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

niwrap_afni/afni/v_3d_lme.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LME_METADATA = Metadata(
-    id="f4d10c5d90b0f7b7397fa43e05d3c57da29fce2c.boutiques",
+    id="31d1a51398f7d40b2fcd22043888f5e84c9f3165.boutiques",
     name="3dLME",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,40 @@ V_3D_LME_METADATA = Metadata(
 
 
 V3dLmeParameters = typing.TypedDict('V3dLmeParameters', {
-    "__STYXTYPE__": typing.Literal["3dLME"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLME"]],
+    "PREFIX": str,
+    "MODEL": str,
+    "DATA_TABLE": str,
+    "BOUNDS": typing.NotRequired[list[float] | None],
+    "CIO_FLAG": bool,
+    "COR_STR": typing.NotRequired[str | None],
+    "CUTOFF": typing.NotRequired[float | None],
+    "DBG_ARGS_FLAG": bool,
+    "JOBS": typing.NotRequired[float | None],
+    "GLT_CODE": typing.NotRequired[str | None],
+    "GLT_LABEL": typing.NotRequired[str | None],
+    "GLF_LABEL": typing.NotRequired[str | None],
+    "GLF_CODE": typing.NotRequired[str | None],
+    "ICC_FLAG": bool,
+    "ICCB_FLAG": bool,
+    "LOG_LIK_FLAG": bool,
+    "LOGIT_FLAG": bool,
+    "ML_FLAG": bool,
+    "QVARS_CENTERS": typing.NotRequired[str | None],
+    "QVARS": typing.NotRequired[str | None],
+    "RANEFF": typing.NotRequired[str | None],
+    "MASK": typing.NotRequired[InputPathType | None],
+    "NUM_GLF": typing.NotRequired[float | None],
+    "NUM_GLT": typing.NotRequired[float | None],
+    "RESID": typing.NotRequired[str | None],
+    "RE": typing.NotRequired[str | None],
+    "REPREFIX": typing.NotRequired[str | None],
+    "RIO_FLAG": bool,
+    "SHOW_OPTIONS_FLAG": bool,
+    "SS_TYPE": typing.NotRequired[float | None],
+})
+V3dLmeParametersTagged = typing.TypedDict('V3dLmeParametersTagged', {
+    "@type": typing.Literal["afni/3dLME"],
     "PREFIX": str,
     "MODEL": str,
     "DATA_TABLE": str,
@@ -46,43 +79,11 @@ V3dLmeParameters = typing.TypedDict('V3dLmeParameters', {
     "SHOW_OPTIONS_FLAG": bool,
     "SS_TYPE": 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 {
-        "3dLME": v_3d_lme_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 {
-        "3dLME": v_3d_lme_outputs,
-    }.get(t)
 
 
 class V3dLmeOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_lme(...)`.
+    Output object returned when calling `V3dLmeParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -121,7 +122,7 @@ def v_3d_lme_params(
     rio_flag: bool = False,
     show_options_flag: bool = False,
     ss_type: float | None = None,
-) -> V3dLmeParameters:
+) -> V3dLmeParametersTagged:
     """
     Build parameters.
     
