Merge pull request #143 from henrypinkard/main

Fix bug that allowed low resolutions on non multi-res datasets
micro-manager · Jun 6, 2024 · 01a8eb8 · 01a8eb8
2 parents 18fc782 + 610d9b4
commit 01a8eb8
Show file tree

Hide file tree

Showing 3 changed files with 22 additions and 8 deletions.
diff --git a/java/pom.xml b/java/pom.xml
@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.ndtiffstorage</groupId>
     <artifactId>NDTiffStorage</artifactId>
-    <version>2.16.0</version>
+    <version>2.16.1</version>
     <packaging>jar</packaging>
     <name>NDTiff Storage file format</name>
     <description>Java-based writer and reader used for NDTiffStorage format</description>
@@ -104,17 +104,24 @@
          </execution>
         </executions>
        </plugin>
-       <plugin>
+      <plugin>
       <groupId>org.sonatype.plugins</groupId>
       <artifactId>nexus-staging-maven-plugin</artifactId>
-      <version>1.6.7</version>
+      <version>1.6.8</version>
       <extensions>true</extensions>
       <configuration>
-         <serverId>ossrh</serverId>
-         <nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
-         <autoReleaseAfterClose>true</autoReleaseAfterClose>
+       <serverId>ossrh</serverId>
+       <nexusUrl>https://s01.oss.sonatype.org/</nexusUrl>
+       <autoReleaseAfterClose>true</autoReleaseAfterClose>
       </configuration>
-    </plugin>
+      <dependencies>
+       <dependency>
+         <groupId>com.thoughtworks.xstream</groupId>
+         <artifactId>xstream</artifactId>
+         <version>1.4.15</version> <!-- apparently this needs to be exactly this version -->
+       </dependency>
+      </dependencies>
+      </plugin>
       </plugins>
      </build>
 

diff --git a/java/src/main/java/org/micromanager/ndtiffstorage/NDTiffStorage.java b/java/src/main/java/org/micromanager/ndtiffstorage/NDTiffStorage.java
@@ -665,6 +665,9 @@ private void populateNewResolutionLevel(int resolutionIndex, boolean addToLowRes
     */
    @Override
    public void increaseMaxResolutionLevel(int newMaxResolutionLevel) {
+      if (!tiled_) {
+         return; // only tiled images support multiple resolutions
+      }
       int oldMaxResolutionLevel = maxResolutionLevel_;
       maxResolutionLevel_ = Math.max(newMaxResolutionLevel, oldMaxResolutionLevel);
       if (fullResStorage_.imageKeys().size() == 0) {

diff --git a/python/ndtiff/nd_tiff_current.py b/python/ndtiff/nd_tiff_current.py
@@ -252,7 +252,7 @@ def __enter__(self):
 
     def __exit__(self, exc_type, exc_val, exc_tb):
         self.close()
-    
+
     def get_channel_names(self):
         """
         :return: list of channel names (strings)
@@ -567,7 +567,11 @@ def _read_single_index_entry(self, data, entries, position=0):
         entries[frozenset(axes.items())] = index_entry
         return position, axes, index_entry
 
+    #TODO: make private
     def read_index(self, path):
+        """
+        Do not use directly -- this function will be made private in the future
+        """
         print("\rReading index...          ", end="")
         with self.file_io.open(path + "NDTiff.index", "rb") as index_file:
             data = index_file.read()