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

niwrap_afni/afni/v_3d_median_filter.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MEDIAN_FILTER_METADATA = Metadata(
-    id="8cec9e9f62ab9dcd134fce2ee61c1b34025a38f7.boutiques",
+    id="617c14931eec5b5191d306af9970a225bbd22fa6.boutiques",
     name="3dMedianFilter",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_MEDIAN_FILTER_METADATA = Metadata(
 
 
 V3dMedianFilterParameters = typing.TypedDict('V3dMedianFilterParameters', {
-    "__STYXTYPE__": typing.Literal["3dMedianFilter"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMedianFilter"]],
+    "irad": typing.NotRequired[float | None],
+    "iter": typing.NotRequired[float | None],
+    "verbose": bool,
+    "prefix": typing.NotRequired[str | None],
+    "automask": bool,
+    "dataset": InputPathType,
+})
+V3dMedianFilterParametersTagged = typing.TypedDict('V3dMedianFilterParametersTagged', {
+    "@type": typing.Literal["afni/3dMedianFilter"],
     "irad": typing.NotRequired[float | None],
     "iter": typing.NotRequired[float | None],
     "verbose": bool,
@@ -22,43 +31,11 @@ V3dMedianFilterParameters = typing.TypedDict('V3dMedianFilterParameters', {
     "automask": bool,
     "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 {
-        "3dMedianFilter": v_3d_median_filter_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 {
-        "3dMedianFilter": v_3d_median_filter_outputs,
-    }.get(t)
 
 
 class V3dMedianFilterOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_median_filter(...)`.
+    Output object returned when calling `V3dMedianFilterParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +52,7 @@ def v_3d_median_filter_params(
     verbose: bool = False,
     prefix: str | None = None,
     automask: bool = False,
-) -> V3dMedianFilterParameters:
+) -> V3dMedianFilterParametersTagged:
     """
     Build parameters.
     
@@ -90,7 +67,7 @@ def v_3d_median_filter_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMedianFilter",
+        "@type": "afni/3dMedianFilter",
         "verbose": verbose,
         "automask": automask,
         "dataset": dataset,
@@ -119,26 +96,26 @@ def v_3d_median_filter_cargs(
     """
     cargs = []
     cargs.append("3dMedianFilter")
-    if params.get("irad") is not None:
+    if params.get("irad", None) is not None:
         cargs.extend([
             "-irad",
-            str(params.get("irad"))
+            str(params.get("irad", None))
         ])
-    if params.get("iter") is not None:
+    if params.get("iter", None) is not None:
         cargs.extend([
             "-iter",
-            str(params.get("iter"))
+            str(params.get("iter", None))
         ])
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    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("automask"):
+    if params.get("automask", False):
         cargs.append("-automask")
-    cargs.append(execution.input_file(params.get("dataset")))
+    cargs.append(execution.input_file(params.get("dataset", None)))
     return cargs
 
 
@@ -157,19 +134,21 @@ def v_3d_median_filter_outputs(
     """
     ret = V3dMedianFilterOutputs(
         root=execution.output_file("."),
-        output_brik=execution.output_file(params.get("prefix") + "+tlrc.BRIK") if (params.get("prefix") is not None) else None,
-        output_head=execution.output_file(params.get("prefix") + "+tlrc.HEAD") if (params.get("prefix") is not None) else None,
+        output_brik=execution.output_file(params.get("prefix", None) + "+tlrc.BRIK") if (params.get("prefix") is not None) else None,
+        output_head=execution.output_file(params.get("prefix", None) + "+tlrc.HEAD") if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_median_filter_execute(
     params: V3dMedianFilterParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMedianFilterOutputs:
     """
-    Computes the median in a spherical neighborhood around each point in the input
-    to produce the output.
+    3dMedianFilter
+    
+    Computes the median in a spherical neighborhood around each point in the
+    input to produce the output.
     
     Author: AFNI Developers
     
@@ -177,10 +156,12 @@ def v_3d_median_filter_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMedianFilterOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEDIAN_FILTER_METADATA)
     params = execution.params(params)
     cargs = v_3d_median_filter_cargs(params, execution)
     ret = v_3d_median_filter_outputs(params, execution)
@@ -198,8 +179,10 @@ def v_3d_median_filter(
     runner: Runner | None = None,
 ) -> V3dMedianFilterOutputs:
     """
-    Computes the median in a spherical neighborhood around each point in the input
-    to produce the output.
+    3dMedianFilter
+    
+    Computes the median in a spherical neighborhood around each point in the
+    input to produce the output.
     