@@ -163,7 +164,7 @@ def v_3d_lme_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLME",
+        "@type": "afni/3dLME",
         "PREFIX": prefix,
         "MODEL": model,
         "DATA_TABLE": data_table,
@@ -233,123 +234,123 @@ def v_3d_lme_cargs(
     cargs.append("3dLME")
     cargs.extend([
         "-prefix",
-        params.get("PREFIX")
+        params.get("PREFIX", None)
     ])
     cargs.extend([
         "-model",
-        params.get("MODEL")
+        params.get("MODEL", None)
     ])
     cargs.extend([
         "-dataTable",
-        params.get("DATA_TABLE")
+        params.get("DATA_TABLE", 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("CIO_FLAG"):
+    if params.get("CIO_FLAG", False):
         cargs.append("-cio")
-    if params.get("COR_STR") is not None:
+    if params.get("COR_STR", None) is not None:
         cargs.extend([
             "-corStr",
-            params.get("COR_STR")
+            params.get("COR_STR", None)
         ])
-    if params.get("CUTOFF") is not None:
+    if params.get("CUTOFF", None) is not None:
         cargs.extend([
             "-cutoff",
-            str(params.get("CUTOFF"))
+            str(params.get("CUTOFF", None))
         ])
-    if params.get("DBG_ARGS_FLAG"):
+    if params.get("DBG_ARGS_FLAG", False):
         cargs.append("-dbgArgs")
-    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))
         ])
-    if params.get("GLT_CODE") is not None:
+    if params.get("GLT_CODE", None) is not None:
         cargs.extend([
             "-gltCode",
-            params.get("GLT_CODE")
+            params.get("GLT_CODE", None)
         ])
-    if params.get("GLT_LABEL") is not None:
+    if params.get("GLT_LABEL", None) is not None:
         cargs.extend([
             "-gltLabel",
-            params.get("GLT_LABEL")
+            params.get("GLT_LABEL", None)
         ])
-    if params.get("GLF_LABEL") is not None:
+    if params.get("GLF_LABEL", None) is not None:
         cargs.extend([
             "-glfLabel",
-            params.get("GLF_LABEL")
+            params.get("GLF_LABEL", None)
         ])
-    if params.get("GLF_CODE") is not None:
+    if params.get("GLF_CODE", None) is not None:
         cargs.extend([
             "-glfCode",
-            params.get("GLF_CODE")
+            params.get("GLF_CODE", None)
         ])
-    if params.get("ICC_FLAG"):
+    if params.get("ICC_FLAG", False):
         cargs.append("-ICC")
-    if params.get("ICCB_FLAG"):
+    if params.get("ICCB_FLAG", False):
         cargs.append("-ICCb")
-    if params.get("LOG_LIK_FLAG"):
+    if params.get("LOG_LIK_FLAG", False):
         cargs.append("-logLik")
-    if params.get("LOGIT_FLAG"):
+    if params.get("LOGIT_FLAG", False):
         cargs.append("-LOGIT")
-    if params.get("ML_FLAG"):
+    if params.get("ML_FLAG", False):
         cargs.append("-ML")
-    if params.get("QVARS_CENTERS") is not None:
+    if params.get("QVARS_CENTERS", None) is not None:
         cargs.extend([
             "-qVarsCenters",
-            params.get("QVARS_CENTERS")
+            params.get("QVARS_CENTERS", 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("RANEFF") is not None:
+    if params.get("RANEFF", None) is not None:
         cargs.extend([
             "-ranEff",
-            params.get("RANEFF")
+            params.get("RANEFF", 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("NUM_GLF") is not None:
+    if params.get("NUM_GLF", None) is not None:
         cargs.extend([
             "-num_glf",
-            str(params.get("NUM_GLF"))
+            str(params.get("NUM_GLF", None))
         ])
-    if params.get("NUM_GLT") is not None:
+    if params.get("NUM_GLT", None) is not None:
         cargs.extend([
             "-num_glt",
-            str(params.get("NUM_GLT"))
+            str(params.get("NUM_GLT", None))
         ])
-    if params.get("RESID") is not None:
+    if params.get("RESID", None) is not None:
         cargs.extend([
             "-resid",
-            params.get("RESID")
+            params.get("RESID", None)
         ])
-    if params.get("RE") is not None:
+    if params.get("RE", None) is not None:
         cargs.extend([
             "-RE",
-            params.get("RE")
+            params.get("RE", None)
         ])
-    if params.get("REPREFIX") is not None:
+    if params.get("REPREFIX", None) is not None:
         cargs.extend([
             "-REprefix",
-            params.get("REPREFIX")
+            params.get("REPREFIX", None)
         ])
-    if params.get("RIO_FLAG"):
+    if params.get("RIO_FLAG", False):
         cargs.append("-Rio")
-    if params.get("SHOW_OPTIONS_FLAG"):
+    if params.get("SHOW_OPTIONS_FLAG", False):
         cargs.append("-show_allowed_options")
-    if params.get("SS_TYPE") is not None:
+    if params.get("SS_TYPE", None) is not None:
         cargs.extend([
             "-SS_type",
-            str(params.get("SS_TYPE"))
+            str(params.get("SS_TYPE", None))
         ])
     return cargs
 
@@ -369,16 +370,18 @@ def v_3d_lme_outputs(
     """
     ret = V3dLmeOutputs(
         root=execution.output_file("."),
-        output_nifti=execution.output_file(params.get("PREFIX") + ".nii"),
+        output_nifti=execution.output_file(params.get("PREFIX", None) + ".nii"),
     )
     return ret
 
 
 def v_3d_lme_execute(
     params: V3dLmeParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLmeOutputs:
     """
+    3dLME
+    
     AFNI Group Analysis Program with Linear Mixed-Effects Modeling Approach.
     
