Add image_diff comparison method for test output verification using images

lib/galaxy/dependencies/pinned-requirements.txt

@@ -126,6 +126,7 @@ parsley==1.3 ; python_version >= "3.8" and python_version < "3.13"
 paste==3.7.1 ; python_version >= "3.8" and python_version < "3.13"
 pastedeploy==3.1.0 ; python_version >= "3.8" and python_version < "3.13"
 pebble==5.0.6 ; python_version >= "3.8" and python_version < "3.13"
+pillow==10.2.0 ; python_version >= "3.8" and python_version < "3.13"
 pkgutil-resolve-name==1.3.10 ; python_version >= "3.8" and python_version < "3.9"
 promise==2.3 ; python_version >= "3.8" and python_version < "3.13"
 prompt-toolkit==3.0.43 ; python_version >= "3.8" and python_version < "3.13"

lib/galaxy/tool_util/linters/tests.py

@@ -278,6 +278,8 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             "decompress": ["diff"],
             "delta": ["sim_size"],
             "delta_frac": ["sim_size"],
+            "metric": ["image_diff"],
+            "eps": ["image_diff"],
         }
         for test_idx, test in enumerate(tests, start=1):
             for output in test.xpath(".//*[self::output or self::element or self::discovered_dataset]"):

lib/galaxy/tool_util/parser/util.py

@@ -3,6 +3,9 @@
 DEFAULT_DELTA = 10000
 DEFAULT_DELTA_FRAC = None
 
+DEFAULT_METRIC = "mae"
+DEFAULT_EPS = 0.01
+
 
 def is_dict(item):
     return isinstance(item, dict) or isinstance(item, OrderedDict)

lib/galaxy/tool_util/parser/xml.py

@@ -19,6 +19,8 @@
 from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA,
     DEFAULT_DELTA_FRAC,
+    DEFAULT_EPS,
+    DEFAULT_METRIC,
 )
 from galaxy.util import (
     Element,
@@ -788,6 +790,9 @@ def __parse_test_attributes(output_elem, attrib, parse_elements=False, parse_dis
     attributes["decompress"] = string_as_bool(attrib.pop("decompress", False))
     # `location` may contain an URL to a remote file that will be used to download `file` (if not already present on disk).
     location = attrib.get("location")
+    # Parameters for "image_diff" comparison
+    attributes["metric"] = attrib.pop("metric", DEFAULT_METRIC)
+    attributes["eps"] = float(attrib.pop("eps", DEFAULT_EPS))
     if location and file is None:
         file = os.path.basename(location)  # If no file specified, try to get filename from URL last component
     attributes["location"] = location

lib/galaxy/tool_util/verify/__init__.py

@@ -5,6 +5,7 @@
 import hashlib
 import json
 import logging
+import math
 import os
 import os.path
 import re
@@ -14,23 +15,38 @@
     Any,
     Callable,
     Dict,
+    List,
     Optional,
+    TYPE_CHECKING,
 )
 
+try:
+    import numpy
+except ImportError:
+    pass
 try:
     import pysam
 except ImportError:
-    pysam = None  # type: ignore[assignment]
+    pass
+try:
+    from PIL import Image
+except ImportError:
+    pass
 
 from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA,
     DEFAULT_DELTA_FRAC,
+    DEFAULT_EPS,
+    DEFAULT_METRIC,
 )
 from galaxy.util import unicodify
 from galaxy.util.compression_utils import get_fileobj
 from .asserts import verify_assertions
 from .test_data import TestDataResolver
 
+if TYPE_CHECKING:
+    import numpy.typing
+
 log = logging.getLogger(__name__)
 
