5 basic image handling

.github/workflows/maven.yml

@@ -15,19 +15,77 @@ on:
     release:
       types: [published, edited]
 
+
+
 jobs:
-  build:
 
+  build:
     runs-on: ubuntu-latest
+    env:
+      AWS_ACCESS_KEY_ID: jj
+      AWS_SECRET_ACCESS_KEY: jj
+      AWS_DEFAULT_REGION: 'site2-low'
+      AWS_ENDPOINT_URL: "http://127.0.0.1:4000"
+
+
+
+#    https://docs.github.com/en/actions/using-containerized-services/about-service-containers
+    services:
+      s3proxy:
+        image: andrewgaul/s3proxy
+        ports:
+          - 4000:80
+        env:
+          JCLOUDS_FILESYSTEM_BASEDIR: /data
+          JCLOUDS_PROVIDER: filesystem
+          JCLOUDS_REGIONS: site2-low
+          S3PROXY_IDENTITY: jj
+          S3PROXY_CREDENTIAL: jj
+
+          LOG_LEVEL: info
+          S3PROXY_ENDPOINT: http://0.0.0.0:80
+          S3PROXY_AUTHORIZATION: "aws-v2-or-v4"
+          S3PROXY_VIRTUALHOST: ""
+          S3PROXY_KEYSTORE_PATH: keystore.jks
+          S3PROXY_KEYSTORE_PASSWORD: password
+          S3PROXY_CORS_ALLOW_ALL: false
+          S3PROXY_CORS_ALLOW_ORIGINS: ""
+          S3PROXY_CORS_ALLOW_METHODS: ""
+          S3PROXY_CORS_ALLOW_HEADERS: ""
+          S3PROXY_IGNORE_UNKNOWN_HEADERS: false
+          S3PROXY_ENCRYPTED_BLOBSTORE: ""
+          S3PROXY_ENCRYPTED_BLOBSTORE_PASSWORD: ""
+          S3PROXY_ENCRYPTED_BLOBSTORE_SALT: ""
+
+          JCLOUDS_ENDPOINT: ""
+          JCLOUDS_REGION: ""
+          JCLOUDS_IDENTITY: remote-identity
+          JCLOUDS_CREDENTIAL: remote-credential
+          JCLOUDS_KEYSTONE_VERSION: ""
+          JCLOUDS_KEYSTONE_SCOPE: ""
+          JCLOUDS_KEYSTONE_PROJECT_DOMAIN_NAME: ""
+        volumes:
+          - /dockerImage/data:/data
 
     steps:
     - uses: actions/checkout@v3
+
+    - name: Put test resources in S3Proxy Container
+      run: |
+        aws s3 mb s3://nfive
+        aws s3 cp ${{ github.workspace }}/src/test/resources/nfive s3://nfive --recursive
+
     - name: Set up JDK 8
       uses: actions/setup-java@v3
       with:
         java-version: '8'
         distribution: 'temurin'
         cache: maven
+
+    #Before building the Repo a docker container needs to intialized such that the test cases can work properly
+#    https://github.com/addnab/docker-run-action
+
+
     - name: Build with Maven
       run: mvn -B package --file pom.xml
 

pom.xml

@@ -117,10 +117,10 @@
             <artifactId>scijava-ui-swing</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>org.scijava</groupId>
-            <artifactId>scijava-ui-awt</artifactId>
-        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>org.scijava</groupId>-->
+<!--            <artifactId>scijava-ui-awt</artifactId>-->
+<!--        </dependency>-->
 
         <dependency>
             <groupId>net.imagej</groupId>
@@ -131,22 +131,67 @@
             <groupId>org.scijava</groupId>
             <artifactId>scijava-plugins-commands</artifactId>
             <scope>runtime</scope>
+             <version>0.2.4</version>
         </dependency>
 
