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Add initial conversion for OME-NGFF keys according to RFC-2 #7

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Add initial conversion for OME-NGFF keys according to RFC-2 #7

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35 changes: 30 additions & 5 deletions src/main/java/com/glencoesoftware/zarr/Convert.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@
import java.util.concurrent.Callable;
import java.util.Arrays;
import java.util.List;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;

Expand All @@ -61,6 +62,13 @@ public class Convert implements Callable<Integer> {

private static final String RESERVED_KEY = "zarr.json";

private static final String[] OME_NGFF_KEYS = new String[]{
"bioformats2raw.layout",
"plate",
"well",
"multiscales"
};

private String inputLocation;
private String outputLocation;
private String logLevel = "INFO";
Expand Down Expand Up @@ -176,6 +184,23 @@ public Integer call() throws Exception {
return 0;
}

/**
* Convert OME-NGFF attributes from 0.4 to 0.5 according to RFC-2
*/
public Map<String, Object> convertToV3(Map<String, Object> attributes) throws Exception {
Map<String, Object> ome = new HashMap<String, Object>();
for (String key: OME_NGFF_KEYS) {
if (attributes.containsKey(key)) {
ome.put(key, attributes.get(key));
attributes.remove(key);
}
}
ome.put("version", "0.5");
attributes.put("ome", ome);
return attributes;
}


/**
* Read v2 input data with jzarr, and write to v3 using zarr-java.
*/
Expand All @@ -199,11 +224,11 @@ public void convertToV3() throws Exception {
LOGGER.debug("opening v3 root group: {}", outputLocation);
FilesystemStore outputStore = new FilesystemStore(outputLocation);
Group outputRootGroup = Group.create(outputStore.resolve());
outputRootGroup.setAttributes(attributes);
outputRootGroup.setAttributes(convertToV3(attributes));

// copy OME-XML file
Group outputOMEGroup = Group.create(outputStore.resolve("OME"));
outputOMEGroup.setAttributes(omeGroup.getAttributes());
outputOMEGroup.setAttributes(convertToV3(omeGroup.getAttributes()));
Files.copy(Paths.get(inputLocation, "OME", "METADATA.ome.xml"),
Paths.get(outputLocation, "OME", "METADATA.ome.xml"));

Expand All @@ -221,7 +246,7 @@ public void convertToV3() throws Exception {
LOGGER.info("got {} series attributes", seriesAttributes.size());

Group outputSeriesGroup = Group.create(outputStore.resolve(seriesGroupKey));
outputSeriesGroup.setAttributes(seriesAttributes);
outputSeriesGroup.setAttributes(convertToV3(seriesAttributes));

Set<String> columnKeys = seriesGroup.getGroupKeys();
// "pass through" if this is not HCS
Expand All @@ -241,7 +266,7 @@ public void convertToV3() throws Exception {
if (!columnKey.isEmpty()) {
Map<String, Object> columnAttributes = column.getAttributes();
Group outputColumnGroup = Group.create(outputStore.resolve(seriesGroupKey, columnKey));
outputColumnGroup.setAttributes(columnAttributes);
outputColumnGroup.setAttributes(convertToV3(columnAttributes));
}

Set<String> fieldKeys = column.getGroupKeys();
Expand All @@ -259,7 +284,7 @@ public void convertToV3() throws Exception {
Map<String, Object> fieldAttributes = field.getAttributes();
if (!fieldKey.isEmpty()) {
Group outputFieldGroup = Group.create(outputStore.resolve(seriesGroupKey, columnKey, fieldKey));
outputFieldGroup.setAttributes(fieldAttributes);
outputFieldGroup.setAttributes(convertToV3(fieldAttributes));
}

// calculate the number of resolutions
Expand Down
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