├── planck ├── __init__.py ├── .gitignore ├── private_template.py ├── cut_planet.pro ├── HFI.py ├── focalplane.py ├── test_planck_LFI_HFI.py ├── hitmap.py ├── utils.py ├── Planck.py ├── LFI.py ├── ps.py ├── pointing.py ├── test_pointing.py └── pointingtools.py ├── .gitignore ├── setup.py ├── README.txt └── gplv3.txt /planck/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | private.py 2 | .svn 3 | *.pyc 4 | -------------------------------------------------------------------------------- /planck/.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | *swp 3 | ipython* 4 | *png 5 | *npy 6 | -------------------------------------------------------------------------------- /planck/private_template.py: -------------------------------------------------------------------------------- 1 | #add all the paths and rename to private.py 2 | LFI_rimo = '' 3 | HFI_rimo = '' 4 | instrument_db = '' 5 | savfilename = '' 6 | AHF_limits = '' 7 | limitsfile ='' 8 | siam = '' 9 | 10 | mKRJ_2_mKcmb = { 11 | } 12 | 13 | mkCMB_2_MJy_sr = { 14 | } 15 | -------------------------------------------------------------------------------- /planck/cut_planet.pro: -------------------------------------------------------------------------------- 1 | result = command_line_args(count=count) 2 | lat = float(result[0]) 3 | lon = float(result[1]) 4 | radius = float(result[2]) 5 | nside = float(result[3]) 6 | 7 | ;glon_glat = [lon 33.75, lat -40.33] ; Jupiter 8 | ;radius = 1.5d ; deg 9 | ;nside = 512 10 | 11 | ang2vec, lat , lon ,vector,/astro 12 | 13 | query_disc,nside,vector,radius,listpix,/nested,/deg,/inclusive 14 | 15 | print, listpix 16 | 17 | exit, status = 0 18 | -------------------------------------------------------------------------------- /planck/HFI.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # Generic python class for dealing with Planck HFI 4 | # by zonca@deepspace.ucsb.edu 5 | 6 | import Planck 7 | import private 8 | 9 | class HFIChannel(Planck.Channel): 10 | 11 | @property 12 | def centralfreq(self): 13 | return self.f.freq 14 | 15 | def Planck_to_RJ(self, data): 16 | return data / private.mKRJ_2_mKcmb[self.f.freq] 17 | 18 | class HFI(Planck.Instrument): 19 | 20 | Channel = HFIChannel 21 | 22 | def __init__(self, name = 'HFI', rimo =private.HFI_rimo): 23 | super(HFI, self).__init__(name,rimo) 24 | 25 | @staticmethod 26 | def freq_from_tag(tag): 27 | return int(tag[:3]) 28 | -------------------------------------------------------------------------------- /planck/focalplane.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import matplotlib.pyplot as plt 3 | from pointingtools import Siam 4 | import re 5 | s=Siam() 6 | plt.figure() 7 | pair = {'a':'b','M':'S'} 8 | for tag,m in s.siam.iteritems(): 9 | 10 | print(tag) 11 | label = tag 12 | 13 | vec=np.dot(m,[1,0,0]) 14 | y=np.dot(m,[0,1,0])*.002 15 | 16 | if y[0] < 0: 17 | y *= -1 18 | 19 | if re.match('.*[abMS].*',tag) is None: 20 | plt.plot(vec[0],vec[1],'bs') 21 | else: 22 | col = 'k' 23 | if re.match('.*[bS].*',tag): 24 | col = 'r' 25 | label = None 26 | else: 27 | label += '+' + pair[tag[-1]] 28 | plt.plot(np.array([0,y[0]])+vec[0],np.array([0,y[1]]+vec[1]),col) 29 | 30 | if label: 31 | plt.text(vec[0]-.002, vec[1]-.005, label, fontsize=6) 32 | plt.grid() 33 | plt.ylim([-.09,.09]) 34 | plt.show() 35 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup, find_packages 2 | setup( 3 | name = "planck", 4 | version = "0.3", 5 | packages = ['planck'], 6 | 7 | # Project uses reStructuredText, so ensure that the docutils get 8 | # installed or upgraded on the target machine 9 | install_requires = ['docutils>=0.3'], 10 | 11 | package_data = { 12 | # If any package contains *.txt or *.rst files, include them: 13 | '': ['*.txt', '*.rst'], 14 | }, 15 | 16 | # metadata for upload to PyPI 17 | author = "Andrea Zonca", 18 | author_email = "code@andreazonca.com", 19 | description = "Python package for working with Planck data", 20 | license = "PSF", 21 | keywords = "Planck science data", 22 | url = "http://andreazonca.com/software/planck/", # project home page, if any 23 | 24 | # could also include long_description, download_url, classifiers, etc. 25 | ) 26 | -------------------------------------------------------------------------------- /README.txt: -------------------------------------------------------------------------------- 1 | Python package for dealing with Planck satellite data 2 | part of the US Planck Test Environment 3 | 4 | license: GPL v3 5 | author: Andrea Zonca 6 | website: http://andreazonca.com 7 | 8 | this software needs data that are not publicly available in 9 | order to work [RIMO, SIAM, AHF], and are not included in the 10 | package, therefore you need to be part of the Planck Collaboration 11 | to use it. 12 | 13 | this software does not include any performance number or any other 14 | information covered by the Planck Data Agreement. 