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

niwrap_afni/afni/{fat_mat_tableize.py → fat_mat_tableize_py.py}

@@ -5,16 +5,29 @@ import typing
 import pathlib
 from styxdefs import *
 
-FAT_MAT_TABLEIZE_METADATA = Metadata(
-    id="54bddb6e07bcdce4629069126b94b563d0162fab.boutiques",
-    name="fat_mat_tableize",
+FAT_MAT_TABLEIZE_PY_METADATA = Metadata(
+    id="df8af0e7bebf2200861007123861520d4b50efb3.boutiques",
+    name="fat_mat_tableize.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-FatMatTableizeParameters = typing.TypedDict('FatMatTableizeParameters', {
-    "__STYXTYPE__": typing.Literal["fat_mat_tableize"],
+FatMatTableizePyParameters = typing.TypedDict('FatMatTableizePyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/fat_mat_tableize.py"]],
+    "input_matrices": list[str],
+    "input_csv": typing.NotRequired[InputPathType | None],
+    "input_list": typing.NotRequired[InputPathType | None],
+    "output_prefix": str,
+    "parameters": typing.NotRequired[list[str] | None],
+    "version": bool,
+    "date": bool,
+    "help": bool,
+    "help_short": bool,
+    "help_view": bool,
+})
+FatMatTableizePyParametersTagged = typing.TypedDict('FatMatTableizePyParametersTagged', {
+    "@type": typing.Literal["afni/fat_mat_tableize.py"],
     "input_matrices": list[str],
     "input_csv": typing.NotRequired[InputPathType | None],
     "input_list": typing.NotRequired[InputPathType | None],
@@ -28,41 +41,9 @@ FatMatTableizeParameters = typing.TypedDict('FatMatTableizeParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_mat_tableize": fat_mat_tableize_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_mat_tableize": fat_mat_tableize_outputs,
-    }.get(t)
-
-
-class FatMatTableizeOutputs(typing.NamedTuple):
+class FatMatTableizePyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_mat_tableize(...)`.
+    Output object returned when calling `FatMatTableizePyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -73,7 +54,7 @@ class FatMatTableizeOutputs(typing.NamedTuple):
     file."""
 
 
-def fat_mat_tableize_params(
+def fat_mat_tableize_py_params(
     input_matrices: list[str],
     output_prefix: str,
     input_csv: InputPathType | None = None,
@@ -84,7 +65,7 @@ def fat_mat_tableize_params(
     help_: bool = False,
     help_short: bool = False,
     help_view: bool = False,
-) -> FatMatTableizeParameters:
+) -> FatMatTableizePyParametersTagged:
     """
     Build parameters.
     
@@ -108,7 +89,7 @@ def fat_mat_tableize_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_mat_tableize",
+        "@type": "afni/fat_mat_tableize.py",
         "input_matrices": input_matrices,
         "output_prefix": output_prefix,
         "version": version,
@@ -126,8 +107,8 @@ def fat_mat_tableize_params(
     return params
 
 
-def fat_mat_tableize_cargs(
-    params: FatMatTableizeParameters,
+def fat_mat_tableize_py_cargs(
+    params: FatMatTableizePyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -143,44 +124,44 @@ def fat_mat_tableize_cargs(
     cargs.append("fat_mat_tableize.py")
     cargs.extend([
         "-in_mat",
-        *params.get("input_matrices")
+        *params.get("input_matrices", None)
     ])
-    if params.get("input_csv") is not None:
+    if params.get("input_csv", None) is not None:
         cargs.extend([
             "-in_csv",
-            execution.input_file(params.get("input_csv"))
+            execution.input_file(params.get("input_csv", None))
         ])
-    if params.get("input_list") is not None:
+    if params.get("input_list", None) is not None:
         cargs.extend([
             "-in_listfile",
-            execution.input_file(params.get("input_list"))
+            execution.input_file(params.get("input_list", None))
         ])
     cargs.extend([
         "-prefix",
-        params.get("output_prefix")
+        params.get("output_prefix", None)
     ])
-    if params.get("parameters") is not None:
+    if params.get("parameters", None) is not None:
         cargs.extend([
             "-pars",
-            *params.get("parameters")
+            *params.get("parameters", None)
         ])
-    if params.get("version"):
+    if params.get("version", False):
         cargs.append("-ver")
-    if params.get("date"):
+    if params.get("date", False):
         cargs.append("-date")
-    if params.get("help"):
+    if params.get("help", False):
         cargs.append("-help")
-    if params.get("help_short"):
+    if params.get("help_short", False):
         cargs.append("-h")
-    if params.get("help_view"):
+    if params.get("help_view", False):
         cargs.append("-hview")
     return cargs
 
