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Flat.py
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Flat.py
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import os
import numpy as np
from scipy.signal import argrelextrema
#from astropy.io import fits
import logging
import coloredlogs
#import traceback
import nirspec_constants
import config
import GratingEq
from DrpException import DrpException
import FlatOrder
import nirspec_lib
import image_lib
from numpy.testing import measure
import matplotlib.pyplot as plt
class Flat:
def __init__(self, fn, baseFns, header, data, logDir=None):
self.fn = fn
self.baseFns = baseFns
self.header = header
self.logDir = logDir
self.baseName = self.getBaseName()
if logDir is None:
self.logger = logging.getLogger('obj')
else:
self.logger = logging.getLogger('flat')
self.initLogger()
self.gratingEq = GratingEq.GratingEq(self.logger)
names = ', '.join(str(x) for x in self.baseFns)
self.logger.info('creating {} from {}'.format(self.fn, names))
if nirspec_constants.upgrade:
self.flatImg = np.rot90(data, k=3)
else:
self.flatImg = data
if nirspec_constants.upgrade:
filtername1, filtername2 = self.header['SCIFILT2'], ''
if self.header['SCIFILT1'] == 'AO-stop': filtername2 = '-AO'
self.filterName = filtername1.upper()+filtername2.upper()
else:
self.filterName = self.header['filname']
self.slit = self.header['slitname']
self.echelleAngle = self.header['echlpos']
self.disperserAngle = self.header['disppos']
self.topEdgeImg = None # top edge image (shift subtract)
self.botEdgeImg = None # bottom edge image (shift subtract)
self.topEdgeProfile = None # top edge profiles
self.botEdgeProfile = None # bottom edge profiles
self.topEdgePeaks = None # filtered top edge profile peaks
self.botEdgePeaks = None # filtered bottom edge profile peaks
self.nOrdersExpected = 0
self.nOrdersFound = 0
self.flatOrders = []
try:
self.reduce()
except Exception as e:
try:
self.logger.error('flat reduction failed: ' + e.message)
except:
self.logger.error('flat reduction failed: ' + '%s' %e)
# traceback.print_tb()
raise
def getShape(self):
return((self.objHeader['NAXIS1'], self.objHeader['NAXIS2']))
def reduce(self):
"""
"""
self.logger.info('reducing flat {}'.format(self.baseName))
self.findEdgeProfilePeaks()
self.nOrdersExpected = 0
firstOrderFound = False
for orderNum in range(config.get_starting_order(self.filterName), 0, -1):
self.logger.info('*'*20 + ' FLAT ORDER {} '.format(orderNum) + '*'*20)
flatOrder = FlatOrder.FlatOrder(self.baseName, orderNum, self.logger)
# get expected location of order on detector
flatOrder.topCalc, flatOrder.botCalc, flatOrder.gratingEqWaveScale = self.gratingEq.evaluate(
orderNum, self.filterName, self.slit, self.echelleAngle, self.disperserAngle)
self.logger.info('predicted top edge location = {:.0f} pixels'.format(flatOrder.topCalc))
self.logger.info('predicted bot edge location = {:.0f} pixels'.format(flatOrder.botCalc))
# TESTING TO PLOT ORDER CUTOUTS XXX
if config.params['debug_tracing'] is True:
print('TOP CALC, BOTTOM CALC:', flatOrder.topCalc, flatOrder.botCalc)
plt.figure(7362)
plt.imshow(self.flatImg, origin='lower', aspect='auto')
