Replace loci_tools.jar with bioformats_package.jar

.gitignore

@@ -9,7 +9,7 @@ dist/*
 pims.egg-info/*
 PIMS.egg-info/*
 pims/version.py
-pims/loci_tools.jar
+pims/bioformats_package.jar
 examples/.ipynb_checkpoints
 pims/tests/data/bulk-water.mov.pims_buffer
 pims/tests/data/bulk-water.mov.pims_meta

doc/source/bioformats.rst

@@ -33,7 +33,7 @@ Or, for windows users,
 download the binary from `Christoph Gohlke's website <http://www.lfd.uci.edu/~gohlke/pythonlibs/#jpype>`_.
 
 On first use of pims.Bioformats(filename), the required java library
-:file:`loci_tools.jar` will be automatically downloaded from
+:file:`bioformats_package.jar` will be automatically downloaded from
 `openmicroscopy.org <http://downloads.openmicroscopy.org/bio-formats/>`__.
 
 Special functions
@@ -44,7 +44,7 @@ switches between them:
 .. code-block:: python
 
    # open a multi-experiment file and read the first experiment
-   reader = pims.BioformatsReader('path/to/file', series=0)
+   reader = pims.bioformats.BioformatsReader('path/to/file', series=0)
    # switch to the third experiment
    reader.series = 2
 
@@ -53,7 +53,7 @@ open a file with for instance 1 GB of java memory:
 
 .. code-block:: python
 
-   reader = BioformatsReader('path/to/file', java_memory='1024m')
+   reader = pims.bioformats.BioformatsReader('path/to/file', java_memory='1024m')
 
 Metadata
 --------
@@ -95,17 +95,17 @@ To update the version of bioformats you are using in pims:
 
 Now you should be able to use pims with the updated bioformats version.
 
-Note: This pims command downloads a bioformats file named `loci_tools.jar`
+Note: This pims command downloads a bioformats file named `bioformats_package.jar`
 to your computer. There are a few possible locations where it might be stored.
 The precedence order is (highest priority first):
 
 1. pims package location
-2. PROGRAMDATA/pims/loci_tools.jar
-3. LOCALAPPDATA/pims/loci_tools.jar
-4. APPDATA/pims/loci_tools.jar
-5. /etc/loci_tools.jar
-6. ~/.config/pims/loci_tools.jar
+2. PROGRAMDATA/pims/bioformats_package.jar
+3. LOCALAPPDATA/pims/bioformats_package.jar
+4. APPDATA/pims/bioformats_package.jar
+5. /etc/bioformats_package.jar
+6. ~/.config/pims/bioformats_package.jar
 
 If you encounter problems updating to the latest version of bioformats,
-you may wish to manually remove `loci_tools.jar` from each of the six locations
+you may wish to manually remove `bioformats_package.jar` from each of the six locations
 and re-run the `pims.bioformats.download_jar` command again.

pims/bioformats.py

@@ -1,3 +1,4 @@
+from turtle import pd
 import numpy as np
 
 from pims.base_frames import FramesSequence, FramesSequenceND
@@ -17,15 +18,15 @@ def available():
 
 def _gen_jar_locations():
     """
-    Generator that yields optional locations of loci_tools.jar.
+    Generator that yields optional locations of bioformats_package.jar.
     The precedence order is (highest priority first):
 
     1. pims package location
-    2. PROGRAMDATA/pims/loci_tools.jar
-    3. LOCALAPPDATA/pims/loci_tools.jar
-    4. APPDATA/pims/loci_tools.jar
-    5. /etc/loci_tools.jar
-    6. ~/.config/pims/loci_tools.jar
+    2. PROGRAMDATA/pims/bioformats_package.jar
+    3. LOCALAPPDATA/pims/bioformats_package.jar
+    4. APPDATA/pims/bioformats_package.jar
+    5. /etc/bioformats_package.jar
+    6. ~/.config/pims/bioformats_package.jar
     """
     yield os.path.dirname(__file__)
     if 'PROGRAMDATA' in os.environ:
@@ -40,18 +41,18 @@ def _gen_jar_locations():
 
 def _find_jar():
     """
-    Finds the location of loci_tools.jar, if necessary download it to a
+    Finds the location of bioformats_package.jar, if necessary download it to a
     writeable location.
     """
     for loc in _gen_jar_locations():
-        if os.path.isfile(os.path.join(loc, 'loci_tools.jar')):
-            return os.path.join(loc, 'loci_tools.jar')
+        if os.path.isfile(os.path.join(loc, 'bioformats_package.jar')):
+            return os.path.join(loc, 'bioformats_package.jar')
 
-    warn('loci_tools.jar not found, downloading')
+    warn('bioformats_package.jar not found, downloading')
     return download_jar()
 
 
-def download_jar(version='6'):
+def download_jar(version='latest'):
     """ Downloads the bioformats distribution of given version. """
     from urllib.request import urlopen
     import hashlib
@@ -68,23 +69,23 @@ def download_jar(version='6'):
     else:
         raise IOError('No writeable location found. In order to use the '
                       'Bioformats reader, please download '
-                      'loci_tools.jar to the pims program folder or one of '
+                      'bioformats_package.jar to the pims program folder or one of '
                       'the locations provided by _gen_jar_locations().')
 
