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Logging

Logging frameworks

Bio-Formats uses SLF4J as a logging API. SLF4J is a facade and needs to be bound to a logging framework at deployment time. Two underlying logging frameworks are currently supported by Bio-Formats. Bio-Formats does not impose any specific SLF4J binding on downstream consumers as per the recommended SLF4J best practices. Some recommended bindings are as follows:

  • logback is the recommended framework and natively implements the SLF4J API. A logback version of 1.2.x is recommended as Bio-Formats has a hard dependency for slf4j-api 1.7.30. This means that logback versions 1.3.x and higher are not yet supported in Bio-Formats as they rely on slf4j-api 2.x.
  • log4j is the other logging framework supported by Bio-Formats and is primarily used in the MATLAB environment <matlab-dev>.

Examples of declaring these dependencies using Maven or Gradle are given in the Bio-Formats examples repository.

Initialization

The :common_javadoc:DebugTools <loci/common/DebugTools.html> class contains a series of framework-agnostic methods for the initialization and control of the logging system. This class uses reflection to detect the underlying logging framework and delegate the method calls to either :common_javadoc:Log4jTools <loci/common/Log4jTools.html> or :common_javadoc:LogbackTools <loci/common/LogbackTools.html>.

The main methods are described below:

  • DebugTools.enableLogging() will initialize the underlying logging framework. This call will result in a no-op if logging has been initialized either via a binding-specific configuration file (see logback configuration) or via a prior call to DebugTools.enableLogging().
  • DebugTools.enableLogging(level) will initialize the logging framework under the same conditions as described above and set the root logger level if the initialization was succesful.
  • DebugTools.setRootLevel(level) will override the level of the root logger independently of how the logging system was initialized.
  • DebugTools.enableIJLogging() (logback-only) will add an ImageJ-specific appender to the root logger.

5.2.0

Prior to Bio-Formats 5.2.0, DebugTools.enableLogging(level) unconditionally set the logging and root logger level. Use DebugTools.setRootLevel(level) to restore this behavior.