# -*- coding: utf-8 -*-

"""

Created on Fri Feb 6 15:36:15 2015

@author: bnorris

This takes the fits files from the Xenics camera and puts the measured waveguide

fluxes into appropriate variables.

"""

import numpy as np

import matplotlib.pyplot as plt

import pyfits as pf

import pdb

from scipy.io.idl import readsav

from circles import circles

from numpy.polynomial.polynomial import polyval

global p1Orp2, nWgsOP, nWgsIN, nBLs, nPists, segmentOrder, showPlots, nonLinCoeffs

p1Orp2 = 1 #Which side of the baseline to piston? (1 or 2)

nWgsOP = 120

nWgsIN = 8

nBLs = 28

nPists = 61

wavelength = 1.55 #microns

showPlots = True

saveFigs = False

nonLinCoeffsFile = 'coeffs_detailed_6.idlvar'

segmentOrder = np.array([23, 25, 27, 9, 29, 36, 31, 33])

outFile = 'extractedFluxes_ipbc_20140930_3_xtr2-nonlin6'

############################################################################################################################################################

# LAB DATA

############################################################################################################################################################

#dataDir='./dragonfly20140930data/'

dataDir='/Volumes/mojito2/snert/dragonfly/labtests/20140930/data_fits/'

darkFrame="ipbc_20140930_3_dark.mat.fits"

singleChannels=['ipbc_20140930_3_SingleWGScan_WG_23.mat.fits','ipbc_20140930_3_SingleWGScan_WG_25.mat.fits',

'ipbc_20140930_3_SingleWGScan_WG_27.mat.fits','ipbc_20140930_3_SingleWGScan_WG_9.mat.fits',

'ipbc_20140930_3_SingleWGScan_WG_29.mat.fits','ipbc_20140930_3_SingleWGScan_WG_36.mat.fits',

'ipbc_20140930_3_SingleWGScan_WG_31.mat.fits','ipbc_20140930_3_SingleWGScan_WG_33.mat.fits']

baselineChannels1=[

'ipbc_20140930_3_BaselineScan_WGs_36_33_p1.mat.fits', 'ipbc_20140930_3_BaselineScan_WGs_31_33_p1.mat.fits']

baselineChannels2=[

'ipbc_20140930_3_BaselineScan_WGs_36_33_p2.mat.fits', 'ipbc_20140930_3_BaselineScan_WGs_31_33_p2.mat.fits']

allOnScans=["ipbc_20140930_3b_AllOnScan_WG_23.mat.fits","ipbc_20140930_3b_AllOnScan_WG_25.mat.fits",

]

#==============================================================================

# Dark Frame, etc.

#==============================================================================

dark=pf.open(dataDir+darkFrame)

dark = dark['PRIMARY'].data

dark=np.average(dark,axis=0)

nonLinCoeffs = readsav(nonLinCoeffsFile).coeffs

if showPlots:

plt.figure(1)

plt.pause(5)

#==============================================================================

# Function to extract fluxes from a given frame

#==============================================================================

# TODO - Rigth now you have to manually put in the following numbers. Make

# an interactive GUI for this.

def fluxesFromIm(image, xstart=86., xend=540., ycoord=234., radius=1.5):

return fluxes

#==============================================================================

# Extract Single Waveguide Scans

#==============================================================================

wgInInds = range(nWgsIN)

singleWGscan_allChipOuts = np.zeros((nPists,nWgsOP,nWgsIN))

print '######## Doing Single Waveguide Scans ########'

for i in wgInInds:

wg2pist = i

print 'Pistoning waveguide %d' % i

filename = dataDir+singleChannels[i]

hdulist=pf.open(filename)

imCube=hdulist['PRIMARY'].data

for pist in range(nPists):

print 'Piston step %d of %d' % (pist+1, nPists)

im=imCube[pist,:,:] - dark

fluxes = fluxesFromIm(im)

singleWGscan_allChipOuts[pist,:,i] = fluxes

if showPlots:

plt.figure(1)

plt.clf()

im2show = singleWGscan_allChipOuts[:,:,i].T

plt.imshow(im2show, interpolation='nearest')

plt.colorbar(orientation='vertical')

plt.pause(0.01)

if saveFigs:

fname="fig_ExtractSingleWGScan_%d.pdf" % i

plt.savefig(fname)

singleWGscan_allChipOuts_avgd = np.average(singleWGscan_allChipOuts, axis=0)

