Update bioformats dependency to 8.0.1 (#231)

* Change URL and hash for jar artifact

* Adapt bioformats logging call to avoid spurious message

Previously we called enableLogging, but under the latest bioformats that emits
one DEBUG-level message during internal logging setup. This message contains a
stack trace from an internally caught exception which looks extra-scary even
though it's irrelevant. Now we use setRootLevel which suppresses even that
message.

* Skip y-axis stage coords flip for InCell reader

Bioformats 6.4.0 added an explicit correction for the stage y-axis.

Author: jmuhlich

MANIFEST.in

@@ -1,3 +1,3 @@
 include versioneer.py
 include ashlar/_version.py
-recursive-include ashlar/jars *.jar
+include ashlar/jars/bioformats_package.jar

ashlar/reg.py

@@ -28,9 +28,9 @@
 
 if not jnius_config.vm_running:
     pkg_root = pathlib.Path(__file__).parent.resolve()
-    bf_jar_path = pkg_root / 'jars' / 'loci_tools.jar'
+    bf_jar_path = pkg_root / 'jars' / 'bioformats_package.jar'
     if not bf_jar_path.exists():
-        raise RuntimeError("loci_tools.jar missing from distribution"
+        raise RuntimeError("bioformats_package.jar missing from distribution"
                            " (expected it at %s)" % bf_jar_path)
     jnius_config.add_classpath(str(bf_jar_path))
     # These settings constrain the memory used by BioFormats to near the minimum
@@ -48,7 +48,7 @@
 ChannelSeparator = jnius.autoclass('loci.formats.ChannelSeparator')
 DynamicMetadataOptions = jnius.autoclass('loci.formats.in.DynamicMetadataOptions')
 UNITS = jnius.autoclass('ome.units.UNITS')
-DebugTools.enableLogging("ERROR")
+DebugTools.setRootLevel("ERROR")
 
 
 # TODO:
@@ -378,9 +378,13 @@ def tile_position(self, i):
                 value = v.doubleValue()
             values.append(value)
         position_microns = np.array(values, dtype=float)
-        # Invert Y so that stage position coordinates and image pixel
-        # coordinates are aligned (most formats seem to work this way).
-        position_microns *= [-1, 1]
+        # Flip the y-axis of the stage coordinate system to align it with the
+        # image coordinate system, as seems to be required for most formats.
+        # Skip this for any formats known not to require it.
+        if self.format_name not in (
+            "InCell 1000/2000", # As of Bioformats 6.4.0
+        ):
+            position_microns *= [-1, 1]
         position_pixels = position_microns / self.pixel_size
         return position_pixels
 

setup.py

@@ -43,32 +43,32 @@
 LICENSE = 'MIT License'
 HOMEPAGE = 'https://github.com/sorgerlab/ashlar'
 
-LOCI_TOOLS_URL = 'https://downloads.openmicroscopy.org/bio-formats/6.3.1/artifacts/loci_tools.jar'
-LOCI_TOOLS_SHA1 = 'bdf1a37b561fea02fd8d1c747bd34db3fc49667b'
+BIOFORMATS_JAR_URL = 'https://downloads.openmicroscopy.org/bio-formats/8.0.1/artifacts/bioformats_package.jar'
+BIOFORMATS_JAR_SHA256 = '8c7557a9357a83bf40272292fbd676beb466a9a8bab34126e92a49d636c64bc2'
 
 def download_bioformats():
     print("Ensuring latest bioformats is present:")
     dist_root = os.path.abspath(os.path.dirname(__file__))
     jar_dir = os.path.join(dist_root, 'ashlar', 'jars')
-    lt_jar_path = os.path.join(jar_dir, 'loci_tools.jar')
+    lt_jar_path = os.path.join(jar_dir, 'bioformats_package.jar')
     if not os.access(jar_dir, os.F_OK):
         os.mkdir(jar_dir)
     try:
         with open(lt_jar_path, 'rb') as f:
-            existing_sha1 = hashlib.sha1(f.read()).hexdigest()
-            if existing_sha1 == LOCI_TOOLS_SHA1:
+            existing_sha256 = hashlib.sha256(f.read()).hexdigest()
+            if existing_sha256 == BIOFORMATS_JAR_SHA256:
                 print("    Up to date!")
                 return
     except IOError:
         pass
-    print("    Downloading BioFormats from %s ..." % LOCI_TOOLS_URL)
+    print("    Downloading BioFormats from %s ..." % BIOFORMATS_JAR_URL)
     # FIXME add progress bar
-    content = urlopen(LOCI_TOOLS_URL).read()
-    content_sha1 = hashlib.sha1(content).hexdigest()
+    content = urlopen(BIOFORMATS_JAR_URL).read()
+    content_sha256 = hashlib.sha256(content).hexdigest()
     with open(lt_jar_path, 'wb') as f:
         f.write(content)
-    if content_sha1 != LOCI_TOOLS_SHA1:
-        raise RuntimeError("loci_tools.jar hash mismatch")
+    if content_sha256 != BIOFORMATS_JAR_SHA256:
+        raise RuntimeError("bioformats_package.jar hash mismatch")
 
 # Define some distutils command subclasses for a few key commands to trigger
 # downloading the BioFormats JAR before they run.