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Commit 6ee4a7d4 authored by Moreau Nicolas's avatar Moreau Nicolas
Browse files

Merge branch 'master' into highcharts

parents 86733526 6199091b
Show whitespace changes
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yafitss/DataBlock.py
View file @ 6ee4a7d4
......@@ -714,7 +714,7 @@ class DataBlock:
aux = [0 for x in range(len(bins))]
for i in range (1, len(aux)):
aux[i] = aux[i-1]+population[i-1]
normfactor = reduce(lambda a,b : a*b, self.__data.shape);
normfactor = np.count_nonzero(~np.isnan(data)) #reduce(lambda a,b : a*b, self.__data.shape);
self.__statistics[key]["cumuldist"] = list(map(lambda x: x/normfactor, aux));
self.__logger.debug(self.__statistics[key]);
self.__logger.debug("__collectStatistics : exiting")
......@@ -1197,6 +1197,43 @@ class DataBlock:
self.__logger.debug("measureContour : exiting")
return result
def measureBox(self, iFREQ, iRA0=None, iRA1=None, iDEC0=None, iDEC1=None):
self.__logger.debug("measureBox: entering")
numDims = len(self.__data.shape)
iDEC0 = iDEC0 if iDEC0 else 0
iDEC1 = iDEC1 if iDEC1 else (self.__data.shape[1] if numDims > 2 else self.__data.shape[0])
iRA0 = iRA0 if iRA0 else 0
iRA1 = iRA1 if iRA1 else (self.__data.shape[2] if numDims > 2 else self.__data.shape[1])
box = self.__getSlice(iFREQ).compute()[iDEC0:iDEC1, iRA0:iRA1]
shape = self.__data.shape
result = {}
bunit = self.__header["BUNIT"]
if bunit == "Jy/beam" :
sumunit = "Jy"
bunit = "Jy/beam"
else:
sumunit = bunit
self.__logger.debug(iRA0);
self.__logger.debug(iRA1);
self.__logger.debug(iDEC0);
self.__logger.debug(iDEC1);
self.__logger.debug(shape)
self.__logger.debug(type(box))
result["sum"] = {"value": np.nansum(box).item() / self.__convert * self.__cdelt , "unit" : sumunit}
result["min"] = {"value": np.nanmin(box).item() , "unit": bunit}
result["max"] = {"value": np.nanmax(box).item() , "unit": bunit}
result["mean"] = {"value": np.nanmean(box).item() , "unit": bunit}
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 = {"status":True, "message":"", "result":result}
self.__logger.debug("measureBox : exiting")
return result
#
# End of DataBlock class definition.
#
yafitss/dataManager_michel.py
View file @ 6ee4a7d4
......@@ -219,11 +219,11 @@ class DataManagerImpl :
self.__logger.debug("getPixelValueAtiFreqiRAiDEC : exiting")
return result
def getSumOverSliceRectArea(self, relFITSFilePath, iFREQ, RAPix0=None, RAPix1=None, DECPix0=None, DECPix1=None):
def getSumOverSliceRectArea(self, relFITSFilePath, iFREQ, iRA0=None, iRA1=None, iDEC0=None, iDEC1=None):
self.__logger.debug("getSumOnSliceRectArea : entering")
result = self.__checkPresence(relFITSFilePath)
if result["status"]:
result=self.__dataBlocks[relFITSFilePath].getSumOverSliceRectArea(iFREQ, RAPix0, RAPix1, DECPix0, DECPix1)
result=self.__dataBlocks[relFITSFilePath].getSumOverSliceRectArea(iFREQ, iRA0, iRA1, iDEC0, iDEC1)
self.__logger.debug("getSumOnSliceRectArea : exiting")
return result
......@@ -268,6 +268,14 @@ class DataManagerImpl :
self.__logger.debug("measureContour - dispatcher : exiting")
return result
def measureBox(self, relFITSFilePath, iFREQ, iRA0, iRA1, iDEC0, iDEC1):
self.__logger.debug("measureBox - dispatcher : entering")
result = self.__checkPresence(relFITSFilePath)
if result["status"] :
result = self.__dataBlocks[relFITSFilePath].measureBox(iFREQ, iRA0, iRA1, iDEC0, iDEC1)
self.__logger.debug("measureBox - dispatcher : exiting")
return result
#
# create fits file containing a spectrum at iRA, iDEC
......