+<!--        <dependency>-->
+<!--            <groupId>org.apache.httpcomponents</groupId>-->
+<!--            <artifactId>httpclient</artifactId>-->
+<!--        </dependency>-->
+
+<!--        <dependency>-->
+<!--            <groupId>org.scijava</groupId>-->
+<!--            <artifactId>scijava-listeners</artifactId>-->
+<!--        </dependency>-->
+
+        <!-- https://mvnrepository.com/artifact/org.janelia.saalfeldlab/n5 -->
         <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpclient</artifactId>
+            <groupId>org.janelia.saalfeldlab</groupId>
+            <artifactId>n5</artifactId>
+            <version>2.5.1</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/org.janelia.saalfeldlab/n5-imglib2 -->
         <dependency>
-            <groupId>org.scijava</groupId>
-            <artifactId>scijava-listeners</artifactId>
+            <groupId>org.janelia.saalfeldlab</groupId>
+            <artifactId>n5-imglib2</artifactId>
+            <version>5.0.0</version>
+        </dependency>
+
+        <!-- https://mvnrepository.com/artifact/net.imglib2/imglib2 -->
+        <dependency>
+            <groupId>net.imglib2</groupId>
+            <artifactId>imglib2</artifactId>
+            <version>6.1.0</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/net.imglib2/imglib2-ij -->
+        <dependency>
+            <groupId>net.imglib2</groupId>
+            <artifactId>imglib2-ij</artifactId>
+            <version>2.0.0</version>
+        </dependency>
+
+
+        <!-- https://mvnrepository.com/artifact/org.janelia.saalfeldlab/n5-aws-s3 -->
+        <dependency>
+            <groupId>org.janelia.saalfeldlab</groupId>
+            <artifactId>n5-aws-s3</artifactId>
+            <version>3.2.0</version>
+        </dependency>
+
+
+        <!-- https://mvnrepository.com/artifact/javax.xml.bind/jaxb-api Used for AWS library to properly parse XML files -->
+<!--        <dependency>-->
+<!--            <groupId>javax.xml.bind</groupId>-->
+<!--            <artifactId>jaxb-api</artifactId>-->
+<!--            <version>2.3.1</version>-->
+<!--        </dependency>-->
+
         <dependency>
             <groupId>org.jsoup</groupId>
             <artifactId>jsoup</artifactId>
-            <version>1.6.1</version>
+            <version>1.16.1</version>
         </dependency>
     </dependencies>
 

