def make_html(coords=[[100, 200], [300, 400]], fileroot='ib2v09kzq'):
'''
Make an html file that gathers all of the images that have been made
'''
# page=markup.page()
title = 'Persistence Removal Evaluation for %s' % fileroot
page = html.begin(title)
# page.init(title='Persistence Removal Evaluation for %s' % fileroot)
# page.h1('Persistence Removal Evaluation for %s' % fileroot)
# page.p('''This page contains images for the evaluation of how well persistence has been removed from an image''')
page = page + html.paragraph(
'''This page contains images for the evaluation of how well persistence has been removed from an image'''
)
# page.hr(size='3',width='100%')
page = page + html.hline(size='3', width='100')
for coord in coords:
# page.p('Images for positions: %3d %3d' % (coord[0],coord[1]))
page = page + html.paragraph('Images for positions: %3d %3d' %
(coord[0], coord[1]))
fig1 = 'Figs/Fig_%s_%04d_%04d_1.png' % (fileroot, coord[0], coord[1])
fig2 = 'Figs/Fig_%s_%04d_%04d_2.png' % (fileroot, coord[0], coord[1])
fig3 = 'Figs/Fig_%s_%04d_%04d_3.png' % (fileroot, coord[0], coord[1])
# page.img( src=fig2, width=900, height=300, alt="Thumbnails" )
page = page + html.image(f2, width=900, height=300, alt="Thumbnails")
# page.p('Left: Original, Center: Persistence model, Right: Subtracted')
page = page + html.paragraph(
'Left: Original, Center: Persistence model, Right: Subtracted')
# page.img( src=fig1, width=400, height=400, alt="Thumbnails" )
page = page + html.image(fig1, width=400, height=400, alt="Thumbnails")
# page.img( src=fig3, width=400, height=400, alt="Thumbnails" )
page = page + html.image(fig3, width=400, height=400, alt="Thumbnails")
# page.p('Left: Original and subtracted data as a function of the estimated persistence, Right: Original and subtracted data as a function of distance from x,y')
page = page + html.paragraph(
'Left: Original and subtracted data as a function of the estimated persistence, Right: Original and subtracted data as a function of distance from x,y'
)
# page.hr(size='3',width='100%')
page = page + hline(size='3', width='100%')
# Write the page to a file
name = xpath + 'Persist_%s.html' % fileroot
g = per_list.open_file(name)
# g=open(name,'w')
# os.chmod(name,0770)
g.write('%s' % page)
g.close()
return fileroot
def make_html(lines, filename='observations.html'):
'''
This routine makes the summary html file.
110428 ksl This routine was writtend because markup.py did not seem to be to handle
a simple table.
'''
header = '''<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html lang="en">
<head>
<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
<title>Summary Evaluation Page of Persistence</title>
</head>
<body>
<p>This page contains links to the individual html files for each
dataset</p>
<hr size="3" width="100%">
<table border="1" cellpadding="2" cellspacing="2" width="100%">
'''
string = header
for line in lines:
row = '<tr>\n'
for word in line:
row = row + '<td> %s </td>\n' % word
row = row + '<tr>\n'
string = string + row
trailer = '''
</tbody>
</table>
<hr size="3" width="100%">
</body>
</html>
'''
string = string + trailer
g = per_list.open_file(filename)
# g=open(filename,'w')
# os.chmod(filename,0770)
g.write('%s\n' % string)
return
def make_reg(sources,regionfile='sources.reg'):
'''
Make a simple region file from a set of
source positions, labelling them by
source number.
