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FileStitcher: do not use detected patterns that include missing files #3129

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Jul 2, 2018
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FileStitcher: do not use detected patterns that include missing files #3129

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36 changes: 32 additions & 4 deletions components/formats-bsd/src/loci/formats/FileStitcher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
package loci.formats;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
Expand Down Expand Up @@ -969,10 +970,28 @@ protected void initFile(String id) throws FormatException, IOException {

String[] patterns = findPatterns(id);
if (patterns.length == 0) patterns = new String[] {id};
externals = new ExternalSeries[patterns.length];

for (int i=0; i<externals.length; i++) {
externals[i] = new ExternalSeries(new FilePattern(patterns[i]));
// catching FileNotFoundException here and during setId below
// allows us to filter out patterns that include missing files
// the exception is caught instead of proactively checking for
// new Location(...).exists() so that patterns consisting of
// .fake files that do not exist on disk continue to be supported
List<ExternalSeries> validExternals = new ArrayList<ExternalSeries>();
for (int i=0; i<patterns.length; i++) {
try {
ExternalSeries e = new ExternalSeries(new FilePattern(patterns[i]));
validExternals.add(e);
}
catch (FileNotFoundException e) {
LOGGER.trace("Could not use pattern " + patterns[i], e);
}
}
if (validExternals.size() == 0) {
patterns = new String[] {id};
externals = new ExternalSeries[] {new ExternalSeries(new FilePattern(id))};
}
else {
externals = validExternals.toArray(new ExternalSeries[validExternals.size()]);
}
fp = new FilePattern(patterns[0]);

Expand All @@ -982,7 +1001,16 @@ protected void initFile(String id) throws FormatException, IOException {
if (!fp.isValid()) {
throw new FormatException("Invalid file pattern: " + fp.getPattern());
}
reader.setId(fp.getFiles()[0]);
try {
reader.setId(fp.getFiles()[0]);
}
catch (FileNotFoundException e) {
LOGGER.trace("Could not use pattern " + patterns[0], e);
patterns = new String[] {id};
fp = new FilePattern(id);
externals = new ExternalSeries[] {new ExternalSeries(fp)};
reader.setId(fp.getFiles()[0]);
}

String msg = " Please rename your files or disable file stitching.";
if (reader.getCoreMetadataList().size() > 1 && externals.length > 1) {
Expand Down