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Rename delta to eps for float-based assertions (#1)
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* Rename `delta` to `eps` for float-based assertions

* Fix tests
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@kostrykin
kostrykin authored Mar 11, 2024
1 parent 00485cc commit fb7bbaa
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Showing 3 changed files with 36 additions and 19 deletions.
14 changes: 7 additions & 7 deletions lib/galaxy/tool_util/verify/asserts/image.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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,
Expand All @@ -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.
Expand All @@ -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(
Expand Down Expand Up @@ -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:
Expand All @@ -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,
Expand Down
19 changes: 10 additions & 9 deletions lib/galaxy/tool_util/xsd/galaxy.xsd
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Original file line number Diff line number Diff line change
Expand Up @@ -2858,7 +2858,7 @@ $attribute_list::5
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image and has a specific mean intensity value of ``value``
plus/minus ``delta`` (e.g., ``<image_has_mean_intensity value="0.83" />``).
plus/minus ``eps`` (e.g., ``<image_has_mean_intensity value="0.83" />``).
Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.
$attribute_list::5
Expand All @@ -2870,9 +2870,9 @@ $attribute_list::5
<xs:documentation xml:lang="en">The required mean value of the image intensities.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="delta" type="xs:float" use="optional" default="0.01">
<xs:attribute name="eps" type="xs:float" use="optional" default="0.01">
<xs:annotation>
<xs:documentation xml:lang="en">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``.</xs:documentation>
<xs:documentation xml:lang="en">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``.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="min" type="xs:float" use="optional">
Expand All @@ -2895,7 +2895,7 @@ $attribute_list::5
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image and has a specific center of mass of ``point``,
or has an Euclidean distance of ``delta`` or less to that point (e.g.,
or has an Euclidean distance of ``eps`` or less to that point (e.g.,
``<has_image_center_of_mass point="511.07, 223.34" />``).
$attribute_list::5
Expand All @@ -2907,7 +2907,7 @@ $attribute_list::5
<xs:documentation xml:lang="en">The required center of mass of the image intensities (horizontal and vertical coordinate, separated by a comma).</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="delta" type="xs:float" use="optional" default="0.01">
<xs:attribute name="eps" type="xs:float" use="optional" default="0.01">
<xs:annotation>
<xs:documentation xml:lang="en">The maximum allowed Euclidean distance to the required center of mass (defaults to ``0.01``).</xs:documentation>
</xs:annotation>
Expand Down Expand Up @@ -2969,8 +2969,9 @@ $attribute_list::5
<xs:complexType name="AssertHasImageMeanObjectSize">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image with labeled objects which have the specified mean size (number of pixels, e.g.,
``<has_image_mean_object_size value="111.87" exclude_labels="0" />``). 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., ``<has_image_mean_object_size value="111.87" exclude_labels="0" />``).
The labels must be unique.
$attribute_list::5
]]>
Expand All @@ -2981,9 +2982,9 @@ $attribute_list::5
<xs:documentation xml:lang="en">The required mean size of the uniquely labeled objects.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="delta" type="xs:float" use="optional" default="0.01">
<xs:attribute name="eps" type="xs:float" use="optional" default="0.01">
<xs:annotation>
<xs:documentation xml:lang="en">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``.</xs:documentation>
<xs:documentation xml:lang="en">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``.</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="min" type="xs:float" use="optional">
Expand Down
22 changes: 19 additions & 3 deletions test/functional/tools/validation_image.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,22 @@
</assert_contents>
</output>
</test>
<test>
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_width value="30" delta="2" />
</assert_contents>
</output>
</test>
<test expect_test_failure="true">
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_width value="29" delta="2" />
</assert_contents>
</output>
</test>
<test>
<param name="input" value="im3_b.tif" />
<output name="output">
Expand Down Expand Up @@ -49,7 +65,7 @@
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_mean_intensity channel="0" value="0.24" delta="0.0100000001" />
<has_image_mean_intensity channel="0" value="0.24" eps="0.0100000001" />
</assert_contents>
</output>
</test>
Expand Down Expand Up @@ -122,7 +138,7 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_mean_object_size value="511" delta="0.9" />
<has_image_mean_object_size value="511" eps="0.9" />
</assert_contents>
</output>
</test>
Expand All @@ -134,7 +150,7 @@
<has_image_height value="32" />
<has_image_channels value="1" />
<has_image_labels value="2" />
<has_image_mean_object_size value="511" delta="1.0" />
<has_image_mean_object_size value="511" eps="1.0" />
</assert_contents>
</output>
</test>
Expand Down

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