15 | 16 | If you are member of the Planck collaboration and interested in using 17 | and contributing to the software please contact me. 18 | 19 | Includes: 20 | 21 | * planck, LFI, HFI: metadata classes for LFI and HFI channels 22 | created dynamically from the Reduced Instrument Model (RIMO), 23 | not publicly available, not even channel names are available in 24 | this package. 25 | 26 | * pointing: pointing library which builds detector pointing from 27 | satellite quaternions, it is based on quaternionarray 28 | [http://github.com/zonca/quaternionarray] 29 | 30 | * utils, ps, hitmap: utilities for date conversion, angular power spectra 31 | and hitmaps 32 | -------------------------------------------------------------------------------- /planck/test_planck_LFI_HFI.py: -------------------------------------------------------------------------------- 1 | import unittest 2 | from Planck import * 3 | 4 | class TestPlanckLFIHFI(unittest.TestCase): 5 | 6 | def setUp(self): 7 | self.Planck = Planck() 8 | self.lfi = self.Planck.inst['LFI'] 9 | self.hfi = self.Planck.inst['HFI'] 10 | 11 | def test_Planck(self): 12 | self.assertEqual(len(self.Planck.ch), 74) 13 | 14 | def test_LFI(self): 15 | self.assertEqual(self.lfi.name , 'LFI') 16 | self.assertEqual(len(self.lfi.ch), 22 ) 17 | self.assertEqual(len(self.lfi.d), 44 ) 18 | self.assertEqual(self.lfi['LFI25M'].tag, 'LFI25M') 19 | self.assertEqual(self.lfi['LFI25M'].arm, 'M') 20 | self.assertEqual(self.lfi['LFI25M'].RCA, 25) 21 | self.assertEqual(self.lfi['LFI27M'][0].tag, 'LFI27M-00') 22 | self.assertEqual(self.lfi['LFI27M'][0].ch.tag, 'LFI27M') 23 | self.assertEqual(self.lfi['LFI28S'].tag, 'LFI28S') 24 | self.assertEqual(self.lfi.ch[0].tag, 'LFI18M') 25 | self.assertEqual(self.lfi.ch[0].tag, 'LFI18M') 26 | 27 | def test_HFI(self): 28 | self.assertEqual(len(self.hfi.ch), 52) 29 | self.assertEqual(self.hfi['217-8a'].tag, '217-8a') 30 | self.assertEqual(self.hfi['545-4'].tag, '545-4') 31 | -------------------------------------------------------------------------------- /planck/hitmap.py: -------------------------------------------------------------------------------- 1 | import matplotlib 2 | matplotlib.use('Agg') 3 | import healpy 4 | import cPickle 5 | import logging as l 6 | import numpy as np 7 | from LFI import LFI 8 | from pointing import Pointing 9 | from testenv.remix import read_exchange 10 | import glob 11 | 12 | def testBit(int_type, offset): 13 | mask = 1 << offset 14 | return(int_type & mask) 15 | 16 | def concat_hitmaps(folder = 'pkl/'): 17 | files = glob.iglob(folder + '*pkl') 18 | for f in files: 19 | print(f) 20 | odhitmap = cPickle.load(open(f,'rb')) 21 | try: 22 | hitmap += odhitmap 23 | except: 24 | hitmap = odhitmap 25 | return hitmap 26 | 27 | 28 | class HitMap(object): 29 | 30 | def __init__(self, freq, od, nside=512, use_flag=True): 31 | LOG_FILENAME = '/u/zonca/p/issues/hitmap/full.log' 32 | l.basicConfig(filename=LOG_FILENAME,level=l.DEBUG) 33 | self.freq = freq 34 | self.od = od 35 | self.use_flag = use_flag 36 | self.lfi = LFI() 37 | self.f = self.lfi.f[self.freq] 38 | self.nside = nside 39 | l.info('%s ready' % self) 40 | 41 | def __repr__(self): 42 | return 'HitMap %d GHz, od %d' % (self.freq, self.od) 43 | 44 | def run(self): 45 | l.debug('Reading data') 46 | read_exchange_obt_flag(self.freq, [self.f.r[0]], ods = [self.od], discard_flag = False,type='R') 47 | obt = np.ma.masked_where(testBit(self.f.commonflag,0)!=0,self.f.obtx) 48 | l.debug('Preparing pointing') 49 | self.pnt = Pointing(obt.compressed(),coord='G') 50 | self.hitmap = np.zeros(healpy.nside2npix(self.nside)) 51 | for rad in self.f.r: 52 | l.debug('Processing rad %s' % rad) 53 | vec = self.pnt.get(rad) 54 | ids = np.bincount(healpy.vec2pix(self.nside, vec[:,0], vec[:,1], vec[:,2])) 55 | self.hitmap[:len(ids)] += ids 56 | l.debug('Writing to file') 57 | cPickle.dump(self.hitmap, open('/u/zonca/p/issues/hitmap/pkl/%d_%d.pkl' % (self.freq,self.od),'wb'),protocol=-1) 58 | 59 | def pix2map(pix, nside, tod=None): 60 | """Pixel array to hitmap, if TOD with same lenght of PIX is provided, 61 | it is binned to a map""" 62 | #TODO test case 63 | pix = pix.astype(np.int) 64 | ids = np.bincount(pix, weights=None) 65 | hitmap = np.ones(healpy.nside2npix(nside)) * healpy.UNSEEN 66 | hitmap[:len(ids)] = ids 67 | hitmap = healpy.ma(hitmap) 68 | if tod is None: 69 | return hitmap 70 | else: 71 | ids_binned = np.bincount(pix, weights=tod) 72 | binned = np.ones(healpy.nside2npix(nside)) * healpy.UNSEEN 73 | binned[:len(ids)] = ids 74 | binned = healpy.ma(binned)/hitmap 75 | return hitmap, binned 76 | 77 | 78 | -------------------------------------------------------------------------------- /planck/utils.