opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Rename assertion attribute value

Browse Source
This commit is contained in:
Leonid Kostrykin
2024-03-13 07:28:48 +00:00
parent fb7bbaaa83
commit 5964f72dfc
3 changed files with 70 additions and 71 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/tool_util/verify/asserts/image.py
+21 -22
View File
@@ -49,7 +49,7 @@ def _assert_float(
def assert_has_image_width(
output_bytes: bytes,
value: Optional[Union[int, str]] = None,
width: Optional[Union[int, str]] = None,
delta: Union[int, str] = 0,
min: Optional[Union[int, str]] = None,
max: Optional[Union[int, str]] = None,
@@ -62,7 +62,7 @@ def assert_has_image_width(
with Image.open(buf) as im:
_assert_number(
im.size[0],
value,
width,
delta,
min,
max,
@@ -74,7 +74,7 @@ def assert_has_image_width(
def assert_has_image_height(
output_bytes: bytes,
value: Optional[Union[int, str]] = None,
height: Optional[Union[int, str]] = None,
delta: Union[int, str] = 0,
min: Optional[Union[int, str]] = None,
max: Optional[Union[int, str]] = None,
@@ -87,7 +87,7 @@ def assert_has_image_height(
with Image.open(buf) as im:
_assert_number(
im.size[1],
value,
height,
delta,
min,
max,
@@ -99,7 +99,7 @@ def assert_has_image_height(
def assert_has_image_channels(
output_bytes: bytes,
value: Optional[Union[int, str]] = None,
channels: Optional[Union[int, str]] = None,
delta: Union[int, str] = 0,
min: Optional[Union[int, str]] = None,
max: Optional[Union[int, str]] = None,
@@ -112,7 +112,7 @@ def assert_has_image_channels(
with Image.open(buf) as im:
_assert_number(
len(im.getbands()),
value,
channels,
delta,
min,
max,
@@ -155,7 +155,7 @@ def _get_image(
def assert_has_image_mean_intensity(
output_bytes: bytes,
channel: Optional[Union[int, str]] = None,
value: Optional[Union[float, str]] = None,
mean_intensity: Optional[Union[float, str]] = None,
eps: Union[float, str] = 0.01,
min: Optional[Union[float, str]] = None,
max: Optional[Union[float, str]] = None,
@@ -168,7 +168,7 @@ def assert_has_image_mean_intensity(
actual=im_arr.mean(),
label="mean intensity",
tolerance=eps,
expected=value,
expected=mean_intensity,
range_min=min,
range_max=max,
)
@@ -176,25 +176,24 @@ def assert_has_image_mean_intensity(
def assert_has_image_center_of_mass(
output_bytes: bytes,
center_of_mass: Union[Tuple[float, float], str],
channel: Optional[Union[int, str]] = None,
point: Optional[Union[Tuple[float, float], str]] = None,
eps: Union[float, str] = 0.01,
) -> None:
"""
Asserts the specified output is an image and has the specified center of mass.
"""
im_arr = _get_image(output_bytes, channel)
if point is not None:
if isinstance(point, str):
point_parts = [c.strip() for c in point.split(",")]
assert len(point_parts) == 2
point = (float(point_parts[0]), float(point_parts[1]))
assert len(point) == 2, "point must have two components"
actual_center_of_mass = _compute_center_of_mass(im_arr)
distance = numpy.linalg.norm(numpy.subtract(point, actual_center_of_mass))
assert distance <= float(
eps
), f"Wrong center of mass: {actual_center_of_mass} (expected {point}, distance: {distance}, eps: {eps})"
if isinstance(center_of_mass, str):
center_of_mass_parts = [c.strip() for c in center_of_mass.split(",")]
assert len(center_of_mass_parts) == 2
center_of_mass = (float(center_of_mass_parts[0]), float(center_of_mass_parts[1]))
assert len(center_of_mass) == 2, "center_of_mass must have two components"
actual_center_of_mass = _compute_center_of_mass(im_arr)
distance = numpy.linalg.norm(numpy.subtract(center_of_mass, actual_center_of_mass))
assert distance <= float(
eps
), f"Wrong center of mass: {actual_center_of_mass} (expected {center_of_mass}, distance: {distance}, eps: {eps})"
def _get_image_labels(
@@ -270,7 +269,7 @@ def assert_has_image_mean_object_size(
channel: Optional[Union[int, str]] = None,
labels: Optional[Union[str, List[int]]] = None,
exclude_labels: Optional[Union[str, List[int]]] = None,
value: Optional[Union[float, str]] = None,
mean_object_size: Optional[Union[float, str]] = None,
eps: Union[float, str] = 0.01,
min: Optional[Union[float, str]] = None,
max: Optional[Union[float, str]] = None,
@@ -284,7 +283,7 @@ def assert_has_image_mean_object_size(
actual=actual_mean_object_size,
label="mean object size",
tolerance=eps,
expected=value,
expected=mean_object_size,
range_min=min,
range_max=max,
)
lib/galaxy/tool_util/xsd/galaxy.xsd
+17 -17
View File
@@ -2758,15 +2758,15 @@ $attribute_list::5
<xs:complexType name="AssertHasImageWidth">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image and has a specific width (in pixels) of ``value``
plus/minus ``delta`` (e.g., ``<has_image_width value="512" delta="2" />``).
