Merge branch 'master' into highcharts

docker-compose.yml

@@ -6,7 +6,6 @@ services:
     ports:
      - "${YAFITSV_PORT}:3000"
     volumes:
-     - "${YAFITS_FITSDIR}:/home/partemix/dataroot/FITS"
      - "${YAFITS_PNGDIR}:/home/partemix/dataroot/PNG"
      - "${YAFITS_OBJDIR}:/home/partemix/dataroot/OBJ"
      - "${YAFITS_SAMPDIR}:/home/partemix/dataroot/SAMP"
@@ -22,16 +21,25 @@ services:
      - yafitss
 
   yafitss:
-    build: ./yafitss
+    build:
+      context: ./yafitss
+      args:
+        YAFITS_FITSDIR: ${YAFITS_FITSDIR}
+        YAFITS_FITSDIR2: ${YAFITS_FITSDIR2}
+
     image: yafitss:${USER}
     ports:
      - "${YAFITSS_PORT}:4251"
     volumes:
-     - "${YAFITS_FITSDIR}:/home/partemix/dataroot/FITS"
+     - "${YAFITS_FITSDIR}:${YAFITS_FITSDIR}"
+     - "${YAFITS_FITSDIR2}:${YAFITS_FITSDIR2}"
      - "${YAFITS_PNGDIR}:/home/partemix/dataroot/PNG"
      - "${YAFITS_OBJDIR}:/home/partemix/dataroot/OBJ"
      - "${YAFITS_LOGDIR}:/home/partemix/log"
+
     environment:
+      - YAFITS_FITSDIR
+      - YAFITS_FITSDIR2
       - YAFITSS_PORT=${YAFITSS_PORT}
       - YAFITSS_MAXIDLE=${YAFITSS_MAXIDLE}
     command: python /home/partemix/yafitss/serverWsgi.py --port 4251

yafits.bashrc.dist

@@ -13,6 +13,13 @@
 #
 export YAFITS_FITSDIR=/datartemix/ALMA/FITS
 
+#
+# A way to extend the disk space allocated to FITS files
+# by using symbolic links defined in YAFITS_FITSDIR towards files
+# or directories located in YAFITS_FITSDIR2
+#
+export YAFITS_FITSDIR2=/datartemix2/ALMA/FITS
+
 #
 # Where will the temporary PNG files and log files be written.
 # Ensure that the directories are writable by anybody or at least

yafitss/DataBlock.py

@@ -1229,6 +1229,7 @@ class DataBlock:
         result["stdev"] = {"value":  np.nanstd(box).item() , "unit": bunit}
         result["numpix"] = {"value":  np.count_nonzero(~np.isnan(box)), "unit" : "pixels (!=Nan)"}
         result["percentage of total number of pixels"] = {"value": (box.shape[0]*box.shape[1]) / (self.__header["NAXIS1"]*self.__header["NAXIS2"]) * 100, "unit": "%"}
+        result["boundingRect"] = {"value":[iRA0, iDEC0, iRA1-iRA0, iDEC1-iDEC0], "unit":"pixels"}
         result = {"status":True, "message":"", "result":result}
 
         self.__logger.debug("measureBox : exiting")

yafitss/Dockerfile

@@ -72,9 +72,20 @@ RUN echo "PATH=$PATH"
 #------------------------------------------------------------#
 
 # Create some directories expected by the application.
+ARG YAFITS_FITSDIR
+ARG YAFITS_FITSDIR2
+
+ENV YAFITS_FITSDIR=$YAFITS_FITSDIR
+ENV YAFITS_FITSDIR2=$YAFITS_FITSDIR2
 
 # The root directory of the FITS files location (readonly). It'll have to be bound to an host directory.
-RUN mkdir -p /home/partemix/dataroot/FITS
+RUN printenv
+RUN sudo mkdir -p ${YAFITS_FITSDIR}
+RUN sudo chown partemix:partemix ${YAFITS_FITSDIR}
+
+# The first extension to the root directory of FITS files location (readonly). It'll have to be bound to an host directory.
+RUN sudo mkdir -p ${YAFITS_FITSDIR2}
+RUN sudo chown partemix:partemix ${YAFITS_FITSDIR2}
 
