niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/{convert_cdiflist_to_grads.py → convert_cdiflist_to_grads_py.py}

@@ -5,16 +5,26 @@ import typing
 import pathlib
 from styxdefs import *
 
-CONVERT_CDIFLIST_TO_GRADS_METADATA = Metadata(
-    id="19cc3a11622aea08b160e07a0c7e99e58530a33b.boutiques",
-    name="convert_cdiflist_to_grads",
+CONVERT_CDIFLIST_TO_GRADS_PY_METADATA = Metadata(
+    id="64ab963d60d406f9d0685d461ee3fcdb60c15e0c.boutiques",
+    name="convert_cdiflist_to_grads.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-ConvertCdiflistToGradsParameters = typing.TypedDict('ConvertCdiflistToGradsParameters', {
-    "__STYXTYPE__": typing.Literal["convert_cdiflist_to_grads"],
+ConvertCdiflistToGradsPyParameters = typing.TypedDict('ConvertCdiflistToGradsPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/convert_cdiflist_to_grads.py"]],
+    "cdiflist": InputPathType,
+    "bval_max": float,
+    "prefix": str,
+    "ver": bool,
+    "date": bool,
+    "help": bool,
+    "hview": bool,
+})
+ConvertCdiflistToGradsPyParametersTagged = typing.TypedDict('ConvertCdiflistToGradsPyParametersTagged', {
+    "@type": typing.Literal["afni/convert_cdiflist_to_grads.py"],
     "cdiflist": InputPathType,
     "bval_max": float,
     "prefix": str,
@@ -25,41 +35,9 @@ ConvertCdiflistToGradsParameters = typing.TypedDict('ConvertCdiflistToGradsParam
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "convert_cdiflist_to_grads": convert_cdiflist_to_grads_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 {
-        "convert_cdiflist_to_grads": convert_cdiflist_to_grads_outputs,
-    }.get(t)
-
-
-class ConvertCdiflistToGradsOutputs(typing.NamedTuple):
+class ConvertCdiflistToGradsPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `convert_cdiflist_to_grads(...)`.
+    Output object returned when calling `ConvertCdiflistToGradsPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -71,7 +49,7 @@ class ConvertCdiflistToGradsOutputs(typing.NamedTuple):
     """Col-format of gradients (scaled by b-values)."""
 
 
-def convert_cdiflist_to_grads_params(
+def convert_cdiflist_to_grads_py_params(
     cdiflist: InputPathType,
     bval_max: float,
     prefix: str,
@@ -79,7 +57,7 @@ def convert_cdiflist_to_grads_params(
     date: bool = False,
     help_: bool = False,
     hview: bool = False,
-) -> ConvertCdiflistToGradsParameters:
+) -> ConvertCdiflistToGradsPyParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +76,7 @@ def convert_cdiflist_to_grads_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "convert_cdiflist_to_grads",
+        "@type": "afni/convert_cdiflist_to_grads.py",
         "cdiflist": cdiflist,
         "bval_max": bval_max,
         "prefix": prefix,
@@ -110,8 +88,8 @@ def convert_cdiflist_to_grads_params(
     return params
 
 
-def convert_cdiflist_to_grads_cargs(
-    params: ConvertCdiflistToGradsParameters,
+def convert_cdiflist_to_grads_py_cargs(
+    params: ConvertCdiflistToGradsPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -127,31 +105,31 @@ def convert_cdiflist_to_grads_cargs(
     cargs.append("convert_cdiflist_to_grads.py")
     cargs.extend([
         "-cdiflist",
-        execution.input_file(params.get("cdiflist"))
+        execution.input_file(params.get("cdiflist", None))
     ])
     cargs.extend([
         "-bval_max",
-        str(params.get("bval_max"))
+        str(params.get("bval_max", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("ver"):
+    if params.get("ver", False):
         cargs.append("-ver")
-    if params.get("date"):
+    if params.get("date", False):
         cargs.append("-date")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("hview"):
+    if params.get("hview", False):
         cargs.append("-h")
     return cargs
 