Asserts the output is an image and has a specific width (in pixels),
plus/minus ``delta`` (e.g., ``<has_image_width width="512" delta="2" />``).
Alternatively the range of the expected width can be specified by ``min`` and/or ``max``.
$attribute_list::5
]]>
</xs:documentation>
</xs:annotation>
<xs:attribute name="value" type="xs:integer" use="optional">
<xs:attribute name="width" type="xs:integer" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Expected width of the image (in pixels).`</xs:documentation>
</xs:annotation>
@@ -2791,15 +2791,15 @@ $attribute_list::5
<xs:complexType name="AssertHasImageHeight">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image and has a specific height (in pixels) of ``value``
plus/minus ``delta`` (e.g., ``<has_image_height value="512" delta="2" />``).
Asserts the output is an image and has a specific height (in pixels),
plus/minus ``delta`` (e.g., ``<has_image_height height="512" delta="2" />``).
Alternatively the range of the expected height can be specified by ``min`` and/or ``max``.
$attribute_list::5
]]>
</xs:documentation>
</xs:annotation>
<xs:attribute name="value" type="xs:integer" use="optional">
<xs:attribute name="height" type="xs:integer" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Expected height of the image (in pixels).`</xs:documentation>
</xs:annotation>
@@ -2824,15 +2824,15 @@ $attribute_list::5
<xs:complexType name="AssertHasImageChannels">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image and has a specific number of channels of ``value``
plus/minus ``delta`` (e.g., ``<has_image_height value="512" delta="2" />``).
Asserts the output is an image and has a specific number of channels,
plus/minus ``delta`` (e.g., ``<has_image_channels channels="3" />``).
Alternatively the range of the expected number of channels can be specified by ``min`` and/or ``max``.
$attribute_list::5
]]>
</xs:documentation>
</xs:annotation>
<xs:attribute name="value" type="xs:integer" use="optional">
<xs:attribute name="channels" type="xs:integer" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">Expected number of channels of the image.`</xs:documentation>
</xs:annotation>
@@ -2857,15 +2857,15 @@ $attribute_list::5
<xs:complexType name="AssertHasImageMeanIntensity">
<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 ``eps`` (e.g., ``<image_has_mean_intensity value="0.83" />``).
Asserts the output is an image and has a specific mean intensity value,
plus/minus ``eps`` (e.g., ``<image_has_mean_intensity mean_intensity="0.83" />``).
Alternatively the range of the expected mean intensity value can be specified by ``min`` and/or ``max``.
$attribute_list::5
]]>
</xs:documentation>
</xs:annotation>
<xs:attribute name="value" type="xs:float" use="optional">
<xs:attribute name="mean_intensity" type="xs:float" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">The required mean value of the image intensities.</xs:documentation>
</xs:annotation>
@@ -2894,15 +2894,15 @@ $attribute_list::5
<xs:complexType name="AssertHasImageCenterOfMass">
<xs:annotation>
<xs:documentation xml:lang="en"><![CDATA[
Asserts the output is an image and has a specific center of mass of ``point``,
Asserts the output is an image and has a specific center of mass,
or has an Euclidean distance of ``eps`` or less to that point (e.g.,
``<has_image_center_of_mass point="511.07, 223.34" />``).
``<has_image_center_of_mass center_of_mass="511.07, 223.34" />``).
$attribute_list::5
]]>
</xs:documentation>
</xs:annotation>
<xs:attribute name="point" type="xs:string" use="optional">
<xs:attribute name="center_of_mass" type="xs:string">
<xs:annotation>
<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>
@@ -2970,14 +2970,14 @@ $attribute_list::5
<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),
plus/minus ``eps`` (e.g., ``<has_image_mean_object_size value="111.87" exclude_labels="0" />``).
plus/minus ``eps`` (e.g., ``<has_image_mean_object_size mean_object_size="111.87" exclude_labels="0" />``).
The labels must be unique.