 # The root directory of the PNG files (read/write). It'll have to be bound to an host directory.
 RUN mkdir -p /home/partemix/dataroot/PNG

yafitss/dataManager_michel.py

@@ -15,8 +15,9 @@ from datetime import datetime
 
 from DataBlock import DataBlock
 
-DataRoot = "dataroot"
-FITSFilePrefix = DataRoot + '/FITS/'
+FITSFilePrefix = os.getenv("YAFITS_FITSDIR")
+
+DataRoot = "/home/partemix/dataroot"
 PNGFilePrefix = DataRoot + '/PNG/'
 OBJFilePrefix = DataRoot + '/OBJ/'
 ApiDocPrefix = DataRoot + '/apidoc/'
@@ -62,19 +63,29 @@ class DataManagerImpl :
         try :
             absFITSFilePrefix = FITSFilePrefix + relKey
             entries = (os.listdir(absFITSFilePrefix))
-            self.__logger.debug("type of entries %s" % (type(entries)))
+            self.__logger.debug("%r" % entries)
             sortedEntries = entries.sort()
             children = []
             for entry in entries:
                 p = absFITSFilePrefix + '/' + entry
-                if entry.startswith(".") or (not os.path.isdir(p) and not p.endswith(".fits")) :
+                condition = (os.path.isfile(p) and p.endswith(".fits"))
+                if not condition :
+                    self.__logger.debug("%s link %r" % (p, os.path.islink(p)))
+                    if os.path.islink(p):
+                        target = os.path.realpath(p)
+                        self.__logger.debug("%s is dir %r" %(target, os.path.isdir(target)))
+                        condition  = os.path.islink(p) # and os.path.isdir(target)
+                    else :
+                        condition = (os.path.isdir(p))
+
+                if not condition :
                     continue
                 elif entry in ["log", "NOFITS", "IGNORE"]:
                     continue
                 else:
                     d = dict()
                     d["key"]    = relKey + '/' + entry
-                    d["folder"] = os.path.isdir(p)
+                    d["folder"] = not os.path.isfile(p)
                     d["lazy"]   = d["folder"]
                     if entry.endswith(".fits") :
                         size = DataBlock.convert_size(os.path.getsize(p))
@@ -86,6 +97,7 @@ class DataManagerImpl :
         except Exception as e :
             result = {"status": False, "message": "Problem while looking for entries under '%s'. Error message was '%s'" % ( relKey, e)}
             self.__logger.debug("%r" % result)
+        self.__logger.debug("%r" % result)
         self.__logger.debug("__getEntries_0: exiting")
         return result
 

yafitsv/public/javascript/olqv_utils.js

@@ -116,7 +116,7 @@ function decLabelFormatter (dec0pix, dec1pix, dec0, dec1) {
 function summedPixelsSpectrumUnit(unit) {
   switch (unit) {
     case "Jy/beam":
-      return "Jy/beam * km/s";
+      return "Jy";
       break;
 
     case "erg/s/cm^2/A/arcsec^2":

yafitsv/views/olqv_2d.ejs

@@ -179,10 +179,16 @@ th, td {
       <div id="FITSHDR" class="overlay" style="overflow:scroll"></div>
       <% include olqv_infosblock %>
       <% include olqv_navbar_external_content %>
+      <% include olqv_settings %>
       <% include olqv_customcontrols %>
       <% include olqv_reset %>
       <% include olqv_samp_publisher %>
+      <% include olqv_shapes %>
+      <% include olqv_contours %>
       <% include olqv_boxes %>
+      <% include olqv_markers %>
+      <% include olqv_keyboardevents %>
+
 <div id="fullscreen" class="fullscreen">
   <div class="sidepanel">
       <nav class="navbar navbar-dark bg-dark">
@@ -251,30 +257,23 @@ var _imageLoadFunction_1 = function(image, src) {
 ** one image built from the content of a 2D FITS file
 */
 var _canvasContext = null;
-var yAFITSContoursViewer;
-var yaFITSContoursGUI;
+var contoursFactory;
+var contoursFactoryGUI;
 
 var reset;
 var settings;
 var boxTool;
-
-var format = function(floatValue) {
-  let result = floatValue;
-  if (typeof result === "number" && !Number.isInteger(result)){
-    result = result.toExponential(4);
-  }
-  return result;
-};
+var keyCodeProcessor;
 
 var infos_line = document.getElementById('infos-line');
 var infos_block = document.getElementById('ModalInfosBlockBody');
 
