niwrap-afni 0.6.2__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/v_3d_mss.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MSS_METADATA = Metadata(
-    id="276226ad44e7a9804c89600a9895d189f8152cd2.boutiques",
+    id="ee1c3e2d4be03aa26d9a69a61da85efaa53d8340.boutiques",
     name="3dMSS",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ V_3D_MSS_METADATA = Metadata(
 
 
 V3dMssParameters = typing.TypedDict('V3dMssParameters', {
-    "__STYXTYPE__": typing.Literal["3dMSS"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMSS"]],
+    "prefix": str,
+    "jobs": typing.NotRequired[float | None],
+    "mrr_formula": typing.NotRequired[str | None],
+    "lme_formula": typing.NotRequired[str | None],
+    "random_effect": typing.NotRequired[str | None],
+    "qvars": typing.NotRequired[str | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "bounds": typing.NotRequired[list[float] | None],
+    "prediction_table": typing.NotRequired[InputPathType | None],
+    "data_table": InputPathType,
+    "cio_flag": bool,
+    "rio_flag": bool,
+    "help_flag": bool,
+    "dbg_args_flag": bool,
+    "if_name": typing.NotRequired[str | None],
+    "show_allowed_options_flag": bool,
+    "sdiff_vars": typing.NotRequired[str | None],
+    "vt_formula": typing.NotRequired[str | None],
+})
+V3dMssParametersTagged = typing.TypedDict('V3dMssParametersTagged', {
+    "@type": typing.Literal["afni/3dMSS"],
     "prefix": str,
     "jobs": typing.NotRequired[float | None],
     "mrr_formula": typing.NotRequired[str | None],
@@ -34,43 +55,11 @@ V3dMssParameters = typing.TypedDict('V3dMssParameters', {
     "sdiff_vars": typing.NotRequired[str | None],
     "vt_formula": 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 {
-        "3dMSS": v_3d_mss_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 {
-        "3dMSS": v_3d_mss_outputs,
-    }.get(t)
 
 
 class V3dMssOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mss(...)`.
+    Output object returned when calling `V3dMssParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -97,7 +86,7 @@ def v_3d_mss_params(
     show_allowed_options_flag: bool = False,
     sdiff_vars: str | None = None,
     vt_formula: str | None = None,
-) -> V3dMssParameters:
+) -> V3dMssParametersTagged:
     """
     Build parameters.
     
@@ -135,7 +124,7 @@ def v_3d_mss_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMSS",
+        "@type": "afni/3dMSS",
         "prefix": prefix,
         "data_table": data_table,
         "cio_flag": cio_flag,
@@ -184,75 +173,75 @@ def v_3d_mss_cargs(
     """
     cargs = []
     cargs.append("3dMSS")
-    cargs.append(params.get("prefix"))
-    if params.get("jobs") is not None:
+    cargs.append(params.get("prefix", None))
+    if params.get("jobs", None) is not None:
         cargs.extend([
             "-jobs",
-            str(params.get("jobs"))
+            str(params.get("jobs", None))
         ])
-    if params.get("mrr_formula") is not None:
+    if params.get("mrr_formula", None) is not None:
         cargs.extend([
             "-mrr",
-            params.get("mrr_formula")
+            params.get("mrr_formula", None)
         ])
-    if params.get("lme_formula") is not None:
+    if params.get("lme_formula", None) is not None:
         cargs.extend([
             "-lme",
-            params.get("lme_formula")
+            params.get("lme_formula", None)
         ])
-    if params.get("random_effect") is not None:
+    if params.get("random_effect", None) is not None:
         cargs.extend([
             "-ranEff",
-            params.get("random_effect")
+            params.get("random_effect", None)
         ])
-    if params.get("qvars") is not None:
+    if params.get("qvars", None) is not None:
         cargs.extend([
             "-qVars",
-            params.get("qvars")
+            params.get("qvars", None)
         ])
-    if params.get("mask") is not None:
+    if params.get("mask", None) is not None:
         cargs.extend([
             "-mask",
-            execution.input_file(params.get("mask"))
+            execution.input_file(params.get("mask", None))
         ])
-    if params.get("bounds") is not None:
+    if params.get("bounds", None) is not None:
         cargs.extend([
             "-bounds",
-            *map(str, params.get("bounds"))
+            *map(str, params.get("bounds", None))
         ])
-    if params.get("prediction_table") is not None:
+    if params.get("prediction_table", None) is not None:
         cargs.extend([
             "-prediction",
-            execution.input_file(params.get("prediction_table"))
+            execution.input_file(params.get("prediction_table", None))
         ])
     cargs.extend([
         "-dataTable",
-        execution.input_file(params.get("data_table"))
+        execution.input_file(params.get("data_table", None))
     ])
-    if params.get("cio_flag"):
+    if params.get("cio_flag", False):
         cargs.append("-cio")
-    if params.get("rio_flag"):
+    if params.get("rio_flag", False):
         cargs.append("-Rio")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-help")
-    if params.get("dbg_args_flag"):
+    if params.get("dbg_args_flag", False):
         cargs.append("-dbgArgs")
-    if params.get("if_name") is not None:
+    if params.get("if_name", None) is not None:
         cargs.extend([
             "-IF",
-            params.get("if_name")
+            params.get("if_name", None)
         ])
-    if params.get("show_allowed_options_flag"):
+    if params.get("show_allowed_options_flag", False):
         cargs.append("-show_allowed_options")
-    if params.get("sdiff_vars") is not None:
+    if params.get("sdiff_vars", None) is not None:
         cargs.extend([
             "-sdiff",
-            params.get("sdiff_vars")
+            params.get("sdiff_vars", None)
         ])
-    if params.get("vt_formula") is not None:
+    if params.get("vt_formula", None) is not None:
         cargs.extend([
             "-vt",
-            params.get("vt_formula")
+            params.get("vt_formula", None)
         ])
     return cargs
 
