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

niwrap_afni/afni/v__rename_panga.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__RENAME_PANGA_METADATA = Metadata(
-    id="667fb48aeb92a9756a0ac4f7c1ba77ceb5554bab.boutiques",
+    id="f6ac5e008e4d183c833a40c6cb0ed7f8a09bb03c.boutiques",
     name="@RenamePanga",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ V__RENAME_PANGA_METADATA = Metadata(
 
 
 VRenamePangaParameters = typing.TypedDict('VRenamePangaParameters', {
-    "__STYXTYPE__": typing.Literal["@RenamePanga"],
+    "@type": typing.NotRequired[typing.Literal["afni/@RenamePanga"]],
+    "dir_number": str,
+    "first_image_number": str,
+    "num_slices": float,
+    "num_reps": float,
+    "output_root": str,
+    "keep_prefix": bool,
+    "interactive": bool,
+    "outliers_check": bool,
+    "slice_pattern": typing.NotRequired[str | None],
+    "output_directory": typing.NotRequired[str | None],
+})
+VRenamePangaParametersTagged = typing.TypedDict('VRenamePangaParametersTagged', {
+    "@type": typing.Literal["afni/@RenamePanga"],
     "dir_number": str,
     "first_image_number": str,
     "num_slices": float,
@@ -26,43 +39,11 @@ VRenamePangaParameters = typing.TypedDict('VRenamePangaParameters', {
     "slice_pattern": typing.NotRequired[str | None],
     "output_directory": 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 {
-        "@RenamePanga": v__rename_panga_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 {
-        "@RenamePanga": v__rename_panga_outputs,
-    }.get(t)
 
 
 class VRenamePangaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__rename_panga(...)`.
+    Output object returned when calling `VRenamePangaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +66,7 @@ def v__rename_panga_params(
     outliers_check: bool = False,
     slice_pattern: str | None = None,
     output_directory: str | None = None,
-) -> VRenamePangaParameters:
+) -> VRenamePangaParametersTagged:
     """
     Build parameters.
     
@@ -110,7 +91,7 @@ def v__rename_panga_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@RenamePanga",
+        "@type": "afni/@RenamePanga",
         "dir_number": dir_number,
         "first_image_number": first_image_number,
         "num_slices": num_slices,
@@ -142,26 +123,26 @@ def v__rename_panga_cargs(
     """
     cargs = []
     cargs.append("@RenamePanga")
-    cargs.append(params.get("dir_number"))
-    cargs.append(params.get("first_image_number"))
-    cargs.append(str(params.get("num_slices")))
-    cargs.append(str(params.get("num_reps")))
-    cargs.append(params.get("output_root"))
-    if params.get("keep_prefix"):
+    cargs.append(params.get("dir_number", None))
+    cargs.append(params.get("first_image_number", None))
+    cargs.append(str(params.get("num_slices", None)))
+    cargs.append(str(params.get("num_reps", None)))
+    cargs.append(params.get("output_root", None))
+    if params.get("keep_prefix", False):
         cargs.append("-kp")
-    if params.get("interactive"):
+    if params.get("interactive", False):
         cargs.append("-i")
-    if params.get("outliers_check"):
+    if params.get("outliers_check", False):
         cargs.append("-oc")
-    if params.get("slice_pattern") is not None:
+    if params.get("slice_pattern", None) is not None:
         cargs.extend([
             "-sp",
-            params.get("slice_pattern")
+            params.get("slice_pattern", None)
         ])
-    if params.get("output_directory") is not None:
+    if params.get("output_directory", None) is not None:
         cargs.extend([
             "-od",
-            params.get("output_directory")
+            params.get("output_directory", None)
         ])
     return cargs
 
@@ -181,18 +162,20 @@ def v__rename_panga_outputs(
     """
     ret = VRenamePangaOutputs(
         root=execution.output_file("."),
-        head_file=execution.output_file(params.get("output_directory") + "/" + params.get("output_root") + "_r#.HEAD") if (params.get("output_directory") is not None) else None,
-        brik_file=execution.output_file(params.get("output_directory") + "/" + params.get("output_root") + "_r#.BRIK") if (params.get("output_directory") is not None) else None,
-        log_file=execution.output_file(params.get("output_directory") + "/MAPLOG_Panga") if (params.get("output_directory") is not None) else None,
+        head_file=execution.output_file(params.get("output_directory", None) + "/" + params.get("output_root", None) + "_r#.HEAD") if (params.get("output_directory") is not None) else None,
+        brik_file=execution.output_file(params.get("output_directory", None) + "/" + params.get("output_root", None) + "_r#.BRIK") if (params.get("output_directory") is not None) else None,
+        log_file=execution.output_file(params.get("output_directory", None) + "/MAPLOG_Panga") if (params.get("output_directory") is not None) else None,
     )
     return ret
 
 
 def v__rename_panga_execute(
     params: VRenamePangaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VRenamePangaOutputs:
     """
+    @RenamePanga
+    
     Creates AFNI bricks from RealTime GE EPI series.
     
     Author: AFNI Developers
@@ -201,10 +184,12 @@ def v__rename_panga_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VRenamePangaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__RENAME_PANGA_METADATA)
     params = execution.params(params)
     cargs = v__rename_panga_cargs(params, execution)
     ret = v__rename_panga_outputs(params, execution)
@@ -226,6 +211,8 @@ def v__rename_panga(
     runner: Runner | None = None,
 ) -> VRenamePangaOutputs:
     """
+    @RenamePanga
+    
     Creates AFNI bricks from RealTime GE EPI series.
     
