Create Package for Library Extensions and Retrieval

Instead of everything being in the top directory, more fine grained categorization is used for clarity.
virtualcell · Oct 1, 2024 · b9ca9fc · b9ca9fc
1 parent 869a4ef
commit b9ca9fc
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Showing 11 changed files with 20 additions and 30 deletions.
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/N5ImageHandler.java b/view-simulation-results/src/main/java/org/vcell/N5/N5ImageHandler.java
@@ -11,13 +11,11 @@
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.vcell.N5.UI.N5ExportTable;
+import org.vcell.N5.retrieving.LoadingFactory;
+import org.vcell.N5.retrieving.SimResultsLoader;
 
 import java.io.*;
-import java.net.MalformedURLException;
-import java.net.URI;
-import java.net.URISyntaxException;
 import java.net.URL;
-import java.util.Stack;
 
 
 /*

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/ImageIntoMemory.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/ImageIntoMemory.java
@@ -4,7 +4,9 @@
 import ij.plugin.Duplicator;
 import org.scijava.log.Logger;
 import org.vcell.N5.N5ImageHandler;
-import org.vcell.N5.SimResultsLoader;
+import org.vcell.N5.retrieving.SimLoadingEventCreator;
+import org.vcell.N5.retrieving.SimLoadingListener;
+import org.vcell.N5.retrieving.SimResultsLoader;
 
 import javax.swing.*;
 import javax.swing.event.EventListenerList;

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java
@@ -3,7 +3,8 @@
 import org.scijava.log.Logger;
 import org.vcell.N5.ExportDataRepresentation;
 import org.vcell.N5.N5ImageHandler;
-import org.vcell.N5.SimResultsLoader;
+import org.vcell.N5.retrieving.SimLoadingListener;
+import org.vcell.N5.retrieving.SimResultsLoader;
 
 import javax.swing.*;
 import javax.swing.border.Border;
@@ -12,7 +13,6 @@
 import javax.swing.event.ListSelectionListener;
 import javax.swing.table.AbstractTableModel;
 import javax.swing.table.DefaultTableCellRenderer;
-import javax.swing.table.TableCellRenderer;
 import javax.swing.table.TableColumn;
 import java.awt.*;
 import java.awt.datatransfer.Clipboard;

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/RemoteFileSelection.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/RemoteFileSelection.java
@@ -1,7 +1,7 @@
 package org.vcell.N5.UI;
 
 import org.vcell.N5.N5ImageHandler;
-import org.vcell.N5.SimResultsLoader;
+import org.vcell.N5.retrieving.SimResultsLoader;
 
 import javax.swing.*;
 import java.awt.*;

diff --git a/...n/java/org/vcell/N5/S3KeyValueAccess.java → .../library/extensions/S3KeyValueAccess.java b/...n/java/org/vcell/N5/S3KeyValueAccess.java → .../library/extensions/S3KeyValueAccess.java
@@ -1,12 +1,9 @@
-package org.vcell.N5;
+package org.vcell.N5.library.extensions;
 
 import com.amazonaws.services.s3.AmazonS3;
 import com.amazonaws.services.s3.model.ListObjectsV2Request;
 import org.janelia.saalfeldlab.n5.N5Exception;
 import org.janelia.saalfeldlab.n5.s3.AmazonS3KeyValueAccess;
-import org.janelia.saalfeldlab.n5.s3.AmazonS3Utils;
-
-import java.net.URI;
 
 public class S3KeyValueAccess extends AmazonS3KeyValueAccess {
     private final String bucketName;

diff --git a/...ain/java/org/vcell/N5/SimCacheLoader.java → ...N5/library/extensions/SimCacheLoader.java b/...ain/java/org/vcell/N5/SimCacheLoader.java → ...N5/library/extensions/SimCacheLoader.java
@@ -1,4 +1,4 @@
-package org.vcell.N5;
+package org.vcell.N5.library.extensions;
 
 import ij.ImagePlus;
 import ij.gui.ImageWindow;

diff --git a/...ain/java/org/vcell/N5/LoadingFactory.java → ...g/vcell/N5/retrieving/LoadingFactory.java b/...ain/java/org/vcell/N5/LoadingFactory.java → ...g/vcell/N5/retrieving/LoadingFactory.java
@@ -1,23 +1,15 @@
-package org.vcell.N5;
+package org.vcell.N5.retrieving;
 
 import ij.ImagePlus;
-import ij.plugin.Duplicator;
 import org.vcell.N5.UI.ImageIntoMemory;
 import org.vcell.N5.UI.N5ExportTable;
-import org.vcell.N5.UI.SimLoadingEventCreator;
-import org.vcell.N5.UI.SimLoadingListener;
 
 import javax.swing.*;
 import javax.swing.event.EventListenerList;
 import java.awt.*;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Set;
 
 public class LoadingFactory implements SimLoadingEventCreator {
     private static final EventListenerList eventListenerList = new EventListenerList();

diff --git a/...g/vcell/N5/UI/SimLoadingEventCreator.java → ...N5/retrieving/SimLoadingEventCreator.java b/...g/vcell/N5/UI/SimLoadingEventCreator.java → ...N5/retrieving/SimLoadingEventCreator.java
@@ -1,8 +1,4 @@
-package org.vcell.N5.UI;
-
-import org.vcell.N5.SimResultsLoader;
-
-import javax.swing.event.EventListenerList;
+package org.vcell.N5.retrieving;
 
 public interface SimLoadingEventCreator {
     public void addSimLoadingListener(SimLoadingListener simLoadingListener);

diff --git a/...a/org/vcell/N5/UI/SimLoadingListener.java → ...ell/N5/retrieving/SimLoadingListener.java b/...a/org/vcell/N5/UI/SimLoadingListener.java → ...ell/N5/retrieving/SimLoadingListener.java
@@ -1,4 +1,4 @@
-package org.vcell.N5.UI;
+package org.vcell.N5.retrieving;
 
 import java.util.EventListener;
 

diff --git a/...n/java/org/vcell/N5/SimResultsLoader.java → ...vcell/N5/retrieving/SimResultsLoader.java b/...n/java/org/vcell/N5/SimResultsLoader.java → ...vcell/N5/retrieving/SimResultsLoader.java
@@ -1,4 +1,4 @@
-package org.vcell.N5;
+package org.vcell.N5.retrieving;
 
 import com.amazonaws.ClientConfiguration;
 import com.amazonaws.auth.AWSStaticCredentialsProvider;
@@ -23,6 +23,9 @@
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
 import org.scijava.log.Logger;
+import org.vcell.N5.N5ImageHandler;
+import org.vcell.N5.library.extensions.S3KeyValueAccess;
+import org.vcell.N5.library.extensions.SimCacheLoader;
 
 import javax.net.ssl.HostnameVerifier;
 import javax.net.ssl.SSLContext;

diff --git a/...java/org/vcell/N5/N5ImageHandlerTest.java → ...ell/N5/retrieving/N5ImageHandlerTest.java b/...java/org/vcell/N5/N5ImageHandlerTest.java → ...ell/N5/retrieving/N5ImageHandlerTest.java
@@ -1,4 +1,4 @@
-package org.vcell.N5;
+package org.vcell.N5.retrieving;
 
 import com.amazonaws.services.s3.AmazonS3ClientBuilder;
 import com.google.gson.internal.LinkedTreeMap;
@@ -11,6 +11,8 @@
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.vcell.N5.N5DataSetFile;
+import org.vcell.N5.N5ImageHandler;
 
 import java.io.File;
 import java.io.IOException;