camel.py 49.9 KB
 bepinat committed Dec 16, 2014 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 ``````#!/usr/bin/env python # -*- coding: utf-8 -*- """ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Created on 12/2014 @author: Benoît Epinat """ import time import os, sys import copy import numpy as np import pyfits as pf from mpfit import mpfit # python 2.7... `````` bepinat committed Dec 18, 2014 28 ``````import ipdb `````` bepinat committed Dec 16, 2014 29 30 31 32 ``````#from matplotlib import pyplot as plt from scipy import ndimage from scipy import constants as ct `````` bepinat committed Dec 18, 2014 33 ``````import argparse `````` bepinat committed Dec 16, 2014 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 `````` def compute_rv(z, zcosmo=None): """This function computes the velocity from local and global redshifts Parameters ---------- z: float (or numpy array of floats) local redshift (local velocity) zcosmo: float cosmological redshift (sytemic velocity) """ if zcosmo == None: v = ((z + 1) ** 2 - 1) / ((z + 1) ** 2 + 1) * ct.c * 1e-3 else: v = (z - zcosmo) / (1 + z) * ct.c * 1e-3 return v def compute_fwhm(dz, z=None, zcosmo=0): """This function computes the velocity variation Parameters ---------- dz: float (or numpy array of floats) local redshift variation (local velocity dispersion) z: float (or numpy array of floats) local redshift (local velocity) zcosmo: float cosmological redshift (sytemic velocity) """ if z == None: z = zcosmo dv = dz * (1 + zcosmo) / (1 + z) ** 2 * ct.c *1e-3 return dv def readconfig(filename, config): """This function reads the configuration file and returns a configuration dictionnary Parameters ---------- filename: string name of the configuration file config: dictionnary contains options with priority on the configuration file """ conf = {} if filename != None: data = open(filename) `````` bepinat committed Mar 23, 2015 86 87 88 `````` count_extral = 0 for raw in data: keyvalcom = raw.split('= ') `````` bepinat committed Dec 16, 2014 89 `````` key = keyvalcom[0].rstrip() # on vire les espaces de fin de keyword `````` bepinat committed Feb 18, 2015 90 `````` value = keyvalcom[1].split('/ ')[0].rstrip('\t').rstrip() # on vire les tabultation et les espaces de fin de keyword `````` bepinat committed Dec 16, 2014 91 92 93 94 95 96 97 98 99 100 `````` value = value.replace("'", '') value = value.replace('"', '') if value == '': value = None elif value.upper() == 'NONE': value = None elif value.upper() == 'FALSE': value = False elif value.upper() == 'TRUE': value = True `````` bepinat committed Mar 23, 2015 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 `````` #elif (value.count('.') == 1) & (value.replace('.', '').isdigit()): #value = float(value) elif (value.count('.') == 1): try: value = float(value) except: value = value #elif value.isdigit(): #value = int(value) elif (value.count('.') == 0): try: value = int(value) except: value = value if (key == 'EXTRAL') & (value != None): if count_extral == 0: conf[key] = np.array([value]) else: conf[key] = np.append(conf[key], value) count_extral += 1 else: conf[key] = value `````` bepinat committed Dec 16, 2014 123 124 125 126 127 128 129 130 131 132 133 134 135 `````` # add input options to configuration dictionnary + check needed keywords if config != None: keys = conf.keys() for key in config: if config[key] != None: conf[key] = config[key] #elif keys.isdisjoint([key]): # c'est du python3 elif (not conf.has_key(key)): # c'est du python 2.7 conf[key] = None # XXX or give an error message but in that case, must test that the keywords have correct values ## XXX more keywords? add default values? `````` bepinat committed Feb 16, 2015 136 `````` needed_keys = ['FITSFILE', 'OUTPUT', 'SKYFILE', 'HALPHA', 'NII6548', 'NII6583', 'SII6716', 'SII6731', 'OIII4959', 'OIII5007', 'HBETA', 'OII3729', 'OII3726', 'COMMW', 'REDSHIFT', 'REDMIN', 'REDMAX', 'INITW', 'WMIN', 'WMAX', 'DFIT', 'DGCTNUM', 'MFIT', 'SCLIP', 'XYCLIP', 'NCLIP', 'SPSF', 'WSMOOTH', 'SSMOOTH', 'THRES', 'MEDIAN', 'FITSPSF', 'XMIN', 'YMIN', 'ZMIN', 'XMAX', 'YMAX', 'ZMAX'] `````` bepinat committed Dec 16, 2014 137 138 139 140 141 142 `````` keys = conf.keys() for key in needed_keys: #if keys.isdisjoint([key]): # c'est du python3 if (not conf.has_key(key)): # c'est du python 2.7 conf[key] = None if conf.has_key('OII'): `````` bepinat committed Feb 18, 2015 143 `````` conf['OII3729'] = conf['OII3726'] = conf.pop('OII') `````` bepinat committed Dec 16, 2014 144 `````` if conf['SPSF'] == None: conf['SPSF'] = 0. `````` bepinat committed Feb 18, 2015 145 `````` if conf['COMMW'] == None: conf['COMMW'] = False `````` bepinat committed Dec 16, 2014 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 `````` # XXX or give an error message but in that case, must test that the keywords have correct values return conf def readcubes(conf, multi_ext=False): """This function reads the input cubes (cube and variance) Parameters ---------- conf: configuration dictionnary multi_ext: bool keyword to indicate if input fits has multiple extensions """ if multi_ext: hdul = pf.open(conf['FITSFILE']) cube = hdul[1].data hdr = hdul[1].header if conf['SKYFILE'] == conf['FITSFILE']: var = hdul[2].data varhdr = hdul[2].header elif (not conf['SKYFILE']): `````` bepinat committed Mar 23, 2015 168 `````` var = None `````` bepinat committed Dec 16, 2014 169 170 171 172 173 174 `````` varhdr = '' else: hdul = pf.open(conf['SKYFILE']) var = hdul[0].data varhdr = hdul[0].header else: `````` bepinat committed Feb 16, 2015 175 176 177 `````` hdul = pf.open(conf['FITSFILE']) cube = hdul[0].data hdr = hdul[0].header `````` bepinat committed Dec 16, 2014 178 `````` if (not conf['SKYFILE']): `````` bepinat committed Mar 23, 2015 179 `````` var = None `````` bepinat committed Dec 16, 2014 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 `````` varhdr = '' else: hdul = pf.open(conf['SKYFILE']) var = hdul[0].data varhdr = hdul[0].header return cube, hdr, var, varhdr def testcubes(cube, var): """This function tests the sizes of the variance data Parameters ---------- cube: ndarray input data cube var: ndarray