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

niwrap_afni/afni/niml_feedme.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NIML_FEEDME_METADATA = Metadata(
-    id="045d80f46fa43e5a4d550a5bf8daeb0c433c5c4f.boutiques",
+    id="5587cd9ad0d1cc56832bc13aa8db7f348d3591d5.boutiques",
     name="niml_feedme",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ NIML_FEEDME_METADATA = Metadata(
 
 
 NimlFeedmeParameters = typing.TypedDict('NimlFeedmeParameters', {
-    "__STYXTYPE__": typing.Literal["niml_feedme"],
+    "@type": typing.NotRequired[typing.Literal["afni/niml_feedme"]],
+    "host": typing.NotRequired[str | None],
+    "interval": typing.NotRequired[float | None],
+    "verbose": bool,
+    "accum": bool,
+    "target_dataset": typing.NotRequired[str | None],
+    "drive_cmds": typing.NotRequired[list[str] | None],
+    "dataset": InputPathType,
+})
+NimlFeedmeParametersTagged = typing.TypedDict('NimlFeedmeParametersTagged', {
+    "@type": typing.Literal["afni/niml_feedme"],
     "host": typing.NotRequired[str | None],
     "interval": typing.NotRequired[float | None],
     "verbose": bool,
@@ -23,42 +33,11 @@ NimlFeedmeParameters = typing.TypedDict('NimlFeedmeParameters', {
     "drive_cmds": typing.NotRequired[list[str] | None],
     "dataset": InputPathType,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "niml_feedme": niml_feedme_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 NimlFeedmeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `niml_feedme(...)`.
+    Output object returned when calling `NimlFeedmeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -72,7 +51,7 @@ def niml_feedme_params(
     accum: bool = False,
     target_dataset: str | None = None,
     drive_cmds: list[str] | None = None,
-) -> NimlFeedmeParameters:
+) -> NimlFeedmeParametersTagged:
     """
     Build parameters.
     
@@ -97,7 +76,7 @@ def niml_feedme_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "niml_feedme",
+        "@type": "afni/niml_feedme",
         "verbose": verbose,
         "accum": accum,
         "dataset": dataset,
@@ -128,31 +107,31 @@ def niml_feedme_cargs(
     """
     cargs = []
     cargs.append("niml_feedme")
-    if params.get("host") is not None:
+    if params.get("host", None) is not None:
         cargs.extend([
             "-host",
-            params.get("host")
+            params.get("host", None)
         ])
-    if params.get("interval") is not None:
+    if params.get("interval", None) is not None:
         cargs.extend([
             "-dt",
-            str(params.get("interval"))
+            str(params.get("interval", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("accum"):
+    if params.get("accum", False):
         cargs.append("-accum")
-    if params.get("target_dataset") is not None:
+    if params.get("target_dataset", None) is not None:
         cargs.extend([
             "-target",
-            params.get("target_dataset")
+            params.get("target_dataset", None)
         ])
-    if params.get("drive_cmds") is not None:
+    if params.get("drive_cmds", None) is not None:
         cargs.extend([
             "-drive",
-            *params.get("drive_cmds")
+            *params.get("drive_cmds", None)
         ])
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -177,9 +156,11 @@ def niml_feedme_outputs(
 
 def niml_feedme_execute(
     params: NimlFeedmeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NimlFeedmeOutputs:
     """
+    niml_feedme
+    
     Sends volumes from the dataset to AFNI via the NIML socket interface.
     
     Author: AFNI Developers
@@ -188,10 +169,12 @@ def niml_feedme_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NimlFeedmeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NIML_FEEDME_METADATA)
     params = execution.params(params)
     cargs = niml_feedme_cargs(params, execution)
     ret = niml_feedme_outputs(params, execution)
@@ -210,6 +193,8 @@ def niml_feedme(
     runner: Runner | None = None,
 ) -> NimlFeedmeOutputs:
     """
+    niml_feedme
+    
     Sends volumes from the dataset to AFNI via the NIML socket interface.
     