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | import numpy as np 3 | from itertools import * 4 | import ephem 5 | import datetime 6 | 7 | OBTSTARTDATE = datetime.datetime(1958,1,1,0,0,0) 8 | LAUNCH = datetime.datetime(2009, 5, 13, 13, 11, 57, 565826) 9 | SECONDSPERDAY = 3600 * 24 10 | 11 | def grouper(n, iterable, padvalue=None): 12 | "grouper(3, 'abcdefg', 'x') --> ('a','b','c'), ('d','e','f'), ('g','x','x')" 13 | return izip(*[chain(iterable, repeat(padvalue, n-1))]*n) 14 | 15 | def ahfdate2obt(ahfdate): 16 | jd = ephem.Date(ahfdate.replace('T',' ').replace('-','/')) - ephem.Date('-4713/1/1 12:00:0') 17 | return jd2obt(jd) 18 | 19 | def time2sample(freq, time): 20 | if freq == 30: 21 | return int((time - 1621174818.021514892578125) * 32.5079365079365) 22 | elif freq == 44: 23 | return int((time - 1621174818.012481689453125) * 46.5454545454545) 24 | elif freq == 70: 25 | return int((time - 1621174818.008087158203125) * 78.7692307692308) 26 | else: 27 | return None 28 | 29 | def ndsample2time(freq, sample): 30 | if freq == 30: 31 | time_flat = 1621174818.021514892578125 + (sample / 32.5079365079365) 32 | BREAK98 = 1629377124.0625305 33 | BREAK98LEN = 3.573974609375 34 | afterbreak, = np.where(time_flat >= BREAK98) 35 | correction = np.zeros_like(time_flat) 36 | correction[afterbreak] = BREAK98LEN 37 | time_corrected = time_flat + correction 38 | return time_corrected 39 | 40 | def sample2time(freq, sample): 41 | if freq == 30: 42 | return 1621174818.021514892578125 + (sample / 32.5079365079365) 43 | elif freq == 44: 44 | return 1621174818.012481689453125 + (sample / 46.5454545454545) 45 | elif freq == 70: 46 | return 1621174818.008087158203125 + (sample / 78.7692307692308) 47 | else: 48 | return None 49 | 50 | def timedelta2seconds(diff): 51 | return diff.days * 24 * 3600 + diff.seconds + diff.microseconds * 1e-3 52 | 53 | def obt2utc(obt): 54 | '''Convert OBT (s) to UTC''' 55 | return OBTSTARTDATE + datetime.timedelta(0,obt) 56 | 57 | def utc2obt(utc): 58 | '''Convert UTC (datetime object) to OBT (s)''' 59 | return timedelta2seconds(utc - OBTSTARTDATE) 60 | 61 | def approxod2utc(od): 62 | return LAUNCH + datetime.timedelta(od) 63 | 64 | def utc2approxod(utc): 65 | return timedelta2seconds(utc - LAUNCH) / SECONDSPERDAY 66 | 67 | def approxod2obt(od): 68 | return utc2obt(approxod2utc(od)) 69 | 70 | def obt2approxod(obt): 71 | return utc2approxod(obt2utc(obt)) 72 | 73 | def powerspectrum(s, Fs): 74 | import matplotlib.pyplot as plt 75 | Pxx, freqs = plt.mlab.psd(s, NFFT=len(s), Fs = Fs) 76 | return freqs, Pxx 77 | 78 | def whitenoise(lenght): 79 | return np.random.standard_normal(size=lenght) 80 | -------------------------------------------------------------------------------- /planck/Planck.py: -------------------------------------------------------------------------------- 1 | import pyfits 2 | import numpy as np 3 | from exceptions import KeyError 4 | import itertools 5 | 6 | class ChannelBase(object): 7 | '''Base for Channel, frequencyset and detector''' 8 | 9 | def __repr__(self): 10 | return self.tag 11 | 12 | class Channel(ChannelBase): 13 | '''Abstract channel class for LFI and HFI channels''' 14 | 15 | def __init__(self, data, inst=None): 16 | self.tag = data[0] 17 | self.rimo = data 18 | self.inst = inst 19 | 20 | @property 21 | def sampling_freq(self): 22 | return self.rimo['F_SAMP'] 23 | 24 | class FrequencySet(ChannelBase): 25 | def __init__(self, freq, ch, inst=None): 26 | self.freq = freq 27 | self.ch = ch 28 | self.inst = inst 29 | for ch in self.ch: 30 | ch.f = self 31 | self.tag = '%d' % self.freq 32 | 33 | def __repr__(self): 34 | return '%d GHz' % self.freq 35 | 36 | @property 37 | def sampling_freq(self): 38 | return self.ch[0].sampling_freq 39 | 40 | @property 41 | def wn(self): 42 | return np.mean([ch.wn for ch in self.ch]) 43 | 44 | class Instrument(object): 45 | '''Common base class for LFI and HFI''' 46 | 47 | Channel = Channel 48 | FrequencySet = FrequencySet 49 | 50 | def __init__(self, name, rimo): 51 | '''Rimo is full path to Reduced Instrument Model FITS file''' 52 | self.name = name 53 | self.rimo = rimo 54 | rimo_file = pyfits.open(rimo)[1].data 55 | rimo_file.sort() 56 | self.rimo_fields = rimo_file.dtype.names 57 | self.ch = map(self.Channel, rimo_file, [self]*len(rimo_file)) 58 | self.chdict = dict( (ch.tag, ch) for ch in self.ch) 59 | self.f = self.create_frequency_sets() 60 | 61 | def create_frequency_sets(self): 62 | freqs = [self.freq_from_tag(ch.tag) for ch in self.ch] 63 | f = {} 64 | for freq in set(freqs): 65 | chlist = [self.ch[i] for i,chfreq in enumerate(freqs) if chfreq == freq] 66 | f[freq] = self.FrequencySet(freq, chlist, self) 67 | return f 68 | 69 | def __getitem__(self, key): 70 | return self.chdict[key] 71 | 72 | 73 | import LFI 74 | import HFI 75 | 76 | class Planck(object): 77 | '''Planck class, gives an iterator .ch for all LFI and HFI channels''' 78 | 79 | def __init__(self): 80 | self.inst = {'LFI':LFI.LFI(), 'HFI':HFI.HFI()} 81 | self.ch = [ch for inst in self.inst.values() for ch in inst.ch] 82 | self.f = dict((freq,f) for inst in self.inst.values() for freq,f in inst.f.iteritems()) 83 | 84 | def __getitem__(self, key): 85 | try: 86 | return self.inst['LFI'][key] 87 | except KeyError: 88 | return self.inst['HFI'][key] 89 | -------------------------------------------------------------------------------- /planck/LFI.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # 3 | # Generic python class for dealing with Planck LFI 4 | # by zonca@deepspace.ucsb.edu 5 | 6 | import numpy as np 7 | import Planck 8 | import private 9 | 10 | def flatten_d(chlist): 11 | return [d for ch in chlist for d in ch.d] 12 | 13 | class LFIChannel(Planck.Channel): 14 | 15 | MS = { 0 : 'M', 1 : 'S' } 16 | fromMS = { 'M' : 0, 'S' : 1} 17 | 18 | def __init__(self, data, inst=None): 19 | super(LFIChannel, self).__init__(data, inst) 20 | self.d = [Detector(self, 0), Detector(self, 1)] 21 | 22 | @property 23 | def RCA(self): 24 | return LFI.RCA_from_tag(self.tag) 25 | 26 | @property 27 | def arm(self): 28 | return self.tag[-1] 29 | 30 | @property 31 | def n(self): 32 | return self.fromMS[self.arm] 33 | 34 | @property 35 | def centralfreq(self): 36 | return self.inst.instrument_db(self).field('nu_cen') 37 | 38 | @property 39 | def wn(self): 40 | return self.inst.instrument_db(self).field('NET_KCMB') 41 | 42 | def __getitem__(self, n): 43 | return self.d[n] 44 | 45 | def Planck_to_RJ(self, data): 46 | from testenv import dipole 47 | return dipole.Planck_to_RJ(data, self.centralfreq) 48 | 49 | class LFIFrequencySet(Planck.FrequencySet): 50 | 51 | @property 52 | def d(self): 53 | return flatten_d(self.ch) 54 | class LFI(Planck.Instrument): 55 | 56 | Channel = LFIChannel 57 | FrequencySet = LFIFrequencySet 58 | 59 | def __init__(self, name = 'LFI', rimo = private.LFI_rimo): 60 | super(LFI, self).__init__(name,rimo) 61 | 62 | @classmethod 63 | def freq_from_tag(cls, tag): 64 | RCA = cls.RCA_from_tag(tag) 65 | if RCA <= 23: 66 | return 70 67 | elif RCA <= 26: 68 | return 44 69 | elif RCA <= 28: 70 | return 30 71 | else: 72 | return None 73 | 74 | @staticmethod 75 | def RCA_from_tag(tag): 76 | return int(tag[3:5]) 77 | 78 | def instrument_db(self,ch): 79 | if not hasattr(self,'_instrument_db'): 80 | import pyfits 81 | self._instrument_db = pyfits.open(private.instrument_db)[1].data 82 | det_index, = np.where(self._instrument_db.field('RADIOMETER').rfind(ch.tag)== 0) 83 | return self._instrument_db[det_index] 84 | 85 | @property 86 | def d(self): 87 | return flatten_d(self.ch) 88 | class Detector(Planck.ChannelBase): 89 | def __init__(self, ch, n): 90 | self.n = n 91 | self.ch = ch 92 | self.tag = '%s-%s%s' % (ch.tag, self.ch.n, self.n) 93 | 94 | def savfilename(self, od): 95 | return private.savfilename % (od, self.ch.RCA, self.ch.n, self.n) 96 | 97 | @property 98 | def cdstag(self): 99 | return 'RCA%s%s%s' % (self.ch.RCA,self.ch.n, self.n) 100 | -------------------------------------------------------------------------------- /planck/ps.py: -------------------------------------------------------------------------------- 1 | import subprocess 2 | import pkgutil 3 | import numpy as np 4 | import os 5 | import pyfits 6 | from configobj import ConfigObj 7 | import math 8 | 9 | import healpy 10 | 11 | from cluster import run_serial 12 | 13 | def apply_mask(mask, m): 14 | m[mask == 0] = healpy.UNSEEN 15 | return m 16 | 17 | def sum_diff_maps(a, b): 18 | '''Returns half-sum and half-difference of input maps on common pixels 19 | ''' 20 | 21 | valid_pixels = np.logical_and(a != healpy.UNSEEN, b != healpy.UNSEEN) 22 | jackmaps = np.zeros_like([a,b]) 23 | jackmaps[:] = healpy.UNSEEN 24 | jackmaps[0][valid_pixels] = ( a[valid_pixels] + b[valid_pixels]) / 2 25 | jackmaps[1][valid_pixels] = ( a[valid_pixels] - b[valid_pixels]) / 2 26 | 27 | return jackmaps 28 | 29 | def smooth(m, arcmin, lmax = None): 30 | '''Utility to smooth a map with smooting by Healpix 