     Author: AFNI Developers
     
@@ -216,8 +199,6 @@ def v_3d_median_filter(
     Returns:
         NamedTuple of outputs (described in `V3dMedianFilterOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MEDIAN_FILTER_METADATA)
     params = v_3d_median_filter_params(
         irad=irad,
         iter_=iter_,
@@ -226,13 +207,13 @@ def v_3d_median_filter(
         automask=automask,
         dataset=dataset,
     )
-    return v_3d_median_filter_execute(params, execution)
+    return v_3d_median_filter_execute(params, runner)
 
 
 __all__ = [
     "V3dMedianFilterOutputs",
-    "V3dMedianFilterParameters",
     "V_3D_MEDIAN_FILTER_METADATA",
     "v_3d_median_filter",
+    "v_3d_median_filter_execute",
     "v_3d_median_filter_params",
 ]

niwrap_afni/afni/v_3d_mema.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MEMA_METADATA = Metadata(
-    id="42d741bde9dc16f04484bfd186884378d78fc8f3.boutiques",
+    id="f041c65105cb28ba9e2c96580eb2aeada384b9ed.boutiques",
     name="3dMEMA",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,37 @@ V_3D_MEMA_METADATA = Metadata(
 
 
 V3dMemaParameters = typing.TypedDict('V3dMemaParameters', {
-    "__STYXTYPE__": typing.Literal["3dMEMA"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dMEMA"]],
+    "prefix": str,
+    "jobs": typing.NotRequired[float | None],
+    "set": list[str],
+    "covariates": typing.NotRequired[InputPathType | None],
+    "covariates_center": typing.NotRequired[str | None],
+    "covariates_model": typing.NotRequired[str | None],
+    "covariates_name": typing.NotRequired[list[str] | None],
+    "groups": typing.NotRequired[list[str] | None],
+    "cio": bool,
+    "HKtest": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "max_zeros": typing.NotRequired[float | None],
+    "missing_data": typing.NotRequired[list[str] | None],
+    "model_outliers": bool,
+    "n_nonzero": typing.NotRequired[float | None],
+    "no_HKtest": bool,
+    "no_model_outliers": bool,
+    "no_residual_Z": bool,
+    "residual_Z": bool,
+    "Rio": bool,
+    "equal_variance": bool,
+    "unequal_variance": bool,
+    "verb": typing.NotRequired[float | None],
+    "dbgArgs": bool,
+    "help": bool,
+    "conditions": typing.NotRequired[list[str] | None],
+    "no_tstat": bool,
+})
+V3dMemaParametersTagged = typing.TypedDict('V3dMemaParametersTagged', {
+    "@type": typing.Literal["afni/3dMEMA"],
     "prefix": str,
     "jobs": typing.NotRequired[float | None],
     "set": list[str],
@@ -43,43 +73,11 @@ V3dMemaParameters = typing.TypedDict('V3dMemaParameters', {
     "conditions": typing.NotRequired[list[str] | None],
     "no_tstat": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dMEMA": v_3d_mema_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 {
-        "3dMEMA": v_3d_mema_outputs,
-    }.get(t)
 
 
 class V3dMemaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_mema(...)`.
+    Output object returned when calling `V3dMemaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -115,7 +113,7 @@ def v_3d_mema_params(
     help_: bool = False,
     conditions: list[str] | None = None,
     no_tstat: bool = False,
-) -> V3dMemaParameters:
+) -> V3dMemaParametersTagged:
     """
     Build parameters.
     