plt.axhline(flatOrder.topCalc, c='r', ls='--')
plt.axhline(flatOrder.botCalc, c='b', ls='--')
plt.show()
#sys.exit()
# TESTING TO PLOT ORDER CUTOUTS XXX
# determine if order is expected to be on the detector
# if this order is off but previous order(s) was/were on then no more orders
# because orders are contiguous
if not self.gratingEq.is_on_detector(flatOrder.topCalc, flatOrder.botCalc):
self.logger.warning('order {} is not on the detector'.format(orderNum))
if firstOrderFound:
break
else:
firstOrderFound = True
self.nOrdersExpected += 1
# determine top and bottom LHS of order by edge detection
if config.params['sowc'] is True:
self.findOrderSowc(flatOrder)
else:
self.findOrder(flatOrder)
if flatOrder.topMeas is None and flatOrder.botMeas is None:
continue
# find spatial trace from edge traces
#if orderNum != 76: continue
try:
self.findSpatialTrace(flatOrder)
except DrpException as e:
self.logger.error('failed to find spatial trace: {}'.format(e.message))
flatOrder.valid = False
continue
# TESTING TO PLOT ORDER CUTOUTS XXX
if config.params['debug_tracing'] is True:
print(flatOrder.topCalc, flatOrder.botCalc)
plt.figure(7363)
plt.imshow(self.flatImg, origin='lower', aspect='auto')
plt.axhline(flatOrder.topCalc, c='r', ls='--')
plt.axhline(flatOrder.botCalc, c='b', ls='--')
try:
plt.axhline(flatOrder.topMeas, c='r', ls=':')
plt.plot(flatOrder.topEdgeTrace)
except:
print('Cannot plot measured top')
try:
plt.axhline(flatOrder.botMeas, c='b', ls=':')
plt.plot(flatOrder.botEdgeTrace)
except:
print('Cannot plot measured bot')
plt.show()
#sys.exit()
# TESTING TO PLOT ORDER CUTOUTS XXX
### TESTING TO PLOT ORDER CUTOUTS XXX
print(flatOrder.botEdgeTrace)
fig = plt.figure(3898)
print('YESYESYES')
plt.imshow(self.flatImg, origin='lower', aspect='auto')
plt.plot(flatOrder.topEdgeTrace, c='r', ls='--')
plt.plot(flatOrder.botEdgeTrace, c='b', ls='--')
plt.minorticks_on()
fig.suptitle('TEST021')
plt.show()
print("NONONO")
#sys.exit()
### TESTING TO PLOT ORDER CUTOUTS XXX
if flatOrder.spatialTraceFitResidual > config.params['max_spatial_trace_res']:
self.logger.info('spatial trace fit residual too large, limit = {}'.format(
config.params['max_spatial_trace_res']))
flatOrder.valid = False
continue
try:
self.cutOutOrder(flatOrder)
except DrpException as e:
self.logger.error('failed to extract flat order {}: {}'.format(
str(orderNum), e.message))
flatOrder.valid = False
continue
try:
flatOrder.reduce()
except DrpException as e:
self.logger.error('failed to reduce flat order{}: {}'.format(
str(orderNum), e.message))
flatOrder.valid = False
continue
flatOrder.valid = True
self.logger.success('flat order {} validated'.format(orderNum))
self.flatOrders.append(flatOrder)
self.logger.success('flat reduction complete')
self.logger.info('n orders expected = {}'.format(self.nOrdersExpected))
self.nOrdersFound = len([p for p in self.flatOrders if p.valid == True])
if self.nOrdersExpected != self.nOrdersFound:
self.logger.warning('n orders found = {}'.format(self.nOrdersFound))
else:
self.logger.success('n orders found = {}'.format(self.nOrdersFound))
return
def getBaseName(self):
return self.fn[self.fn.rfind('/') + 1:self.fn.rfind('.')]