31 | ''' 32 | unseen = m == healpy.UNSEEN 33 | healpy.write_map('tempmap.fits', m, nest = False) 34 | config_filename = 'config_smooth.txt' 35 | config = ConfigObj() 36 | config.filename = config_filename 37 | config['simul_type'] = 1 38 | if lmax: 39 | config['nlmax'] = lmax 40 | config['infile'] = 'tempmap.fits' 41 | config['outfile'] = 'tempmap_smoothed.fits' 42 | config['fwhm_arcmin'] = arcmin 43 | config.write() 44 | if os.path.exists('tempmap_smoothed.fits'): 45 | os.remove('tempmap_smoothed.fits') 46 | callstring = 'smoothing --double %s' % config_filename 47 | subprocess.call(callstring, shell=True) 48 | smoothed_m = healpy.read_map('tempmap_smoothed.fits') 49 | smoothed_m[unseen] = healpy.UNSEEN 50 | return smoothed_m 51 | 52 | def remove_dipole(m, gal_cut = 30): 53 | #module abs path 54 | abspath = os.path.dirname(__file__) 55 | if os.path.exists('tempmap.fits'): 56 | os.remove('tempmap.fits') 57 | healpy.write_map('tempmap.fits',m,nest = False) 58 | callstring = 'idl %s/fixmap.pro -IDL_QUIET 1 -quiet -args tempmap.fits %d' % (abspath,gal_cut) 59 | subprocess.call(callstring, shell=True) 60 | out = healpy.read_map('no_dipole_tempmap.fits', nest=True) 61 | os.remove('no_dipole_tempmap.fits') 62 | return out 63 | 64 | def anafast(m, gal_cut = 30, lmax = None): 65 | '''Utility to run anafast by Healpix''' 66 | healpy.write_map('tempmap.fits', m, nest = False) 67 | config_filename = 'anafastconfig.txt' 68 | config = ConfigObj() 69 | config.filename = config_filename 70 | config['simul_type'] = 1 71 | if gal_cut: 72 | config['theta_cut_deg'] = gal_cut 73 | if lmax: 74 | config['nlmax'] = lmax 75 | config['infile'] = 'tempmap.fits' 76 | config['outfile'] = 'tempcl.fits' 77 | config['won'] = 0 78 | config.write() 79 | if os.path.exists('tempcl.fits'): 80 | os.remove('tempcl.fits') 81 | callstring = 'anafast --double %s' % config_filename 82 | subprocess.call(callstring, shell=True) 83 | cl = pyfits.open('tempcl.fits')[1].data.field('TEMPERATURE') 84 | os.remove('tempcl.fits') 85 | return cl 86 | 87 | def cut_planet(lat, lon, radius = 1.5, nside = 512): 88 | '''Cut planet 89 | 90 | Example: 91 | Jupiter [lat -40.33,lon 33.75] radius = 1.5 deg''' 92 | 93 | callstring = 'idl cut_planet.pro -IDL_QUIET 1 -quiet -args %f %f %f %f' % (lat, lon, radius, nside) 94 | popen = subprocess.Popen(callstring, shell=True, stdout=subprocess.PIPE, cwd = os.path.dirname(__file__)) 95 | output = popen.communicate()[0] 96 | return map(float, output.strip().split()) 97 | -------------------------------------------------------------------------------- /planck/pointing.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | 3 | import pyfits 4 | import logging as l 5 | from Quaternion import Quat as quat 6 | import numpy as np 7 | from LFI import LFI 8 | #from IPython.Debugger import Tracer; debug_here = Tracer() 9 | import re 10 | import quaternionarray as qarray 11 | from utils import grouper 12 | import Planck 13 | import private 14 | from pointingtools import * 15 | 16 | class Pointing(object): 17 | '''Pointing interpolation and rotation class 18 | 19 | usage: 20 | >>> ch= Planck()['100-1a'] 21 | >>> pnt = Pointing(obt, coord='G') #interpolates AHF to obt 22 | >>> vec = pnt.get(ch) #rotates to detector frame and gives x,y,z vector 23 | >>> pix = pnt.get_pix(ch, 2048, nest=True) #healpix pixel number nside 2048 24 | ''' 25 | 26 | def __init__(self,obt,coord='G', AHF_d=None, nointerp=False): 27 | '''AHF_d is the pyfits AHF data if already loaded in the main file 28 | nointerp to use the AHF OBT stamps''' 29 | l.warning('Pointing setup, coord:%s' % coord) 30 | #get ahf limits 31 | 32 | if AHF_d is None: 33 | AHF_data_iter = (pyfits.open(file)[1].data for file in AHF_btw_OBT(obt)) 34 | else: 35 | AHF_data_iter = [AHF_d] 36 | 37 | ahfobt = np.array([]) 38 | qsat = None 39 | for AHF_data in AHF_data_iter: 40 | 41 | obt_spl = AHF_data.field('OBT_SPL')/2.**16 42 | i_start = max(obt_spl.searchsorted(obt[0])-1,0) 43 | i_end = min(obt_spl.searchsorted(obt[-1])+1,len(obt_spl)-1) 44 | AHF = AHF_data[i_start:i_end] 45 | 46 | allquat = np.hstack([AHF.field('QUATERNION_X')[:,np.newaxis], AHF.field('QUATERNION_Y')[:,np.newaxis], AHF.field('QUATERNION_Z')[:,np.newaxis], AHF.field('QUATERNION_S')[:,np.newaxis]]) 47 | 48 | if qsat is None: 49 | qsat = allquat 50 | else: 51 | qsat = np.vstack([qsat,allquat]) 52 | ahfobt = np.concatenate([ahfobt, AHF.field('OBT_SPL')/2.