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

niwrap_afni/afni/tfim.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TFIM_METADATA = Metadata(
-    id="38e322eb579d3ffa906fe84891ae928a1b57f743.boutiques",
+    id="e87b2aa4efb80b1f5b57aa6c492c17c5946f1793.boutiques",
     name="tfim",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ TFIM_METADATA = Metadata(
 
 
 TfimParameters = typing.TypedDict('TfimParameters', {
-    "__STYXTYPE__": typing.Literal["tfim"],
+    "@type": typing.NotRequired[typing.Literal["afni/tfim"]],
+    "prefix": typing.NotRequired[str | None],
+    "pthresh": typing.NotRequired[float | None],
+    "eqcorr": typing.NotRequired[float | None],
+    "paired": bool,
+    "set1_images": list[InputPathType],
+    "set2_images": list[InputPathType],
+    "base1_value": typing.NotRequired[float | None],
+})
+TfimParametersTagged = typing.TypedDict('TfimParametersTagged', {
+    "@type": typing.Literal["afni/tfim"],
     "prefix": typing.NotRequired[str | None],
     "pthresh": typing.NotRequired[float | None],
     "eqcorr": typing.NotRequired[float | None],
@@ -23,43 +33,11 @@ TfimParameters = typing.TypedDict('TfimParameters', {
     "set2_images": list[InputPathType],
     "base1_value": 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 {
-        "tfim": tfim_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 {
-        "tfim": tfim_outputs,
-    }.get(t)
 
 
 class TfimOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `tfim(...)`.
+    Output object returned when calling `TfimParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +57,7 @@ def tfim_params(
     eqcorr: float | None = None,
     paired: bool = False,
     base1_value: float | None = None,
-) -> TfimParameters:
+) -> TfimParametersTagged:
     """
     Build parameters.
     
@@ -100,7 +78,7 @@ def tfim_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "tfim",
+        "@type": "afni/tfim",
         "paired": paired,
         "set1_images": set1_images,
         "set2_images": set2_images,
@@ -131,35 +109,35 @@ def tfim_cargs(
     """
     cargs = []
     cargs.append("tfim")
-    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("pthresh") is not None:
+    if params.get("pthresh", None) is not None:
         cargs.extend([
             "-pthresh",
-            str(params.get("pthresh"))
+            str(params.get("pthresh", None))
         ])
-    if params.get("eqcorr") is not None:
+    if params.get("eqcorr", None) is not None:
         cargs.extend([
             "-eqcorr",
-            str(params.get("eqcorr"))
+            str(params.get("eqcorr", None))
         ])
-    if params.get("paired"):
+    if params.get("paired", False):
         cargs.append("-paired")
     cargs.extend([
         "-set1",
-        *[execution.input_file(f) for f in params.get("set1_images")]
+        *[execution.input_file(f) for f in params.get("set1_images", None)]
     ])
     cargs.extend([
         "-set2",
-        *[execution.input_file(f) for f in params.get("set2_images")]
+        *[execution.input_file(f) for f in params.get("set2_images", None)]
     ])
-    if params.get("base1_value") is not None:
+    if params.get("base1_value", None) is not None:
         cargs.extend([
             "-base1",
-            str(params.get("base1_value"))
+            str(params.get("base1_value", None))
         ])
     return cargs
 
@@ -179,18 +157,20 @@ def tfim_outputs(
     """
     ret = TfimOutputs(
         root=execution.output_file("."),
-        diff_output=execution.output_file(params.get("prefix") + ".diff") if (params.get("prefix") is not None) else None,
-        tspm_output=execution.output_file(params.get("prefix") + ".tspm") if (params.get("prefix") is not None) else None,
-        corr_output=execution.output_file(params.get("prefix") + ".corr") if (params.get("prefix") is not None) else None,
+        diff_output=execution.output_file(params.get("prefix", None) + ".diff") if (params.get("prefix") is not None) else None,
+        tspm_output=execution.output_file(params.get("prefix", None) + ".tspm") if (params.get("prefix") is not None) else None,
+        corr_output=execution.output_file(params.get("prefix", None) + ".corr") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def tfim_execute(
     params: TfimParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TfimOutputs:
     """
+    tfim
+    
     MCW TFIM: t-tests on sets of functional images.
     
     Author: AFNI Developers
@@ -199,10 +179,12 @@ def tfim_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TfimOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TFIM_METADATA)
     params = execution.params(params)
     cargs = tfim_cargs(params, execution)
     ret = tfim_outputs(params, execution)
@@ -221,6 +203,8 @@ def tfim(
     runner: Runner | None = None,
 ) -> TfimOutputs:
     """
+    tfim
+    
     MCW TFIM: t-tests on sets of functional images.
     