@@ -153,7 +151,7 @@ def v_3d_mema_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dMEMA",
+        "@type": "afni/3dMEMA",
         "prefix": prefix,
         "set": set_,
         "cio": cio,
@@ -214,97 +212,97 @@ def v_3d_mema_cargs(
     cargs.append("3dMEMA")
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("jobs") is not None:
+    if params.get("jobs", None) is not None:
         cargs.extend([
             "-jobs",
-            str(params.get("jobs"))
+            str(params.get("jobs", None))
         ])
     cargs.extend([
         "-set",
-        *params.get("set")
+        *params.get("set", None)
     ])
-    if params.get("covariates") is not None:
+    if params.get("covariates", None) is not None:
         cargs.extend([
             "-covariates",
-            execution.input_file(params.get("covariates"))
+            execution.input_file(params.get("covariates", None))
         ])
-    if params.get("covariates_center") is not None:
+    if params.get("covariates_center", None) is not None:
         cargs.extend([
             "-covariates_center",
-            params.get("covariates_center")
+            params.get("covariates_center", None)
         ])
-    if params.get("covariates_model") is not None:
+    if params.get("covariates_model", None) is not None:
         cargs.extend([
             "-covariates_model",
-            params.get("covariates_model")
+            params.get("covariates_model", None)
         ])
-    if params.get("covariates_name") is not None:
+    if params.get("covariates_name", None) is not None:
         cargs.extend([
             "-covariates_name",
-            *params.get("covariates_name")
+            *params.get("covariates_name", None)
         ])
-    if params.get("groups") is not None:
+    if params.get("groups", None) is not None:
         cargs.extend([
             "-groups",
-            *params.get("groups")
+            *params.get("groups", None)
         ])
-    if params.get("cio"):
+    if params.get("cio", False):
         cargs.append("-cio")
-    if params.get("HKtest"):
+    if params.get("HKtest", False):
         cargs.append("-HKtest")
-    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("max_zeros") is not None:
+    if params.get("max_zeros", None) is not None:
         cargs.extend([
             "-max_zeros",
-            str(params.get("max_zeros"))
+            str(params.get("max_zeros", None))
         ])
-    if params.get("missing_data") is not None:
+    if params.get("missing_data", None) is not None:
         cargs.extend([
             "-missing_data",
-            *params.get("missing_data")
+            *params.get("missing_data", None)
         ])
-    if params.get("model_outliers"):
+    if params.get("model_outliers", False):
         cargs.append("-model_outliers")
-    if params.get("n_nonzero") is not None:
+    if params.get("n_nonzero", None) is not None:
         cargs.extend([
             "-n_nonzero",
-            str(params.get("n_nonzero"))
+            str(params.get("n_nonzero", None))
         ])
-    if params.get("no_HKtest"):
+    if params.get("no_HKtest", False):
         cargs.append("-no_HKtest")
-    if params.get("no_model_outliers"):
+    if params.get("no_model_outliers", False):
         cargs.append("-no_model_outliers")
-    if params.get("no_residual_Z"):
+    if params.get("no_residual_Z", False):
         cargs.append("-no_residual_Z")
-    if params.get("residual_Z"):
+    if params.get("residual_Z", False):
         cargs.append("-residual_Z")
-    if params.get("Rio"):
+    if params.get("Rio", False):
         cargs.append("-Rio")
-    if params.get("equal_variance"):
+    if params.get("equal_variance", False):
         cargs.append("-equal_variance")
-    if params.get("unequal_variance"):
+    if params.get("unequal_variance", False):
         cargs.append("-unequal_variance")
-    if params.get("verb") is not None:
+    if params.get("verb", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verb"))
+            str(params.get("verb", None))
         ])
-    if params.get("dbgArgs"):
+    if params.get("dbgArgs", False):
         cargs.append("-dbgArgs")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("conditions") is not None:
+    if params.get("conditions", None) is not None:
         cargs.extend([
             "-conditions",
-            *params.get("conditions")
+            *params.get("conditions", None)
         ])
-    if params.get("no_tstat"):
+    if params.get("no_tstat", False):
         cargs.append("-no_tstat")
     return cargs
 
@@ -324,18 +322,20 @@ def v_3d_mema_outputs(
     """
     ret = V3dMemaOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz"),
     )
     return ret
 
 
 def v_3d_mema_execute(
     params: V3dMemaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dMemaOutputs:
     """
-    3dMEMA is a program for performing Mixed Effects Meta Analysis at group level
-    that models both within- and across-subjects variability.
+    3dMEMA
+    
+    3dMEMA is a program for performing Mixed Effects Meta Analysis at group
+    level that models both within- and across-subjects variability.
     
     Author: AFNI Developers
     
@@ -343,10 +343,12 @@ def v_3d_mema_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dMemaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_MEMA_METADATA)
     params = execution.params(params)
     cargs = v_3d_mema_cargs(params, execution)
     ret = v_3d_mema_outputs(params, execution)
@@ -385,8 +387,10 @@ def v_3d_mema(
     runner: Runner | None = None,
 ) -> V3dMemaOutputs:
     """
-    3dMEMA is a program for performing Mixed Effects Meta Analysis at group level
-    that models both within- and across-subjects variability.
+    3dMEMA
+    
+    3dMEMA is a program for performing Mixed Effects Meta Analysis at group
+    level that models both within- and across-subjects variability.
     
     Author: AFNI Developers
     
@@ -426,8 +430,6 @@ def v_3d_mema(
     Returns:
         NamedTuple of outputs (described in `V3dMemaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_MEMA_METADATA)
     params = v_3d_mema_params(
         prefix=prefix,
         jobs=jobs,
@@ -457,13 +459,13 @@ def v_3d_mema(
         conditions=conditions,
         no_tstat=no_tstat,
     )
-    return v_3d_mema_execute(params, execution)
+    return v_3d_mema_execute(params, runner)
 
 
 __all__ = [
     "V3dMemaOutputs",
-    "V3dMemaParameters",
     "V_3D_MEMA_METADATA",
     "v_3d_mema",
+    "v_3d_mema_execute",
     "v_3d_mema_params",
 ]