     Author: AFNI Developers
@@ -253,8 +240,6 @@ def v__rename_panga(
     Returns:
         NamedTuple of outputs (described in `VRenamePangaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__RENAME_PANGA_METADATA)
     params = v__rename_panga_params(
         dir_number=dir_number,
         first_image_number=first_image_number,
@@ -267,13 +252,13 @@ def v__rename_panga(
         slice_pattern=slice_pattern,
         output_directory=output_directory,
     )
-    return v__rename_panga_execute(params, execution)
+    return v__rename_panga_execute(params, runner)
 
 
 __all__ = [
     "VRenamePangaOutputs",
-    "VRenamePangaParameters",
     "V__RENAME_PANGA_METADATA",
     "v__rename_panga",
+    "v__rename_panga_execute",
     "v__rename_panga_params",
 ]

niwrap_afni/afni/v__reorder.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__REORDER_METADATA = Metadata(
-    id="ef9c00baf613311acb5352e7a897dfe4418a1739.boutiques",
+    id="cd46479c358c4447d40503c639bbd80f9c31e06b.boutiques",
     name="@Reorder",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V__REORDER_METADATA = Metadata(
 
 
 VReorderParameters = typing.TypedDict('VReorderParameters', {
-    "__STYXTYPE__": typing.Literal["@Reorder"],
+    "@type": typing.NotRequired[typing.Literal["afni/@Reorder"]],
+    "input_dataset": InputPathType,
+    "mapfile": InputPathType,
+    "prefix": str,
+    "offset": typing.NotRequired[float | None],
+    "save_work": bool,
+    "test": bool,
+    "help": bool,
+})
+VReorderParametersTagged = typing.TypedDict('VReorderParametersTagged', {
+    "@type": typing.Literal["afni/@Reorder"],
     "input_dataset": InputPathType,
     "mapfile": InputPathType,
     "prefix": str,
@@ -23,43 +33,11 @@ VReorderParameters = typing.TypedDict('VReorderParameters', {
     "test": bool,
     "help": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "@Reorder": v__reorder_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 {
-        "@Reorder": v__reorder_outputs,
-    }.get(t)
 
 
 class VReorderOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v__reorder(...)`.
+    Output object returned when calling `VReorderParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def v__reorder_params(
     save_work: bool = False,
     test: bool = False,
     help_: bool = False,
-) -> VReorderParameters:
+) -> VReorderParametersTagged:
     """
     Build parameters.
     
@@ -91,7 +69,7 @@ def v__reorder_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "@Reorder",
+        "@type": "afni/@Reorder",
         "input_dataset": input_dataset,
         "mapfile": mapfile,
         "prefix": prefix,
@@ -119,19 +97,19 @@ def v__reorder_cargs(
     """
     cargs = []
     cargs.append("@Reorder")
-    cargs.append(execution.input_file(params.get("input_dataset")))
-    cargs.append(execution.input_file(params.get("mapfile")))
-    cargs.append(params.get("prefix"))
-    if params.get("offset") is not None:
+    cargs.append(execution.input_file(params.get("input_dataset", None)))
+    cargs.append(execution.input_file(params.get("mapfile", None)))
+    cargs.append(params.get("prefix", None))
+    if params.get("offset", None) is not None:
         cargs.extend([
             "-offset",
-            str(params.get("offset"))
+            str(params.get("offset", None))
         ])
-    if params.get("save_work"):
+    if params.get("save_work", False):
         cargs.append("-save_work")
-    if params.get("test"):
+    if params.get("test", False):
         cargs.append("-test")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -151,18 +129,20 @@ def v__reorder_outputs(
     """
     ret = VReorderOutputs(
         root=execution.output_file("."),
-        output_dataset=execution.output_file(params.get("prefix") + "+tlrc"),
+        output_dataset=execution.output_file(params.get("prefix", None) + "+tlrc"),
     )
     return ret
 
 
 def v__reorder_execute(
     params: VReorderParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> VReorderOutputs:
     """
-    Reorder sub-bricks of a dataset based on event mapping. Works similarly to the
-    Reorder plugin.
+    @Reorder
+    
+    Reorder sub-bricks of a dataset based on event mapping. Works similarly to
+    the Reorder plugin.
     
     Author: AFNI Developers
     
@@ -170,10 +150,12 @@ def v__reorder_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VReorderOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V__REORDER_METADATA)
     params = execution.params(params)
     cargs = v__reorder_cargs(params, execution)
     ret = v__reorder_outputs(params, execution)
@@ -192,8 +174,10 @@ def v__reorder(
     runner: Runner | None = None,
 ) -> VReorderOutputs:
     """
-    Reorder sub-bricks of a dataset based on event mapping. Works similarly to the
-    Reorder plugin.
+    @Reorder
+    
+    Reorder sub-bricks of a dataset based on event mapping. Works similarly to
+    the Reorder plugin.
     
     Author: AFNI Developers
     
@@ -211,8 +195,6 @@ def v__reorder(
     Returns:
         NamedTuple of outputs (described in `VReorderOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V__REORDER_METADATA)
     params = v__reorder_params(
         input_dataset=input_dataset,
         mapfile=mapfile,
@@ -222,13 +204,13 @@ def v__reorder(
         test=test,
         help_=help_,
     )
-    return v__reorder_execute(params, execution)
+    return v__reorder_execute(params, runner)
 
 
 __all__ = [
     "VReorderOutputs",
-    "VReorderParameters",
     "V__REORDER_METADATA",
     "v__reorder",
+    "v__reorder_execute",
     "v__reorder_params",
 ]