How to use tb_frame method in Slash
Best Python code snippet using slash
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)...
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