yafitss/serverWsgi.py
View file @ 6ee4a7d4
......@@ -560,12 +560,12 @@ def getSumOverSliceRectArea():
logger.debug("getSumOverSliceRectArea - wrapper : entering" )
try:
relFITSFilePath = rebuildFilename(request.GET['relFITSFilePath'])
DECPix0 = getIntValue(request.GET['DECPix0'])
DECPix1 = getIntValue(request.GET['DECPix1'])
RAPix0 = getIntValue(request.GET['RAPix0'])
RAPix1 = getIntValue(request.GET['RAPix1'])
iDEC0 = getIntValue(request.GET['iDEC0'])
iDEC1 = getIntValue(request.GET['iDEC1'])
iRA0 = getIntValue(request.GET['iRA0'])
iRA1 = getIntValue(request.GET['iRA1'])
iFREQ = getIntValue(request.GET['iFREQ'])
result = json.dumps(dm.getSumOverSliceRectArea(relFITSFilePath, iFREQ, RAPix0, RAPix1, DECPix0, DECPix1))
result = json.dumps(dm.getSumOverSliceRectArea(relFITSFilePath, iFREQ, iRA0, iRA1, iDEC0, iDEC1))
except Exception as e:
exc_type, exc_value, exc_traceback = sys.exc_info()
message = "%s ! %s" % (type(e), "".join(traceback.format_list(traceback.extract_tb(exc_traceback))))
......@@ -881,6 +881,29 @@ def measureContour():
logger.debug("measureContour - wrapper : exiting")
return json.dumps(result)
@route( baseUrl+'/measureBox', name='measureBox', method='POST')
@enable_cors
def measureBox():
logger.debug("measureContour - wrapper : entering")
try:
body = byteify(json.loads(request.body.read()))
relFITSFilePath = rebuildFilename(body['relFITSFilePath'])
iFREQ = getIntValue(body['iFREQ'])
iRA0 = getIntValue(body['iRA0']) if 'iRA0' in body else None
iRA1 = getIntValue(body['iRA1']) if 'iRA1' in body else None
iDEC0 = getIntValue(body['iDEC0']) if 'iDEC0' in body else None
iDEC1 = getIntValue(body['iDEC1']) if 'iDEC1' in body else None
result = dm.measureBox(relFITSFilePath, iFREQ, iDEC0, iDEC1, iRA0, iRA1)
except Exception as e:
exc_type, exc_value, exc_traceback = sys.exc_info()
message = "%s ! %s" % (type(e), "".join(traceback.format_list(traceback.extract_tb(exc_traceback))))
logger.debug(message)
result = {"status": False, "message": message}
response.content_type = "application/json; charset=utf-8"
logger.debug("measureContour - wrapper : exiting")
return json.dumps(result)
"""
Given the values of a spectrum 'ydata' passed with the corresponding frequency values 'xdata'
......
