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

niwrap_afni/afni/abids_json_info_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ABIDS_JSON_INFO_PY_METADATA = Metadata(
-    id="dbe784da9ea0070ea74b0200f0a71ea570de859e.boutiques",
+    id="cdac5506c8cbb0e985bd9b452999658837f91d6a.boutiques",
     name="abids_json_info.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ ABIDS_JSON_INFO_PY_METADATA = Metadata(
 
 
 AbidsJsonInfoPyParameters = typing.TypedDict('AbidsJsonInfoPyParameters', {
-    "__STYXTYPE__": typing.Literal["abids_json_info.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/abids_json_info.py"]],
+    "json_files": list[InputPathType],
+    "tr_flag": bool,
+    "te_flag": bool,
+    "te_sec_flag": bool,
+    "match_nii_flag": bool,
+    "field_list": typing.NotRequired[list[str] | None],
+    "list_fields_flag": bool,
+    "help_flag": bool,
+})
+AbidsJsonInfoPyParametersTagged = typing.TypedDict('AbidsJsonInfoPyParametersTagged', {
+    "@type": typing.Literal["afni/abids_json_info.py"],
     "json_files": list[InputPathType],
     "tr_flag": bool,
     "te_flag": bool,
@@ -24,42 +35,11 @@ AbidsJsonInfoPyParameters = typing.TypedDict('AbidsJsonInfoPyParameters', {
     "list_fields_flag": bool,
     "help_flag": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "abids_json_info.py": abids_json_info_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 AbidsJsonInfoPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `abids_json_info_py(...)`.
+    Output object returned when calling `AbidsJsonInfoPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -74,7 +54,7 @@ def abids_json_info_py_params(
     field_list: list[str] | None = None,
     list_fields_flag: bool = False,
     help_flag: bool = False,
-) -> AbidsJsonInfoPyParameters:
+) -> AbidsJsonInfoPyParametersTagged:
     """
     Build parameters.
     
@@ -95,7 +75,7 @@ def abids_json_info_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "abids_json_info.py",
+        "@type": "afni/abids_json_info.py",
         "json_files": json_files,
         "tr_flag": tr_flag,
         "te_flag": te_flag,
@@ -124,23 +104,23 @@ def abids_json_info_py_cargs(
     """
     cargs = []
     cargs.append("abids_json_info.py")
-    cargs.extend([execution.input_file(f) for f in params.get("json_files")])
-    if params.get("tr_flag"):
+    cargs.extend([execution.input_file(f) for f in params.get("json_files", None)])
+    if params.get("tr_flag", False):
         cargs.append("-TR")
-    if params.get("te_flag"):
+    if params.get("te_flag", False):
         cargs.append("-TE")
-    if params.get("te_sec_flag"):
+    if params.get("te_sec_flag", False):
         cargs.append("-TE_sec")
-    if params.get("match_nii_flag"):
+    if params.get("match_nii_flag", False):
         cargs.append("-match_nii")
-    if params.get("field_list") is not None:
+    if params.get("field_list", None) is not None:
         cargs.extend([
             "-field",
-            *params.get("field_list")
+            *params.get("field_list", None)
         ])
-    if params.get("list_fields_flag"):
+    if params.get("list_fields_flag", False):
         cargs.append("-list_fields")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
     return cargs
 
@@ -166,9 +146,11 @@ def abids_json_info_py_outputs(
 
 def abids_json_info_py_execute(
     params: AbidsJsonInfoPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AbidsJsonInfoPyOutputs:
     """
+    abids_json_info.py
+    
     A tool to extract information from BIDS formatted json files.
     
     Author: AFNI Developers
@@ -177,10 +159,12 @@ def abids_json_info_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AbidsJsonInfoPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ABIDS_JSON_INFO_PY_METADATA)
     params = execution.params(params)
     cargs = abids_json_info_py_cargs(params, execution)
     ret = abids_json_info_py_outputs(params, execution)
@@ -200,6 +184,8 @@ def abids_json_info_py(
     runner: Runner | None = None,
 ) -> AbidsJsonInfoPyOutputs:
     """
+    abids_json_info.py
+    
     A tool to extract information from BIDS formatted json files.
     