-    url = ('http://downloads.openmicroscopy.org/bio-formats/' + version +
-           '/artifacts/loci_tools.jar')
+    url = ('https://downloads.openmicroscopy.org/bio-formats/' + version +
+           '/artifacts/bioformats_package.jar')
 
-    path = os.path.join(loc, 'loci_tools.jar')
-    loci_tools = urlopen(url).read()
+    path = os.path.join(loc, 'bioformats_package.jar')
+    bioformats_package = urlopen(url).read()
     sha1_checksum = urlopen(url + '.sha1').read().split(b' ')[0].decode()
 
-    downloaded = hashlib.sha1(loci_tools).hexdigest()
+    downloaded = hashlib.sha1(bioformats_package).hexdigest()
     if downloaded != sha1_checksum:
-        raise IOError("Downloaded loci_tools.jar has invalid checksum. "
+        raise IOError("Downloaded bioformats_package.jar has invalid checksum. "
                       "Please try again.")
 
     with open(path, 'wb') as output:
-        output.write(loci_tools)
+        output.write(bioformats_package)
 
     return path
 
@@ -330,27 +331,30 @@ def __init__(self, filename, meta=True, java_memory='512m',
 
         # Start java VM and initialize logger (globally)
         if not jpype.isJVMStarted():
-            from distutils.version import LooseVersion
+            from packaging.specifiers import SpecifierSet
+            from packaging.version import Version
 
-            loci_path = _find_jar()
+            bioformats_package_path = _find_jar()
             # If we can turn off string auto-conversion, do so,
             # since this is the recommended practice.
-            if LooseVersion(jpype.__version__) >= LooseVersion('0.7.0'):
+            version_spec = SpecifierSet(">=0.7.0")
+            if Version(jpype.__version__) in version_spec:
                 startJVM_kwargs = {'convertStrings': False}
             else:
                 startJVM_kwargs = {}  # convertStrings kwarg not supported for earlier jpype versions
             jpype.startJVM(jpype.getDefaultJVMPath(), '-ea',
-                           '-Djava.class.path=' + loci_path,
+                           '-Djava.class.path=' + bioformats_package_path,
                            '-Xmx' + java_memory, **startJVM_kwargs)
-            log4j = jpype.JPackage('org.apache.log4j')
-            log4j.BasicConfigurator.configure()
-            log4j_logger = log4j.Logger.getRootLogger()
-            log4j_logger.setLevel(log4j.Level.ERROR)
+            logback = jpype.JPackage('ch.qos.logback.classic')
+            logger_context = logback.LoggerContext()
+            logback.BasicConfigurator().setContext(logger_context)
+            logback.BasicConfigurator().configure(logger_context)
 
-        if not jpype.isThreadAttachedToJVM():
-            jpype.attachThreadToJVM()
+        if not jpype.java.lang.Thread.isAttached():
+            jpype.java.lang.Thread.attach()
 
         loci = jpype.JPackage('loci')
+        loci.common.DebugTools.enableLogging('ERROR')
 
         # Initialize reader and metadata
         self.filename = str(filename)
@@ -407,8 +411,8 @@ def __init__(self, filename, meta=True, java_memory='512m',
             if isinstance(Jarr[:], np.ndarray):
                 read_mode = 'jpype'
             else:
-                warn('Due to an issue with JPype 0.6.0, reading is slower. '
-                     'Please consider upgrading JPype to 0.6.1 or later.')
+                # warn('Due to an issue with JPype 0.6.0, reading is slower. '
+                #      'Please consider upgrading JPype to 0.6.1 or later.')
                 try:
                     im = self._jbytearr_stringbuffer(Jarr)
                     im.reshape(self._sizeRGB, self._sizeX, self._sizeY)

pims/tests/test_bioformats.py

@@ -504,5 +504,4 @@ def test_metadata_tags(self):
         assert 'PixelsPhysicalSizeX' in fields
 
 if __name__ == '__main__':
-    unittest.runmodule(argv=[__file__, '-vvs'],
-                   exit=False)
+    unittest.main(verbosity=2)