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

niwrap_afni/afni/{gen_ss_review_scripts.py → gen_ss_review_scripts_py.py}

@@ -5,16 +5,38 @@ import typing
 import pathlib
 from styxdefs import *
 
-GEN_SS_REVIEW_SCRIPTS_METADATA = Metadata(
-    id="19293a431a3099e1044a725ff53be407555c7b79.boutiques",
-    name="gen_ss_review_scripts",
+GEN_SS_REVIEW_SCRIPTS_PY_METADATA = Metadata(
+    id="039be4dfc322a0c1878b8ece0ddefa12e6e5b637.boutiques",
+    name="gen_ss_review_scripts.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-GenSsReviewScriptsParameters = typing.TypedDict('GenSsReviewScriptsParameters', {
-    "__STYXTYPE__": typing.Literal["gen_ss_review_scripts"],
+GenSsReviewScriptsPyParameters = typing.TypedDict('GenSsReviewScriptsPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/gen_ss_review_scripts.py"]],
+    "subject_id": typing.NotRequired[str | None],
+    "rm_trs": typing.NotRequired[float | None],
+    "num_stim": typing.NotRequired[float | None],
+    "mb_level": typing.NotRequired[float | None],
+    "slice_pattern": typing.NotRequired[str | None],
+    "motion_dset": typing.NotRequired[InputPathType | None],
+    "outlier_dset": typing.NotRequired[InputPathType | None],
+    "enorm_dset": typing.NotRequired[InputPathType | None],
+    "mot_limit": typing.NotRequired[float | None],
+    "out_limit": typing.NotRequired[float | None],
+    "xmat_regress": typing.NotRequired[InputPathType | None],
+    "xmat_uncensored": typing.NotRequired[InputPathType | None],
+    "stats_dset": typing.NotRequired[InputPathType | None],
+    "final_anat": typing.NotRequired[InputPathType | None],
+    "final_view": typing.NotRequired[str | None],
+    "prefix": typing.NotRequired[str | None],
+    "verbosity": typing.NotRequired[float | None],
+    "uvars_json": typing.NotRequired[InputPathType | None],
+    "init_uvars_json": typing.NotRequired[InputPathType | None],
+})
+GenSsReviewScriptsPyParametersTagged = typing.TypedDict('GenSsReviewScriptsPyParametersTagged', {
+    "@type": typing.Literal["afni/gen_ss_review_scripts.py"],
     "subject_id": typing.NotRequired[str | None],
     "rm_trs": typing.NotRequired[float | None],
     "num_stim": typing.NotRequired[float | None],
@@ -37,41 +59,9 @@ GenSsReviewScriptsParameters = typing.TypedDict('GenSsReviewScriptsParameters',
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gen_ss_review_scripts": gen_ss_review_scripts_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 {
-        "gen_ss_review_scripts": gen_ss_review_scripts_outputs,
-    }.get(t)
-
-
-class GenSsReviewScriptsOutputs(typing.NamedTuple):
+class GenSsReviewScriptsPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gen_ss_review_scripts(...)`.
+    Output object returned when calling `GenSsReviewScriptsPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -83,7 +73,7 @@ class GenSsReviewScriptsOutputs(typing.NamedTuple):
     """Driver commands script output"""
 
 
-def gen_ss_review_scripts_params(
+def gen_ss_review_scripts_py_params(
     subject_id: str | None = None,
     rm_trs: float | None = None,
     num_stim: float | None = None,
@@ -103,7 +93,7 @@ def gen_ss_review_scripts_params(
     verbosity: float | None = None,
     uvars_json: InputPathType | None = None,
     init_uvars_json: InputPathType | None = None,
-) -> GenSsReviewScriptsParameters:
+) -> GenSsReviewScriptsPyParametersTagged:
     """
     Build parameters.
     
