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

Reduce number of fields in memo file #78

Merged
merged 3 commits into from
Feb 20, 2024
Merged

Reduce number of fields in memo file #78

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
153a466
Reduce number of fields in memo file
dgault Feb 8, 2024
0130777
Don't populate originalMetadata by default
dgault Feb 11, 2024
75814b4
Don't copy over any original annotations
dgault Feb 11, 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
79 changes: 47 additions & 32 deletions src/loci/formats/in/ZarrReader.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -99,15 +99,18 @@ public class ZarrReader extends FormatReader {
public static final boolean INCLUDE_LABELS_DEFAULT = false;
protected transient ZarrService zarrService;
private ArrayList<String> arrayPaths = new ArrayList<String>();
private ArrayList<String> groupKeys = new ArrayList<String>();
private HashMap<Integer, ArrayList<String>> resSeries = new HashMap<Integer, ArrayList<String>>();
private HashMap<String, Integer> resCounts = new HashMap<String, Integer>();
private HashSet<Integer> uniqueResCounts = new HashSet<Integer>();
private HashMap<String, Integer> resIndexes = new HashMap<String, Integer>();

// The below fields are only required for initialization and are not required to be serialized
private transient ArrayList<String> groupKeys = new ArrayList<String>();
private transient HashMap<Integer, ArrayList<String>> resSeries = new HashMap<Integer, ArrayList<String>>(); // can be removed
private transient HashMap<String, Integer> resCounts = new HashMap<String, Integer>(); // can be removed
private transient HashSet<Integer> uniqueResCounts = new HashSet<Integer>(); // can be removed
private transient HashMap<String, Integer> resIndexes = new HashMap<String, Integer>(); // can be removed
private transient HashMap<String, ArrayList<String>> pathArrayDimensions = new HashMap<String, ArrayList<String>>(); // can be removed

private String dimensionOrder = "XYZCT";
private int wellCount = 0;
private int wellSamplesCount = 0;
private HashMap<String, ArrayList<String>> pathArrayDimensions = new HashMap<String, ArrayList<String>>();
private boolean planesPrePopulated = false;
private boolean hasSPW = false;
private transient int currentOpenZarr = -1;
Expand Down Expand Up @@ -200,15 +203,17 @@ protected void initFile(String id) throws FormatException, IOException {
if (attr != null && !attr.isEmpty()) {
parseResolutionCount(zarrRootPath, "", attr);
parseOmeroMetadata(zarrRootPath, attr);
String jsonAttr;
try {
jsonAttr = ZarrUtils.toJson(attr, true);
store.setXMLAnnotationValue(jsonAttr, attrIndex);
String xml_id = MetadataTools.createLSID("Annotation", attrIndex);
store.setXMLAnnotationID(xml_id, attrIndex);
} catch (JZarrException e) {
LOGGER.warn("Failed to convert attributes to JSON");
e.printStackTrace();
if (saveAnnotations()) {
String jsonAttr;
try {
jsonAttr = ZarrUtils.toJson(attr, true);
store.setXMLAnnotationValue(jsonAttr, attrIndex);
String xml_id = MetadataTools.createLSID("Annotation", attrIndex);
store.setXMLAnnotationID(xml_id, attrIndex);
} catch (JZarrException e) {
LOGGER.warn("Failed to convert attributes to JSON");
e.printStackTrace();
}
}
}
generateGroupKeys(attr, canonicalPath);
Expand Down Expand Up @@ -961,8 +966,10 @@ private void parseOMEXML(Location omeMetaFile, MetadataStore store, ArrayList<St
{
service = new ServiceFactory().getInstance( OMEXMLService.class );
omexmlMeta = service.createOMEXMLMetadata( xml );
Hashtable originalMetadata = service.getOriginalMetadata(omexmlMeta);
if (originalMetadata != null) metadata = originalMetadata;
if (saveAnnotations()) {
Hashtable originalMetadata = service.getOriginalMetadata(omexmlMeta);
if (originalMetadata != null) metadata = originalMetadata;
}
planesPrePopulated = true;
}
catch (DependencyException | ServiceException | NullPointerException e1 )
Expand Down Expand Up @@ -1034,24 +1041,32 @@ private void parseOMEXML(Location omeMetaFile, MetadataStore store, ArrayList<St
}
setSeries(oldSeries);

// Remove old PyramidResolution annotations
OME root = (OME) omexmlMeta.getRoot();
StructuredAnnotations annotations = root.getStructuredAnnotations();
if (annotations != null) {
int numMapAnnotations = annotations.sizeOfMapAnnotationList();
int index = 0;
for (int i = 0; i < numMapAnnotations; i++) {
MapAnnotation mapAnnotation = annotations.getMapAnnotation(index);
String namespace = mapAnnotation.getNamespace();
if (namespace != null && namespace.toLowerCase().contains("pyramidresolution")) {
annotations.removeMapAnnotation(mapAnnotation);
}
else {
index++;

// Optionally remove all annotations
if (!saveAnnotations()) {
root.setStructuredAnnotations(null);
omexmlMeta.setRoot((MetadataRoot) root);
}
else {
// Remove old PyramidResolution annotations
StructuredAnnotations annotations = root.getStructuredAnnotations();
if (annotations != null) {
int numMapAnnotations = annotations.sizeOfMapAnnotationList();
int index = 0;
for (int i = 0; i < numMapAnnotations; i++) {
MapAnnotation mapAnnotation = annotations.getMapAnnotation(index);
String namespace = mapAnnotation.getNamespace();
if (namespace != null && namespace.toLowerCase().contains("pyramidresolution")) {
annotations.removeMapAnnotation(mapAnnotation);
}
else {
index++;
}
}
root.setStructuredAnnotations(annotations);
omexmlMeta.setRoot((MetadataRoot) root);
}
root.setStructuredAnnotations(annotations);
omexmlMeta.setRoot((MetadataRoot) root);
}

// Remove old Screen and Plate metadata
Expand Down
Loading