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

niwrap_afni/afni/retro_ts_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RETRO_TS_PY_METADATA = Metadata(
-    id="79fe337b0aef3f964a4c552f4dbbd2809f5b1792.boutiques",
+    id="bb079d91adb04385514019ae3540d64ee4d39c7a.boutiques",
     name="RetroTS.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,35 @@ RETRO_TS_PY_METADATA = Metadata(
 
 
 RetroTsPyParameters = typing.TypedDict('RetroTsPyParameters', {
-    "__STYXTYPE__": typing.Literal["RetroTS.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/RetroTS.py"]],
+    "resp_file": typing.NotRequired[InputPathType | None],
+    "card_file": typing.NotRequired[InputPathType | None],
+    "phys_fs": typing.NotRequired[float | None],
+    "num_slices": float,
+    "volume_tr": float,
+    "phys_file": typing.NotRequired[InputPathType | None],
+    "phys_json": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "rvt_shifts": typing.NotRequired[str | None],
+    "rvt_out": bool,
+    "resp_cutoff_freq": typing.NotRequired[float | None],
+    "cardiac_cutoff_freq": typing.NotRequired[float | None],
+    "cardiac_out": bool,
+    "respiration_out": bool,
+    "interp_style": typing.NotRequired[str | None],
+    "fir_order": typing.NotRequired[float | None],
+    "quiet": bool,
+    "demo": bool,
+    "show_graphs": bool,
+    "debug": bool,
+    "slice_offset": typing.NotRequired[str | None],
+    "slice_major": typing.NotRequired[float | None],
+    "slice_order": typing.NotRequired[str | None],
+    "zero_phase_offset": bool,
+    "legacy_transform": typing.NotRequired[float | None],
+})
+RetroTsPyParametersTagged = typing.TypedDict('RetroTsPyParametersTagged', {
+    "@type": typing.Literal["afni/RetroTS.py"],
     "resp_file": typing.NotRequired[InputPathType | None],
     "card_file": typing.NotRequired[InputPathType | None],
     "phys_fs": typing.NotRequired[float | None],
@@ -41,43 +69,11 @@ RetroTsPyParameters = typing.TypedDict('RetroTsPyParameters', {
     "zero_phase_offset": bool,
     "legacy_transform": 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 {
-        "RetroTS.py": retro_ts_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 {
-        "RetroTS.py": retro_ts_py_outputs,
-    }.get(t)
 
 
 class RetroTsPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `retro_ts_py(...)`.
+    Output object returned when calling `RetroTsPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -111,7 +107,7 @@ def retro_ts_py_params(
     slice_order: str | None = None,
     zero_phase_offset: bool = False,
     legacy_transform: float | None = None,
-) -> RetroTsPyParameters:
+) -> RetroTsPyParametersTagged:
     """
     Build parameters.
     
