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How to use tb_frame method in Slash

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cosmo-serv.py

Source:cosmo-serv.py

1import eventlet2eventlet.monkey_patch()3# app.py4import multiprocessing5import threading6from flask import Flask, jsonify, request, render_template, session, copy_current_request_context7from flask_compress import Compress8import yt9from yt import YTArray10import trident11import numpy as np12from astropy.io import fits13from astropy.table import Table14import json15import yt.units as units16from yt.visualization.volume_rendering.api import PointSource17from yt.units import kpc18import pylab19from itertools import product20from flask import Response21from flask_socketio import SocketIO, emit, join_room, leave_room, close_room, rooms, disconnect22import random23import mpi4py24from mpi4py import MPI25import os.path26from os import path27from trident.config import trident_path28from scipy import interpolate29import sys,os30import copy31import pprint32import psutil33import time34#Flask is used as web framework to run python scripts35#Flask-io / socketio :  gives Flask applications 36# access to low latency bi-directional communications37# between the clients and the server.38 39async_mode = 'eventlet'40app = Flask(__name__)41app.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0 # clears cache on load for debugging42app.config['SECRET_KEY'] = 'secret!'43app.config['TEMPLATES_AUTO_RELOAD'] = True44Compress(app)45# socketio = SocketIO(app, cors_allowed_origins="*", async_mode=async_mode,async_handlers=True,upgradeTimeout=240000,logger=True, engineio_logger=True)46socketio = SocketIO(app,cors_allowed_origins="https://cosmovis-dev.nrp-nautilus.io", async_mode=async_mode,async_handlers=True,upgradeTimeout=240000)#,logger=True, engineio_logger=True)47# thread = None48# thread_lock = Lock()49multiprocessing.set_start_method('spawn')50yt.enable_parallelism()51sgs = []52rpts = {}53spectrum_hdul = fits.HDUList()54try:55    EAGLE_12Mpc = yt.load('static/data/RefL0012N0188/snapshot_028_z000p000/snap_028_z000p000.0.hdf5')56    EAGLE_12Mpc_ad = EAGLE_12Mpc.all_data()57except Exception as e:58    print('error: '+ str( e ))59    exc_type, exc_obj, exc_tb = sys.exc_info()60    fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]61    print(exc_type, fname, exc_tb.tb_lineno) 62try:63    EAGLE_25Mpc = yt.load('static/data/RefL0025N0376/snapshot_028_z000p000/snap_028_z000p000.0.hdf5')64    #EAGLE_25Mpc = yt.load('/cv-vol/EAGLE25_z0_0/RefL0025N0376/snapshot_028_z000p000/snap_028_z000p000.0.hdf5')65    EAGLE_25Mpc_ad = EAGLE_25Mpc.all_data()66except Exception as e:67    print('error: '+ str( e ))68    exc_type, exc_obj, exc_tb = sys.exc_info()69    fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]70    print(exc_type, fname, exc_tb.tb_lineno) 71try:72    EAGLE_100Mpc = yt.load('static/data/RefL0100N1504/snapshot/RefL0100N1504/snapshot_028_z000p000/snap_028_z000p000.0.hdf5')73    # EAGLE_100Mpc = yt.load('/cv-vol/EAGLE100_z0_0/RefL0100N1504/snapshot_028_z000p000/snap_028_z000p000.0.hdf5')74    EAGLE_100Mpc_ad = EAGLE_100Mpc.all_data()75except Exception as e:76    print('error: '+ str( e ))77    exc_type, exc_obj, exc_tb = sys.exc_info()78    fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]79    print(exc_type, fname, exc_tb.tb_lineno)80try:81    TNG100_snap030 = yt.load('static/data/TNG100_z2.3/snapshot/snap_030.0.hdf5')82    # TNG100_snap030 = yt.load('/cv-vol/TNG100_z2_3/snap_030.0.hdf5')83    TNG100_snap030_ad = TNG100_snap030.all_data()84except Exception as e:85    print('error: '+ str( e ))86    exc_type, exc_obj, exc_tb = sys.exc_info()87    fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]88    print(exc_type, fname, exc_tb.tb_lineno) 89try:90    TNG100_snap099 = yt.load('static/data/TNG100_z0.0/snapshot/snap_099.0.hdf5')91    # TNG100_snap099 = yt.load('/cv-vol/TNG100_z0.0/snap_099.0.hdf5')92    TNG100_snap099_ad = TNG100_snap099.all_data()93except Exception as e:94    print('error: '+ str( e ))95    exc_type, exc_obj, exc_tb = sys.exc_info()96    fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]97    print(exc_type, fname, exc_tb.tb_lineno) 98def truncate(f, n):99    '''Truncates/pads a float f to n decimal places without rounding'''100    s = '{}'.format(f)101    if 'e' in s or 'E' in s:102        return '{0:.{1}f}'.format(f, n)103    i, p, d = s.partition('.')104    return '.'.join([i, (d+'0'*n)[:n]])105def interpol8(oldx,oldy,newdx):106    107    # H_I = n.array([np.array(ray.r[('gas', 'l')].to('kpc').tolist()),np.array(ray.r[('gas', 'H_p0_number_density')] * ray.r[('gas', 'dl')].to('kpc').tolist())])108    oldx = np.array(oldx.tolist())109    oldy = np.array(oldy.tolist())110    # newdx = 1111    terpfunc = interpolate.interp1d(oldx, oldy,fill_value="extrapolate")112    newx = np.arange(np.min(oldx), np.max(oldx)+newdx, newdx)113    newy = terpfunc(newx)114    return newx.tolist(), newy.tolist()115# createLookup()116# import pdb; pdb.set_trace()117# host the index.html web page118# default is localhost:5000119@app.route('/webhook', methods=['POST'])120def webhook():121    if request.headers['Content-Type'] == 'application/json':122        info = json.dumps(request.json)123        print(info)124#         threading.Thread(target=lambda: [time.sleep(2), os.system('systemctl restart cosmovis.service')]).start()125        os.system('/bin/bash update.sh')126        return info127@app.route('/')128def index():129    return render_template('index.html', async_mode=socketio.async_mode)130#getSkewerSimpleRay -- this function is used to get the 'quick' data along the skewer and sends it back to the frontend131@socketio.on('getSkewerSimpleRay',namespace="/test")132def handle_ray_selection(simID,idx, start, end):133    # try:134   135    print(multiprocessing.cpu_count())136    sys.stdout.flush()137    socketio.start_background_task(handle_skewer_simple_ray,simID,idx, start, end)138        # th = multiprocessing.Process(target=handle_skewer_simple_ray(simID,idx, start, end))139        # th.start()140        # th.join()141    # except Exception as e:142    #     print('error: '+ str( e ))143    #     exc_type, exc_obj, exc_tb = sys.exc_info()144    #     fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]145    #     print(exc_type, fname, exc_tb.tb_lineno) 146def handle_skewer_simple_ray(simID,idx,start,end):147    yt.enable_parallelism()148    print('system cpu cores: ' + str(multiprocessing.cpu_count()))149    sys.stdout.flush()150    print('cpu cores available to python: ' + str(len(psutil.Process().cpu_affinity())))151    sys.stdout.flush()152    print('mpi parallelism: ' + str(yt.enable_parallelism()))153    sys.stdout.flush()154    print('received simple ray request')155    socketio.emit( 'retrievingLineData', {'index': idx}, namespace = '/test' )156    socketio.sleep(0)157    fn = ''158    # ds = []159    160    if simID == 'RefL0012N0188':161        ds = EAGLE_12Mpc162    elif simID == 'RefL0025N0376':163        ds = EAGLE_25Mpc164    elif simID == 'RefL0100N1504':165        ds = EAGLE_100Mpc166    elif simID == 'TNG100_z2.3':167        ds = TNG100_snap030168    elif simID == 'TNG100_z0.0':169        ds = TNG100_snap099170    else:171        # if 'RefL' in simID:172        #     fn = 'static/data/'+simID+'/snapshot_028_z000p000/snap_028_z000p000.0.hdf5'173        # if 'TNG' in simID:174        #     fn = 'static/data/'+simID+'/snapshot/snap_030.0.hdf5'175        # print("loading" + str(fn))176        print(fn)177        ds = yt.load(fn)178    socketio.sleep(0)179    ad = ds.all_data()180    socketio.sleep(0)181    print(simID)182    socketio.sleep(0)183    sim_width = np.float(ds.domain_right_edge[0].in_units('Mpc') - ds.domain_left_edge[0].in_units('Mpc'))184    # print(ds.domain_right_edge)185    ray_start = np.float_(start)186    ray_end   = np.float_(end)187    # print('ray start: ' + str(ray_start))188    # print('ray end  : ' + str(ray_end))189    ray_start = ds.arr(ray_start/sim_width * np.float(ds.domain_right_edge[0]), 'code_length') #list(np.float_(start))190    ray_end   = ds.arr(ray_end/sim_width * np.float(ds.domain_right_edge[0]), 'code_length')   #list(np.float_(end))191    # ray_start = ds.arr(ray_start, 'Mpc')/sim_width #list(np.float_(start))192    # ray_end   = ds.arr(ray_end, 'Mpc')/sim_width  #list(np.float_(end))193    print(ray_start.in_units('Mpc'))194    print(ray_end.in_units('Mpc'))195    line_list = ['H', 'C', 'N', 'O', 'Mg']196    socketio.sleep(0)197    # This LightRay object is a yt dataset of a 1D data structure representing the skewer path as it traverses the dataset. 