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

niwrap_afni/afni/v_3d_reg_ana.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_REG_ANA_METADATA = Metadata(
-    id="d0f5f9773868694c40c8514ea58aae0c0f7243a6.boutiques",
+    id="6831e3fbaee6f2899266f38b3f5966413f97b912.boutiques",
     name="3dRegAna",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_REG_ANA_METADATA = Metadata(
 
 
 V3dRegAnaParameters = typing.TypedDict('V3dRegAnaParameters', {
-    "__STYXTYPE__": typing.Literal["3dRegAna"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dRegAna"]],
+    "rows": float,
+    "cols": float,
+    "xydata": list[str],
+    "model": str,
+    "diskspace": bool,
+    "workmem": typing.NotRequired[float | None],
+    "rmsmin": typing.NotRequired[float | None],
+    "fdisp": typing.NotRequired[float | None],
+    "flof": typing.NotRequired[float | None],
+    "fcoef": typing.NotRequired[list[str] | None],
+    "rcoef": typing.NotRequired[list[str] | None],
+    "tcoef": typing.NotRequired[list[str] | None],
+    "bucket": typing.NotRequired[str | None],
+    "brick": typing.NotRequired[list[str] | None],
+    "datum": typing.NotRequired[str | None],
+})
+V3dRegAnaParametersTagged = typing.TypedDict('V3dRegAnaParametersTagged', {
+    "@type": typing.Literal["afni/3dRegAna"],
     "rows": float,
     "cols": float,
     "xydata": list[str],
@@ -31,43 +49,11 @@ V3dRegAnaParameters = typing.TypedDict('V3dRegAnaParameters', {
     "brick": typing.NotRequired[list[str] | None],
     "datum": 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 {
-        "3dRegAna": v_3d_reg_ana_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 {
-        "3dRegAna": v_3d_reg_ana_outputs,
-    }.get(t)
 
 
 class V3dRegAnaOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_reg_ana(...)`.
+    Output object returned when calling `V3dRegAnaParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -99,7 +85,7 @@ def v_3d_reg_ana_params(
     bucket: str | None = None,
     brick: list[str] | None = None,
     datum: str | None = None,
-) -> V3dRegAnaParameters:
+) -> V3dRegAnaParametersTagged:
     """
     Build parameters.
     
@@ -130,7 +116,7 @@ def v_3d_reg_ana_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dRegAna",
+        "@type": "afni/3dRegAna",
         "rows": rows,
         "cols": cols,
         "xydata": xydata,
@@ -177,71 +163,71 @@ def v_3d_reg_ana_cargs(
     cargs.append("3dRegAna")
     cargs.extend([
         "-rows",
-        str(params.get("rows"))
+        str(params.get("rows", None))
     ])
     cargs.extend([
         "-cols",
-        str(params.get("cols"))
+        str(params.get("cols", None))
     ])
     cargs.extend([
         "-xydata",
-        *params.get("xydata")
+        *params.get("xydata", None)
     ])
     cargs.extend([
         "-model",
-        params.get("model")
+        params.get("model", None)
     ])
-    if params.get("diskspace"):
+    if params.get("diskspace", False):
         cargs.append("-diskspace")
-    if params.get("workmem") is not None:
+    if params.get("workmem", None) is not None:
         cargs.extend([
             "-workmem",
-            str(params.get("workmem"))
+            str(params.get("workmem", None))
         ])
-    if params.get("rmsmin") is not None:
+    if params.get("rmsmin", None) is not None:
         cargs.extend([
             "-rmsmin",
-            str(params.get("rmsmin"))
+            str(params.get("rmsmin", None))
         ])
-    if params.get("fdisp") is not None:
+    if params.get("fdisp", None) is not None:
         cargs.extend([
             "-fdisp",
-            str(params.get("fdisp"))
+            str(params.get("fdisp", None))
         ])
-    if params.get("flof") is not None:
+    if params.get("flof", None) is not None:
         cargs.extend([
             "-flof",
-            str(params.get("flof"))
+            str(params.get("flof", None))
         ])
-    if params.get("fcoef") is not None:
+    if params.get("fcoef", None) is not None:
         cargs.extend([
             "-fcoef",
-            *params.get("fcoef")
+            *params.get("fcoef", None)
         ])
-    if params.get("rcoef") is not None:
+    if params.get("rcoef", None) is not None:
         cargs.extend([
             "-rcoef",
-            *params.get("rcoef")
+            *params.get("rcoef", None)
         ])
-    if params.get("tcoef") is not None:
+    if params.get("tcoef", None) is not None:
         cargs.extend([
             "-tcoef",
-            *params.get("tcoef")
+            *params.get("tcoef", None)
         ])
-    if params.get("bucket") is not None:
+    if params.get("bucket", None) is not None:
         cargs.extend([
             "-bucket",
-            params.get("bucket")
+            params.get("bucket", None)
         ])
-    if params.get("brick") is not None:
+    if params.get("brick", None) is not None:
         cargs.extend([
             "-brick",
-            *params.get("brick")
+            *params.get("brick", None)
         ])
-    if params.get("datum") is not None:
+    if params.get("datum", None) is not None:
         cargs.extend([
             "-datum",
-            params.get("datum")
+            params.get("datum", None)
         ])
     return cargs
 
@@ -272,9 +258,11 @@ def v_3d_reg_ana_outputs(
 
 def v_3d_reg_ana_execute(
     params: V3dRegAnaParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRegAnaOutputs:
     """
+    3dRegAna
+    
     Multiple linear regression analysis for AFNI datasets.
     