     Author: AFNI Developers
@@ -387,10 +390,12 @@ def v_3d_lme_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLmeOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LME_METADATA)
     params = execution.params(params)
     cargs = v_3d_lme_cargs(params, execution)
     ret = v_3d_lme_outputs(params, execution)
@@ -432,6 +437,8 @@ def v_3d_lme(
     runner: Runner | None = None,
 ) -> V3dLmeOutputs:
     """
+    3dLME
+    
     AFNI Group Analysis Program with Linear Mixed-Effects Modeling Approach.
     
     Author: AFNI Developers
@@ -476,8 +483,6 @@ def v_3d_lme(
     Returns:
         NamedTuple of outputs (described in `V3dLmeOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LME_METADATA)
     params = v_3d_lme_params(
         prefix=prefix,
         model=model,
@@ -510,13 +515,13 @@ def v_3d_lme(
         show_options_flag=show_options_flag,
         ss_type=ss_type,
     )
-    return v_3d_lme_execute(params, execution)
+    return v_3d_lme_execute(params, runner)
 
 
 __all__ = [
     "V3dLmeOutputs",
-    "V3dLmeParameters",
     "V_3D_LME_METADATA",
     "v_3d_lme",
+    "v_3d_lme_execute",
     "v_3d_lme_params",
 ]

niwrap_afni/afni/v_3d_lmer.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LMER_METADATA = Metadata(
-    id="8a20ec1dad15f735378cd37a5c99e69b69118bc1.boutiques",
+    id="716346bea5e7c26c346b9be754d889886a9feaa2.boutiques",
     name="3dLMEr",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,32 @@ V_3D_LMER_METADATA = Metadata(
 
 
 V3dLmerParameters = typing.TypedDict('V3dLmerParameters', {
-    "__STYXTYPE__": typing.Literal["3dLMEr"],
+    "@type": typing.NotRequired[typing.Literal["afni/3dLMEr"]],
+    "bound_lower": typing.NotRequired[float | None],
+    "bound_upper": typing.NotRequired[float | None],
+    "cio": bool,
+    "data_table": InputPathType,
+    "debug_args": bool,
+    "glf_code": typing.NotRequired[str | None],
+    "glt_code": typing.NotRequired[str | None],
+    "help": bool,
+    "input_file_column": typing.NotRequired[str | None],
+    "jobs": typing.NotRequired[float | None],
+    "mask": typing.NotRequired[InputPathType | None],
+    "model": str,
+    "prefix": str,
+    "qvar_centers": typing.NotRequired[str | None],
+    "qvars": typing.NotRequired[str | None],
+    "resid": typing.NotRequired[str | None],
+    "rio": bool,
+    "show_options": bool,
+    "ss_type": typing.NotRequired[float | None],
+    "trr": bool,
+    "vvar_centers": typing.NotRequired[str | None],
+    "vvars": typing.NotRequired[str | None],
+})
+V3dLmerParametersTagged = typing.TypedDict('V3dLmerParametersTagged', {
+    "@type": typing.Literal["afni/3dLMEr"],
     "bound_lower": typing.NotRequired[float | None],
     "bound_upper": typing.NotRequired[float | None],
     "cio": bool,
@@ -38,43 +63,11 @@ V3dLmerParameters = typing.TypedDict('V3dLmerParameters', {
     "vvar_centers": typing.NotRequired[str | None],
     "vvars": 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 {
-        "3dLMEr": v_3d_lmer_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 {
-        "3dLMEr": v_3d_lmer_outputs,
-    }.get(t)
 
 
 class V3dLmerOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `v_3d_lmer(...)`.
+    Output object returned when calling `V3dLmerParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +100,7 @@ def v_3d_lmer_params(
     trr: bool = False,
     vvar_centers: str | None = None,
     vvars: str | None = None,
-) -> V3dLmerParameters:
+) -> V3dLmerParametersTagged:
     """
     Build parameters.
     