'''
# g=open(regionfile,'w')
# os.chmod(regionfile,0770)
# g.write(regionheader)
g=per_list.open_file(regionfile)
i=1
for source in sources:
g.write('circle(%6.2f,%6.2f ,5) # text={%03d}\n' % (source[1]+1,source[0]+1,i))
i=i+1
g.close()
return
def do_dataset(dataset='ia21h2e9q',model_type=0,norm=0.3,alpha=0.2,gamma=0.8,e_fermi=80000,kT=20000,fileroot='observations',ds9='yes',local='no',parameter_file='persist.pf',lookback_time=16):
'''
Create a persistence image for this dataset. This version works by creating using the
persistance model from each of the previous images. It assumes that the only one which
matters is the image which created the most persistence according toe the modeld
model_type=0 is our our orignal model which has a modified fermi distributioon, controlled by the values of norm, etc.
model_type=1 is our purely describtive model defined in terms of amplitudes and power laws
model_type=2 for the fermi model that interpolates bewtween cureves for different expsoure times
All returns from this program should be:
OK: something
NOK: something
Outputs:
If there were IR observations that preceded the observation being analyzed
then this routines creates various fits files:
rootname_persist.fits - The model for the total of internal and external persistnce
rootname_extper.fits - The model for persistence from earlier visits, aka
external persistence
rootname_flt_cor.fits - The corrected flt file
rootname_stim.fits - The stimulus that caused the persistence
rootname_dt.fits - The time at which the stimulus occurred
Plots of the various images are also created, as well as a log file for
the data set
Notes:
This is really the main routine of the program. When run_persist.py calls this modeule.
this is the routine that is called.
In practice, the only difference between model types 1 and 2 is the calibration file that is read in. The same interpolation
routine is used for both. At present the calibration file names for this are hardwired.
History
100905 ksl Added disgnostic files to record the time of the stimulus and the
value of the stimulus
101015 ksl Moved the location of where the output files are stored and
added a history file, so we would know what had happened
110122 ksl Added a switch to turn off displaying with ds9
110324 ksl Changed call to accommodate new persistence model
110602 ksl Incorporated the possibility of providing a correction file xynorm to account
for spatial variations across the detector persistence model
140606 ksl Added correction which puts the correct units in the stimulus file.
140611 ksl Began to add in new persistnce model, initially just by short-circuiting everything
140803 ksl Switched to fits version of data files
141124 ksl Small change to handle situations were the flat field correction is not found
'''
cur_time=date.get_gmt()
xfile=locate_file(parameter_file)
if xfile=='':
print '# Error: Could not locate parameter file %s ' % parameter_file
else:
parameter_file=xfile
if model_type==0:
print '# Processing dataset %s with fermi model: Norm %4.2f alpha %4.2f gamma %4.2f e_fermi %6.0f kT %6.0f ' % (dataset,norm,alpha,gamma,e_fermi,kT)
elif model_type==1:
print '# Processing dataset %s with A gamma model' % dataset
elif model_type==2:
print '# Processing dataset %s with a time-variable fermi model' % dataset
else:
print '# Error: run_persist: Unknown model type %d' % model_type
return 'NOK'
# Read the observations file to get the data set of interest
delta=lookback_time # Datasets which occurred more than delta hours earlier not considered.
records=per_list.read_ordered_list2(fileroot,dataset,interval=[-delta,0],outroot='none')
# Check the length of records
if len(records)==0:
string = 'NOK: subtract_persist.do_dataset :There are no records associated with dataset %s. Check name in %s.ls' % (dataset,fileroot)
sum_string='NOK - No record associated with this dataset'
per_list.update_summary(dataset,'ERROR',sum_string,append='no')
return string
# So now we have the list that we need.
science_record=records[len(records)-1] # The science record is the last record
sci_progid=science_record[2]
words=science_record[3].split('.')