input variance data """ `````` bepinat committed Mar 23, 2015 198 199 `````` if var == None: return `````` bepinat committed Dec 16, 2014 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 `````` if var.ndim == 3: if var.shape != cube.shape: sys.exit(2) if var.ndim == 1: if var.shape[0] != cube.shape[0]: sys.exit(2) return def writedata(data, hdr, filename): """This function writes the output data Parameters ---------- data: ndarray data to be written hdr: fits header fits header to be written filename: string name of the output """ hdu = pf.PrimaryHDU(data, hdr) hdulist = pf.HDUList(hdu) hdulist.writeto(filename, clobber=True) return hdulist[0].header def cutcube(cube, hdr, conf): """This function cuts the cube according to the limits requested Parameters ---------- cube: array input data cube or variance array hdr: fits header input data cube header conf: configuration dictionnary """ if conf['XMIN'] == None: conf['XMIN'] = 0 if conf['YMIN'] == None: conf['YMIN'] = 0 if conf['ZMIN'] == None: conf['ZMIN'] = 0 if conf['XMAX'] == None: conf['XMAX'] = cube.shape[2] - 1 if conf['YMAX'] == None: conf['YMAX'] = cube.shape[1] - 1 if conf['ZMAX'] == None: conf['ZMAX'] = cube.shape[0] - 1 conf['ZMIN'], conf['YMIN'], conf['XMIN'] = np.max([[conf['ZMIN'], conf['YMIN'], conf['XMIN']], [0, 0, 0]],axis=0) conf['ZMAX'], conf['YMAX'], conf['XMAX'] = np.min([[conf['ZMAX'], conf['YMAX'], conf['XMAX']], np.array(cube.shape) - 1],axis=0) conf['ZMIN'], conf['YMIN'], conf['XMIN'] = np.min([[conf['ZMIN'], conf['YMIN'], conf['XMIN']], [conf['ZMAX'], conf['YMAX'], conf['XMAX']]],axis=0) conf['ZMAX'], conf['YMAX'], conf['XMAX'] = np.max([[conf['ZMAX'], conf['YMAX'], conf['XMAX']], [conf['ZMIN'], conf['YMIN'], conf['XMIN']]],axis=0) if cube.ndim == 3: cubecut = cube[conf['ZMIN']:conf['ZMAX'] + 1, conf['YMIN']:conf['YMAX'] + 1, conf['XMIN']:conf['XMAX'] + 1] hdr['CRPIX1'] -= conf['XMIN'] hdr['CRPIX2'] -= conf['YMIN'] hdr['CRPIX3'] -= conf['ZMIN'] elif cube.ndim == 1: cubecut = cube[conf['ZMIN']:conf['ZMAX'] + 1] hdr['CRPIX1'] -= conf['ZMIN'] return cubecut, hdr `````` bepinat committed Feb 18, 2015 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 ``````def remove_nanvar(var): """This function removes nan in variance cube if any and replaces them by median variance (spectrally) Parameters ---------- var: array input variance cube Returns ------- corrected variance """ cnan = np.isnan(var) nanmap = cnan.prod(axis=0) indnan = np.where(nanmap == 1) indnum = np.where(nanmap == 0) qvar = var[:, indnum[0], indnum[1]].reshape(var.shape[0], np.size(indnum[0])) medianvar = np.median(qvar, axis=1) if np.size(indnan[0]) == 0: print('Variance cube contains NaN and has been corrected') for ind in range(np.size(indnan[0])): var[:, indnan[0][ind], indnan[1][ind]] = medianvar return var `````` bepinat committed Dec 16, 2014 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 ``````def clipcube(cube, hdr, xy=3, sclip=3, npass=10): """This function performs a sigma clipping on the cube Parameters ---------- cube: array input datacube hdr: fits header input data cube header xy: integer size of the box in pixels in which the clipping is done sclip: float value of the clipping (n sigma) npass: integer number of pass to perform the clipping `````` bepinat committed Feb 18, 2015 307 `````` `````` bepinat committed Dec 16, 2014 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 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initialization of output cube sigma = fwhm / (2. * np.sqrt(2. * np.log(2.))) for z in range(cube.shape[0]): # loop on the z range cube1[z,:] = ndimage.gaussian_filter(cube[z,:], sigma) hdr.append(('SSMOOTH', fwhm, 'FWHM in pixels of 2D Gaussian spatial smoothing')) return cube1, hdr def spectralsmooth(cube, hdr, fwhm): """This function performs a Gaussian spectral smoothing on the cube Parameters ---------- cube: array input datacube hdr: fits header input data cube header fwhm: float full width half maximum of the 1D Gaussian kernel """ cube1 = np.zeros(cube.shape) # initialization of output cube sigma = fwhm / (2. * np.sqrt(2. * np.log(2.))) for x in range(cube.shape[2]): # loop on the x range for y in range(cube.shape[1]): # loop on the y range cube1[:, y, x] = ndimage.gaussian_filter(cube[:, y, x], sigma) hdr.append(('WSMOOTH', fwhm, 'FWHM in pixels of Gaussian spectral smoothing')) # XXX add Hanning, Gauss, ... return cube1, hdr class line: """This class is the basic for defining a line. A line is defined by its name, its wavelength and the reference line to which it is attached if the ratio has to be constrained. """ def __init__(self, name, wave, ref=None, fit=False, low=0, up=None, th=None, index=None): self.index = index self.name = name self.wave = wave self.fit = fit if ref == None: ref = name self.ref = ref if ref == name: self.low = 1 self.up = 1 self.th = 1 else: self.low = low self.up = up self.th = th class lines: """This class enables to deal with lines. A dictionnary stored in lines will contain informations on each lines. """ def append(self, line): self.lines[line.name] = line self.lines[line.name].index = self.index self.index += 1 def __init__(self): self.index = 0 self.lines = {} `````` bepinat committed Feb 16, 2015 404 405 `````` self.append(line('HALPHA', 6562.801, ref='HBETA', low=2.75, th=2.85)) self.append(line('HBETA', 4861.363)) `````` bepinat committed Feb 16, 2015 406 `````` self.append(line('HGAMMA', 4340.47, ref='HBETA', low=0.44, up=0.5, th=0.468)) `````` bepinat committed Feb 18, 2015 407 408 `````` self.append(line('HDELTA', 4101.73, ref='HBETA', low=0.23, up=0.29, th=0.259)) self.append(line('HEPS', 3970.07, ref='HBETA', low=0.13, up=0.19, th=0.159)) `````` bepinat committed Feb 16, 2015 409 `````` self.append(line('NII6583', 6583.45, ref='NII6548', low=2.7, up=3.3, th=3.)) `````` bepinat committed Feb 16, 2015 410 411 412 413 `````` #self.append(line('NII6583', 6583., ref='NII6548', low=2.7, up=3.3, th=3.)) self.append(line('NII6548', 6548.05)) self.append(line('SII6731', 6730.82)) self.append(line('SII6716', 6716.44, ref='SII6731', low=0.45, up=1.45, th=1.)) `````` bepinat committed Feb 18, 2015 