yafitsv/routes/olqv.js
View file @ 6ee4a7d4
......@@ -99,14 +99,14 @@ var clienthttp = {
});
},
getSumOverSliceRectArea : function(relFITSFilePath, sessionID, iFREQ, RAPix0, RAPix1, DECPix0, DECPix1, callback) {
getSumOverSliceRectArea : function(relFITSFilePath, sessionID, iFREQ, iRA0, iRA1, iDEC0, iDEC1, callback) {
request(this.server+"/getSumOverSliceRectArea?relFITSFilePath="+relFITSFilePath+
"&sessionID="+sessionID+
"&iFREQ="+iFREQ+
"&RAPix0="+RAPix0+
"&RAPix1="+RAPix1+
"&DECPix0="+DECPix0+
"&DECPix1="+DECPix1,
"&iRA0="+iRA0+
"&iRA1="+iRA1+
"&iDEC0="+iDEC0+
"&iDEC1="+iDEC1,
{json: true},
function(error, response, body){
callback(error, response, body)
......@@ -184,6 +184,16 @@ var clienthttp = {
});
},
measureBox: function(relFITSFilePath, iFREQ, iRA0, iRA1, iDEC0, iDEC1, callback) {
let input = {"relFITSFilePath": relFITSFilePath,
"iFREQ": iFREQ,
"iRA0" : iRA0, "iRA1" : iRA1,
"iDEC0" : iDEC0, "iDEC1" : iDEC1};
request.post(this.server+"/measureBox", {json:true, body:input}, function(error, response, body){
callback(error, response, body);
});
},
renderingCapabilities: function(callback) {
request(this.server+"/renderingCapabilities", {json: true}, function (error, response, body){
callback(error, response, body);
......@@ -542,10 +552,10 @@ router.post('/', function(req, res, next) {
req.body.relFITSFilePath,
req.body.sessionID ? req.body.sessionID : 0,
req.body.iFREQ ? parseInt(req.body.iFREQ) : 0,
req.body.RAPix0 ? parseInt(req.body.RAPix0) : 0,
req.body.RAPix1 ? parseInt(req.body.RAPix1) : null,
req.body.DECPix0 ? parseInt(req.body.DECPix0) : 0,
req.body.DECPix1 ? parseInt(req.body.DECPix1) : null,
req.body.iRA0 ? parseInt(req.body.iRA0) : 0,
req.body.iRA1 ? parseInt(req.body.iRA1) : null,
req.body.iDEC0 ? parseInt(req.body.iDEC0) : 0,
req.body.iDEC1 ? parseInt(req.body.iDEC1) : null,
(error, response, body) => {
console.log("getSumOverSliceRectArea callback : entering");
if (error) {
......@@ -761,6 +771,22 @@ router.post('/measureContour', function(req, res, next){
console.log("router.post('/measureContour', function(req, res, next){: exiting");
});
router.post('/measureBox', function(req, res, next){
console.log("router.post('/measureBox', function(req, res, next){: entering");
clienthttp.measureBox(req.body.relFITSFilePath, req.body.iFREQ, req.body.iRA0, req.body.iRA1, req.body.iDEC0, req.body.iDEC1, (error, response, body) => {
console.log("measureBox callback entering");
if (error) {
console.log(error);
}
else {
console.log(body);
res.send(body);
}
console.log("measureBox callback exiting");
});
console.log("router.post('/measureBox', function(req, res, next){: exiting");
});
router.get("/getYtObj", function(req, res, next) {
console.log('router.get("/", function(req, res, next) { : entering ');
clienthttp.getYtObj(req.query.relFITSFilePath,req.query.iRA0, req.query.iRA1, req.query.iDEC0,
......
yafitsv/views/olqv_2d.ejs
View file @ 6ee4a7d4
......@@ -182,6 +182,7 @@ th, td {
<% include olqv_customcontrols %>
<% include olqv_reset %>
<% include olqv_samp_publisher %>
<% include olqv_boxes %>
<div id="fullscreen" class="fullscreen">
<div class="sidepanel">
<nav class="navbar navbar-dark bg-dark">
......@@ -255,8 +256,27 @@ var yaFITSContoursGUI;
var reset;
var settings;
var boxTool;
function SliceViewer ( relFITSFilePath, width, height, RADECRangeInDegrees, FITSHeader, divSlice) {
var format = function(floatValue) {
let result = floatValue;
if (typeof result === "number" && !Number.isInteger(result)){
result = result.toExponential(4);
}
return result;
};
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>";
}
}
function SliceViewer (relFITSFilePath, width, height, RADECRangeInDegrees, FITSHeader, divSlice) {
console.log("SliceViewer : entering");
let _relFITSFilePath = null;
......@@ -345,6 +365,14 @@ function SliceViewer ( relFITSFilePath, width, height, RADECRangeInDegrees, FITS
return result;
};
this.getSliceIndex = function () {
return _sliceIndex;
}
this.getRelFITSFilePath = function() {
return _relFITSFilePath;
}
this.reset = function() {
_map_1.getView().setCenter(ol.extent.getCenter(_extent));
_map_1.getView().setResolution(1);
......@@ -566,44 +594,22 @@ var _marker_styles_f = function(feature) {
_selected_features_1 = event.target.getFeatures();
_deselected_features_1 = event.deselected;
let infos_line = document.getElementById('infos-line');
let infos_block = document.getElementById('ModalInfosBlockBody');
// Update the displayed integrated flux accordingly with the selected box.