 DEFAULT_TEST_DATA_RESOLVER = TestDataResolver()
@@ -171,6 +187,8 @@ def get_filename(filename: str) -> str:
                 files_delta(local_name, temp_name, attributes=attributes)
             elif compare == "contains":
                 files_contains(local_name, temp_name, attributes=attributes)
+            elif compare == "image_diff":
+                files_image_diff(local_name, temp_name, attributes=attributes)
             else:
                 raise Exception(f"Unimplemented Compare type: {compare}")
         except AssertionError as err:
@@ -432,3 +450,68 @@ def files_contains(file1, file2, attributes=None):
             line_diff_count += 1
         if line_diff_count > lines_diff:
             raise AssertionError(f"Failed to find '{contains}' in history data. (lines_diff={lines_diff}).")
+
+
+def _multiobject_intersection_over_union(
+    mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray", repeat_reverse: bool = True
+) -> List["numpy.floating"]:
+    iou_list = []
+    for label1 in numpy.unique(mask1):
+        cc1 = mask1 == label1
+        cc1_iou_list = []
+        for label2 in numpy.unique(mask2[cc1]):
+            cc2 = mask2 == label2
+            cc1_iou_list.append(intersection_over_union(cc1, cc2))
+        iou_list.append(max(cc1_iou_list))
+    if repeat_reverse:
+        iou_list.extend(_multiobject_intersection_over_union(mask2, mask1, repeat_reverse=False))
+    return iou_list
+
+
+def intersection_over_union(mask1: "numpy.typing.NDArray", mask2: "numpy.typing.NDArray") -> "numpy.floating":
+    assert mask1.dtype == mask2.dtype
+    assert mask1.ndim == mask2.ndim == 2
+    assert mask1.shape == mask2.shape
+    if mask1.dtype == bool:
+        return numpy.logical_and(mask1, mask2).sum() / numpy.logical_or(mask1, mask2).sum()
+    else:
+        return min(_multiobject_intersection_over_union(mask1, mask2))
+
+
+def get_image_metric(
+    attributes: Dict[str, Any]
+) -> Callable[["numpy.typing.NDArray", "numpy.typing.NDArray"], "numpy.floating"]:
+    metric_name = attributes.get("metric", DEFAULT_METRIC)
+    metrics = {
+        "mae": lambda arr1, arr2: numpy.abs(arr1 - arr2).mean(),
+        # Convert to float before squaring to prevent overflows
+        "mse": lambda arr1, arr2: numpy.square((arr1 - arr2).astype(float)).mean(),
+        "rms": lambda arr1, arr2: math.sqrt(numpy.square((arr1 - arr2).astype(float)).mean()),
+        "fro": lambda arr1, arr2: numpy.linalg.norm((arr1 - arr2).reshape(1, -1), "fro"),
+        "iou": lambda arr1, arr2: 1 - intersection_over_union(arr1, arr2),
+    }
+    try:
+        return metrics[metric_name]
+    except KeyError:
+        raise ValueError(f'No such metric: "{metric_name}"')
+
+
+def files_image_diff(file1: str, file2: str, attributes: Optional[Dict[str, Any]] = None) -> None:
+    """Check the pixel data of 2 image files for differences."""
+    attributes = attributes or {}
+
+    with Image.open(file1) as im1:
+        arr1 = numpy.array(im1)
+    with Image.open(file2) as im2:
+        arr2 = numpy.array(im2)
+
+    if arr1.dtype != arr2.dtype:
+        raise AssertionError(f"Image data types did not match ({arr1.dtype}, {arr2.dtype}).")
+
+    if arr1.shape != arr2.shape:
+        raise AssertionError(f"Image dimensions did not match ({arr1.shape}, {arr2.shape}).")
+
+    distance = get_image_metric(attributes)(arr1, arr2)
+    distance_eps = attributes.get("eps", DEFAULT_EPS)
+    if distance > distance_eps:
+        raise AssertionError(f"Image difference {distance} exceeds eps={distance_eps}.")

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -1659,7 +1659,7 @@ Different methods can be chosen for the comparison with the local file specified
 by ``file`` using the ``compare`` attribute:
 
 - ``diff``: uses diff to compare the history data set and the file provided by
-  ``file``. Compressed files are decompressed before the compariopm if
+  ``file``. Compressed files are decompressed before the comparison if
   ``decompress`` is set to ``true``. BAM files are converted to SAM before the
   comparision and for pdf some special rules are implemented. The number of
   allowed differences can be set with ``lines_diff``.  If ``sort="true"`` history
@@ -1677,6 +1677,10 @@ by ``file`` using the ``compare`` attribute:
 - ``sim_size``: compares the size of the history dataset and the ``file`` subject to
   the values of the ``delta`` and ``delta_frac`` attributes. Note that a ``has_size``
   content assertion should be preferred, because this avoids storing the test file.
+- ``image_diff``: compares the pixel data of the history data set and the file
+  provided by ``file``. The difference of the images is quantified according to their
+  pixel-wise distance with respect to a specific ``metric``. The check passes if the
+  distance is not larger than the value set for ``eps``. Only 2-D images can be used.
 