-var populateInfosBlock = function(title, collection) {
-  infos_block.innerHTML = "<b>"+title+" <br><br>";
-  for (var k in collection) {
-    infos_block.innerHTML += k + ":" + format(collection[k]["value"]) + " " + collection[k]["unit"] + "<br>";
-  }
-}
+// var populateInfosBlock = function(title, collection) {
+//   infos_block.innerHTML = "<b>"+title+" <br><br>";
+//   for (var k in collection) {
+//     infos_block.innerHTML += k + ":" + format(collection[k]["value"]) + " " + collection[k]["unit"] + "<br>";
+//   }
+// }
 
 function SliceViewer (relFITSFilePath, width, height, RADECRangeInDegrees, FITSHeader, divSlice) {
     console.log("SliceViewer : entering");
@@ -336,6 +335,9 @@ function SliceViewer (relFITSFilePath, width, height, RADECRangeInDegrees, FITSH
     let _naxis  = parseInt(header["NAXIS"]);
     let _naxis1 = parseInt(header["NAXIS1"]);
     let _naxis2 = parseInt(header["NAXIS2"]);
+    if (_naxis > 2) _naxis3 = parseInt(header["NAXIS3"]);
+    if (_naxis > 4) _naxis4 = parseInt(header["NAXIS4"]);
+
     let _crpix = [parseFloat(header["CRPIX1"]), parseFloat(header["CRPIX2"])];
     let _crval = [parseFloat(header["CRVAL1"]), parseFloat(header["CRVAL2"])];
     let _cdelt = [parseFloat(header["CDELT1"]), parseFloat(header["CDELT2"])];
@@ -365,6 +367,10 @@ function SliceViewer (relFITSFilePath, width, height, RADECRangeInDegrees, FITSH
       return result;
     };
 
+    this.is3D = function() {
+      return  (_naxis==3 && _naxis3>1) || (_naxis==4 && _naxis3>1 && _naxis4==1);
+    }
+
     this.getSliceIndex = function () {
       return _sliceIndex;
     }
@@ -609,7 +615,7 @@ var _marker_styles_f = function(feature) {
             let properties = selectedFeature.get("properties");
             let level = properties["level"]["value"].toExponential(3);
             if ("measurements" in properties) {
-              yAFITSContoursViewer.selected(selectedFeature);
+              contoursFactory.selected(selectedFeature);
             }
             else {
               document.getElementById('loading').style.display="block";
@@ -624,7 +630,7 @@ var _marker_styles_f = function(feature) {
                   console.log(resp["result"]);
                   properties["measurements"]=resp["result"];
                   selectedFeature.set("properties",properties);
-                  yAFITSContoursViewer.selected(selectedFeature);
+                  contoursFactory.selected(selectedFeature);
                 }
                 console.log('measureContour callback : exiting');
               });
@@ -1115,7 +1121,10 @@ $( document ).ready(function() {
       sliceViewer = new SliceViewer (relFITSFilePath, width, height, RADECRangeInDegrees, header, "slice");
       sliceViewer.display();
 
-      document.addEventListener('keydown', sliceViewer.processKeyCode, false);
+      //document.addEventListener('keydown', sliceViewer.processKeyCode, false);
+
+      keyCodeProcessor = new KeyCodeProcessor(sliceViewer);
+      keyCodeProcessor.open();
 
       infosBlock = new InfosBlock(sliceViewer);
 
@@ -1135,11 +1144,11 @@ $( document ).ready(function() {
       markerFactory = new MarkerFactory(sliceViewer);
       customControls.addButton(markerFactory.getButton());
 
-      yAFITSContoursViewer = new ContoursViewer(sliceViewer, infosBlock);
-      customControls.addButton(yAFITSContoursViewer.getButton());
+      contoursFactory = new ContoursFactory(sliceViewer, infosBlock);
+      customControls.addButton(contoursFactory.getButton());
 