     Author: AFNI Developers
@@ -283,10 +271,12 @@ def v_3d_reg_ana_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRegAnaOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_REG_ANA_METADATA)
     params = execution.params(params)
     cargs = v_3d_reg_ana_cargs(params, execution)
     ret = v_3d_reg_ana_outputs(params, execution)
@@ -313,6 +303,8 @@ def v_3d_reg_ana(
     runner: Runner | None = None,
 ) -> V3dRegAnaOutputs:
     """
+    3dRegAna
+    
     Multiple linear regression analysis for AFNI datasets.
     
     Author: AFNI Developers
@@ -346,8 +338,6 @@ def v_3d_reg_ana(
     Returns:
         NamedTuple of outputs (described in `V3dRegAnaOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_REG_ANA_METADATA)
     params = v_3d_reg_ana_params(
         rows=rows,
         cols=cols,
@@ -365,13 +355,13 @@ def v_3d_reg_ana(
         brick=brick,
         datum=datum,
     )
-    return v_3d_reg_ana_execute(params, execution)
+    return v_3d_reg_ana_execute(params, runner)
 
 
 __all__ = [
     "V3dRegAnaOutputs",
-    "V3dRegAnaParameters",
     "V_3D_REG_ANA_METADATA",
     "v_3d_reg_ana",
+    "v_3d_reg_ana_execute",
     "v_3d_reg_ana_params",
 ]

niwrap_afni/afni/v_3d_remlfit.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_REMLFIT_METADATA = Metadata(
-    id="c3d94a2363ffc8ce0deb6c202c023dd3b848f3ec.boutiques",
+    id="036315e0f46a70dcc3f52e76a3cbd09391a7e811.boutiques",
     name="3dREMLfit",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,25 @@ V_3D_REMLFIT_METADATA = Metadata(
 
 
 V3dRemlfitParameters = typing.TypedDict('V3dRemlfitParameters', {
-    "__STYXTYPE__": typing.Literal["3dREMLfit"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dREMLfit"]],
+    "input_file": InputPathType,
+    "regression_matrix": InputPathType,
+    "baseline_files": typing.NotRequired[list[str] | None],
+    "sort_nods": bool,
+    "temp_storage": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "output_prefix": typing.NotRequired[str | None],
+    "no_fdr_curve": bool,
+    "go_for_it": bool,
+    "max_a_param": typing.NotRequired[float | None],
+    "max_b_param": typing.NotRequired[float | None],
+    "grid_param": typing.NotRequired[float | None],
+    "negative_corr": bool,
+    "quiet": bool,
+    "verbose": bool,
+})
+V3dRemlfitParametersTagged = typing.TypedDict('V3dRemlfitParametersTagged', {
+    "@type": typing.Literal["afni/3dREMLfit"],
     "input_file": InputPathType,
     "regression_matrix": InputPathType,
     "baseline_files": typing.NotRequired[list[str] | None],
@@ -31,43 +49,11 @@ V3dRemlfitParameters = typing.TypedDict('V3dRemlfitParameters', {
     "quiet": bool,
     "verbose": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "3dREMLfit": v_3d_remlfit_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 {
-        "3dREMLfit": v_3d_remlfit_outputs,
-    }.get(t)
 
 
 class V3dRemlfitOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_remlfit(...)`.
+    Output object returned when calling `V3dRemlfitParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +87,7 @@ def v_3d_remlfit_params(
     negative_corr: bool = False,
     quiet: bool = False,
     verbose: bool = False,
-) -> V3dRemlfitParameters:
+) -> V3dRemlfitParametersTagged:
     """
     Build parameters.
     
