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

niwrap_afni/afni/v_3d_grayplot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_GRAYPLOT_METADATA = Metadata(
-    id="9cc45e81af02b7ce8653e8e48c2ead1d99631336.boutiques",
+    id="f6e3887ef52f450f8f7c42c285ca11d1dca72962.boutiques",
     name="3dGrayplot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_GRAYPLOT_METADATA = Metadata(
 
 
 V3dGrayplotParameters = typing.TypedDict('V3dGrayplotParameters', {
-    "__STYXTYPE__": typing.Literal["3dGrayplot"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dGrayplot"]],
+    "input": InputPathType,
+    "mask": typing.NotRequired[InputPathType | None],
+    "prefix": typing.NotRequired[str | None],
+    "dimensions": typing.NotRequired[list[float] | None],
+    "resample_old": bool,
+    "polort": typing.NotRequired[float | None],
+    "fwhm": typing.NotRequired[float | None],
+    "pvorder": bool,
+    "LJorder": bool,
+    "peelorder": bool,
+    "ijkorder": bool,
+    "range": typing.NotRequired[float | None],
+    "percent": bool,
+    "raw_with_bounds": typing.NotRequired[list[float] | None],
+})
+V3dGrayplotParametersTagged = typing.TypedDict('V3dGrayplotParametersTagged', {
+    "@type": typing.Literal["afni/3dGrayplot"],
     "input": InputPathType,
     "mask": typing.NotRequired[InputPathType | None],
     "prefix": typing.NotRequired[str | None],
@@ -30,43 +47,11 @@ V3dGrayplotParameters = typing.TypedDict('V3dGrayplotParameters', {
     "percent": bool,
     "raw_with_bounds": typing.NotRequired[list[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 {
-        "3dGrayplot": v_3d_grayplot_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 {
-        "3dGrayplot": v_3d_grayplot_outputs,
-    }.get(t)
 
 
 class V3dGrayplotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_grayplot(...)`.
+    Output object returned when calling `V3dGrayplotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -89,7 +74,7 @@ def v_3d_grayplot_params(
     range_: float | None = None,
     percent: bool = False,
     raw_with_bounds: list[float] | None = None,
-) -> V3dGrayplotParameters:
+) -> V3dGrayplotParametersTagged:
     """
     Build parameters.
     
@@ -122,7 +107,7 @@ def v_3d_grayplot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dGrayplot",
+        "@type": "afni/3dGrayplot",
         "input": input_,
         "resample_old": resample_old,
         "pvorder": pvorder,
@@ -163,53 +148,53 @@ def v_3d_grayplot_cargs(
     """
     cargs = []
     cargs.append("3dGrayplot")
-    cargs.append(execution.input_file(params.get("input")))
-    if params.get("mask") is not None:
+    cargs.append(execution.input_file(params.get("input", 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("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("dimensions") is not None:
+    if params.get("dimensions", None) is not None:
         cargs.extend([
             "-dimen",
-            *map(str, params.get("dimensions"))
+            *map(str, params.get("dimensions", None))
         ])
-    if params.get("resample_old"):
+    if params.get("resample_old", False):
         cargs.append("-oldresam")
-    if params.get("polort") is not None:
+    if params.get("polort", None) is not None:
         cargs.extend([
             "-polort",
-            str(params.get("polort"))
+            str(params.get("polort", None))
         ])
-    if params.get("fwhm") is not None:
+    if params.get("fwhm", None) is not None:
         cargs.extend([
             "-fwhm",
-            str(params.get("fwhm"))
+            str(params.get("fwhm", None))
         ])
-    if params.get("pvorder"):
+    if params.get("pvorder", False):
         cargs.append("-pvorder")
-    if params.get("LJorder"):
+    if params.get("LJorder", False):
         cargs.append("-LJorder")
-    if params.get("peelorder"):
+    if params.get("peelorder", False):
         cargs.append("-peelorder")
-    if params.get("ijkorder"):
+    if params.get("ijkorder", False):
         cargs.append("-ijkorder")
-    if params.get("range") is not None:
+    if params.get("range", None) is not None:
         cargs.extend([
             "-range",
-            str(params.get("range"))
+            str(params.get("range", None))
         ])
-    if params.get("percent"):
+    if params.get("percent", False):
         cargs.append("-percent")
-    if params.get("raw_with_bounds") is not None:
+    if params.get("raw_with_bounds", None) is not None:
         cargs.extend([
             "-raw_with_bounds",
-            *map(str, params.get("raw_with_bounds"))
+            *map(str, params.get("raw_with_bounds", None))
         ])
     return cargs
 