def findEdgeProfilePeaks(self):
# make top and bottom edge profile images
rolled = np.roll(self.flatImg, 5, axis=0)
self.topEdgeImg = rolled - self.flatImg
self.botEdgeImg = self.flatImg - rolled
self.topEdgeProfile = np.median(self.topEdgeImg[:, 40:60], axis=1)
self.botEdgeProfile = np.median(self.botEdgeImg[:, 40:60], axis=1)
self.topEdgePeaks = self.findPeaks(self.topEdgeProfile)
self.botEdgePeaks = self.findPeaks(self.botEdgeProfile)
### TEST PLOT ORDER EDGE PEAKS XXX
if config.params['debug_tracing'] is True:
print(rolled)
print(self.topEdgeImg)
print(self.botEdgeImg)
print(self.topEdgeProfile)
print(self.botEdgeProfile)
print(self.topEdgePeaks)
print(self.botEdgePeaks)
fig1 = plt.figure(2647, figsize=(10,6))
ax1 = fig1.add_subplot(121)
ax2 = fig1.add_subplot(122)
ax1.set_title('Top Peaks')
ax2.set_title('Bottom Peaks')
ax1.plot(self.topEdgeProfile)
for i in self.topEdgePeaks: ax1.axvline(i, color='r', ls='--')
ax2.plot(self.botEdgeProfile)
for i in self.botEdgePeaks: ax2.axvline(i, color='r', ls='--')
plt.show()
#sys.exit()
### TEST PLOT ORDER EDGE PEAKS XXX
return
def findPeaks(self, edgeProfile):
edgeProfile[0:15] = 0 # mask out the first few pixels (maybe this is a dirty fix)
peak_rows = argrelextrema(edgeProfile, np.greater, order=35)[0]
peak_intensities = edgeProfile[peak_rows]
tall_peaks_i = np.where(peak_intensities > (np.amax(peak_intensities) * 0.05)) # made this lower to find more orders
return(peak_rows[tall_peaks_i[0]])
def findOrderSowc(self, flatOrder):
flatOrder.topMeas = None
flatOrder.botMeas = None
w = flatOrder.topCalc - flatOrder.botCalc
maxDelta = config.get_max_edge_location_error(self.filterName, self.slit)
flatOrder.topMeas = self.findEdge(flatOrder.topCalc, maxDelta, 'top')
if flatOrder.topMeas is not None:
flatOrder.botMeas = self.findEdge(flatOrder.topMeas - w, maxDelta, 'bot')
else:
flatOrder.botMeas = self.findEdge(flatOrder.botCalc, maxDelta, 'bot')
if flatOrder.topMeas is not None and flatOrder.botMeas is None:
flatOrder.botMeas = self.findEdge(flatOrder.topMeas - w, maxDelta, 'bot')
elif flatOrder.topMeas is None and flatOrder.botMeas is not None:
flatOrder.topMeas = self.findEdge(flatOrder.botMeas + w, maxDelta, 'top')
if flatOrder.topMeas is None:
self.logger.warning('top edge not found')
else:
self.logger.info('measured top edge location = {:.0f} pixels'.format(flatOrder.topMeas))
self.logger.info(' top edge location delta = {:.0f} pixels'.format(
flatOrder.topCalc - flatOrder.topMeas))
if flatOrder.botMeas is None:
self.logger.warning('bottom edge not found')
else:
self.logger.info('measured bot edge location = {:.0f} pixels'.format(flatOrder.botMeas))
self.logger.info(' bot edge location delta = {:.0f} pixels'.format(
flatOrder.botCalc - flatOrder.botMeas))
return
def findEdge(self, calc, maxDelta, topOrBot):
if topOrBot == 'bot':
meas = min((abs(calc - i), i) for i in self.botEdgePeaks)[1]
else:
meas = min((abs(calc - i), i) for i in self.topEdgePeaks)[1]
if meas is None or abs(meas - calc) > maxDelta:
self.logger.debug('{} edge not found at {:.0f} +/- {:.0f}'.format(
topOrBot, calc, maxDelta))
return None
else:
return meas
def findOrder(self, flatOrder):
flatOrder.topMeas = min((abs(flatOrder.topCalc - i), i) for i in self.topEdgePeaks)[1]
flatOrder.botMeas = min((abs(flatOrder.botCalc - i), i) for i in self.botEdgePeaks)[1]
max_delta = config.get_max_edge_location_error(self.filterName, self.slit)
if flatOrder.topMeas is None or abs(flatOrder.topMeas - flatOrder.topCalc) > max_delta:
self.logger.info('measured top edge location too far from expected location')