 
-def convert_cdiflist_to_grads_outputs(
-    params: ConvertCdiflistToGradsParameters,
+def convert_cdiflist_to_grads_py_outputs(
+    params: ConvertCdiflistToGradsPyParameters,
     execution: Execution,
-) -> ConvertCdiflistToGradsOutputs:
+) -> ConvertCdiflistToGradsPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -161,20 +139,22 @@ def convert_cdiflist_to_grads_outputs(
     Returns:
         Outputs object.
     """
-    ret = ConvertCdiflistToGradsOutputs(
+    ret = ConvertCdiflistToGradsPyOutputs(
         root=execution.output_file("."),
-        output_rvec=execution.output_file(params.get("prefix") + "_rvec.dat"),
-        output_bval=execution.output_file(params.get("prefix") + "_bval.dat"),
-        output_cvec=execution.output_file(params.get("prefix") + "_cvec.dat"),
+        output_rvec=execution.output_file(params.get("prefix", None) + "_rvec.dat"),
+        output_bval=execution.output_file(params.get("prefix", None) + "_bval.dat"),
+        output_cvec=execution.output_file(params.get("prefix", None) + "_cvec.dat"),
     )
     return ret
 
 
-def convert_cdiflist_to_grads_execute(
-    params: ConvertCdiflistToGradsParameters,
-    execution: Execution,
-) -> ConvertCdiflistToGradsOutputs:
+def convert_cdiflist_to_grads_py_execute(
+    params: ConvertCdiflistToGradsPyParameters,
+    runner: Runner | None = None,
+) -> ConvertCdiflistToGradsPyOutputs:
     """
+    convert_cdiflist_to_grads.py
+    
     This program reads in a GE cdiflist and outputs gradient file and file of
     bvalues for subsequent processing.
     
@@ -184,18 +164,20 @@ def convert_cdiflist_to_grads_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `ConvertCdiflistToGradsOutputs`).
+        NamedTuple of outputs (described in `ConvertCdiflistToGradsPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVERT_CDIFLIST_TO_GRADS_PY_METADATA)
     params = execution.params(params)
-    cargs = convert_cdiflist_to_grads_cargs(params, execution)
-    ret = convert_cdiflist_to_grads_outputs(params, execution)
+    cargs = convert_cdiflist_to_grads_py_cargs(params, execution)
+    ret = convert_cdiflist_to_grads_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def convert_cdiflist_to_grads(
+def convert_cdiflist_to_grads_py(
     cdiflist: InputPathType,
     bval_max: float,
     prefix: str,
@@ -204,8 +186,10 @@ def convert_cdiflist_to_grads(
     help_: bool = False,
     hview: bool = False,
     runner: Runner | None = None,
-) -> ConvertCdiflistToGradsOutputs:
+) -> ConvertCdiflistToGradsPyOutputs:
     """
+    convert_cdiflist_to_grads.py
+    
     This program reads in a GE cdiflist and outputs gradient file and file of
     bvalues for subsequent processing.
     
@@ -226,11 +210,9 @@ def convert_cdiflist_to_grads(
         hview: Display help in terminal.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `ConvertCdiflistToGradsOutputs`).
+        NamedTuple of outputs (described in `ConvertCdiflistToGradsPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONVERT_CDIFLIST_TO_GRADS_METADATA)
-    params = convert_cdiflist_to_grads_params(
+    params = convert_cdiflist_to_grads_py_params(
         cdiflist=cdiflist,
         bval_max=bval_max,
         prefix=prefix,
@@ -239,13 +221,13 @@ def convert_cdiflist_to_grads(
         help_=help_,
         hview=hview,
     )
-    return convert_cdiflist_to_grads_execute(params, execution)
+    return convert_cdiflist_to_grads_py_execute(params, runner)
 
 
 __all__ = [
-    "CONVERT_CDIFLIST_TO_GRADS_METADATA",
-    "ConvertCdiflistToGradsOutputs",
-    "ConvertCdiflistToGradsParameters",
-    "convert_cdiflist_to_grads",
-    "convert_cdiflist_to_grads_params",
+    "CONVERT_CDIFLIST_TO_GRADS_PY_METADATA",
+    "ConvertCdiflistToGradsPyOutputs",
+    "convert_cdiflist_to_grads_py",
+    "convert_cdiflist_to_grads_py_execute",
+    "convert_cdiflist_to_grads_py_params",
 ]

niwrap_afni/afni/convert_dset.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 CONVERT_DSET_METADATA = Metadata(
-    id="4beee4c1c48b313053c056b039eaf7a92a5a5c03.boutiques",
+    id="9106f18145f0a080b4b236102317c71eb1c34ffe.boutiques",
     name="ConvertDset",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,31 @@ CONVERT_DSET_METADATA = Metadata(
 
