Merge pull request #69 from StingraySoftware/Sprint_Week_36

Sprint week 36

Author: pbalm

README.md

@@ -20,7 +20,9 @@ You will see that there's plenty left to do!
 
 NOTE: Mac OSX dependencies
 * At least Homebrew installed (http://brew.sh/) or MacPorts installed (https://www.macports.org)
-* Administrator rights are required for using MacPorts, please run Dave using: sudo DAVEApp.app/Contents/MacOS/DAVEApp 
+* If MacPorts will be used, you have two available options:
+* 1 - Install LibMagic by yourself running this MacPorts command `sudo /opt/local/bin/port install file` on the terminal and then launch DAVE running `DAVEApp.app/Contents/MacOS/DAVEApp`.
+* 2 - Launch DAVE as root running this command on the terminal: `sudo DAVEApp.app/Contents/MacOS/DAVEApp`
 
 
 ## Contribute

setup/setup.bash

@@ -3,6 +3,11 @@
 # Source this script to set up the environment for developing DAVE.
 # - Download miniconda and install packages and virtual env
 # - Download node and install packages
+# - Install Python dependencies
+# - Install Stingray and Astropy Helpers
+# - Install Hendrics
+# - Install LibMagic
+# - Install node modules
 
 # First check if the script is being sourced...
 if [[ "${BASH_SOURCE[0]}" == "${0}" ]] ; then
@@ -114,7 +119,7 @@ NODE_FILENAME="node-v$NODE_VERSION"
 			fi
 		fi
 
-		sudo installer -pkg $NODE_TAR -target /
+		installer -pkg $NODE_TAR -target /
 
 	else
 		# Unknown.
@@ -169,8 +174,8 @@ source activate dave
 STINGRAY_FOLDER=$DIR/stingray
 STINGRAY_URL=https://github.com/StingraySoftware/stingray.git
 # Sets the specific commit to checkout:
-# Oct 22th, 2017 -> https://github.com/StingraySoftware/stingray/commit/b64aceb3197062ffd65bfd735ebff190a34e1066
-STINGRAY_COMMIT_HASH=b64aceb3197062ffd65bfd735ebff190a34e1066
+# Nov 7th, 2017 -> https://github.com/StingraySoftware/stingray/commit/0870c2051dadd9fd921fe286132971eb31b6a199
+STINGRAY_COMMIT_HASH=0870c2051dadd9fd921fe286132971eb31b6a199
 LINUX_COMPILATION=lib.linux-x86_64-3.5
 DARWIN_COMPILATION=lib.macosx-10.5-x86_64-3.5
 
@@ -220,12 +225,12 @@ if [ ! -e $STINGRAY_FOLDER ]; then
 		# Mac OSX
 
 		#Build stingray
-		sudo python setup.py install
+		python setup.py install
 
 		cd $STINGRAY_FOLDER/astropy_helpers
 
 		#Build astropy_helpers
-		sudo python setup.py install
+		python setup.py install
 
 		cd $DIR/..
 
@@ -239,8 +244,8 @@ fi
 HENDRICS_FOLDER=$DIR/hendrics
 HENDRICS_URL=https://github.com/StingraySoftware/HENDRICS.git
 # Sets the specific commit to checkout:
-# Oct 20th, 2017 -> https://github.com/StingraySoftware/HENDRICS/commit/9c4f95ec30837bc0bc8077b369e4957bcccefb16
-HENDRICS_COMMIT_HASH=9c4f95ec30837bc0bc8077b369e4957bcccefb16
+# Oct 27th, 2017 -> https://github.com/StingraySoftware/HENDRICS/commit/53ebffd826583027acc7ccad565029babd08d24d
+HENDRICS_COMMIT_HASH=53ebffd826583027acc7ccad565029babd08d24d
 
 if [ ! -e $HENDRICS_FOLDER ]; then
 
@@ -275,7 +280,7 @@ if [ ! -e $HENDRICS_FOLDER ]; then
 		# Mac OSX
 
 		#Build HENDRICS
-		sudo python setup.py install
+		python setup.py install
 
 		cd $DIR/..
 