@@ -131,7 +121,7 @@ def gen_ss_review_scripts_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gen_ss_review_scripts",
+        "@type": "afni/gen_ss_review_scripts.py",
     }
     if subject_id is not None:
         params["subject_id"] = subject_id
@@ -174,8 +164,8 @@ def gen_ss_review_scripts_params(
     return params
 
 
-def gen_ss_review_scripts_cargs(
-    params: GenSsReviewScriptsParameters,
+def gen_ss_review_scripts_py_cargs(
+    params: GenSsReviewScriptsPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -189,108 +179,108 @@ def gen_ss_review_scripts_cargs(
     """
     cargs = []
     cargs.append("gen_ss_review_scripts.py")
-    if params.get("subject_id") is not None:
+    if params.get("subject_id", None) is not None:
         cargs.extend([
             "-subj",
-            params.get("subject_id")
+            params.get("subject_id", None)
         ])
-    if params.get("rm_trs") is not None:
+    if params.get("rm_trs", None) is not None:
         cargs.extend([
             "-rm_trs",
-            str(params.get("rm_trs"))
+            str(params.get("rm_trs", None))
         ])
-    if params.get("num_stim") is not None:
+    if params.get("num_stim", None) is not None:
         cargs.extend([
             "-num_stim",
-            str(params.get("num_stim"))
+            str(params.get("num_stim", None))
         ])
-    if params.get("mb_level") is not None:
+    if params.get("mb_level", None) is not None:
         cargs.extend([
             "-mb_level",
-            str(params.get("mb_level"))
+            str(params.get("mb_level", None))
         ])
-    if params.get("slice_pattern") is not None:
+    if params.get("slice_pattern", None) is not None:
         cargs.extend([
             "-slice_pattern",
-            params.get("slice_pattern")
+            params.get("slice_pattern", None)
         ])
-    if params.get("motion_dset") is not None:
+    if params.get("motion_dset", None) is not None:
         cargs.extend([
             "-motion_dset",
-            execution.input_file(params.get("motion_dset"))
+            execution.input_file(params.get("motion_dset", None))
         ])
-    if params.get("outlier_dset") is not None:
+    if params.get("outlier_dset", None) is not None:
         cargs.extend([
             "-outlier_dset",
-            execution.input_file(params.get("outlier_dset"))
+            execution.input_file(params.get("outlier_dset", None))
         ])
-    if params.get("enorm_dset") is not None:
+    if params.get("enorm_dset", None) is not None:
         cargs.extend([
             "-enorm_dset",
-            execution.input_file(params.get("enorm_dset"))
+            execution.input_file(params.get("enorm_dset", None))
         ])
-    if params.get("mot_limit") is not None:
+    if params.get("mot_limit", None) is not None:
         cargs.extend([
             "-mot_limit",
-            str(params.get("mot_limit"))
+            str(params.get("mot_limit", None))
         ])
-    if params.get("out_limit") is not None:
+    if params.get("out_limit", None) is not None:
         cargs.extend([
             "-out_limit",
-            str(params.get("out_limit"))
+            str(params.get("out_limit", None))
         ])
-    if params.get("xmat_regress") is not None:
+    if params.get("xmat_regress", None) is not None:
         cargs.extend([
             "-xmat_regress",
-            execution.input_file(params.get("xmat_regress"))
+            execution.input_file(params.get("xmat_regress", None))
         ])
-    if params.get("xmat_uncensored") is not None:
+    if params.get("xmat_uncensored", None) is not None:
         cargs.extend([
             "-xmat_uncensored",
-            execution.input_file(params.get("xmat_uncensored"))
+            execution.input_file(params.get("xmat_uncensored", None))
         ])
-    if params.get("stats_dset") is not None:
+    if params.get("stats_dset", None) is not None:
         cargs.extend([
             "-stats_dset",
-            execution.input_file(params.get("stats_dset"))
+            execution.input_file(params.get("stats_dset", None))
         ])
-    if params.get("final_anat") is not None:
+    if params.get("final_anat", None) is not None:
         cargs.extend([
             "-final_anat",
-            execution.input_file(params.get("final_anat"))
+            execution.input_file(params.get("final_anat", None))
         ])
-    if params.get("final_view") is not None:
+    if params.get("final_view", None) is not None:
         cargs.extend([
             "-final_view",
-            params.get("final_view")
+            params.get("final_view", 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("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
-    if params.get("uvars_json") is not None:
+    if params.get("uvars_json", None) is not None:
         cargs.extend([
             "-write_uvars_json",
-            execution.input_file(params.get("uvars_json"))
+            execution.input_file(params.get("uvars_json", None))
         ])
-    if params.get("init_uvars_json") is not None:
+    if params.get("init_uvars_json", None) is not None:
         cargs.extend([
             "-init_uvars_json",
-            execution.input_file(params.get("init_uvars_json"))
+            execution.input_file(params.get("init_uvars_json", None))
         ])
     return cargs
 
