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

niwrap_afni/afni/make_color_map.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_COLOR_MAP_METADATA = Metadata(
-    id="74bc2813713e1afd72d384800e82892e19f26459.boutiques",
+    id="b166ea43fbf7c4fe260b5ab62d4e4a681005db1c.boutiques",
     name="MakeColorMap",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,30 @@ MAKE_COLOR_MAP_METADATA = Metadata(
 
 
 MakeColorMapParameters = typing.TypedDict('MakeColorMapParameters', {
-    "__STYXTYPE__": typing.Literal["MakeColorMap"],
+    "@type": typing.NotRequired[typing.Literal["afni/MakeColorMap"]],
+    "fiducials_ncol": typing.NotRequired[InputPathType | None],
+    "fiducials": typing.NotRequired[InputPathType | None],
+    "num_colors": typing.NotRequired[float | None],
+    "std_mapname": typing.NotRequired[str | None],
+    "palette_file": typing.NotRequired[InputPathType | None],
+    "cmap_name": typing.NotRequired[str | None],
+    "fscolut_labels": typing.NotRequired[list[float] | None],
+    "fscolut_file": typing.NotRequired[InputPathType | None],
+    "afni_hex": typing.NotRequired[str | None],
+    "afni_hex_complete": typing.NotRequired[str | None],
+    "suma_colormap": typing.NotRequired[str | None],
+    "user_colut_file": typing.NotRequired[InputPathType | None],
+    "sdset": typing.NotRequired[InputPathType | None],
+    "sdset_prefix": typing.NotRequired[str | None],
+    "flipupdown": bool,
+    "skip_last": bool,
+    "show_fscolut": bool,
+    "help_flag": bool,
+    "help_full_flag": bool,
+    "flip_map_updside_down": bool,
+})
+MakeColorMapParametersTagged = typing.TypedDict('MakeColorMapParametersTagged', {
+    "@type": typing.Literal["afni/MakeColorMap"],
     "fiducials_ncol": typing.NotRequired[InputPathType | None],
     "fiducials": typing.NotRequired[InputPathType | None],
     "num_colors": typing.NotRequired[float | None],
@@ -36,43 +59,11 @@ MakeColorMapParameters = typing.TypedDict('MakeColorMapParameters', {
     "help_full_flag": bool,
     "flip_map_updside_down": bool,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "MakeColorMap": make_color_map_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 {
-        "MakeColorMap": make_color_map_outputs,
-    }.get(t)
 
 
 class MakeColorMapOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_color_map(...)`.
+    Output object returned when calling `MakeColorMapParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -103,7 +94,7 @@ def make_color_map_params(
     help_flag: bool = False,
     help_full_flag: bool = False,
     flip_map_updside_down: bool = False,
-) -> MakeColorMapParameters:
+) -> MakeColorMapParametersTagged:
     """
     Build parameters.
     