src/main/js/electron/main.js

@@ -8,11 +8,14 @@ var rq = require('request-promise');
 var Config = require('config-js');
 var Menu = require("menu");
 var request = require('request');
+var fs = require('fs');
 
 let mainWindow,
     windowParams = {
         width:1200,
         height: 700,
+        minHeight: 300,
+        minWidth: 768,
         icon: "resources/resources/static/img/icon.png"
     };
 var retryInterval = 0.5 * 1000;
@@ -85,7 +88,7 @@ function launchPythonServer(config, callback) {
       } else if (config.pythonEnabled) {
         launchProcess ("python", [config.pythonPath, '/tmp', '..', port, 'PY_ENV'], "Python");
       } else if (config.envEnabled) {
-        launchProcess ("/bin/bash", [config.envScriptPath], "Env&Python");
+        launchProcess ("/bin/bash", [config.envScriptPath], "E&P");
       }
 
       if (callback != null) {
@@ -261,15 +264,17 @@ function connectionLost (){
 }
 
 function getTailFromLogFile (logFilePath) {
-  log('Getting log info from: ' + logFilePath, "Warn");
-  var tailProc = cp.spawn("tail", [ "-10", logFilePath ]);
-  var stdout = "";
-  tailProc.stdout.on('data', (data) => {
-    stdout += data;
-  });
-  tailProc.on('close', (code) => {
-    log("LOGFILE: " + stdout);
-  });
+  if (fs.existsSync(logFilePath)) {
+    log('Getting log info from: ' + logFilePath, "Warn");
+    var tailProc = cp.spawn("tail", [ "-10", logFilePath ]);
+    var stdout = "";
+    tailProc.stdout.on('data', (data) => {
+      stdout += data;
+    });
+    tailProc.on('close', (code) => {
+      log("LOGFILE: " + stdout);
+    });
+  }
 }
 
 function escapeSpecialChars (text) {

src/main/python/server.py

@@ -101,7 +101,7 @@ def append_file_to_dataset():
 
 @app.route('/apply_rmf_file_to_dataset', methods=['GET'])
 def apply_rmf_file_to_dataset():
-    return DaveEndpoint.apply_rmf_file_to_dataset(request.args['filename'], request.args['rmf_filename'], UPLOADS_TARGET)
+    return DaveEndpoint.apply_rmf_file_to_dataset(request.args['filename'], request.args['rmf_filename'], request.args['column'], UPLOADS_TARGET)
 
 
 @app.route('/get_plot_data', methods=['POST'])
@@ -202,6 +202,15 @@ def get_rms_spectrum():
             request.json['freq_range'], request.json['energy_range'], int(request.json['n_bands']))
 
 
+@app.route('/get_rms_vs_countrate', methods=['POST'])
+def get_rms_vs_countrate():
+    return DaveEndpoint.get_rms_vs_countrate(request.json['filename'],
+            request.json['bck_filename'], request.json['gti_filename'], UPLOADS_TARGET,
+            request.json['filters'], request.json['axis'], float(request.json['dt']),
+            int(request.json['n_bands']), float(request.json['df']),
+            request.json['freq_range'], request.json['energy_range'])
+
+
 @app.route('/get_plot_data_from_models', methods=['POST'])
 def get_plot_data_from_models():
     return DaveEndpoint.get_plot_data_from_models(request.json['models'], request.json['x_values'])
@@ -284,10 +293,16 @@ def get_pulse_search():
 
 @app.route('/get_phaseogram', methods=['POST'])
 def get_phaseogram():
+
+    binary_params= None
+    if "binary_params" in request.json:
+        binary_params = request.json['binary_params']
+
     return DaveEndpoint.get_phaseogram(request.json['filename'],
             request.json['bck_filename'], request.json['gti_filename'], UPLOADS_TARGET,
             request.json['filters'], request.json['axis'], float(request.json['dt']),
-            float(request.json['f']), int(request.json['nph']), int(request.json['nt']))
+            float(request.json['f']), int(request.json['nph']), int(request.json['nt']),
+            float(request.json['fdot']), float(request.json['fddot']), binary_params)
 