self.logger.info('\tcalc={:.0f}, meas={:.0f}, delta={:.0f}, max delta={:.0f}'.format(
flatOrder.topCalc, flatOrder.topMeas,
abs(flatOrder.topMeas - flatOrder.topCalc), max_delta))
flatOrder.topMeas = None
topStr = 'not found'
else:
topStr = str(flatOrder.topMeas)
if flatOrder.botMeas is None or abs(flatOrder.botMeas - flatOrder.botCalc) > max_delta:
self.logger.info('measured bottom edge location too far from expected location')
self.logger.info('\tcalc={:.0f}, meas={:.0f}, delta={:.0f}, max delta={:.0f}'.format(
flatOrder.botCalc, flatOrder.botMeas,
abs(flatOrder.botMeas - flatOrder.botCalc), max_delta))
flatOrder.botMeas = None
botStr = 'not found'
else:
botStr = str(flatOrder.botMeas)
self.logger.info('measured y location: top = ' + topStr + ', bottom = ' + botStr)
return
def findSpatialTrace(self, flatOrder):
if flatOrder.topMeas is not None:
self.logger.debug('tracing top of order')
flatOrder.topEdgeTrace = nirspec_lib.trace_order_edge(self.topEdgeImg, flatOrder.topMeas)
if flatOrder.botMeas is not None:
self.logger.debug('tracing bottom of order')
flatOrder.botEdgeTrace = nirspec_lib.trace_order_edge(self.botEdgeImg, flatOrder.botMeas)
if flatOrder.topEdgeTrace is None and flatOrder.botEdgeTrace is None:
raise DrpException('could not trace top or bottom edge')
if flatOrder.topEdgeTrace is not None and flatOrder.botEdgeTrace is not None:
self.logger.success('using top and bottom trace')
flatOrder.avgEdgeTrace = (flatOrder.topEdgeTrace + flatOrder.botEdgeTrace) / 2.0
elif flatOrder.botEdgeTrace is None:
self.logger.warning('using top trace only')
flatOrder.avgEdgeTrace = flatOrder.topEdgeTrace - \
((flatOrder.topMeas - flatOrder.botCalc) / 2.0) + 1.0
else:
self.logger.warning('using bottom trace only')
flatOrder.avgEdgeTrace = flatOrder.botEdgeTrace + \
((flatOrder.topCalc - flatOrder.botMeas) / 2.0) + 1.0
# apply long slit edge margin correction to raw traces
if '24' in self.slit:
self.logger.info('applying long slit edge margins of {} pixels'.format(
config.params['long_slit_edge_margin']))
if flatOrder.topEdgeTrace is not None:
flatOrder.topEdgeTrace -= config.params['long_slit_edge_margin']
if flatOrder.botEdgeTrace is not None:
flatOrder.botEdgeTrace += config.params['long_slit_edge_margin']
# apply K-AO correction to raw traces
if 'K-AO' in self.filterName:
self.logger.info('applying K-AO filter edge margins of {} pixels'.format(
config.params['K-AO_edge_margin']))
if flatOrder.topEdgeTrace is not None:
flatOrder.topEdgeTrace -= config.params['K-AO_edge_margin']
#if flatOrder.botEdgeTrace is not None:
# flatOrder.botEdgeTrace += config.params['K-AO_edge_margin']
# if bottom edge trace successful, use to refine LHS bottom location
if flatOrder.botEdgeTrace is not None:
flatOrder.botMeas = flatOrder.botEdgeTrace[1]
# smooth spatial trace
flatOrder.smoothedSpatialTrace, flatOrder.spatialTraceMask = \
nirspec_lib.smooth_spatial_trace(flatOrder.avgEdgeTrace)
"""
# smooth spatial trace for A and B frames (maybe implement later)
flatOrder.smoothedSpatialTraceA, flatOrder.spatialTraceMaskA = \
nirspec_lib.smooth_spatial_trace(flatOrder.topEdgeTrace)
flatOrder.smoothedSpatialTraceB, flatOrder.spatialTraceMaskB = \
nirspec_lib.smooth_spatial_trace(flatOrder.botEdgeTrace)
"""
self.logger.info('spatial trace smoothed, ' + \
str(self.flatImg.shape[1] - np.count_nonzero(flatOrder.spatialTraceMask)) +
' points ignored')
flatOrder.spatialTraceFitResidual = np.sqrt(
np.mean(np.square(flatOrder.avgEdgeTrace - flatOrder.smoothedSpatialTrace)))
self.logger.info('spatial trace smoothing rms fit residual = {:.2f}'.format(
