@ -22,43 +31,11 @@ VSumaMakeSpecCaretParameters = typing.TypedDict('VSumaMakeSpecCaretParameters',
     "surface_path": typing.NotRequired[str | None],
     "side_labels_style": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@SUMA_Make_Spec_Caret": v__suma_make_spec_caret_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_Make_Spec_Caret": v__suma_make_spec_caret_outputs,
-    }.get(t)
 
 
 class VSumaMakeSpecCaretOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__suma_make_spec_caret(...)`.
+    Output object returned when calling `VSumaMakeSpecCaretParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v__suma_make_spec_caret_params(
     echo: bool = False,
     surface_path: str | None = None,
     side_labels_style: int | None = None,
-) -> VSumaMakeSpecCaretParameters:
+) -> VSumaMakeSpecCaretParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def v__suma_make_spec_caret_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SUMA_Make_Spec_Caret",
+        "@type": "afni/@SUMA_Make_Spec_Caret",
         "subject_id": subject_id,
         "help": help_,
         "echo": echo,
@@ -123,26 +100,26 @@ def v__suma_make_spec_caret_cargs(
     cargs.append("@SUMA_Make_Spec_Caret")
     cargs.extend([
         "-sid",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("echo"):
+    if params.get("echo", False):
         cargs.append("-echo")
-    if params.get("surface_path") is not None:
+    if params.get("surface_path", None) is not None:
         cargs.extend([
             "-sfpath",
-            params.get("surface_path")
+            params.get("surface_path", None)
         ])
-    if params.get("side_labels_style") is not None:
+    if params.get("side_labels_style", None) is not None:
         cargs.extend([
             "-side_labels_style",
-            str(params.get("side_labels_style"))
+            str(params.get("side_labels_style", None))
         ])
     return cargs
 
@@ -162,17 +139,19 @@ def v__suma_make_spec_caret_outputs(
     """
     ret = VSumaMakeSpecCaretOutputs(
         root=execution.output_file("."),
-        left_hemisphere_spec=execution.output_file(params.get("subject_id") + "_lh.spec"),
-        right_hemisphere_spec=execution.output_file(params.get("subject_id") + "_rh.spec"),
+        left_hemisphere_spec=execution.output_file(params.get("subject_id", None) + "_lh.spec"),
+        right_hemisphere_spec=execution.output_file(params.get("subject_id", None) + "_rh.spec"),
     )
     return ret
 
 
 def v__suma_make_spec_caret_execute(
     params: VSumaMakeSpecCaretParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSumaMakeSpecCaretOutputs:
     """
+    @SUMA_Make_Spec_Caret
+    
     Prepare surfaces for viewing in SUMA, tested with Caret-5.2 surfaces.
     
     Author: AFNI Developers
@@ -181,10 +160,12 @@ def v__suma_make_spec_caret_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecCaretOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_MAKE_SPEC_CARET_METADATA)
     params = execution.params(params)
     cargs = v__suma_make_spec_caret_cargs(params, execution)
     ret = v__suma_make_spec_caret_outputs(params, execution)
@@ -202,6 +183,8 @@ def v__suma_make_spec_caret(
     runner: Runner | None = None,
 ) -> VSumaMakeSpecCaretOutputs:
     """
+    @SUMA_Make_Spec_Caret
+    
     Prepare surfaces for viewing in SUMA, tested with Caret-5.2 surfaces.
     
     Author: AFNI Developers
@@ -221,8 +204,6 @@ def v__suma_make_spec_caret(
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecCaretOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SUMA_MAKE_SPEC_CARET_METADATA)
     params = v__suma_make_spec_caret_params(
         subject_id=subject_id,
         help_=help_,
@@ -231,13 +212,13 @@ def v__suma_make_spec_caret(
         surface_path=surface_path,
         side_labels_style=side_labels_style,
     )
-    return v__suma_make_spec_caret_execute(params, execution)
+    return v__suma_make_spec_caret_execute(params, runner)
 
