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

niwrap_afni/afni/{fat_roi_row.py → fat_roi_row_py.py}

@@ -5,16 +5,23 @@ import typing
 import pathlib
 from styxdefs import *
 
-FAT_ROI_ROW_METADATA = Metadata(
-    id="739c802e1b22c2e198a3d50de14679a6f269f722.boutiques",
-    name="fat_roi_row",
+FAT_ROI_ROW_PY_METADATA = Metadata(
+    id="962a18899af088da3ff1ac68aa693ceff0dc586c.boutiques",
+    name="fat_roi_row.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
 )
 
 
-FatRoiRowParameters = typing.TypedDict('FatRoiRowParameters', {
-    "__STYXTYPE__": typing.Literal["fat_roi_row"],
+FatRoiRowPyParameters = typing.TypedDict('FatRoiRowPyParameters', {
+    "@type": typing.NotRequired[typing.Literal["afni/fat_roi_row.py"]],
+    "roi": str,
+    "matrix_files": typing.NotRequired[str | None],
+    "list_file": typing.NotRequired[InputPathType | None],
+    "extern_labs_no": bool,
+})
+FatRoiRowPyParametersTagged = typing.TypedDict('FatRoiRowPyParametersTagged', {
+    "@type": typing.Literal["afni/fat_roi_row.py"],
     "roi": str,
     "matrix_files": typing.NotRequired[str | None],
     "list_file": typing.NotRequired[InputPathType | None],
@@ -22,41 +29,9 @@ FatRoiRowParameters = typing.TypedDict('FatRoiRowParameters', {
 })
 
 
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fat_roi_row": fat_roi_row_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_roi_row": fat_roi_row_outputs,
-    }.get(t)
-
-
-class FatRoiRowOutputs(typing.NamedTuple):
+class FatRoiRowPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fat_roi_row(...)`.
+    Output object returned when calling `FatRoiRowPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -64,12 +39,12 @@ class FatRoiRowOutputs(typing.NamedTuple):
     """Selected ROI row output file in .row format."""
 
 
-def fat_roi_row_params(
+def fat_roi_row_py_params(
     roi: str,
     matrix_files: str | None = None,
     list_file: InputPathType | None = None,
     extern_labs_no: bool = False,
-) -> FatRoiRowParameters:
+) -> FatRoiRowPyParametersTagged:
     """
     Build parameters.
     
@@ -89,7 +64,7 @@ def fat_roi_row_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fat_roi_row",
+        "@type": "afni/fat_roi_row.py",
         "roi": roi,
         "extern_labs_no": extern_labs_no,
     }
@@ -100,8 +75,8 @@ def fat_roi_row_params(
     return params
 
 
-def fat_roi_row_cargs(
-    params: FatRoiRowParameters,
+def fat_roi_row_py_cargs(
+    params: FatRoiRowPyParameters,
     execution: Execution,
 ) -> list[str]:
     """
@@ -117,27 +92,27 @@ def fat_roi_row_cargs(
     cargs.append("fat_roi_row.py")
     cargs.extend([
         "-r",
-        params.get("roi")
+        params.get("roi", 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_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))
         ])
-    if params.get("extern_labs_no"):
+    if params.get("extern_labs_no", False):
         cargs.append("-E")
     return cargs
 
 
-def fat_roi_row_outputs(
-    params: FatRoiRowParameters,
+def fat_roi_row_py_outputs(
+    params: FatRoiRowPyParameters,
     execution: Execution,
-) -> FatRoiRowOutputs:
+) -> FatRoiRowPyOutputs:
     """
     Build outputs object containing output file paths and possibly stdout/stderr.
     
@@ -147,20 +122,22 @@ def fat_roi_row_outputs(
     Returns:
         Outputs object.
     """
-    ret = FatRoiRowOutputs(
+    ret = FatRoiRowPyOutputs(
         root=execution.output_file("."),
-        output_file=execution.output_file(params.get("roi") + "_selected.row"),
+        output_file=execution.output_file(params.get("roi", None) + "_selected.row"),
     )
     return ret
 
 
-def fat_roi_row_execute(
-    params: FatRoiRowParameters,
-    execution: Execution,
-) -> FatRoiRowOutputs:
+def fat_roi_row_py_execute(
+    params: FatRoiRowPyParameters,
+    runner: Runner | None = None,
+) -> FatRoiRowPyOutputs:
     """
-    Select a single ROI's row out of a connectivity matrix file (*.grid or *.netcc)
-    for viewing and/or further analysis.
+    fat_roi_row.py
+    
+    Select a single ROI's row out of a connectivity matrix file (*.grid or
+    *.netcc) for viewing and/or further analysis.
     
