Merge pull request #3580 from chris-allan/no-stats-info-option-develop

Add no StatsInfo option to importer

components/blitz/resources/omero/Repositories.ice

@@ -285,6 +285,11 @@ module omero {
               **/
              omero::RBool doThumbnails;
 
+             /**
+              * Whether we are to disable StatsInfo population.
+              **/
+             omero::RBool noStatsInfo;
+
              /**
               * User choice of checksum algorithm for verifying upload.
               **/

components/blitz/src/ome/formats/importer/ImportCandidates.java

@@ -422,6 +422,7 @@ protected ImportContainer singleFile(File file, ImportConfig config)
                         file, null, null,
                         readerClassName, usedFiles, isSPW);
                 ic.setDoThumbnails(config.doThumbnails.get());
+                ic.setNoStatsInfo(config.noStatsInfo.get());
                 String configImageName = config.userSpecifiedName.get();
                 if (configImageName == null)
                 {
@@ -482,33 +483,6 @@ private List<String> getImageNames() {
         return toReturn;
     }
 
-    /**
-     * Creates a Pixels object populated with the dimensions for each image
-     * that Bio-Formats has detected.
-     * @return A list of Pixels objects, in the order of <i>series</i>
-     * populated with dimensions X, Y, Z, C and T.
-     */
-    private List<Pixels> getPixelsWithDimensions()
-    {
-        List<Pixels> toReturn = new ArrayList<Pixels>();
-        for (int i = 0; i < reader.getSeriesCount(); i++)
-        {
-            reader.setSeries(i);
-            Pixels pixels = new PixelsI();
-            PixelsType pixelsType = new PixelsTypeI();
-            pixelsType.setValue(rstring(
-                    FormatTools.getPixelTypeString(reader.getPixelType())));
-            pixels.setSizeX(rint(reader.getSizeX()));
-            pixels.setSizeY(rint(reader.getSizeY()));
-            pixels.setSizeZ(rint(reader.getSizeZ()));
-            pixels.setSizeC(rint(reader.getSizeC()));
-            pixels.setSizeT(rint(reader.getSizeT()));
-            pixels.setPixelsType(pixelsType);
-            toReturn.add(pixels);
-        }
-        return toReturn;
-    }
-
     /**
      * This method uses the {@link FileInfo#usedToInitialize} flag to re-order
      * used files. All files which can be used to initialize a fileset are

components/blitz/src/ome/formats/importer/ImportConfig.java

@@ -107,6 +107,7 @@ public class ImportConfig {
     public final StrValue sessionKey;
     public final LongValue group;
     public final BoolValue doThumbnails;
+    public final BoolValue noStatsInfo;
     public final StrValue email;
     public final StrValue userSpecifiedName;
     public final StrValue userSpecifiedDescription;
@@ -244,6 +245,7 @@ public synchronized void load() {
         sessionKey   = new StrValue("session", this);
         group		 = new LongValue("group", this, null);
         doThumbnails = new BoolValue("doThumbnails", this, true);
+        noStatsInfo  = new BoolValue("noStatsInfo", this, false);
         email        = new StrValue("email", this);
         qaBaseURL    = new StrValue("qaBaseURL", this, DEFAULT_QABASEURL);
         userSpecifiedName = new StrValue("userSpecifiedName", this);

components/blitz/src/ome/formats/importer/ImportContainer.java

@@ -59,6 +59,7 @@ public class ImportContainer
     private String userSpecifiedName;
     private String userSpecifiedDescription;
     private boolean doThumbnails = true;
+    private boolean noStatsInfo = false;
     private List<Annotation> customAnnotationList;
     private IObject target;
     private String checksumAlgorithm;
@@ -86,7 +87,7 @@ public ImportContainer(ImportConfig config,
     /**
      * Retrieves whether or not we are performing thumbnail creation upon
      * import completion.
-     * return <code>true</code> if we are to perform thumbnail creation and
+     * @return <code>true</code> if we are to perform thumbnail creation and
      * <code>false</code> otherwise.
      * @since OMERO Beta 4.3.0.
      */
@@ -107,6 +108,28 @@ public void setDoThumbnails(boolean v)
         doThumbnails = v;
     }
 
