Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bump dependencies #68

Merged
merged 2 commits into from
Jun 4, 2024
Merged

Bump dependencies #68

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
6328bd5
Update dependencies
DavidStirling May 30, 2024
95b45a5
Fix inversion
DavidStirling May 30, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 13 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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:
Expand Down
8 changes: 4 additions & 4 deletions build.gradle
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
24 changes: 23 additions & 1 deletion src/main/java/com/glencoesoftware/convert/tasks/CreateNGFF.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
}


Expand Down Expand Up @@ -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;
Expand Down Expand Up @@ -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());
Expand Down Expand Up @@ -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())
Expand Down Expand Up @@ -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());
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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) {
Expand Down Expand Up @@ -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()));
Expand Down Expand Up @@ -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());
Expand Down Expand Up @@ -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());

Expand Down
Loading