198    if simID[:3] == 'Ref':199        ray = trident.make_simple_ray(ds, start_position=ray_start,200                                end_position=ray_end,201                                data_filename="ray.h5",202                                lines=line_list,203                                ftype='gas',204                                fields=[('PartType0','Entropy')])205    elif simID[:3] == 'TNG':206        ray = trident.make_simple_ray(ds, start_position=ray_start,207                                end_position=ray_end,208                                data_filename="ray.h5",209                                lines=line_list)210    socketio.sleep(0)211    trident.add_ion_fields(ray, ions=['O VI', 'C IV', 'N', 'He I', 'He II', 'He III', 'O II', 'O III', 'O V', 'Ne III', 'Ne IV', 'Ne V', 'Ne VI', 'Ne VIII', 'Na I', 'Na IX', 'Mg X', 'Si II', 'Si III', 'Si IV', 'Si XII', 'S II', 'S III', 'S IV', 'S V', 'S VI', 'O IV'], ftype="PartType0")212    socketio.sleep(0)213    # for field in ray.derived_field_list: print(field)214    # ('gas', 'l') -- the 1D location of the gas going from nearby (0) to faraway along the LightRay215    # convert to kpc216    l = ray.r[('gas', 'l')].to('kpc')217    print(ray)218    # ('gas', 'temperature') -- the gas temperature along l (K)219    # the way trident+yt represents ions as fields is a little weird220    # ex: For H I, which is neutral hydrogen, which is H (plus zero energy state), it's represented as H_p0221    # multiply number density by path length (dl) to get column density of ions (units cm^-2)222    socketio.sleep(0)223    dx = 4224    # n_density in units of particles/cm^3225    226    dl_cm = ray.r[('gas', 'dl')].to('cm')227    ## FULL RANGE VALUES228    ## used for graphing229    socketio.sleep(0)230    try:231        H_I = (ray.r[('gas', 'H_p0_number_density')] * dl_cm).tolist()232        i_H_I   = interpol8(l,ray.r[('gas', 'H_p0_number_density')] *  dl_cm,dx)[1]233    except Exception as e:234        H_I = []   235        i_H_I = []236        print('error: '+ str( e ))237        exc_type, exc_obj, exc_tb = sys.exc_info()238        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]239        print(exc_type, fname, exc_tb.tb_lineno) 240    241    socketio.sleep(0)242    try:243        H_II   = (ray.r[('gas', 'H_p1_number_density')]   * dl_cm).tolist()244        i_H_II  = interpol8(l,ray.r[('gas', 'H_p1_number_density')] *  dl_cm,dx)[1]245    except Exception as e:246        H_II  = []247        i_H_II= []248        print('error: '+ str( e ))249        exc_type, exc_obj, exc_tb = sys.exc_info()250        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]251        print(exc_type, fname, exc_tb.tb_lineno) 252    socketio.sleep(0)253    try:254        C_I    = (ray.r[('gas', 'C_p0_number_density')]   * dl_cm).tolist()255        i_C_I   = interpol8(l,ray.r[('gas', 'C_p0_number_density')] *  dl_cm,dx)[1]256    except Exception as e:257        C_I    = []258        i_C_I  = []259        print('error: '+ str( e ))260        exc_type, exc_obj, exc_tb = sys.exc_info()261        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]262        print(exc_type, fname, exc_tb.tb_lineno) 263    socketio.sleep(0)264    try:265        C_II   = (ray.r[('gas', 'C_p1_number_density')]   * dl_cm).tolist()266        i_C_II  = interpol8(l,ray.r[('gas', 'C_p1_number_density')] *  dl_cm,dx)[1]267    except Exception as e:268        C_II  = []269        i_C_II= []270        print('error: '+ str( e ))271        exc_type, exc_obj, exc_tb = sys.exc_info()272        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]273        print(exc_type, fname, exc_tb.tb_lineno) 274    socketio.sleep(0)275    try:276        C_III  = (ray.r[('gas', 'C_p2_number_density')]   * dl_cm).tolist()277        i_C_III = interpol8(l,ray.r[('gas', 'C_p2_number_density')] *  dl_cm,dx)[1]278    except Exception as e:279        C_III  = []280        i_C_III= []281        print('error: '+ str( e ))282        exc_type, exc_obj, exc_tb = sys.exc_info()283        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]284        print(exc_type, fname, exc_tb.tb_lineno) 285    socketio.sleep(0)286    try:287        C_IV   = (ray.r[('gas', 'C_p3_number_density')]   * dl_cm).tolist()288        i_C_IV  = interpol8(l,ray.r[('gas', 'C_p3_number_density')] *  dl_cm,dx)[1]289    except Exception as e:290        C_IV  = []291        i_C_IV= []292        print('error: '+ str( e ))293        exc_type, exc_obj, exc_tb = sys.exc_info()294        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]295        print(exc_type, fname, exc_tb.tb_lineno) 296    socketio.sleep(0)297    try:298        C_V    = (ray.r[('gas', 'C_p4_number_density')]   * dl_cm).tolist()299        i_C_V   = interpol8(l,ray.r[('gas', 'C_p4_number_density')] *  dl_cm,dx)[1]300    except Exception as e:301        C_V   = []302        i_C_V = []303        print('error: '+ str( e ))304        exc_type, exc_obj, exc_tb = sys.exc_info()305        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]306        print(exc_type, fname, exc_tb.tb_lineno) 307    socketio.sleep(0)308    try:309        C_VI   = (ray.r[('gas', 'C_p5_number_density')]   * dl_cm).tolist()310        i_C_VI  = interpol8(l,ray.r[('gas', 'C_p5_number_density')] *  dl_cm,dx)[1]311    except Exception as e:312        C_VI   = []313        i_C_VI = []314        print('error: '+ str( e ))315        exc_type, exc_obj, exc_tb = sys.exc_info()316        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]317        print(exc_type, fname, exc_tb.tb_lineno) 318    socketio.sleep(0)319    try:320        He_I   = (ray.r[('gas', 'He_p0_number_density')]  * dl_cm).tolist()321        i_He_I  = interpol8(l,ray.r[('gas', 'He_p0_number_density')] * dl_cm,dx)[1]322    except Exception as e:323        He_I   = []324        i_He_I = []325        print('error: '+ str( e ))326        exc_type, exc_obj, exc_tb = sys.exc_info()327        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]328        print(exc_type, fname, exc_tb.tb_lineno) 329    socketio.sleep(0)330    try:331        He_II  = (ray.r[('gas', 'He_p1_number_density')]  * dl_cm).tolist()332        i_He_II = interpol8(l,ray.r[('gas', 'He_p1_number_density')] * dl_cm,dx)[1]333    except Exception as e:334        He_II  = []335        i_He_II= []336        print('error: '+ str( e ))337        exc_type, exc_obj, exc_tb = sys.exc_info()338        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]339        print(exc_type, fname, exc_tb.tb_lineno) 340    socketio.sleep(0)341    try:342        He_III = (ray.r[('gas', 'He_p2_number_density')]  * dl_cm).tolist()343        i_He_III= interpol8(l,ray.r[('gas', 'He_p2_number_density')] * dl_cm,dx)[1]344    except Exception as e:345        He_III = []346        i_He_III= []347        print('error: '+ str( e ))348        exc_type, exc_obj, exc_tb = sys.exc_info()349        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]350        print(exc_type, fname, exc_tb.tb_lineno) 351    socketio.sleep(0)352    try:353        Mg_I   = (ray.r[('gas', 'Mg_p0_number_density')]  * dl_cm).tolist()354        i_Mg_I  = interpol8(l,ray.r[('gas', 'Mg_p0_number_density')] * dl_cm,dx)[1]355    except Exception as e:356        Mg_I  = []357        i_Mg_I= []358        print('error: '+ str( e ))359        