niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

niwrap_afni/afni/{fat_mvm_prep.py → fat_mvm_prep_py.py}

@@ -5,16 +5,26 @@ import typing
 import pathlib
 from styxdefs import *
 
-FAT_MVM_PREP_METADATA = Metadata(
-    id="be0a3158fe3df52caf8c7307710e4bd60769efcd.boutiques",
-    name="fat_mvm_prep",
+FAT_MVM_PREP_PY_METADATA = Metadata(
+    id="54af44a0131490c3e76aabb802ff1e00c7d8f153.boutiques",
+    name="fat_mvm_prep.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-FatMvmPrepParameters = typing.TypedDict('FatMvmPrepParameters', {
-    "__STYXTYPE__": typing.Literal["fat_mvm_prep"],
+FatMvmPrepPyParameters = typing.TypedDict('FatMvmPrepPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/fat_mvm_prep.py"]],
+    "prefix": str,
+    "csv_file": InputPathType,
+    "matrix_files": typing.NotRequired[str | None],
+    "list_match": typing.NotRequired[InputPathType | None],
+    "unionize_rois": bool,
+    "na_warn_off": bool,
+    "extern_labels_no": bool,
+})
+FatMvmPrepPyParametersTagged = typing.TypedDict('FatMvmPrepPyParametersTagged', {
+    "@type": typing.Literal["afni/fat_mvm_prep.py"],
     "prefix": str,
     "csv_file": InputPathType,
     "matrix_files": typing.NotRequired[str | None],
@@ -25,41 +35,9 @@ FatMvmPrepParameters = typing.TypedDict('FatMvmPrepParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_mvm_prep": fat_mvm_prep_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 {
-        "fat_mvm_prep": fat_mvm_prep_outputs,
-    }.get(t)
-
-
-class FatMvmPrepOutputs(typing.NamedTuple):
+class FatMvmPrepPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_mvm_prep(...)`.
+    Output object returned when calling `FatMvmPrepPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +47,7 @@ class FatMvmPrepOutputs(typing.NamedTuple):
     """Log file detailing subject matching and ROI list."""
 
 
-def fat_mvm_prep_params(
+def fat_mvm_prep_py_params(
     prefix: str,
     csv_file: InputPathType,
     matrix_files: str | None = None,
@@ -77,7 +55,7 @@ def fat_mvm_prep_params(
     unionize_rois: bool = False,
     na_warn_off: bool = False,
     extern_labels_no: bool = False,
-) -> FatMvmPrepParameters:
+) -> FatMvmPrepPyParametersTagged:
     """
     Build parameters.
     
@@ -98,7 +76,7 @@ def fat_mvm_prep_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_mvm_prep",
+        "@type": "afni/fat_mvm_prep.py",
         "prefix": prefix,
         "csv_file": csv_file,
         "unionize_rois": unionize_rois,
@@ -112,8 +90,8 @@ def fat_mvm_prep_params(
     return params
 
 
-def fat_mvm_prep_cargs(
-    params: FatMvmPrepParameters,
+def fat_mvm_prep_py_cargs(
+    params: FatMvmPrepPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -129,35 +107,35 @@ def fat_mvm_prep_cargs(
     cargs.append("fat_mvm_prep.py")
     cargs.extend([
         "-p",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "-c",
-        execution.input_file(params.get("csv_file"))
+        execution.input_file(params.get("csv_file", None))
     ])
-    if params.get("matrix_files") is not None:
+    if params.get("matrix_files", None) is not None:
         cargs.extend([
             "-m",
-            params.get("matrix_files")
+            params.get("matrix_files", None)
         ])
-    if params.get("list_match") is not None:
+    if params.get("list_match", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("list_match"))
+            execution.input_file(params.get("list_match", None))
         ])
-    if params.get("unionize_rois"):
+    if params.get("unionize_rois", False):
         cargs.append("-u")
-    if params.get("na_warn_off"):
+    if params.get("na_warn_off", False):
         cargs.append("-N")
-    if params.get("extern_labels_no"):
+    if params.get("extern_labels_no", False):
         cargs.append("-E")
     return cargs
 
 
-def fat_mvm_prep_outputs(
-    params: FatMvmPrepParameters,
+def fat_mvm_prep_py_outputs(
+    params: FatMvmPrepPyParameters,
     execution: Execution,
-) -> FatMvmPrepOutputs:
+) -> FatMvmPrepPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -167,19 +145,21 @@ def fat_mvm_prep_outputs(
     Returns:
         Outputs object.
     """
-    ret = FatMvmPrepOutputs(
+    ret = FatMvmPrepPyOutputs(
         root=execution.output_file("."),
-        mvmtbl=execution.output_file(params.get("prefix") + "_MVMtbl.txt"),
-        mvmprep_log=execution.output_file(params.get("prefix") + "_MVMprep.log"),
+        mvmtbl=execution.output_file(params.get("prefix", None) + "_MVMtbl.txt"),
+        mvmprep_log=execution.output_file(params.get("prefix", None) + "_MVMprep.log"),
     )
     return ret
 
 
-def fat_mvm_prep_execute(
-    params: FatMvmPrepParameters,
-    execution: Execution,
-) -> FatMvmPrepOutputs:
+def fat_mvm_prep_py_execute(
+    params: FatMvmPrepPyParameters,
+    runner: Runner | None = None,
+) -> FatMvmPrepPyOutputs:
     """
+    fat_mvm_prep.py
+    
     Combine FATCAT output with CSV data for statistical modeling.
     
