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BDV: store relative path instead of absolute #4440

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BDV: store relative path instead of absolute #4440

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18 changes: 13 additions & 5 deletions components/formats-bsd/src/loci/formats/in/BDVReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -154,7 +154,7 @@ protected void initFile(String id) throws FormatException, IOException {
store.setXMLAnnotationValue(bdvxml, 0);
String xml_id = MetadataTools.createLSID("XMLAnnotation", 0);
store.setXMLAnnotationID(xml_id, 0);
initializeJHDFService(h5Id);
initializeJHDFService(fetchH5Path());
parseStructure();

// The ImageJ RoiManager can not distinguish ROIs from different
Expand All @@ -181,6 +181,15 @@ private String fetchXMLId() throws FormatException {
return xmlId;
}

private String fetchH5Path() {
Location location = new Location(currentId).getAbsoluteFile();
Location parent = location.getParentFile();
if (h5Id != null) {
return new Location(parent, h5Id).getAbsolutePath();
}
return null;
}

/* @see loci.formats.IFormatReader#getUsedFiles(boolean) */
@Override
public String[] getUsedFiles(boolean noPixels) {
Expand All @@ -193,7 +202,7 @@ public String[] getUsedFiles(boolean noPixels) {
LOGGER.error("Unable to locate associated BDV XML for file: " + currentId);
}
}
return new String[] {xmlId, h5Id};
return new String[] {xmlId, fetchH5Path()};
}

/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
Expand Down Expand Up @@ -362,7 +371,7 @@ public void close(boolean fileOnly) throws IOException {
@Override
public void reopenFile() throws IOException {
try {
initializeJHDFService(h5Id);
initializeJHDFService(fetchH5Path());
}
catch (MissingLibraryException e) {
throw new IOException(e);
Expand Down Expand Up @@ -795,8 +804,7 @@ public void characters(char[] ch, int start, int length) {
if (currentQName.toLowerCase().equals("hdf5")) {
String hdf5Contents = new String(ch, start, length);
if (checkSuffix(hdf5Contents, "h5")) {
String parent = new Location(currentId).getAbsoluteFile().getParent();
h5Id = parent + File.separator + hdf5Contents;
h5Id = hdf5Contents;
}
}
if (parsingTimepoints && currentQName.toLowerCase().equals("first")) {
Expand Down
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