414 415 `````` self.append(line('OIII5007', 5006.843, ref='OIII4959', low=2.7, up=3.3, th=3.)) self.append(line('OIII4959', 4958.911)) `````` bepinat committed Dec 16, 2014 416 `````` self.append(line('OIII4363', 4363., ref='OIII4959')) # XXX low=, up=, th= `````` bepinat committed Feb 16, 2015 417 418 `````` self.append(line('OII3729', 3728.80, ref='OII3726', low=0.3, up=1.5, th=1.)) self.append(line('OII3726', 3726.04)) `````` bepinat committed Dec 16, 2014 419 420 421 422 423 424 425 `````` self.append(line('HEI4471', 4471.)) self.append(line('HEI5876', 5876., ref='HEI4471', low=2.5, th=2.5)) self.append(line('HEII4686', 4686.)) self.append(line('OI6300', 6300.)) self.append(line('NEIII3868', 3868.)) #self['Ha'] = `````` bepinat committed Feb 16, 2015 426 `````` #self.names = ['Ha', 'Hb', 'Hga', 'Hd', 'Heps', 'NII6583', 'NII6548', 'SII6731', 'SII6716', 'OIII5007', 'OIII4959', 'OIII4363', 'OII3729', 'OII3726', 'HeI4471', 'HeI5876', 'HeII4686', 'OI6300', 'NeIII3868'] `````` bepinat committed Dec 16, 2014 427 428 429 `````` #self.waves = [6562.8, 4861., 4340., 4101., 3968., 6583., 6548., 6731., 6717., 5007., 4959., 4363., 3729., 3726., 4471., 5876., 4686., 6300., 3868.] #self.ref = ['Hb', 'Hb', 'Hb', 'Hb', 'Hb', 'NII6548', 'NII6548', 'SII6731', 'SII6731', 'OIII4959', 'OIII4959', 'OIII4959', 'OII3726', 'OII3726', 'HeI4471', 'HeI4471', 'HeII4686', 'OI6300', 'NeIII3868'] `````` bepinat committed Feb 16, 2015 430 `````` #lines={'Ha':6562.8,'Hb':4861.,'Hga':4340.,'Hd':4101.,'Heps':3968.,'NII6583':6583.,'NII6548':6548.,'SII6731':6731.,'SII6716':6717.,'OIII5007':5007.,'OIII4959':4959.,'OIII4363':4363.,'OII3729':3729.,'OII3726':3726.,'HeI4471':4471.,'HeI5876':5876.,'HeII4686':4686.,'OI6300':6300.,'NeIII3868':3868.} `````` bepinat committed Dec 16, 2014 431 `````` ##Initialisation of groups of lines `````` bepinat committed Feb 16, 2015 432 `````` #sgroup={'Ha':'Hb','Hb':'Hb','Hga':'Hb','Hd':'Hb','Heps':'Hb','NII6583':'NII6548','NII6548':'NII6548','SII6731':'SII6731','SII6716':'SII6731','OIII5007':'OIII4959','OIII4959':'OIII4959','OIII4363':'OIII4959','OII3729':'OII3726','OII3726':'OII3726','HeI4471':'HeI4471','HeI5876':'HeI4471','HeII4686':'HeII4686','OI6300':'OI6300','NeIII3868':'NeIII3868'} `````` bepinat committed Dec 16, 2014 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 `````` def waveindgen(hdr): ''' This function returns the wavelength index in angstroms from the header information and the conversion factor from header data to angstroms. ''' cunit = hdr['CUNIT3'] if cunit.strip().lower() in {'microns', 'micrometers', 'mum'}: lconvfac=1e4 if cunit.strip().lower() in {'angstroms', 'angstrom'}: lconvfac=1 if cunit.strip().lower() in {'nanometers', 'nm'}: lconvfac=1e3 if 'CDELT3' in hdr.ascard.keys(): sclp = hdr['CDELT3'] elif 'CD3_3' in hdr.ascard.keys(): sclp = hdr['CD3_3'] wave = lconvfac * (sclp * (np.arange(hdr['NAXIS3']) - hdr['CRPIX3'] + 1) + hdr['CRVAL3']) return wave, lconvfac, sclp def elspectrum(p, wave=None, lines=None, psf=None, degc=None): wavel = wave.reshape(1, wave.size) deg = np.arange(degc + 1).reshape(degc + 1, 1) coefs = p[lines.size * 3 + 1:lines.size * 3 + 1 + degc + 1].reshape(degc + 1, 1) continuum = (coefs * (wavel - wave[0]) ** deg).sum(axis=0) wlines = lines.reshape(lines.size, 1) dlines = (p[1:lines.size + 1] * lines).reshape(lines.size, 1) coefs = (p[lines.size + 1:lines.size * 2 + 1] * p[lines.size *2 + 1:lines.size * 3 + 1]).reshape(lines.size, 1) slines = (coefs * np.exp( -0.5 * (wavel - wlines * (p[0] + 1)) ** 2 / (dlines ** 2 + psf ** 2))).sum(axis=0) return (continuum + slines) def myelspectrum(p, fjac=None, wave=None, spectrum= None, err=None, lines=None, psf=None, degc=None): model = elspectrum(p, wave=wave, lines=lines, psf=psf, degc=degc) status = 0 return [status, (spectrum - model) / err] def buildmaps(conf, cube, hdr, var=None, plot=False, debug=False, free_ratio=False): """ """ #Initialisation of lines els = lines() `````` bepinat committed Mar 23, 2015 474 `````` for lline in els.lines: `````` bepinat committed Dec 16, 2014 475 476 `````` #check the line name is set in the configuration file #if (not conf.keys().isdisjoint([line])): # c'est du python3 `````` bepinat committed Mar 23, 2015 477 478 `````` if conf.has_key(lline): # python 2.7 els.lines[lline].fit = conf[lline] `````` bepinat committed Dec 16, 2014 479 480 481 482 483 484 485 486 487 488 489 490 491 `````` if conf['EXTRAL'] != None: for i in np.arange(np.shape(conf['EXTRAL'])[0]): els.append(line('EXTRAL%i'%(i+1), conf['EXTRAL'][i], fit=True)) #Construction of wavelength index wave0, lconvfac, sclp = waveindgen(hdr) # wavelength array in Angstrom and convertion factor #Condition on the wavelength to be within the redshift cuts #XXX try zmin > zmax? zcosmo = conf['REDSHIFT'] zmax = conf['REDMAX'] zmin = conf['REDMIN'] `````` bepinat committed Mar 23, 2015 492 `````` zrange = zmax - zmin `````` bepinat committed Dec 16, 2014 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 `````` argsorted = np.argsort(np.array([els.lines[i].index for i in els.lines])) lineindex = np.array([els.lines[i].index for i in els.lines])[argsorted] linefit = np.array([els.lines[i].fit for i in els.lines])[argsorted] linewave = np.array([els.lines[i].wave for i in els.lines])[argsorted] linename = np.array([els.lines[i].name for i in els.lines])[argsorted] indok = np.zeros(0, dtype = int) firstind = np.zeros(linefit.size) lastind = np.zeros(linefit.size) firstind0 = np.zeros(linefit.size) lastind0 = np.zeros(linefit.size) for i in range(linefit.size): if (not linefit[i]): continue linf = np.max([(zmin - zrange / 2. + 1) * linewave[i] , np.min(wave0)]) lsup = np.min([(zmax + zrange / 2. + 1) * linewave[i] , np.max(wave0)]) condo = np.where((wave0 >= linf) & (wave0 <= lsup)) if np.size(condo) != 0: firstind0[i] = condo[0][0] lastind0[i] = condo[0][np.size(condo) - 1] indok = np.append(indok, condo) indok = np.unique(indok) wave = wave0[indok] for i in range(linefit.size): if (not linefit[i]): continue linf = np.max([(zmin - zrange / 2. + 1) * linewave[i] , np.min(wave0)]) lsup = np.min([(zmax + zrange / 2. + 1) * linewave[i] , np.max(wave0)]) condo = np.where((wave >= linf) & (wave <= lsup)) if np.size(condo) != 0: firstind[i] = condo[0][0] lastind[i] = condo[0][np.size(condo) - 1] #firstind = np.zeros(np.size(cond)) #lastind = np.zeros(np.size(cond)) #firstind0 = np.zeros(np.size(cond)) #lastind0 = np.zeros(np.size(cond)) #for i in range(np.size(cond)): #linf = np.max([(zmin - zrange / 2. + 1) * linewave[cond[0][i]] , np.min(wave0)]) #lsup = np.min([(zmax + zrange / 2. + 1) * linewave[cond[0][i]] , np.max(wave0)]) #condo = np.where((wave0 >= linf) & (wave0 <= lsup)) #if np.size(condo) != 0: #firstind0[i] = condo[0][0] #lastind0[i] = condo[0][np.size(condo) - 1] #indok = np.append(indok, condo) #indok = np.unique(indok) #wave = wave0[indok] #for i in range(np.size(cond)): #linf = np.max([(zmin - zrange / 2. + 1) * linewave[cond[0][i]] , np.min(wave0)]) #lsup = np.min([(zmax + zrange / 2. + 1) * linewave[cond[0][i]] , np.max(wave0)]) #condo = np.where((wave >= linf) & (wave <= lsup)) #if np.size(condo) != 0: #firstind[i] = condo[0][0] #lastind[i] = condo[0][np.size(condo) - 1] #Weights `````` bepinat committed Mar 23, 2015 548 549 `````` #if var == None: var = np.ones([indok.size, cube.shape[1], cube.shape[2]]) if var == None: var = np.ones(cube.shape) `````` bepinat committed Dec 16, 2014 550 551 552 553 554 555 `````` if var.ndim == 1: var = np.tile(var.reshape(var.size, 1, 1), (1, cube.shape[1], cube.shape[2])) #if var.ndim == 3: weight = ((1. / var[indok,:,:]) / np.sum(1. / var[indok,:,:], axis=0)) * indok.size if var.ndim == 3: weight = ((1. / var) / np.sum(1. / var, axis=0)) * var.shape[0] #Redshift step zstep = (conf['DFIT'] * 1e3 / ct.c + zcosmo) / (1 - conf['DFIT'] * 1e3 / ct.c) - zcosmo `````` bepinat committed Mar 23, 2015 556 557 558 559 560 `````` if zstep >= (zmax - zmin) / 2: zstep = (zmax - zmin) / 2. zmean = (zmax + zmin) / 2. zzmax = zmean + (np.round(zmean / zstep) + 1) * zstep zzmin = zmean - np.round(zmean / zstep) * zstep `````` bepinat committed Dec 16, 2014 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 `````` #Parameters contraints and informations params = np.zeros(1 + els.index * 3 + conf['DGCTNUM'] + 1) parbase = {'value':0., 'fixed':1, 'limited':[0,0], 'limits':[0.,0.], 'tied':'', 'mpmaxstep':0, 'mpminstep':0, 'parname':''} parinfo = [] for i in range(len(params)): parinfo.append(copy.deepcopy(parbase)) #Redshift range parinfo[0]['limited'] = [1, 1] parinfo[0]['limits'] = [zmin, zmax] parinfo[0]['fixed'] = 0 #Line parameters #When common dispersion, we determine the reference line for the width and set the dispersion as free parameter commwindex = -1 if conf['COMMW']: commwindex = np.min(lineindex[np.where(linefit)]) parinfo[1 + commwindex]['fixed'] = 0 linew = np.zeros(els.index) `````` bepinat committed Mar 23, 2015 581 `````` `````` bepinat committed Dec 16, 2014 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 `````` for i in range(els.index): name = linename[i] j = els.lines[els.lines[name].ref].index #Dispersion parinfo[1 + i]['limited'] = [1, 1] parinfo[1 + i]['limits'] = [(conf['WMIN'] * 1e3 / ct.c + zcosmo) / (1 - conf['WMIN'] * 1e3 / ct.c) - zcosmo, (conf['WMAX'] * 1e3 / ct.c + zcosmo) / (1 - conf['WMAX'] * 1e3 / ct.c) - zcosmo] #in redshift unit parinfo[1 + i]['value'] = params[1 + i] = (conf['INITW'] * 1e3 / ct.c + zcosmo) / (1 - conf['INITW'] * 1e3 / ct.c) - zcosmo #When dispersion is common for all lines, widths are tied to the first free line (the first free width is free) if (conf['COMMW']) & (i != commwindex): parinfo[1 + i]['tied'] = 'p[%i]'%(1 + commwindex) #When dispersion is independant for all lines (common by groups), widths are tied to the reference line and the ref width is free if (not conf['COMMW']) & (i != j): parinfo[1 + i]['tied'] = 'p[%i]'%(1 + j) if els.lines[name].fit: parinfo[1 + j]['fixed'] = 0 # the width of the reference line is free if (not conf['COMMW']) & (i == j) & (els.lines[name].fit is True): parinfo[1 + i]['fixed'] = 0 # the width of the reference line is free #XXX When dispersion is completely independant, widths are not tied and are free #if (not conf['COMMW']): #if els.lines[name].fit: parinfo[1 + i]['fixed'] = 0 # the width of the reference line is free #Intensity parinfo[els.index + 1 + i]['limited'][0] = 1 parinfo[els.index + 1 + i]['limits'][0] = 0. #When line ratio is free: all ratios are fixed (= 1) and lines intensities are not tied and free parameters if free_ratio: parinfo[2 * els.index + 1 + i]['value'] = 1 if els.lines[name].fit is True: parinfo[els.index + 1 + i]['fixed'] = 0 #When line ratio is constrained: line intensities are tied and ratios are free, except for the reference line (the ref intensity is free, the ref ratio is fixed = 1) if (not free_ratio) & (i != j): parinfo[els.index + 1 + i]['tied'] = 'p[%i]'%(els.index + 1 + j) # line intensity is tied to reference #Ratio limits parinfo[2 * els.index + 1 + i]['limited'][0] = 1 if els.lines[name].low != None: parinfo[2 * els.index + 1 + i]['limits'][0] = els.lines[name].low if els.lines[name].up != None: parinfo[2 * els.index + 1 + i]['limited'][1] = 1 parinfo[2 * els.index + 1 + i]['limits'][1] = els.lines[name].up if els.lines[name].th != None: `````` bepinat committed Dec 18, 2014 628 629 `````` parinfo[2 * els.index + 1 + i]['value'] = els.lines[name].th params[2 * els.index + 1 + i] = els.lines[name].th `````` bepinat committed Dec 16, 2014 630 `````` else: `````` bepinat committed Dec 18, 2014 631 `````` parinfo[2 * els.index + 1 + i]['value'] = 1 `````` bepinat committed Dec 16, 2014 632 633 634 635 636 637 638 639 640 641 642 `````` params[2 * els.index + 1 + i] = 1 #Free parameters if els.lines[name].fit is True: parinfo[els.index + 1 + j]['fixed'] = 0 # the intensity of the reference line is free parinfo[2 * els.index + 1 + i]['fixed'] = 0 # line ratio is free #XXX When reference line is not fitted, we have to find a solution if several lines of a group are fitted if (not free_ratio) & (i == j) & (els.lines[name].fit is True): #When line is reference line, the ratio is fixed equal to 1 parinfo[2 * els.index + 1 + i]['limited'] = [0, 0] `````` bepinat committed Dec 18, 2014 643 644 `````` parinfo[2 * els.index + 1 + i]['value'] = 1 params[2 * els.index + 1 + i] = 1 `````` bepinat committed Dec 16, 2014 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 `````` parinfo[els.index + 1 + i]['fixed'] = 0 #XXX When line ratio is fixed: all ratios are fixed equal to theoretical values and intensities are tied (the ref intensity is free) #if (not free_ratio) & (i!