     Author: AFNI Developers
@@ -244,8 +228,6 @@ def tfim(
     Returns:
         NamedTuple of outputs (described in `TfimOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TFIM_METADATA)
     params = tfim_params(
         prefix=prefix,
         pthresh=pthresh,
@@ -255,13 +237,13 @@ def tfim(
         set2_images=set2_images,
         base1_value=base1_value,
     )
-    return tfim_execute(params, execution)
+    return tfim_execute(params, runner)
 
 
 __all__ = [
     "TFIM_METADATA",
     "TfimOutputs",
-    "TfimParameters",
     "tfim",
+    "tfim_execute",
     "tfim_params",
 ]

niwrap_afni/afni/timing_tool_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TIMING_TOOL_PY_METADATA = Metadata(
-    id="a4ec6d467d16a0ee7788f24ba2104b0d64b24601.boutiques",
+    id="c6a750e559b7e1a87795b8b6883c0238bf717721.boutiques",
     name="timing_tool.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,29 @@ TIMING_TOOL_PY_METADATA = Metadata(
 
 
 TimingToolPyParameters = typing.TypedDict('TimingToolPyParameters', {
-    "__STYXTYPE__": typing.Literal["timing_tool.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/timing_tool.py"]],
+    "timing_file": typing.NotRequired[InputPathType | None],
+    "output_file": typing.NotRequired[str | None],
+    "run_length": typing.NotRequired[list[float] | None],
+    "tr": typing.NotRequired[float | None],
+    "offset": typing.NotRequired[float | None],
+    "extend_file": typing.NotRequired[InputPathType | None],
+    "sort": bool,
+    "scale_data": typing.NotRequired[float | None],
+    "shift_to_run_offset": typing.NotRequired[float | None],
+    "timing_to_1D_file": typing.NotRequired[str | None],
+    "stim_duration": typing.NotRequired[float | None],
+    "multi_timing_files": typing.NotRequired[list[InputPathType] | None],
+    "multi_show_isi_stats": bool,
+    "multi_show_timing": bool,
+    "show_timing": bool,
+    "multi_stim_duration": typing.NotRequired[list[float] | None],
+    "round_times_frac": typing.NotRequired[float | None],
+    "truncate_times": bool,
+    "multi_timing_event_list": typing.NotRequired[str | None],
+})
+TimingToolPyParametersTagged = typing.TypedDict('TimingToolPyParametersTagged', {
+    "@type": typing.Literal["afni/timing_tool.py"],
     "timing_file": typing.NotRequired[InputPathType | None],
     "output_file": typing.NotRequired[str | None],
     "run_length": typing.NotRequired[list[float] | None],
@@ -35,43 +57,11 @@ TimingToolPyParameters = typing.TypedDict('TimingToolPyParameters', {
     "truncate_times": bool,
     "multi_timing_event_list": 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 {
-        "timing_tool.py": timing_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 {
-        "timing_tool.py": timing_tool_py_outputs,
-    }.get(t)
 
 
 class TimingToolPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `timing_tool_py(...)`.
+    Output object returned when calling `TimingToolPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +91,7 @@ def timing_tool_py_params(
     round_times_frac: float | None = None,
     truncate_times: bool = False,
     multi_timing_event_list: str | None = None,
-) -> TimingToolPyParameters:
+) -> TimingToolPyParametersTagged:
     """
     Build parameters.
     
