Bump dependencies (#68)

* Update dependencies

* Fix inversion

Author: DavidStirling

CHANGELOG.md

@@ -1,3 +1,16 @@
+# v2.0.2 (2024-05-30)
+
+### Bugfixes/Maintenance:
+* Updated component package versions
+  * bioformats 7.3.0
+  * bioformats2raw 0.9.3
+  * raw2ometiff 0.7.1
+* CreateNGFF has a new option to omit original metadata from METADATA.ome.xml within the .zarr file
+* raw2ometiff now scans .zarr files much faster
+
+### Known issues:
+* The underlying bioformats package is currently unable to read some formats on ARM-based MacOS systems.
+
 # v2.0.1 (2024-05-02)
 
 ### Bugfixes/Maintenance:

build.gradle

@@ -7,10 +7,10 @@ plugins {
     id "com.github.hierynomus.license-report" version "0.16.1"
 }
 
-version = '2.0.1'
-String bfversion = "7.2.0"
-String b2rversion = "0.9.2"
-String r2oversion = "0.7.0"
+version = '2.0.2'
+String bfversion = "7.3.0"
+String b2rversion = "0.9.3"
+String r2oversion = "0.7.1"
 
 mainClassName = 'com.glencoesoftware.convert.Launcher'
 applicationName = 'NGFF-Converter'

src/main/java/com/glencoesoftware/convert/tasks/CreateNGFF.java

@@ -57,7 +57,7 @@ public enum prefKeys {LOG_LEVEL, MAX_WORKERS, COMPRESSION, TILE_WIDTH, TILE_HEIG
         DIMENSION_ORDER, DOWNSAMPLING, MIN_IMAGE_SIZE, REUSE_RES, CHUNK_DEPTH, SCALE_FORMAT_STRING, SCALE_FORMAT_CSV,
         FILL_VALUE, BLOSC_CNAME, BLOSC_CLEVEL, BLOSC_BLOCKSIZE, BLOSC_SHUFFLE, ZLIB_LEVEL,
         MAX_CACHED_TILES, MIN_MAX, HCS, NESTED, OME_META, NO_ROOT, PYRAMID_NAME, KEEP_MEMOS, MEMO_DIR,
-        READER_OPTS, OUTPUT_OPTS, EXTRA_READERS
+        READER_OPTS, OUTPUT_OPTS, EXTRA_READERS, WRITE_METADATA
     }
 
 
@@ -91,6 +91,7 @@ public enum prefKeys {LOG_LEVEL, MAX_WORKERS, COMPRESSION, TILE_WIDTH, TILE_HEIG
     private static final ToggleSwitch disableMinMax;
     private static final ToggleSwitch disableHCS;
     private static final ToggleSwitch nested;
+    private static final ToggleSwitch originalMeta;
     private static final ToggleSwitch noOMEMeta;
     private static final ToggleSwitch noRoot;
     private static final TextField pyramidName;
@@ -175,6 +176,7 @@ public void prepareForDisplay() {
         disableMinMax.setSelected(converter.getCalculateOMEROMetadata());
         disableHCS.setSelected(converter.getNoHCS());
         nested.setSelected(converter.getNested());
+        originalMeta.setSelected(converter.getOriginalMetadata());
         noOMEMeta.setSelected(converter.getNoOMEMeta());
         noRoot.setSelected(converter.getNoRootGroup());
         pyramidName.setText(converter.getPyramidName());
@@ -263,6 +265,7 @@ public int applySettings() {
         converter.setNoHCS(disableHCS.isSelected());
 