-      yAFITSContoursGUI = new ContoursGUI();
-      yAFITSContoursGUI.connect(yAFITSContoursViewer, sliceViewer);
+      contoursFactoryGUI = new ContoursFactoryGUI();
+      contoursFactoryGUI.connect(contoursFactory, sliceViewer);
 
       boxFactory = new BoxFactory(sliceViewer, infosBlock);
       customControls.addButton(boxFactory.getButton());

yafitsv/views/olqv_boxes.ejs

 <script>
-class BoxFactory {
+class BoxFactory extends ShapesFactory {
   constructor (sliceViewer, infosBlock) {
+    super(sliceViewer, infosBlock);
+    ShapesFactory.enter(this.constructor.name);
     console.log("BoxFactory ctor: entering");
 
     this.source;
@@ -13,53 +15,8 @@ class BoxFactory {
     let target = this.map.getTarget();
     this.jTarget = typeof target === "string" ? $("#" + target) : $(target);
     this.lastSelectedBox = null;
-    this.highlightStyle = new ol.style.Style({
-      fill: new ol.style.Fill({
-        color: 'rgba(255,255,255,0.7)'
-      }),
-      stroke: new ol.style.Stroke({
-        color: '#3399CC',
-        width: 3
-      })
-    });
 
-    this.style = {
-      'LineString': new ol.style.Style({
-        stroke: new ol.style.Stroke({
-          color: 'lightblue',
-          //lineDash: [2],
-          width: 2
-        }),
-        fill: new ol.style.Fill({
-          color: 'rgba(0, 0, 255, 0.6)'
-        })
-      }),
-      'Polygon': new ol.style.Style({
-        stroke: new ol.style.Stroke({
-          color: 'lightblue',
-          //lineDash: [2],
-          width: 2
-        }),
-        fill: new ol.style.Fill({
-          color: 'rgba(0, 0, 255, 0.1)'
-        })
-      })
-    };
-
-    this.style_f = (feature) => {
-      return this.style[feature.getGeometry().getType()];
-    };
-
-    this.source = new ol.source.Vector();
-    this.layer = new ol.layer.Vector({source: this.source, style: this.style_f});
-    this.map.addLayer(this.layer);
     this.layer.setZIndex(12);
-    this.visible = true;
-
-    this.overlay = null;
-    this.container = document.getElementById('popup');
-    this.content = document.getElementById('popup-content');
-    this.closer = document.getElementById('popup-closer');
 
     this.lastSelectedContour = null;
 
@@ -73,77 +30,46 @@ class BoxFactory {
     this.button.onclick = f.bind(this);
     this.isOpened = false;
 
-    this.infosBlock = infosBlock;
-
     /*
     ** This is our dragbox interaction
     */
     this.dragBox = new ol.interaction.DragBox({condition: ol.events.condition.platformModifierKeyOnly});
     this.dragBox.on('boxend', () => {
-      console.log("this.dragBox.on('boxend', function() { : entering");
+      ShapesFactory.enter("this.dragBox.on('boxend', function() { : entering");
       var extent = this.dragBox.getGeometry().getExtent();
 
       // The real work when a drag box interaction reach its end is done below ( saynchronously )
       //this.createAndMeasureBox(this.relFITSFilePath, this.sliceIndex, extent[0], extent[2], extent[1], extent[3]);
       let box = this.prepareBox(extent[0], extent[2], extent[1], extent[3]);
       this.measure(box);
-      console.log("this.dragBox.on('boxend', function() { : exiting");
+      ShapesFactory.exit();
     });
-    console.log("BoxFactory ctor: exiting");
+    ShapesFactory.exit();
   }
 
   getButton() {
     return this.button;
   }
 
-  highlight(feature) {
-      console.log("highlight : entering");
-      if (this.lastSelectedBox !== null) {
-        this.lastSelectedBox.setStyle(undefined);
-      }
-      feature.setStyle(this.highlightStyle);
-      this.lastSelectedBox = feature;
-      console.log("highlight : exiting");
-  }
-
   open() {
-    console.log('open: entering');
-      this.map.addInteraction(this.dragBox);
-      this.jTarget.css('cursor','nwse-resize');
-      this.isOpened = true;
-      console.log('open: exiting');
+    ShapesFactory.enter(this.open.name);
+    this.map.addInteraction(this.dragBox);
+    this.jTarget.css('cursor','nwse-resize');
+    this.isOpened = true;
+    ShapesFactory.exit();
   }
 
   close() {
-    console.log('close: open');
+    ShapesFactory.enter(this.close.name);
     this.map.removeInteraction(this.dragBox);
     this.jTarget.css('cursor','pointer');
     this.isOpened = false;
-    console.log('close: exiting');
+    ShapesFactory.exit();
   }
 