if (_selected_features_1.getLength() == 1) {
let selectedFeature = _selected_features_1.item(0);
let featureType = selectedFeature.getGeometry().getType();
let format = function(floatValue) {
let result = floatValue;
if (typeof result === "number" && !Number.isInteger(result)){
result = result.toExponential(4);
}
return result;
};
let 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>";
}
}
switch (featureType) {
case 'Polygon':
infos_line.innerHTML = 'Integrated flux : ' + _box_infos_1[_selected_features_1.item(0).getId()]["flux"].toExponential(3) + ' Jy';
boxFactory.selected(selectedFeature);
break;
case 'LineString':
var coordinates = selectedFeature.getGeometry().getCoordinates();
let properties = selectedFeature.get("properties");
let level = properties["level"]["value"].toExponential(3);
let levelUnit = properties["level"]["unit"];
let title = 'Contour level at ' + level + ' ' + levelUnit;
infos_line.innerHTML = title;
if ("measurements" in properties) {
populateInfosBlock(title, properties["measurements"]);
infos_line.innerHTML += ' <button type="button" class="btn btn-outline-link btn-sm" data-toggle="modal" data-target="#ModalInfosBlock">etc.</button>';
yAFITSContoursViewer.highlight(selectedFeature);
yAFITSContoursViewer.selected(selectedFeature);
}
else {
document.getElementById('loading').style.display="block";
......@@ -618,9 +624,7 @@ var _marker_styles_f = function(feature) {
console.log(resp["result"]);
properties["measurements"]=resp["result"];
selectedFeature.set("properties",properties);
populateInfosBlock(title, properties["measurements"]);
infos_line.innerHTML += ' <button type="button" class="btn btn-outline-link btn-sm" data-toggle="modal" data-target="#ModalInfosBlock">etc.</button>';
yAFITSContoursViewer.highlight(selectedFeature);
yAFITSContoursViewer.selected(selectedFeature);
}
console.log('measureContour callback : exiting');
});
......@@ -681,21 +685,21 @@ var _marker_styles_f = function(feature) {
/*
** This is our dragbox interaction
*/
_dragBox_1 = new ol.interaction.DragBox();
//_dragBox_1 = new ol.interaction.DragBox();
/*
** And its behaviour.
*/
_dragBox_1.on('boxend', function() {
console.log(" _dragBox_1.on('boxend', function() { : entering");
var extent = _dragBox_1.getGeometry().getExtent();
// The real work when a drag box interaction reach its end is done below
_getSumOverSliceRectAreaWithPOST(_relFITSFilePath, 0, 0, extent);
console.log(JSON.stringify(extent));
console.log(" _dragBox_1.on('boxend', function() { : exiting");
});
// _dragBox_1.on('boxend', function() {
// console.log(" _dragBox_1.on('boxend', function() { : entering");
// var extent = _dragBox_1.getGeometry().getExtent();
//
// // The real work when a drag box interaction reach its end is done below
// _getSumOverSliceRectAreaWithPOST(_relFITSFilePath, 0, 0, extent);
//
// console.log(JSON.stringify(extent));
// console.log(" _dragBox_1.on('boxend', function() { : exiting");
// });
let _updateSliceWithPOST = function () {
......@@ -863,22 +867,22 @@ var _marker_styles_f = function(feature) {
break;
// B
case 66 :
if (_interaction_mode == "") { // Has to see with boxes
_interaction_mode = "box";
_map_1.removeInteraction(_select_1); // Enter box mode
_map_1.addInteraction(_dragBox_1);
jTarget.css('cursor','nwse-resize');
}
else if (_interaction_mode == "box") { // Leave box mode
_interaction_mode = "";
_map_1.removeInteraction(_dragBox_1);
_map_1.addInteraction(_select_1);
jTarget.css('cursor','pointer');
}
break;
// case 66 :
// if (_interaction_mode == "") { // Has to see with boxes
// _interaction_mode = "box";
// _map_1.removeInteraction(_select_1); // Enter box mode
// _map_1.addInteraction(_dragBox_1);
//
// jTarget.css('cursor','nwse-resize');
// }
// else if (_interaction_mode == "box") { // Leave box mode