#==============================================================================

# Extract Baseline Scans

#==============================================================================

bl2wg = np.array([ [23,25 ],

[31,33] ])

blInds = range(nBLs)

BLscan_allChipOuts = np.zeros((nPists,nWgsOP,nBLs))

BLscan_pistVals = np.zeros((nPists,nBLs))

print '######## Doing Baseline Scans ########'

for i in blInds:

wg2pist = bl2wg[i, p1Orp2-1]

print 'Baseline %d, pistoning waveguide %d' % (i, wg2pist)

if p1Orp2 == 1:

filename = dataDir+baselineChannels1[i]

else:

filename = dataDir+baselineChannels2[i]

hdulist=pf.open(filename)

imCube=hdulist['PRIMARY'].data

# Put pistvals in radians. NB *2 is because OPL = 2*MEMS_piston

BLscan_pistVals[:,i] = (imCube[:,0,0]*2. / wavelength) * 2.*np.pi

print BLscan_pistVals[:,i]

for pist in range(nPists):

print 'Piston step %d of %d' % (pist+1, nPists)

im=imCube[pist,:,:] - dark

fluxes = fluxesFromIm(im)

BLscan_allChipOuts[pist,:,i] = fluxes

if showPlots:

plt.figure(1)

plt.clf()

im2show = BLscan_allChipOuts[:,:,i].T

plt.imshow(im2show, interpolation='nearest')

plt.colorbar(orientation='vertical')

plt.pause(0.01)

if saveFigs:

fname="fig_ExtractBLScan_%d.pdf" % i

plt.savefig(fname)

#==============================================================================

# Extract AllOn Scans (for later testing)

#==============================================================================

wgInInds = range(nWgsIN)

allOnWGscan_allChipOuts = np.zeros((nPists,nWgsOP,nWgsIN))

print '######## Doing AllOn Scans ########'

for i in wgInInds:

wg2pist = i

print 'Pistoning waveguide %d' % i

filename = dataDir+allOnScans[i]

hdulist=pf.open(filename)

imCube=hdulist['PRIMARY'].data

for pist in range(nPists):

print 'Piston step %d of %d' % (pist+1, nPists)

im=imCube[pist,:,:] - dark

fluxes = fluxesFromIm(im)

allOnWGscan_allChipOuts[pist,:,i] = fluxes

if showPlots:

plt.figure(1)

plt.clf()

im2show = allOnWGscan_allChipOuts[:,:,i].T

plt.imshow(im2show, interpolation='nearest')

plt.colorbar(orientation='vertical')

plt.pause(0.01)

if saveFigs:

fname="fig_ExtractAllOnScan_%d.pdf" % i

plt.savefig(fname)

#==============================================================================

# Save everything

#==============================================================================

#FIXME

np.savez(outFile, singleWGscan_allChipOuts_avgd=singleWGscan_allChipOuts_avgd,

singleWGscan_allChipOuts=singleWGscan_allChipOuts,

BLscan_allChipOuts=BLscan_allChipOuts,

BLscan_pistVals=BLscan_pistVals,

allOnWGscan_allChipOuts=allOnWGscan_allChipOuts)

#==============================================================================

# To restore, you'd do:

#file='extractedFluxes_ipbc_20140930_3_xtr1.npz'

#npzfile=np.load(file)

#singleWGscan_allChipOuts=npzfile['singleWGscan_allChipOuts']

#etc.

#npzfile.files will tell you what variables are in there (by name)

#==============================================================================