     Author: AFNI Developers
@@ -223,8 +209,6 @@ def abids_json_info_py(
     Returns:
         NamedTuple of outputs (described in `AbidsJsonInfoPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ABIDS_JSON_INFO_PY_METADATA)
     params = abids_json_info_py_params(
         json_files=json_files,
         tr_flag=tr_flag,
@@ -235,13 +219,13 @@ def abids_json_info_py(
         list_fields_flag=list_fields_flag,
         help_flag=help_flag,
     )
-    return abids_json_info_py_execute(params, execution)
+    return abids_json_info_py_execute(params, runner)
 
 
 __all__ = [
     "ABIDS_JSON_INFO_PY_METADATA",
     "AbidsJsonInfoPyOutputs",
-    "AbidsJsonInfoPyParameters",
     "abids_json_info_py",
+    "abids_json_info_py_execute",
     "abids_json_info_py_params",
 ]

niwrap_afni/afni/abids_json_tool_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 ABIDS_JSON_TOOL_PY_METADATA = Metadata(
-    id="a9dbf330af1f3822b5e39734d477a5a6979179ef.boutiques",
+    id="1ad32b5a1f97747be06e8fea3d5e1f88bb402d1c.boutiques",
     name="abids_json_tool.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ ABIDS_JSON_TOOL_PY_METADATA = Metadata(
 
 
 AbidsJsonToolPyParameters = typing.TypedDict('AbidsJsonToolPyParameters', {
-    "__STYXTYPE__": typing.Literal["abids_json_tool.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/abids_json_tool.py"]],
+    "input_file": InputPathType,
+    "prefix": str,
+    "txt2json": bool,
+    "json2txt": bool,
+    "add_json": typing.NotRequired[list[str] | None],
+    "del_json": typing.NotRequired[str | None],
+    "force_add": bool,
+    "overwrite": bool,
+    "help": bool,
+    "delimiter_major": typing.NotRequired[str | None],
+    "delimiter_minor": typing.NotRequired[str | None],
+    "literal_keys": bool,
+    "values_stay_str": bool,
+})
+AbidsJsonToolPyParametersTagged = typing.TypedDict('AbidsJsonToolPyParametersTagged', {
+    "@type": typing.Literal["afni/abids_json_tool.py"],
     "input_file": InputPathType,
     "prefix": str,
     "txt2json": bool,
@@ -29,42 +45,11 @@ AbidsJsonToolPyParameters = typing.TypedDict('AbidsJsonToolPyParameters', {
     "literal_keys": bool,
     "values_stay_str": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "abids_json_tool.py": abids_json_tool_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 AbidsJsonToolPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `abids_json_tool_py(...)`.
+    Output object returned when calling `AbidsJsonToolPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -84,7 +69,7 @@ def abids_json_tool_py_params(
     delimiter_minor: str | None = None,
     literal_keys: bool = False,
     values_stay_str: bool = False,
-) -> AbidsJsonToolPyParameters:
+) -> AbidsJsonToolPyParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +98,7 @@ def abids_json_tool_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "abids_json_tool.py",
+        "@type": "afni/abids_json_tool.py",
         "input_file": input_file,
         "prefix": prefix,
         "txt2json": txt2json,
@@ -152,45 +137,45 @@ def abids_json_tool_py_cargs(
     cargs.append("abids_json_tool.py")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("txt2json"):
+    if params.get("txt2json", False):
         cargs.append("-txt2json")
-    if params.get("json2txt"):
+    if params.get("json2txt", False):
         cargs.append("-json2txt")
-    if params.get("add_json") is not None:
+    if params.get("add_json", None) is not None:
         cargs.extend([
             "-add_json",
-            *params.get("add_json")
+            *params.get("add_json", None)
         ])
-    if params.get("del_json") is not None:
+    if params.get("del_json", None) is not None:
         cargs.extend([
             "-del_json",
-            params.get("del_json")
+            params.get("del_json", None)
         ])
-    if params.get("force_add"):
+    if params.get("force_add", False):
         cargs.append("-f")
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("delimiter_major") is not None:
+    if params.get("delimiter_major", None) is not None:
         cargs.extend([
             "-delimiter_major",
-            params.get("delimiter_major")
+            params.get("delimiter_major", None)
         ])
-    if params.get("delimiter_minor") is not None:
+    if params.get("delimiter_minor", None) is not None:
         cargs.extend([
             "-delimiter_minor",
-            params.get("delimiter_minor")
+            params.get("delimiter_minor", None)
         ])
-    if params.get("literal_keys"):
+    if params.get("literal_keys", False):
         cargs.append("-literal_keys")
-    if params.get("values_stay_str"):
+    if params.get("values_stay_str", False):
         cargs.append("-values_stay_str")
     return cargs
 
@@ -216,9 +201,11 @@ def abids_json_tool_py_outputs(
 
 def abids_json_tool_py_execute(
     params: AbidsJsonToolPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> AbidsJsonToolPyOutputs:
     """
+    abids_json_tool.py
+    
     This script helps to manipulate json files in various ways.
     