// _interaction_mode = "";
// _map_1.removeInteraction(_dragBox_1);
// _map_1.addInteraction(_select_1);
//
// jTarget.css('cursor','pointer');
// }
// break;
// X
case 88:
......@@ -1123,20 +1127,22 @@ $( document ).ready(function() {
settings = new Settings(sliceViewer);
customControls.addButton(settings.getButton());
markerFactory = new MarkerFactory(sliceViewer);
customControls.addButton(markerFactory.getButton());
yAFITSContoursViewer = new ContoursViewer(relFITSFilePath, sliceViewer);
customControls.addButton(yAFITSContoursViewer.getButton());
<%if(useSAMP){%>
publishSAMP = new PublishSAMP(sAMPPublisher);
customControls.addButton(publishSAMP.getButton());
<%}%>
markerFactory = new MarkerFactory(sliceViewer);
customControls.addButton(markerFactory.getButton());
yAFITSContoursViewer = new ContoursViewer(sliceViewer, infosBlock);
customControls.addButton(yAFITSContoursViewer.getButton());
yAFITSContoursGUI = new ContoursGUI();
yAFITSContoursGUI.connect(yAFITSContoursViewer, sliceViewer);
boxFactory = new BoxFactory(sliceViewer, infosBlock);
customControls.addButton(boxFactory.getButton());
$('a#rccap').click(function () {sliceViewer.refresh()});
console.log('$.post("", {"method": "RADECRangeInDegrees", "fileName": relFITSFilePath}).done(function (resp) { : exiting');
......
yafitsv/views/olqv_boxes.ejs 0 → 100644
View file @ 6ee4a7d4
<script>
class BoxFactory {
constructor (sliceViewer, infosBlock) {
console.log("BoxFactory ctor: entering");
this.source;
this.layer;
this.dragBox;
this.relFITSFilePath = sliceViewer.getRelFITSFilePath();
this.sliceIndex = sliceViewer.getSliceIndex();
this.map = sliceViewer.getMap();
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;
this.button = document.createElement("button");
this.button.setAttribute("type","button");
this.button.setAttribute("class", "btn btn-primary btn-sm");
this.button.setAttribute("data-tooltip", "tooltip");
this.button.setAttribute("title", "Work with boxes");
this.button.append("B");
let f = function(event) {event.stopPropagation(); if (this.isOpened) this.close(); else this.open();};
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");
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");
});
console.log("BoxFactory ctor: exiting");
}
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');
}
close() {
console.log('close: open');
this.map.removeInteraction(this.dragBox);
this.jTarget.css('cursor','pointer');
this.isOpened = false;
console.log('close: exiting');
}
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");
document.getElementById('loading').style.display='block';
var tl = [iRA0, iDEC1];
var tr = [iRA1, iDEC1];
var br = [iRA1, iDEC0];
var bl = [iRA0, iDEC0];
var corners = [];
corners.push(tl,tr, br, bl, tl);
let feature = new ol.Feature({geometry : new ol.geom.Polygon([corners])});
let properties = {};
properties["type"]="box";
feature.set("properties",properties);
console.log("createBox: exiting");
return feature;
}
measure(feature, addFeature=true) {
console.log("measure: entering");
let properties = feature.get("properties");
if (properties.hasOwnProperty("type") && properties["type"] === "box") {
document.getElementById('loading').style.display="block";
let corners = feature.getGeometry().getCoordinates()[0];
console.log(corners[0]);
let iRA0 = Math.round(corners[0][0]);
let iDEC1 = Math.round(corners[0][1]);
let iRA1 = Math.round(corners[1][0]);
let iDEC0 = Math.round(corners[2][1]);
console.log(iRA0, iRA1, iDEC0, iDEC1);
$.post("measureBox", {'relFITSFilePath': this.relFITSFilePath,
'iFREQ': this.sliceIndex,
'iRA0': iRA0,
'iRA1': iRA1,
'iDEC0': iDEC0,
'iDEC1': iDEC1 },
(resp) => {
console.log('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"]+"'");
}
else {
properties["measurements"]=resp["result"];