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

niwrap_afni/afni/nicat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NICAT_METADATA = Metadata(
-    id="f07ebd8a4a69a3eed0a7d3aacc42caa99277edd7.boutiques",
+    id="ca9eebfe58a16733378505aca09b8609d16496d5.boutiques",
     name="nicat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,24 @@ NICAT_METADATA = Metadata(
 
 
 NicatParameters = typing.TypedDict('NicatParameters', {
-    "__STYXTYPE__": typing.Literal["nicat"],
+    "@type": typing.NotRequired[typing.Literal["afni/nicat"]],
+    "stream_spec": str,
+    "reopen": typing.NotRequired[str | None],
+    "copy_stream": bool,
+    "read_only": bool,
+})
+NicatParametersTagged = typing.TypedDict('NicatParametersTagged', {
+    "@type": typing.Literal["afni/nicat"],
     "stream_spec": str,
     "reopen": typing.NotRequired[str | None],
     "copy_stream": bool,
     "read_only": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "nicat": nicat_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 NicatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `nicat(...)`.
+    Output object returned when calling `NicatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def nicat_params(
     reopen: str | None = None,
     copy_stream: bool = False,
     read_only: bool = False,
-) -> NicatParameters:
+) -> NicatParametersTagged:
     """
     Build parameters.
     
@@ -81,7 +57,7 @@ def nicat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "nicat",
+        "@type": "afni/nicat",
         "stream_spec": stream_spec,
         "copy_stream": copy_stream,
         "read_only": read_only,
@@ -106,15 +82,15 @@ def nicat_cargs(
     """
     cargs = []
     cargs.append("nicat")
-    cargs.append(params.get("stream_spec"))
-    if params.get("reopen") is not None:
+    cargs.append(params.get("stream_spec", None))
+    if params.get("reopen", None) is not None:
         cargs.extend([
             "-reopen",
-            params.get("reopen")
+            params.get("reopen", None)
         ])
-    if params.get("copy_stream"):
+    if params.get("copy_stream", False):
         cargs.append("-r")
-    if params.get("read_only"):
+    if params.get("read_only", False):
         cargs.append("-R")
     return cargs
 
@@ -140,9 +116,11 @@ def nicat_outputs(
 
 def nicat_execute(
     params: NicatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NicatOutputs:
     """
+    nicat
+    
     Copies stdin to the NIML stream, which will be opened for writing.
     
     Author: AFNI Developers
@@ -151,10 +129,12 @@ def nicat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NicatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NICAT_METADATA)
     params = execution.params(params)
     cargs = nicat_cargs(params, execution)
     ret = nicat_outputs(params, execution)
@@ -170,6 +150,8 @@ def nicat(
     runner: Runner | None = None,
 ) -> NicatOutputs:
     """
+    nicat
+    
     Copies stdin to the NIML stream, which will be opened for writing.
     
     Author: AFNI Developers
@@ -187,21 +169,19 @@ def nicat(
     Returns:
         NamedTuple of outputs (described in `NicatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NICAT_METADATA)
     params = nicat_params(
         stream_spec=stream_spec,
         reopen=reopen,
         copy_stream=copy_stream,
         read_only=read_only,
     )
-    return nicat_execute(params, execution)
+    return nicat_execute(params, runner)
 
 
 __all__ = [
     "NICAT_METADATA",
     "NicatOutputs",
-    "NicatParameters",
     "nicat",
+    "nicat_execute",
     "nicat_params",
 ]

niwrap_afni/afni/niccc.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NICCC_METADATA = Metadata(
-    id="0537b5f7fdbe5bd7d26d518f7b08fae562a93852.boutiques",
+    id="38ab5aeadd2358c30dcd70e6045a73c5e0e67cb5.boutiques",
     name="niccc",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ NICCC_METADATA = Metadata(
 
 
 NicccParameters = typing.TypedDict('NicccParameters', {
-    "__STYXTYPE__": typing.Literal["niccc"],
+    "@type": typing.NotRequired[typing.Literal["afni/niccc"]],
+    "streamspec": str,
+    "duplicate": bool,
+    "nodata": bool,
+    "attribute": typing.NotRequired[str | None],
+    "match": typing.NotRequired[str | None],
+    "file": bool,
+    "string": bool,
+    "stdout": bool,
+    "hash": bool,
+    "quiet": bool,
+    "find_attr": typing.NotRequired[list[str] | None],
+    "skip_attr": typing.NotRequired[list[str] | None],
+})
+NicccParametersTagged = typing.TypedDict('NicccParametersTagged', {
+    "@type": typing.Literal["afni/niccc"],
     "streamspec": str,
     "duplicate": bool,
     "nodata": bool,
@@ -28,43 +43,11 @@ NicccParameters = typing.TypedDict('NicccParameters', {
     "find_attr": typing.NotRequired[list[str] | None],
     "skip_attr": typing.NotRequired[list[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 {
-        "niccc": niccc_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 {
-        "niccc": niccc_outputs,
-    }.get(t)
 
 
 class NicccOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `niccc(...)`.
+    Output object returned when calling `NicccParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def niccc_params(
     quiet: bool = False,
     find_attr: list[str] | None = None,
     skip_attr: list[str] | None = None,
-) -> NicccParameters:
+) -> NicccParametersTagged:
     """
     Build parameters.
     