+    /**
+     * Retrieves whether or not we disabling <codeStatsInfo</code> population.
+     * @returns <code>true</code> if we are to disable <code>StatsInfo</code>
+     * population. <code>false</code> otherwise.
+     * @since OMERO 5.1.
+     */
+    public boolean getNoStatsInfo()
+    {
+        return noStatsInfo;
+    }
+
+    /**
+     * Sets whether or not we disabling <codeStatsInfo</code> population.
+     * @param v <code>true</code> if we are to disable <code>StatsInfo</code>
+     * population. <code>false</code> otherwise.
+     * @since OMERO 5.1.
+     */
+    public void setNoStatsInfo(boolean v)
+    {
+        noStatsInfo = v;
+    }
+
     /**
      * Retrieves the current custom image/plate name string.
      * @return As above. <code>null</code> if it has not been set.
@@ -298,6 +321,7 @@ public void fillData(ImportConfig config, ImportSettings settings, Fileset fs,
         // TODO: These should possible be a separate option like
         // ImportUserSettings rather than misusing ImportContainer.
         settings.doThumbnails = rbool(getDoThumbnails());
+        settings.noStatsInfo = rbool(getNoStatsInfo());
         settings.userSpecifiedTarget = getTarget();
         settings.userSpecifiedName = getUserSpecifiedName() == null ? null
                 : rstring(getUserSpecifiedName());

components/blitz/src/ome/formats/importer/cli/CommandLineImporter.java

@@ -515,11 +515,14 @@ public static void main(String[] args) throws Exception {
         LongOpt qaBaseURL = new LongOpt(
                 "qa_baseurl", LongOpt.REQUIRED_ARGUMENT, null, 21);
 
+        LongOpt noStatsInfo =
+                new LongOpt("no_stats_info", LongOpt.NO_ARGUMENT, null, 22);
+
         // DEPRECATED OPTIONS
         LongOpt plateName = new LongOpt(
-                "plate_name", LongOpt.REQUIRED_ARGUMENT, null, 22);
+                "plate_name", LongOpt.REQUIRED_ARGUMENT, null, 90);
         LongOpt plateDescription = new LongOpt(
-                "plate_description", LongOpt.REQUIRED_ARGUMENT, null, 23);
+                "plate_description", LongOpt.REQUIRED_ARGUMENT, null, 91);
 
         Getopt g = new Getopt(APP_NAME, args, "cfl:s:u:w:d:r:k:x:n:p:h",
                 new LongOpt[] { debug, report, upload, logs, email,
@@ -528,7 +531,7 @@ public static void main(String[] args) throws Exception {
                                 annotationLink, transferOpt, advancedHelp,
                                 checksumAlgorithm, minutesWait,
                                 closeCompleted, waitCompleted, autoClose,
-                                exclude,
+                                exclude, noStatsInfo,
                                 qaBaseURL, plateName, plateDescription});
         int a;
 
@@ -653,17 +656,21 @@ public static void main(String[] args) throws Exception {
                 config.qaBaseURL.set(g.getOptarg());
                 break;
             }
+            case 22: {
+                config.noStatsInfo.set(true);
+                break;
+            }
             // ADVANCED END ---------------------------------------------------
             // DEPRECATED OPTIONS
-            case 22: {
+            case 90: {
                 if (userSpecifiedNameAlreadySet) {
                     usage();
                 }
                 config.userSpecifiedName.set(g.getOptarg());
                 userSpecifiedNameAlreadySet = true;
                 break;
             }
-            case 23: {
+            case 91: {
                 if (userSpecifiedDescriptionAlreadySet) {
                     usage();
                 }

components/blitz/src/ome/services/blitz/repo/ManagedImportRequestI.java

@@ -88,7 +88,7 @@
  */
 public class ManagedImportRequestI extends ImportRequest implements IRequest {
 
-    private static final long serialVersionUID = -303948503984L;
+    private static final long serialVersionUID = -303948503985L;
 
     private static Logger log = LoggerFactory.getLogger(ManagedImportRequestI.class);
 
@@ -134,6 +134,8 @@ public class ManagedImportRequestI extends ImportRequest implements IRequest {
 
     private boolean doThumbnails = true;
 
