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Fix class cast and labels issue. #98

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Fix class cast and labels issue. #98

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3b3cda8
Update all actions to v4
melissalinkert Oct 24, 2024
0adcd0b
Channel coeff can be Integer or Double
dominikl Oct 28, 2024
6a2f882
Fix issue if 'labels' part of filename
dominikl Oct 29, 2024
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6 changes: 3 additions & 3 deletions .github/workflows/maven.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
run: mvn ${{ env.maven_commands }}
- name: Upload JAR as artifact
if: matrix.os == 'ubuntu-latest' && matrix.java == '1.8'
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: ZarrReader
path: target/*.jar
Expand Down Expand Up @@ -71,7 +71,7 @@ jobs:
needs: build
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
- name: Retrieve version
id: get_version
run: |
Expand All @@ -86,7 +86,7 @@ jobs:
echo server='ome.releases' >> $GITHUB_OUTPUT
fi
- name: Set up Repository
uses: actions/setup-java@v3
uses: actions/setup-java@v4
with:
java-version: 8
distribution: 'zulu'
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29 changes: 16 additions & 13 deletions src/loci/formats/in/ZarrReader.java
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Expand Up @@ -5,7 +5,7 @@
* #%L
* Implementation of Bio-Formats readers for the next-generation file formats
* %%
* Copyright (C) 2020 - 2022 Open Microscopy Environment
* Copyright (C) 2020 - 2024 Open Microscopy Environment
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
Expand Down Expand Up @@ -44,7 +44,6 @@
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Stream;

import javax.xml.parsers.ParserConfigurationException;
Expand All @@ -68,17 +67,13 @@
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.in.DynamicMetadataOptions;
import loci.formats.in.MetadataOptions;
import loci.formats.meta.MetadataStore;
import loci.formats.ome.OMEXMLMetadata;
import loci.formats.services.JZarrServiceImpl;
import ome.xml.meta.MetadataConverter;
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 @@ -930,7 +925,9 @@ private void parseOmeroMetadata(String root, Map<String, Object> attr) throws IO
for (int i = 0; i < channels.size(); i++) {
Map<String, Object> channel = (Map<String, Object>) channels.get(i);
Boolean channelActive = (Boolean) channel.get("active");
Double channelCoefficient = (Double) channel.get("coefficient");
Double channelCoefficient = channel.get("coefficient") instanceof Double ?
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See also #95 an alternative to the intanceof check would be to read these as Number

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Ah thanks, so that actually already has been fixed in another PR, should have checked properly. Maybe we could merge the other PR first...

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Only obvious caveat is that #95 needs additional work to get the test to compile first. But if that was the preferred option, no objection from my side to splitting these fixes into 2 separate PRs.

((Double) channel.get("coefficient")) :
((Integer) channel.get("coefficient")).doubleValue();
String channelColor = (String) channel.get("color");
String channelFamily = (String) channel.get("family");
Boolean channelInverted = (Boolean) channel.get("inverted");
Expand Down Expand Up @@ -1125,19 +1122,25 @@ private Double getDouble(Map<String, Object> src, String key) {
public String[] getUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
String zarrRootPath = currentId.substring(0, currentId.indexOf(".zarr") + 5);
int rootPathLength = zarrRootPath.length();
ArrayList<String> usedFiles = new ArrayList<String>();
reloadOptionsFile(zarrRootPath);

boolean skipPixels = noPixels || !listPixels() || !systemEnvListPixels();
boolean includeLabels = includeLabels();
try (Stream<Path> paths = Files.walk(Paths.get(zarrRootPath), FileVisitOption.FOLLOW_LINKS)) {
paths.filter(Files::isRegularFile)
.forEach(path -> {if ((!skipPixels && includeLabels) ||
(!skipPixels && !includeLabels && !path.toString().toLowerCase().contains("labels")) ||
(skipPixels && includeLabels && (path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))) ||
(skipPixels && !includeLabels && !path.toString().toLowerCase().contains("labels") &&(path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))))
usedFiles.add(path.toFile().getAbsolutePath());
});
.forEach(path -> {
if (
(!skipPixels && includeLabels) ||
(!skipPixels && !includeLabels && (path.toString().toLowerCase().lastIndexOf("labels")<rootPathLength) ||
(skipPixels && includeLabels && (path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml"))) ||
(skipPixels && !includeLabels && (path.toString().toLowerCase().lastIndexOf("labels")<rootPathLength) &&(path.endsWith(".zgroup") || path.endsWith(".zattrs") || path.endsWith(".xml")))))
{
usedFiles.add(path.toFile().getAbsolutePath());
}
}
);
} catch (IOException e) {
e.printStackTrace();
}
Expand Down