@@ -272,16 +261,18 @@ def v_3d_mss_outputs(
     """
     ret = V3dMssOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii"),
+        output_file=execution.output_file(params.get("prefix", None) + ".nii"),
     )
     return ret
 
 
 def v_3d_mss_execute(
     params: V3dMssParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMssOutputs:
     """
+    3dMSS
+    
     Voxelwise Multilevel Smoothing Spline (MSS) Analysis.
     
     Author: AFNI Developers
@@ -290,10 +281,12 @@ def v_3d_mss_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMssOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MSS_METADATA)
     params = execution.params(params)
     cargs = v_3d_mss_cargs(params, execution)
     ret = v_3d_mss_outputs(params, execution)
@@ -323,6 +316,8 @@ def v_3d_mss(
     runner: Runner | None = None,
 ) -> V3dMssOutputs:
     """
+    3dMSS
+    
     Voxelwise Multilevel Smoothing Spline (MSS) Analysis.
     
     Author: AFNI Developers
@@ -363,8 +358,6 @@ def v_3d_mss(
     Returns:
         NamedTuple of outputs (described in `V3dMssOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MSS_METADATA)
     params = v_3d_mss_params(
         prefix=prefix,
         jobs=jobs,
@@ -385,13 +378,13 @@ def v_3d_mss(
         sdiff_vars=sdiff_vars,
         vt_formula=vt_formula,
     )
-    return v_3d_mss_execute(params, execution)
+    return v_3d_mss_execute(params, runner)
 
 
 __all__ = [
     "V3dMssOutputs",
-    "V3dMssParameters",
     "V_3D_MSS_METADATA",
     "v_3d_mss",
+    "v_3d_mss_execute",
     "v_3d_mss_params",
 ]

niwrap_afni/afni/v_3d_multi_thresh.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MULTI_THRESH_METADATA = Metadata(
-    id="0cd522f82df292e38bac580f53ce63e58f4d0ba1.boutiques",
+    id="f72f5d78b27fbaeb74d57fefdb1f807e2d3688b6.boutiques",
     name="3dMultiThresh",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,21 @@ V_3D_MULTI_THRESH_METADATA = Metadata(
 
 
 V3dMultiThreshParameters = typing.TypedDict('V3dMultiThreshParameters', {
-    "__STYXTYPE__": typing.Literal["3dMultiThresh"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMultiThresh"]],
+    "mthresh_file": InputPathType,
+    "input_file": InputPathType,
+    "index": typing.NotRequired[float | None],
+    "signed_flag": typing.NotRequired[str | None],
+    "positive_sign_flag": bool,
+    "negative_sign_flag": bool,
+    "prefix": typing.NotRequired[str | None],
+    "mask_only_flag": bool,
+    "all_mask": typing.NotRequired[str | None],
+    "no_zero_flag": bool,
+    "quiet_flag": bool,
+})
+V3dMultiThreshParametersTagged = typing.TypedDict('V3dMultiThreshParametersTagged', {
+    "@type": typing.Literal["afni/3dMultiThresh"],
     "mthresh_file": InputPathType,
     "input_file": InputPathType,
     "index": typing.NotRequired[float | None],
@@ -27,43 +41,11 @@ V3dMultiThreshParameters = typing.TypedDict('V3dMultiThreshParameters', {
     "no_zero_flag": bool,
     "quiet_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 {
-        "3dMultiThresh": v_3d_multi_thresh_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 {
-        "3dMultiThresh": v_3d_multi_thresh_outputs,
-    }.get(t)
 