exc_type, exc_obj, exc_tb = sys.exc_info()360        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]361        print(exc_type, fname, exc_tb.tb_lineno) 362    socketio.sleep(0)363    try:364        Mg_II  = (ray.r[('gas', 'Mg_p1_number_density')]  * dl_cm).tolist()365        i_Mg_II = interpol8(l,ray.r[('gas', 'Mg_p1_number_density')] * dl_cm,dx)[1]366    except Exception as e:367        Mg_II  = []368        i_Mg_II= []369        print('error: '+ str( e ))370        exc_type, exc_obj, exc_tb = sys.exc_info()371        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]372        print(exc_type, fname, exc_tb.tb_lineno) 373    socketio.sleep(0)374    try:375        Mg_X   = (ray.r[('gas', 'Mg_p9_number_density')]  * dl_cm).tolist()376        i_Mg_X  = interpol8(l,ray.r[('gas', 'Mg_p9_number_density')] * dl_cm,dx)[1]377    except Exception as e:378        Mg_X  = []379        i_Mg_X= []380        print('error: '+ str( e ))381        exc_type, exc_obj, exc_tb = sys.exc_info()382        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]383        print(exc_type, fname, exc_tb.tb_lineno) 384    socketio.sleep(0)385    try:386        N_II   = (ray.r[('gas', 'N_p1_number_density')]   * dl_cm).tolist()387        i_N_II  = interpol8(l,ray.r[('gas', 'N_p1_number_density')] *  dl_cm,dx)[1]388        389    except Exception as e:390        N_II  = []391        i_N_II= []392        print('error: '+ str( e ))393        exc_type, exc_obj, exc_tb = sys.exc_info()394        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]395        print(exc_type, fname, exc_tb.tb_lineno) 396    socketio.sleep(0)397    try:398        N_III  = (ray.r[('gas', 'N_p2_number_density')]   * dl_cm).tolist()399        i_N_III = interpol8(l,ray.r[('gas', 'N_p2_number_density')] *  dl_cm,dx)[1]400    except Exception as e:401        N_III  = []402        i_N_III= []403        print('error: '+ str( e ))404        exc_type, exc_obj, exc_tb = sys.exc_info()405        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]406        print(exc_type, fname, exc_tb.tb_lineno) 407    socketio.sleep(0)408    try:409        N_IV   = (ray.r[('gas', 'N_p3_number_density')]   * dl_cm).tolist()410        i_N_IV  = interpol8(l,ray.r[('gas', 'N_p3_number_density')] *  dl_cm,dx)[1]411    except Exception as e:412        N_IV  = []413        i_N_IV= []414        print('error: '+ str( e ))415        exc_type, exc_obj, exc_tb = sys.exc_info()416        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]417        print(exc_type, fname, exc_tb.tb_lineno) 418    socketio.sleep(0)419    try:420        N_V    = (ray.r[('gas', 'N_p4_number_density')]   * dl_cm).tolist()421        i_N_V   = interpol8(l,ray.r[('gas', 'N_p4_number_density')] *  dl_cm,dx)[1]422    except Exception as e:423        N_V   = []424        i_N_V = []425        print('error: '+ str( e ))426        exc_type, exc_obj, exc_tb = sys.exc_info()427        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]428        print(exc_type, fname, exc_tb.tb_lineno) 429    socketio.sleep(0)430    try:431        N_VI   = (ray.r[('gas', 'N_p5_number_density')]   * dl_cm).tolist()432        i_N_VI  = interpol8(l,ray.r[('gas', 'N_p5_number_density')] *  dl_cm,dx)[1]433    except Exception as e:434        N_VI   = []435        i_N_VI = []436        print('error: '+ str( e ))437        exc_type, exc_obj, exc_tb = sys.exc_info()438        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]439        print(exc_type, fname, exc_tb.tb_lineno) 440    socketio.sleep(0)441    try:442        N_VII  = (ray.r[('gas', 'N_p6_number_density')]   * dl_cm).tolist()443        i_N_VII = interpol8(l,ray.r[('gas', 'N_p6_number_density')] *  dl_cm,dx)[1]444    except Exception as e:445        N_VII  = []446        i_N_VII= []447        print('error: '+ str( e ))448        exc_type, exc_obj, exc_tb = sys.exc_info()449        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]450        print(exc_type, fname, exc_tb.tb_lineno) 451    socketio.sleep(0)452    try:453        Na_I   = (ray.r[('gas', 'Na_p0_number_density')]  * dl_cm).tolist()454        i_Na_I  = interpol8(l,ray.r[('gas', 'Na_p0_number_density')] * dl_cm,dx)[1]455    except Exception as e:456        Na_I  = []457        i_Na_I= []458        print('error: '+ str( e ))459        exc_type, exc_obj, exc_tb = sys.exc_info()460        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]461        print(exc_type, fname, exc_tb.tb_lineno) 462    socketio.sleep(0)463    try:464        Na_IX  = (ray.r[('gas', 'Na_p8_number_density')]  * dl_cm).tolist()465        i_Na_IX = interpol8(l,ray.r[('gas', 'Na_p8_number_density')] * dl_cm,dx)[1]466    except Exception as e:467        Na_IX  = []468        i_Na_IX= []469        print('error: '+ str( e ))470        exc_type, exc_obj, exc_tb = sys.exc_info()471        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]472        print(exc_type, fname, exc_tb.tb_lineno) 473    socketio.sleep(0)474    try:475        Ne_III = (ray.r[('gas', 'Ne_p2_number_density')]  * dl_cm).tolist()476        i_Ne_III= interpol8(l,ray.r[('gas', 'Ne_p2_number_density')] * dl_cm,dx)[1]477    except Exception as e:478        Ne_III = []479        i_Ne_III= []480        print('error: '+ str( e ))481        exc_type, exc_obj, exc_tb = sys.exc_info()482        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]483        print(exc_type, fname, exc_tb.tb_lineno) 484    socketio.sleep(0)485    try:486        Ne_IV  = (ray.r[('gas', 'Ne_p3_number_density')]  * dl_cm).tolist()487        i_Ne_IV = interpol8(l,ray.r[('gas', 'Ne_p3_number_density')] * dl_cm,dx)[1]488    except Exception as e:489        Ne_IV  = []490        i_Ne_IV= []491        print('error: '+ str( e ))492        exc_type, exc_obj, exc_tb = sys.exc_info()493        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]494        print(exc_type, fname, exc_tb.tb_lineno) 495    socketio.sleep(0)496    try:497        Ne_V   = (ray.r[('gas', 'Ne_p4_number_density')]  * dl_cm).tolist()498        i_Ne_V  = interpol8(l,ray.r[('gas', 'Ne_p4_number_density')] * dl_cm,dx)[1]499    except Exception as e:500        Ne_V  = []501        i_Ne_V= []502        print('error: '+ str( e ))503        exc_type, exc_obj, exc_tb = sys.exc_info()504        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]505        print(exc_type, fname, exc_tb.tb_lineno) 506    socketio.sleep(0)507    try:508        Ne_VI  = (ray.r[('gas', 'Ne_p5_number_density')]  * dl_cm).tolist()509        i_Ne_VI = interpol8(l,ray.r[('gas', 'Ne_p5_number_density')] * dl_cm,dx)[1]510    except Exception as e:511        Ne_VI  = []512        i_Ne_VI= []513        print('error: '+ str( e ))514        exc_type, exc_obj, exc_tb = sys.exc_info()515        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]516        print(exc_type, fname, exc_tb.tb_lineno) 517    socketio.sleep(0)518    try:519        Ne_VIII= (ray.r[('gas', 'Ne_p7_number_density')]  * dl_cm).tolist()520        i_Ne_VIII=interpol8(l,ray.r[('gas', 'Ne_p7_number_density')] * dl_cm,dx)[1]521    except Exception as e:522        Ne_VIII = []523        i_Ne_VIII= []524        print('error: '+ str( e ))525        exc_type, exc_obj, exc_tb = sys.exc_info()526        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]527        print(exc_type, fname, exc_tb.tb_lineno) 528    socketio.sleep(0)529    try:530        O_I    = (ray.r[('gas', 'O_p0_number_density')]   * dl_cm).tolist()531        i_O_I   = interpol8(l,ray.r[('gas', 'O_p0_number_density')] *  dl_cm,dx)[1]532    except Exception as e:533        O_I   = []534        i_O_I = []535        print('error: '+ str( e ))536        exc_type, exc_obj, exc_tb = sys.exc_info()537        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]538        print(exc_type, fname, exc_tb.tb_lineno) 539    socketio.sleep(0)540    try:541        O_II   = (ray.r[('gas', 'O_p1_number_density')]   * dl_cm).tolist()542        i_O_II  = interpol8(l,ray.r[('gas', 