Merge branch 'dev' into document_formatter

Author: CodyCBakerPhD

nwbinspector/checks/images.py

@@ -0,0 +1,24 @@
+from hdmf.utils import get_data_shape
+
+from pynwb.base import Images
+
+from ..register_checks import register_check, Importance, InspectorMessage
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Images)
+def check_order_of_images_unique(images: Images):
+    if images.order_of_images is None:
+        return
+    if not len(set(images.order_of_images)) == len(images.order_of_images):
+        return InspectorMessage(message="order_of_images should have unique values.")
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=Images)
+def check_order_of_images_len(images: Images):
+    if images.order_of_images is None:
+        return
+    if not len(images.order_of_images) == len(images.images):
+        return InspectorMessage(
+            message=f"Length of order_of_images ({len(images.order_of_images)}) does not match the number of images ("
+            f"{len(images.images)})."
+        )

setup.py

@@ -5,7 +5,7 @@
     long_description = f.read()
 setup(
     name="nwbinspector",
-    version="0.4.7",
+    version="0.4.8",
     description="Tool to inspect NWB files for best practices compliance.",
     long_description=long_description,
     long_description_content_type="text/markdown",

tests/unit_tests/test_images.py

@@ -0,0 +1,57 @@
+import numpy as np
+
+from pynwb.base import Images, ImageReferences
+from pynwb.image import GrayscaleImage
+
+from nwbinspector import InspectorMessage, Importance
+from nwbinspector.checks.images import check_order_of_images_unique, check_order_of_images_len
+
+
+def test_check_order_of_images_unique():
+
+    imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
+    img_refs = ImageReferences(name="order_of_images", data=imgs + [imgs[0]])
+    images = Images(name="my_images", images=imgs, order_of_images=img_refs)
+
+    assert check_order_of_images_unique(images) == InspectorMessage(
+        message="order_of_images should have unique values.",
+        importance=Importance.BEST_PRACTICE_VIOLATION,
+        check_function_name="check_order_of_images_unique",
+        object_type="Images",
+        object_name="my_images",
+        location="/",
+    )
+
+
+def test_pass_check_order_of_images_unique():
+
+    imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
+    img_refs = ImageReferences(name="order_of_images", data=imgs)
+    images = Images(name="my_images", images=imgs, order_of_images=img_refs)
+
+    assert check_order_of_images_unique(images) is None
+
+
+def test_check_order_of_images_len():
+
+    imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
+    img_refs = ImageReferences(name="order_of_images", data=imgs + [imgs[0]])
+    images = Images(name="my_images", images=imgs, order_of_images=img_refs)
+
+    assert check_order_of_images_len(images) == InspectorMessage(
+        message=f"Length of order_of_images (6) does not match the number of images (5).",
+        importance=Importance.BEST_PRACTICE_VIOLATION,
+        check_function_name="check_order_of_images_len",
+        object_type="Images",
+        object_name="my_images",
+        location="/",
+    )
+
+
+def test_pass_check_order_of_images_len():
+
+    imgs = [GrayscaleImage(name=f"image{i}", data=np.random.randn(10, 10)) for i in range(5)]
+    img_refs = ImageReferences(name="order_of_images", data=imgs)
+    images = Images(name="my_images", images=imgs, order_of_images=img_refs)
+
+    assert check_order_of_images_len(images) is None