@@ -153,7 +149,7 @@ def retro_ts_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "RetroTS.py",
+        "@type": "afni/RetroTS.py",
         "num_slices": num_slices,
         "volume_tr": volume_tr,
         "rvt_out": rvt_out,
@@ -213,104 +209,104 @@ def retro_ts_py_cargs(
     """
     cargs = []
     cargs.append("RetroTS.py")
-    if params.get("resp_file") is not None:
+    if params.get("resp_file", None) is not None:
         cargs.extend([
             "-r",
-            execution.input_file(params.get("resp_file"))
+            execution.input_file(params.get("resp_file", None))
         ])
-    if params.get("card_file") is not None:
+    if params.get("card_file", None) is not None:
         cargs.extend([
             "-c",
-            execution.input_file(params.get("card_file"))
+            execution.input_file(params.get("card_file", None))
         ])
-    if params.get("phys_fs") is not None:
+    if params.get("phys_fs", None) is not None:
         cargs.extend([
             "-p",
-            str(params.get("phys_fs"))
+            str(params.get("phys_fs", None))
         ])
     cargs.extend([
         "-n",
-        str(params.get("num_slices"))
+        str(params.get("num_slices", None))
     ])
     cargs.extend([
         "-v",
-        str(params.get("volume_tr"))
+        str(params.get("volume_tr", None))
     ])
-    if params.get("phys_file") is not None:
+    if params.get("phys_file", None) is not None:
         cargs.extend([
             "-phys_file",
-            execution.input_file(params.get("phys_file"))
+            execution.input_file(params.get("phys_file", None))
         ])
-    if params.get("phys_json") is not None:
+    if params.get("phys_json", None) is not None:
         cargs.extend([
             "-phys_json",
-            execution.input_file(params.get("phys_json"))
+            execution.input_file(params.get("phys_json", 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("rvt_shifts") is not None:
+    if params.get("rvt_shifts", None) is not None:
         cargs.extend([
             "-rvt_shifts",
-            params.get("rvt_shifts")
+            params.get("rvt_shifts", None)
         ])
-    if params.get("rvt_out"):
+    if params.get("rvt_out", False):
         cargs.append("-rvt_out")
-    if params.get("resp_cutoff_freq") is not None:
+    if params.get("resp_cutoff_freq", None) is not None:
         cargs.extend([
             "-respiration_cutoff_frequency",
-            str(params.get("resp_cutoff_freq"))
+            str(params.get("resp_cutoff_freq", None))
         ])
-    if params.get("cardiac_cutoff_freq") is not None:
+    if params.get("cardiac_cutoff_freq", None) is not None:
         cargs.extend([
             "-cardiac_cutoff_frequency",
-            str(params.get("cardiac_cutoff_freq"))
+            str(params.get("cardiac_cutoff_freq", None))
         ])
-    if params.get("cardiac_out"):
+    if params.get("cardiac_out", False):
         cargs.append("-cardiac_out")
-    if params.get("respiration_out"):
+    if params.get("respiration_out", False):
         cargs.append("-respiration_out")
-    if params.get("interp_style") is not None:
+    if params.get("interp_style", None) is not None:
         cargs.extend([
             "-interpolation_style",
-            params.get("interp_style")
+            params.get("interp_style", None)
         ])
-    if params.get("fir_order") is not None:
+    if params.get("fir_order", None) is not None:
         cargs.extend([
             "-fir_order",
-            str(params.get("fir_order"))
+            str(params.get("fir_order", None))
         ])
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("demo"):
+    if params.get("demo", False):
         cargs.append("-demo")
-    if params.get("show_graphs"):
+    if params.get("show_graphs", False):
         cargs.append("-show_graphs")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("slice_offset") is not None:
+    if params.get("slice_offset", None) is not None:
         cargs.extend([
             "-slice_offset",
-            params.get("slice_offset")
+            params.get("slice_offset", None)
         ])
-    if params.get("slice_major") is not None:
+    if params.get("slice_major", None) is not None:
         cargs.extend([
             "-slice_major",
-            str(params.get("slice_major"))
+            str(params.get("slice_major", None))
         ])
-    if params.get("slice_order") is not None:
+    if params.get("slice_order", None) is not None:
         cargs.extend([
             "-slice_order",
-            params.get("slice_order")
+            params.get("slice_order", None)
         ])
-    if params.get("zero_phase_offset"):
+    if params.get("zero_phase_offset", False):
         cargs.append("-zero_phase_offset")
-    if params.get("legacy_transform") is not None:
+    if params.get("legacy_transform", None) is not None:
         cargs.extend([
             "-legacy_transform",
-            str(params.get("legacy_transform"))
+            str(params.get("legacy_transform", None))
         ])
     return cargs
 
@@ -330,16 +326,18 @@ def retro_ts_py_outputs(
     """
     ret = RetroTsPyOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".slibase.1D") if (params.get("prefix") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".slibase.1D") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def retro_ts_py_execute(
     params: RetroTsPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RetroTsPyOutputs:
     """
+    RetroTS.py
+    
     Creates slice-based regressors for regressing out components of heart rate,
     respiration, and respiration volume per time using independent data files or
     BIDS formatted files.
@@ -350,10 +348,12 @@ def retro_ts_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RetroTsPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RETRO_TS_PY_METADATA)
     params = execution.params(params)
     cargs = retro_ts_py_cargs(params, execution)
     ret = retro_ts_py_outputs(params, execution)
@@ -390,6 +390,8 @@ def retro_ts_py(
     runner: Runner | None = None,
 ) -> RetroTsPyOutputs:
     """
+    RetroTS.py
+    
     Creates slice-based regressors for regressing out components of heart rate,
     respiration, and respiration volume per time using independent data files or
     BIDS formatted files.
@@ -436,8 +438,6 @@ def retro_ts_py(
     Returns:
         NamedTuple of outputs (described in `RetroTsPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RETRO_TS_PY_METADATA)
     params = retro_ts_py_params(
         resp_file=resp_file,
         card_file=card_file,
@@ -465,13 +465,13 @@ def retro_ts_py(
         zero_phase_offset=zero_phase_offset,
         legacy_transform=legacy_transform,
     )
-    return retro_ts_py_execute(params, execution)
+    return retro_ts_py_execute(params, runner)
 
