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get_wcs_angles.py
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get_wcs_angles.py
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# -*- coding: utf-8 -*-
#import Interpol
#import getImages
import pyfits
import os
import string
import gzip
import csv
import utils
import inpaint
from astLib import astWCS
import numpy as np
import sdss_photo_check as sdss
#import plot_survey as plot
#import photometry as phot
from math import ceil
#import readAtlas
#import circle
import db
import os
import sdss
#import imtools
#import scipy.misc
dbDir = '../db/'
class GalaxyParameters:
@staticmethod
def SDSS(listFile, ID):
ret = GalaxyParameters()
CALIFAID_col = 0
ra_col = 1
dec_col = 2
run_col = 7
rerun_col = 8
camcol_col = 9
field_col = 10
ID = ID - 1
with open(listFile, 'rb') as f:
mycsv = csv.reader(f)
mycsv = list(mycsv)
ret.CALIFAID = string.strip(mycsv[ID][CALIFAID_col])
ret.ra = string.strip(mycsv[ID][ra_col])
ret.dec = string.strip(mycsv[ID][dec_col])
ret.run = string.strip(mycsv[ID][run_col])
ret.rerun = string.strip(mycsv[ID][rerun_col])
ret.camcol = string.strip(mycsv[ID][camcol_col])
ret.field = string.strip(mycsv[ID][field_col])
ret.runstr = utils.run2string(ret.run)
ret.field_str = utils.field2string(ret.field)
return ret
@staticmethod
def getSDSSUrl(listFile, dataDir, ID):
band = setBand()
camcol = GalaxyParameters.SDSS(listFile, ID).camcol
field = GalaxyParameters.SDSS(listFile, ID).field
field_str = GalaxyParameters.SDSS(listFile, ID).field_str
runstr = GalaxyParameters.SDSS(listFile, ID).runstr
fpCFile = dataDir+'/SDSS/'+band+'/fpC-'+runstr+'-'+band+camcol+'-'+field_str+'.fit.gz'
return fpCFile
@staticmethod
def getFilledUrl(listFile, dataDir, ID):
sdssFilename = GalaxyParameters.getSDSSUrl(listFile, dataDir, ID)
return dataDir+filledDir+utils.createOutputFilename(sdssFilename)
@staticmethod
def getMaskUrl(listFile, dataDir, simpleFile, ID):
NedName = GalaxyParameters.getNedName(listFile, simpleFile, ID).NedName
print NedName
maskFile = dataDir+'/MASKS/'+NedName+'_mask_r.fits'
return maskFile
@staticmethod
def getNedName(listFile, simpleFile, ID):
ret = GalaxyParameters()
with open(simpleFile, 'rb') as f:
NEDNAME_col = 2
mycsv = csv.reader(f)
mycsv = list(mycsv)
ret.NedName = string.strip(mycsv[ID][NEDNAME_col])
return ret
#class Inpaint():
class Interpolation():
@staticmethod
def rotateYourOwl(inputArray, n):
return np.rot90(inputArray, n)
@staticmethod
def runInpainting(maskFile, listFile, dataDir, ID, log):
maskFilename = dataDir+utils.getMask(maskFile, ID)
sdssFilename = GalaxyParameters.getSDSSUrl(listFile, dataDir, ID)
outputFilename = utils.createOutputFilename(sdssFilename, dataDir)
outputDir = dataDir+'/filled'
print 'output filename', outputFilename
#try:
#with open(dataDir+'/filled2/'+outputFilename) as f: pass
#print 'skipping', ID
#except IOError as e:
print 'inpainting', ID
sdssImage = pyfits.open(sdssFilename)
imageData = sdssImage[0].data
imageData = imageData - 1000 #soft bias subtraction, comment out if needed
head = sdssImage[0].header
maskFile = pyfits.open(maskFilename)
print 'MASK', maskFilename
mask = maskFile[0].data
callInpaint(imageData, mask, outputDir)
return log
@staticmethod