 
-def fat_mat_tableize_outputs(
-    params: FatMatTableizeParameters,
+def fat_mat_tableize_py_outputs(
+    params: FatMatTableizePyParameters,
     execution: Execution,
-) -> FatMatTableizeOutputs:
+) -> FatMatTableizePyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -190,22 +171,24 @@ def fat_mat_tableize_outputs(
     Returns:
         Outputs object.
     """
-    ret = FatMatTableizeOutputs(
+    ret = FatMatTableizePyOutputs(
         root=execution.output_file("."),
-        output_table=execution.output_file(params.get("output_prefix") + "_tbl.txt"),
-        output_log=execution.output_file(params.get("output_prefix") + "_prep.log"),
+        output_table=execution.output_file(params.get("output_prefix", None) + "_tbl.txt"),
+        output_log=execution.output_file(params.get("output_prefix", None) + "_prep.log"),
     )
     return ret
 
 
-def fat_mat_tableize_execute(
-    params: FatMatTableizeParameters,
-    execution: Execution,
-) -> FatMatTableizeOutputs:
+def fat_mat_tableize_py_execute(
+    params: FatMatTableizePyParameters,
+    runner: Runner | None = None,
+) -> FatMatTableizePyOutputs:
     """
+    fat_mat_tableize.py
+    
     Make tables for AFNI group analysis programs from 3dNetCorr (*.netcc) and
-    3dTrackID (*.grid) outputs, with optional additional subject information from
-    CSV files.
+    3dTrackID (*.grid) outputs, with optional additional subject information
+    from CSV files.
     
     Author: AFNI Developers
     
@@ -213,18 +196,20 @@ def fat_mat_tableize_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FatMatTableizeOutputs`).
+        NamedTuple of outputs (described in `FatMatTableizePyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MAT_TABLEIZE_PY_METADATA)
     params = execution.params(params)
-    cargs = fat_mat_tableize_cargs(params, execution)
-    ret = fat_mat_tableize_outputs(params, execution)
+    cargs = fat_mat_tableize_py_cargs(params, execution)
+    ret = fat_mat_tableize_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def fat_mat_tableize(
+def fat_mat_tableize_py(
     input_matrices: list[str],
     output_prefix: str,
     input_csv: InputPathType | None = None,
@@ -236,11 +221,13 @@ def fat_mat_tableize(
     help_short: bool = False,
     help_view: bool = False,
     runner: Runner | None = None,
-) -> FatMatTableizeOutputs:
+) -> FatMatTableizePyOutputs:
     """
+    fat_mat_tableize.py
+    
     Make tables for AFNI group analysis programs from 3dNetCorr (*.netcc) and
-    3dTrackID (*.grid) outputs, with optional additional subject information from
-    CSV files.
+    3dTrackID (*.grid) outputs, with optional additional subject information
+    from CSV files.
     
     Author: AFNI Developers
     
@@ -264,11 +251,9 @@ def fat_mat_tableize(
         help_view: Display help in a separate text editor.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FatMatTableizeOutputs`).
+        NamedTuple of outputs (described in `FatMatTableizePyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_MAT_TABLEIZE_METADATA)
-    params = fat_mat_tableize_params(
+    params = fat_mat_tableize_py_params(
         input_matrices=input_matrices,
         input_csv=input_csv,
         input_list=input_list,
@@ -280,13 +265,13 @@ def fat_mat_tableize(
         help_short=help_short,
         help_view=help_view,
     )
-    return fat_mat_tableize_execute(params, execution)
+    return fat_mat_tableize_py_execute(params, runner)
 
 
 __all__ = [
-    "FAT_MAT_TABLEIZE_METADATA",
-    "FatMatTableizeOutputs",
-    "FatMatTableizeParameters",
-    "fat_mat_tableize",
-    "fat_mat_tableize_params",
+    "FAT_MAT_TABLEIZE_PY_METADATA",
+    "FatMatTableizePyOutputs",
+    "fat_mat_tableize_py",
+    "fat_mat_tableize_py_execute",
+    "fat_mat_tableize_py_params",
 ]

niwrap_afni/afni/fat_mvm_gridconv_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FAT_MVM_GRIDCONV_PY_METADATA = Metadata(
-    id="60500ab4b4a40d9048e813ee764c1f1904d6bbcf.boutiques",
+    id="b082285800362f5644c0f2275c7fb8980bd9cc47.boutiques",
     name="fat_mvm_gridconv.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,59 +14,29 @@ FAT_MVM_GRIDCONV_PY_METADATA = Metadata(
 