**16]) 53 | 54 | if coord == 'E': 55 | qsatgal = qsat 56 | elif coord == 'G': 57 | hfobt = np.array([]) 58 | qsatgal = quaternion_ecl2gal(qsat) 59 | 60 | if nointerp: 61 | self.qsatgal_interp = qsatgal 62 | else: 63 | l.info('Interpolating quaternions') 64 | #nlerp 65 | self.qsatgal_interp = qarray.nlerp(obt, ahfobt, qsatgal) 66 | 67 | l.info('Quaternions interpolated') 68 | self.siam = Siam() 69 | 70 | self.ahfobt = ahfobt 71 | self.obt = obt 72 | 73 | def interp_get(self, rad): 74 | '''Interpolation after rotation to gal frame''' 75 | from Quaternion import Quat 76 | l.info('Rotating to detector %s' % rad) 77 | siam_quat = Quat(self.siam.get(rad)).q 78 | totquat = qarray.mult(self.qsatgal_interp, siam_quat) 79 | totquat_interp = qarray.nlerp(self.obt, self.ahfobt, totquat) 80 | x = np.array([1, 0, 0]) 81 | vec = qarray.rotate(totquat_interp, x) 82 | l.info('Rotated to detector %s' % rad) 83 | return vec 84 | 85 | def get(self, rad): 86 | l.info('Rotating to detector %s' % rad) 87 | x = np.dot(self.siam.get(rad),[1, 0, 0]) 88 | vec = qarray.norm(qarray.rotate(self.qsatgal_interp, x)) 89 | l.info('Rotated to detector %s' % rad) 90 | return vec 91 | 92 | def get_pix(self, rad, nside=1024, nest=True): 93 | from healpy import vec2pix 94 | vec = self.get(rad) 95 | return vec2pix(nside, vec[:,0], vec[:,1], vec[:,2], nest) 96 | 97 | def get_ang(self, rad, degrees=False): 98 | from healpy import vec2ang 99 | vec = self.get(rad) 100 | ang = vec2ang(vec) 101 | if degrees: 102 | return map(np.rad2deg, ang) 103 | else: 104 | return ang 105 | -------------------------------------------------------------------------------- /planck/test_pointing.py: -------------------------------------------------------------------------------- 1 | import cPickle 2 | import healpy 3 | import logging as l 4 | import unittest 5 | import matplotlib.pyplot as plt 6 | 7 | from pointing import * 8 | from LFI import LFI 9 | from testenv.remix import read_exchange 10 | 11 | class TestPointing(unittest.TestCase): 12 | 13 | def setUp(self): 14 | 15 | l.basicConfig(level=l.DEBUG, 16 | format='%(asctime)s %(levelname)s %(message)s') 17 | self.chlfi = LFI()['LFI28M'] 18 | self.TOLERANCE = 1e-7 19 | 20 | def test_prepare_for_dipole(self): 21 | '''Saves pointing array for testing dipole generation''' 22 | read_exchange([self.chlfi], ods = [100], discard_flag = False,type='R') 23 | pnt = Pointing(self.chlfi.f.obtx,coord='G') 24 | vec = pnt.get(self.chlfi) 25 | np.save('vec_LFI28M_OD100_G',vec) 26 | assert True 27 | 28 | def test_prepare_for_M3(self): 29 | '''Saves pointing array for comparing with M3''' 30 | read_exchange([self.chlfi], ods = [100], discard_flag = False,type='R') 31 | span = 56300 32 | obt = self.chlfi.f.obtx[:span] 33 | pnt = Pointing(obt, coord='E') 34 | vec = pnt.get(self.chlfi) 35 | np.save('vec_LFI28M_OD100_E',vec) 36 | np.save('obt_LFI28M_OD100_E',obt) 37 | assert True 38 | 39 | def test_pointing_vs_dpc(self): 40 | '''Check pointing against LFI DPC''' 41 | # pointing extracted from DPC trieste 42 | dpc=cPickle.load(open('/u/zonca/p/issues/pointing/pointing100_DPC.pkl')) 43 | i_dpc = dpc['sampleOBT'].searchsorted(106793429004442.0) 44 | thetadpc=dpc['theta'][i_dpc] 45 | phidpc=dpc['phi'][i_dpc] 46 | dpc['theta'] = dpc['theta'][i_dpc:] 47 | dpc['phi'] = dpc['phi'][i_dpc:] 48 | dpc['sampleOBT'] = dpc['sampleOBT'][i_dpc:]/2**16 49 | dpc['name'] = 'dpc' 50 | 51 | read_exchange([self.chlfi], ods = [100], discard_flag = False,type='R') 52 | i_te = 697 53 | te = {'sampleOBT':self.chlfi.f.obtx[i_te:],'name':'te'} 54 | #pnt = Pointing(self.chlfi.f.obtx[697:698],coord='E') 55 | pnt = Pointing(te['sampleOBT'],coord='E') 56 | vec = pnt.get(self.chlfi) 57 | thetav, phiv = healpy.vec2ang(vec) 58 | te['theta'] = thetav 59 | te['phi'] = phiv 60 | theta, phi = thetav[0], phiv[0] 61 | print('Theta DPC %f testenv %f' % (thetadpc, theta)) 62 | print('Phi DPC %f testenv %f' % (phidpc, phi)) 63 | span = 32.5 * 60 * 10 64 | for angle in ['theta','phi','diff_theta','diff_phi']: 65 | plt.figure() 66 | if angle.startswith('diff'): 67 | a = angle.split('_')[1] 68 | plt.plot(d['sampleOBT'][:span], dpc[a][:span]-te[a][:span],label=a.capitalize() + ' difference') 69 | else: 70 | for d in [dpc,te]: 71 | plt.plot(d['sampleOBT'][:span], d[angle][:span], label=d['name']) 72 | plt.legend();plt.grid() 73 | plt.title(angle.capitalize().replace('_',' ')) 74 | plt.xlabel('OBT') 75 | plt.ylabel('%s [rad]' % angle) 76 | plt.savefig('%s_dpc_te.png' % angle) 77 | assert abs(thetadpc - theta) < self.TOLERANCE 78 | assert abs(phidpc - phi) < self.TOLERANCE 79 | 80 | def test_quaternion_ecl2gal(self): 81 | #from Quaternion module .transform 82 | ecl2gal_matrix = np.matrix([[ -5.48755398e-02, -9.93821384e-01, -9.64765918e-02], 83 | [ 4.94109453e-01, -1.10990693e-01, 8.62285866e-01], 84 | [ -8.67666136e-01, -3.51593739e-04, 4.97147215e-01]]) 