-  hide() {
-    console.log("hide : entering");
-    this.layer.setVisible(false);
-    console.log("hide : exiting");
-  };
-
-  show() {
-    console.log("show : entering");
-    this.layer.setVisible(true);
-    console.log("show : exiting");
-  };
-
-  clear() {
-    console.log("clear : entering");
-    if (this.lastSelectedBox) this.lastSelectedBox.setStyle(undefined);
-    this.lastSelectedBox = null;
-    this.source.clear();
-    console.log("clear : exiting");
-  };
 
   prepareBox(iRA0, iRA1, iDEC0, iDEC1){
-    console.log("createBox: entering");
+    ShapesFactory.enter(this.prepareBox.name);
     document.getElementById('loading').style.display='block';
     var tl = [iRA0, iDEC1];
     var tr = [iRA1, iDEC1];
@@ -157,12 +83,12 @@ class BoxFactory {
     let properties = {};
     properties["type"]="box";
     feature.set("properties",properties);
-    console.log("createBox: exiting");
+    ShapesFactory.exit();
     return feature;
   }
 
   measure(feature, addFeature=true) {
-    console.log("measure: entering");
+    ShapesFactory.enter(this.measure.name);
     let properties = feature.get("properties");
     if (properties.hasOwnProperty("type") && properties["type"] === "box") {
       document.getElementById('loading').style.display="block";
@@ -180,7 +106,7 @@ class BoxFactory {
       'iDEC0': iDEC0,
       'iDEC1': iDEC1 },
       (resp) => {
-        console.log('measure callback: entering');
+        ShapesFactory.enter('measure callback: entering');
         document.getElementById('loading').style.display="none";
         if ( resp["status"]  == false ){
           alert ("Something went wrong with the measurements of contour. The message was '" + resp["message"]+"'");
@@ -193,23 +119,24 @@ class BoxFactory {
             this.selected(feature);
           }
         }
-        console.log('measureBox callback: exiting');
+        ShapesFactory.exit();
       } );
     }
     else {
       console.log("Unable to measure such a feature") ;
     }
-    console.log("measure : exiting");
+    ShapesFactory.exit();
   }
 
-  selected(feature) {
-    console.log("selected : entering");
-    let properties = feature.get("properties");
+  selected(box) {
+    ShapesFactory.enter(this.selected.name);
+    let properties = box.get("properties");
     let title = "Flux in box : " + properties["measurements"]["sum"]["value"].toExponential(4) + " " + properties["measurements"]["sum"]["unit"];
     this.infosBlock.headline(title)
     this.infosBlock.populate(title, properties["measurements"]);
-    this.highlight(feature);
-    console.log("selected : exiting");
+    this.highlight(box);
+    ShapesFactory.selection = box;
+    ShapesFactory.exit();
   }
 }
 </script>

yafitsv/views/olqv_contours.ejs

 <script>
-class ContoursViewer {
-
+class ContoursFactory extends ShapesFactory {
   constructor (sliceViewer, infosBlock) {
-    console.log("ContoursViewer ctor: entering");console.trace();
-    this.infosBlock = infosBlock;
+    super(sliceViewer, infosBlock);
+    ShapesFactory.enter(this.constructor.name);
+
     this.source;
     this.layer;
-    this.sliceViewer = sliceViewer;
     this.relFITSFilePath = this.sliceViewer.getRelFITSFilePath();
     this.sliceIndex = this.sliceViewer.getSliceIndex();
-    this.map = sliceViewer.getMap();
-    this.infosBlock = infosBlock;
-
-    this.highlightStyle = new ol.style.Style({
-      fill: new ol.style.Fill({
-        color: 'rgba(255,255,255,0.7)'
-      }),
-      stroke: new ol.style.Stroke({
-        color: '#3399CC',
-        width: 3
-      })
-    });
 