src/main/java/org/vcell/vcellfiji/N5ImageHandler.java

@@ -0,0 +1,231 @@
+package org.vcell.vcellfiji;
+
+
+import com.amazonaws.auth.AWSStaticCredentialsProvider;
+import com.amazonaws.auth.AnonymousAWSCredentials;
+import com.amazonaws.auth.BasicAWSCredentials;
+import com.amazonaws.client.builder.AwsClientBuilder;
+import com.amazonaws.services.s3.AmazonS3;
+import com.amazonaws.services.s3.AmazonS3ClientBuilder;
+import com.amazonaws.services.s3.AmazonS3URI;
+import ij.ImagePlus;
+import ij.plugin.Duplicator;
+import net.imglib2.cache.img.CachedCellImg;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.numeric.integer.*;
+import net.imglib2.type.numeric.real.DoubleType;
+import net.imglib2.type.numeric.real.FloatType;
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
+import org.scijava.command.Command;
+import org.scijava.plugin.Plugin;
+import org.janelia.saalfeldlab.n5.*;
+import org.vcell.vcellfiji.UI.VCellGUI;
+
+import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+
+
+/*
+    Able to open N5 files locally, display the datasets that can be chosen from it, and open the datasets within ImageJ.
+    Flow of operations is select an N5 file, get dataset list, select a dataset and then open it.
+ */
+
+@Plugin(type = Command.class, menuPath = "Plugins>VCell>N5 Dataset Viewer")
+public class N5ImageHandler implements Command{
+    private VCellGUI vGui;
+    private File selectedLocalFile;
+    private AmazonS3 s3Client;
+    private String bucketName;
+
+    private String s3ObjectKey;
+
+    @Override
+    public void run() {
+        this.vGui = new VCellGUI();
+        this.vGui.localFileDialog.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                selectedLocalFile = vGui.localFileDialog.getSelectedFile();
+                displayN5Results(getN5DatasetList());
+            }
+        });
+
+        this.vGui.okayButton.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                try{
+                    loadN5Dataset(vGui.datasetList.getSelectedValue());
+                }
+                catch (IOException ex){
+                    return;
+                }
+            }
+        });
+
+        this.vGui.remoteFileSelection.submitS3Info.addActionListener(new ActionListener() {
+            @Override
+            public void actionPerformed(ActionEvent e) {
+                createS3Client(vGui.remoteFileSelection.getS3URL(), vGui.remoteFileSelection.returnCredentials(), vGui.remoteFileSelection.returnEndpoint());
+                ArrayList<String> list = getS3N5DatasetList();
+                displayN5Results(list);
+            }
+        });
+    }
+
+    public ArrayList<String> getN5DatasetList(){
+        // auto closes reader
+        try (N5FSReader n5Reader = new N5FSReader(selectedLocalFile.getPath())) {
+            String[] metaList = n5Reader.deepList("/");
+            ArrayList<String> fList = new ArrayList<>();
+            for (String s : metaList) {
+                if (n5Reader.datasetExists(s)) {
+                    fList.add(s);
+                };
+            }
+            return fList;
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    public void displayN5Results(ArrayList<String> datasetList){
+        SwingUtilities.invokeLater(() ->{
+            this.vGui.updateDatasetList(datasetList);
+        });
+    }
+
+
+    public ImagePlus getImgPlusFromN5File(String selectedDataset, N5Reader n5Reader) throws IOException {
+        // Theres definitly a better way to do this, I trie using a variable to change the cached cells first parameter type but it didn't seem to work :/
+        switch (n5Reader.getDatasetAttributes(selectedDataset).getDataType()){
+            case UINT8:
+                return ImageJFunctions.wrap((CachedCellImg<UnsignedByteType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case UINT16:
+                return ImageJFunctions.wrap((CachedCellImg<UnsignedShortType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case UINT32:
+                return ImageJFunctions.wrap((CachedCellImg<UnsignedIntType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case INT8:
+                return ImageJFunctions.wrap((CachedCellImg<ByteType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case INT16:
+                return ImageJFunctions.wrap((CachedCellImg<ShortType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case INT32:
+                return ImageJFunctions.wrap((CachedCellImg<IntType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case FLOAT32:
+                return ImageJFunctions.wrap((CachedCellImg<FloatType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+            case FLOAT64:
+                return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>)N5Utils.open(n5Reader, selectedDataset), "");
+//                final ARGBARGBDoubleConverter<ARGBDoubleType> converters = new ARGBARGBDoubleConverter<>();
+//                final CachedCellImg<DoubleType, ?> cachedCellImg = N5Utils.open(n5Reader, selectedDataset);
+//                return ImageJFunctions.showRGB(cachedCellImg, converters, "");
+        }
+        return null;
+    }
+
+
+    private void displayN5Dataset(ImagePlus imagePlus){
+        if (this.vGui.openVirtualCheckBox.isSelected()){
+            imagePlus.show();
+        }
+        else{
+            ImagePlus memoryImagePlus = new Duplicator().run(imagePlus);
+            memoryImagePlus.show();
+        }
+    }
+
+    public N5AmazonS3Reader getN5AmazonS3Reader(){
+        try(N5AmazonS3Reader n5AmazonS3Reader = new N5AmazonS3Reader(this.s3Client, this.bucketName, this.s3ObjectKey)){
+            return n5AmazonS3Reader;
+        }
+        catch (IOException e){
+            throw new RuntimeException(e);
+        }
+    }
+
+    public N5FSReader getN5FSReader(){
+        try (N5FSReader n5FSReader = new N5FSReader(selectedLocalFile.getPath())) {
+            return n5FSReader;
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    public void loadN5Dataset(String selectedDataset) throws IOException {
+        if(selectedLocalFile != null) {
+            ImagePlus imagePlus = this.getImgPlusFromN5File(selectedDataset, this.getN5FSReader());
+            this.displayN5Dataset(imagePlus);
+        }
+        else {
+            ImagePlus imagePlus = this.getImgPlusFromN5File(selectedDataset, this.getN5AmazonS3Reader());
+            this.displayN5Dataset(imagePlus);
+        }
+    }
+
+    //When creating client's try to make one for an Amazon link, otherwise use our custom url scheme
+    public void createS3Client(String url, HashMap<String, String> credentials, HashMap<String, String> endpoint){
+        AmazonS3ClientBuilder s3ClientBuilder = AmazonS3ClientBuilder.standard();
+        URI uri = URI.create(url);
+        String defaultRegion = "site2-low";
+
+        // believe that it's a s3 URL
+        try{
+            AmazonS3URI s3URI = new AmazonS3URI(uri);
+            this.s3ObjectKey = s3URI.getKey();
+            this.bucketName = s3URI.getBucket();
+            defaultRegion = s3URI.getRegion();
+        }
+        // otherwise assume it is one of our URLs
+        catch (IllegalArgumentException e){
+            String[] pathSubStrings = uri.getPath().split("/", 3);
+            this.s3ObjectKey = pathSubStrings[2];
+            this.bucketName = pathSubStrings[1];
+        }
+
+        if(credentials != null){
+            s3ClientBuilder.withCredentials(new AWSStaticCredentialsProvider(new BasicAWSCredentials(credentials.get("AccessKey"), credentials.get("SecretKey"))));
+        }
+        if(endpoint != null){
+            s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(endpoint.get("Endpoint"), endpoint.get("Region")));
+            this.s3Client = s3ClientBuilder.build();
+            return;
+        }
+        // if nothing is given, default user and return so that code after if statement does not execute
+        if(endpoint == null && credentials == null){
+            this.s3Client = AmazonS3ClientBuilder.standard().withRegion(defaultRegion).withCredentials(new AWSStaticCredentialsProvider(new AnonymousAWSCredentials())).build();
+            return;
+        }
+
+        //creds not null, but region is
+        this.s3Client = s3ClientBuilder.withRegion(defaultRegion).build();
+    }
+
+
+    public ArrayList<String> getS3N5DatasetList(){
+
+        // used as a flag to tell that remote access is occurring, and that there is no local files
+        selectedLocalFile = null;
+
+        try(N5AmazonS3Reader n5AmazonS3Reader = new N5AmazonS3Reader(this.s3Client, this.bucketName)) {
+            return new ArrayList<>(Arrays.asList(n5AmazonS3Reader.deepListDatasets(this.s3ObjectKey)));
+        }
+        catch (IOException e){
+            throw new RuntimeException(e);
+        }
+    }
+
+
+    public void setSelectedLocalFile(File selectedLocalFile){
+        this.selectedLocalFile = selectedLocalFile;
+    }
+    public File getSelectedLocalFile() {
+        return selectedLocalFile;
+    }
+
+}