Merge branch 'master' into multi_channel

# Conflicts: # render-app/src/main/java/org/janelia/alignment/Render.java # render-app/src/main/java/org/janelia/alignment/util/ImageProcessorCache.java # render-app/src/main/java/org/janelia/alignment/util/LabelImageProcessorCache.java # render-app/src/test/java/org/janelia/alignment/RenderRawTileTest.java # render-ws-spark-client/src/main/java/org/janelia/render/client/spark/ScapeClient.java
djkapner · Jun 12, 2017 · ce40772 · ce40772
2 parents 9cc3b2a + 78cef36
commit ce40772
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Showing 12 changed files with 498 additions and 124 deletions.
diff --git a/render-app/src/main/java/org/janelia/alignment/spec/SectionData.java b/render-app/src/main/java/org/janelia/alignment/spec/SectionData.java
@@ -1,6 +1,10 @@
 package org.janelia.alignment.spec;
 
+import java.beans.Transient;
 import java.io.Serializable;
+import java.util.Comparator;
+
+import org.janelia.alignment.json.JsonUtils;
 
 /**
  * Maps a section identifier to its z value.
@@ -68,4 +72,35 @@ public Double getMinX() {
     public Double getMinY() {
         return minY;
     }
+
+    @Transient
+    public int getWidth() {
+        return (int) (maxX - minX + 0.5);
+    }
+
+    @Transient
+    public int getHeight() {
+        return (int) (maxY - minY + 0.5);
+    }
+
+    public String toJson() {
+        return JSON_HELPER.toJson(this);
+    }
+
+    @Override
+    public String toString() {
+        return this.toJson();
+    }
+
+    public static final Comparator<SectionData> Z_COMPARATOR = new Comparator<SectionData>() {
+        @Override
+        public int compare(final SectionData o1,
+                           final SectionData o2) {
+            return o1.z.compareTo(o2.z);
+        }
+    };
+
+    private static final JsonUtils.Helper<SectionData> JSON_HELPER =
+            new JsonUtils.Helper<>(SectionData.class);
+
 }
diff --git a/render-app/src/main/java/org/janelia/alignment/spec/stack/StackId.java b/render-app/src/main/java/org/janelia/alignment/spec/stack/StackId.java
@@ -1,5 +1,7 @@
 package org.janelia.alignment.spec.stack;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 import java.io.Serializable;
 
 import org.janelia.alignment.util.CollectionNameUtil;
@@ -74,14 +76,17 @@ public int compareTo(final StackId that) {
         return v;
     }
 
+    @JsonIgnore
     public String getSectionCollectionName() {
         return getCollectionName(SECTION_COLLECTION_SUFFIX);
     }
 
+    @JsonIgnore
     public String getTileCollectionName() {
         return getCollectionName(TILE_COLLECTION_SUFFIX);
     }
 
+    @JsonIgnore
     public String getTransformCollectionName() {
         return getCollectionName(TRANSFORM_COLLECTION_SUFFIX);
     }

diff --git a/render-app/src/main/java/org/janelia/alignment/spec/stack/StackMetaData.java b/render-app/src/main/java/org/janelia/alignment/spec/stack/StackMetaData.java
@@ -59,6 +59,10 @@ public boolean isLoading() {
         return LOADING.equals(state);
     }
 
+    public boolean isOffline() {
+        return OFFLINE.equals(state);
+    }
+
     public boolean isReadOnly() {
         return READ_ONLY.equals(state);
     }
@@ -280,6 +284,15 @@ public static StackMetaData fromJson(final String json) {
         return JSON_HELPER.fromJson(json);
     }
 
+    public static StackMetaData buildDerivedMetaData(final StackId stackId,
+                                                     final StackMetaData fromStackMetaData) {
+        final StackMetaData derivedMetaData = new StackMetaData(stackId, fromStackMetaData.getCurrentVersion());
+        derivedMetaData.state = fromStackMetaData.state;
+        derivedMetaData.currentVersionNumber = fromStackMetaData.currentVersionNumber;
+        derivedMetaData.stats = fromStackMetaData.stats;
+        return derivedMetaData;
+    }
+
     private static final JsonUtils.Helper<StackMetaData> JSON_HELPER =
             new JsonUtils.Helper<>(StackMetaData.class);
 }
diff --git a/render-app/src/main/java/org/janelia/alignment/util/ImageProcessorCache.java b/render-app/src/main/java/org/janelia/alignment/util/ImageProcessorCache.java
@@ -306,7 +306,7 @@ public String getUri() {
         }
         public boolean isConvertTo16Bit(){
             return convertTo16Bit;
-        }
+	    }
         public int getDownSampleLevels() {
             return downSampleLevels;
         }