 
 class V3dMultiThreshOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_multi_thresh(...)`.
+    Output object returned when calling `V3dMultiThreshParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -88,7 +70,7 @@ def v_3d_multi_thresh_params(
     all_mask: str | None = None,
     no_zero_flag: bool = False,
     quiet_flag: bool = False,
-) -> V3dMultiThreshParameters:
+) -> V3dMultiThreshParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +96,7 @@ def v_3d_multi_thresh_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMultiThresh",
+        "@type": "afni/3dMultiThresh",
         "mthresh_file": mthresh_file,
         "input_file": input_file,
         "positive_sign_flag": positive_sign_flag,
@@ -151,41 +133,41 @@ def v_3d_multi_thresh_cargs(
     cargs.append("3dMultiThresh")
     cargs.extend([
         "-mthresh",
-        execution.input_file(params.get("mthresh_file"))
+        execution.input_file(params.get("mthresh_file", None))
     ])
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
-    if params.get("index") is not None:
+    if params.get("index", None) is not None:
         cargs.extend([
             "-1tindex",
-            str(params.get("index"))
+            str(params.get("index", None))
         ])
-    if params.get("signed_flag") is not None:
+    if params.get("signed_flag", None) is not None:
         cargs.extend([
             "-signed",
-            params.get("signed_flag")
+            params.get("signed_flag", None)
         ])
-    if params.get("positive_sign_flag"):
+    if params.get("positive_sign_flag", False):
         cargs.append("-pos")
-    if params.get("negative_sign_flag"):
+    if params.get("negative_sign_flag", False):
         cargs.append("-neg")
-    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("mask_only_flag"):
+    if params.get("mask_only_flag", False):
         cargs.append("-maskonly")
-    if params.get("all_mask") is not None:
+    if params.get("all_mask", None) is not None:
         cargs.extend([
             "-allmask",
-            params.get("all_mask")
+            params.get("all_mask", None)
         ])
-    if params.get("no_zero_flag"):
+    if params.get("no_zero_flag", False):
         cargs.append("-nozero")
-    if params.get("quiet_flag"):
+    if params.get("quiet_flag", False):
         cargs.append("-quiet")
     return cargs
 
@@ -205,18 +187,20 @@ def v_3d_multi_thresh_outputs(
     """
     ret = V3dMultiThreshOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
-        mask_output=execution.output_file(params.get("prefix") + "_mask.nii.gz") if (params.get("prefix") is not None) else None,
-        all_mask_output=execution.output_file(params.get("all_mask") + ".nii.gz") if (params.get("all_mask") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
+        mask_output=execution.output_file(params.get("prefix", None) + "_mask.nii.gz") if (params.get("prefix") is not None) else None,
+        all_mask_output=execution.output_file(params.get("all_mask", None) + ".nii.gz") if (params.get("all_mask") is not None) else None,
     )
     return ret
 
 
 def v_3d_multi_thresh_execute(
     params: V3dMultiThreshParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMultiThreshOutputs:
     """
+    3dMultiThresh
+    
     Program to apply a multi-threshold (mthresh) dataset to an input dataset.
     
     Author: AFNI Developers
@@ -225,10 +209,12 @@ def v_3d_multi_thresh_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMultiThreshOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MULTI_THRESH_METADATA)
     params = execution.params(params)
     cargs = v_3d_multi_thresh_cargs(params, execution)
     ret = v_3d_multi_thresh_outputs(params, execution)
@@ -251,6 +237,8 @@ def v_3d_multi_thresh(
     runner: Runner | None = None,
 ) -> V3dMultiThreshOutputs:
     """
+    3dMultiThresh
+    
     Program to apply a multi-threshold (mthresh) dataset to an input dataset.
     
     Author: AFNI Developers
@@ -279,8 +267,6 @@ def v_3d_multi_thresh(
     Returns:
         NamedTuple of outputs (described in `V3dMultiThreshOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MULTI_THRESH_METADATA)
     params = v_3d_multi_thresh_params(
         mthresh_file=mthresh_file,
         input_file=input_file,
@@ -294,13 +280,13 @@ def v_3d_multi_thresh(
         no_zero_flag=no_zero_flag,
         quiet_flag=quiet_flag,
     )
-    return v_3d_multi_thresh_execute(params, execution)
+    return v_3d_multi_thresh_execute(params, runner)
 
 
 __all__ = [
     "V3dMultiThreshOutputs",
-    "V3dMultiThreshParameters",
     "V_3D_MULTI_THRESH_METADATA",
     "v_3d_multi_thresh",
+    "v_3d_multi_thresh_execute",
     "v_3d_multi_thresh_params",
 ]