'O_p1_number_density')] *  dl_cm,dx)[1]543    except Exception as e:544        O_II  = []545        i_O_II= []546        print('error: '+ str( e ))547        exc_type, exc_obj, exc_tb = sys.exc_info()548        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]549        print(exc_type, fname, exc_tb.tb_lineno) 550    socketio.sleep(0)551    try:552        O_III  = (ray.r[('gas', 'O_p2_number_density')]   * dl_cm).tolist()553        i_O_III = interpol8(l,ray.r[('gas', 'O_p2_number_density')] *  dl_cm,dx)[1]554    except Exception as e:555        O_III  = []556        i_O_III= []557        print('error: '+ str( e ))558        exc_type, exc_obj, exc_tb = sys.exc_info()559        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]560        print(exc_type, fname, exc_tb.tb_lineno) 561    socketio.sleep(0)562    try:563        O_IV   = (ray.r[('gas', 'O_p3_number_density')]   * dl_cm).tolist()564        i_O_IV  = interpol8(l,ray.r[('gas', 'O_p3_number_density')] *  dl_cm,dx)[1]565    except Exception as e:566        O_IV  = []567        i_O_IV= []568        print('error: '+ str( e ))569        exc_type, exc_obj, exc_tb = sys.exc_info()570        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]571        print(exc_type, fname, exc_tb.tb_lineno) 572    socketio.sleep(0)573    try:574        O_V    = (ray.r[('gas', 'O_p4_number_density')]   * dl_cm).tolist()575        i_O_V   = interpol8(l,ray.r[('gas', 'O_p4_number_density')] *  dl_cm,dx)[1]576    except Exception as e:577        O_V  = []578        i_O_V= []579        print('error: '+ str( e ))580        exc_type, exc_obj, exc_tb = sys.exc_info()581        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]582        print(exc_type, fname, exc_tb.tb_lineno) 583    socketio.sleep(0)584    try:585        O_VI   = (ray.r[('gas', 'O_p5_number_density')]   * dl_cm).tolist()586        i_O_VI  = interpol8(l,ray.r[('gas', 'O_p5_number_density')] *  dl_cm,dx)[1]587    except Exception as e:588        O_VI  = []589        i_O_VI= []590        print('error: '+ str( e ))591        exc_type, exc_obj, exc_tb = sys.exc_info()592        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]593        print(exc_type, fname, exc_tb.tb_lineno) 594    socketio.sleep(0)595    try:596        O_VII  = (ray.r[('gas', 'O_p6_number_density')]   * dl_cm).tolist()597        i_O_VII = interpol8(l,ray.r[('gas', 'O_p6_number_density')] *  dl_cm,dx)[1]598    except Exception as e:599        O_VII  = []600        i_O_VII= []601        print('error: '+ str( e ))602        exc_type, exc_obj, exc_tb = sys.exc_info()603        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]604        print(exc_type, fname, exc_tb.tb_lineno) 605    socketio.sleep(0)606    try:607        O_VIII = (ray.r[('gas', 'O_p7_number_density')]   * dl_cm).tolist()608        i_O_VIII= interpol8(l,ray.r[('gas', 'O_p7_number_density')] *  dl_cm,dx)[1]609    except Exception as e:610        O_VIII = []611        i_O_VIII= []612        print('error: '+ str( e ))613        exc_type, exc_obj, exc_tb = sys.exc_info()614        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]615        print(exc_type, fname, exc_tb.tb_lineno) 616    socketio.sleep(0)617    try:618        S_II   = (ray.r[('gas', 'S_p1_number_density')]   * dl_cm).tolist()619        i_S_II  = interpol8(l,ray.r[('gas', 'S_p1_number_density')] *  dl_cm,dx)[1]620    except Exception as e:621        S_II  = []622        i_S_II= []623        print('error: '+ str( e ))624        exc_type, exc_obj, exc_tb = sys.exc_info()625        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]626        print(exc_type, fname, exc_tb.tb_lineno) 627    socketio.sleep(0)628    try:629        S_III  = (ray.r[('gas', 'S_p2_number_density')]   * dl_cm).tolist()630        i_S_III = interpol8(l,ray.r[('gas', 'S_p2_number_density')] *  dl_cm,dx)[1]631    except Exception as e:632        S_III  = []633        i_S_III= []634        print('error: '+ str( e ))635        exc_type, exc_obj, exc_tb = sys.exc_info()636        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]637        print(exc_type, fname, exc_tb.tb_lineno) 638    socketio.sleep(0)639    try:640        S_IV   = (ray.r[('gas', 'S_p3_number_density')]   * dl_cm).tolist()641        i_S_IV  = interpol8(l,ray.r[('gas', 'S_p3_number_density')] *  dl_cm,dx)[1]642    except Exception as e:643        S_IV  = []644        i_S_IV= []645        print('error: '+ str( e ))646        exc_type, exc_obj, exc_tb = sys.exc_info()647        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]648        print(exc_type, fname, exc_tb.tb_lineno) 649    socketio.sleep(0)650    try:651        S_V    = (ray.r[('gas', 'S_p4_number_density')]   * dl_cm).tolist()652        i_S_V   = interpol8(l,ray.r[('gas', 'S_p4_number_density')] *  dl_cm,dx)[1]653    except Exception as e:654        S_V  = []655        i_S_V= []656        print('error: '+ str( e ))657        exc_type, exc_obj, exc_tb = sys.exc_info()658        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]659        print(exc_type, fname, exc_tb.tb_lineno) 660    socketio.sleep(0)661    try:662        S_VI   = (ray.r[('gas', 'S_p5_number_density')]   * dl_cm).tolist()663        i_S_VI  = interpol8(l,ray.r[('gas', 'S_p5_number_density')] *  dl_cm,dx)[1]664    except Exception as e:665        S_VI  = []666        i_S_VI= []667        print('error: '+ str( e ))668        exc_type, exc_obj, exc_tb = sys.exc_info()669        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]670        print(exc_type, fname, exc_tb.tb_lineno) 671    socketio.sleep(0)672    try:673        Si_II  = (ray.r[('gas', 'Si_p1_number_density')]  * dl_cm).tolist()674        i_Si_II = interpol8(l,ray.r[('gas', 'Si_p1_number_density')] * dl_cm,dx)[1]675    except Exception as e:676        Si_II  = []677        i_Si_II= []678        print('error: '+ str( e ))679        exc_type, exc_obj, exc_tb = sys.exc_info()680        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]681        print(exc_type, fname, exc_tb.tb_lineno) 682    socketio.sleep(0)683    try:684        Si_III = (ray.r[('gas', 'Si_p2_number_density')]  * dl_cm).tolist()685        i_Si_III= interpol8(l,ray.r[('gas', 'Si_p2_number_density')] * dl_cm,dx)[1]686    except Exception as e:687        Si_III = []688        i_Si_III= []689        print('error: '+ str( e ))690        exc_type, exc_obj, exc_tb = sys.exc_info()691        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]692        print(exc_type, fname, exc_tb.tb_lineno) 693    socketio.sleep(0)694    try:695        Si_IV  = (ray.r[('gas', 'Si_p3_number_density')]  * dl_cm).tolist()696        i_Si_IV = interpol8(l,ray.r[('gas', 'Si_p3_number_density')] * dl_cm,dx)[1]697    except Exception as e:698        Si_IV  = []699        i_Si_IV= []700        print('error: '+ str( e ))701        exc_type, exc_obj, exc_tb = sys.exc_info()702        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]703        print(exc_type, fname, exc_tb.tb_lineno) 704    socketio.sleep(0)705    try:706        Si_XII = (ray.r[('gas', 'Si_p11_number_density')] * dl_cm).tolist()707        i_Si_XII= interpol8(l,ray.r[('gas', 'Si_p11_number_density')] *dl_cm,dx)[1]708    except Exception as e:709        Si_XII   = []710        i_Si_XII = []711        print('error: '+ str( e ))712        exc_type, exc_obj, exc_tb = sys.exc_info()713        fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]714        print(exc_type, fname, exc_tb.tb_lineno) 715    716    finally:717        socketio.sleep(0)718        log_density = np.log10(ray.r[('gas', 'density')])+23.77+0.21 # dividing by mean molecular mass, mass of proton719        density     = (10**log_density).tolist() # divide by mean molecular mass... somewhere between ~(10^-6, 1)720        try:721            if simID[:3] == 'Ref':722                entropy   = (ray.r[('gas', 'Entropy')]).tolist()723                i_entropy = interpol8(l,ray.r[('gas', 'Entropy')],dx)[1]724            elif simID[:3] == 