 
 __all__ = [
     "VSumaMakeSpecCaretOutputs",
-    "VSumaMakeSpecCaretParameters",
     "V__SUMA_MAKE_SPEC_CARET_METADATA",
     "v__suma_make_spec_caret",
+    "v__suma_make_spec_caret_execute",
     "v__suma_make_spec_caret_params",
 ]

niwrap_afni/afni/v__suma_make_spec_fs.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SUMA_MAKE_SPEC_FS_METADATA = Metadata(
-    id="10445ccc3d3a66bb5ebcc9fc5b2ee7040da06041.boutiques",
+    id="3293dfa2ded1817daff81673a2443e32143e7a7b.boutiques",
     name="@SUMA_Make_Spec_FS",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,26 @@ V__SUMA_MAKE_SPEC_FS_METADATA = Metadata(
 
 
 VSumaMakeSpecFsParameters = typing.TypedDict('VSumaMakeSpecFsParameters', {
-    "__STYXTYPE__": typing.Literal["@SUMA_Make_Spec_FS"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SUMA_Make_Spec_FS"]],
+    "subject_id": str,
+    "debug": typing.NotRequired[int | None],
+    "fs_setup": bool,
+    "filesystem_path": typing.NotRequired[str | None],
+    "extra_annot_labels": typing.NotRequired[list[str] | None],
+    "extra_fs_dsets": typing.NotRequired[list[str] | None],
+    "make_rank_dsets": bool,
+    "use_mgz": bool,
+    "neuro": bool,
+    "gnifti": bool,
+    "nifti": bool,
+    "inflate": typing.NotRequired[float | None],
+    "set_space": typing.NotRequired[str | None],
+    "ld": typing.NotRequired[float | None],
+    "ldpref": typing.NotRequired[str | None],
+    "no_ld": bool,
+})
+VSumaMakeSpecFsParametersTagged = typing.TypedDict('VSumaMakeSpecFsParametersTagged', {
+    "@type": typing.Literal["afni/@SUMA_Make_Spec_FS"],
     "subject_id": str,
     "debug": typing.NotRequired[int | None],
     "fs_setup": bool,
@@ -32,47 +51,15 @@ VSumaMakeSpecFsParameters = typing.TypedDict('VSumaMakeSpecFsParameters', {
     "ldpref": typing.NotRequired[str | None],
     "no_ld": 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_Make_Spec_FS": v__suma_make_spec_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_Make_Spec_FS": v__suma_make_spec_fs_outputs,
-    }.get(t)
 
 
 class VSumaMakeSpecFsOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__suma_make_spec_fs(...)`.
+    Output object returned when calling `VSumaMakeSpecFsParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    suma_output: OutputPathType
+    suma_output_dir: OutputPathType
     """All created files are stored in a new SUMA directory"""
 
 
@@ -93,7 +80,7 @@ def v__suma_make_spec_fs_params(
     ld: float | None = None,
     ldpref: str | None = None,
     no_ld: bool = False,
-) -> VSumaMakeSpecFsParameters:
+) -> VSumaMakeSpecFsParametersTagged:
     """
     Build parameters.
     
