Remove log4j log supression, Add slf4j log supression

Author: XericZephyr

bioformats/__init__.py

@@ -88,15 +88,14 @@
 from . import omexml
 
 def init_logger():
-    javabridge.static_call("org/apache/log4j/BasicConfigurator",
-                           "configure", "()V")
-    log4j_logger = javabridge.static_call("org/apache/log4j/Logger",
-                                          "getRootLogger",
-                                          "()Lorg/apache/log4j/Logger;")
-    warn_level = javabridge.get_static_field("org/apache/log4j/Level", "WARN",
-                                             "Lorg/apache/log4j/Level;")
-    javabridge.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V", 
-                    warn_level)
+    rootLoggerName = javabridge.get_static_field("org/slf4j/Logger",
+                                                 "ROOT_LOGGER_NAME", "Ljava/lang/String;")
+    rootLogger = javabridge.static_call("org/slf4j/LoggerFactory",
+                                       "getLogger", "(Ljava/lang/String;)Lorg/slf4j/Logger;", rootLoggerName)
+    logLevel = javabridge.get_static_field("ch/qos/logback/classic/Level",
+                                                "WARN", "Lch/qos/logback/classic/Level;")
+    javabridge.call(rootLogger, "setLevel", "(Lch/qos/logback/classic/Level;)V",
+                    logLevel)
 
 
 if __name__ == "__main__":

bioformats/log4j.py

@@ -16,14 +16,13 @@
 
 import javabridge as J
 import bioformats.formatreader as F
-from bioformats import log4j
 import bioformats
 
 class TestFormatReader(unittest.TestCase):
     def setUp(self):
         J.start_vm(class_path=bioformats.JARS)
         J.attach()
-        log4j.basic_config()
+        bioformats.init_logger()
 
     def tearDown(self):
         J.detach()

bioformats/tests/test_formatreader.py

@@ -15,14 +15,13 @@
 import bioformats.formatreader as formatreader
 import bioformats.metadatatools as metadatatools
 from bioformats import load_image, load_image_url
-from bioformats import log4j
 import urllib
 
 class TestLoadUsingBioformats(unittest.TestCase):
 
     def setUp(self):
         javabridge.attach()
-        log4j.basic_config()
+        bioformats.init_logger()
 
     def tearDown(self):
         javabridge.detach()
@@ -42,7 +41,7 @@ def test_file_not_found(self):
 class TestLoadUsingBioformatsURL(unittest.TestCase):
     def setUp(self):
         javabridge.attach()
-        log4j.basic_config()
+        bioformats.init_logger()
 
     def tearDown(self):
         javabridge.detach()