-    this.style = {
-      'LineString': new ol.style.Style({
-        stroke: new ol.style.Stroke({
-          color: 'blue',
-          lineDash: [2],
-          width: 1
-        }),
-        fill: new ol.style.Fill({
-          color: 'rgba(0, 0, 255, 0.6)'
-        })
-      }),
-      'Polygon': new ol.style.Style({
-        stroke: new ol.style.Stroke({
-          color: 'green',
-          lineDash: [2],
-          width: 1
-        }),
-        fill: new ol.style.Fill({
-          color: 'rgba(0, 0, 255, 0.1)'
-        })
-      })
-    };
-
-    this.style_f = (feature) => {
-      return this.style[feature.getGeometry().getType()];
-    };
-
-    this.source = new ol.source.Vector();
-    this.layer = new ol.layer.Vector({source: this.source, style: this.style_f});
-    this.map.addLayer(this.layer);
     this.layer.setZIndex(10);
-    this.visible = true;
 
-    this.overlay = null;
-    this.container = document.getElementById('popup');
-    this.content = document.getElementById('popup-content');
-    this.closer = document.getElementById('popup-closer');
-
-    this.lastSelectedContour = null;
     this.lastBox = null;
 
     $(this.map.getTargetElement()).append($("#ModalContoursForm"));
@@ -74,37 +24,21 @@ class ContoursViewer {
     this.button.setAttribute("title", "Draw contours");
     this.button.append("C");
 
-    console.log("ContoursViewer ctor: exiting");console.trace();
+    ShapesFactory.exit();
   }
 
   getButton() {
     return this.button;
   }
 
-  highlight(feature) {
-      console.log("highlight : entering");
-      if (this.lastSelectedContour !== null) {
-        this.lastSelectedContour.setStyle(undefined);
-        if (this.lastBox !== null) {
-          this.source.removeFeature(this.lastBox);
-          this.lastBox = null;
-        }
-      }
-      feature.setStyle(this.highlightStyle);
-      this.box(feature);
-      //this.grid(feature);
-      this.lastSelectedContour = feature;
-      console.log("highlight : exiting");
-  }
-
   box(feature) {
     console.log("box : entering");
     let br = feature.get("properties")["measurements"]["boundingRect"]["value"];
     let corners=[[br[0], br[1]],
-                  [br[0]+br[2]-1, br[1]],
-                  [br[0]+br[2]-1, br[1]+br[3]-1],
-                  [br[0], br[1]+br[3]-1],
-                  [br[0], br[1]]];
+    [br[0]+br[2]-1, br[1]],
+    [br[0]+br[2]-1, br[1]+br[3]-1],
+    [br[0], br[1]+br[3]-1],
+    [br[0], br[1]]];
 
     this.lastBox = new ol.Feature({geometry: new ol.geom.Polygon([corners])});
     this.source.addFeature(this.lastBox);
@@ -126,54 +60,47 @@ class ContoursViewer {
   }
 
   importYAFITSContours(yAFITSContours) {
+    ShapesFactory.enter(this.importYAFITSContours.name);
     console.log("importYAFITSContours: entering");
     this.clear();
     var features = new Array();
     yAFITSContours.forEach((contour) => {
       let  coordinates = contour["coordinates"];
-      coordinates.push(coordinates[0]);
+      coordinates.push(coordinates[0]);;
+      let properties = contour["properties"];
+      properties["type"] = "contour"
       features.push(new ol.Feature( { geometry : new ol.geom.LineString(coordinates),
-                                      properties : contour["properties"]}))});
+        properties : properties}))}
+      );
     this.source.addFeatures(features);
     this.show();
-    console.log("importYAFITSContours: exiting");
+    ShapesFactory.exit()
   }
 
-  hide() {
-    console.log("hide : entering");
-    this.layer.setVisible(false);
-    console.log("hide : exiting");
+  selected(contour) {
+    ShapesFactory.enter(this.selected.name);
+    let properties = contour.get("properties");
+    let level = properties["level"]["value"].toExponential(3);
+    let levelUnit = properties["level"]["unit"];
+    let title = 'Contour level at ' + level + ' ' + levelUnit;
+    this.infosBlock.headline(title)
+    this.infosBlock.populate(title, properties["measurements"]);
+    this.highlight(contour);
+    ShapesFactory.selection = contour;
+    ShapesFactory.exit()
   }
+}; // End of class ContoursFactory
 
-  show() {
-    console.log("show : entering");
-    this.layer.setVisible(true);
-    console.log("show : exiting");
+class ContoursFactoryGUI {