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

niwrap_afni/afni/fsread_annot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FSREAD_ANNOT_METADATA = Metadata(
-    id="119c7f16e85967567c34d369d4ee5cf158ea2364.boutiques",
+    id="f43f4505849178213f22484e025190c164fdc8b0.boutiques",
     name="FSread_annot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ FSREAD_ANNOT_METADATA = Metadata(
 
 
 FsreadAnnotParameters = typing.TypedDict('FsreadAnnotParameters', {
-    "__STYXTYPE__": typing.Literal["FSread_annot"],
+    "@type": typing.NotRequired[typing.Literal["afni/FSread_annot"]],
+    "infile": InputPathType,
+    "hemi": typing.NotRequired[str | None],
+    "fscmap": typing.NotRequired[InputPathType | None],
+    "fscmap_range": typing.NotRequired[list[float] | None],
+    "fsversion": typing.NotRequired[str | None],
+    "col_1d": typing.NotRequired[str | None],
+    "roi_1d": typing.NotRequired[str | None],
+    "cmap_1d": typing.NotRequired[str | None],
+    "show_fscmap": bool,
+    "dset": typing.NotRequired[str | None],
+    "help": bool,
+})
+FsreadAnnotParametersTagged = typing.TypedDict('FsreadAnnotParametersTagged', {
+    "@type": typing.Literal["afni/FSread_annot"],
     "infile": InputPathType,
     "hemi": typing.NotRequired[str | None],
     "fscmap": typing.NotRequired[InputPathType | None],
@@ -27,43 +41,11 @@ FsreadAnnotParameters = typing.TypedDict('FsreadAnnotParameters', {
     "dset": typing.NotRequired[str | None],
     "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 {
-        "FSread_annot": fsread_annot_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 {
-        "FSread_annot": fsread_annot_outputs,
-    }.get(t)
 
 
 class FsreadAnnotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fsread_annot(...)`.
+    Output object returned when calling `FsreadAnnotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +71,7 @@ def fsread_annot_params(
     show_fscmap: bool = False,
     dset: str | None = None,
     help_: bool = False,
-) -> FsreadAnnotParameters:
+) -> FsreadAnnotParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +96,7 @@ def fsread_annot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "FSread_annot",
+        "@type": "afni/FSread_annot",
         "infile": infile,
         "show_fscmap": show_fscmap,
         "help": help_,
@@ -155,51 +137,51 @@ def fsread_annot_cargs(
     cargs.append("FSread_annot")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("infile"))
+        execution.input_file(params.get("infile", None))
     ])
-    if params.get("hemi") is not None:
+    if params.get("hemi", None) is not None:
         cargs.extend([
             "-hemi",
-            params.get("hemi")
+            params.get("hemi", None)
         ])
-    if params.get("fscmap") is not None:
+    if params.get("fscmap", None) is not None:
         cargs.extend([
             "-FScmap",
-            execution.input_file(params.get("fscmap"))
+            execution.input_file(params.get("fscmap", None))
         ])
-    if params.get("fscmap_range") is not None:
+    if params.get("fscmap_range", None) is not None:
         cargs.extend([
             "-FScmaprange",
-            *map(str, params.get("fscmap_range"))
+            *map(str, params.get("fscmap_range", None))
         ])
-    if params.get("fsversion") is not None:
+    if params.get("fsversion", None) is not None:
         cargs.extend([
             "-FSversion",
-            params.get("fsversion")
+            params.get("fsversion", None)
         ])
-    if params.get("col_1d") is not None:
+    if params.get("col_1d", None) is not None:
         cargs.extend([
             "-col_1D",
-            params.get("col_1d")
+            params.get("col_1d", None)
         ])
-    if params.get("roi_1d") is not None:
+    if params.get("roi_1d", None) is not None:
         cargs.extend([
             "-roi_1D",
-            params.get("roi_1d")
+            params.get("roi_1d", None)
         ])
-    if params.get("cmap_1d") is not None:
+    if params.get("cmap_1d", None) is not None:
         cargs.extend([
             "-cmap_1D",
-            params.get("cmap_1d")
+            params.get("cmap_1d", None)
         ])
-    if params.get("show_fscmap"):
+    if params.get("show_fscmap", False):
         cargs.append("-show_FScmap")
-    if params.get("dset") is not None:
+    if params.get("dset", None) is not None:
         cargs.extend([
             "-dset",
-            params.get("dset")
+            params.get("dset", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
     return cargs
 