     Author: AFNI Developers
@@ -227,10 +214,12 @@ def abids_json_tool_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `AbidsJsonToolPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ABIDS_JSON_TOOL_PY_METADATA)
     params = execution.params(params)
     cargs = abids_json_tool_py_cargs(params, execution)
     ret = abids_json_tool_py_outputs(params, execution)
@@ -255,6 +244,8 @@ def abids_json_tool_py(
     runner: Runner | None = None,
 ) -> AbidsJsonToolPyOutputs:
     """
+    abids_json_tool.py
+    
     This script helps to manipulate json files in various ways.
     
     Author: AFNI Developers
@@ -286,8 +277,6 @@ def abids_json_tool_py(
     Returns:
         NamedTuple of outputs (described in `AbidsJsonToolPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ABIDS_JSON_TOOL_PY_METADATA)
     params = abids_json_tool_py_params(
         input_file=input_file,
         prefix=prefix,
@@ -303,13 +292,13 @@ def abids_json_tool_py(
         literal_keys=literal_keys,
         values_stay_str=values_stay_str,
     )
-    return abids_json_tool_py_execute(params, execution)
+    return abids_json_tool_py_execute(params, runner)
 
 
 __all__ = [
     "ABIDS_JSON_TOOL_PY_METADATA",
     "AbidsJsonToolPyOutputs",
-    "AbidsJsonToolPyParameters",
     "abids_json_tool_py",
+    "abids_json_tool_py_execute",
     "abids_json_tool_py_params",
 ]

niwrap_afni/afni/{abids_tool.py → abids_tool_py.py}

@@ -5,16 +5,25 @@ import typing
 import pathlib
 from styxdefs import *
 
-ABIDS_TOOL_METADATA = Metadata(
-    id="623988e726ff6bf6b4972b1940f6f0b4f38877f2.boutiques",
-    name="abids_tool",
+ABIDS_TOOL_PY_METADATA = Metadata(
+    id="0cec3da978793786b74a6ef0ab3a3f167672d68f.boutiques",
+    name="abids_tool.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-AbidsToolParameters = typing.TypedDict('AbidsToolParameters', {
-    "__STYXTYPE__": typing.Literal["abids_tool"],
+AbidsToolPyParameters = typing.TypedDict('AbidsToolPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/abids_tool.py"]],
+    "input_files": list[InputPathType],
+    "tr_match": bool,
+    "add_tr": bool,
+    "add_slice_times": bool,
+    "copy_prefix": typing.NotRequired[list[str] | None],
+    "help_flag": bool,
+})
+AbidsToolPyParametersTagged = typing.TypedDict('AbidsToolPyParametersTagged', {
+    "@type": typing.Literal["afni/abids_tool.py"],
     "input_files": list[InputPathType],
     "tr_match": bool,
     "add_tr": bool,
@@ -24,53 +33,22 @@ AbidsToolParameters = typing.TypedDict('AbidsToolParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "abids_tool": abids_tool_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 AbidsToolOutputs(typing.NamedTuple):
+class AbidsToolPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `abids_tool(...)`.
+    Output object returned when calling `AbidsToolPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
 
 
-def abids_tool_params(
+def abids_tool_py_params(
     input_files: list[InputPathType],
     tr_match: bool = False,
     add_tr: bool = False,
     add_slice_times: bool = False,
     copy_prefix: list[str] | None = None,
     help_flag: bool = False,
-) -> AbidsToolParameters:
+) -> AbidsToolPyParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +67,7 @@ def abids_tool_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "abids_tool",
+        "@type": "afni/abids_tool.py",
         "input_files": input_files,
         "tr_match": tr_match,
         "add_tr": add_tr,
@@ -101,8 +79,8 @@ def abids_tool_params(
     return params
 