def plotFilled(inputImage, i):
CALIFA_ID = str(int(i)+1)
outputImage = inputImage
#outputImage, cdf = imtools.histeq(outputImage)
#scipy.misc.imsave('img/g/'+CALIFA_ID+'_image.jpg', outputImage)
@staticmethod
def callInpaint(img, mask, outputFilename, i):
maskedImg = np.ma.array(img, mask = mask)
NANMask = maskedImg.filled(np.NaN)
filled = inpaint.replace_nans(NANMask)
#outputFilename = utils.createOutputFilename(sdssFilename, dataDir)
hdu = pyfits.PrimaryHDU(filled)
if os.path.exists(outputFilename):
print outputFilename
outputFilename = outputFilename+"B"
hdu.writeto(outputFilename)
else:
hdu.writeto(outputFilename)
#Interpolation.plotFilled(filled, i)
def setBand():
return 'r'
def checkInput(listFile, dataDir, ID, run, rerun, camcol, runstr, band, field_str, fitsDir):
try:
f = open(GalaxyParameters.getSDSSUrl(listFile, dataDir, ID-1))
print 'it is here', ID - 1
pass
except IOError as e:
print e, ID - 1
os.system('wget -P '+fitsDir+band+' http://das.sdss.org/imaging/'+run+'/'+rerun+'/corr/'+camcol+'/fpC-'+runstr+'-'+band+camcol+'-'+field_str+'.fit.gz')
pass
try:
f = open(fitsDir+'r/fpC-'+runstr+'-r'+camcol+'-'+field_str+'.fit.gz')
print 'it is here', 'r', ID - 1
pass
except IOError as e:
print e, 'r', ID - 1
os.system('wget -P '+fitsDir+'r/ http://das.sdss.org/imaging/'+run+'/'+rerun+'/corr/'+camcol+'/fpC-'+runstr+'-r'+camcol+'-'+field_str+'.fit.gz')
pass
def checkOutput(dataDir, ID, run, rerun, camcol, runstr, band, field_str, fitsDir, filledDir):
outputFilename = dataDir+'/'+filledDir+'fpC-'+runstr+'-'+band+camcol+'-'+field_str+'.fits'
print outputFilename
try:
f = open(outputFilename)
#print 'musu', ID
except IOError as e:
out = [ID]
utils.writeOut(out, 'missing_'+setBand()+'.csv')
pass
def main():
iso25D = 40 / 0.396
#dataDir = '/media/46F4A27FF4A2713B_/work2/data/'
dataDir = '../data'
band = setBand()
#outputFile = dataDir+'/growthCurvePhotometry.csv'
listFile = dataDir+'/SDSS_photo_match.csv'
fitsDir = dataDir+'/SDSS/'
#filledDir = 'filled_'+band+'/'
filledDir = 'filled2/'
imgDir = 'img/'+band
simpleFile = dataDir+'/CALIFA_mother_simple.csv'
maskFile = dataDir+'/maskFilenames.csv'
dataFile = 'list.txt'
for ID in range(1, 940):
print 'id,', int(ID)
ra = GalaxyParameters.SDSS(listFile, int(ID)).ra
dec = GalaxyParameters.SDSS(listFile, int(ID)).dec
run = GalaxyParameters.SDSS(listFile, int(ID)).run
rerun = GalaxyParameters.SDSS(listFile, int(ID)).rerun
camcol = GalaxyParameters.SDSS(listFile, int(ID)).camcol
field = GalaxyParameters.SDSS(listFile, int(ID)).field
runstr = GalaxyParameters.SDSS(listFile, int(ID)).runstr
field_str = sdss.field2string(field)
print 'getting header info...'
rFile = fitsDir+'r/fpC-'+runstr+'-r'+camcol+'-'+field_str+'.fit.gz'
WCS=astWCS.WCS(rFile)
pa = utils.convert(db.dbUtils.getFromDB('pa', dbDir+'CALIFA.sqlite', 'nadine', ' where califa_id = '+str(ID)))[0][0]
pa_align = utils.convert(db.dbUtils.getFromDB('pa_align', dbDir+'CALIFA.sqlite', 'nadine', ' where califa_id = '+str(ID)))[0][0]
ang = WCS.getRotationDeg()
print ang
pa_align2 = (360 - ang) - 90 + pa
#if pa_align2 >= 180:
# pa_align2 = pa_align2 - 180
# if pa_align2 <= 0:
# pa_align2 = pa_align2 + 180
out = int(ID), pa, pa_align2
print out
utils.writeOut(out, "align_pa.csv")
if __name__ == "__main__":
main()