@@ -140,7 +133,7 @@ def v_3d_lmer_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "3dLMEr",
+        "@type": "afni/3dLMEr",
         "cio": cio,
         "data_table": data_table,
         "debug_args": debug_args,
@@ -195,88 +188,88 @@ def v_3d_lmer_cargs(
     """
     cargs = []
     cargs.append("3dLMEr")
-    if params.get("bound_lower") is not None:
-        cargs.append(str(params.get("bound_lower")))
-    if params.get("bound_upper") is not None:
-        cargs.append(str(params.get("bound_upper")))
-    if params.get("cio"):
+    if params.get("bound_lower", None) is not None:
+        cargs.append(str(params.get("bound_lower", None)))
+    if params.get("bound_upper", None) is not None:
+        cargs.append(str(params.get("bound_upper", None)))
+    if params.get("cio", False):
         cargs.append("-cio")
     cargs.extend([
         "-dataTable",
-        execution.input_file(params.get("data_table"))
+        execution.input_file(params.get("data_table", None))
     ])
-    if params.get("debug_args"):
+    if params.get("debug_args", False):
         cargs.append("-dbgArgs")
-    if params.get("glf_code") is not None:
+    if params.get("glf_code", None) is not None:
         cargs.extend([
             "-glfCode",
-            params.get("glf_code")
+            params.get("glf_code", None)
         ])
-    if params.get("glt_code") is not None:
+    if params.get("glt_code", None) is not None:
         cargs.extend([
             "-gltCode",
-            params.get("glt_code")
+            params.get("glt_code", None)
         ])
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("input_file_column") is not None:
+    if params.get("input_file_column", None) is not None:
         cargs.extend([
             "-IF",
-            params.get("input_file_column")
+            params.get("input_file_column", 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))
         ])
-    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))
         ])
     cargs.extend([
         "-model",
-        params.get("model")
+        params.get("model", None)
     ])
     cargs.extend([
         "-prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
-    if params.get("qvar_centers") is not None:
+    if params.get("qvar_centers", None) is not None:
         cargs.extend([
             "-qVarCenters",
-            params.get("qvar_centers")
+            params.get("qvar_centers", 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("resid") is not None:
+    if params.get("resid", None) is not None:
         cargs.extend([
             "-resid",
-            params.get("resid")
+            params.get("resid", None)
         ])
-    if params.get("rio"):
+    if params.get("rio", False):
         cargs.append("-Rio")
-    if params.get("show_options"):
+    if params.get("show_options", False):
         cargs.append("-show_allowed_options")
-    if params.get("ss_type") is not None:
+    if params.get("ss_type", None) is not None:
         cargs.extend([
             "-SS_type",
-            str(params.get("ss_type"))
+            str(params.get("ss_type", None))
         ])
-    if params.get("trr"):
+    if params.get("trr", False):
         cargs.append("-TRR")
-    if params.get("vvar_centers") is not None:
+    if params.get("vvar_centers", None) is not None:
         cargs.extend([
             "-vVarCenters",
-            params.get("vvar_centers")
+            params.get("vvar_centers", None)
         ])
-    if params.get("vvars") is not None:
+    if params.get("vvars", None) is not None:
         cargs.extend([
             "-vVars",
-            params.get("vvars")
+            params.get("vvars", None)
         ])
     return cargs
 
@@ -296,17 +289,19 @@ def v_3d_lmer_outputs(
     """
     ret = V3dLmerOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("prefix") + ".nii.gz"),
-        residuals_file=execution.output_file(params.get("resid") + ".nii.gz") if (params.get("resid") is not None) else None,
+        output_file=execution.output_file(params.get("prefix", None) + ".nii.gz"),
+        residuals_file=execution.output_file(params.get("resid", None) + ".nii.gz") if (params.get("resid") is not None) else None,
     )
     return ret
 
 
 def v_3d_lmer_execute(
     params: V3dLmerParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> V3dLmerOutputs:
     """
+    3dLMEr
+    
     Program for Voxelwise Linear Mixed-Effects (LME) Analysis.
     
     Author: AFNI Developers
@@ -315,10 +310,12 @@ def v_3d_lmer_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLmerOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(V_3D_LMER_METADATA)
     params = execution.params(params)
     cargs = v_3d_lmer_cargs(params, execution)
     ret = v_3d_lmer_outputs(params, execution)
@@ -352,6 +349,8 @@ def v_3d_lmer(
     runner: Runner | None = None,
 ) -> V3dLmerOutputs:
     """
+    3dLMEr
+    
     Program for Voxelwise Linear Mixed-Effects (LME) Analysis.
     
     Author: AFNI Developers
@@ -387,8 +386,6 @@ def v_3d_lmer(
     Returns:
         NamedTuple of outputs (described in `V3dLmerOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(V_3D_LMER_METADATA)
     params = v_3d_lmer_params(
         bound_lower=bound_lower,
         bound_upper=bound_upper,
@@ -413,13 +410,13 @@ def v_3d_lmer(
         vvar_centers=vvar_centers,
         vvars=vvars,
     )
-    return v_3d_lmer_execute(params, execution)
+    return v_3d_lmer_execute(params, runner)
 
 
 __all__ = [
     "V3dLmerOutputs",
-    "V3dLmerParameters",
     "V_3D_LMER_METADATA",
     "v_3d_lmer",
+    "v_3d_lmer_execute",
     "v_3d_lmer_params",
 ]