=j): #parinfo[els.index + 1 + i]['tied'] = 'p[%i]'%(els.index + 1 + j) #parinfo[2 * els.index + 1 + i]['limited'][0] = 1 #if els.lines[name].low != None: #parinfo[2 * els.index + 1 + i]['limits'][0] = els.lines[name].low #if els.lines[name].up != None: #parinfo[2 * els.index + 1 + i]['limited'][1] = 1 #parinfo[2 * els.index + 1 + i]['limits'][1] = els.lines[name].up #if els.lines[name].th != None: #parinfo[2 * els.index + 1 + i]['value'] = params[2 * els.index + 1 + i] = els.lines[name].th #else: #params[2 * els.index + 1 + i] = 1 #if els.lines[name].fit is True: #parinfo[els.index + 1 + j]['fixed'] = 0 # the intensity of the reference line is free #if (not free_ratio) & (i == j) & (els.lines[name].fit is True): ##When line is reference line, the ratio is fixed equal to 1 #parinfo[2 * els.index + 1 + i]['limited'] = [0, 0] #parinfo[2 * els.index + 1 + i]['value'] = params[2 * els.index + 1 + i] = 1 #parinfo[els.index + 1 + i]['fixed'] = 0 `````` bepinat committed Dec 18, 2014 668 669 `````` #ipdb.set_trace() `````` bepinat committed Dec 16, 2014 670 671 672 673 674 675 676 `````` #Continuum parametres for i in range(conf['DGCTNUM'] + 1): parinfo[1 + els.index * 3 + i]['fixed'] = 0 #Output initialisation to be filled paramscube = np.zeros(np.append(len(params), cube.shape[1:])) perrorcube = np.zeros(np.append(len(params), cube.shape[1:])) `````` bepinat committed Dec 18, 2014 677 `````` statusmap = np.zeros(cube.shape[1:]) `````` bepinat committed Dec 16, 2014 678 679 680 681 682 683 684 685 686 `````` dofmap = np.zeros(cube.shape[1:]) fnormmap = np.zeros(cube.shape[1:]) modcube = np.zeros(cube.shape) #List of extra parameters #xxx Ajuster wave et spectrum pour ne garder que ce qui nous intéresse? fa = {'wave': wave, 'spectrum': None, 'err': None, 'lines': linewave, 'psf': conf['SPSF'], 'degc': conf['DGCTNUM']} #Loop on pixels `````` bepinat committed Dec 18, 2014 687 `````` counter = 0 `````` bepinat committed Jan 27, 2015 688 689 `````` fac_prev = -1 number_of_pixels = np.float(cube.shape[2] * cube.shape[1]) `````` bepinat committed Dec 16, 2014 690 691 `````` for x in range(cube.shape[2]): for y in range(cube.shape[1]): `````` bepinat committed Jan 27, 2015 692 693 694 695 696 697 `````` if np.int((counter / number_of_pixels) * 100) != fac_prev: fac_prev = np.int((counter / number_of_pixels) * 100) sys.stdout.write("Progress => {:3d}%\r".format(fac_prev)) sys.stdout.flush() #if (counter / 10.) == np.int(counter / 10.): print('pixel %i / %i'%(counter, number_of_pixels)) `````` bepinat committed Dec 18, 2014 698 `````` counter += 1 `````` bepinat committed Dec 16, 2014 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 `````` fa['spectrum'] = cube[indok,y,x] # Spectrum fa['err'] = np.sqrt(var[indok,y,x]) # Error #fa['weight'] = np.sqrt(weight[indok,y,x]) # Weight if (np.min(fa['spectrum']) == np.max(fa['spectrum'])) & (np.min(fa['spectrum']) == 0): continue # No need for fitting minfnorm = np.infty #index = None std = np.std(fa['spectrum']) #Parameters initialisation p = np.copy(params) #Line intensity initisalisation for i in range(els.index): p[els.index + 1 + i] = 2 * std #Inititalisation of continuum (degree 0) p[1 + els.index * 3] = np.median(fa['spectrum']) `````` bepinat committed Mar 23, 2015 718 `````` for z in np.arange(zzmin, zzmax, zstep): `````` bepinat committed Dec 16, 2014 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 `````` p[0] = z pstart = np.copy(p) fit0 = mpfit.mpfit(myelspectrum, xall=pstart, functkw=fa, quiet=True, parinfo=parinfo) if fit0.status == 0: continue if fit0.status == -16: continue if fit0.fnorm <= minfnorm: minfnorm = fit0.fnorm fit = copy.copy(fit0) if minfnorm == np.infty: continue #print(fit.params[2 * els.index + 1 + 12], parinfo[2 * els.index + 1 + 12]['limits'], fit.params[2 * els.index + 1 + 13]) paramscube[:, y, x] = fit.params[:] perrorcube[:, y, x] = fit.perror[:] fnormmap[y, x] = fit.fnorm dofmap[y, x] = fit.dof statusmap[y, x] = fit.status modcube[indok, y, x] = elspectrum(fit.params, wave=wave, lines=linewave, psf=conf['SPSF'], degc=conf['DGCTNUM']) #Creating outputs #Error normalisation by reduced chi2 perrorcube = perrorcube * np.sqrt(fnormmap / dofmap) #Continuum #if we want the coefficient, we must multiply them by factor + give lambda[0] contcube = np.zeros(cube.shape) econtcube = np.zeros(cube.shape) for i in range(conf['DGCTNUM'] + 1): contcube += paramscube[1 + els.index * 3 + i,:,:] * (wave0 - wave[0]).reshape(wave0.size, 1, 1) ** i econtcube += perrorcube[1 + els.index * 3 + i,:,:] * (wave0 - wave[0]).reshape(wave0.size, 1, 1) ** i #contmap #; continuum is computed at the longest wavelength, not necessarily optimal #cont[m,n]+=pfinal[2*n_elements(l)+1+i]*double(lambda[n_elements(lambda)-1]-lambda[0])^i/double(lambda[n_elements(lambda)-1]-lambda[0]) #econt[m,n]+=(paramerr[2*n_elements(l)+1+i]*double(lambda[n_elements(lambda)-1]-lambda[0])^i/double(lambda[n_elements(lambda)-1]-lambda[0]))^2 #Residual cube #residual residualcube = np.zeros(cube.shape) residualcube[indok,:,:] = cube[indok,:,:] - modcube[indok,:,:] #dispcont dispcontmap = np.std(cube[indok,:,:] - modcube[indok,:,:], axis=0) #Chi2 chi2map = fnormmap / dofmap #Velocity field zmap = paramscube[0,:,:] ezmap = perrorcube[0,:,:] rvmap = compute_rv(zmap, zcosmo=zcosmo) ervmap = compute_fwhm(ezmap, z=zmap, zcosmo=zcosmo) #Lines wavemaps = np.zeros(np.append(els.index, cube.shape[1:])) ewavemaps = np.zeros(np.append(els.index, cube.shape[1:])) wavedispmaps = np.zeros(np.append(els.index, cube.shape[1:])) ewavedispmaps = np.zeros(np.append(els.index, cube.shape[1:])) dispmaps = np.zeros(np.append(els.index, cube.shape[1:])) edispmaps = np.zeros(np.append(els.index, cube.shape[1:])) intmaps = np.zeros(np.append(els.index, cube.shape[1:])) eintmaps = np.zeros(np.append(els.index, cube.shape[1:])) fluxmaps = np.zeros(np.append(els.index, cube.shape[1:])) efluxmaps = np.zeros(np.append(els.index, cube.shape[1:])) snrmaps = np.zeros(np.append(els.index, cube.shape[1:])) # dzmap and edzmap are intermediate products if conf['COMMW']: dzmap = paramscube[1 + commwindex,:,:] edzmap = perrorcube[1 + commwindex,:,:] for i in range(els.index): if (not linefit[i]): continue name = linename[i] j = els.lines[els.lines[name].ref].index `````` bepinat committed Mar 27, 2015 793 794 795 796 `````` #if (not conf['COMMW']) & (i != j): #dzmap = paramscube[1 + j,:,:] #edzmap = perrorcube[1 + j,:,:] if (not conf['COMMW']): `````` bepinat committed Dec 16, 2014 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 `````` dzmap = paramscube[1 + j,:,:] edzmap = perrorcube[1 + j,:,:] wavemaps[i,:,:] = (zmap + 1) * linewave[i] ewavemaps[i,:,:] = ezmap * linewave[i] wavedispmaps[i,:,:] = dzmap * linewave[i] ewavedispmaps[i,:,:] = edzmap * linewave[i] dispmaps[i,:,:] = compute_fwhm(dzmap, z=zmap, zcosmo=zcosmo) edispmaps[i,:,:] = compute_fwhm(edzmap, z=zmap, zcosmo=zcosmo) intmaps[i,:,:] = paramscube[1 + els.index + i,:,:] * paramscube[1 + 2 * els.index + i,:,:] fluxmaps[i,:,:] = np.sum(intmaps[i,:,:] * np.exp(-0.5 * (wave.reshape(wave.size, 1, 1) - linewave[i] * (1 + zmap)) ** 2 / ((dzmap * linewave[i]) ** 2 + conf['SPSF'] ** 2)) * sclp * lconvfac, axis=0) snrmaps[i,:,:] = np.sum(weight[firstind0[i]:lastind0[i],:,:] * (modcube[firstind0[i]:lastind0[i],:,:] - contcube[firstind0[i]:lastind0[i],:,:]), axis=0) * sclp * lconvfac / (np.sqrt(np.pi * 2) * np.sqrt((linewave[i] * dzmap) ** 2 + conf['SPSF'] ** 2) * np.sqrt(np.sum(weight[firstind0[i]:lastind0[i],:,:] * (cube[firstind0[i]:lastind0[i],:,:] - modcube[firstind0[i]:lastind0[i],:,:]) ** 2, axis=0) / np.sum(weight[firstind0[i]:lastind0[i],:,:], axis=0))) * (lastind0[i] - firstind0[i]) / np.sum(weight[firstind0[i]:lastind0[i],:,:], axis=0) if free_ratio: eintmaps[i,:,:] = perrorcube[1 + els.index + i,:,:] elif i != j: eintmaps[i,:,:] = np.sqrt((paramscube[1 + els.index + i,:,:] * perrorcube[1 + 2 * els.index + i,:,:]) ** 2 + (perrorcube[1 + els.index + j,:,:] * paramscube[1 + 2 * els.index + i,:,:]) ** 2) else: eintmaps[i,:,:] = perrorcube[1 + els.index + i,:,:] efluxmaps[i,:,:] = np.sqrt(np.pi * 2) * np.sqrt((eintmaps[i,:,:] * np.sqrt((linewave[i] * dzmap) ** 2 + conf['SPSF'] ** 2)) ** 2 + (linewave[i] * dzmap / np.sqrt((linewave[i] * dzmap) ** 2 + conf['SPSF'] ** 2) * intmaps[i,:,:] * edzmap) ** 2) snrmap = np.sum(weight[indok,:,:] * (modcube[indok,:,:] - contcube[indok,:,:]), axis = 0) * sclp * lconvfac / (np.sqrt(np.pi * 2) * np.sqrt((dzmap * np.median(wave) / (1 + zmap)) ** 2 + conf['SPSF'] ** 2) * np.sqrt( np.sum(weight[indok,:,:] * (cube[indok,:,:] - modcube[indok,:,:]) ** 2, axis=0) / np.sum(weight[indok,:,:], axis=0))) #Output writing #Cubes hh = writedata(residualcube, hdr, conf['OUTPUT'] + '_residualcube.fits') hh = writedata(modcube, hdr, conf['OUTPUT'] + '_modcube.fits') hh = writedata(contcube, hdr, conf['OUTPUT'] + '_contcube.fits') hh = writedata(econtcube, hdr, conf['OUTPUT'] + '_econtcube.fits') #Images if 'CTYPE3' in hdr.ascard.keys(): del hdr['CTYPE3'] if 'CRVAL3' in hdr.ascard.keys(): del hdr['CRVAL3'] if 'CRPIX3' in hdr.ascard.keys(): del hdr['CRPIX3'] if 'CUNIT3' in hdr.ascard.keys(): del hdr['CUNIT3'] if 'CD3_3' in hdr.ascard.keys(): del hdr['CD3_3'] if 'CD3_2' in hdr.ascard.keys(): del hdr['CD3_2'] if 'CD3_1' in hdr.ascard.keys(): del hdr['CD3_1'] if 'CD2_3' in hdr.ascard.keys(): del hdr['CD2_3'] if 'CD1_3' in hdr.ascard.keys(): del hdr['CD1_3'] suffixe = '' if conf['COMMW']: suffixe = '_common' else: suffixe = '_indep' #paramscube #perrorcube hh = writedata(dofmap, hdr, conf['OUTPUT'] + '_dof' + suffixe + '.fits') hh = writedata(fnormmap, hdr, conf['OUTPUT'] + '_fnorm' + suffixe + '.fits') hh = writedata(statusmap, hdr, conf['OUTPUT'] + '_status' + suffixe + '.fits') hh = writedata(chi2map, hdr, conf['OUTPUT'] + '_chi2' + suffixe + '.fits') hh = writedata(dispcontmap, hdr, conf['OUTPUT'] + '_distcont' + suffixe + '.fits') hh = writedata(zmap, hdr, conf['OUTPUT'] + '_z' + suffixe + '.fits') hh = writedata(ezmap, hdr, conf['OUTPUT'] + '_ez' + suffixe + '.fits') hh = writedata(rvmap, hdr, conf['OUTPUT'] + '_vel' + suffixe + '.fits') hh = writedata(ervmap, hdr, conf['OUTPUT'] + '_evel' + suffixe + '.fits') hh = writedata(snrmap, hdr, conf['OUTPUT'] + '_snr' + suffixe + '.fits') for i in range(els.index): if (not linefit[i]): continue hh = writedata(wavemaps[i,:,:], hdr, conf['OUTPUT'] + '_wave' + suffixe + '_' + linename[i] + '.fits') hh = writedata(ewavemaps[i,:,:], hdr, conf['OUTPUT'] + '_ewave' + suffixe + '_' + linename[i] + '.fits') hh = writedata(wavedispmaps[i,:,:], hdr, conf['OUTPUT'] + '_wavedisp' + suffixe + '_' + linename[i] + '.fits') hh = writedata(ewavedispmaps[i,:,:], hdr, conf['OUTPUT'] + '_ewavedisp' + suffixe + '_' + linename[i] + '.fits') hh = writedata(dispmaps[i,:,:], hdr, conf['OUTPUT'] + '_disp' + suffixe + '_' + linename[i] + '.fits') hh = writedata(edispmaps[i,:,:], hdr, conf['OUTPUT'] + '_edisp' + suffixe + '_' + linename[i] + '.fits') hh = writedata(intmaps[i,:,:], hdr, conf['OUTPUT'] + '_int' + suffixe + '_' + linename[i] + '.fits') hh = writedata(eintmaps[i,:,:], hdr, conf['OUTPUT'] + '_eint' + suffixe + '_' + linename[i] + '.fits') hh = writedata(fluxmaps[i,:,:], hdr, conf['OUTPUT'] + '_flux' + suffixe + '_' + linename[i] + '.fits') hh = writedata(efluxmaps[i,:,:], hdr, conf['OUTPUT'] + '_eflux' + suffixe + '_' + linename[i] + '.fits') hh = writedata(snrmaps[i,:,:], hdr, conf['OUTPUT'] + '_snr' + suffixe + '_' + linename[i] + '.fits') return rvmap def camel(filename, plot=False, debug=False, free_ratio=False, multi_ext=False, config=None): """CAMEL (Cube Analysis: Moment maps of Emission Lines) computes moment maps Parameters ---------- filename: string name of the configuration file plot: bool keyword to plot fits during the process (not implemented yet) debug: bool keyword to show debug information (not implemented yet) free_ratio: bool keyword to allow unconstrained line ratio multi_ext: bool keyword to indicate if input fits has multiple extensions config: dictionnary optional dictionnary that contains options usually stored in the configuration file """ # XXX gérer message d'erreur si on trouve pas le fichier d'input, s'il n'y a aucune raie, si un paramètre a un problème (e.g. de formatage)... # XXX gérer cas avec une LSF donnée en input (non bruitée) t0 = time.time() #Reading of configuration file print("Reading configuration file " + filename) try: conf = readconfig(filename, config) except: print("Configuration file problem") return #Reading data `````` bepinat committed Mar 23, 2015 909 910 911 912 `````` try: print("Reading data cube " + conf['FITSFILE'] + " and variance " + conf['SKYFILE']) except: print("Reading data cube " + conf['FITSFILE'] + ". No variance data.") `````` bepinat committed Dec 16, 2014 913 914 915 916 917 918 919 920 921 `````` try: cube, hdr, var, varhdr = readcubes(conf, multi_ext=multi_ext) except: print("Input cube problem") return try: testcubes(cube, var) except: `````` bepinat committed Mar 23, 2015 922 `````` print("Variance shape: %i; Data cube shape: %i"%(np.shape(var), cube.shape)) `````` bepinat committed Dec 16, 2014 923 924 925 926 927 928 929 930 931 932 `````` print("Variance size problem") return #Cutting the cubes print("Cutting data cube") cube, hdr = cutcube(cube, hdr, conf) hdr = writedata(cube, hdr, conf['OUTPUT']+'_cube_cut.fits') if var != None: print("Cutting variance") var, varhdr = cutcube(var, varhdr, conf) `````` bepinat committed Feb 18, 2015 933 934 `````` if var.ndim == 3: var = remove_nanvar(var) `````` bepinat committed Dec 16, 2014 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 `````` varhdr = writedata(var, varhdr, conf['OUTPUT']+'_var_cut.fits') #Clipping the cube if (conf['SCLIP'] != 0) & (conf['SCLIP'] != None): print('Performing %3.1f-sigma clipping using box of size %i. Number of pass: %i'%(conf['SCLIP'], conf['XYCLIP'], conf['NCLIP'])) cube, hdr = clipcube(cube, hdr, xy=conf['XYCLIP'], sclip=conf['SCLIP'], npass=conf['NCLIP']) hdr = writedata(cube, hdr, conf['OUTPUT'] + '_cube_cut_clip.fits') #Smoothing the cubes if (conf['WSMOOTH'] != 0) & (conf['WSMOOTH'] != None): print('Performing %3.1f pixels 1D spectral smoothing'%conf['WSMOOTH']) cube, hdr = spectralsmooth(cube, hdr, conf['WSMOOTH']) conf['OUTPUT'] = conf['OUTPUT'] + '_wsmooth' hdr = writedata(cube, hdr, conf['OUTPUT'] + '_cube.fits') if var != None: if var.ndim == 3: var, varhdr = spectralsmooth(var, varhdr, conf['WSMOOTH']) varhdr = writedata(var, varhdr, conf['OUTPUT'] + '_var.fits') if (conf['SSMOOTH'] != 0) & (conf['SSMOOTH'] != None): print('Performing %3.1f pixels 2D gaussian spatial smoothing'%conf['SSMOOTH'] ) cube, hdr = spatialsmooth(cube, hdr, conf['SSMOOTH']) conf['OUTPUT'] = conf['OUTPUT'] + '_ssmooth' hdr = writedata(cube, hdr, conf['OUTPUT'] + '_cube.fits') if var != None: if var.ndim == 3: var, varhdr = spatialsmooth(var, varhdr, conf['SSMOOTH']) varhdr = writedata(var, varhdr, conf['OUTPUT'] + '_var.fits') #Creating the maps rv = buildmaps(conf, cube, hdr, var=var, plot=plot, debug=debug, free_ratio=free_ratio) t1 = time.time() #print(t1-t0) return #def usage(option, opt, value, parser): def usage(): """CAMEL (Cube Analysis: Moment maps of Emission Lines) can by launched from command line or from a python console. ######################### #Python console solution# ######################### Syntaxe: -------- import camel camel(filename, plot=False, debug=False, free_ratio=False, multi_ext=False, config=None) Parameters ---------- filename: string name of the configuration file plot: bool keyword to plot fits during the process (not implemented yet) debug: bool keyword to show debug information (not implemented yet) free_ratio: bool keyword to allow unconstrained line ratio multi_ext: bool keyword to indicate if input fits has multiple extensions config: dictionnary optional dictionnary that contains options usually stored in the configuration file ####################### #Command line solution# ####################### Syntaxe: -------- """ print(usage.__doc__) def main(argv): """ """ `````` bepinat committed Dec 18, 2014 1015 1016 1017 1018 1019 1020 1021 1022 1023 `````` parser = argparse.ArgumentParser(description=usage()) parser.add_argument('--file', '-f', action="store", dest="filename", default=None, help="name of the configuration file") parser.add_argument('--plot', '-p', action="store_true", dest="plot", default=False, help="keyword to plot fits during the process (not implemented yet)") parser.add_argument('--debug', '-d', action="store_true", dest="debug", default=False, help="keyword to show debug information (not implemented yet)") parser.add_argument('--free_line_ratio', '-r', action="store_true", dest="free_ratio", default=False, help="keyword to allow unconstrained line ratio") parser.add_argument('--multi_ext', '-m', action="store_true", dest="multi_ext", default=False, help="keyword to indicate if input fits has multiple extensions") parser.add_argument('--FITSFILE', action="store", dest="FITSFILE", default=None, help="name of the input cube") parser.add_argument('--OUTPUT', action="store", dest="OUTPUT", default=None, help="generic output name") parser.add_argument('--SKYFILE', action="store", dest="SKYFILE", default=None, help="name of the variance cube (can be a sky cube)") `````` bepinat committed Feb 16, 2015 1024 1025 1026 `````` parser.add_argument('--HALPHA', action="store_true", dest="HALPHA", default=None, help="keyword to fit Halpha@6562.801 line") parser.add_argument('--HBETA', action="store_true", dest="HBETA", default=None, help="keyword to fit Hbeta@4861.363 line") parser.add_argument('--HGAMMA', action="store_true", dest="HGAMMA", default=None, help="keyword to fit Hgamma@4340.47 line") `````` bepinat committed Feb 18, 2015 1027 1028 `````` parser.add_argument('--HDELTA', action="store_true", dest="HDELTA", default=None, help="keyword to fit Hdelta@4101.73 line") parser.add_argument('--HEPS', action="store_true", dest="HEPS", default=None, help="keyword to fit Hepsilon@3970.07 line") `````` bepinat committed Feb 16, 