         converter.setUnnested(!nested.isSelected());
+        converter.setNoOriginalMetadata(!originalMeta.isSelected());
         converter.setNoOMEMeta(noOMEMeta.isSelected());
         converter.setNoRootGroup(noRoot.isSelected());
         if (pyramidName.getText() != null && !pyramidName.getText().isEmpty())
@@ -323,6 +326,7 @@ public void cloneValues(BaseTask sourceInstance) {
         converter.setCalculateOMEROMetadata(source.converter.getCalculateOMEROMetadata());
         converter.setNoHCS(source.converter.getNoHCS());
         converter.setUnnested(!source.converter.getNested());
+        converter.setNoOriginalMetadata(!source.converter.getOriginalMetadata());
         converter.setNoOMEMeta(source.converter.getNoOMEMeta());
         converter.setNoRootGroup(source.converter.getNoRootGroup());
         converter.setPyramidName(source.converter.getPyramidName());
@@ -652,6 +656,16 @@ Default value to fill in for missing tiles (0-255)
                 """
         ));
 
+        originalMeta = new ToggleSwitch();
+        advancedSettings.add(getSettingContainer(
+                originalMeta,
+                "Write original metadata",
+                """
+                Write original metadata key/values
+                into NGFF file OME-XML metadata.
+                """
+        ));
+
         noOMEMeta = new ToggleSwitch();
         advancedSettings.add(getSettingContainer(
                 noOMEMeta,
@@ -890,6 +904,7 @@ public void setDefaults() throws BackingStoreException {
         taskPreferences.putBoolean(prefKeys.MIN_MAX.name(), converter.getCalculateOMEROMetadata());
         taskPreferences.putBoolean(prefKeys.HCS.name(), converter.getNoHCS());
         taskPreferences.putBoolean(prefKeys.NESTED.name(), converter.getNested());
+        taskPreferences.putBoolean(prefKeys.WRITE_METADATA.name(), converter.getOriginalMetadata());
         taskPreferences.putBoolean(prefKeys.OME_META.name(), converter.getNoOMEMeta());
         taskPreferences.putBoolean(prefKeys.NO_ROOT.name(), converter.getNoRootGroup());
         if (converter.getPyramidName() != null) {
@@ -957,6 +972,8 @@ public void applyDefaults() {
                 prefKeys.MIN_MAX.name(), converter.getCalculateOMEROMetadata()));
         converter.setNoHCS(taskPreferences.getBoolean(prefKeys.HCS.name(), converter.getNoHCS()));
         converter.setUnnested(!taskPreferences.getBoolean(prefKeys.NESTED.name(), converter.getNested()));
+        converter.setNoOriginalMetadata(
+                !taskPreferences.getBoolean(prefKeys.WRITE_METADATA.name(), converter.getOriginalMetadata()));
         converter.setNoOMEMeta(taskPreferences.getBoolean(prefKeys.OME_META.name(), converter.getNoOMEMeta()));
         converter.setNoRootGroup(taskPreferences.getBoolean(prefKeys.NO_ROOT.name(), converter.getNoRootGroup()));
         converter.setPyramidName(taskPreferences.get(prefKeys.PYRAMID_NAME.name(), converter.getPyramidName()));
@@ -1064,6 +1081,8 @@ public void exportSettings(JsonGenerator generator) throws IOException {
         generator.writeBoolean(converter.getNoHCS());
         generator.writeFieldName(prefKeys.NESTED.name());
         generator.writeBoolean(converter.getNested());
+        generator.writeFieldName(prefKeys.WRITE_METADATA.name());
+        generator.writeBoolean(converter.getOriginalMetadata());
         generator.writeFieldName(prefKeys.OME_META.name());
         generator.writeBoolean(converter.getNoOMEMeta());
         generator.writeFieldName(prefKeys.NO_ROOT.name());
@@ -1169,6 +1188,9 @@ public void importSettings(JsonNode mainNode) {
         subject = settings.get(prefKeys.NESTED.name());
         if (subject != null) nested.setSelected(subject.booleanValue());
 
+        subject = settings.get(prefKeys.WRITE_METADATA.name());
+        if (subject != null) originalMeta.setSelected(subject.booleanValue());
+
         subject = settings.get(prefKeys.OME_META.name());
         if (subject != null) noOMEMeta.setSelected(subject.booleanValue());