85 | q = np.array([0, 0, 0, 1]) 86 | vecl = np.array([ 0.29192658, 0.45464871, 0.84147098]) 87 | qgal = quaternion_ecl2gal(q) 88 | vgal_ecl2gal = qarray.rotate(qgal,vecl) 89 | vgal_matrix = np.asarray(ecl2gal_matrix * vecl[:,np.newaxis]).flatten() 90 | print(vgal_ecl2gal) 91 | print(vgal_matrix) 92 | assert (vgal_ecl2gal - vgal_matrix).std() < 1e-8 93 | 94 | def test_vector_ecl2gal(self): 95 | #from Quaternion module .transform 96 | ecl2gal_matrix = np.matrix([[ -5.48755398e-02, -9.93821384e-01, -9.64765918e-02], 97 | [ 4.94109453e-01, -1.10990693e-01, 8.62285866e-01], 98 | [ -8.67666136e-01, -3.51593739e-04, 4.97147215e-01]]) 99 | vecl = np.array([ 0.29192658, 0.45464871, 0.84147098]) 100 | vgal_ecl2gal = vector_ecl2gal(vecl) 101 | vgal_matrix = np.asarray(ecl2gal_matrix * vecl[:,np.newaxis]).flatten() 102 | print(vgal_ecl2gal) 103 | print(vgal_matrix) 104 | assert (vgal_ecl2gal - vgal_matrix).std() < 1e-8 105 | -------------------------------------------------------------------------------- /planck/pointingtools.py: -------------------------------------------------------------------------------- 1 | from __future__ import division 2 | 3 | #TODO remove useless imports 4 | import math 5 | import pyfits 6 | import logging as l 7 | import csv 8 | import glob 9 | from itertools import * 10 | from Quaternion import Quat as quat 11 | import numpy as np 12 | #from IPython.Debugger import Tracer; debug_here = Tracer() 13 | import re 14 | import quaternionarray as qarray 15 | from utils import grouper 16 | import private 17 | from cgkit.cgtypes import * 18 | from pointingtools import * 19 | 20 | 21 | QECL2GAL = np.array((-0.37382079227204573, 0.33419217216073838, 0.64478939348298625, 0.57690575088960561)) 22 | 23 | def ahf_limits(odrange = range(90,481 +1), folder = private.AHF_limits): 24 | from IPython.kernel import client 25 | tc = client.TaskClient() 26 | files = [glob.glob(folder + '/%04d/att_hist_high*' % od)[0] for od in odrange] 27 | lims = tc.map(get_ahf_lim, files) 28 | outfile = open('/u/zonca/p/remix/AHF-limits.txt','w') 29 | out = csv.writer(outfile) 30 | for f,l in zip(files,lims): 31 | out.writerow([f,'%f' % l[0],'%f' % l[1]]) 32 | outfile.close() 33 | 34 | def get_ahf_lim(AHF): 35 | import pyfits 36 | f = pyfits.open(AHF) 37 | return f[1].data.field('OBT_SPL')[[0,-1]]/2.**16 38 | 39 | class Siam(object): 40 | 41 | def __init__(self): 42 | siamfile = private.siam 43 | l.debug('using SIAM %s' % siamfile) 44 | f = open(siamfile) 45 | lines = f.readlines() 46 | self.siam = {} 47 | for line in grouper(4,lines[1:]): 48 | chtag = line[0].split()[0] 49 | m = np.array(np.matrix(';'.join(line[1:])).T) 50 | self.siam[chtag] = m 51 | def get(self, ch): 52 | if ch.inst.name == 'HFI': 53 | return self.siam[ch.tag] 54 | else: 55 | l.warning('For LFI using instrument DB angles') 56 | return SiamAngles().get(ch) 57 | 58 | class SiamAngles(object): 59 | 60 | SPIN2BORESIGHT = 85.0 61 | 62 | def __init__(self): 63 | pass 64 | 65 | def get(self, ch): 66 | mat_spin2boresight=mat3.rotation(np.pi/2-self.SPIN2BORESIGHT/180.*np.pi,vec3(0,1,0)) 67 | theta = ch.rimo['THETA_UV']/180.*np.pi 68 | phi = ch.rimo['PHI_UV']/180.*np.pi 69 | psi = ch.rimo['PSI_UV']/180.*np.pi 70 | mat_theta_phi = mat3.rotation(theta,vec3(-math.sin(phi),math.cos(phi),0)) 71 | mat_psi = mat3.rotation(psi,vec3(0,0,1)) 72 | # detector points to X axis 73 | total = mat_spin2boresight * (mat_theta_phi * mat_psi) 74 | total_mat = np.matrix(np.split(np.array(total.toList(rowmajor=True)),3)) 75 | # siam is defined as pointing to Z axis 76 | return np.array(total_mat * np.matrix([[0,0,1],[0,1,0],[1,0,0]])) 77 | 78 | def AHF_filename2od(filename): 79 | return int(re.findall('/(\d{4})/',filename)[0]) 80 | 81 | def get_AHF_limits(filenames = True): 82 | limitsfile = private.limitsfile 83 | if filenames: 84 | dt=np.dtype({'names':['filename','start','end'],'formats':['S100',np.float,np.float]}) 85 | return np.loadtxt(open(limitsfile),delimiter=',',dtype=dt) 86 | else: 87 | dt=np.dtype({'names':['od','start','end'],'formats':[np.int,np.float,np.float]}) 88 | return np.loadtxt(open(limitsfile),delimiter=',',dtype=dt, converters={0: AHF_filename2od}) 89 | 90 | def AHF_btw_OBT(obt): 91 | 92 | limits = get_AHF_limits() 93 | 94 | first_file_index = limits['start'].searchsorted(obt[0]) - 1 95 | last_file_index = limits['end'].searchsorted(obt[-1]) 96 | if first_file_index == -1: 97 | first_file_index = 0 98 | if last_file_index > len(limits) -1: 99 | last_file_index -= 1 100 | 101 | files = limits['filename'][first_file_index:last_file_index + 1] 102 | l.debug('Opening %s' % files) 103 | return files 104 | 105 | def generate_repointing_flag(obt): 106 | flag = np.zeros_like(obt) 107 | files = [pyfits.open(file)[1].data for file in AHF_btw_OBT(obt)] 108 | 109 | files[-1] = files[-1][:(files[-1].field('OBT_SPL')/2.