 
-def gen_ss_review_scripts_outputs(
-    params: GenSsReviewScriptsParameters,
+def gen_ss_review_scripts_py_outputs(
+    params: GenSsReviewScriptsPyParameters,
     execution: Execution,
-) -> GenSsReviewScriptsOutputs:
+) -> GenSsReviewScriptsPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -300,7 +290,7 @@ def gen_ss_review_scripts_outputs(
     Returns:
         Outputs object.
     """
-    ret = GenSsReviewScriptsOutputs(
+    ret = GenSsReviewScriptsPyOutputs(
         root=execution.output_file("."),
         basic_review=execution.output_file("./@ss_review_basic"),
         driver_review=execution.output_file("./@ss_review_driver"),
@@ -309,11 +299,13 @@ def gen_ss_review_scripts_outputs(
     return ret
 
 
-def gen_ss_review_scripts_execute(
-    params: GenSsReviewScriptsParameters,
-    execution: Execution,
-) -> GenSsReviewScriptsOutputs:
+def gen_ss_review_scripts_py_execute(
+    params: GenSsReviewScriptsPyParameters,
+    runner: Runner | None = None,
+) -> GenSsReviewScriptsPyOutputs:
     """
+    gen_ss_review_scripts.py
+    
     Generate single subject analysis review scripts.
     
     Author: AFNI Developers
@@ -322,18 +314,20 @@ def gen_ss_review_scripts_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `GenSsReviewScriptsOutputs`).
+        NamedTuple of outputs (described in `GenSsReviewScriptsPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GEN_SS_REVIEW_SCRIPTS_PY_METADATA)
     params = execution.params(params)
-    cargs = gen_ss_review_scripts_cargs(params, execution)
-    ret = gen_ss_review_scripts_outputs(params, execution)
+    cargs = gen_ss_review_scripts_py_cargs(params, execution)
+    ret = gen_ss_review_scripts_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def gen_ss_review_scripts(
+def gen_ss_review_scripts_py(
     subject_id: str | None = None,
     rm_trs: float | None = None,
     num_stim: float | None = None,
@@ -354,8 +348,10 @@ def gen_ss_review_scripts(
     uvars_json: InputPathType | None = None,
     init_uvars_json: InputPathType | None = None,
     runner: Runner | None = None,
-) -> GenSsReviewScriptsOutputs:
+) -> GenSsReviewScriptsPyOutputs:
     """
+    gen_ss_review_scripts.py
+    
     Generate single subject analysis review scripts.
     
     Author: AFNI Developers
@@ -384,11 +380,9 @@ def gen_ss_review_scripts(
         init_uvars_json: Initialize user variables from the given JSON file.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `GenSsReviewScriptsOutputs`).
+        NamedTuple of outputs (described in `GenSsReviewScriptsPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GEN_SS_REVIEW_SCRIPTS_METADATA)
-    params = gen_ss_review_scripts_params(
+    params = gen_ss_review_scripts_py_params(
         subject_id=subject_id,
         rm_trs=rm_trs,
         num_stim=num_stim,
@@ -409,13 +403,13 @@ def gen_ss_review_scripts(
         uvars_json=uvars_json,
         init_uvars_json=init_uvars_json,
     )
-    return gen_ss_review_scripts_execute(params, execution)
+    return gen_ss_review_scripts_py_execute(params, runner)
 