'TNG':725                entropy   = (ray.r[('gas', 'entropy')]).tolist()726                i_entropy = interpol8(l,ray.r[('gas', 'entropy')],dx)[1]727        except Exception as e:728            entropy = []729            i_entropy = []730            print('error: '+ str( e ))731            exc_type, exc_obj, exc_tb = sys.exc_info()732            fname = os.path.split(exc_tb.tb_frame.f_code.co_filename)[1]733            print(exc_type, fname, exc_tb.tb_lineno) 734        socketio.sleep(0)735        metallicity = (ray.r[('gas', 'metallicity')].to('Zsun')).tolist()736        temperature = (ray.r[('gas', 'temperature')]).tolist()737        log_density = np.log10(ray.r[('gas', 'density')])+23.77+0.21 # dividing by mean molecular mass, mass of proton738        i_density       = (10**np.array(interpol8(l, log_density,dx)[1])).tolist() # divide by mean molecular mass... somewhere between ~(10^-6, 1)739        i_metallicity   = interpol8(l,ray.r[('gas', 'metallicity')].to('Zsun'),dx)[1]740        i_l, i_temperature = interpol8(l,ray.r[('gas', 'temperature')],dx)741        socketio.sleep(0)742        socketio.emit('simple_line_data',{  'index':         idx,743                                         'start':         start,744                                         'end':           end,745                                         'l':             l.tolist(),746                                         'N(H I)':        H_I,747                                         'N(H II)':       H_II,748                                         'N(C I)':        C_I,749                                         'N(C II)':       C_II,750                                         'N(C III)':      C_III,751                                         'N(C IV)':       C_IV,752                                         'N(C V)':        C_V,753                                         'N(C VI)':       C_VI,754                                         'N(He I)':       He_I,755                                         'N(He II)':      He_II,756                                         'N(He III)':     He_III,757                                         'N(Mg I)':       Mg_I,758                                         'N(Mg II)':      Mg_II,759                                         'N(Mg X)':       Mg_X,760                                         'N(N II)':       N_II,761                                         'N(N III)':      N_III,762                                         'N(N IV)':       N_IV,763                                         'N(N V)':        N_V,764                                         'N(N VI)':       N_VI,765                                         'N(N VII)':      N_VII,766                                         'N(Na I)':       Na_I,767                                         'N(Na IX)':      Na_IX,768                                         'N(Ne III)':     Ne_III,769                                         'N(Ne IV)':      Ne_IV,770                                         'N(Ne V)':       Ne_V,771                                         'N(Ne VI)':      Ne_VI,772                                         'N(Ne VIII)':    Ne_VIII,773                                         'N(O I)':        O_I,774                                         'N(O II)':       O_II,775                                         'N(O III)':      O_III,776                                         'N(O IV)':       O_IV,777                                         'N(O V)':        O_V,778                                         'N(O VI)':       O_VI,779                                         'N(O VII)':      O_VII,780                                         'N(O VIII)':     O_VIII,781                                         'N(S II)':       S_II,782                                         'N(S III)':      S_III,783                                         'N(S IV)':       S_IV,784                                         'N(S V)':        S_V,785                                         'N(S VI)':       S_VI,786                                         'N(Si II)':      Si_II,787                                         'N(Si III)':     Si_III,788                                         'N(Si IV)':      Si_IV,789                                         'N(Si XII)':     Si_XII,790                                         'density':       density,791                                         'entropy':       entropy,792                                         'metallicity':   metallicity,793                                         'temperature':   temperature,794                                         'i_l':           i_l,795                                         'i_N(H I)':      i_H_I,796                                         'i_N(H II)':     i_H_II,797                                         'i_N(C I)':      i_C_I,798                                         'i_N(C II)':     i_C_II,799                                         'i_N(C III)':    i_C_III,800                                         'i_N(C IV)':     i_C_IV,801                                         'i_N(C V)':      i_C_V,802                                         'i_N(C VI)':     i_C_VI,803                                         'i_N(He I)':     i_He_I,804                                         'i_N(He II)':    i_He_II,805                                         'i_N(He III)':   i_He_III,806                                         'i_N(Mg I)':     i_Mg_I,807                                         'i_N(Mg II)':    i_Mg_II,808                                         'i_N(Mg X)':     i_Mg_X,809                                         'i_N(N II)':     i_N_II,810                                         'i_N(N III)':    i_N_III,811                                         'i_N(N IV)':     i_N_IV,812                                         'i_N(N V)':      i_N_V,813                                         'i_N(N VI)':     i_N_VI,814                                         'i_N(N VII)':    i_N_VII,815                                         'i_N(Na I)':     i_Na_I,816                                         'i_N(Na IX)':    i_Na_IX,817                                         'i_N(Ne III)':   i_Ne_III,818                                         'i_N(Ne IV)':    i_Ne_IV,819                                         'i_N(Ne V)':     i_Ne_V,820                                         'i_N(Ne VI)':    i_Ne_VI,821                                         'i_N(Ne VIII)':  i_Ne_VIII,822                                         'i_N(O I)':      i_O_I,823                                         'i_N(O II)':     i_O_II,824                                         'i_N(O III)':    i_O_III,825                                         'i_N(O IV)':     i_O_IV,826                                         'i_N(O V)':      i_O_V,827                                         'i_N(O VI)':     i_O_VI,828                                         'i_N(O VII)':    i_O_VII,829                                         'i_N(O VIII)':   i_O_VIII,830                                         'i_N(S II)':     i_S_II,831                                         'i_N(S III)':    i_S_III,832                                         'i_N(S IV)':     i_S_IV,833                                         'i_N(S V)':      i_S_V,834                                         'i_N(S VI)':     i_S_VI,835                                         'i_N(Si II)':    i_Si_II,836                                         'i_N(Si III)':   i_Si_III,837                                         'i_N(Si IV)':    i_Si_IV,838                                         'i_N(Si XII)':   i_Si_XII,839                                         'i_density':     i_density,840                                         'i_entropy':     i_entropy,841                                         'i_metallicity': i_metallicity,842                                         'i_temperature': i_temperature843                                        }, namespace='/test')844    socketio.sleep(0)845    print('sent simple ray data')846# selectRay is called from index.html when 847@socketio.on('selectRay', namespace='/test')848def handle_ray_selection(simID,idx, start, end):849    try:850        if path.exists('static/data/skewers/'+simID+'_'+str(idx)+'_'+str(start)+'_'+str(end)+'.json'):851            socketio.emit( 'synthetic_spectrum_saved', {'index': 'static/data/skewers/'+simID+'_'+str(idx)+'_'+str(start)+'_'+str(end)+'.json'}, namespace = '/test' )852        else:853            socketio.start_background_task(handle_ray_selection_background,simID,idx, start, end)854    except:855        socketio.emit( 'spectrumError', {'index': idx}, namespace = '/test' )856    857def handle_ray_selection_background(simID,idx,start,end):858    # socketio = SocketIO(message_queue='amqp://')859    socketio.emit( 'processingRay', {'index': idx}, namespace = '/test' )860    eventlet.sleep()861    socketio.sleep(0)862    # fn = ''863    # if 'RefL' in simID:864    #     fn = 'static/data/'+simID+'/snapshot_028_z000p000/snap_028_z000p000.0.hdf5'865    # if 'TNG' in simID:866    #     fn = 'static/data/'+simID+'/snapshot/snap_030.0.hdf5'867    # # ds = yt.load(fn)868    # socketio.sleep(0)869    # # ad = ds.all_data()870    fn = ''871    # ds = []872    873    if simID == 'RefL0012N0188':874        ds = EAGLE_12Mpc875    elif simID == 'RefL0025N0376':876        ds = EAGLE_25Mpc877    elif simID == 'RefL0100N1504':878        ds = EAGLE_100Mpc879    elif simID == 'TNG100_z2.3':880        ds = TNG100_snap030881    elif simID == 'TNG100_z0.0':882        ds = TNG100_snap099883    else:884        # if 'RefL' in simID:885        #     fn = 'static/data/'+simID+'/snapshot_028_z000p000/snap_028_z000p000.0.hdf5'886        # if 'TNG' in simID:887        #     fn = 'static/data/'+simID+'/snapshot/snap_030.0.hdf5'888        # print("loading" + str(fn))889        print(fn)890        ds = yt.load(fn)891    ad = ds.all_data()892    print(simID)893    print('received args: ' + str(start) + str(end))894    ray_start = np.float_(start)895    ray_end = np.float_(end)896    sim_width = np.float(ds.domain_right_edge[0].in_units('Mpc') - ds.domain_left_edge[0].in_units('Mpc'))897    # ray_start = ds.arr(ray_start, 'Mpc') #list(np.float_(start))898    # ray_end   = ds.arr(ray_end, 'Mpc')899    ray_start = ds.arr(ray_start/sim_width * np.float(ds.domain_right_edge[0]), 'code_length') #list(np.float_(start))900    ray_end   = ds.arr(ray_end/sim_width * np.float(ds.domain_right_edge[0]), 'code_length')   #list(np.float_(end))901    print(ray_start.in_units('Mpc'))902    print(ray_end.in_units('Mpc'))903    line_list = ['H', 'C', 'N', 'O', 'Mg']904    instrument = 'COS'905    grating = 'G130M'906    inst = instrument + '-' + grating907    lambda_min = float(trident.valid_instruments[inst].lambda_min)908    lambda_max = float(trident.valid_instruments[inst].lambda_max)909    path = trident_path() + '/data/line_lists/lines.txt'910    path2 = trident_path() + '/data/line_lists/lines_subset_test.txt'911    912    lines_data = open(path,"r")913    open(path2, 'w').close()914    lines_subset_test = open(path2,"a")915    socketio.sleep(0)916    c = 0917    lines = {} # keeps track of lines and whether or not they are added to the subset918    for line in lines_data:919        if c == 0:920            lines_subset_test.write(line)921            c+=1922            continue923        field = line.split()924        # print(field)925        wavelength = float(field[2])926        element = field[0] + field[1] + truncate(wavelength,0)927        element = element[:-1]928        if (wavelength >= lambda_min) and (wavelength <= lambda_max):929            lines_subset_test.write(line)930            lines[element] = True931        else:932            lines[element] = False933            continue934        # import pdb; pdb.set_trace()935    936    lines_data.close()937    lines_subset_test.close()938    print("making simple ray")939    socketio.sleep(0)940    ray = trident.make_simple_ray(ds, start_position=ray_start,941                               end_position=ray_end,942                               data_filename="ray.h5", # update file name if we need multiple943                               lines=line_list)944    socketio.sleep(0)945    sg = trident.SpectrumGenerator(inst ,line_database="lines_subset_test.txt")#, dlambda=1)946    # sg = trident.SpectrumGenerator('COS-G130M',line_database="lines.txt")947    948    # emit('my_response', {'data': 'Connected', 'count': -1})949    socketio.sleep(0)950    print('making spectrum')951    sg.make_spectrum(ray, lines=line_list) #spitting information through std_out, scrape information952    socketio.sleep(0)953    # sg.add_qso_spectrum(emitting_redshift=0.5)954    955    MW = False956    if MW == True:957        sg.add_milky_way_foreground() #fine with COS G130M958    socketio.sleep(0)959    sg.apply_lsf() #instrumental profile960    socketio.sleep(0)961    noise = True962    SNR = 50963    if noise == True:964        sg.add_gaussian_noise(SNR)965    socketio.sleep(0)966    error = sg.error_func(sg.flux_field)967    968    socketio.sleep(0)969    sgs.append([start,end,sg,idx])970    socketio.sleep(0)971    socketio.emit( 'sentRay', {'index': idx}, namespace = '/test' )972    socketio.sleep(0)973    print('emitting spectrum')974    socketio.sleep(0)975    socketio.emit('synthetic_spectrum',{'index':idx,'start':start,'end':end,'lambda':sgs[-1][2].lambda_field.tolist(),'flux':sgs[-1][2].flux_field.tolist()}, namespace='/test')976    socketio.sleep(0)977    print('sent spectrum')978    # sg.save_spectrum('spec_raw.txt')979    # sg.plot_spectrum('spec_raw.png')980    # print(jsonify(sg.lambda_field.tolist()))981    # print(sg.flux_field.tolist())982    tab = Table((sgs[-1][2].lambda_field.tolist(), sgs[-1][2].flux_field.tolist(), error.tolist() ), names=["lambda","flux","error"])983    # tab = Table((sgs[-1][2].lambda_field.tolist(), sgs[-1][2].flux_field.tolist() ), names=["lambda","flux"])984    hdul = fits.table_to_hdu(tab)985    hdr = hdul.header986    # Software987    hdr['COSMOVIS'] = 0.1 # Cosmovis version988    hdr['TRIDENT'] =  trident.__version__   # Trident version989    hdr['YT'] = yt.__version__    # Yt version990    # Simulation991    hdr['SIM'] = 'EAGLE'    # Simulation (EAGLE, FIRE, etc.)992    hdr['SIM_VERS'] = 'RefL0012N0188'    # Sim version993    hdr['BOX_SIZE'] = ds.parameters['BoxSize']  # Box size994    hdr['Z'] = ds.parameters['Redshift']   # Redshift995    # Spectrum996    hdr['X1Y1Z1'] = str(start[0]) + ', ' + str(start[1]) + ', ' + str(start[2])           997                                    # X1, Y1, Z1998    hdr['X2Y2Z2'] = str(end[0]) + ', ' + str(end[1]) + ', '  + str(end[2])          999                                    # X2, Y2, Z2    1000    hdr['MW_FRGND'] = MW            # MWforeground (True, False)1001    hdr['NOISEADD'] = noise         # NoiseAdded (True, False)1002    hdr['NOISETYP'] = 'Gaussian'    # NoiseType (Gaussian, custom)1003    hdr['SNR'] = SNR                # SNR1004    hdr['SEED'] = False             # NoiseSeed1005    hdr['INSTRMNT'] = instrument    # Instrument1006    hdr['GRATING'] = grating        # Grating1007    hdr['ROTATION'] = 'null'        # Grating rotation1008    hdr['RESOLUTN'] = float(sg.dlambda*6)    # Spectral resolution (Angstroms)1009    # Lines added (each boolean)1010    for line in lines:1011        # print(lines[line])1012        hdr[line] = lines[line]1013        # HI12151014        # HI10251015        # HI9721016        # OVI10311017        # OVI10371018    spectrum_hdul.append(hdul)1019    spectrum_hdul.writeto('static/data/spectra.fits', overwrite=True)1020    1021    socketio.sleep(0)1022    spec = {'index':idx,'start':start,'end':end,'lambda':sgs[-1][2].lambda_field.tolist(),'flux':sgs[-1][2].flux_field.tolist()}1023    socketio.sleep()1024    with open('static/data/skewers/'+simID+'_'+str(idx)+'_'+str(start)+'_'+str(end)+'.json', 'w') as