     Author: AFNI Developers
@@ -188,18 +168,20 @@ def fat_mvm_prep_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FatMvmPrepOutputs`).
+        NamedTuple of outputs (described in `FatMvmPrepPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MVM_PREP_PY_METADATA)
     params = execution.params(params)
-    cargs = fat_mvm_prep_cargs(params, execution)
-    ret = fat_mvm_prep_outputs(params, execution)
+    cargs = fat_mvm_prep_py_cargs(params, execution)
+    ret = fat_mvm_prep_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def fat_mvm_prep(
+def fat_mvm_prep_py(
     prefix: str,
     csv_file: InputPathType,
     matrix_files: str | None = None,
@@ -208,8 +190,10 @@ def fat_mvm_prep(
     na_warn_off: bool = False,
     extern_labels_no: bool = False,
     runner: Runner | None = None,
-) -> FatMvmPrepOutputs:
+) -> FatMvmPrepPyOutputs:
     """
+    fat_mvm_prep.py
+    
     Combine FATCAT output with CSV data for statistical modeling.
     
     Author: AFNI Developers
@@ -231,11 +215,9 @@ def fat_mvm_prep(
             the *.grid/*.netcc files.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FatMvmPrepOutputs`).
+        NamedTuple of outputs (described in `FatMvmPrepPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_MVM_PREP_METADATA)
-    params = fat_mvm_prep_params(
+    params = fat_mvm_prep_py_params(
         prefix=prefix,
         csv_file=csv_file,
         matrix_files=matrix_files,
@@ -244,13 +226,13 @@ def fat_mvm_prep(
         na_warn_off=na_warn_off,
         extern_labels_no=extern_labels_no,
     )
-    return fat_mvm_prep_execute(params, execution)
+    return fat_mvm_prep_py_execute(params, runner)
 
 
 __all__ = [
-    "FAT_MVM_PREP_METADATA",
-    "FatMvmPrepOutputs",
-    "FatMvmPrepParameters",
-    "fat_mvm_prep",
-    "fat_mvm_prep_params",
+    "FAT_MVM_PREP_PY_METADATA",
+    "FatMvmPrepPyOutputs",
+    "fat_mvm_prep_py",
+    "fat_mvm_prep_py_execute",
+    "fat_mvm_prep_py_params",
 ]

niwrap_afni/afni/fat_mvm_scripter_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_MVM_SCRIPTER_PY_METADATA = Metadata(
-    id="da61b76b3f825a46611c99151eed256c6fae9763.boutiques",
+    id="9b3bc9fd729815c1d4263ce94ba8f03463293f18.boutiques",
     name="fat_mvm_scripter.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,23 @@ FAT_MVM_SCRIPTER_PY_METADATA = Metadata(
 
 
 FatMvmScripterPyParameters = typing.TypedDict('FatMvmScripterPyParameters', {
-    "__STYXTYPE__": typing.Literal["fat_mvm_scripter.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_mvm_scripter.py"]],
+    "prefix": str,
+    "table": InputPathType,
+    "log": InputPathType,
+    "vars": typing.NotRequired[str | None],
+    "file_vars": typing.NotRequired[InputPathType | None],
+    "Pars": typing.NotRequired[str | None],
+    "file_Pars": typing.NotRequired[InputPathType | None],
+    "rois": typing.NotRequired[str | None],
+    "file_rois": typing.NotRequired[InputPathType | None],
+    "no_posthoc": bool,
+    "NA_warn_off": bool,
+    "subnet_pref": typing.NotRequired[str | None],
+    "cat_pair_off": bool,
+})
+FatMvmScripterPyParametersTagged = typing.TypedDict('FatMvmScripterPyParametersTagged', {
+    "@type": typing.Literal["afni/fat_mvm_scripter.py"],
     "prefix": str,
     "table": InputPathType,
     "log": InputPathType,
@@ -29,43 +45,11 @@ FatMvmScripterPyParameters = typing.TypedDict('FatMvmScripterPyParameters', {
     "subnet_pref": typing.NotRequired[str | None],
     "cat_pair_off": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_mvm_scripter.py": fat_mvm_scripter_py_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 {
-        "fat_mvm_scripter.py": fat_mvm_scripter_py_outputs,
-    }.get(t)
 
 
 class FatMvmScripterPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_mvm_scripter_py(...)`.
+    Output object returned when calling `FatMvmScripterPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -90,7 +74,7 @@ def fat_mvm_scripter_py_params(
     na_warn_off: bool = False,
     subnet_pref: str | None = None,
     cat_pair_off: bool = False,
-) -> FatMvmScripterPyParameters:
+) -> FatMvmScripterPyParametersTagged:
     """
     Build parameters.
     