 
 __all__ = [
-    "GEN_SS_REVIEW_SCRIPTS_METADATA",
-    "GenSsReviewScriptsOutputs",
-    "GenSsReviewScriptsParameters",
-    "gen_ss_review_scripts",
-    "gen_ss_review_scripts_params",
+    "GEN_SS_REVIEW_SCRIPTS_PY_METADATA",
+    "GenSsReviewScriptsPyOutputs",
+    "gen_ss_review_scripts_py",
+    "gen_ss_review_scripts_py_execute",
+    "gen_ss_review_scripts_py_params",
 ]

niwrap_afni/afni/gen_ss_review_table_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 GEN_SS_REVIEW_TABLE_PY_METADATA = Metadata(
-    id="6cb69af99777b33cd9b767e710e49b813e80d5c6.boutiques",
+    id="86e0a4a60a7307fdbdac8e970d36b74509c7924f.boutiques",
     name="gen_ss_review_table.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ GEN_SS_REVIEW_TABLE_PY_METADATA = Metadata(
 
 
 GenSsReviewTablePyParameters = typing.TypedDict('GenSsReviewTablePyParameters', {
-    "__STYXTYPE__": typing.Literal["gen_ss_review_table.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/gen_ss_review_table.py"]],
+    "infiles": list[InputPathType],
+    "write_table": typing.NotRequired[InputPathType | None],
+    "write_outliers": typing.NotRequired[InputPathType | None],
+    "overwrite": bool,
+    "empty_is_outlier": bool,
+    "outlier_sep": typing.NotRequired[str | None],
+    "separator": typing.NotRequired[str | None],
+    "showlabs": bool,
+    "show_infiles": bool,
+    "show_keepers": bool,
+    "report_outliers": typing.NotRequired[list[str] | None],
+    "report_outliers_fill_style": typing.NotRequired[str | None],
+    "show_missing": bool,
+    "verbosity": typing.NotRequired[int | None],
+})
+GenSsReviewTablePyParametersTagged = typing.TypedDict('GenSsReviewTablePyParametersTagged', {
+    "@type": typing.Literal["afni/gen_ss_review_table.py"],
     "infiles": list[InputPathType],
     "write_table": typing.NotRequired[InputPathType | None],
     "write_outliers": typing.NotRequired[InputPathType | None],
@@ -30,43 +47,11 @@ GenSsReviewTablePyParameters = typing.TypedDict('GenSsReviewTablePyParameters',
     "show_missing": bool,
     "verbosity": typing.NotRequired[int | None],
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "gen_ss_review_table.py": gen_ss_review_table_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 {
-        "gen_ss_review_table.py": gen_ss_review_table_py_outputs,
-    }.get(t)
 
 
 class GenSsReviewTablePyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `gen_ss_review_table_py(...)`.
+    Output object returned when calling `GenSsReviewTablePyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -91,7 +76,7 @@ def gen_ss_review_table_py_params(
     report_outliers_fill_style: str | None = None,
     show_missing: bool = False,
     verbosity: int | None = None,
-) -> GenSsReviewTablePyParameters:
+) -> GenSsReviewTablePyParametersTagged:
     """
     Build parameters.
     
