diff --git a/lib/galaxy/tool_util/verify/asserts/image.py b/lib/galaxy/tool_util/verify/asserts/image.py index ff2ea64654a0..6f9c1609c343 100644 --- a/lib/galaxy/tool_util/verify/asserts/image.py +++ b/lib/galaxy/tool_util/verify/asserts/image.py @@ -156,7 +156,7 @@ def assert_has_image_mean_intensity( output_bytes: bytes, channel: Optional[Union[int, str]] = None, value: Optional[Union[float, str]] = None, - delta: Union[float, str] = 0.01, + eps: Union[float, str] = 0.01, min: Optional[Union[float, str]] = None, max: Optional[Union[float, str]] = None, ) -> None: @@ -167,7 +167,7 @@ def assert_has_image_mean_intensity( _assert_float( actual=im_arr.mean(), label="mean intensity", - tolerance=delta, + tolerance=eps, expected=value, range_min=min, range_max=max, @@ -178,7 +178,7 @@ def assert_has_image_center_of_mass( output_bytes: bytes, channel: Optional[Union[int, str]] = None, point: Optional[Union[Tuple[float, float], str]] = None, - delta: Union[float, str] = 0.01, + eps: Union[float, str] = 0.01, ) -> None: """ Asserts the specified output is an image and has the specified center of mass. @@ -193,8 +193,8 @@ def assert_has_image_center_of_mass( actual_center_of_mass = _compute_center_of_mass(im_arr) distance = numpy.linalg.norm(numpy.subtract(point, actual_center_of_mass)) assert distance <= float( - delta - ), f"Wrong center of mass: {actual_center_of_mass} (expected {point}, distance: {distance}, delta: {delta})" + eps + ), f"Wrong center of mass: {actual_center_of_mass} (expected {point}, distance: {distance}, eps: {eps})" def _get_image_labels( @@ -271,7 +271,7 @@ def assert_has_image_mean_object_size( labels: Optional[Union[str, List[int]]] = None, exclude_labels: Optional[Union[str, List[int]]] = None, value: Optional[Union[float, str]] = None, - delta: Union[float, str] = 0.01, + eps: Union[float, str] = 0.01, min: Optional[Union[float, str]] = None, max: Optional[Union[float, str]] = None, ) -> None: @@ -283,7 +283,7 @@ def assert_has_image_mean_object_size( _assert_float( actual=actual_mean_object_size, label="mean object size", - tolerance=delta, + tolerance=eps, expected=value, range_min=min, range_max=max, diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd index 0d107df49ee0..b6b6fb10279c 100644 --- a/lib/galaxy/tool_util/xsd/galaxy.xsd +++ b/lib/galaxy/tool_util/xsd/galaxy.xsd @@ -2858,7 +2858,7 @@ $attribute_list::5 ``). +plus/minus ``eps`` (e.g., ````). Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``. $attribute_list::5 @@ -2870,9 +2870,9 @@ $attribute_list::5 The required mean value of the image intensities. - + - The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- delta``. + The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean value of the image intensities has to be in the range ``value +- eps``. @@ -2895,7 +2895,7 @@ $attribute_list::5 ``). $attribute_list::5 @@ -2907,7 +2907,7 @@ $attribute_list::5 The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma). - + The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``). @@ -2969,8 +2969,9 @@ $attribute_list::5 ``). The labels must be unique. +Asserts the output is an image with labeled objects which have the specified mean size (number of pixels), +plus/minus ``eps`` (e.g., ````). +The labels must be unique. $attribute_list::5 ]]> @@ -2981,9 +2982,9 @@ $attribute_list::5 The required mean size of the uniquely labeled objects. - + - The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- delta``. + The absolute tolerance to be used for ``value`` (defaults to ``0.01``). The observed mean size of the uniquely labeled objects has to be in the range ``value +- eps``. diff --git a/test/functional/tools/validation_image.xml b/test/functional/tools/validation_image.xml index 840ffdfa7719..c63584796862 100644 --- a/test/functional/tools/validation_image.xml +++ b/test/functional/tools/validation_image.xml @@ -21,6 +21,22 @@ + + + + + + + + + + + + + + + + @@ -49,7 +65,7 @@ - + @@ -122,7 +138,7 @@ - + @@ -134,7 +150,7 @@ - +