sci_visit=words[0]
sci_fil=science_record[10]
sci_exp=eval(science_record[11])
sci_obj=science_record[14]
# Create the Persist directory if it does not already exist
path=per_list.set_path(science_record[0],'yes',local)
if path.count('NOK'): # Then we were not able to create a plausible directory to put the data ink
return path
# Open a history file. Note that one needs the path before one can do this
# The reason for calling this via the per_list routine, is that this routine sets the permissions
# for the file
history=per_list.open_file(path+science_record[1]+'.txt')
history.write('START: Persistence processing of file %s\n\n' % science_record[1])
history.write('! Processed: %s\n' % date.get_gmt())
history.write('! ProgramID: %s\n' % sci_progid)
history.write('! Visit: %s\n' % sci_visit)
history.write('! FltFile: %s\n' % science_record[1])
history.write('! Filter: %s\n' % sci_fil)
history.write('! Exposure: %6.1f\n' % sci_exp)
history.write('! Object: %s\n' % sci_obj)
history.write('\n! Using Version %s of the perstence S/W' % VERSION)
history.write('\n! Using a lookback time for observations that might cause persistence of %.1f hours\n' % lookback_time)
if model_type==0:
history.write('\n! Processing dataset %s with fermi model: norm %6.2f alpha %6.2f e_fermi %6.0f kT %6.0f\n' % (dataset,norm,alpha,e_fermi,kT))
elif model_type==1:
history.write('\n! Processing dataset %s with A gamma model\n' % dataset)
elif model_type==2:
history.write('\n! Processing dataset %s with time-variable fermi model\n' % dataset)
# Check whether there is anything to do
if len(records)==1:
string='subtract_persist: No persistence for this dataset. No earlier observations within %4.1f hours\n' % (delta)
history.write('%s\n' % string)
history.write('! Persistence: None\n')
string='OK: subtract_persist: -- None'
print string
history.close()
xstring=' %6.2f %6.2f %6.2f %6.2f %6.2f %6.2f' % (0,0,0,0,0,0)
per_list.update_summary(dataset,'Persist',xstring,append='no')
return string
# Persistence is calculated for the middle of the interval in which the expousre
# was taking place
[t1,t2]=get_times(science_record[0])
tscience=0.5*(t1+t2)
# establish which record is the last record that comes from a different visit than the current one
i=0
while i<len(records)-1:
cur_progid=records[i][2]
words=records[i][3].split('.')
cur_visit=words[0]
# print 'OK',cur_progid,cur_visit
if cur_progid==sci_progid and cur_visit==sci_visit:
# then we are now into earlier exposures of the same visit
break
i=i+1
# if i = 0, all the exposures being evaluated for persistence create self_persistence
# if i= len(records), all exposures being evaluated for persistence are from other visits
last_external=i-1 # This is the last record that created external persistence
ext_values=[] # A place to store information about the persistence due to other observers
ext_persist=[] # This is a place holder for storing the extenal persistence
xynorm=read_parameter(parameter_file,'xynorm')
if xynorm!='':
xynorm=locate_file(xynorm)
xcorr=get_image(xynorm,1)
if len(xcorr)==0:
xynorm='' # This is an error because we were unable to find the file
history.write('! Error: Could not find correction file %s containing spatial dependence. Continuing anyway' % xynorm)
else:
history.write('! Reference file containing spatial dependence: %s\n' % xynorm)
else:
string='! Processing without spatially dependent correction'
print string
history.write('%s\n' % string )
# This is the beginning of the loop for calculating the persistence model
i=0
while i<len(records)-1:
record=records[i]
# print 'subtract: %30s %6.1f model_type %d' % (record[0],eval(record[11]),model_type)
# dt is measured from the end of the stimulus image to the middle of the
# science image
[t1,t2]=get_times(record[0])
dt=(tscience-t2)*86400
cur_progid=record[2]
words=record[3].split('.')