@@ -114,7 +99,7 @@ def gen_ss_review_table_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "gen_ss_review_table.py",
+        "@type": "afni/gen_ss_review_table.py",
         "infiles": infiles,
         "overwrite": overwrite,
         "empty_is_outlier": empty_is_outlier,
@@ -155,53 +140,53 @@ def gen_ss_review_table_py_cargs(
     """
     cargs = []
     cargs.append("gen_ss_review_table.py")
-    cargs.extend([execution.input_file(f) for f in params.get("infiles")])
-    if params.get("write_table") is not None:
+    cargs.extend([execution.input_file(f) for f in params.get("infiles", None)])
+    if params.get("write_table", None) is not None:
         cargs.extend([
             "-write_table",
-            execution.input_file(params.get("write_table"))
+            execution.input_file(params.get("write_table", None))
         ])
-    if params.get("write_outliers") is not None:
+    if params.get("write_outliers", None) is not None:
         cargs.extend([
             "-write_outliers",
-            execution.input_file(params.get("write_outliers"))
+            execution.input_file(params.get("write_outliers", None))
         ])
-    if params.get("overwrite"):
+    if params.get("overwrite", False):
         cargs.append("-overwrite")
-    if params.get("empty_is_outlier"):
+    if params.get("empty_is_outlier", False):
         cargs.append("-empty_is_outlier")
-    if params.get("outlier_sep") is not None:
+    if params.get("outlier_sep", None) is not None:
         cargs.extend([
             "-outlier_sep",
-            params.get("outlier_sep")
+            params.get("outlier_sep", None)
         ])
-    if params.get("separator") is not None:
+    if params.get("separator", None) is not None:
         cargs.extend([
             "-separator",
-            params.get("separator")
+            params.get("separator", None)
         ])
-    if params.get("showlabs"):
+    if params.get("showlabs", False):
         cargs.append("-showlabs")
-    if params.get("show_infiles"):
+    if params.get("show_infiles", False):
         cargs.append("-show_infiles")
-    if params.get("show_keepers"):
+    if params.get("show_keepers", False):
         cargs.append("-show_keepers")
-    if params.get("report_outliers") is not None:
+    if params.get("report_outliers", None) is not None:
         cargs.extend([
             "-report_outliers",
-            *params.get("report_outliers")
+            *params.get("report_outliers", None)
         ])
-    if params.get("report_outliers_fill_style") is not None:
+    if params.get("report_outliers_fill_style", None) is not None:
         cargs.extend([
             "-report_outliers_fill_style",
-            params.get("report_outliers_fill_style")
+            params.get("report_outliers_fill_style", None)
         ])
-    if params.get("show_missing"):
+    if params.get("show_missing", False):
         cargs.append("-show_missing")
-    if params.get("verbosity") is not None:
+    if params.get("verbosity", None) is not None:
         cargs.extend([
             "-verb",
-            str(params.get("verbosity"))
+            str(params.get("verbosity", None))
         ])
     return cargs
 
@@ -221,17 +206,19 @@ def gen_ss_review_table_py_outputs(
     """
     ret = GenSsReviewTablePyOutputs(
         root=execution.output_file("."),
-        output_table=execution.output_file(pathlib.Path(params.get("write_table")).name) if (params.get("write_table") is not None) else None,
-        output_outliers=execution.output_file(pathlib.Path(params.get("write_outliers")).name) if (params.get("write_outliers") is not None) else None,
+        output_table=execution.output_file(pathlib.Path(params.get("write_table", None)).name) if (params.get("write_table") is not None) else None,
+        output_outliers=execution.output_file(pathlib.Path(params.get("write_outliers", None)).name) if (params.get("write_outliers") is not None) else None,
     )
     return ret
 
 
 def gen_ss_review_table_py_execute(
     params: GenSsReviewTablePyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> GenSsReviewTablePyOutputs:
     """
+    gen_ss_review_table.py
+    
     Generate a table from ss_review_basic output files.
     
     Author: AFNI Developers
@@ -240,10 +227,12 @@ def gen_ss_review_table_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `GenSsReviewTablePyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(GEN_SS_REVIEW_TABLE_PY_METADATA)
     params = execution.params(params)
     cargs = gen_ss_review_table_py_cargs(params, execution)
     ret = gen_ss_review_table_py_outputs(params, execution)
@@ -269,6 +258,8 @@ def gen_ss_review_table_py(
     runner: Runner | None = None,
 ) -> GenSsReviewTablePyOutputs:
     """
+    gen_ss_review_table.py
+    
     Generate a table from ss_review_basic output files.
     
     Author: AFNI Developers
@@ -294,8 +285,6 @@ def gen_ss_review_table_py(
     Returns:
         NamedTuple of outputs (described in `GenSsReviewTablePyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(GEN_SS_REVIEW_TABLE_PY_METADATA)
     params = gen_ss_review_table_py_params(
         infiles=infiles,
         write_table=write_table,
@@ -312,13 +301,13 @@ def gen_ss_review_table_py(
         show_missing=show_missing,
         verbosity=verbosity,
     )
-    return gen_ss_review_table_py_execute(params, execution)
+    return gen_ss_review_table_py_execute(params, runner)
 
 
 __all__ = [
     "GEN_SS_REVIEW_TABLE_PY_METADATA",
     "GenSsReviewTablePyOutputs",
-    "GenSsReviewTablePyParameters",
     "gen_ss_review_table_py",
+    "gen_ss_review_table_py_execute",
     "gen_ss_review_table_py_params",
 ]