@@ -113,7 +96,7 @@ def niccc_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "niccc",
+        "@type": "afni/niccc",
         "streamspec": streamspec,
         "duplicate": duplicate,
         "nodata": nodata,
@@ -149,40 +132,40 @@ def niccc_cargs(
     """
     cargs = []
     cargs.append("niccc")
-    cargs.append(params.get("streamspec"))
-    if params.get("duplicate"):
+    cargs.append(params.get("streamspec", None))
+    if params.get("duplicate", False):
         cargs.append("-dup")
-    if params.get("nodata"):
+    if params.get("nodata", False):
         cargs.append("-nodata")
-    if params.get("attribute") is not None:
+    if params.get("attribute", None) is not None:
         cargs.extend([
             "-attribute",
-            params.get("attribute")
+            params.get("attribute", None)
         ])
-    if params.get("match") is not None:
+    if params.get("match", None) is not None:
         cargs.extend([
             "-match",
-            params.get("match")
+            params.get("match", None)
         ])
-    if params.get("file"):
+    if params.get("file", False):
         cargs.append("-f")
-    if params.get("string"):
+    if params.get("string", False):
         cargs.append("-s")
-    if params.get("stdout"):
+    if params.get("stdout", False):
         cargs.append("-stdout")
-    if params.get("hash"):
+    if params.get("hash", False):
         cargs.append("-#")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("find_attr") is not None:
+    if params.get("find_attr", None) is not None:
         cargs.extend([
             "-find_nel_with_attr",
-            *params.get("find_attr")
+            *params.get("find_attr", None)
         ])
-    if params.get("skip_attr") is not None:
+    if params.get("skip_attr", None) is not None:
         cargs.extend([
             "-skip_nel_with_attr",
-            *params.get("skip_attr")
+            *params.get("skip_attr", None)
         ])
     return cargs
 
@@ -209,11 +192,13 @@ def niccc_outputs(
 
 def niccc_execute(
     params: NicccParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NicccOutputs:
     """
-    A program for conducting certain NIML tests on input from streamspec and write
-    the results to stderr.
+    niccc
+    
+    A program for conducting certain NIML tests on input from streamspec and
+    write the results to stderr.
     
     Author: AFNI Developers
     
@@ -221,10 +206,12 @@ def niccc_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NicccOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NICCC_METADATA)
     params = execution.params(params)
     cargs = niccc_cargs(params, execution)
     ret = niccc_outputs(params, execution)
@@ -248,8 +235,10 @@ def niccc(
     runner: Runner | None = None,
 ) -> NicccOutputs:
     """
-    A program for conducting certain NIML tests on input from streamspec and write
-    the results to stderr.
+    niccc
+    
+    A program for conducting certain NIML tests on input from streamspec and
+    write the results to stderr.
     
     Author: AFNI Developers
     
@@ -279,8 +268,6 @@ def niccc(
     Returns:
         NamedTuple of outputs (described in `NicccOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NICCC_METADATA)
     params = niccc_params(
         streamspec=streamspec,
         duplicate=duplicate,
@@ -295,13 +282,13 @@ def niccc(
         find_attr=find_attr,
         skip_attr=skip_attr,
     )
-    return niccc_execute(params, execution)
+    return niccc_execute(params, runner)
 
 
 __all__ = [
     "NICCC_METADATA",
     "NicccOutputs",
-    "NicccParameters",
     "niccc",
+    "niccc_execute",
     "niccc_params",
 ]

niwrap_afni/afni/nifti_tool.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NIFTI_TOOL_METADATA = Metadata(
-    id="9789f342be7ffa2a9b170901d7f6938dde505424.boutiques",
+    id="c38dcd8a1c8c213776e12797ae1106aacaa014e6.boutiques",
     name="nifti_tool",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,22 @@ NIFTI_TOOL_METADATA = Metadata(
 
 
 NiftiToolParameters = typing.TypedDict('NiftiToolParameters', {
-    "__STYXTYPE__": typing.Literal["nifti_tool"],
+    "@type": typing.NotRequired[typing.Literal["afni/nifti_tool"]],
+    "action": str,
+    "input_files": typing.NotRequired[list[InputPathType] | None],
+    "field": typing.NotRequired[str | None],
+    "mod_field": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "debug": typing.NotRequired[float | None],
+    "overwrite": bool,
+    "convert2dtype": typing.NotRequired[str | None],
+    "convert_fail_choice": typing.NotRequired[str | None],
+    "convert_verify": bool,
+    "add_comment_ext": typing.NotRequired[str | None],
+    "rm_ext": typing.NotRequired[str | None],
+})
+NiftiToolParametersTagged = typing.TypedDict('NiftiToolParametersTagged', {
+    "@type": typing.Literal["afni/nifti_tool"],
     "action": str,
     "input_files": typing.NotRequired[list[InputPathType] | None],
     "field": typing.NotRequired[str | None],
@@ -28,43 +43,11 @@ NiftiToolParameters = typing.TypedDict('NiftiToolParameters', {
     "add_comment_ext": typing.NotRequired[str | None],
     "rm_ext": 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 {
-        "nifti_tool": nifti_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 {
-        "nifti_tool": nifti_tool_outputs,
-    }.get(t)
 