file:1025        json.dump(spec, file)1026    socketio.sleep(0)1027    socketio.emit( 'synthetic_spectrum_saved', {'index': 'static/data/skewers/'+simID+'_'+str(idx)+'_'+str(start)+'_'+str(end)+'.json'}, namespace = '/test' )1028    socketio.sleep(0)1029    print("spectrum saved")1030    1031@socketio.on('simIDtoServer', namespace='/test')1032def updateSimID(simID):1033             1034    global fn1035    global ds1036    global fl 1037    global ad1038    global right_edge 1039    global left_edge1040    if simID == 'RefL0012N0188':1041        if fn != 'static/data/RefL0012N0188/snapshot_028_z000p000/snap_028_z000p000.0.hdf5':1042            fn = 'static/data/RefL0012N0188/snapshot_028_z000p000/snap_028_z000p000.0.hdf5'1043            # ds = yt.load(fn)1044            fl = sorted(ds.field_list) # contains list of fields in the dataset1045            ad = ds.all_data()1046            right_edge = [float(ad.right_edge[0]),float(ad.right_edge[1]),float(ad.right_edge[2])]1047            left_edge = [float(ad.left_edge[0]),float(ad.left_edge[1]),float(ad.left_edge[2])]1048            emit('field_list', {'data': fl},namespace='/test')1049            emit('domain_edges', {'left_edge': left_edge, 'right_edge': right_edge},namespace='/test')1050    elif simID == 'RefL0025N0376':1051        if fn != 'static/data/RefL0025N0376/snapshot_028_z000p000/snap_028_z000p000.0.hdf5':1052            fn = 'static/data/RefL0025N0376/snapshot_028_z000p000/snap_028_z000p000.0.hdf5'1053            # ds = yt.load(fn)1054            fl = sorted(ds.field_list) # contains list of fields in the dataset1055            ad = ds.all_data()1056            right_edge = [float(ad.right_edge[0]),float(ad.right_edge[1]),float(ad.right_edge[2])]1057            left_edge = [float(ad.left_edge[0]),float(ad.left_edge[1]),float(ad.left_edge[2])]1058            emit('field_list', {'data': fl},namespace='/test')1059            emit('domain_edges', {'left_edge': left_edge, 'right_edge': right_edge},namespace='/test')1060    with open('static/data/'+simID+'/simMetadata.json', 'w') as file:1061        simMetadata = {1062            "left_edge": left_edge,1063            "right_edge": right_edge,1064            "field_list": fl1065        }1066        json.dump(simMetadata, file)1067@socketio.on('connect', namespace='/test')1068def test_connect():1069    print("connected")1070    emit('my_response', {'data': 'Connected', 'count': 0})1071if __name__ == '__main__':1072    # socketio.run(app, debug=False)1073    # socketio.run(app, host='0.0.0.0', debug=True)...

__init__.py

Source:__init__.py

1import re2import sys3from types import CodeType4from types import FrameType5from types import TracebackType6try:7    from __pypy__ import tproxy8except ImportError:9    tproxy = None10try:11    from .cpython import tb_set_next12except ImportError:13    tb_set_next = None14if not tb_set_next and not tproxy:15    raise ImportError("Cannot use tblib. Runtime not supported.")16__version__ = '1.7.0'17__all__ = 'Traceback', 'TracebackParseError', 'Frame', 'Code'18PY3 = sys.version_info[0] == 319FRAME_RE = re.compile(r'^\s*File "(?P<co_filename>.+)", line (?P<tb_lineno>\d+)(, in (?P<co_name>.+))?$')20class _AttrDict(dict):21    __slots__ = ()22    def __getattr__(self, name):23        try:24            return self[name]25        except KeyError:26            raise AttributeError(name)27# noinspection PyPep8Naming28class __traceback_maker(Exception):29    pass30class TracebackParseError(Exception):31    pass32class Code(object):33    """34    Class that replicates just enough of the builtin Code object to enable serialization and traceback rendering.35    """36    co_code = None37    def __init__(self, code):38        self.co_filename = code.co_filename39        self.co_name = code.co_name40        self.co_argcount = 041        self.co_kwonlyargcount = 042        self.co_varnames = ()43        self.co_nlocals = 044        self.co_stacksize = 045        self.co_flags = 6446        self.co_firstlineno = 047    # noinspection SpellCheckingInspection48    def __tproxy__(self, operation, *args, **kwargs):49        """50        Necessary for PyPy's tproxy.51        """52        if operation in ('__getattribute__', '__getattr__'):53            return getattr(self, args[0])54        else:55            return getattr(self, operation)(*args, **kwargs)56class Frame(object):57    """58    Class that replicates just enough of the builtin Frame object to enable serialization and traceback rendering.59    """60    def __init__(self, frame):61        self.f_locals = {}62        self.f_globals = {63            k: v64            for k, v in frame.f_globals.items()65            if k in ("__file__", "__name__")66        }67        self.f_code = Code(frame.f_code)68        self.f_lineno = frame.f_lineno69    def clear(self):70        """71        For compatibility with PyPy 3.5;72        clear() was added to frame in Python 3.473        and is called by traceback.clear_frames(), which74        in turn is called by unittest.TestCase.assertRaises75        """76    # noinspection SpellCheckingInspection77    def __tproxy__(self, operation, *args, **kwargs):78        """79        Necessary for PyPy's tproxy.80        """81        if operation in ('__getattribute__', '__getattr__'):82            if args[0] == 'f_code':83                return tproxy(CodeType, self.f_code.__tproxy__)84            else:85                return getattr(self, args[0])86        else:87            return getattr(self, operation)(*args, **kwargs)88class Traceback(object):89    """90    Class that wraps builtin Traceback objects.91    """92    tb_next = None93    def __init__(self, tb):94        self.tb_frame = Frame(tb.tb_frame)95        # noinspection SpellCheckingInspection96        self.tb_lineno = int(tb.tb_lineno)97        # Build in place to avoid exceeding the recursion limit98        tb = tb.tb_next99        prev_traceback = self100        cls = type(self)101        while tb is not None:102            traceback = object.__new__(cls)103            traceback.tb_frame = Frame(tb.tb_frame)104            traceback.tb_lineno = int(tb.tb_lineno)105            prev_traceback.tb_next = traceback106            prev_traceback = traceback107            tb = tb.tb_next108    def as_traceback(self):109        """110        Convert to a builtin Traceback object that is usable for raising or rendering a stacktrace.111        """112        if tproxy:113            return tproxy(TracebackType, self.__tproxy__)114        if not tb_set_next:115            raise RuntimeError("Unsupported Python interpreter!")116        current = self117        top_tb = None118        tb = None119        while current:120            f_code = current.tb_frame.f_code121            code = compile('\n' * (current.tb_lineno - 1) + 'raise __traceback_maker', current.tb_frame.f_code.co_filename, 'exec')122            if hasattr(code, "replace"):123                # Python 3.8 and newer124                code = code.replace(co_argcount=0,125                                    co_filename=f_code.co_filename, co_name=f_code.co_name,126                                    co_freevars=(), co_cellvars=())127            elif PY3:128                code = CodeType(129                    0, code.co_kwonlyargcount,130                    code.co_nlocals, code.co_stacksize, code.co_flags,131                    code.co_code, code.co_consts, code.co_names, code.co_varnames,132                    f_code.co_filename, f_code.co_name,133                    code.co_firstlineno, code.co_lnotab, (), ()134                )135            else:136                code = CodeType(137                    0,138                    code.co_nlocals, code.co_stacksize, code.co_flags,139                    code.co_code, code.co_consts, code.co_names, code.co_varnames,140                    f_code.co_filename.encode(), f_code.co_name.encode(),141                    code.co_firstlineno, code.co_lnotab, (), ()142                )143            # noinspection PyBroadException144            try:145                exec(code, dict(current.tb_frame.f_globals), {})146            except Exception:147                next_tb = sys.exc_info()[2].tb_next148                if top_tb is None:149                    top_tb = next_tb150                if tb is not None:151                    tb_set_next(tb, next_tb)152                tb = next_tb153                del next_tb154            current = current.tb_next155        try:156            return top_tb157        finally:158            del top_tb159            del tb160    to_traceback = as_traceback161    # noinspection SpellCheckingInspection162    def __tproxy__(self, operation, *args, **kwargs):163        """164        Necessary for PyPy's tproxy.165        """166        if operation in ('__getattribute__', '__getattr__'):167            if args[0] == 'tb_next':168                return self.tb_next and self.tb_next.as_traceback()169            elif args[0] == 'tb_frame':170                return tproxy(FrameType, self.tb_frame.