+    private boolean noStatsInfo = false;
+
     private String fileName = null;
 
     private String shortName = null;
@@ -215,6 +217,8 @@ public void init(Helper helper) {
             annotationList = settings.userSpecifiedAnnotationList;
             doThumbnails = settings.doThumbnails == null ? true :
                 settings.doThumbnails.getValue();
+            noStatsInfo = settings.noStatsInfo == null ? false :
+                settings.noStatsInfo.getValue();
 
             detectAutoClose();
 
@@ -570,7 +574,7 @@ public Object pixelData(PixelDataJob pdj) throws Throwable {
 
         store.updatePixels(pixList);
 
-        if (!reader.isMinMaxSet())
+        if (!reader.isMinMaxSet() && !noStatsInfo)
         {
             store.populateMinMax();
         }

components/common/test/ome/testing/ObjectFactory.java

@@ -121,6 +121,7 @@ public static Pixels createPixelGraphWithChannels(Pixels example, int channelCou
             pi.setValue("RGB");
 
             pt.setValue("int8");
+            pt.setBitSize(8);
 
             dO.setValue("XYZTC");
 

components/rendering/src/omeis/providers/re/HSBStrategy.java

@@ -187,11 +187,14 @@ private List<QuantumStrategy> getStrategies() {
     	if (overlays != null)
     	{
     		QuantumDef def = new QuantumDef();  // Just to fulfill interface
+    		Pixels pixels = new Pixels();
     		PixelsType bitType = new PixelsType();
     		bitType.setValue(PlaneFactory.BIT);
+    		bitType.setBitSize(1);
+    		pixels.setPixelsType(bitType);
     		for (int i = 0; i < overlays.size(); i++)
     		{
-    			strats.add(new BinaryMaskQuantizer(def, bitType));
+    			strats.add(new BinaryMaskQuantizer(def, pixels));
     		}
     	}
         return strats;

components/rendering/src/omeis/providers/re/QuantumManager.java

@@ -69,15 +69,12 @@ class QuantumManager {
      * 
      * @param qd
      *            The quantum definition which dictates what strategy to use.
-     * @param type
-     *            The pixels' type.
      * @param waves
      *            Rendering settings associated to each wavelength (channel).
      */
-    void initStrategies(QuantumDef qd, PixelsType type,
-            List<ChannelBinding> waves) {
+    void initStrategies(QuantumDef qd, List<ChannelBinding> waves) {
         ChannelBinding[] cb = waves.toArray(new ChannelBinding[waves.size()]);
-        initStrategies(qd, type, cb);
+        initStrategies(qd, cb);
     }
 
     /**
@@ -87,12 +84,10 @@ void initStrategies(QuantumDef qd, PixelsType type,
      * 
      * @param qd
      *            The quantum definition which dictates what strategy to use.
-     * @param type
-     *            The pixels' type.
      * @param waves
      *            Rendering settings associated to each wavelength (channel).
      */
-    void initStrategies(QuantumDef qd, PixelsType type, ChannelBinding[] waves) {
+    void initStrategies(QuantumDef qd, ChannelBinding[] waves) {
         QuantumStrategy stg;
         double gMin, gMax;
         int w = 0;
@@ -101,10 +96,10 @@ void initStrategies(QuantumDef qd, PixelsType type, ChannelBinding[] waves) {
         double[] minmax;
         for (Iterator<Channel> i = metadata.iterateChannels(); i.hasNext();) {
             channel = i.next();
-            stg = factory.getStrategy(qd, type);
+            stg = factory.getStrategy(qd, metadata);
             StatsInfo statsInfo = channel.getStatsInfo();
             if (statsInfo == null) {
-                minmax = sf.initPixelsRange(type);
+                minmax = sf.initPixelsRange(metadata);
                 gMin = minmax[0];
                 gMax = minmax[1];
             } else {

components/rendering/src/omeis/providers/re/Renderer.java

@@ -349,7 +349,7 @@ public Renderer(QuantumFactory quantumFactory,
         QuantumDef qd = rndDef.getQuantization();
         quantumManager = new QuantumManager(metadata, quantumFactory);
         ChannelBinding[] cBindings = getChannelBindings();
-        quantumManager.initStrategies(qd, metadata.getPixelsType(), cBindings);
+        quantumManager.initStrategies(qd, cBindings);
 