@@ -136,7 +127,7 @@ def make_color_map_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "MakeColorMap",
+        "@type": "afni/MakeColorMap",
         "flipupdown": flipupdown,
         "skip_last": skip_last,
         "show_fscolut": show_fscolut,
@@ -190,87 +181,87 @@ def make_color_map_cargs(
     """
     cargs = []
     cargs.append("MakeColorMap")
-    if params.get("fiducials_ncol") is not None:
+    if params.get("fiducials_ncol", None) is not None:
         cargs.extend([
             "-fn",
-            execution.input_file(params.get("fiducials_ncol"))
+            execution.input_file(params.get("fiducials_ncol", None))
         ])
-    if params.get("fiducials") is not None:
+    if params.get("fiducials", None) is not None:
         cargs.extend([
             "-f",
-            execution.input_file(params.get("fiducials"))
+            execution.input_file(params.get("fiducials", None))
         ])
-    if params.get("num_colors") is not None:
+    if params.get("num_colors", None) is not None:
         cargs.extend([
             "-nc",
-            str(params.get("num_colors"))
+            str(params.get("num_colors", None))
         ])
-    if params.get("std_mapname") is not None:
+    if params.get("std_mapname", None) is not None:
         cargs.extend([
             "-std",
-            params.get("std_mapname")
+            params.get("std_mapname", None)
         ])
-    if params.get("palette_file") is not None:
+    if params.get("palette_file", None) is not None:
         cargs.extend([
             "-cmapdb",
-            execution.input_file(params.get("palette_file"))
+            execution.input_file(params.get("palette_file", None))
         ])
-    if params.get("cmap_name") is not None:
+    if params.get("cmap_name", None) is not None:
         cargs.extend([
             "-cmap",
-            params.get("cmap_name")
+            params.get("cmap_name", None)
         ])
-    if params.get("fscolut_labels") is not None:
+    if params.get("fscolut_labels", None) is not None:
         cargs.extend([
             "-fscolut",
-            *map(str, params.get("fscolut_labels"))
+            *map(str, params.get("fscolut_labels", None))
         ])
-    if params.get("fscolut_file") is not None:
+    if params.get("fscolut_file", None) is not None:
         cargs.extend([
             "-fscolutfile",
-            execution.input_file(params.get("fscolut_file"))
+            execution.input_file(params.get("fscolut_file", None))
         ])
-    if params.get("afni_hex") is not None:
+    if params.get("afni_hex", None) is not None:
         cargs.extend([
             "-ah",
-            params.get("afni_hex")
+            params.get("afni_hex", None)
         ])
-    if params.get("afni_hex_complete") is not None:
+    if params.get("afni_hex_complete", None) is not None:
         cargs.extend([
             "-ahc",
-            params.get("afni_hex_complete")
+            params.get("afni_hex_complete", None)
         ])
-    if params.get("suma_colormap") is not None:
+    if params.get("suma_colormap", None) is not None:
         cargs.extend([
             "-suma_cmap",
-            params.get("suma_colormap")
+            params.get("suma_colormap", None)
         ])
-    if params.get("user_colut_file") is not None:
+    if params.get("user_colut_file", None) is not None:
         cargs.extend([
             "-usercolutfile",
-            execution.input_file(params.get("user_colut_file"))
+            execution.input_file(params.get("user_colut_file", None))
         ])
-    if params.get("sdset") is not None:
+    if params.get("sdset", None) is not None:
         cargs.extend([
             "-sdset",
-            execution.input_file(params.get("sdset"))
+            execution.input_file(params.get("sdset", None))
         ])
-    if params.get("sdset_prefix") is not None:
+    if params.get("sdset_prefix", None) is not None:
         cargs.extend([
             "-sdset_prefix",
-            params.get("sdset_prefix")
+            params.get("sdset_prefix", None)
         ])
-    if params.get("flipupdown"):
+    if params.get("flipupdown", False):
         cargs.append("-flipud")
-    if params.get("skip_last"):
+    if params.get("skip_last", False):
         cargs.append("-sl")
-    if params.get("show_fscolut"):
+    if params.get("show_fscolut", False):
         cargs.append("-show_fscolut")
-    if params.get("help_flag"):
+    if params.get("help_flag", False):
         cargs.append("-h")
-    if params.get("help_full_flag"):
+    if params.get("help_full_flag", False):
         cargs.append("-help")
-    if params.get("flip_map_updside_down"):
+    if params.get("flip_map_updside_down", False):
         cargs.append("-flipud")
     return cargs
 
@@ -290,7 +281,7 @@ def make_color_map_outputs(
     """
     ret = MakeColorMapOutputs(
         root=execution.output_file("."),
-        afni_hex_output_prefix=execution.output_file(params.get("afni_hex") + "_01") if (params.get("afni_hex") is not None) else None,
+        afni_hex_output_prefix=execution.output_file(params.get("afni_hex", None) + "_01") if (params.get("afni_hex") is not None) else None,
         palette_file_output=execution.output_file("TestPalette.pal"),
     )
     return ret
@@ -298,11 +289,13 @@ def make_color_map_outputs(
 
 def make_color_map_execute(
     params: MakeColorMapParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakeColorMapOutputs:
     """
-    Utility for creating and modifying colormaps with various formats and fiducial
-    points.
+    MakeColorMap
+    
+    Utility for creating and modifying colormaps with various formats and
+    fiducial points.
     
     Author: AFNI Developers
     
@@ -310,10 +303,12 @@ def make_color_map_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakeColorMapOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_COLOR_MAP_METADATA)
     params = execution.params(params)
     cargs = make_color_map_cargs(params, execution)
     ret = make_color_map_outputs(params, execution)
@@ -345,8 +340,10 @@ def make_color_map(
     runner: Runner | None = None,
 ) -> MakeColorMapOutputs:
     """
-    Utility for creating and modifying colormaps with various formats and fiducial
-    points.
+    MakeColorMap
+    
+    Utility for creating and modifying colormaps with various formats and
+    fiducial points.
     
     Author: AFNI Developers
     
@@ -381,8 +378,6 @@ def make_color_map(
     Returns:
         NamedTuple of outputs (described in `MakeColorMapOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_COLOR_MAP_METADATA)
     params = make_color_map_params(
         fiducials_ncol=fiducials_ncol,
         fiducials=fiducials,
@@ -405,13 +400,13 @@ def make_color_map(
         help_full_flag=help_full_flag,
         flip_map_updside_down=flip_map_updside_down,
     )
-    return make_color_map_execute(params, execution)
+    return make_color_map_execute(params, runner)
 
 
 __all__ = [
     "MAKE_COLOR_MAP_METADATA",
     "MakeColorMapOutputs",
-    "MakeColorMapParameters",
     "make_color_map",
+    "make_color_map_execute",
     "make_color_map_params",
 ]

niwrap_afni/afni/make_pq_script_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 MAKE_PQ_SCRIPT_PY_METADATA = Metadata(
-    id="92e2566b52307fc16bead6a8f031cd5f8c8b9b62.boutiques",
+    id="00368a745377b383a6791b40eb2356c9208093f7.boutiques",
     name="make_pq_script.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,49 +14,24 @@ MAKE_PQ_SCRIPT_PY_METADATA = Metadata(
 