@@ -133,7 +123,7 @@ def timing_tool_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "timing_tool.py",
+        "@type": "afni/timing_tool.py",
         "sort": sort,
         "multi_show_isi_stats": multi_show_isi_stats,
         "multi_show_timing": multi_show_timing,
@@ -186,85 +176,85 @@ def timing_tool_py_cargs(
     """
     cargs = []
     cargs.append("timing_tool.py")
-    if params.get("timing_file") is not None:
+    if params.get("timing_file", None) is not None:
         cargs.extend([
             "-timing",
-            execution.input_file(params.get("timing_file"))
+            execution.input_file(params.get("timing_file", None))
         ])
-    if params.get("output_file") is not None:
+    if params.get("output_file", None) is not None:
         cargs.extend([
             "-write_timing",
-            params.get("output_file")
+            params.get("output_file", None)
         ])
-    if params.get("run_length") is not None:
+    if params.get("run_length", None) is not None:
         cargs.extend([
             "-run_len",
-            *map(str, params.get("run_length"))
+            *map(str, params.get("run_length", None))
         ])
-    if params.get("tr") is not None:
+    if params.get("tr", None) is not None:
         cargs.extend([
             "-tr",
-            str(params.get("tr"))
+            str(params.get("tr", None))
         ])
-    if params.get("offset") is not None:
+    if params.get("offset", None) is not None:
         cargs.extend([
             "-add_offset",
-            str(params.get("offset"))
+            str(params.get("offset", None))
         ])
-    if params.get("extend_file") is not None:
+    if params.get("extend_file", None) is not None:
         cargs.extend([
             "-extend",
-            execution.input_file(params.get("extend_file"))
+            execution.input_file(params.get("extend_file", None))
         ])
-    if params.get("sort"):
+    if params.get("sort", False):
         cargs.append("-sort")
-    if params.get("scale_data") is not None:
+    if params.get("scale_data", None) is not None:
         cargs.extend([
             "-scale_data",
-            str(params.get("scale_data"))
+            str(params.get("scale_data", None))
         ])
-    if params.get("shift_to_run_offset") is not None:
+    if params.get("shift_to_run_offset", None) is not None:
         cargs.extend([
             "-shift_to_run_offset",
-            str(params.get("shift_to_run_offset"))
+            str(params.get("shift_to_run_offset", None))
         ])
-    if params.get("timing_to_1D_file") is not None:
+    if params.get("timing_to_1D_file", None) is not None:
         cargs.extend([
             "-timing_to_1D",
-            params.get("timing_to_1D_file")
+            params.get("timing_to_1D_file", None)
         ])
-    if params.get("stim_duration") is not None:
+    if params.get("stim_duration", None) is not None:
         cargs.extend([
             "-stim_dur",
-            str(params.get("stim_duration"))
+            str(params.get("stim_duration", None))
         ])
-    if params.get("multi_timing_files") is not None:
+    if params.get("multi_timing_files", None) is not None:
         cargs.extend([
             "-multi_timing",
-            *[execution.input_file(f) for f in params.get("multi_timing_files")]
+            *[execution.input_file(f) for f in params.get("multi_timing_files", None)]
         ])
-    if params.get("multi_show_isi_stats"):
+    if params.get("multi_show_isi_stats", False):
         cargs.append("-multi_show_isi_stats")
-    if params.get("multi_show_timing"):
+    if params.get("multi_show_timing", False):
         cargs.append("-multi_show_timing_ele")
-    if params.get("show_timing"):
+    if params.get("show_timing", False):
         cargs.append("-show_timing_ele")
-    if params.get("multi_stim_duration") is not None:
+    if params.get("multi_stim_duration", None) is not None:
         cargs.extend([
             "-multi_stim_dur",
-            *map(str, params.get("multi_stim_duration"))
+            *map(str, params.get("multi_stim_duration", None))
         ])
-    if params.get("round_times_frac") is not None:
+    if params.get("round_times_frac", None) is not None:
         cargs.extend([
             "-round_times",
-            str(params.get("round_times_frac"))
+            str(params.get("round_times_frac", None))
         ])
-    if params.get("truncate_times"):
+    if params.get("truncate_times", False):
         cargs.append("-truncate_times")
-    if params.get("multi_timing_event_list") is not None:
+    if params.get("multi_timing_event_list", None) is not None:
         cargs.extend([
             "-multi_timing_to_event_list",
-            params.get("multi_timing_event_list")
+            params.get("multi_timing_event_list", None)
         ])
     return cargs
 
@@ -284,17 +274,19 @@ def timing_tool_py_outputs(
     """
     ret = TimingToolPyOutputs(
         root=execution.output_file("."),
-        output_timing_file=execution.output_file(params.get("output_file")) if (params.get("output_file") is not None) else None,
-        timing_to_1_d_output=execution.output_file(params.get("timing_to_1D_file")) if (params.get("timing_to_1D_file") is not None) else None,
+        output_timing_file=execution.output_file(params.get("output_file", None)) if (params.get("output_file") is not None) else None,
+        timing_to_1_d_output=execution.output_file(params.get("timing_to_1D_file", None)) if (params.get("timing_to_1D_file") is not None) else None,
     )
     return ret
 
 
 def timing_tool_py_execute(
     params: TimingToolPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> TimingToolPyOutputs:
     """
+    timing_tool.py
+    
     Tool for manipulating and evaluating stimulus timing files.
     
     Author: AFNI Developers
@@ -303,10 +295,12 @@ def timing_tool_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TimingToolPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(TIMING_TOOL_PY_METADATA)
     params = execution.params(params)
     cargs = timing_tool_py_cargs(params, execution)
     ret = timing_tool_py_outputs(params, execution)
@@ -337,6 +331,8 @@ def timing_tool_py(
     runner: Runner | None = None,
 ) -> TimingToolPyOutputs:
     """
+    timing_tool.py
+    
     Tool for manipulating and evaluating stimulus timing files.
     
     Author: AFNI Developers
@@ -371,8 +367,6 @@ def timing_tool_py(
     Returns:
         NamedTuple of outputs (described in `TimingToolPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(TIMING_TOOL_PY_METADATA)
     params = timing_tool_py_params(
         timing_file=timing_file,
         output_file=output_file,
@@ -394,13 +388,13 @@ def timing_tool_py(
         truncate_times=truncate_times,
         multi_timing_event_list=multi_timing_event_list,
     )
-    return timing_tool_py_execute(params, execution)
+    return timing_tool_py_execute(params, runner)
 
 
 __all__ = [
     "TIMING_TOOL_PY_METADATA",
     "TimingToolPyOutputs",
-    "TimingToolPyParameters",
     "timing_tool_py",
+    "timing_tool_py_execute",
     "timing_tool_py_params",
 ]