 
 ConvertDsetParameters = typing.TypedDict('ConvertDsetParameters', {
-    "__STYXTYPE__": typing.Literal["ConvertDset"],
+    "@type": typing.NotRequired[typing.Literal["afni/ConvertDset"]],
+    "output_type": list[typing.Literal["niml_asc", "niml_bi", "1D", "1Dp", "1Dpt", "gii", "gii_asc", "gii_b64", "gii_b64gz", "1D_stderr", "1D_stdout", "niml_stderr", "niml_stdout", "1Dp_stdout", "1Dp_stderr", "1Dpt_stdout", "1Dpt_stderr"]],
+    "input_dataset": InputPathType,
+    "input_type": typing.NotRequired[typing.Literal["niml", "1D", "dx"] | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "dset_labels": typing.NotRequired[str | None],
+    "add_node_index": bool,
+    "node_index_file": typing.NotRequired[InputPathType | None],
+    "node_select_file": typing.NotRequired[InputPathType | None],
+    "prepend_node_index": bool,
+    "pad_to_node": typing.NotRequired[str | None],
+    "labelize": typing.NotRequired[InputPathType | None],
+    "graphize": bool,
+    "graph_nodelist": typing.NotRequired[str | None],
+    "graph_full_nodelist": typing.NotRequired[InputPathType | None],
+    "graph_named_nodelist": typing.NotRequired[str | None],
+    "graph_xyz_lpi": bool,
+    "graph_edgelist": typing.NotRequired[InputPathType | None],
+    "onegraph": bool,
+    "multigraph": bool,
+    "split": typing.NotRequired[int | None],
+    "no_history": bool,
+})
+ConvertDsetParametersTagged = typing.TypedDict('ConvertDsetParametersTagged', {
+    "@type": typing.Literal["afni/ConvertDset"],
     "output_type": list[typing.Literal["niml_asc", "niml_bi", "1D", "1Dp", "1Dpt", "gii", "gii_asc", "gii_b64", "gii_b64gz", "1D_stderr", "1D_stdout", "niml_stderr", "niml_stdout", "1Dp_stdout", "1Dp_stderr", "1Dpt_stdout", "1Dpt_stderr"]],
     "input_dataset": InputPathType,
     "input_type": typing.NotRequired[typing.Literal["niml", "1D", "dx"] | None],
@@ -37,43 +61,11 @@ ConvertDsetParameters = typing.TypedDict('ConvertDsetParameters', {
     "split": typing.NotRequired[int | None],
     "no_history": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "ConvertDset": convert_dset_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 {
-        "ConvertDset": convert_dset_outputs,
-    }.get(t)
 
 
 class ConvertDsetOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `convert_dset(...)`.
+    Output object returned when calling `ConvertDsetParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +95,7 @@ def convert_dset_params(
     multigraph: bool = False,
     split: int | None = None,
     no_history: bool = False,
-) -> ConvertDsetParameters:
+) -> ConvertDsetParametersTagged:
     """
     Build parameters.
     
