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Add setFilePatternIds method to ImporterOptions #3019

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merged 1 commit into from Jan 18, 2018
Merged

Add setFilePatternIds method to ImporterOptions #3019

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7 changes: 5 additions & 2 deletions components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java
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Expand Up @@ -48,6 +48,7 @@
import loci.formats.ChannelSeparator;
import loci.formats.ClassList;
import loci.formats.DimensionSwapper;
import loci.formats.FilePattern;
import loci.formats.FileStitcher;
import loci.formats.FormatException;
import loci.formats.FormatTools;
Expand Down Expand Up @@ -495,7 +496,8 @@ private void initializeFile() throws FormatException, IOException {
baseReader.getMetadataOptions().setMetadataLevel(
MetadataLevel.NO_OVERLAYS);
}
baseReader.setId(options.getId());
baseReader.setId(options.isUsingPatternIds() ?
new FilePattern(options.getId()).getFiles()[0] : options.getId());

boolean mustGroup = baseReader.fileGroupOption(options.getId()) == FormatTools.MUST_GROUP;
options.setMustGroup(mustGroup);
Expand Down Expand Up @@ -615,7 +617,8 @@ private void createBaseReader() throws FormatException, IOException {
if (options.isLocal() || options.isHTTP()) {
BF.status(options.isQuiet(), "Identifying " + idName);
imageReader = LociPrefs.makeImageReader();
baseReader = imageReader.getReader(options.getId());
baseReader = imageReader.getReader(options.isUsingPatternIds() ?
new FilePattern(options.getId()).getFiles()[0] : options.getId());
}
else if (options.isOMERO()) {
BF.status(options.isQuiet(), "Establishing server connection");
Expand Down
6 changes: 6 additions & 0 deletions components/bio-formats-plugins/src/loci/plugins/in/ImporterOptions.java
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Expand Up @@ -154,6 +154,9 @@ public class ImporterOptions extends OptionsList {
private List<List<DoubleOption>> customColors =
new ArrayList<List<DoubleOption>>();

// whether to treat the given id as a file pattern directly
private boolean usePatternIds;

// -- Constructor --

public ImporterOptions() throws IOException {
Expand Down Expand Up @@ -510,6 +513,9 @@ public String getCustomColorKey(int s, int c) {
return s + "_" + c;
}

public boolean isUsingPatternIds() { return usePatternIds; }
public void setUsingPatternIds(boolean b) { usePatternIds = b; }

// -- Helper methods --

private <T extends Object> void set(List<T> list,
Expand Down