         ]]></xs:documentation>
     </xs:annotation>
@@ -1813,6 +1817,13 @@ will be infered from the last component of the location URL. For example, `locat
 If you specify a `checksum`, it will be also used to check the integrity of the download.</xs:documentation>
       </xs:annotation>
     </xs:attribute>
+    <xs:attribute name="metric" type="TestOutputMetricType" default="mae">
+    </xs:attribute>
+    <xs:attribute name="eps" type="xs:float" default="0.01">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">If ``compare`` is set to ``image_diff``, this is the maximum allowed distance between the data set that is generated in the test and the file in ``test-data/`` that is referenced by the ``file`` attribute, with distances computed with respect to the specified ``metric``. Default value is 0.01.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
   </xs:complexType>
   <xs:group name="TestOutputElement">
     <xs:choice>
@@ -7450,15 +7461,29 @@ and ``bibtex`` are the only supported options.</xs:documentation>
     <xs:annotation>
       <xs:documentation xml:lang="en">Type of comparison to use when comparing
 test generated output files to expected output files. Currently valid value are
-``diff`` (the default), ``re_match``, ``re_match_multiline``,
-and ``contains``. In addition there is ``sim_size`` which is discouraged in favour of a ``has_size`` assertion.</xs:documentation>
+``diff`` (the default), ``re_match``, ``re_match_multiline``, ``contains``,
+and ``image_diff``. In addition there is ``sim_size`` which is discouraged in
+favour of a ``has_size`` assertion.</xs:documentation>
     </xs:annotation>
     <xs:restriction base="xs:string">
       <xs:enumeration value="diff"/>
       <xs:enumeration value="re_match"/>
       <xs:enumeration value="sim_size"/>
       <xs:enumeration value="re_match_multiline"/>
       <xs:enumeration value="contains"/>
+      <xs:enumeration value="image_diff"/>
+    </xs:restriction>
+  </xs:simpleType>
+  <xs:simpleType name="TestOutputMetricType">
+    <xs:annotation>
+      <xs:documentation xml:lang="en">If ``compare`` is set to ``image_diff``, this is the metric used to compute the distance between images for quantification of their difference. For intensity images, possible metrics are *mean absolute error* (``mae``, the default), *mean squared error* (``mse``), *root mean squared* error (``rms``), and the *Frobenius norm* (``fro``). In addition, for binary images and label maps (with multiple objects), ``iou`` can be used to compute *one minus* the *intersection over the union* (IoU). Object correspondances are established by taking the pair of objects, for which the IoU is highest, and the distance of the images is the worst value determined for any pair of corresponding objects.</xs:documentation>
+    </xs:annotation>
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="mae"/>
+      <xs:enumeration value="mse"/>
+      <xs:enumeration value="rms"/>
+      <xs:enumeration value="fro"/>
+      <xs:enumeration value="iou"/>
     </xs:restriction>
   </xs:simpleType>
   <xs:simpleType name="PermissiveBoolean">

lib/galaxy/util/checkers.py

@@ -187,11 +187,9 @@ def iter_zip(file_path: str):
             yield (z.open(f), f)
 
 
-def check_image(file_path: str):
+def check_image(file_path: str) -> bool:
     """Simple wrapper around image_type to yield a True/False verdict"""
-    if image_type(file_path):
-        return True
-    return False
+    return bool(image_type(file_path))
 
 
 COMPRESSION_CHECK_FUNCTIONS: Dict[str, CompressionChecker] = {

lib/galaxy/util/image_util.py

@@ -2,25 +2,25 @@
 
 import imghdr
 import logging
+from typing import (
+    List,
+    Optional,
+)
 
 try:
-    import Image as PIL
+    from PIL import Image
 except ImportError:
-    try:
-        from PIL import Image as PIL
-    except ImportError:
-        PIL = None
+    PIL = None
 
 log = logging.getLogger(__name__)
 
