DM-5793: Mask overlay support

src/firefly/html/firefly.html

@@ -10,7 +10,10 @@
     <title>IRSA Viewer</title>
 
     <script>
-        window.firefly = {app: {}};
+        window.firefly = {
+            app: {},
+            MenuItemKeys: {maskOverlay:true}
+        };
     </script>
     <script  type="text/javascript" src="firefly_loader.js"></script>
 </head>
@@ -19,6 +22,9 @@
 <!-- attached loaction for firefly app -->
 <div id='app'/>
 
+
+
+
 </body>
 
 </html>

src/firefly/java/edu/caltech/ipac/firefly/server/ServerContext.java

@@ -48,7 +48,7 @@ public class ServerContext {
     private static final int PFX_START_LEN= PFX_START.length();
     public static final String PFX_END= "}";
     private static final int PFX_TOTAL_CHAR= 3;
-    public static final boolean FITS_SECURITY = AppProperties.getBooleanProperty("visualize.fits.Security", true);
+    public static boolean FITS_SECURITY;
     public static final String VIS_SEARCH_PATH= "visualize.fits.search.path";
     public final static Map<File, Long> _visSessionDirs= new ConcurrentHashMap<File, Long>(617);
     public static boolean DEBUG_MODE;
@@ -146,6 +146,10 @@ public static void configInit() {
         // disable caching is it's a preference
         CacheManager.setDisabled(AppProperties.getBooleanProperty(CACHEMANAGER_DISABLED_PROP, false));
 
+
+        // Must be done after property init
+        FITS_SECURITY = AppProperties.getBooleanProperty("visualize.fits.Security", true);
+
         // use EhCache for caching.
         CacheManager.setCacheProvider(EhcacheProvider.class.getName());
 

src/firefly/java/edu/caltech/ipac/firefly/server/visualize/ImagePlotBuilder.java

@@ -287,6 +287,7 @@ private static ImagePlotInfo[] makeNewPlots(String workingCtxStr,
                 VisContext.purgeOtherPlots(state);
                 state.setOriginalImageIdx(idx, NO_BAND);
                 state.setImageIdx(idx, NO_BAND);
+                state.setMultiImageFile(true,Band.NO_BAND);
                 //todo: here
                 plotInfo[0] = ImagePlotCreator.makeOneImagePerBand(workingCtxStr, state, readInfoMap, zoomChoice);
                 break;

src/firefly/java/edu/caltech/ipac/firefly/server/visualize/ImagePlotCreator.java

@@ -166,8 +166,9 @@ static ImagePlot createImagePlot(PlotState state,
             if (plot.getImageDataWidth()!=rWidth || plot.getImageDataWidth()!=rHeight) {
                 String primDim= rWidth+"x"+rHeight;
                 String overDim= plot.getImageDataWidth()+"x"+plot.getImageDataHeight();
-                throw new FitsException("Mask Overlay does not match the primary plot dimensions ("+
-                                         overDim+" vs "+primDim+")");
+//                throw new FitsException("Mask Overlay does not match the primary plot dimensions ("+
+//                                         overDim+" vs "+primDim+")");
+                _log.warn( "Mask Overlay does not match the primary plot dimensions ("+ overDim+" vs "+primDim+")");
             }
         }
         else { // standard

src/firefly/java/edu/caltech/ipac/firefly/server/visualize/PlotStateUtil.java

@@ -73,6 +73,12 @@ public static void initRequestFromState(WebPlotRequest req, PlotState oldState,
         req.setInitialRangeValues(oldState.getRangeValues(band));
         req.setInitialColorTable(oldState.getColorTableId());
         req.setInitialZoomLevel(oldState.getZoomLevel());
+        WebPlotRequest oldReq= oldState.getPrimaryRequest();
+        if (oldReq.isPlotAsMask()) {
+            req.setPlotAsMask(true);
+            req.setMaskBits(req.getMaskBits());
+            req.setMaskColors(req.getMaskColors().toArray(new String[3]));
+        }
     }
 
 

src/firefly/java/edu/caltech/ipac/firefly/server/visualize/VisJsonSerializer.java