@@ -124,7 +111,7 @@ def v__suma_make_spec_fs_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SUMA_Make_Spec_FS",
+        "@type": "afni/@SUMA_Make_Spec_FS",
         "subject_id": subject_id,
         "fs_setup": fs_setup,
         "make_rank_dsets": make_rank_dsets,
@@ -170,61 +157,61 @@ def v__suma_make_spec_fs_cargs(
     cargs.append("@SUMA_Make_Spec_FS")
     cargs.extend([
         "-sid",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
-    if params.get("debug") is not None:
+    if params.get("debug", None) is not None:
         cargs.extend([
             "-debug",
-            str(params.get("debug"))
+            str(params.get("debug", None))
         ])
-    if params.get("fs_setup"):
+    if params.get("fs_setup", False):
         cargs.append("-fs_setup")
-    if params.get("filesystem_path") is not None:
+    if params.get("filesystem_path", None) is not None:
         cargs.extend([
             "-fspath",
-            params.get("filesystem_path")
+            params.get("filesystem_path", None)
         ])
-    if params.get("extra_annot_labels") is not None:
+    if params.get("extra_annot_labels", None) is not None:
         cargs.extend([
             "-extra_annot_labels",
-            *params.get("extra_annot_labels")
+            *params.get("extra_annot_labels", None)
         ])
-    if params.get("extra_fs_dsets") is not None:
+    if params.get("extra_fs_dsets", None) is not None:
         cargs.extend([
             "-extra_fs_dsets",
-            *params.get("extra_fs_dsets")
+            *params.get("extra_fs_dsets", None)
         ])
-    if params.get("make_rank_dsets"):
+    if params.get("make_rank_dsets", False):
         cargs.append("-make_rank_dsets")
-    if params.get("use_mgz"):
+    if params.get("use_mgz", False):
         cargs.append("-use_mgz")
-    if params.get("neuro"):
+    if params.get("neuro", False):
         cargs.append("-neuro")
-    if params.get("gnifti"):
+    if params.get("gnifti", False):
         cargs.append("-GNIFTI")
-    if params.get("nifti"):
+    if params.get("nifti", False):
         cargs.append("-NIFTI")
-    if params.get("inflate") is not None:
+    if params.get("inflate", None) is not None:
         cargs.extend([
             "-inflate",
-            str(params.get("inflate"))
+            str(params.get("inflate", None))
         ])
-    if params.get("set_space") is not None:
+    if params.get("set_space", None) is not None:
         cargs.extend([
             "-set_space",
-            params.get("set_space")
+            params.get("set_space", None)
         ])
-    if params.get("ld") is not None:
+    if params.get("ld", None) is not None:
         cargs.extend([
             "-ld",
-            str(params.get("ld"))
+            str(params.get("ld", None))
         ])
-    if params.get("ldpref") is not None:
+    if params.get("ldpref", None) is not None:
         cargs.extend([
             "-ldpref",
-            params.get("ldpref")
+            params.get("ldpref", None)
         ])
-    if params.get("no_ld"):
+    if params.get("no_ld", False):
         cargs.append("-no_ld")
     return cargs
 
@@ -244,16 +231,18 @@ def v__suma_make_spec_fs_outputs(
     """
     ret = VSumaMakeSpecFsOutputs(
         root=execution.output_file("."),
-        suma_output=execution.output_file("SUMA/*"),
+        suma_output_dir=execution.output_file("SUMA"),
     )
     return ret
 
 
 def v__suma_make_spec_fs_execute(
     params: VSumaMakeSpecFsParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSumaMakeSpecFsOutputs:
     """
+    @SUMA_Make_Spec_FS
+    
     Prepare for surface viewing in SUMA.
     
     Author: AFNI Developers
@@ -262,10 +251,12 @@ def v__suma_make_spec_fs_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecFsOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_MAKE_SPEC_FS_METADATA)
     params = execution.params(params)
     cargs = v__suma_make_spec_fs_cargs(params, execution)
     ret = v__suma_make_spec_fs_outputs(params, execution)
@@ -293,6 +284,8 @@ def v__suma_make_spec_fs(
     runner: Runner | None = None,
 ) -> VSumaMakeSpecFsOutputs:
     """
+    @SUMA_Make_Spec_FS
+    
     Prepare for surface viewing in SUMA.
     
     Author: AFNI Developers
@@ -326,8 +319,6 @@ def v__suma_make_spec_fs(
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecFsOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SUMA_MAKE_SPEC_FS_METADATA)
     params = v__suma_make_spec_fs_params(
         subject_id=subject_id,
         debug=debug,
@@ -346,13 +337,13 @@ def v__suma_make_spec_fs(
         ldpref=ldpref,
         no_ld=no_ld,
     )
-    return v__suma_make_spec_fs_execute(params, execution)
+    return v__suma_make_spec_fs_execute(params, runner)
 
 
 __all__ = [
     "VSumaMakeSpecFsOutputs",
-    "VSumaMakeSpecFsParameters",
     "V__SUMA_MAKE_SPEC_FS_METADATA",
     "v__suma_make_spec_fs",
+    "v__suma_make_spec_fs_execute",
     "v__suma_make_spec_fs_params",
 ]

niwrap_afni/afni/v__suma_make_spec_sf.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SUMA_MAKE_SPEC_SF_METADATA = Metadata(
-    id="b2f1fc4d123e03415cf587f26d4d91d1d54dd486.boutiques",
+    id="2e386638a118532e0161e64bba78fad27856fccb.boutiques",
     name="@SUMA_Make_Spec_SF",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,52 +14,26 @@ V__SUMA_MAKE_SPEC_SF_METADATA = Metadata(
 