@@ -229,11 +211,13 @@ def fsread_annot_outputs(
 
 def fsread_annot_execute(
     params: FsreadAnnotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FsreadAnnotOutputs:
     """
-    Reads a FreeSurfer annotation file and outputs an equivalent ROI file and/or a
-    colormap file for use with SUMA.
+    FSread_annot
+    
+    Reads a FreeSurfer annotation file and outputs an equivalent ROI file and/or
+    a colormap file for use with SUMA.
     
     Author: AFNI Developers
     
@@ -241,10 +225,12 @@ def fsread_annot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FsreadAnnotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FSREAD_ANNOT_METADATA)
     params = execution.params(params)
     cargs = fsread_annot_cargs(params, execution)
     ret = fsread_annot_outputs(params, execution)
@@ -267,8 +253,10 @@ def fsread_annot(
     runner: Runner | None = None,
 ) -> FsreadAnnotOutputs:
     """
-    Reads a FreeSurfer annotation file and outputs an equivalent ROI file and/or a
-    colormap file for use with SUMA.
+    FSread_annot
+    
+    Reads a FreeSurfer annotation file and outputs an equivalent ROI file and/or
+    a colormap file for use with SUMA.
     
     Author: AFNI Developers
     
@@ -295,8 +283,6 @@ def fsread_annot(
     Returns:
         NamedTuple of outputs (described in `FsreadAnnotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FSREAD_ANNOT_METADATA)
     params = fsread_annot_params(
         infile=infile,
         hemi=hemi,
@@ -310,13 +296,13 @@ def fsread_annot(
         dset=dset,
         help_=help_,
     )
-    return fsread_annot_execute(params, execution)
+    return fsread_annot_execute(params, runner)
 
 
 __all__ = [
     "FSREAD_ANNOT_METADATA",
     "FsreadAnnotOutputs",
-    "FsreadAnnotParameters",
     "fsread_annot",
+    "fsread_annot_execute",
     "fsread_annot_params",
 ]

niwrap_afni/afni/gen_epi_review_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GEN_EPI_REVIEW_PY_METADATA = Metadata(
-    id="d8d2bfa4cbebb23bdbab47bb389c8686d9524ec8.boutiques",
+    id="6789f4ee958948df08713dc79f981e6501a16f41.boutiques",
     name="gen_epi_review.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,20 @@ GEN_EPI_REVIEW_PY_METADATA = Metadata(
 