@@ -16,7 +16,6 @@
 import edu.caltech.ipac.firefly.visualize.InsertBandInitializer;
 import edu.caltech.ipac.firefly.visualize.PlotImages;
 import edu.caltech.ipac.firefly.visualize.PlotState;
-import edu.caltech.ipac.firefly.visualize.ProjectionSerializer;
 import edu.caltech.ipac.firefly.visualize.StretchData;
 import edu.caltech.ipac.firefly.visualize.WebFitsData;
 import edu.caltech.ipac.firefly.visualize.WebPlotInitializer;
@@ -71,7 +70,8 @@ public static JSONObject serializeWebPlotInitializerDeep(WebPlotInitializer wpIn
     }
 
     public static JSONObject serializeProjection(WebPlotInitializer wpInit) {
-        Projection proj= ProjectionSerializer.deserializeProjection(wpInit.getProjectionSerialized());
+//        Projection proj= ProjectionSerializer.deserializeProjection(wpInit.getProjectionSerialized());
+        Projection proj= wpInit.getProjection();
         if (proj==null) return null;
         JSONObject map = new JSONObject();
         map.put("coorindateSys", proj.getCoordinateSys().toString());
@@ -133,6 +133,10 @@ public static JSONObject serializeProjectionParams(ProjectionParams p) {
         map.put("map_distortion", p.map_distortion);
         map.put("keyword", p.keyword);
 
+        for(Map.Entry<String,String> e : p.additionalHeaders.entrySet() ) {
+            map.put(e.getKey(),e.getValue());
+        }
+
         return map;
 
     }

src/firefly/java/edu/caltech/ipac/firefly/server/visualize/VisServerCommands.java

@@ -8,10 +8,8 @@
  * Time: 1:27 PM
  */
 
-import edu.caltech.ipac.firefly.data.DataEntry;
 import edu.caltech.ipac.firefly.data.ServerParams;
 import edu.caltech.ipac.firefly.data.TableServerRequest;
-import edu.caltech.ipac.firefly.data.table.TableMeta;
 import edu.caltech.ipac.firefly.server.ServerCommandAccess;
 import edu.caltech.ipac.firefly.server.servlets.CommandService;
 import edu.caltech.ipac.firefly.server.util.Logger;
@@ -23,18 +21,18 @@
 import edu.caltech.ipac.firefly.visualize.WebPlotRequest;
 import edu.caltech.ipac.firefly.visualize.WebPlotResult;
 import edu.caltech.ipac.firefly.visualize.draw.StaticDrawInfo;
-import edu.caltech.ipac.util.FileUtil;
 import edu.caltech.ipac.util.DataGroup;
 import edu.caltech.ipac.visualize.plot.ImagePt;
-
 import nom.tam.fits.FitsException;
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
 
-import java.io.BufferedReader;
 import java.io.IOException;
-import java.net.URL;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * @author Trey Roby
@@ -77,16 +75,28 @@ public String doCommand(Map<String, String[]> paramMap) throws IllegalArgumentEx
 
 
             SrvParam sp= new SrvParam(paramMap);
-            PlotState state= sp.getState();
+//            PlotState state= sp.getState();
+            PlotState stateAry[]= sp.getStateAry();
+            PlotState state= stateAry[0];
             ImagePt pt = sp.getRequiredImagePt("pt");
 
             FileAndHeaderInfo fahAry[];
             List<FileAndHeaderInfo> list = new ArrayList<FileAndHeaderInfo>(state.getBands().length);
             for(Band b : state.getBands()) {
                 list.add(state.getFileAndHeaderInfo(b));
             }
+
+            if (stateAry.length>1) {
+                for(int i=1; (i<stateAry.length);i++) {
+                    list.add(stateAry[i].getFileAndHeaderInfo(Band.NO_BAND) );
+                }
+            }
+
+
+
             fahAry = list.toArray(new FileAndHeaderInfo[list.size()]);
 
+
             String[] res = VisServerOps.getFileFlux(fahAry, pt);
 
 
@@ -96,9 +106,19 @@ public String doCommand(Map<String, String[]> paramMap) throws IllegalArgumentEx
 
             JSONObject data= new JSONObject();
             Band[] bands = state.getBands();
-            for (int i=0; i<res.length; i++){
-                data.put(bands[i].toString(), res[i]);
+            int resultCnt=0;
+            for (;resultCnt<res.length && resultCnt<bands.length; resultCnt++){
+                data.put(bands[resultCnt].toString(), res[resultCnt]);
+            }
+
+
+            if (stateAry.length>1) {
+                for(int i=1; (i<stateAry.length);i++) {
+                    data.put("overlay-"+(i-1), res[resultCnt++]);
+                }
             }
+
+
             data.put("success", true);
 