cur_visit=words[0]
cur_sci_fil=record[10]
cur_sci_exp=eval(record[11])
cur_sci_obj=record[14]
scan=record[4]
xfile=record[0]
# Use the ima file, if file calusing persistence is a scan object
if scan=='scan':
xfile=xfile.replace('flt','ima')
print 'Using ima file for ',record[0],xfile,scan
x=get_image(xfile,1,'e',fileref=science_record[0]) # Convert this to electrons
if len(x)==0:
xstring='NOK: Problem with science extension of %s' % record[0]
history.write('%s\n' % xstring)
print xstring
return xstring
dq=get_image(xfile,3,fileref=science_record[0]) # Get the dq
if len(dq)==0:
xstring = 'NOK: Problem with dq extension of %s' % record[0]
history.write('%s\n' % xstring)
print xstring
# 110926 - ksl - modified to allow this to process the image even if there was no dq array
# return xstring
if model_type==0:
model_persistence=calc_persist(x,dq,dt,norm,alpha,gamma,e_fermi,kT)
elif model_type==1:
# print 'Model type is 1'
xfile=read_parameter(parameter_file,'a_gamma')
# The next lines are awkward, becuate the parameter file name is read multiple times
if i==0:
history.write('! Reference file containing spatially-averaged peristence model: %s' % xfile)
model_persistence=make_persistence_image(x,cur_sci_exp,dt,xfile)
elif model_type==2:
# print 'Model type is 2'
xfile=read_parameter(parameter_file,'fermi')
if i==0:
history.write('! Reference file containing Spatially-averaged peristence model: %s' % xfile)
model_persistence=make_persistence_image(x,cur_sci_exp,dt,xfile)
else:
print 'Error: subtract_persist: Unknown model type %d' % model_type
return 'NOK'
values=how_much(model_persistence)
if i==0:
persist=model_persistence
stimulus=x # This is an array which contains the maximum counts in a pixel
xtimes=numpy.ones_like(persist)
xtimes=xtimes*dt # This is an array containing the delta time at which the stimulus occured
else:
xpersist=model_persistence
stimulus=numpy.select([xpersist>persist],[x],default=stimulus)
xtimes=numpy.select([xpersist>persist],[dt],default=xtimes)
persist=numpy.select([xpersist>persist],[xpersist],default=persist)
# Get some elementary statistics on the stimulus
xvalues=get_stats(x,70000)
history.write('\nsubtract_persist: Stimulus by %30s from program %s Visit %s\n' % (record[0],cur_progid,cur_visit))
history.write('\nsubtract_persist: The filter was %s and exposure was %6.1f for target %s\n' % (cur_sci_fil,cur_sci_exp,cur_sci_obj))
history.write('subtract_persist: The exposure was %8.0f s earlier than the current exposure\n' % dt)
history.write('subtract_persist: The median value in the stimulus image was %6.1f and the number of saturated pixels was %d\n' % (xvalues[0],xvalues[1]))
history.write('subtract_persist: The maximum value for persistence is %f\n' % values[4])
history.write('subtract_persist: The median value for persistence is %f\n' % values[5])
history.write('subtract_persist: 90 percent of persist values less than %f\n' % values[6])
history.write('subtract_persist: 99 percent of persist values less than %f\n' % values[7])
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.10 e/s\n' % (values[1],values[1]*100./values[0]))
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.03 e/s\n' % (values[2],values[2]*100./values[0]))
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.01 e/s\n' % (values[3],values[3]*100./values[0]))
string = 'subtract_persist: Finished (%2d of %2d) %s' % (i+1,len(records)-1,record[0])
#130909 Removed print statement as unnneessary. The string still goes to the history file
# print string
history.write('%s\n' % string)
# Summarize the Stiumulus printing out the filename, prog_id, visit_name, target, dt and the number of pixels above saturation of 70000
scan='No'
if record[4]=='scan':
scan='Yes'
stimulus_summary='Stimulus: %40s %10s %10s %20s %8.0f %3d %3s %6s\n' % (record[0],cur_progid,cur_visit,cur_sci_obj,dt,xvalues[1],record[9],scan)
history.write('! %s\n' % stimulus_summary)
if i==last_external:
ext_values=how_much(persist)
ext_persist=numpy.copy(persist)
i=i+1
# This is the end of the loop where the persistence model is calculated
# First report on the external persistence for this file;
# Now apply the fix to account for spatial variations in persistence
if xynorm !='' and numpy.shape(xcorr)==numpy.shape(persist):