     Author: AFNI Developers
     
@@ -168,27 +145,31 @@ def fat_roi_row_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FatRoiRowOutputs`).
+        NamedTuple of outputs (described in `FatRoiRowPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FAT_ROI_ROW_PY_METADATA)
     params = execution.params(params)
-    cargs = fat_roi_row_cargs(params, execution)
-    ret = fat_roi_row_outputs(params, execution)
+    cargs = fat_roi_row_py_cargs(params, execution)
+    ret = fat_roi_row_py_outputs(params, execution)
     execution.run(cargs)
     return ret
 
 
-def fat_roi_row(
+def fat_roi_row_py(
     roi: str,
     matrix_files: str | None = None,
     list_file: InputPathType | None = None,
     extern_labs_no: bool = False,
     runner: Runner | None = None,
-) -> FatRoiRowOutputs:
+) -> FatRoiRowPyOutputs:
     """
-    Select a single ROI's row out of a connectivity matrix file (*.grid or *.netcc)
-    for viewing and/or further analysis.
+    fat_roi_row.py
+    
+    Select a single ROI's row out of a connectivity matrix file (*.grid or
+    *.netcc) for viewing and/or further analysis.
     
     Author: AFNI Developers
     
@@ -208,23 +189,21 @@ def fat_roi_row(
             labels in the *.grid/*.netcc files.
         runner: Command runner.
     Returns:
-        NamedTuple of outputs (described in `FatRoiRowOutputs`).
+        NamedTuple of outputs (described in `FatRoiRowPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FAT_ROI_ROW_METADATA)
-    params = fat_roi_row_params(
+    params = fat_roi_row_py_params(
         roi=roi,
         matrix_files=matrix_files,
         list_file=list_file,
         extern_labs_no=extern_labs_no,
     )
-    return fat_roi_row_execute(params, execution)
+    return fat_roi_row_py_execute(params, runner)
 
 
 __all__ = [
-    "FAT_ROI_ROW_METADATA",
-    "FatRoiRowOutputs",
-    "FatRoiRowParameters",
-    "fat_roi_row",
-    "fat_roi_row_params",
+    "FAT_ROI_ROW_PY_METADATA",
+    "FatRoiRowPyOutputs",
+    "fat_roi_row_py",
+    "fat_roi_row_py_execute",
+    "fat_roi_row_py_params",
 ]

niwrap_afni/afni/fatcat_matplot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FATCAT_MATPLOT_METADATA = Metadata(
-    id="804cde808f328b2d1b8ec82db978eeac78490b19.boutiques",
+    id="ea9e34c417e4d60f8cb488d20b44ee9b288b0053.boutiques",
     name="FATCAT_matplot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,46 +14,20 @@ FATCAT_MATPLOT_METADATA = Metadata(
 
 
 FatcatMatplotParameters = typing.TypedDict('FatcatMatplotParameters', {
-    "__STYXTYPE__": typing.Literal["FATCAT_matplot"],
+    "@type": typing.NotRequired[typing.Literal["afni/FATCAT_matplot"]],
+    "directory": str,
+    "shiny_folder": bool,
+})
+FatcatMatplotParametersTagged = typing.TypedDict('FatcatMatplotParametersTagged', {
+    "@type": typing.Literal["afni/FATCAT_matplot"],
     "directory": str,
     "shiny_folder": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "FATCAT_matplot": fatcat_matplot_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 {
-    }.get(t)
 
 
 class FatcatMatplotOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fatcat_matplot(...)`.
+    Output object returned when calling `FatcatMatplotParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -62,7 +36,7 @@ class FatcatMatplotOutputs(typing.NamedTuple):
 def fatcat_matplot_params(
     directory: str,
     shiny_folder: bool = False,
-) -> FatcatMatplotParameters:
+) -> FatcatMatplotParametersTagged:
     """
     Build parameters.
     
@@ -73,7 +47,7 @@ def fatcat_matplot_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "FATCAT_matplot",
+        "@type": "afni/FATCAT_matplot",
         "directory": directory,
         "shiny_folder": shiny_folder,
     }
@@ -95,8 +69,8 @@ def fatcat_matplot_cargs(
     """
     cargs = []
     cargs.append("FATCAT_matplot")
-    cargs.append(params.get("directory"))
-    if params.get("shiny_folder"):
+    cargs.append(params.get("directory", None))
+    if params.get("shiny_folder", False):
         cargs.append("-ShinyFolder")
     return cargs
 
@@ -122,9 +96,11 @@ def fatcat_matplot_outputs(
 
 def fatcat_matplot_execute(
     params: FatcatMatplotParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FatcatMatplotOutputs:
     """
+    FATCAT_matplot
+    
     Launch a shiny app to visualize .netcc and/or .grid files.
     
     Author: AFNI Developers
@@ -133,10 +109,12 @@ def fatcat_matplot_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FatcatMatplotOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FATCAT_MATPLOT_METADATA)
     params = execution.params(params)
     cargs = fatcat_matplot_cargs(params, execution)
     ret = fatcat_matplot_outputs(params, execution)
@@ -150,6 +128,8 @@ def fatcat_matplot(
     runner: Runner | None = None,
 ) -> FatcatMatplotOutputs:
     """
+    FATCAT_matplot
+    
     Launch a shiny app to visualize .netcc and/or .grid files.
     