     Author: AFNI Developers
@@ -237,8 +222,6 @@ def niml_feedme(
     Returns:
         NamedTuple of outputs (described in `NimlFeedmeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NIML_FEEDME_METADATA)
     params = niml_feedme_params(
         host=host,
         interval=interval,
@@ -248,13 +231,13 @@ def niml_feedme(
         drive_cmds=drive_cmds,
         dataset=dataset,
     )
-    return niml_feedme_execute(params, execution)
+    return niml_feedme_execute(params, runner)
 
 
 __all__ = [
     "NIML_FEEDME_METADATA",
     "NimlFeedmeOutputs",
-    "NimlFeedmeParameters",
     "niml_feedme",
+    "niml_feedme_execute",
     "niml_feedme_params",
 ]

niwrap_afni/afni/nsize.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 NSIZE_METADATA = Metadata(
-    id="a9d2ae05ed0705b6b163c901233146b3b789bc31.boutiques",
+    id="3ce24bfc99036870491608926e2af290bef3ada3.boutiques",
     name="nsize",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,47 +14,20 @@ NSIZE_METADATA = Metadata(
 
 
 NsizeParameters = typing.TypedDict('NsizeParameters', {
-    "__STYXTYPE__": typing.Literal["nsize"],
+    "@type": typing.NotRequired[typing.Literal["afni/nsize"]],
+    "image_in": InputPathType,
+    "image_out": str,
+})
+NsizeParametersTagged = typing.TypedDict('NsizeParametersTagged', {
+    "@type": typing.Literal["afni/nsize"],
     "image_in": InputPathType,
     "image_out": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "nsize": nsize_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 {
-        "nsize": nsize_outputs,
-    }.get(t)
 
 
 class NsizeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `nsize(...)`.
+    Output object returned when calling `NsizeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -65,7 +38,7 @@ class NsizeOutputs(typing.NamedTuple):
 def nsize_params(
     image_in: InputPathType,
     image_out: str,
-) -> NsizeParameters:
+) -> NsizeParametersTagged:
     """
     Build parameters.
     
@@ -76,7 +49,7 @@ def nsize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "nsize",
+        "@type": "afni/nsize",
         "image_in": image_in,
         "image_out": image_out,
     }
@@ -98,8 +71,8 @@ def nsize_cargs(
     """
     cargs = []
     cargs.append("nsize")
-    cargs.append(execution.input_file(params.get("image_in")))
-    cargs.append(params.get("image_out"))
+    cargs.append(execution.input_file(params.get("image_in", None)))
+    cargs.append(params.get("image_out", None))
     return cargs
 
 
@@ -118,16 +91,18 @@ def nsize_outputs(
     """
     ret = NsizeOutputs(
         root=execution.output_file("."),
-        image_out_file=execution.output_file(params.get("image_out")),
+        image_out_file=execution.output_file(params.get("image_out", None)),
     )
     return ret
 
 
 def nsize_execute(
     params: NsizeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> NsizeOutputs:
     """
+    nsize
+    
     Zero pads an input image to the nearest larger NxN dimensions.
     
     Author: AFNI Developers
@@ -136,10 +111,12 @@ def nsize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `NsizeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(NSIZE_METADATA)
     params = execution.params(params)
     cargs = nsize_cargs(params, execution)
     ret = nsize_outputs(params, execution)
@@ -153,6 +130,8 @@ def nsize(
     runner: Runner | None = None,
 ) -> NsizeOutputs:
     """
+    nsize
+    
     Zero pads an input image to the nearest larger NxN dimensions.
     
     Author: AFNI Developers
@@ -166,19 +145,17 @@ def nsize(
     Returns:
         NamedTuple of outputs (described in `NsizeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(NSIZE_METADATA)
     params = nsize_params(
         image_in=image_in,
         image_out=image_out,
     )
-    return nsize_execute(params, execution)
+    return nsize_execute(params, runner)
 
 
 __all__ = [
     "NSIZE_METADATA",
     "NsizeOutputs",
-    "NsizeParameters",
     "nsize",
+    "nsize_execute",
     "nsize_params",
 ]

niwrap_afni/afni/p2dsetstat.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 P2DSETSTAT_METADATA = Metadata(
-    id="bf97782e51f33e92fa4f622b20ca100db34f1437.boutiques",
+    id="2d263db81db9ab4c4b01892dae28a9649f9c93a3.boutiques",
     name="p2dsetstat",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ P2DSETSTAT_METADATA = Metadata(
 