 
 class NiftiToolOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `nifti_tool(...)`.
+    Output object returned when calling `NiftiToolParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +68,7 @@ def nifti_tool_params(
     convert_verify: bool = False,
     add_comment_ext: str | None = None,
     rm_ext: str | None = None,
-) -> NiftiToolParameters:
+) -> NiftiToolParametersTagged:
     """
     Build parameters.
     
@@ -106,7 +89,7 @@ def nifti_tool_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "nifti_tool",
+        "@type": "afni/nifti_tool",
         "action": action,
         "overwrite": overwrite,
         "convert_verify": convert_verify,
@@ -147,55 +130,55 @@ def nifti_tool_cargs(
     """
     cargs = []
     cargs.append("nifti_tool")
-    cargs.append(params.get("action"))
-    if params.get("input_files") is not None:
+    cargs.append(params.get("action", None))
+    if params.get("input_files", None) is not None:
         cargs.extend([
             "-infiles",
-            *[execution.input_file(f) for f in params.get("input_files")]
+            *[execution.input_file(f) for f in params.get("input_files", None)]
         ])
-    if params.get("field") is not None:
+    if params.get("field", None) is not None:
         cargs.extend([
             "-field",
-            params.get("field")
+            params.get("field", None)
         ])
-    if params.get("mod_field") is not None:
+    if params.get("mod_field", None) is not None:
         cargs.extend([
             "-mod_field",
-            params.get("mod_field")
+            params.get("mod_field", None)
         ])
-    if params.get("prefix") is not None:
+    if params.get("prefix", None) is not None:
         cargs.extend([
             "-prefix",
-            params.get("prefix")
+            params.get("prefix", 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("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("convert2dtype") is not None:
+    if params.get("convert2dtype", None) is not None:
         cargs.extend([
             "-convert2dtype",
-            params.get("convert2dtype")
+            params.get("convert2dtype", None)
         ])
-    if params.get("convert_fail_choice") is not None:
+    if params.get("convert_fail_choice", None) is not None:
         cargs.extend([
             "-convert_fail_choice",
-            params.get("convert_fail_choice")
+            params.get("convert_fail_choice", None)
         ])
-    if params.get("convert_verify"):
+    if params.get("convert_verify", False):
         cargs.append("-convert_verify")
-    if params.get("add_comment_ext") is not None:
+    if params.get("add_comment_ext", None) is not None:
         cargs.extend([
             "-add_comment_ext",
-            params.get("add_comment_ext")
+            params.get("add_comment_ext", None)
         ])
-    if params.get("rm_ext") is not None:
+    if params.get("rm_ext", None) is not None:
         cargs.extend([
             "-rm_ext",
-            params.get("rm_ext")
+            params.get("rm_ext", None)
         ])
     return cargs
 
@@ -215,16 +198,18 @@ def nifti_tool_outputs(
     """
     ret = NiftiToolOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def nifti_tool_execute(
     params: NiftiToolParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NiftiToolOutputs:
     """
+    nifti_tool
+    
     Display, modify, or compare nifti headers.
     
     Author: AFNI Developers
@@ -233,10 +218,12 @@ def nifti_tool_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NiftiToolOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NIFTI_TOOL_METADATA)
     params = execution.params(params)
     cargs = nifti_tool_cargs(params, execution)
     ret = nifti_tool_outputs(params, execution)
@@ -260,6 +247,8 @@ def nifti_tool(
     runner: Runner | None = None,
 ) -> NiftiToolOutputs:
     """
+    nifti_tool
+    
     Display, modify, or compare nifti headers.
     
     Author: AFNI Developers
@@ -283,8 +272,6 @@ def nifti_tool(
     Returns:
         NamedTuple of outputs (described in `NiftiToolOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NIFTI_TOOL_METADATA)
     params = nifti_tool_params(
         action=action,
         input_files=input_files,
@@ -299,13 +286,13 @@ def nifti_tool(
         add_comment_ext=add_comment_ext,
         rm_ext=rm_ext,
     )
-    return nifti_tool_execute(params, execution)
+    return nifti_tool_execute(params, runner)
 
 
 __all__ = [
     "NIFTI_TOOL_METADATA",
     "NiftiToolOutputs",
-    "NiftiToolParameters",
     "nifti_tool",
+    "nifti_tool_execute",
     "nifti_tool_params",
 ]