 
 MakePqScriptPyParameters = typing.TypedDict('MakePqScriptPyParameters', {
-    "__STYXTYPE__": typing.Literal["make_pq_script.py"],
+    "@type": typing.NotRequired[typing.Literal["afni/make_pq_script.py"]],
+    "dataset": InputPathType,
+    "brick_index": float,
+    "mask": InputPathType,
+    "out_script": str,
+})
+MakePqScriptPyParametersTagged = typing.TypedDict('MakePqScriptPyParametersTagged', {
+    "@type": typing.Literal["afni/make_pq_script.py"],
     "dataset": InputPathType,
     "brick_index": float,
     "mask": InputPathType,
     "out_script": str,
 })
-
-
-def dyn_cargs(
-    t: str,
-) -> typing.Any:
-    """
-    Get build cargs function by command type.
-    
-    Args:
-        t: Command type.
-    Returns:
-        Build cargs function.
-    """
-    return {
-        "make_pq_script.py": make_pq_script_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 {
-        "make_pq_script.py": make_pq_script_py_outputs,
-    }.get(t)
 
 
 class MakePqScriptPyOutputs(typing.NamedTuple):
     """
-    Output object returned when calling `make_pq_script_py(...)`.
+    Output object returned when calling `MakePqScriptPyParameters(...)`.
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
@@ -69,7 +44,7 @@ def make_pq_script_py_params(
     brick_index: float,
     mask: InputPathType,
     out_script: str,
-) -> MakePqScriptPyParameters:
+) -> MakePqScriptPyParametersTagged:
     """
     Build parameters.
     
@@ -82,7 +57,7 @@ def make_pq_script_py_params(
         Parameter dictionary
     """
     params = {
-        "__STYXTYPE__": "make_pq_script.py",
+        "@type": "afni/make_pq_script.py",
         "dataset": dataset,
         "brick_index": brick_index,
         "mask": mask,
@@ -106,10 +81,10 @@ def make_pq_script_py_cargs(
     """
     cargs = []
     cargs.append("make_pq_script.py")
-    cargs.append(execution.input_file(params.get("dataset")))
-    cargs.append(str(params.get("brick_index")))
-    cargs.append(execution.input_file(params.get("mask")))
-    cargs.append(params.get("out_script"))
+    cargs.append(execution.input_file(params.get("dataset", None)))
+    cargs.append(str(params.get("brick_index", None)))
+    cargs.append(execution.input_file(params.get("mask", None)))
+    cargs.append(params.get("out_script", None))
     return cargs
 
 
@@ -128,16 +103,18 @@ def make_pq_script_py_outputs(
     """
     ret = MakePqScriptPyOutputs(
         root=execution.output_file("."),
-        script=execution.output_file(params.get("out_script")),
+        script=execution.output_file(params.get("out_script", None)),
     )
     return ret
 
 
 def make_pq_script_py_execute(
     params: MakePqScriptPyParameters,
-    execution: Execution,
+    runner: Runner | None = None,
 ) -> MakePqScriptPyOutputs:
     """
+    make_pq_script.py
+    
     Creates a script to compute p-value and q-value curves.
     
     Author: AFNI Developers
@@ -146,10 +123,12 @@ def make_pq_script_py_execute(
     
     Args:
         params: The parameters.
-        execution: The execution object.
+        runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `MakePqScriptPyOutputs`).
     """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(MAKE_PQ_SCRIPT_PY_METADATA)
     params = execution.params(params)
     cargs = make_pq_script_py_cargs(params, execution)
     ret = make_pq_script_py_outputs(params, execution)
@@ -165,6 +144,8 @@ def make_pq_script_py(
     runner: Runner | None = None,
 ) -> MakePqScriptPyOutputs:
     """
+    make_pq_script.py
+    
     Creates a script to compute p-value and q-value curves.
     
     Author: AFNI Developers
@@ -180,21 +161,19 @@ def make_pq_script_py(
     Returns:
         NamedTuple of outputs (described in `MakePqScriptPyOutputs`).
     """
-    runner = runner or get_global_runner()
-    execution = runner.start_execution(MAKE_PQ_SCRIPT_PY_METADATA)
     params = make_pq_script_py_params(
         dataset=dataset,
         brick_index=brick_index,
         mask=mask,
         out_script=out_script,
     )
-    return make_pq_script_py_execute(params, execution)
+    return make_pq_script_py_execute(params, runner)
 
 
 __all__ = [
     "MAKE_PQ_SCRIPT_PY_METADATA",
     "MakePqScriptPyOutputs",
-    "MakePqScriptPyParameters",
     "make_pq_script_py",
+    "make_pq_script_py_execute",
     "make_pq_script_py_params",
 ]