 
 P2dsetstatParameters = typing.TypedDict('P2dsetstatParameters', {
-    "__STYXTYPE__": typing.Literal["p2dsetstat"],
+    "@type": typing.NotRequired[typing.Literal["afni/p2dsetstat"]],
+    "dataset": str,
+    "pvalue": float,
+    "bisided": bool,
+    "twosided": bool,
+    "onesided": bool,
+    "quiet": bool,
+})
+P2dsetstatParametersTagged = typing.TypedDict('P2dsetstatParametersTagged', {
+    "@type": typing.Literal["afni/p2dsetstat"],
     "dataset": str,
     "pvalue": float,
     "bisided": bool,
@@ -22,43 +31,11 @@ P2dsetstatParameters = typing.TypedDict('P2dsetstatParameters', {
     "onesided": bool,
     "quiet": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "p2dsetstat": p2dsetstat_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 {
-        "p2dsetstat": p2dsetstat_outputs,
-    }.get(t)
 
 
 class P2dsetstatOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `p2dsetstat(...)`.
+    Output object returned when calling `P2dsetstatParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +50,7 @@ def p2dsetstat_params(
     twosided: bool = False,
     onesided: bool = False,
     quiet: bool = False,
-) -> P2dsetstatParameters:
+) -> P2dsetstatParametersTagged:
     """
     Build parameters.
     
@@ -92,7 +69,7 @@ def p2dsetstat_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "p2dsetstat",
+        "@type": "afni/p2dsetstat",
         "dataset": dataset,
         "pvalue": pvalue,
         "bisided": bisided,
@@ -120,19 +97,19 @@ def p2dsetstat_cargs(
     cargs.append("p2dsetstat")
     cargs.extend([
         "-inset",
-        params.get("dataset")
+        params.get("dataset", None)
     ])
     cargs.extend([
         "-pval",
-        str(params.get("pvalue"))
+        str(params.get("pvalue", None))
     ])
-    if params.get("bisided"):
+    if params.get("bisided", False):
         cargs.append("-bisided")
-    if params.get("twosided"):
+    if params.get("twosided", False):
         cargs.append("-2sided")
-    if params.get("onesided"):
+    if params.get("onesided", False):
         cargs.append("-1sided")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
     return cargs
 
@@ -159,10 +136,13 @@ def p2dsetstat_outputs(
 
 def p2dsetstat_execute(
     params: P2dsetstatParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> P2dsetstatOutputs:
     """
-    Convert a p-value to a statistic of choice with reference to a specific dataset.
+    p2dsetstat
+    
+    Convert a p-value to a statistic of choice with reference to a specific
+    dataset.
     
     Author: AFNI Developers
     
@@ -170,10 +150,12 @@ def p2dsetstat_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `P2dsetstatOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(P2DSETSTAT_METADATA)
     params = execution.params(params)
     cargs = p2dsetstat_cargs(params, execution)
     ret = p2dsetstat_outputs(params, execution)
@@ -191,7 +173,10 @@ def p2dsetstat(
     runner: Runner | None = None,
 ) -> P2dsetstatOutputs:
     """
-    Convert a p-value to a statistic of choice with reference to a specific dataset.
+    p2dsetstat
+    
+    Convert a p-value to a statistic of choice with reference to a specific
+    dataset.
     
     Author: AFNI Developers
     
@@ -212,8 +197,6 @@ def p2dsetstat(
     Returns:
         NamedTuple of outputs (described in `P2dsetstatOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(P2DSETSTAT_METADATA)
     params = p2dsetstat_params(
         dataset=dataset,
         pvalue=pvalue,
@@ -222,13 +205,13 @@ def p2dsetstat(
         onesided=onesided,
         quiet=quiet,
     )
-    return p2dsetstat_execute(params, execution)
+    return p2dsetstat_execute(params, runner)
 
 
 __all__ = [
     "P2DSETSTAT_METADATA",
     "P2dsetstatOutputs",
-    "P2dsetstatParameters",
     "p2dsetstat",
+    "p2dsetstat_execute",
     "p2dsetstat_params",
 ]

niwrap_afni/afni/parse_fs_lt_log_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 PARSE_FS_LT_LOG_PY_METADATA = Metadata(
-    id="eea3154b221cecc946f3e7770034475288b7026a.boutiques",
+    id="4a69eeba6f91f13034077316927725321424fc4f.boutiques",
     name="parse_fs_lt_log.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,26 @@ PARSE_FS_LT_LOG_PY_METADATA = Metadata(
 
