Commit 2e92f510 authored by Moreau Nicolas's avatar Moreau Nicolas
Browse files

Merge branch 'master' into highcharts

parents 11bfdcc4 5328a223
......@@ -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=${YAFITSS_MAXIDLE}
command: python /home/partemix/yafitss/serverWsgi.py --port 4251
......@@ -13,6 +13,13 @@
#
export YAFITS_FITSDIR=/datartemix/ALMA/FITS
#
# A way to extend the disk space allocated to FITS files
# by using symbolic links defined in YAFITS_FITSDIR towards files
# or directories located in YAFITS_FITSDIR2
#
export YAFITS_FITSDIR2=/datartemix2/ALMA/FITS
#
# Where will the temporary PNG files and log files be written.
# Ensure that the directories are writable by anybody or at least
......
......@@ -1229,6 +1229,7 @@ class DataBlock:
result["stdev"] = {"value": np.nanstd(box).item() , "unit": bunit}
result["numpix"] = {"value": np.count_nonzero(~np.isnan(box)), "unit" : "pixels (!=Nan)"}
result["percentage of total number of pixels"] = {"value": (box.shape[0]*box.shape[1]) / (self.__header["NAXIS1"]*self.__header["NAXIS2"]) * 100, "unit": "%"}
result["boundingRect"] = {"value":[iRA0, iDEC0, iRA1-iRA0, iDEC1-iDEC0], "unit":"pixels"}
result = {"status":True, "message":"", "result":result}
self.__logger.debug("measureBox : exiting")
......
......@@ -72,9 +72,20 @@ RUN echo "PATH=$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
......
......@@ -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
......
......@@ -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":
......
......@@ -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());
......
<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>
<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 {
static enter(what) {
console.group(this.name + "." + what);
}