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Add new option to list pixels in getUsedFiles #58

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Add new option to list pixels in getUsedFiles #58

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c1f4a2b
Add new option to list pixels in getUsedFiles
dgault Jul 7, 2023
8230a39
GetUsedFiles: Update logic to skip pixel files
dgault Jul 7, 2023
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28 changes: 26 additions & 2 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -93,6 +93,9 @@ public class ZarrReader extends FormatReader {
private HashMap<String, ArrayList<String>> pathArrayDimensions = new HashMap<String, ArrayList<String>>();
private boolean planesPrePopulated = false;
private boolean hasSPW = false;

public static final String LIST_PIXELS_KEY = "omezarr.list_pixels";
public static final boolean LIST_PIXELS_DEFAULT = false;

public ZarrReader() {
super("Zarr", "zarr");
Expand Down Expand Up @@ -863,9 +866,13 @@ public String[] getUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
ArrayList<String> usedFiles = new ArrayList<String>();
boolean skipPixels = noPixels || !listPixels();
try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath), FileVisitOption.FOLLOW_LINKS)) {
paths.filter(Files::isRegularFile)
.forEach(path -> usedFiles.add(path.toFile().getAbsolutePath()));
paths.filter(Files::isRegularFile)
.forEach(path -> {if (!skipPixels ||
(skipPixels && (path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))))
usedFiles.add(path.toFile().getAbsolutePath());
});
} catch (IOException e) {
e.printStackTrace();
}
Expand All @@ -883,4 +890,21 @@ public String[] getDomains() {
FormatTools.NON_SPECIAL_DOMAINS;
}

/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected ArrayList<String> getAvailableOptions() {
ArrayList<String> optionsList = super.getAvailableOptions();
optionsList.add(LIST_PIXELS_KEY);
return optionsList;
}

public boolean listPixels() {
MetadataOptions options = getMetadataOptions();
if (options instanceof DynamicMetadataOptions) {
return ((DynamicMetadataOptions) options).getBoolean(
LIST_PIXELS_KEY, LIST_PIXELS_DEFAULT);
}
return LIST_PIXELS_DEFAULT;
}

}