 
 FatMvmGridconvPyParameters = typing.TypedDict('FatMvmGridconvPyParameters', {
-    "__STYXTYPE__": typing.Literal["fat_mvm_gridconv.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/fat_mvm_gridconv.py"]],
+    "matrix_files": typing.NotRequired[str | None],
+    "list_file": typing.NotRequired[InputPathType | None],
+})
+FatMvmGridconvPyParametersTagged = typing.TypedDict('FatMvmGridconvPyParametersTagged', {
+    "@type": typing.Literal["afni/fat_mvm_gridconv.py"],
     "matrix_files": typing.NotRequired[str | None],
     "list_file": typing.NotRequired[InputPathType | None],
 })
-
-
-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_gridconv.py": fat_mvm_gridconv_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_gridconv.py": fat_mvm_gridconv_py_outputs,
-    }.get(t)
 
 
 class FatMvmGridconvPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_mvm_gridconv_py(...)`.
+    Output object returned when calling `FatMvmGridconvPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    converted_grid_files: OutputPathType
-    """Output converted grid files, with '_MOD.grid' postfix or custom output
-    name provided in the list file."""
 
 
 def fat_mvm_gridconv_py_params(
     matrix_files: str | None = None,
     list_file: InputPathType | None = None,
-) -> FatMvmGridconvPyParameters:
+) -> FatMvmGridconvPyParametersTagged:
     """
     Build parameters.
     
@@ -83,7 +53,7 @@ def fat_mvm_gridconv_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_mvm_gridconv.py",
+        "@type": "afni/fat_mvm_gridconv.py",
     }
     if matrix_files is not None:
         params["matrix_files"] = matrix_files
@@ -107,15 +77,15 @@ def fat_mvm_gridconv_py_cargs(
     """
     cargs = []
     cargs.append("fat_mvm_gridconv.py")
-    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_file") is not None:
+    if params.get("list_file", None) is not None:
         cargs.extend([
             "-l",
-            execution.input_file(params.get("list_file"))
+            execution.input_file(params.get("list_file", None))
         ])
     return cargs
 
@@ -135,16 +105,17 @@ def fat_mvm_gridconv_py_outputs(
     """
     ret = FatMvmGridconvPyOutputs(
         root=execution.output_file("."),
-        converted_grid_files=execution.output_file("*_MOD.grid"),
     )
     return ret
 
 
 def fat_mvm_gridconv_py_execute(
     params: FatMvmGridconvPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatMvmGridconvPyOutputs:
     """
+    fat_mvm_gridconv.py
+    
     Preprocess 'old school' *.grid files for statistical modeling using 3dMVM.
     
     Author: AFNI Developers
@@ -153,10 +124,12 @@ def fat_mvm_gridconv_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatMvmGridconvPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_MVM_GRIDCONV_PY_METADATA)
     params = execution.params(params)
     cargs = fat_mvm_gridconv_py_cargs(params, execution)
     ret = fat_mvm_gridconv_py_outputs(params, execution)
@@ -170,6 +143,8 @@ def fat_mvm_gridconv_py(
     runner: Runner | None = None,
 ) -> FatMvmGridconvPyOutputs:
     """
+    fat_mvm_gridconv.py
+    
     Preprocess 'old school' *.grid files for statistical modeling using 3dMVM.
     
     Author: AFNI Developers
@@ -189,19 +164,17 @@ def fat_mvm_gridconv_py(
     Returns:
         NamedTuple of outputs (described in `FatMvmGridconvPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_MVM_GRIDCONV_PY_METADATA)
     params = fat_mvm_gridconv_py_params(
         matrix_files=matrix_files,
         list_file=list_file,
     )
-    return fat_mvm_gridconv_py_execute(params, execution)
+    return fat_mvm_gridconv_py_execute(params, runner)
 
 
 __all__ = [
     "FAT_MVM_GRIDCONV_PY_METADATA",
     "FatMvmGridconvPyOutputs",
-    "FatMvmGridconvPyParameters",
     "fat_mvm_gridconv_py",
+    "fat_mvm_gridconv_py_execute",
     "fat_mvm_gridconv_py_params",
 ]