 
-def image_type(filename):
+def image_type(filename: str) -> Optional[str]:
     fmt = None
-    if PIL is not None:
+    if Image is not None:
         try:
-            im = PIL.open(filename)
-            fmt = im.format
-            im.close()
+            with Image.open(filename) as im:
+                fmt = im.format
         except Exception:
             # We continue to try with imghdr, so this is a rare case of an
             # exception we expect to happen frequently, so we're not logging
@@ -30,10 +30,10 @@ def image_type(filename):
     if fmt:
         return fmt.upper()
     else:
-        return False
+        return None
 
 
-def check_image_type(filename, types):
+def check_image_type(filename: str, types: List[str]) -> bool:
     fmt = image_type(filename)
     if fmt in types:
         return True

packages/data/setup.cfg

@@ -34,6 +34,7 @@ include_package_data = True
 install_requires =
     galaxy-files
     galaxy-objectstore
+    galaxy-tool-util
     galaxy-util[template]
     alembic
     alembic-utils

packages/test.sh

@@ -51,7 +51,7 @@ while read -r package_dir || [ -n "$package_dir" ]; do  # https://stackoverflow.
     if [ "$package_dir" = "util" ]; then
         pip install -e '.[template,jstree]'
     elif [ "$package_dir" = "tool_util" ]; then
-        pip install -e '.[cwl,mulled,edam]'
+        pip install -e '.[cwl,mulled,edam,extended-assertions]'
     else
         pip install -e '.'
     fi

packages/tool_util/setup.cfg

@@ -66,6 +66,10 @@ mulled =
     Whoosh
 edam =
     edam-ontology
+extended-assertions =
+    numpy
+    pysam
+    pillow
 
 [options.packages.find]
 exclude =

pyproject.toml

@@ -85,6 +85,7 @@ paramiko = "!=2.9.0, !=2.9.1"  # https://github.com/paramiko/paramiko/issues/196
 Parsley = "*"
 Paste = "*"
 pebble = "*"
+pillow = "*"
 psutil = "*"
 pulsar-galaxy-lib = ">=0.15.0.dev0"
 pycryptodome = "*"

test/functional/tools/image_diff.xml

@@ -0,0 +1,36 @@
+<tool id="image_diff" name="image_diff" version="0.1.0">
+  <command><![CDATA[
+    cp '$in' '$out'
+  ]]></command>
+  <inputs>
+    <param name="in" type="data" format="data"/>
+  </inputs>
+  <outputs>
+    <data name="out" format="data"/>
+  </outputs>
+  <tests>
+    <!-- test pair of equal images (but different formats) -->
+    <test>
+      <param name="in" value="im1_uint8.png" />
+      <output name="out" value="im1_uint8.png" compare="image_diff" metric="mae" />
+    </test>
+    <test>
+      <param name="in" value="im1_uint8.tif" />
+      <output name="out" value="im1_uint8.png" compare="image_diff" metric="mse" eps="0" />
+    </test>
+    <test>
+      <param name="in" value="im1_uint8.png" />
+      <output name="out" value="im1_uint8.png" compare="image_diff" metric="rms" eps="0" />
+    </test>
+    <!-- test pair of different images -->
+    <test>
+      <param name="in" value="im2_a.png" />
+      <output name="out" value="im2_b.png" compare="image_diff" metric="mae" eps="0.25" />
+    </test>
+    <!-- test RGB data -->
+    <test>
+      <param name="in" value="im3_a.png" />
+      <output name="out" value="im3_b.tif" compare="image_diff" metric="fro" eps="256" />
+    </test>
+  </tests>
+</tool>

test/functional/tools/sample_tool_conf.xml

@@ -8,6 +8,7 @@
     <tool file="param_text_option.xml" />
     <tool file="column_param.xml" />
   </section>
+  <tool file="image_diff.xml"/>
   <tool file="output_format_input.xml"/>
   <tool file="ucsc_tablebrowser.xml"/>
   <tool file="test_data_source.xml"/>