**16).searchsorted(obt[-1])+1] 110 | files[0] = files[0][(files[0].field('OBT_SPL')/2.**16).searchsorted(obt[0])-1:] 111 | AHF = np.concatenate(files) 112 | 113 | i_start_repointing, = np.nonzero(np.diff(AHF['OBT_BEG'])) 114 | start_repointing = AHF['OBT_SPL'][i_start_repointing+1]/2.**16 115 | end_repointing = AHF['OBT_BEG'][i_start_repointing+1]/2.**16 116 | for start, end in zip(start_repointing,end_repointing): 117 | flag[obt.searchsorted(start):obt.searchsorted(end)] = 1 118 | return flag 119 | 120 | def quaternion_ecl2gal(qsat): 121 | '''Convert array of quaternions from Ecliptic to Galactic''' 122 | l.info('Rotating to Galactic frame') 123 | qsatgal = qarray.mult(QECL2GAL ,qsat) 124 | # renormalizing to unity 125 | qsatgal = qarray.norm(qsatgal) 126 | return qsatgal 127 | 128 | def vector_ecl2gal(vecl): 129 | '''Convert arrays from Ecliptic to Galactic''' 130 | l.info('Rotating to Galactic frame') 131 | return qarray.rotate(QECL2GAL ,vecl) 132 | 133 | def vector_gal2ecl(vecl): 134 | '''Convert arrays from Ecliptic to Galactic''' 135 | l.info('Rotating to Galactic frame') 136 | return qarray.rotate(qarray.inv(QECL2GAL) ,vecl) 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No Surrender of Others' Freedom. 541 | 542 | If conditions are imposed on you (whether by court order, agreement or 543 | otherwise) that contradict the conditions of this License, they do not 544 | excuse you from the conditions of this License. If you cannot convey a 545 | covered work so as to satisfy simultaneously your obligations under this 546 | License and any other pertinent obligations, then as a consequence you may 547 | not convey it at all. For example, if you agree to terms that obligate you 548 | to collect a royalty for further conveying from those to whom you convey 549 | the Program, the only way you could satisfy both those terms and this 550 | License would be to refrain entirely from conveying the Program. 551 | 552 | 13. Use with the GNU Affero General Public License. 553 | 554 | Notwithstanding any other provision of this License, you have 555 | permission to link or combine any covered work with a work licensed 556 | under version 3 of the GNU Affero General Public License into a single 557 | combined work, and to convey the resulting work. The terms of this 558 | License will continue to apply to the part which is the covered work, 559 | but the special requirements of the GNU Affero General Public License, 560 | section 13, concerning interaction through a network will apply to the 561 | combination as such. 562 | 563 | 14. Revised Versions of this License. 564 | 565 | The Free Software Foundation may publish revised and/or new versions of 566 | the GNU General Public License from time to time. Such new versions will 567 | be similar in spirit to the present version, but may differ in detail to 568 | address new problems or concerns. 569 | 570 | Each version is given a distinguishing version number. If the 571 | Program specifies that a certain numbered version of the GNU General 572 | Public License "or any later version" applies to it, you have the 573 | option of following the terms and conditions either of that numbered 574 | version or of any later version published by the Free Software 575 | Foundation. If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT 593 | HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY 594 | OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, 595 | THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR 596 | PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM 597 | IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF 598 | ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 599 | 600 | 16. Limitation of Liability. 601 | 602 | IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING 603 | WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS 604 | THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY 605 | GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE 606 | USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF 607 | DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD 608 | PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), 609 | EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF 610 | SUCH DAMAGES. 611 | 612 | 17. Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | --------------------------------------------------------------------------------