persist=persist*xcorr
if len(ext_values)>0:
f1=ext_values[1]*100./ext_values[0]
f2=ext_values[2]*100./ext_values[0]
f3=ext_values[3]*100./ext_values[0]
emeasure='%6.2f %6.2f %6.2f' % (f1,f2,f3)
history.write('\nsubtract_persist: Estimate of persistence from earlier visits\n')
history.write('subtract_persist: The maximum value for persistence is %f\n' % ext_values[4])
history.write('subtract_persist: The median value for persistence is %f\n' % ext_values[5])
history.write('subtract_persist: 90 percent of persist values less than %f\n' % ext_values[6])
history.write('subtract_persist: 99 percent of persist values less than %f\n' % ext_values[7])
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.10 e/s\n' % (ext_values[1],f1))
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.03 e/s\n' % (ext_values[2],f2))
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.01 e/s\n' % (ext_values[3],f3))
else:
emeasure='%6.2f %6.2f %6.2f' % (0 ,0,0)
history.write('\nsubtract_persist: This exposure has no persistence from earlier visits. All persistence is self-induced\n')
# Now evaluate the total persistence
values=how_much(persist)
f1=values[1]*100./values[0]
f2=values[2]*100./values[0]
f3=values[3]*100./values[0]
measure='%6.2f %6.2f %6.2f' % (f1,f2,f3)
history.write('\nsubtract_persist: Estimate of total persistence for this file\n')
history.write('subtract_persist: The maximum value for persistence is %f\n' % values[4])
history.write('subtract_persist: The median value for persistence is %f\n' % values[5])
history.write('subtract_persist: 90 percent of persist values less than %f\n' % values[6])
history.write('subtract_persist: 99 percent of persist values less than %f\n' % values[7])
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.10 e/s\n' % (values[1],f1))
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.03 e/s\n' % (values[2],f2))
history.write('subtract_persist: %7d pixels (or %6.3f percent) greater than 0.01 e/s\n' % (values[3],f3))
history.write('! PersistenceSum: External %s\n'% emeasure)
history.write('! PersistenceSum: Total %s\n'% measure)
# Now write out all of the new fits files
# First find out the units of the science image
units=get_keyword(science_record[0],1,'bunit')
# print 'test',units
if units[0]=='COUNTS/S':
print 'Reducing model to match units for dataset %s to match %s ' % (dataset,units)
persist/=2.4
# subtract and write out the corrected image
science=get_image(science_record[0],1,'no')
original=numpy.copy(science)
science=science-persist
xname=parse_fitsname(science_record[0])
persist_file=path+dataset+'_persist.fits'
ext_persist_file=path+dataset+'_extper.fits'
# Note: Do not use some with an extension like flt.fits because it will interfere with making list
corrected_file=path+dataset+'_flt_cor.fits'
stimulus_file=path+dataset+'_stim.fits'
time_file=path+dataset+'_dt.fits'
rewrite_fits(xname[0],persist_file,1,persist)
rewrite_fits(xname[0],corrected_file,1,science)
rewrite_fits(xname[0],stimulus_file,1,stimulus)
# 140606 - Fix added to put stimulus file in the correct units.
put_keyword(stimulus_file,1,'bunit','ELECTRONS')
rewrite_fits(xname[0],time_file,1,xtimes)
if len(ext_persist)>0:
rewrite_fits(xname[0],ext_persist_file,1,ext_persist)
# This completes the section which writes out all of the fits files
# Get statistics on the images and make the 4 panel plot
xmed=numpy.median(original)
zmed=numpy.median(persist)
zmax=numpy.max(persist)
pylab.figure(1,[12,12])
pylab.title(dataset)
pylab.subplot(221)
pylab.imshow(original,origin='lower',cmap=pylab.cm.gray,vmin=xmed-0.1,vmax=xmed+0.1)
pylab.title('Original')
pylab.subplot(222)
pylab.imshow(science,origin='lower',cmap=pylab.cm.gray,vmin=xmed-0.1,vmax=xmed+0.1)
pylab.title('Subtracted')
pylab.subplot(223)
pylab.imshow(persist,origin='lower',cmap=pylab.cm.gray,vmin=zmed-0.1,vmax=zmed+0.1)
pylab.title('Total Persistence')
if len(ext_persist)>0:
pylab.subplot(224)
pylab.imshow(ext_persist,origin='lower',cmap=pylab.cm.gray,vmin=zmed-0.1,vmax=zmed+0.1)
pylab.title('External Persistence')
else:
pylab.subplot(224)
pylab.imshow(stimulus,origin='lower',cmap=pylab.cm.gray,vmin=0.0,vmax=200000)
pylab.title('Stimulus')
fig1=path+'Figs/'+dataset+'_subtract.png'
if os.path.isfile(fig1):