     Author: AFNI Developers
@@ -163,19 +143,17 @@ def fatcat_matplot(
     Returns:
         NamedTuple of outputs (described in `FatcatMatplotOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FATCAT_MATPLOT_METADATA)
     params = fatcat_matplot_params(
         directory=directory,
         shiny_folder=shiny_folder,
     )
-    return fatcat_matplot_execute(params, execution)
+    return fatcat_matplot_execute(params, runner)
 
 
 __all__ = [
     "FATCAT_MATPLOT_METADATA",
     "FatcatMatplotOutputs",
-    "FatcatMatplotParameters",
     "fatcat_matplot",
+    "fatcat_matplot_execute",
     "fatcat_matplot_params",
 ]

niwrap_afni/afni/fdrval.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 FDRVAL_METADATA = Metadata(
-    id="a0de8ec4e0e3a36fbc893d3b8b4292e32543fc80.boutiques",
+    id="6580e1aa03a1bd1fe5cac6a65e7103bb65bb0dd7.boutiques",
     name="fdrval",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ FDRVAL_METADATA = Metadata(
 
 
 FdrvalParameters = typing.TypedDict('FdrvalParameters', {
-    "__STYXTYPE__": typing.Literal["fdrval"],
+    "@type": typing.NotRequired[typing.Literal["afni/fdrval"]],
+    "dset": InputPathType,
+    "sub": float,
+    "val_list": list[float],
+    "pval": bool,
+    "ponly": bool,
+    "qonly": bool,
+    "qinput": bool,
+    "inverse": bool,
+})
+FdrvalParametersTagged = typing.TypedDict('FdrvalParametersTagged', {
+    "@type": typing.Literal["afni/fdrval"],
     "dset": InputPathType,
     "sub": float,
     "val_list": list[float],
@@ -24,43 +35,11 @@ FdrvalParameters = typing.TypedDict('FdrvalParameters', {
     "qinput": bool,
     "inverse": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "fdrval": fdrval_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 {
-        "fdrval": fdrval_outputs,
-    }.get(t)
 
 
 class FdrvalOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `fdrval(...)`.
+    Output object returned when calling `FdrvalParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def fdrval_params(
     qonly: bool = False,
     qinput: bool = False,
     inverse: bool = False,
-) -> FdrvalParameters:
+) -> FdrvalParametersTagged:
     """
     Build parameters.
     
@@ -96,7 +75,7 @@ def fdrval_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "fdrval",
+        "@type": "afni/fdrval",
         "dset": dset,
         "sub": sub,
         "val_list": val_list,
@@ -124,18 +103,18 @@ def fdrval_cargs(
     """
     cargs = []
     cargs.append("fdrval")
-    cargs.append(execution.input_file(params.get("dset")))
-    cargs.append(str(params.get("sub")))
-    cargs.extend(map(str, params.get("val_list")))
-    if params.get("pval"):
+    cargs.append(execution.input_file(params.get("dset", None)))
+    cargs.append(str(params.get("sub", None)))
+    cargs.extend(map(str, params.get("val_list", None)))
+    if params.get("pval", False):
         cargs.append("-pval")
-    if params.get("ponly"):
+    if params.get("ponly", False):
         cargs.append("-ponly")
-    if params.get("qonly"):
+    if params.get("qonly", False):
         cargs.append("-qonly")
-    if params.get("qinput"):
+    if params.get("qinput", False):
         cargs.append("-qinput")
-    if params.get("inverse"):
+    if params.get("inverse", False):
         cargs.append("-inverse")
     return cargs
 
@@ -162,9 +141,11 @@ def fdrval_outputs(
 
 def fdrval_execute(
     params: FdrvalParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> FdrvalOutputs:
     """
+    fdrval
+    
     Computes q-values from FDR curve data stored in dataset headers.
     
     Author: AFNI Developers
@@ -173,10 +154,12 @@ def fdrval_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `FdrvalOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(FDRVAL_METADATA)
     params = execution.params(params)
     cargs = fdrval_cargs(params, execution)
     ret = fdrval_outputs(params, execution)
@@ -196,6 +179,8 @@ def fdrval(
     runner: Runner | None = None,
 ) -> FdrvalOutputs:
     """
+    fdrval
+    
     Computes q-values from FDR curve data stored in dataset headers.
     
     Author: AFNI Developers
@@ -217,8 +202,6 @@ def fdrval(
     Returns:
         NamedTuple of outputs (described in `FdrvalOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(FDRVAL_METADATA)
     params = fdrval_params(
         dset=dset,
         sub=sub,
@@ -229,13 +212,13 @@ def fdrval(
         qinput=qinput,
         inverse=inverse,
     )
-    return fdrval_execute(params, execution)
+    return fdrval_execute(params, runner)
 
 
 __all__ = [
     "FDRVAL_METADATA",
     "FdrvalOutputs",
-    "FdrvalParameters",
     "fdrval",
+    "fdrval_execute",
     "fdrval_params",
 ]