flatOrder.spatialTraceFitResidual))
return
def cutOutOrder(self, flatOrder):
# determine cutout padding
flatOrder.cutoutPadding = config.get_cutout_padding(self.filterName, self.slit)
# get the extra cutout if any
flatOrder.extraCutout = config.get_extra_cutout(self.filterName, self.slit)
# add extra padding for orders with large tilt
tilt = abs(flatOrder.avgEdgeTrace[0] - flatOrder.avgEdgeTrace[-1])
if tilt > config.params['large_tilt_threshold']:
self.logger.info('large order tilt detected, tilt = ' + str(round(tilt, 1)) +
' threshold = ' + str(config.params['large_tilt_threshold']) +
' extra padding = ' + str(config.params['large_tilt_extra_padding']))
flatOrder.cutoutPadding += config.params['large_tilt_extra_padding']
if config.params['extra_cutout']:
self.logger.info('extra order cutout detected,' +
' extra cutout = ' + str(flatOrder.extraCutout) + ' pixels')
self.logger.debug('cutout padding = ' + str(round(flatOrder.cutoutPadding, 0)))
# determine highest point of top trace (ignore edge)
if flatOrder.topEdgeTrace is None:
flatOrder.topEdgeTrace = flatOrder.botEdgeTrace + \
(flatOrder.topCalc - flatOrder.botCalc) - 5
flatOrder.highestPoint = np.amax(flatOrder.topEdgeTrace[0:-config.params['overscan_width']])
if flatOrder.botEdgeTrace is None:
flatOrder.botEdgeTrace = flatOrder.topEdgeTrace - \
(flatOrder.topCalc - flatOrder.botCalc) + 5
flatOrder.lowestPoint = np.amin(flatOrder.botEdgeTrace[0:-config.params['overscan_width']])
flatOrder.cutout = np.array(image_lib.cut_out(
self.flatImg, flatOrder.highestPoint, flatOrder.lowestPoint,
flatOrder.cutoutPadding))
if float(flatOrder.lowestPoint) > float(flatOrder.cutoutPadding):
flatOrder.onOrderMask, flatOrder.offOrderMask = get_masks(
flatOrder.cutout.shape,
flatOrder.topEdgeTrace - flatOrder.lowestPoint + flatOrder.cutoutPadding,
flatOrder.botEdgeTrace - flatOrder.lowestPoint + flatOrder.cutoutPadding)
else:
flatOrder.onOrderMask, flatOrder.offOrderMask = get_masks(
flatOrder.cutout.shape, flatOrder.topEdgeTrace, flatOrder.botEdgeTrace)
flatOrder.cutout = np.ma.masked_array(flatOrder.cutout, mask=flatOrder.offOrderMask)
return
def initLogger(self):
self.logger.handlers = []
if config.params['debug']:
self.logger.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s ' +
'%(levelname)s - %(filename)s:%(lineno)s - %(message)s')
else:
self.logger.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s %(levelname)s - %(message)s')
fn = self.logDir + '/' + self.baseName + '.log'
if os.path.exists(fn):
os.rename(fn, fn + '.prev')
fh = logging.FileHandler(filename=fn)
fh.setLevel(logging.DEBUG)
fh.setFormatter(formatter)
self.logger.addHandler(fh)
if config.params['verbose'] is True:
if config.params['debug']:
#sformatter = logging.Formatter('%(asctime)s %(levelname)s - %(filename)s:%(lineno)s - %(message)s')
sformatter = coloredlogs.ColoredFormatter(fmt='%(asctime)s,%(msecs)03d %(levelname)s - %(filename)s:%(lineno)s - %(message)s',
field_styles={'levelname': {'color': 'cyan'}})
else:
#sformatter = logging.Formatter('%(asctime)s %(levelname)s - %(message)s')
sformatter = coloredlogs.ColoredFormatter(fmt='%(asctime)s,%(msecs)03d %(levelname)s - %(message)s',
field_styles={'levelname': {'color': 'cyan'}})
sh = logging.StreamHandler()
sh.setLevel(logging.DEBUG)
sh.setFormatter(sformatter)
self.logger.addHandler(sh)
def get_masks(shape, top_trace, bot_trace):
y, x = np.indices(shape, dtype=np.float32)
off_top = y > top_trace
off_bot = y < bot_trace
off_order = off_top | off_bot
belowtop = y < top_trace
abovebot = y > bot_trace
on_order = belowtop & abovebot
return on_order, off_order