 
-def abids_tool_cargs(
-    params: AbidsToolParameters,
+def abids_tool_py_cargs(
+    params: AbidsToolPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -116,27 +94,27 @@ def abids_tool_cargs(
     """
     cargs = []
     cargs.append("abids_tool.py")
-    cargs.extend([execution.input_file(f) for f in params.get("input_files")])
-    if params.get("tr_match"):
+    cargs.extend([execution.input_file(f) for f in params.get("input_files", None)])
+    if params.get("tr_match", False):
         cargs.append("-TR_match")
-    if params.get("add_tr"):
+    if params.get("add_tr", False):
         cargs.append("-add_TR")
-    if params.get("add_slice_times"):
+    if params.get("add_slice_times", False):
         cargs.append("-add_slice_times")
-    if params.get("copy_prefix") is not None:
+    if params.get("copy_prefix", None) is not None:
         cargs.extend([
             "-copy",
-            *params.get("copy_prefix")
+            *params.get("copy_prefix", None)
         ])
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
     return cargs
 
 
-def abids_tool_outputs(
-    params: AbidsToolParameters,
+def abids_tool_py_outputs(
+    params: AbidsToolPyParameters,
     execution: Execution,
-) -> AbidsToolOutputs:
+) -> AbidsToolPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -146,20 +124,22 @@ def abids_tool_outputs(
     Returns:
         Outputs object.
     """
-    ret = AbidsToolOutputs(
+    ret = AbidsToolPyOutputs(
         root=execution.output_file("."),
     )
     return ret
 
 
-def abids_tool_execute(
-    params: AbidsToolParameters,
-    execution: Execution,
-) -> AbidsToolOutputs:
+def abids_tool_py_execute(
+    params: AbidsToolPyParameters,
+    runner: Runner | None = None,
+) -> AbidsToolPyOutputs:
     """
+    abids_tool.py
+    
     A tool to work with BIDS formatted datasets created with dcm2niix_afni or
-    dcm2niix, mainly to pull information from the matching JSON file and refit the
-    input dataset using 3drefit.
+    dcm2niix, mainly to pull information from the matching JSON file and refit
+    the input dataset using 3drefit.
     
     Author: AFNI Developers
     
@@ -167,18 +147,20 @@ def abids_tool_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `AbidsToolOutputs`).
+        NamedTuple of outputs (described in `AbidsToolPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(ABIDS_TOOL_PY_METADATA)
     params = execution.params(params)
-    cargs = abids_tool_cargs(params, execution)
-    ret = abids_tool_outputs(params, execution)
+    cargs = abids_tool_py_cargs(params, execution)
+    ret = abids_tool_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def abids_tool(
+def abids_tool_py(
     input_files: list[InputPathType],
     tr_match: bool = False,
     add_tr: bool = False,
@@ -186,11 +168,13 @@ def abids_tool(
     copy_prefix: list[str] | None = None,
     help_flag: bool = False,
     runner: Runner | None = None,
-) -> AbidsToolOutputs:
+) -> AbidsToolPyOutputs:
     """
+    abids_tool.py
+    
     A tool to work with BIDS formatted datasets created with dcm2niix_afni or
-    dcm2niix, mainly to pull information from the matching JSON file and refit the
-    input dataset using 3drefit.
+    dcm2niix, mainly to pull information from the matching JSON file and refit
+    the input dataset using 3drefit.
     
     Author: AFNI Developers
     
@@ -209,11 +193,9 @@ def abids_tool(
         help_flag: Show help information and exit.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `AbidsToolOutputs`).
+        NamedTuple of outputs (described in `AbidsToolPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(ABIDS_TOOL_METADATA)
-    params = abids_tool_params(
+    params = abids_tool_py_params(
         input_files=input_files,
         tr_match=tr_match,
         add_tr=add_tr,
@@ -221,13 +203,13 @@ def abids_tool(
         copy_prefix=copy_prefix,
         help_flag=help_flag,
     )
-    return abids_tool_execute(params, execution)
+    return abids_tool_py_execute(params, runner)
 
 
 __all__ = [
-    "ABIDS_TOOL_METADATA",
-    "AbidsToolOutputs",
-    "AbidsToolParameters",
-    "abids_tool",
-    "abids_tool_params",
+    "ABIDS_TOOL_PY_METADATA",
+    "AbidsToolPyOutputs",
+    "abids_tool_py",
+    "abids_tool_py_execute",
+    "abids_tool_py_params",
 ]