             JSONArray wrapperAry= new JSONArray();
@@ -392,8 +412,9 @@ public static class FlipImageOnY extends ServerCommandAccess.ServCommand {
 
         public String doCommand(Map<String, String[]> paramMap) throws IllegalArgumentException {
             SrvParam sp= new SrvParam(paramMap);
-            PlotState state= sp.getState();
-            WebPlotResult result = VisServerOps.flipImageOnY(state);
+            PlotState stateAry[]= sp.getStateAry();
+//            PlotState state= sp.getState();
+            WebPlotResult result = VisServerOps.flipImageOnY(stateAry);
             return WebPlotResultSerializer.createJson(result, sp.isJsonDeep());
         }
     }

src/firefly/java/edu/caltech/ipac/firefly/server/visualize/VisServerOps.java

@@ -461,7 +461,8 @@ public static WebPlotResult crop(PlotState state, ImagePt c1, ImagePt c2, boolea
 
                 File workingFilsFile = PlotStateUtil.getWorkingFitsFile(state, bands[i]);
                 String fName = workingFilsFile.getName();
-                File cropFile = File.createTempFile(FileUtil.getBase(fName) + "-crop",
+                String multiStr= state.isMultiImageFile(bands[i]) ? "-multi" : "-"+state.getImageIdx(bands[i]);
+                File cropFile = File.createTempFile(FileUtil.getBase(fName) + multiStr + "-crop",
                         "." + FileUtil.FITS,
                         ServerContext.getVisSessionDir());
 

src/firefly/java/edu/caltech/ipac/firefly/visualize/WebPlotInitializer.java

@@ -34,6 +34,7 @@ public class WebPlotInitializer implements Serializable, DataEntry {
     private WebFitsData   _fitsData[];
     private String        _desc;
     private String        _dataDesc;
+    private transient Projection _projection;
 
 
 
@@ -55,6 +56,7 @@ public WebPlotInitializer(PlotState plotState,
         _initImages= images;
         _imageCoordSys= imageCoordSys;
         _projectionSerialized= ProjectionSerializer.serializeProjection(projection);
+        _projection= projection;
         _dataWidth= dataWidth;
         _dataHeight= dataHeight;
         _imageScaleFactor= imageScaleFactor;
@@ -73,7 +75,7 @@ public WebPlotInitializer(PlotState plotState,
 
     public Projection getProjection() {
 //        return _projection;
-        return ProjectionSerializer.deserializeProjection(_projectionSerialized);
+        return _projection!=null ? _projection : ProjectionSerializer.deserializeProjection(_projectionSerialized);
     }
 
     public String getProjectionSerialized() { return _projectionSerialized; }

src/firefly/java/edu/caltech/ipac/firefly/visualize/WebPlotRequest.java

@@ -1149,7 +1149,12 @@ public void setMaskColors(String colors[]) {
     public List<String> getMaskColors() {
         if (containsParam(MASK_COLORS)) {
             String data= getParam(MASK_COLORS);
-            return StringUtils.parseStringList(data,";");
+            List<String> retval= StringUtils.parseStringList(data,";");
+            if (retval.size()==0 && data.length()>0) {
+                retval= new ArrayList<>(1);
+                retval.add(data);
+            }
+            return retval;
         }
         else {
             return Collections.emptyList();

src/firefly/java/edu/caltech/ipac/visualize/plot/FitsRead.java

@@ -68,7 +68,7 @@ public class FitsRead implements Serializable {
     private final int extension_number;
     private final BasicHDU hdu;
     private float[] float1d;
-    private Fits fits;
+//    private Fits fits;
     private ImageHeader imageHeader;
     private Header header;
     private int indexInFile = -1;  // -1 unknown, >=0 index in file
@@ -89,8 +89,8 @@ public class FitsRead implements Serializable {
     private FitsRead(Fits fits, ImageHDU imageHdu) throws FitsException {
 
         //assign some instant variables
-        this.fits = fits;
-        hdu = imageHdu;
+//        this.fits = fits;
+        this.hdu = imageHdu;
         header = imageHdu.getHeader();
 
         planeNumber = header.getIntValue("SPOT_PL", 0);
@@ -132,8 +132,8 @@ private FitsRead(Fits fits, ImageHDU imageHdu) throws FitsException {
      private FitsRead(Fits fits, ImageHDU imageHdu, int maskExtension) throws FitsException {
 