2015 1029 1030 1031 1032 `````` parser.add_argument('--NII6548', action="store_true", dest="NII6548", default=None, help="keyword to fit NII@6548.05 line") parser.add_argument('--NII6583', action="store_true", dest="NII6583", default=None, help="keyword to fit NII@6583.45 line") parser.add_argument('--SII6716', action="store_true", dest="SII6716", default=None, help="keyword to fit SII@6716.44 line") parser.add_argument('--SII6731', action="store_true", dest="SII6731", default=None, help="keyword to fit SII@6730.82 line") `````` bepinat committed Dec 18, 2014 1033 `````` parser.add_argument('--OIII4363', action="store_true", dest="OIII4363", default=None, help="keyword to fit OIII@4363 line") `````` bepinat committed Feb 16, 2015 1034 1035 1036 `````` parser.add_argument('--OIII4959', action="store_true", dest="OIII4959", default=None, help="keyword to fit OIII@4958.911 line") parser.add_argument('--OIII5007', action="store_true", dest="OIII5007", default=None, help="keyword to fit OIII@5006.843 line") parser.add_argument('--OII', action="store_true", dest="OII3729", default=None, help="keyword to fit OII doublet @3726.04,3728.80") # ['OII3729','OII3726'] `````` bepinat committed Dec 18, 2014 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 `````` parser.add_argument('--OI6300', action="store_true", dest="OI6300", default=None, help="keyword to fit OI@6300 line") parser.add_argument('--HEI4471', action="store_true", dest="HeI4471", default=None, help="keyword to fit HeI@4471 line") parser.add_argument('--HEI5876', action="store_true", dest="HeI5876", default=None, help="keyword to fit HeI@5876 line") parser.add_argument('--HEII4686', action="store_true", dest="HeII4686", default=None, help="keyword to fit HeII@4686 line") parser.add_argument('--NEIII3868', action="store_true", dest="NeIII3868", default=None, help="keyword to fit NeIII@3868 line") parser.add_argument('--EXTRAL', action="append", dest="EXTRAL", default=None, type=float, help="keyword to add a new line (wavelength in angstrom) - multiple extra wavelengths can be added") parser.add_argument('--COMMW', action="store_true", dest="COMMW", default=None, help="keyword to fix common widths (in velocity) between several fitted lines") parser.add_argument('--REDSHIFT', action="store", dest="REDSHIFT", default=None, type=float, help="mean redshift of the object") parser.add_argument('--REDMIN', action="store", dest="REDMIN", default=None, type=float, help="minimum redshift allowed for fitting") parser.add_argument('--REDMAX', action="store", dest="REDMAX", default=None, type=float, help="maximum redshift allowed for fitting") parser.add_argument('--INITW', action="store", dest="INITW", default=None, type=float, help="initial linewidth in km/s") parser.add_argument('--WMIN', action="store", dest="WMIN", default=None, type=float, help="minimum width allowed for fitting in km/s") parser.add_argument('--WMAX', action="store", dest="WMAX", default=None, type=float, help="maximum width allowed for fitting in km/s") parser.add_argument('--DFIT', action="store", dest="DFIT", default=None, type=float, help="bin in km/s for searching the position of the lines") parser.add_argument('--DGCTNUM', action="store", dest="DGCTNUM", default=None, type=int, help="continuum degree") parser.add_argument('--SCLIP', action="store", dest="SCLIP", default=None, type=float, help="sigma-clipping threshold to clean the cube") parser.add_argument('--XYCLIP', action="store", dest="XYCLIP", default=None, type=int, help="width of the box to compute the median for the sigma-clipping") parser.add_argument('--NCLIP', action="store", dest="NCLIP", default=None, type=int, help="number of pass for clipping") parser.add_argument('--LSF', action="store", dest="SPSF", default=None, type=float, help="spectral PSF width in angstroms (dispersion of the gaussian)") parser.add_argument('--WSMOOTH', action="store", dest="WSMOOTH", default=None, type=float, help="width for Gaussian spectral smoothing in pixel") # options? gaussian uniquement? parser.add_argument('--SSMOOTH', action="store", dest="SSMOOTH", default=None, type=float, help="width for Gaussian spatial smoothing in pixel") parser.add_argument('--XMIN', action="store", dest="XMIN", default=None, type=int, help="lower cut window in x direction of the cube in pixel") parser.add_argument('--YMIN', action="store", dest="YMIN", default=None, type=int, help="upper cut window in x direction of the cube in pixel") parser.add_argument('--ZMIN', action="store", dest="ZMIN", default=None, type=int, help="lower cut window in y direction of the cube in pixel") parser.add_argument('--XMAX', action="store", dest="XMAX", default=None, type=int, help="upper cut window in y direction of the cube in pixel") parser.add_argument('--YMAX', action="store", dest="YMAX", default=None, type=int, help="lower cut window in z direction of the cube in pixel") parser.add_argument('--ZMAX', action="store", dest="ZMAX", default=None, type=int, help="upper cut window in z direction of the cube in pixel") #parser.add_argument('--MFIT', action="store", dest="MFIT", default=None) #parser.add_argument('--THRES', action="store", dest="THRES", default=None, type=float) #parser.add_argument('--MEDIAN', action="store", dest="MEDIAN", default=None, type=float) #parser.add_argument('--FITSPSF', action="store", dest="FITSPSF", default=None, type=float) `````` bepinat committed Dec 16, 2014 1069 1070 `````` try: `````` bepinat committed Dec 18, 2014 1071 `````` options = parser.parse_args() `````` bepinat committed Dec 16, 2014 1072 1073 1074 `````` except: sys.exit(2) `````` bepinat committed Dec 18, 2014 1075 `````` if np.size(argv) < 1: `````` bepinat committed Dec 16, 2014 1076 `````` sys.exit(2) `````` bepinat committed Dec 18, 2014 1077 `````` `````` bepinat committed Dec 16, 2014 1078 1079 1080 1081 1082 1083 1084 `````` opts = vars(options) # this is a dictionnary opts['OII3726'] = opts['OII3729'] camel(options.filename, plot=options.plot, debug=options.debug, free_ratio=options.free_ratio, multi_ext=options.multi_ext, config=opts) return if __name__ == "__main__": main(sys.argv[1:])``````