 
 GenEpiReviewPyParameters = typing.TypedDict('GenEpiReviewPyParameters', {
-    "__STYXTYPE__": typing.Literal["gen_epi_review.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/gen_epi_review.py"]],
+    "datasets": list[str],
+    "script_name": typing.NotRequired[str | None],
+    "windows": typing.NotRequired[list[str] | None],
+    "verbosity": typing.NotRequired[float | None],
+    "image_size": typing.NotRequired[list[float] | None],
+    "image_xoffset": typing.NotRequired[float | None],
+    "image_yoffset": typing.NotRequired[float | None],
+    "graph_size": typing.NotRequired[list[float] | None],
+    "graph_xoffset": typing.NotRequired[float | None],
+    "graph_yoffset": typing.NotRequired[float | None],
+})
+GenEpiReviewPyParametersTagged = typing.TypedDict('GenEpiReviewPyParametersTagged', {
+    "@type": typing.Literal["afni/gen_epi_review.py"],
     "datasets": list[str],
     "script_name": typing.NotRequired[str | None],
     "windows": typing.NotRequired[list[str] | None],
@@ -26,42 +39,11 @@ GenEpiReviewPyParameters = typing.TypedDict('GenEpiReviewPyParameters', {
     "graph_xoffset": typing.NotRequired[float | None],
     "graph_yoffset": typing.NotRequired[float | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gen_epi_review.py": gen_epi_review_py_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 GenEpiReviewPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gen_epi_review_py(...)`.
+    Output object returned when calling `GenEpiReviewPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -78,7 +60,7 @@ def gen_epi_review_py_params(
     graph_size: list[float] | None = None,
     graph_xoffset: float | None = None,
     graph_yoffset: float | None = None,
-) -> GenEpiReviewPyParameters:
+) -> GenEpiReviewPyParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +79,7 @@ def gen_epi_review_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gen_epi_review.py",
+        "@type": "afni/gen_epi_review.py",
         "datasets": datasets,
     }
     if script_name is not None:
@@ -138,52 +120,52 @@ def gen_epi_review_py_cargs(
     cargs.append("gen_epi_review.py")
     cargs.extend([
         "-dsets",
-        *params.get("datasets")
+        *params.get("datasets", None)
     ])
-    if params.get("script_name") is not None:
+    if params.get("script_name", None) is not None:
         cargs.extend([
             "-script",
-            params.get("script_name")
+            params.get("script_name", None)
         ])
-    if params.get("windows") is not None:
+    if params.get("windows", None) is not None:
         cargs.extend([
             "-windows",
-            *params.get("windows")
+            *params.get("windows", None)
         ])
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
-    if params.get("image_size") is not None:
+    if params.get("image_size", None) is not None:
         cargs.extend([
             "-im_size",
-            *map(str, params.get("image_size"))
+            *map(str, params.get("image_size", None))
         ])
-    if params.get("image_xoffset") is not None:
+    if params.get("image_xoffset", None) is not None:
         cargs.extend([
             "-im_xoff",
-            str(params.get("image_xoffset"))
+            str(params.get("image_xoffset", None))
         ])
-    if params.get("image_yoffset") is not None:
+    if params.get("image_yoffset", None) is not None:
         cargs.extend([
             "-im_yoff",
-            str(params.get("image_yoffset"))
+            str(params.get("image_yoffset", None))
         ])
-    if params.get("graph_size") is not None:
+    if params.get("graph_size", None) is not None:
         cargs.extend([
             "-gr_size",
-            *map(str, params.get("graph_size"))
+            *map(str, params.get("graph_size", None))
         ])
-    if params.get("graph_xoffset") is not None:
+    if params.get("graph_xoffset", None) is not None:
         cargs.extend([
             "-gr_xoff",
-            str(params.get("graph_xoffset"))
+            str(params.get("graph_xoffset", None))
         ])
-    if params.get("graph_yoffset") is not None:
+    if params.get("graph_yoffset", None) is not None:
         cargs.extend([
             "-gr_yoff",
-            str(params.get("graph_yoffset"))
+            str(params.get("graph_yoffset", None))
         ])
     return cargs
 
@@ -209,9 +191,11 @@ def gen_epi_review_py_outputs(
 
 def gen_epi_review_py_execute(
     params: GenEpiReviewPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GenEpiReviewPyOutputs:
     """
+    gen_epi_review.py
+    
     Generate an AFNI processing script to review EPI data.
     
     Author: AFNI Developers
@@ -220,10 +204,12 @@ def gen_epi_review_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GenEpiReviewPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GEN_EPI_REVIEW_PY_METADATA)
     params = execution.params(params)
     cargs = gen_epi_review_py_cargs(params, execution)
     ret = gen_epi_review_py_outputs(params, execution)
@@ -245,6 +231,8 @@ def gen_epi_review_py(
     runner: Runner | None = None,
 ) -> GenEpiReviewPyOutputs:
     """
+    gen_epi_review.py
+    
     Generate an AFNI processing script to review EPI data.
     
     Author: AFNI Developers
@@ -266,8 +254,6 @@ def gen_epi_review_py(
     Returns:
         NamedTuple of outputs (described in `GenEpiReviewPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GEN_EPI_REVIEW_PY_METADATA)
     params = gen_epi_review_py_params(
         datasets=datasets,
         script_name=script_name,
@@ -280,13 +266,13 @@ def gen_epi_review_py(
         graph_xoffset=graph_xoffset,
         graph_yoffset=graph_yoffset,
     )
-    return gen_epi_review_py_execute(params, execution)
+    return gen_epi_review_py_execute(params, runner)
 
 
 __all__ = [
     "GEN_EPI_REVIEW_PY_METADATA",
     "GenEpiReviewPyOutputs",
-    "GenEpiReviewPyParameters",
     "gen_epi_review_py",
+    "gen_epi_review_py_execute",
     "gen_epi_review_py_params",
 ]