         //assign some instant variables
-        this.fits = fits;
-        hdu = imageHdu;
+//        this.fits = fits;
+        this.hdu = imageHdu;
         header = imageHdu.getHeader();
         planeNumber = header.getIntValue("SPOT_PL", 0);
         extension_number = header.getIntValue("SPOT_EXT", -1);
@@ -146,7 +146,7 @@ private FitsRead(Fits fits, ImageHDU imageHdu, int maskExtension) throws FitsExc
         }
         //get the data and store into float array
         float1d = getImageHDUDataInFloatArray(imageHdu);
-        masks = getMasksInFits(maskExtension);
+        masks = getMasksInFits(fits, maskExtension);
 
         hist= computeHistogram();
 
@@ -162,7 +162,7 @@ private FitsRead(Fits fits, ImageHDU imageHdu, int maskExtension) throws FitsExc
 
      }
 
-    private short[] getMasksInFits(int maskExtension) throws FitsException {
+    private short[] getMasksInFits(Fits fits, int maskExtension) throws FitsException {
 
         //get all the Header Data Unit from the fits file
         BasicHDU[] HDUs = fits.read();
@@ -281,8 +281,10 @@ public static FitsImageCube createFitsImageCube(Fits fits)throws FitsException {
 
     public static FitsRead createFitsReadFlipLR(FitsRead aFitsReader)
             throws FitsException, GeomException {
-        FlipLR flipLr = new FlipLR();
-        return (flipLr.do_flip(aFitsReader));
+
+        return new FlipXY(aFitsReader,"yAxis").doFlip();
+//        FlipLR flipLr = new FlipLR();
+//        return (flipLr.do_flip(aFitsReader));
     }
 
     /**
@@ -1653,9 +1655,9 @@ public boolean isSameProjection(FitsRead secondFitsread) {
     }
 
 
-    public Fits getFits() {
-        return (fits);
-    }
+//    public Fits getFits() {
+//        return (fits);
+//    }
 
     public BasicHDU getHDU() {
         return hdu;
@@ -1838,7 +1840,7 @@ public static float[][] getDataFloat(ImageHDU imageHDU)
 
     public void freeResources() {
         float1d = null;
-        fits = null;
+//        fits = null;
         imageHeader = null;
         header = null;
 

src/firefly/java/edu/caltech/ipac/visualize/plot/ImageHeader.java

@@ -11,8 +11,12 @@
 import edu.caltech.ipac.visualize.plot.projection.ProjectionParams;
 import nom.tam.fits.FitsException;
 import nom.tam.fits.Header;
+import nom.tam.fits.HeaderCard;
+import nom.tam.util.Cursor;
 
 import java.io.Serializable;
+import java.util.HashMap;
+import java.util.Map;
 
 
 public class ImageHeader implements Serializable
@@ -73,6 +77,7 @@ public class ImageHeader implements Serializable
     public double bp[][] = new double[ProjectionParams.MAX_SIP_LENGTH][ProjectionParams.MAX_SIP_LENGTH];
     public boolean map_distortion = false;
     public String keyword;
+	public Map<String,String> additionalHeaders= new HashMap<>(77);
 
 
     public ImageHeader()
@@ -101,6 +106,18 @@ public ImageHeader(Header header, long HDU_offset, int _plane_number)
 	String ctype1_trim = null;
 
 	long header_size = header.getOriginalSize();
+
+	Cursor extraIter= header.iterator();
+	for(;extraIter.hasNext();) {
+		HeaderCard hc= (HeaderCard)extraIter.next();
+		if (hc.getKey().startsWith("MP") || hc.getKey().startsWith("HIERARCH.MP")) {
+			additionalHeaders.put(hc.getKey(), hc.getValue());
+		}
+	}
+
+
+
+
 	data_offset = HDU_offset + header_size;
 	plane_number = _plane_number;
 
@@ -709,6 +726,7 @@ public Projection createProjection(CoordinateSys csys) {
     public static ProjectionParams createProjectionParams(ImageHeader hdr) {
         ProjectionParams params= new ProjectionParams();
 
+		params.additionalHeaders= hdr.additionalHeaders;
         params.bitpix= hdr.bitpix;
         params.naxis = hdr.naxis;
         params.naxis1= hdr.naxis1;
@@ -765,6 +783,8 @@ public static ProjectionParams createProjectionParams(ImageHeader hdr) {
         params.map_distortion= hdr.map_distortion;
         params.keyword= hdr.keyword;
 
+
+
         return params;
 
     }