diff --git a/render-app/src/main/java/org/janelia/alignment/util/LabelImageProcessorCache.java b/render-app/src/main/java/org/janelia/alignment/util/LabelImageProcessorCache.java
@@ -137,7 +137,7 @@ protected ImageProcessor loadImageProcessor(final String url,
         ImageProcessor imageProcessor;
 
         if (isMask) {
-            imageProcessor = super.loadImageProcessor(url, downSampleLevels, true, false);
+            imageProcessor = super.loadImageProcessor(url, downSampleLevels, true, convertTo16Bit);
         } else {
 
             final Color labelColor = getColorForUrl(url);

diff --git a/render-app/src/test/java/org/janelia/alignment/TransformMeshTest.java b/render-app/src/test/java/org/janelia/alignment/TransformMeshTest.java
@@ -35,6 +35,7 @@
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.BeforeClass;
+import org.junit.Ignore;
 import org.junit.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -44,6 +45,7 @@
  *
  * @author Eric Trautman
  */
+@Ignore
 public class TransformMeshTest {
 
     // increase this to 10 (or more) to see average times

diff --git a/render-ws-java-client/src/main/java/org/janelia/render/client/FileUtil.java b/render-ws-java-client/src/main/java/org/janelia/render/client/FileUtil.java
@@ -2,6 +2,7 @@
 
 import java.io.BufferedInputStream;
 import java.io.BufferedOutputStream;
+import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
@@ -90,6 +91,25 @@ public static void saveJsonFile(final String path,
         LOG.info("saveJsonFile: exit, wrote data to {}", toPath);
     }
 
+    public static void ensureWritableDirectory(final File directory) {
+        // try twice to work around concurrent access issues
+        if (! directory.exists()) {
+            if (! directory.mkdirs()) {
+                if (! directory.exists()) {
+                    // last try
+                    if (! directory.mkdirs()) {
+                        if (! directory.exists()) {
+                            throw new IllegalArgumentException("failed to create " + directory);
+                        }
+                    }
+                }
+            }
+        }
+        if (! directory.canWrite()) {
+            throw new IllegalArgumentException("not allowed to write to " + directory);
+        }
+    }
+
     private static final Logger LOG = LoggerFactory.getLogger(FileUtil.class);
 
     private static final int DEFAULT_BUFFER_SIZE = 65536;

diff --git a/render-ws-java-client/src/main/java/org/janelia/render/client/RenderSectionClient.java b/render-ws-java-client/src/main/java/org/janelia/render/client/RenderSectionClient.java
@@ -98,7 +98,7 @@ public RenderSectionClient(final Parameters clientParameters) {
                                            sectionsAtScaleName).toAbsolutePath();
 
         this.sectionDirectory = sectionPath.toFile();
-        ensureWritableDirectory(this.sectionDirectory);
+        FileUtil.ensureWritableDirectory(this.sectionDirectory);
 
         // set cache size to 50MB so that masks get cached but most of RAM is left for target image
         final int maxCachedPixels = 50 * 1000000;
@@ -155,29 +155,11 @@ private File getSectionFile(final Double z) {
         final int hundreds = (z.intValue() % 1000) / 100;
         final File hundredsDir = new File(thousandsDir, String.valueOf(hundreds));
 
-        ensureWritableDirectory(hundredsDir);
+        FileUtil.ensureWritableDirectory(hundredsDir);
 
         return new File(hundredsDir, z + "." + clientParameters.format.toLowerCase());
     }
 
-    private void ensureWritableDirectory(final File directory) {
-        // try twice to work around concurrent access issues
-        if (! directory.exists()) {
-            if (! directory.mkdirs()) {
-                if (! directory.exists()) {
-                    // last try
-                    if (! directory.mkdirs()) {
-                        if (! directory.exists()) {
-                            throw new IllegalArgumentException("failed to create " + directory);
-                        }
-                    }
-                }
-            }
-        }
-        if (! directory.canWrite()) {
-            throw new IllegalArgumentException("not allowed to write to " + directory);
-        }
-    }
 
     private String getNumericDirectoryName(final int value) {
         String pad = "00";