__tproxy__)171            else:172                return getattr(self, args[0])173        else:174            return getattr(self, operation)(*args, **kwargs)175    def as_dict(self):176        """177        Converts to a dictionary representation. You can serialize the result to JSON as it only has178        builtin objects like dicts, lists, ints or strings.179        """180        if self.tb_next is None:181            tb_next = None182        else:183            tb_next = self.tb_next.to_dict()184        code = {185            'co_filename': self.tb_frame.f_code.co_filename,186            'co_name': self.tb_frame.f_code.co_name,187        }188        frame = {189            'f_globals': self.tb_frame.f_globals,190            'f_code': code,191            'f_lineno': self.tb_frame.f_lineno,192        }193        return {194            'tb_frame': frame,195            'tb_lineno': self.tb_lineno,196            'tb_next': tb_next,197        }198    to_dict = as_dict199    @classmethod200    def from_dict(cls, dct):201        """202        Creates an instance from a dictionary with the same structure as ``.as_dict()`` returns.203        """204        if dct['tb_next']:205            tb_next = cls.from_dict(dct['tb_next'])206        else:207            tb_next = None208        code = _AttrDict(209            co_filename=dct['tb_frame']['f_code']['co_filename'],210            co_name=dct['tb_frame']['f_code']['co_name'],211        )212        frame = _AttrDict(213            f_globals=dct['tb_frame']['f_globals'],214            f_code=code,215            f_lineno=dct['tb_frame']['f_lineno'],216        )217        tb = _AttrDict(218            tb_frame=frame,219            tb_lineno=dct['tb_lineno'],220            tb_next=tb_next,221        )222        return cls(tb)223    @classmethod224    def from_string(cls, string, strict=True):225        """226        Creates an instance by parsing a stacktrace. Strict means that parsing stops when lines are not indented by at least two spaces227        anymore.228        """229        frames = []230        header = strict231        for line in string.splitlines():232            line = line.rstrip()233            if header:234                if line == 'Traceback (most recent call last):':235                    header = False236                continue237            frame_match = FRAME_RE.match(line)238            if frame_match:239                frames.append(frame_match.groupdict())240            elif line.startswith('  '):241                pass242            elif strict:243                break  # traceback ended244        if frames:245            previous = None246            for frame in reversed(frames):247                previous = _AttrDict(248                    frame,249                    tb_frame=_AttrDict(250                        frame,251                        f_globals=_AttrDict(252                            __file__=frame['co_filename'],253                            __name__='?',254                        ),255                        f_code=_AttrDict(frame),256                        f_lineno=int(frame['tb_lineno']),257                    ),258                    tb_next=previous,259                )260            return cls(previous)261        else:...

exception_test.py

Source:exception_test.py

1# -*- coding: UTF-8 -*-2#3# Copyright 2015-2022 Flavio Garcia4#5# Licensed under the Apache License, Version 2.0 (the "License");6# you may not use this file except in compliance with the License.7# You may obtain a copy of the License at8#9#    http://www.apache.org/licenses/LICENSE-2.010#11# Unless required by applicable law or agreed to in writing, software12# distributed under the License is distributed on an "AS IS" BASIS,13# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.14# See the License for the specific language governing permissions and15# limitations under the License.16"""17Datetime tests18"""19from tests import WarningsHandler20from cartola import exception21import logging22import warnings23import unittest24logger = logging.getLogger(__name__)25class MockLoggingHandler(logging.Handler):26    """Mock logging handler to check for expected logs.27    Messages are available from an instance's ``messages`` dict, in order,28    indexed by a lowercase log level string (e.g., 'debug', 'info', etc.).29    SEE: https://stackoverflow.com/a/20553331/288798930    """31    def __init__(self, *args, **kwargs):32        self.messages = {'debug': [], 'info': [], 'warning': [], 'error': [],33                         'critical': []}34        super(MockLoggingHandler, self).__init__(*args, **kwargs)35    def emit(self, record):36        """Store a message from ``record`` in the instance's ``messages``37        dict."""38        try:39            self.messages[record.levelname.lower()].append(record)40        except Exception:41            self.handleError(record)42    def reset(self):43        self.acquire()44        try:45            for message_list in self.messages.values():46                message_list.clear()47        finally:48            self.release()49class ExceptionTestCase(unittest.TestCase):50    @classmethod51    def setUpClass(cls):52        super(ExceptionTestCase, cls).setUpClass()53        # Assuming you follow Python's logging module's documentation's54        # recommendation about naming your module's logs after the module's55        # __name__,the following getLogger call should fetch the same logger56        # you use in the foo module57        exception_log = logging.getLogger(__name__)58        cls._exception_log_handler = MockLoggingHandler(level='DEBUG')59        exception_log.addHandler(cls._exception_log_handler)60        cls.exception_log_messages = cls._exception_log_handler.messages61    def setUp(self):62        super(ExceptionTestCase, self).setUp()63        self._exception_log_handler.reset()  # So each test is independent64    def test_stack(self):65        """ Checking if full_exc_info will return the division by 0 error at66        line 83. If the line changes this test will fail."""67        try:68            1/069        except:70            logger.warning("The message", exc_info=exception.full_exc_info())71            for record in self.exception_log_messages['warning']:72                tb_frame = record.exc_info[2]73                while tb_frame.tb_next:74                    tb_frame = tb_frame.tb_next75                self.assertEqual(76                    tb_frame.tb_frame.f_locals['record'].filename,77                    "exception_test.py")78                self.assertEqual(79                    tb_frame.tb_frame.f_locals['record'].funcName,80                    "test_stack")81                self.assertEqual(82                    tb_frame.tb_frame.f_locals['record'].exc_info[0],83                    ZeroDivisionError)...

Automation Testing Tutorials

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