 
 # Receives a message from client and send it to all subscribers

src/main/python/utils/dave_endpoint.py

@@ -121,8 +121,9 @@ def append_file_to_dataset(filename, nextfile, target):
 #                            Creates a new column E with Enery data on dataset
 # @param: filename: filename or dataset cache key
 # @param: rmf_filename: rmf file to apply
+# @param: column: column to use for the conversion: PHA, or PI for NuSTAR
 #
-def apply_rmf_file_to_dataset(filename, rmf_filename, target):
+def apply_rmf_file_to_dataset(filename, rmf_filename, column, target):
     destination = get_destination(filename, target)
     if not destination:
         return common_error("Invalid file or cache key")
@@ -134,7 +135,7 @@ def apply_rmf_file_to_dataset(filename, rmf_filename, target):
     if not FileUtils.is_valid_file(rmf_destination):
         return common_error("Invalid RMF file")
 
-    result = DaveEngine.apply_rmf_file_to_dataset(destination, rmf_destination)
+    result = DaveEngine.apply_rmf_file_to_dataset(destination, rmf_destination, column)
     return json.dumps(result)
 
 
@@ -572,6 +573,43 @@ def get_rms_spectrum(src_filename, bck_filename, gti_filename, target,
     return json.dumps(data, cls=NPEncoder)
 
 
+def get_rms_vs_countrate(src_filename, bck_filename, gti_filename, target,
+                    filters, axis, dt, nsegm, df, freq_range, energy_range):
+    src_destination = get_destination(src_filename, target)
+    if not src_destination:
+        return common_error("Invalid file or cache key for source data")
+
+    bck_destination = ""
+    if bck_filename:
+        bck_destination = get_destination(bck_filename, target)
+        if not bck_destination:
+            return common_error("Invalid file or cache key for backgrund data")
+
+    gti_destination = ""
+    if gti_filename:
+        gti_destination = get_destination(gti_filename, target)
+        if not gti_destination:
+            return common_error("Invalid file or cache key for gti data")
+
+    logging.debug("get_rms_vs_countrate src: %s" % src_filename)
+    logging.debug("get_rms_vs_countrate bck: %s" % bck_filename)
+    logging.debug("get_rms_vs_countrate gti: %s" % gti_filename)
+    logging.debug("get_rms_vs_countrate: filters %s" % filters)
+    logging.debug("get_rms_vs_countrate: axis %s" % axis)
+    logging.debug("get_rms_vs_countrate: dt %s" % dt)
+    logging.debug("get_rms_vs_countrate: nsegm %f" % nsegm)
+    logging.debug("get_rms_vs_countrate: df %s" % df)
+    logging.debug("get_rms_vs_countrate: freq_range %s" % freq_range)
+    logging.debug("get_rms_vs_countrate: energy_range %s" % energy_range)
+
+    data = DaveEngine.get_rms_vs_countrate(src_destination, bck_destination, gti_destination,
+                                        filters, axis, dt, nsegm, df, freq_range, energy_range)
+
+    logging.debug("get_rms_vs_countrate: Finish!")
+
+    return json.dumps(data, cls=NPEncoder)
+
+
 def get_plot_data_from_models(models, x_values):
 
     logging.debug("get_plot_data_from_models models: %s" % models)
@@ -826,7 +864,8 @@ def get_pulse_search(src_filename, bck_filename, gti_filename, target,
 
 
 def get_phaseogram(src_filename, bck_filename, gti_filename, target,
-                    filters, axis, dt, f, nph, nt):
+                    filters, axis, dt, f, nph, nt, fdot=0, fddot=0,
+                    binary_parameters=None):
 
     src_destination = get_destination(src_filename, target)
     if not src_destination:
@@ -853,9 +892,12 @@ def get_phaseogram(src_filename, bck_filename, gti_filename, target,
     logging.debug("get_phaseogram: f %s" % f)
     logging.debug("get_phaseogram: nph %s" % nph)
     logging.debug("get_phaseogram: nt %s" % nt)
+    logging.debug("get_phaseogram: fdot %s" % fdot)
+    logging.debug("get_phaseogram: fddot %s" % fddot)
+    logging.debug("get_phaseogram: binary_parameters %s" % binary_parameters)
 
     data = DaveEngine.get_phaseogram(src_destination, bck_destination, gti_destination,
-                                    filters, axis, dt, f, nph, nt)
+                                    filters, axis, dt, f, nph, nt, fdot, fddot, binary_parameters)
 
     logging.debug("get_phaseogram: Finish!")