issue #17 load_image_url raises exception if file url and unicode

Author: Lee Kamentsky

bioformats/formatreader.py

@@ -545,7 +545,10 @@ def __init__(self, path=None, url=None, perform_init=True):
         self.using_temp_file = False
         if url is not None and url.lower().startswith(file_scheme):
             utf8_url = urllib.url2pathname(url[len(file_scheme):])
-            path = unicode(utf8_url, 'utf-8')
+            if isinstance(utf8_url, str):
+                path = unicode(utf8_url, 'utf-8')
+            else:
+                path = utf8_url
         self.path = path
         if path is None:
             if url.lower().startswith("omero:"):

bioformats/tests/test_load_using_bioformats.py

@@ -14,8 +14,9 @@
 
 import bioformats.formatreader as formatreader
 import bioformats.metadatatools as metadatatools
-from bioformats import load_image
+from bioformats import load_image, load_image_url
 from bioformats import log4j
+import urllib
 
 class TestLoadUsingBioformats(unittest.TestCase):
 
@@ -38,4 +39,37 @@ def test_file_not_found(self):
         self.assertRaises(exceptions.IOError, 
                           lambda :load_image(path))
 
+class TestLoadUsingBioformatsURL(unittest.TestCase):
+    def setUp(self):
+        javabridge.attach()
+        log4j.basic_config()
+        
+    def tearDown(self):
+        javabridge.detach()
 
+    def test_01_01_open_file(self):
+        path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
+        url = "file:" + urllib.pathname2url(path).encode("utf-8")
+        image, scale = load_image_url(
+            url, rescale=False, wants_max_intensity=True)
+        self.assertEqual(image.shape[0], 640)
+        
+    def test_01_02_open_http(self):
+        url = "https://github.com/CellProfiler/python-bioformats"+\
+            "/raw/master/bioformats/tests/Channel1-01-A-01.tif"
+        image, scale = load_image_url(
+            url, rescale=False, wants_max_intensity=True)
+        self.assertEqual(image.shape[0], 640)
+
+    def test_01_03_unicode_url(self):
+        #
+        # Regression test of issue #17: ensure that this does not
+        # raise an exception when converting URL to string
+        #
+        path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
+        url = u"file:" + urllib.pathname2url(path).encode("utf-8")
+        image, scale = load_image_url(
+            url, rescale=False, wants_max_intensity=True)
+        self.assertEqual(image.shape[0], 640)
+        
+