@@ -229,18 +214,20 @@ def v_3d_grayplot_outputs(
     """
     ret = V3dGrayplotOutputs(
         root=execution.output_file("."),
-        grayplot_img=execution.output_file(params.get("prefix")) if (params.get("prefix") is not None) else None,
+        grayplot_img=execution.output_file(params.get("prefix", None)) if (params.get("prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_grayplot_execute(
     params: V3dGrayplotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dGrayplotOutputs:
     """
-    Make a grayplot from a 3D+time dataset, like a carpet plot. Result is saved to a
-    PNG image.
+    3dGrayplot
+    
+    Make a grayplot from a 3D+time dataset, like a carpet plot. Result is saved
+    to a PNG image.
     
     Author: AFNI Developers
     
@@ -248,10 +235,12 @@ def v_3d_grayplot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dGrayplotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GRAYPLOT_METADATA)
     params = execution.params(params)
     cargs = v_3d_grayplot_cargs(params, execution)
     ret = v_3d_grayplot_outputs(params, execution)
@@ -277,8 +266,10 @@ def v_3d_grayplot(
     runner: Runner | None = None,
 ) -> V3dGrayplotOutputs:
     """
-    Make a grayplot from a 3D+time dataset, like a carpet plot. Result is saved to a
-    PNG image.
+    3dGrayplot
+    
+    Make a grayplot from a 3D+time dataset, like a carpet plot. Result is saved
+    to a PNG image.
     
     Author: AFNI Developers
     
@@ -313,8 +304,6 @@ def v_3d_grayplot(
     Returns:
         NamedTuple of outputs (described in `V3dGrayplotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_GRAYPLOT_METADATA)
     params = v_3d_grayplot_params(
         input_=input_,
         mask=mask,
@@ -331,13 +320,13 @@ def v_3d_grayplot(
         percent=percent,
         raw_with_bounds=raw_with_bounds,
     )
-    return v_3d_grayplot_execute(params, execution)
+    return v_3d_grayplot_execute(params, runner)
 
 
 __all__ = [
     "V3dGrayplotOutputs",
-    "V3dGrayplotParameters",
     "V_3D_GRAYPLOT_METADATA",
     "v_3d_grayplot",
+    "v_3d_grayplot_execute",
     "v_3d_grayplot_params",
 ]

niwrap_afni/afni/v_3d_group_in_corr.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_GROUP_IN_CORR_METADATA = Metadata(
-    id="783e0b2b58c72c469e00378de705788029b59277.boutiques",
+    id="5a246eddb950c28c8d77eb5f8f6b372d0071a89d.boutiques",
     name="3dGroupInCorr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,38 @@ V_3D_GROUP_IN_CORR_METADATA = Metadata(
 