 
 ParseFsLtLogPyParameters = typing.TypedDict('ParseFsLtLogPyParameters', {
-    "__STYXTYPE__": typing.Literal["parse_fs_lt_log.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/parse_fs_lt_log.py"]],
+    "logfile": InputPathType,
+    "labels": list[str],
+    "show_orig": bool,
+    "show_all_orig": bool,
+    "verbosity": typing.NotRequired[float | None],
+})
+ParseFsLtLogPyParametersTagged = typing.TypedDict('ParseFsLtLogPyParametersTagged', {
+    "@type": typing.Literal["afni/parse_fs_lt_log.py"],
     "logfile": InputPathType,
     "labels": list[str],
     "show_orig": bool,
     "show_all_orig": bool,
     "verbosity": 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 {
-        "parse_fs_lt_log.py": parse_fs_lt_log_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 ParseFsLtLogPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `parse_fs_lt_log_py(...)`.
+    Output object returned when calling `ParseFsLtLogPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -68,7 +45,7 @@ def parse_fs_lt_log_py_params(
     show_orig: bool = False,
     show_all_orig: bool = False,
     verbosity: float | None = None,
-) -> ParseFsLtLogPyParameters:
+) -> ParseFsLtLogPyParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +59,7 @@ def parse_fs_lt_log_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "parse_fs_lt_log.py",
+        "@type": "afni/parse_fs_lt_log.py",
         "logfile": logfile,
         "labels": labels,
         "show_orig": show_orig,
@@ -110,20 +87,20 @@ def parse_fs_lt_log_py_cargs(
     cargs.append("parse_fs_lt_log.py")
     cargs.extend([
         "-logfile",
-        execution.input_file(params.get("logfile"))
+        execution.input_file(params.get("logfile", None))
     ])
     cargs.extend([
         "-labels",
-        *params.get("labels")
+        *params.get("labels", None)
     ])
-    if params.get("show_orig"):
+    if params.get("show_orig", False):
         cargs.append("-show_orig")
-    if params.get("show_all_orig"):
+    if params.get("show_all_orig", False):
         cargs.append("-show_all_orig")
-    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))
         ])
     return cargs
 
@@ -149,9 +126,11 @@ def parse_fs_lt_log_py_outputs(
 
 def parse_fs_lt_log_py_execute(
     params: ParseFsLtLogPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> ParseFsLtLogPyOutputs:
     """
+    parse_fs_lt_log.py
+    
     Parses FreeSurfer labeltable log file and retrieves labeltable indices.
     
     Author: AFNI Developers
@@ -160,10 +139,12 @@ def parse_fs_lt_log_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `ParseFsLtLogPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(PARSE_FS_LT_LOG_PY_METADATA)
     params = execution.params(params)
     cargs = parse_fs_lt_log_py_cargs(params, execution)
     ret = parse_fs_lt_log_py_outputs(params, execution)
@@ -180,6 +161,8 @@ def parse_fs_lt_log_py(
     runner: Runner | None = None,
 ) -> ParseFsLtLogPyOutputs:
     """
+    parse_fs_lt_log.py
+    
     Parses FreeSurfer labeltable log file and retrieves labeltable indices.
     
     Author: AFNI Developers
@@ -196,8 +179,6 @@ def parse_fs_lt_log_py(
     Returns:
         NamedTuple of outputs (described in `ParseFsLtLogPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(PARSE_FS_LT_LOG_PY_METADATA)
     params = parse_fs_lt_log_py_params(
         logfile=logfile,
         labels=labels,
@@ -205,13 +186,13 @@ def parse_fs_lt_log_py(
         show_all_orig=show_all_orig,
         verbosity=verbosity,
     )
-    return parse_fs_lt_log_py_execute(params, execution)
+    return parse_fs_lt_log_py_execute(params, runner)
 
 
 __all__ = [
     "PARSE_FS_LT_LOG_PY_METADATA",
     "ParseFsLtLogPyOutputs",
-    "ParseFsLtLogPyParameters",
     "parse_fs_lt_log_py",
+    "parse_fs_lt_log_py_execute",
     "parse_fs_lt_log_py_params",
 ]