os.remove(fig1)
pylab.savefig(fig1)
os.chmod(fig1,0770)
# Eliminated to prevent an error on linux having to do with tkinter
# pylab.close('all')
if ds9=='yes':
LoadFrame(science_record[0],1,0,2,'histequ')
LoadFrame(persist_file,2,0,2,'histequ')
LoadFrame(corrected_file,3,0,2,'histequ')
if len(ext_persist)>0:
LoadFrame(ext_persist_file,4,0,2,'histequ')
else:
LoadFrame(stimulus_file,4,0,1e5,'histequ')
# Finished plots
# Finished everything so wrap it up
history.write('# Finished Persistence processing of file %s\n' % science_record[1])
history.close()
# Upadete the summary file
string='%20s %20s' % (emeasure,measure)
per_list.update_summary(dataset,'Persist',string,fileroot,append='no')
return string
def do_dataset(dataset='ia21h2eaq', fileroot='observations', local='no'):
'''
Make html files for a single dataset
110203 ksl Added local swithch which controls where the
real working directory is to make testing
easier
140307 ksl Added information about scans and subarray observations
'''
record = per_list.read_ordered_list_one(fileroot, dataset)
if len(record) == 0:
return 'NOK: make_html failed becaouse could not find dataset %s' % dataset
work_dir = per_list.set_path(
record[0], 'no',
local) # This will be the Persist directory for the dataset
fig_dir = work_dir + '/Figs/' # This will be the directory where figures are stored
html_filename = work_dir + dataset + '_persist.html'
# page=markup.page()
title = 'Persistence Removal Evaluation for dataset %s' % dataset
page = html.begin(title)
# page.init(title='Persistence Removal Evaluation for dataset %s' % dataset)
# page.h1('Persistence Removal Evaluation for %s' % dataset)
# page.p('''This page contains images for the evaluation of how well persistence has been removed from an image''')
page = page + html.paragraph(
'''This page contains images for the evaluation of how well persistence has been removed from an image'''
)
# Look for the history file for this dataset
history_file = dataset + '.txt'
if os.path.exists(work_dir + history_file):
string = '''The history file for the processing of this dataset is '''
string = string + html.link("here", href=history_file)
page = page + html.paragraph(string)
# read history simply returns all of the lines in the history file that begin with !
# And so any processing of these lines still has to be done
lines, table1, table2 = read_history(work_dir + history_file)
for line in lines:
page = page + html.paragraph(line)
if len(table1) > 0:
page = page + html.h2(
'Earlier exposures that could affect this image')
page = page + html.table(table1)
if len(table2) > 0:
page = page + html.h2(
'External and total persistence for this image')
string = '''External persistence is persistance from previous visits; internal persistence
is persistence induced from exposures in this vist. Total persistence includes both
internal and external persistence. . Generally, self-induced or internal persistence is
only important if the dithers larger than the psf have been used within the visit'''
page = page + html.paragraph(string)
page = page + html.table(table2)
else:
page = page + html.paragraph(
''' The history file for this dataset appears to be missing. Check that the file has been processed'''
)
page = page + html.hline(size='3', width='100')
string = '''The next 4-panel image shows the original flt image (upper left), the corrected flt image (upper right),
the persistence model (lower left) and the stimulus (lower right). The stimulus is simply the image constructed
maximum value in electrons of any of the images that went into the stimulus model'''
# Look for the summary image
xname = dataset + '_subtract.png'
if os.path.exists(fig_dir + xname):
# page.img(src='Figs/'+xname,width=600,height=600,alt="Thumbnails")
page = page + html.image(
image='Figs/' + xname, width=600, height=600, alt="Thumbnails")
else:
# page.p('''The summary image is missing''')
page = page + html.paragraph('''The summary image is missing''')
# page.hr(size='3',width='100%')
page = page + html.hline(size='3', width='100')
# Now include the evaluation images
string = '''As a qualitative indicator of how well the persistence correction has worked, some of the regions with
the highest predicted persistence have been examined.