@@ -127,7 +111,7 @@ def fat_mvm_scripter_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_mvm_scripter.py",
+        "@type": "afni/fat_mvm_scripter.py",
         "prefix": prefix,
         "table": table,
         "log": log,
@@ -169,56 +153,56 @@ def fat_mvm_scripter_py_cargs(
     cargs.append("fat_mvm_scripter.py")
     cargs.extend([
         "--prefix",
-        params.get("prefix")
+        params.get("prefix", None)
     ])
     cargs.extend([
         "--table",
-        execution.input_file(params.get("table"))
+        execution.input_file(params.get("table", None))
     ])
     cargs.extend([
         "--log",
-        execution.input_file(params.get("log"))
+        execution.input_file(params.get("log", None))
     ])
-    if params.get("vars") is not None:
+    if params.get("vars", None) is not None:
         cargs.extend([
             "--vars",
-            params.get("vars")
+            params.get("vars", None)
         ])
-    if params.get("file_vars") is not None:
+    if params.get("file_vars", None) is not None:
         cargs.extend([
             "--file_vars",
-            execution.input_file(params.get("file_vars"))
+            execution.input_file(params.get("file_vars", None))
         ])
-    if params.get("Pars") is not None:
+    if params.get("Pars", None) is not None:
         cargs.extend([
             "--Pars",
-            params.get("Pars")
+            params.get("Pars", None)
         ])
-    if params.get("file_Pars") is not None:
+    if params.get("file_Pars", None) is not None:
         cargs.extend([
             "--File_Pars",
-            execution.input_file(params.get("file_Pars"))
+            execution.input_file(params.get("file_Pars", None))
         ])
-    if params.get("rois") is not None:
+    if params.get("rois", None) is not None:
         cargs.extend([
             "--rois",
-            params.get("rois")
+            params.get("rois", None)
         ])
-    if params.get("file_rois") is not None:
+    if params.get("file_rois", None) is not None:
         cargs.extend([
             "--file_rois",
-            execution.input_file(params.get("file_rois"))
+            execution.input_file(params.get("file_rois", None))
         ])
-    if params.get("no_posthoc"):
+    if params.get("no_posthoc", False):
         cargs.append("--no_posthoc")
-    if params.get("NA_warn_off"):
+    if params.get("NA_warn_off", False):
         cargs.append("--NA_warn_off")
-    if params.get("subnet_pref") is not None:
+    if params.get("subnet_pref", None) is not None:
         cargs.extend([
             "--subnet_pref",
-            params.get("subnet_pref")
+            params.get("subnet_pref", None)
         ])
-    if params.get("cat_pair_off"):
+    if params.get("cat_pair_off", False):
         cargs.append("--cat_pair_off")
     return cargs
 
@@ -238,17 +222,19 @@ def fat_mvm_scripter_py_outputs(
     """
     ret = FatMvmScripterPyOutputs(
         root=execution.output_file("."),
-        generated_script=execution.output_file(params.get("prefix") + "_scri.tcsh"),
-        results_file=execution.output_file(params.get("prefix") + "_MVM.txt"),
+        generated_script=execution.output_file(params.get("prefix", None) + "_scri.tcsh"),
+        results_file=execution.output_file(params.get("prefix", None) + "_MVM.txt"),
     )
     return ret
 
 
 def fat_mvm_scripter_py_execute(
     params: FatMvmScripterPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatMvmScripterPyOutputs:
     """
+    fat_mvm_scripter.py
+    
     Automated tool to create command scripts for 3dMVM statistical modeling.
     
     Author: AFNI Developers
@@ -257,10 +243,12 @@ def fat_mvm_scripter_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatMvmScripterPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MVM_SCRIPTER_PY_METADATA)
     params = execution.params(params)
     cargs = fat_mvm_scripter_py_cargs(params, execution)
     ret = fat_mvm_scripter_py_outputs(params, execution)
@@ -285,6 +273,8 @@ def fat_mvm_scripter_py(
     runner: Runner | None = None,
 ) -> FatMvmScripterPyOutputs:
     """
+    fat_mvm_scripter.py
+    
     Automated tool to create command scripts for 3dMVM statistical modeling.
     
     Author: AFNI Developers
@@ -324,8 +314,6 @@ def fat_mvm_scripter_py(
     Returns:
         NamedTuple of outputs (described in `FatMvmScripterPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_MVM_SCRIPTER_PY_METADATA)
     params = fat_mvm_scripter_py_params(
         prefix=prefix,
         table=table,
@@ -341,13 +329,13 @@ def fat_mvm_scripter_py(
         subnet_pref=subnet_pref,
         cat_pair_off=cat_pair_off,
     )
-    return fat_mvm_scripter_py_execute(params, execution)
+    return fat_mvm_scripter_py_execute(params, runner)
 
 
 __all__ = [
     "FAT_MVM_SCRIPTER_PY_METADATA",
     "FatMvmScripterPyOutputs",
-    "FatMvmScripterPyParameters",
     "fat_mvm_scripter_py",
+    "fat_mvm_scripter_py_execute",
     "fat_mvm_scripter_py_params",
 ]