 
 VSumaMakeSpecSfParameters = typing.TypedDict('VSumaMakeSpecSfParameters', {
-    "__STYXTYPE__": typing.Literal["@SUMA_Make_Spec_SF"],
+    "@type": typing.NotRequired[typing.Literal["afni/@SUMA_Make_Spec_SF"]],
+    "debug_level": typing.NotRequired[int | None],
+    "surface_path": typing.NotRequired[str | None],
+    "subject_id": str,
+})
+VSumaMakeSpecSfParametersTagged = typing.TypedDict('VSumaMakeSpecSfParametersTagged', {
+    "@type": typing.Literal["afni/@SUMA_Make_Spec_SF"],
     "debug_level": typing.NotRequired[int | None],
     "surface_path": typing.NotRequired[str | None],
     "subject_id": 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_Make_Spec_SF": v__suma_make_spec_sf_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_Make_Spec_SF": v__suma_make_spec_sf_outputs,
-    }.get(t)
 
 
 class VSumaMakeSpecSfOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__suma_make_spec_sf(...)`.
+    Output object returned when calling `VSumaMakeSpecSfParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_files: OutputPathType
+    output_directory: OutputPathType
     """All created files are stored in SURFACES directory"""
 
 
@@ -67,7 +41,7 @@ def v__suma_make_spec_sf_params(
     subject_id: str,
     debug_level: int | None = None,
     surface_path: str | None = None,
-) -> VSumaMakeSpecSfParameters:
+) -> VSumaMakeSpecSfParametersTagged:
     """
     Build parameters.
     
@@ -80,7 +54,7 @@ def v__suma_make_spec_sf_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@SUMA_Make_Spec_SF",
+        "@type": "afni/@SUMA_Make_Spec_SF",
         "subject_id": subject_id,
     }
     if debug_level is not None:
@@ -105,19 +79,19 @@ def v__suma_make_spec_sf_cargs(
     """
     cargs = []
     cargs.append("@SUMA_Make_Spec_SF")
-    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("surface_path") is not None:
+    if params.get("surface_path", None) is not None:
         cargs.extend([
             "-sfpath",
-            params.get("surface_path")
+            params.get("surface_path", None)
         ])
     cargs.extend([
         "-sid",
-        params.get("subject_id")
+        params.get("subject_id", None)
     ])
     return cargs
 
@@ -137,16 +111,18 @@ def v__suma_make_spec_sf_outputs(
     """
     ret = VSumaMakeSpecSfOutputs(
         root=execution.output_file("."),
-        output_files=execution.output_file("SURFACES/*"),
+        output_directory=execution.output_file("SURFACES"),
     )
     return ret
 
 
 def v__suma_make_spec_sf_execute(
     params: VSumaMakeSpecSfParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VSumaMakeSpecSfOutputs:
     """
+    @SUMA_Make_Spec_SF
+    
     Prepare for surface viewing in SUMA.
     
     Author: AFNI Developers
@@ -155,10 +131,12 @@ def v__suma_make_spec_sf_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecSfOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__SUMA_MAKE_SPEC_SF_METADATA)
     params = execution.params(params)
     cargs = v__suma_make_spec_sf_cargs(params, execution)
     ret = v__suma_make_spec_sf_outputs(params, execution)
@@ -173,6 +151,8 @@ def v__suma_make_spec_sf(
     runner: Runner | None = None,
 ) -> VSumaMakeSpecSfOutputs:
     """
+    @SUMA_Make_Spec_SF
+    
     Prepare for surface viewing in SUMA.
     
     Author: AFNI Developers
@@ -188,20 +168,18 @@ def v__suma_make_spec_sf(
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecSfOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__SUMA_MAKE_SPEC_SF_METADATA)
     params = v__suma_make_spec_sf_params(
         debug_level=debug_level,
         surface_path=surface_path,
         subject_id=subject_id,
     )
-    return v__suma_make_spec_sf_execute(params, execution)
+    return v__suma_make_spec_sf_execute(params, runner)
 
 
 __all__ = [
     "VSumaMakeSpecSfOutputs",
-    "VSumaMakeSpecSfParameters",
     "V__SUMA_MAKE_SPEC_SF_METADATA",
     "v__suma_make_spec_sf",
+    "v__suma_make_spec_sf_execute",
     "v__suma_make_spec_sf_params",
 ]