         // Create and configure the codomain chain.
         codomainChain = new CodomainChain(qd.getCdStart().intValue(), qd
@@ -429,7 +429,7 @@ public Map<byte[], Integer> getOverlays() {
     public void updateQuantumManager() {
         QuantumDef qd = rndDef.getQuantization();
         ChannelBinding[] cb = getChannelBindings();
-        quantumManager.initStrategies(qd, metadata.getPixelsType(), cb);
+        quantumManager.initStrategies(qd, cb);
     }
 
     /**

components/rendering/src/omeis/providers/re/metadata/StatsFactory.java

@@ -220,22 +220,41 @@ private double accumulateCloseToMax(int[] totals, BasicSegment[] segments,
         return s;
     }
 
-
     /** 
      * Determines the minimum and maximum corresponding to the passed
-     * pixels type.
+     * pixels.
      * 
-     * @param type The pixels type to handle.
+     * @param metadata The pixels to handle.
      */
-    public double[] initPixelsRange(PixelsType type)
+    public double[] initPixelsRange(Pixels metadata)
     {
+        PixelsType type = metadata.getPixelsType();
         double[] minmax = new double[] {0, 1};
         if (type == null) return minmax;
         String typeAsString = type.getValue();
-        long[] values = FormatTools.defaultMinMax(
-                FormatTools.pixelTypeFromString(typeAsString));
-        minmax[0] = values[0];
-        minmax[1] = values[1];
+        int bfPixelsType = FormatTools.pixelTypeFromString(typeAsString);
+
+        // Handle floating point types first
+        if (FormatTools.isFloatingPoint(bfPixelsType)) {
+            long[] values = FormatTools.defaultMinMax(bfPixelsType);
+            minmax[0] = values[0];
+            minmax[1] = values[1];
+            return minmax;
+        }
+
+        // Use significant bits if they are available for integral pixel types.
+        Integer significantBits = metadata.getSignificantBits();
+        if (significantBits == null) {
+            significantBits = type.getBitSize();
+        }
+        significantBits = Math.min(significantBits, type.getBitSize());
+        if (FormatTools.isSigned(bfPixelsType)) {
+            minmax[0] = -Math.pow(2, significantBits - 1);
+            minmax[1] = Math.pow(2,  significantBits - 1) - 1;
+        } else {
+            minmax[0] = 0;
+            minmax[1] = Math.pow(2, significantBits) - 1;
+        }
         return minmax;
     }
 
@@ -258,7 +277,7 @@ public void computeLocationStats(final Pixels metadata,
         inputStart = 0;
         inputEnd = 1;
         if (stats == null) {
-            double[] values = initPixelsRange(metadata.getPixelsType());
+            double[] values = initPixelsRange(metadata);
             inputStart = values[0];
             inputEnd = values[1];
         } else {

components/rendering/src/omeis/providers/re/quantum/BinaryMaskQuantizer.java

@@ -12,6 +12,7 @@
 // Third-party libraries
 
 // Application-internal dependencies
+import ome.model.core.Pixels;
 import ome.model.display.QuantumDef;
 import ome.model.enums.PixelsType;
 import omeis.providers.re.data.PlaneFactory;
@@ -27,12 +28,13 @@ public class BinaryMaskQuantizer extends QuantumStrategy
      * Creates a new strategy.
      * 
      * @param qd Quantum definition object, contained mapping data.
-     * @param type The pixel type. Must be of type <code>bit</code>.
+     * @param type The pixels. Must be of type <code>bit</code>.
      */
-    public BinaryMaskQuantizer(QuantumDef qd, PixelsType type)
+    public BinaryMaskQuantizer(QuantumDef qd, Pixels pixels)
     {
-        super(qd, type);
-        if (!PlaneFactory.BIT.equals(type))
+        super(qd, pixels);
+        PixelsType type = pixels.getPixelsType();
+        if (!PlaneFactory.BIT.equals(type.getValue()))
         {
         	throw new IllegalArgumentException(
         			"The type " + type.getValue() + " != 'bit'.");