 
 V3dGroupInCorrParameters = typing.TypedDict('V3dGroupInCorrParameters', {
-    "__STYXTYPE__": typing.Literal["3dGroupInCorr"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dGroupInCorr"]],
+    "set_a": InputPathType,
+    "set_b": typing.NotRequired[InputPathType | None],
+    "apair": bool,
+    "label_a": typing.NotRequired[str | None],
+    "label_b": typing.NotRequired[str | None],
+    "pooled": bool,
+    "unpooled": bool,
+    "paired": bool,
+    "nosix": bool,
+    "covariates_file": typing.NotRequired[InputPathType | None],
+    "center": typing.NotRequired[str | None],
+    "seed_radius": typing.NotRequired[float | None],
+    "sendall": bool,
+    "donocov": bool,
+    "dospcov": bool,
+    "cluster": typing.NotRequired[str | None],
+    "read": bool,
+    "ztest": bool,
+    "ah": typing.NotRequired[str | None],
+    "port_offset": typing.NotRequired[float | None],
+    "port_offset_quiet": typing.NotRequired[float | None],
+    "port_bloc": typing.NotRequired[float | None],
+    "suma": bool,
+    "quiet": bool,
+    "verbose": bool,
+    "very_verbose": bool,
+    "debug": bool,
+    "batch": typing.NotRequired[str | None],
+})
+V3dGroupInCorrParametersTagged = typing.TypedDict('V3dGroupInCorrParametersTagged', {
+    "@type": typing.Literal["afni/3dGroupInCorr"],
     "set_a": InputPathType,
     "set_b": typing.NotRequired[InputPathType | None],
     "apair": bool,
@@ -44,43 +75,11 @@ V3dGroupInCorrParameters = typing.TypedDict('V3dGroupInCorrParameters', {
     "debug": bool,
     "batch": 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 {
-        "3dGroupInCorr": v_3d_group_in_corr_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 {
-        "3dGroupInCorr": v_3d_group_in_corr_outputs,
-    }.get(t)
 
 
 class V3dGroupInCorrOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_group_in_corr(...)`.
+    Output object returned when calling `V3dGroupInCorrParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -117,7 +116,7 @@ def v_3d_group_in_corr_params(
     very_verbose: bool = False,
     debug: bool = False,
     batch: str | None = None,
-) -> V3dGroupInCorrParameters:
+) -> V3dGroupInCorrParametersTagged:
     """
     Build parameters.
     
@@ -161,7 +160,7 @@ def v_3d_group_in_corr_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dGroupInCorr",
+        "@type": "afni/3dGroupInCorr",
         "set_a": set_a,
         "apair": apair,
         "pooled": pooled,
@@ -223,97 +222,97 @@ def v_3d_group_in_corr_cargs(
     cargs.append("3dGroupInCorr")
     cargs.extend([
         "-setA",
-        execution.input_file(params.get("set_a"))
+        execution.input_file(params.get("set_a", None))
     ])
-    if params.get("set_b") is not None:
+    if params.get("set_b", None) is not None:
         cargs.extend([
             "-setB",
-            execution.input_file(params.get("set_b"))
+            execution.input_file(params.get("set_b", None))
         ])
-    if params.get("apair"):
+    if params.get("apair", False):
         cargs.append("-Apair")
-    if params.get("label_a") is not None:
+    if params.get("label_a", None) is not None:
         cargs.extend([
             "-labelA",
-            params.get("label_a")
+            params.get("label_a", None)
         ])
-    if params.get("label_b") is not None:
+    if params.get("label_b", None) is not None:
         cargs.extend([
             "-labelB",
-            params.get("label_b")
+            params.get("label_b", None)
         ])
-    if params.get("pooled"):
+    if params.get("pooled", False):
         cargs.append("-pooled")
-    if params.get("unpooled"):
+    if params.get("unpooled", False):
         cargs.append("-unpooled")
-    if params.get("paired"):
+    if params.get("paired", False):
         cargs.append("-paired")
-    if params.get("nosix"):
+    if params.get("nosix", False):
         cargs.append("-nosix")
-    if params.get("covariates_file") is not None:
+    if params.get("covariates_file", None) is not None:
         cargs.extend([
             "-covariates",
-            execution.input_file(params.get("covariates_file"))
+            execution.input_file(params.get("covariates_file", None))
         ])
-    if params.get("center") is not None:
+    if params.get("center", None) is not None:
         cargs.extend([
             "-center",
-            params.get("center")
+            params.get("center", None)
         ])
-    if params.get("seed_radius") is not None:
+    if params.get("seed_radius", None) is not None:
         cargs.extend([
             "-seedrad",
-            str(params.get("seed_radius"))
+            str(params.get("seed_radius", None))
         ])
-    if params.get("sendall"):
+    if params.get("sendall", False):
         cargs.append("-sendall")
-    if params.get("donocov"):
+    if params.get("donocov", False):
         cargs.append("-donocov")
-    if params.get("dospcov"):
+    if params.get("dospcov", False):
         cargs.append("-dospcov")
-    if params.get("cluster") is not None:
+    if params.get("cluster", None) is not None:
         cargs.extend([
             "-clust",
-            params.get("cluster")
+            params.get("cluster", None)
         ])
-    if params.get("read"):
+    if params.get("read", False):
         cargs.append("-read")
-    if params.get("ztest"):
+    if params.get("ztest", False):
         cargs.append("-ztest")
-    if params.get("ah") is not None:
+    if params.get("ah", None) is not None:
         cargs.extend([
             "-ah",
-            params.get("ah")
+            params.get("ah", None)
         ])
-    if params.get("port_offset") is not None:
+    if params.get("port_offset", None) is not None:
         cargs.extend([
             "-np",
-            str(params.get("port_offset"))
+            str(params.get("port_offset", None))
         ])
-    if params.get("port_offset_quiet") is not None:
+    if params.get("port_offset_quiet", None) is not None:
         cargs.extend([
             "-npq",
-            str(params.get("port_offset_quiet"))
+            str(params.get("port_offset_quiet", None))
         ])
-    if params.get("port_bloc") is not None:
+    if params.get("port_bloc", None) is not None:
         cargs.extend([
             "-npb",
-            str(params.get("port_bloc"))
+            str(params.get("port_bloc", None))
         ])
-    if params.get("suma"):
+    if params.get("suma", False):
         cargs.append("-suma")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("-quiet")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
-    if params.get("very_verbose"):
+    if params.get("very_verbose", False):
         cargs.append("-VERB")
-    if params.get("debug"):
+    if params.get("debug", False):
         cargs.append("-debug")
-    if params.get("batch") is not None:
+    if params.get("batch", None) is not None:
         cargs.extend([
             "-batch",
-            params.get("batch")
+            params.get("batch", None)
         ])
     return cargs
 