@@ -139,7 +131,7 @@ def convert_dset_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "ConvertDset",
+        "@type": "afni/ConvertDset",
         "output_type": output_type,
         "input_dataset": input_dataset,
         "add_node_index": add_node_index,
@@ -194,85 +186,85 @@ def convert_dset_cargs(
     cargs.append("ConvertDset")
     cargs.extend([
         "-o_",
-        *params.get("output_type")
+        *params.get("output_type", None)
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_dataset"))
+        execution.input_file(params.get("input_dataset", None))
     ])
-    if params.get("input_type") is not None:
+    if params.get("input_type", None) is not None:
         cargs.extend([
             "-i_",
-            params.get("input_type")
+            params.get("input_type", None)
         ])
-    if params.get("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("dset_labels") is not None:
+    if params.get("dset_labels", None) is not None:
         cargs.extend([
             "-dset_labels",
-            params.get("dset_labels")
+            params.get("dset_labels", None)
         ])
-    if params.get("add_node_index"):
+    if params.get("add_node_index", False):
         cargs.append("-add_node_index")
-    if params.get("node_index_file") is not None:
+    if params.get("node_index_file", None) is not None:
         cargs.extend([
             "-node_index_1D",
-            execution.input_file(params.get("node_index_file"))
+            execution.input_file(params.get("node_index_file", None))
         ])
-    if params.get("node_select_file") is not None:
+    if params.get("node_select_file", None) is not None:
         cargs.extend([
             "-node_select_1D",
-            execution.input_file(params.get("node_select_file"))
+            execution.input_file(params.get("node_select_file", None))
         ])
-    if params.get("prepend_node_index"):
+    if params.get("prepend_node_index", False):
         cargs.append("-prepend_node_index_1D")
-    if params.get("pad_to_node") is not None:
+    if params.get("pad_to_node", None) is not None:
         cargs.extend([
             "-pad_to_node",
-            params.get("pad_to_node")
+            params.get("pad_to_node", None)
         ])
-    if params.get("labelize") is not None:
+    if params.get("labelize", None) is not None:
         cargs.extend([
             "-labelize",
-            execution.input_file(params.get("labelize"))
+            execution.input_file(params.get("labelize", None))
         ])
-    if params.get("graphize"):
+    if params.get("graphize", False):
         cargs.append("-graphize")
-    if params.get("graph_nodelist") is not None:
+    if params.get("graph_nodelist", None) is not None:
         cargs.extend([
             "-graph_nodelist_1D",
-            params.get("graph_nodelist")
+            params.get("graph_nodelist", None)
         ])
-    if params.get("graph_full_nodelist") is not None:
+    if params.get("graph_full_nodelist", None) is not None:
         cargs.extend([
             "-graph_full_nodelist_1D",
-            execution.input_file(params.get("graph_full_nodelist"))
+            execution.input_file(params.get("graph_full_nodelist", None))
         ])
-    if params.get("graph_named_nodelist") is not None:
+    if params.get("graph_named_nodelist", None) is not None:
         cargs.extend([
             "-graph_named_nodelist_txt",
-            params.get("graph_named_nodelist")
+            params.get("graph_named_nodelist", None)
         ])
-    if params.get("graph_xyz_lpi"):
+    if params.get("graph_xyz_lpi", False):
         cargs.append("-graph_XYZ_LPI")
-    if params.get("graph_edgelist") is not None:
+    if params.get("graph_edgelist", None) is not None:
         cargs.extend([
             "-graph_edgelist_1D",
-            execution.input_file(params.get("graph_edgelist"))
+            execution.input_file(params.get("graph_edgelist", None))
         ])
-    if params.get("onegraph"):
+    if params.get("onegraph", False):
         cargs.append("-onegraph")
-    if params.get("multigraph"):
+    if params.get("multigraph", False):
         cargs.append("-multigraph")
-    if params.get("split") is not None:
+    if params.get("split", None) is not None:
         cargs.extend([
             "-split",
-            str(params.get("split"))
+            str(params.get("split", None))
         ])
-    if params.get("no_history"):
+    if params.get("no_history", False):
         cargs.append("-no_history")
     return cargs
 
@@ -292,16 +284,18 @@ def convert_dset_outputs(
     """
     ret = ConvertDsetOutputs(
         root=execution.output_file("."),
-        converted_dataset=execution.output_file(params.get("output_prefix")) if (params.get("output_prefix") is not None) else None,
+        converted_dataset=execution.output_file(params.get("output_prefix", None)) if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def convert_dset_execute(
     params: ConvertDsetParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ConvertDsetOutputs:
     """
+    ConvertDset
+    
     Converts a surface dataset from one format to another.
     
     Author: AFNI Developers
@@ -310,10 +304,12 @@ def convert_dset_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ConvertDsetOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(CONVERT_DSET_METADATA)
     params = execution.params(params)
     cargs = convert_dset_cargs(params, execution)
     ret = convert_dset_outputs(params, execution)
@@ -346,6 +342,8 @@ def convert_dset(
     runner: Runner | None = None,
 ) -> ConvertDsetOutputs:
     """
+    ConvertDset
+    
     Converts a surface dataset from one format to another.
     
     Author: AFNI Developers
@@ -384,8 +382,6 @@ def convert_dset(
     Returns:
         NamedTuple of outputs (described in `ConvertDsetOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(CONVERT_DSET_METADATA)
     params = convert_dset_params(
         output_type=output_type,
         input_dataset=input_dataset,
@@ -409,13 +405,13 @@ def convert_dset(
         split=split,
         no_history=no_history,
     )
-    return convert_dset_execute(params, execution)
+    return convert_dset_execute(params, runner)
 
 
 __all__ = [
     "CONVERT_DSET_METADATA",
     "ConvertDsetOutputs",
-    "ConvertDsetParameters",
     "convert_dset",
+    "convert_dset_execute",
     "convert_dset_params",
 ]