$attribute_list::5
]]>
</xs:documentation>
</xs:annotation>
<xs:attribute name="value" type="xs:float" use="optional">
<xs:attribute name="mean_object_size" type="xs:float" use="optional">
<xs:annotation>
<xs:documentation xml:lang="en">The required mean size of the uniquely labeled objects.</xs:documentation>
</xs:annotation>
test/functional/tools/validation_image.xml
+32 -32
View File
@@ -14,10 +14,10 @@
<param name="input" value="im1_uint8.tif" />
<output name="output">
<assert_contents>
<has_image_width value="32" />
<has_image_height value="32" />
<has_image_channels value="1" />
<has_image_center_of_mass point="15.61, 15.48" />
<has_image_width width="32" />
<has_image_height height="32" />
<has_image_channels channels="1" />
<has_image_center_of_mass center_of_mass="15.61, 15.48" />
</assert_contents>
</output>
</test>
@@ -25,7 +25,7 @@
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_width value="30" delta="2" />
<has_image_width width="30" delta="2" />
</assert_contents>
</output>
</test>
@@ -33,7 +33,7 @@
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_width value="29" delta="2" />
<has_image_width width="29" delta="2" />
</assert_contents>
</output>
</test>
@@ -41,15 +41,15 @@
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_width value="32" />
<has_image_height value="32" />
<has_image_channels value="3" />
<has_image_center_of_mass channel="0" point="7.5, 7.5" />
<has_image_mean_intensity channel="0" value="0.25" />
<has_image_mean_intensity channel="1" value="0.0" />
<has_image_mean_intensity channel="2" value="0" />
<has_image_center_of_mass point="7.5, 7.5" />
<has_image_mean_intensity value="0.08333333333" />
<has_image_width width="32" />
<has_image_height height="32" />
<has_image_channels channels="3" />
<has_image_center_of_mass channel="0" center_of_mass="7.5, 7.5" />
<has_image_mean_intensity channel="0" mean_intensity="0.25" />
<has_image_mean_intensity channel="1" mean_intensity="0.0" />
<has_image_mean_intensity channel="2" mean_intensity="0" />
<has_image_center_of_mass center_of_mass="7.5, 7.5" />
<has_image_mean_intensity mean_intensity="0.08333333333" />
</assert_contents>
</output>
</test>
@@ -57,7 +57,7 @@
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_mean_intensity channel="0" value="0.24" />
<has_image_mean_intensity channel="0" mean_intensity="0.24" />
</assert_contents>
</output>
</test>
@@ -65,7 +65,7 @@
<param name="input" value="im3_b.tif" />
<output name="output">
<assert_contents>
<has_image_mean_intensity channel="0" value="0.24" eps="0.0100000001" />
<has_image_mean_intensity channel="0" mean_intensity="0.24" eps="0.0100000001" />
</assert_contents>
</output>
</test>
@@ -98,11 +98,11 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_width value="32" />
<has_image_height value="32" />
<has_image_channels value="1" />
<has_image_width width="32" />
<has_image_height height="32" />
<has_image_channels channels="1" />
<has_image_labels value="1" exclude_labels="0" />
<has_image_mean_object_size value="256" exclude_labels="0" />
<has_image_mean_object_size mean_object_size="256" exclude_labels="0" />
</assert_contents>
</output>
</test>
@@ -110,11 +110,11 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_width value="32" />
<has_image_height value="32" />
<has_image_channels value="1" />
<has_image_width width="32" />
<has_image_height height="32" />
<has_image_channels channels="1" />
<has_image_labels value="2" />
<has_image_mean_object_size value="512" />
<has_image_mean_object_size mean_object_size="512" />
</assert_contents>
</output>
</test>
@@ -122,7 +122,7 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_mean_object_size labels="0" value="768" />
<has_image_mean_object_size labels="0" mean_object_size="768" />
</assert_contents>
</output>
</test>
@@ -130,7 +130,7 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_mean_object_size labels="0, 1" value="512" />
<has_image_mean_object_size labels="0, 1" mean_object_size="512" />
</assert_contents>
</output>
</test>
@@ -138,7 +138,7 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_mean_object_size value="511" eps="0.9" />
<has_image_mean_object_size mean_object_size="511" eps="0.9" />
</assert_contents>
</output>
</test>
@@ -146,11 +146,11 @@
<param name="input" value="im2_b.png" />
<output name="output">
<assert_contents>
<has_image_width value="32" />
<has_image_height value="32" />
<has_image_channels value="1" />
<has_image_width width="32" />
<has_image_height height="32" />
<has_image_channels channels="1" />
<has_image_labels value="2" />
<has_image_mean_object_size value="511" eps="1.0" />
<has_image_mean_object_size mean_object_size="511" eps="1.0" />
</assert_contents>
</output>
</test>