@@ -333,16 +332,18 @@ def v_3d_group_in_corr_outputs(
     """
     ret = V3dGroupInCorrOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(pathlib.Path(params.get("set_a")).name + ".results.nii"),
+        output_file=execution.output_file(pathlib.Path(params.get("set_a", None)).name + ".results.nii"),
     )
     return ret
 
 
 def v_3d_group_in_corr_execute(
     params: V3dGroupInCorrParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dGroupInCorrOutputs:
     """
+    3dGroupInCorr
+    
     Functional connectivity analysis in group of subjects.
     
     Author: AFNI Developers
@@ -351,10 +352,12 @@ def v_3d_group_in_corr_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dGroupInCorrOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_GROUP_IN_CORR_METADATA)
     params = execution.params(params)
     cargs = v_3d_group_in_corr_cargs(params, execution)
     ret = v_3d_group_in_corr_outputs(params, execution)
@@ -394,6 +397,8 @@ def v_3d_group_in_corr(
     runner: Runner | None = None,
 ) -> V3dGroupInCorrOutputs:
     """
+    3dGroupInCorr
+    
     Functional connectivity analysis in group of subjects.
     
     Author: AFNI Developers
@@ -440,8 +445,6 @@ def v_3d_group_in_corr(
     Returns:
         NamedTuple of outputs (described in `V3dGroupInCorrOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_GROUP_IN_CORR_METADATA)
     params = v_3d_group_in_corr_params(
         set_a=set_a,
         set_b=set_b,
@@ -472,13 +475,13 @@ def v_3d_group_in_corr(
         debug=debug,
         batch=batch,
     )
-    return v_3d_group_in_corr_execute(params, execution)
+    return v_3d_group_in_corr_execute(params, runner)
 
 
 __all__ = [
     "V3dGroupInCorrOutputs",
-    "V3dGroupInCorrParameters",
     "V_3D_GROUP_IN_CORR_METADATA",
     "v_3d_group_in_corr",
+    "v_3d_group_in_corr_execute",
     "v_3d_group_in_corr_params",
 ]