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ZarrReader: Update handling of pre-existing plate metadata #49

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Mar 23, 2023
Merged

ZarrReader: Update handling of pre-existing plate metadata #49

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71 changes: 46 additions & 25 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,8 @@
import ome.xml.meta.MetadataRoot;
import ome.xml.model.MapAnnotation;
import ome.xml.model.OME;
import ome.xml.model.Plate;
import ome.xml.model.Screen;
import ome.xml.model.StructuredAnnotations;
import ome.xml.model.primitives.NonNegativeInteger;
import ome.xml.model.primitives.PositiveInteger;
Expand Down Expand Up @@ -548,19 +550,31 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
}
}
}
for (int c = 0; c < columns.size(); c++) {
Map<String, Object> column = (Map<String, Object>) columns.get(c);
String colName = (String) column.get("name");
}

// TODO: Likely remove as values unused
// for (int c = 0; c < columns.size(); c++) {
// Map<String, Object> column = (Map<String, Object>) columns.get(c);
// String colName = (String) column.get("name");
// }
// for (int r = 0; r < rows.size(); r++) {
// Map<String, Object> row = (Map<String, Object>) rows.get(r);
// String rowName = (String) row.get("name");
// }

//Create empty wells for each row and column
wellCount = rows.size() * columns.size();
for (int r = 0; r < rows.size(); r++) {
Map<String, Object> row = (Map<String, Object>) rows.get(r);
String rowName = (String) row.get("name");
for (int c = 0; c < columns.size(); c++) {
int wellIndex = (r * columns.size()) + c;
String well_id = MetadataTools.createLSID("Well", 0, wellIndex);
store.setWellID(well_id, 0, wellIndex);
store.setWellRow(new NonNegativeInteger(r), 0, wellIndex);
store.setWellColumn(new NonNegativeInteger(c), 0, wellIndex);
}
}
for (int w = 0; w < wells.size(); w++) {
Map<String, Object> well = (Map<String, Object>) wells.get(w);
String wellPath = (String) well.get("path");
String well_id = MetadataTools.createLSID("Well", wellCount);
store.setWellID(well_id, 0, w);

// column_index & row_index stored as Integer in bioformats2raw 0.3
Integer wellColIndex = (Integer) well.get("column_index");
Expand All @@ -570,29 +584,23 @@ private void parsePlate(String root, String key, MetadataStore store) throws IOE
wellColIndex = (Integer) well.get("columnIndex");
wellRowIndex = (Integer) well.get("rowIndex");
}
if (wellColIndex != null && wellRowIndex != null) {
store.setWellRow(new NonNegativeInteger(wellRowIndex), 0, w);
store.setWellColumn(new NonNegativeInteger(wellColIndex), 0, w);
}
else {
if (wellColIndex == null || wellRowIndex == null) {
// for OME-NGFF v0.2 parse row and column index from the path
String[] parts = wellPath.split("/");
String wellRow = parts[parts.length - 2];
String wellCol = parts[parts.length - 1];
int rowIndex = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".indexOf(wellRow.toUpperCase());
if (rowIndex == -1) {
rowIndex = Integer.parseInt(wellRow);
wellRowIndex = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".indexOf(wellRow.toUpperCase());
if (wellRowIndex == -1) {
wellRowIndex = Integer.parseInt(wellRow);
}
int colIndex = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".indexOf(wellCol.toUpperCase());
if (colIndex == -1) {
colIndex = Integer.parseInt(wellCol);
wellColIndex = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".indexOf(wellCol.toUpperCase());
if (wellColIndex == -1) {
wellColIndex = Integer.parseInt(wellCol);
}
store.setWellRow(new NonNegativeInteger(rowIndex), 0, w);
store.setWellColumn(new NonNegativeInteger(colIndex), 0, w);
}
store.setWellExternalIdentifier(wellPath, 0, w);
parseWells(root, wellPath, store, 0, w, acqIdsIndexMap);
wellCount++;
int wellIndex = (wellRowIndex * columns.size()) + wellColIndex;
store.setWellExternalIdentifier(wellPath, 0, wellIndex);
parseWells(root, wellPath, store, 0, wellIndex, acqIdsIndexMap);
}
}
}
Expand All @@ -611,7 +619,7 @@ private void parseWells(String root, String key, MetadataStore store, int plateI
if (acqIdsIndexMap.containsKey(acquisition)) {
acquisition = acqIdsIndexMap.get(acquisition);
}
String site_id = MetadataTools.createLSID("WellSample", wellSamplesCount);
String site_id = MetadataTools.createLSID("WellSample", plateIndex, wellIndex, i);
store.setWellSampleID(site_id, plateIndex, wellIndex, i);
store.setWellSampleIndex(new NonNegativeInteger(i), plateIndex, wellIndex, i);
String imageRefPath = "" + i;
Expand Down Expand Up @@ -814,6 +822,19 @@ private void parseOMEXML(Location omeMetaFile, MetadataStore store) throws IOExc
root.setStructuredAnnotations(annotations);
omexmlMeta.setRoot((MetadataRoot) root);
}

// Remove old Screen and Plate metadata
int screenSize = root.sizeOfScreenList();
for (int i = 0; i < screenSize; i++) {
root.removeScreen(root.getScreen(i));
}

int plateSize = root.sizeOfPlateList();
for (int i = 0; i < plateSize; i++) {
root.removePlate(root.getPlate(i));
}

omexmlMeta.setRoot((MetadataRoot) root);

MetadataConverter.convertMetadata( omexmlMeta, store );
}
Expand Down