 
 __all__ = [
     "RETRO_TS_PY_METADATA",
     "RetroTsPyOutputs",
-    "RetroTsPyParameters",
     "retro_ts_py",
+    "retro_ts_py_execute",
     "retro_ts_py_params",
 ]

niwrap_afni/afni/rmz.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 RMZ_METADATA = Metadata(
-    id="7b3623e5a5e9b6c5f11ff499f54a7ef56d132993.boutiques",
+    id="3b8f3cf4c3c1f22210c3b2448f1539b6a30c6f8e.boutiques",
     name="rmz",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,48 +14,24 @@ RMZ_METADATA = Metadata(
 
 
 RmzParameters = typing.TypedDict('RmzParameters', {
-    "__STYXTYPE__": typing.Literal["rmz"],
+    "@type": typing.NotRequired[typing.Literal["afni/rmz"]],
+    "quiet": bool,
+    "hash_flag": typing.NotRequired[float | None],
+    "keep_flag": bool,
+    "filenames": list[InputPathType],
+})
+RmzParametersTagged = typing.TypedDict('RmzParametersTagged', {
+    "@type": typing.Literal["afni/rmz"],
     "quiet": bool,
     "hash_flag": typing.NotRequired[float | None],
     "keep_flag": bool,
     "filenames": list[InputPathType],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "rmz": rmz_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 RmzOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `rmz(...)`.
+    Output object returned when calling `RmzParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -66,7 +42,7 @@ def rmz_params(
     quiet: bool = False,
     hash_flag: float | None = None,
     keep_flag: bool = False,
-) -> RmzParameters:
+) -> RmzParametersTagged:
     """
     Build parameters.
     
@@ -79,7 +55,7 @@ def rmz_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "rmz",
+        "@type": "afni/rmz",
         "quiet": quiet,
         "keep_flag": keep_flag,
         "filenames": filenames,
@@ -104,16 +80,16 @@ def rmz_cargs(
     """
     cargs = []
     cargs.append("rmz")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-q")
-    if params.get("hash_flag") is not None:
+    if params.get("hash_flag", None) is not None:
         cargs.extend([
             "-#",
-            str(params.get("hash_flag"))
+            str(params.get("hash_flag", None))
         ])
-    if params.get("keep_flag"):
+    if params.get("keep_flag", False):
         cargs.append("-k")
-    cargs.extend([execution.input_file(f) for f in params.get("filenames")])
+    cargs.extend([execution.input_file(f) for f in params.get("filenames", None)])
     return cargs
 
 
@@ -138,9 +114,11 @@ def rmz_outputs(
 
 def rmz_execute(
     params: RmzParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> RmzOutputs:
     """
+    rmz
+    
     Zeros out files before removing them.
     
     Author: AFNI Developers
@@ -149,10 +127,12 @@ def rmz_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `RmzOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(RMZ_METADATA)
     params = execution.params(params)
     cargs = rmz_cargs(params, execution)
     ret = rmz_outputs(params, execution)
@@ -168,6 +148,8 @@ def rmz(
     runner: Runner | None = None,
 ) -> RmzOutputs:
     """
+    rmz
+    
     Zeros out files before removing them.
     
     Author: AFNI Developers
@@ -183,21 +165,19 @@ def rmz(
     Returns:
         NamedTuple of outputs (described in `RmzOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(RMZ_METADATA)
     params = rmz_params(
         quiet=quiet,
         hash_flag=hash_flag,
         keep_flag=keep_flag,
         filenames=filenames,
     )
-    return rmz_execute(params, execution)
+    return rmz_execute(params, runner)
 
 
 __all__ = [
     "RMZ_METADATA",
     "RmzOutputs",
-    "RmzParameters",
     "rmz",
+    "rmz_execute",
     "rmz_params",
 ]