@@ -132,7 +118,7 @@ def v_3d_remlfit_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dREMLfit",
+        "@type": "afni/3dREMLfit",
         "input_file": input_file,
         "regression_matrix": regression_matrix,
         "sort_nods": sort_nods,
@@ -175,55 +161,55 @@ def v_3d_remlfit_cargs(
     cargs.append("3dREMLfit")
     cargs.extend([
         "-input",
-        execution.input_file(params.get("input_file"))
+        execution.input_file(params.get("input_file", None))
     ])
     cargs.extend([
         "-matrix",
-        execution.input_file(params.get("regression_matrix"))
+        execution.input_file(params.get("regression_matrix", None))
     ])
-    if params.get("baseline_files") is not None:
+    if params.get("baseline_files", None) is not None:
         cargs.extend([
             "-addbase",
-            *params.get("baseline_files")
+            *params.get("baseline_files", None)
         ])
-    if params.get("sort_nods"):
+    if params.get("sort_nods", False):
         cargs.append("-dsort_nods")
-    if params.get("temp_storage"):
+    if params.get("temp_storage", False):
         cargs.append("-usetemp")
-    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("output_prefix") is not None:
+    if params.get("output_prefix", None) is not None:
         cargs.extend([
             "-Rvar",
-            params.get("output_prefix")
+            params.get("output_prefix", None)
         ])
-    if params.get("no_fdr_curve"):
+    if params.get("no_fdr_curve", False):
         cargs.append("-noFDR")
-    if params.get("go_for_it"):
+    if params.get("go_for_it", False):
         cargs.append("-GOFORIT")
-    if params.get("max_a_param") is not None:
+    if params.get("max_a_param", None) is not None:
         cargs.extend([
             "-MAXa",
-            str(params.get("max_a_param"))
+            str(params.get("max_a_param", None))
         ])
-    if params.get("max_b_param") is not None:
+    if params.get("max_b_param", None) is not None:
         cargs.extend([
             "-MAXb",
-            str(params.get("max_b_param"))
+            str(params.get("max_b_param", None))
         ])
-    if params.get("grid_param") is not None:
+    if params.get("grid_param", None) is not None:
         cargs.extend([
             "-Grid",
-            str(params.get("grid_param"))
+            str(params.get("grid_param", None))
         ])
-    if params.get("negative_corr"):
+    if params.get("negative_corr", False):
         cargs.append("-NEGcor")
-    if params.get("quiet"):
+    if params.get("quiet", False):
         cargs.append("quiet")
-    if params.get("verbose"):
+    if params.get("verbose", False):
         cargs.append("-verb")
     return cargs
 
@@ -243,23 +229,25 @@ def v_3d_remlfit_outputs(
     """
     ret = V3dRemlfitOutputs(
         root=execution.output_file("."),
-        outfile=execution.output_file(params.get("output_prefix") + ".nii.gz") if (params.get("output_prefix") is not None) else None,
-        rvar_file=execution.output_file(params.get("output_prefix") + "_Rvar.nii.gz") if (params.get("output_prefix") is not None) else None,
-        rbeta_file=execution.output_file(params.get("output_prefix") + "_Rbeta.nii.gz") if (params.get("output_prefix") is not None) else None,
-        rbuck_file=execution.output_file(params.get("output_prefix") + "_Rbuck.nii.gz") if (params.get("output_prefix") is not None) else None,
-        rfitts_file=execution.output_file(params.get("output_prefix") + "_Rfitts.nii.gz") if (params.get("output_prefix") is not None) else None,
-        rerrts_file=execution.output_file(params.get("output_prefix") + "_Rerrts.nii.gz") if (params.get("output_prefix") is not None) else None,
+        outfile=execution.output_file(params.get("output_prefix", None) + ".nii.gz") if (params.get("output_prefix") is not None) else None,
+        rvar_file=execution.output_file(params.get("output_prefix", None) + "_Rvar.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rbeta_file=execution.output_file(params.get("output_prefix", None) + "_Rbeta.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rbuck_file=execution.output_file(params.get("output_prefix", None) + "_Rbuck.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rfitts_file=execution.output_file(params.get("output_prefix", None) + "_Rfitts.nii.gz") if (params.get("output_prefix") is not None) else None,
+        rerrts_file=execution.output_file(params.get("output_prefix", None) + "_Rerrts.nii.gz") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
 
 def v_3d_remlfit_execute(
     params: V3dRemlfitParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dRemlfitOutputs:
     """
-    Generalized least squares time series fit, with REML estimation of the temporal
-    auto-correlation structure.
+    3dREMLfit
+    
+    Generalized least squares time series fit, with REML estimation of the
+    temporal auto-correlation structure.
     
     Author: AFNI Developers
     
@@ -267,10 +255,12 @@ def v_3d_remlfit_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dRemlfitOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_REMLFIT_METADATA)
     params = execution.params(params)
     cargs = v_3d_remlfit_cargs(params, execution)
     ret = v_3d_remlfit_outputs(params, execution)
@@ -297,8 +287,10 @@ def v_3d_remlfit(
     runner: Runner | None = None,
 ) -> V3dRemlfitOutputs:
     """
-    Generalized least squares time series fit, with REML estimation of the temporal
-    auto-correlation structure.
+    3dREMLfit
+    
+    Generalized least squares time series fit, with REML estimation of the
+    temporal auto-correlation structure.
     
     Author: AFNI Developers
     
@@ -331,8 +323,6 @@ def v_3d_remlfit(
     Returns:
         NamedTuple of outputs (described in `V3dRemlfitOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_REMLFIT_METADATA)
     params = v_3d_remlfit_params(
         input_file=input_file,
         regression_matrix=regression_matrix,
@@ -350,13 +340,13 @@ def v_3d_remlfit(
         quiet=quiet,
         verbose=verbose,
     )
-    return v_3d_remlfit_execute(params, execution)
+    return v_3d_remlfit_execute(params, runner)
 
 
 __all__ = [
     "V3dRemlfitOutputs",
-    "V3dRemlfitParameters",
     "V_3D_REMLFIT_METADATA",
     "v_3d_remlfit",
+    "v_3d_remlfit_execute",
     "v_3d_remlfit_params",
 ]