The next two images give an indication of how well the persistence has been subtracted from the images.
Both images have the original data in red and the persistence-subtracted data in blue. The first image is
a plot of flux vs the persisence model, the second is flux as a function of the stimulus. Ideally the blue
curves would all center around 0. The utility of these plots depends on how isolated the persistence peaks
are from stars in the image. If these plots are empty, no good regions for evaluation persistence were found.'''
page = page + html.paragraph(string)
xname = dataset + '.sum1.png'
if os.path.exists(fig_dir + xname):
# page.img(src='Figs/'+xname,width=300,height=300,alt="Thumbnails")
page = page + html.image(
'Figs/' + xname, width=300, height=300, alt="Thumbnails")
else:
# page.p('''The first evaluation image showing the subtraction is missing''')
page = page + '''The first evaluation image showing the subtraction is missing'''
xname = dataset + '.sum2.png'
if os.path.exists(fig_dir + xname):
# page.img(src='Figs/'+xname,width=300,height=300,alt="Thumbnails")
page = page + html.image(
'Figs/' + xname, width=300, height=300, alt="Thumbnails")
else:
# page.p('''The second evaluation image showing the subtraction is missing''')
page = page + html.paragraph(
'''The second evaluation image showing the subtraction is missing'''
)
# page.hr(size='3',width='100%')
page = page + html.hline(size=3, width=100)
# Look for the peaks summary
string = '''This figures indicates what regions were selected for evaluation. The two panels are
identical except the regions selected are indicated in the lower panel. '''
page = page + html.paragraph(string)
xname = dataset + '_persist.peaks.png'
if os.path.exists(fig_dir + xname):
# page.img(src='Figs/'+xname,width=600,height=1000,alt="Thumbnails")
page = page + html.image(
'Figs/' + xname, width=900, height=900, alt="Thumbnails")
else:
# page.p('''The summary figure for peak identification is missing''')
page = page + html.paragraph(
'''The summary figure for peak identification is missing''')
# Now find all of the individual peak files:
searchstring = fig_dir + dataset + '.peak.*.1.png'
print searchstring
try:
peaks_file = work_dir + dataset + '_persist.peaks.dat'
p = open(peaks_file, 'r')
lines = p.readlines()
p.close
except IOError:
print 'Warning: %s not found' % peaks_file
lines = []
xlines = []
for one in lines:
one = one.strip()
if one[0] != '#' and len(one) > 0:
xlines.append(one)
if len(xlines) > 0:
string = '''The results for individual regions are shown below. The four panels are a subsection of the original flt file, the predicted persistence in that region, the persistence subtracted flt file, and a plot of pixel values as a function of predicted persistence in the region. Green points are the original values; yellow point are the corrected values. The red and blue lines show the mean values in the original and corrected and corrected images, respectively.'''
page = page + html.paragraph(string)
page = page + html.hline(size='3', width='100')
for one in xlines:
word = one.split()
x = int(word[0])
y = int(word[1])
z = eval(word[2])
zz = eval(word[3])
# page.p('Persistence at x = %3d, y=%3d' %(x,y))
page = page + html.paragraph(
'Persistence at x = %3d, y=%3d is about %6.3f e/s compared to science image flux of %6.3f e/s'
% (x, y, z, zz))
xname = '%s.peak.%03d_%03d.1.png' % (dataset, x, y)
if os.path.exists(fig_dir + xname):
# page.img(src='Figs/'+xname,width=400,height=400,alt="Thumbnails")
page = page + html.image(
'Figs/' + xname, width=400, height=400, alt="Thumbnails")
else:
# page.p('Figure %s not present' % (work_dir+xname))
page = page + html.paragraph('Figure %s not present' %
(work_dir + xname))
# page.hr(size='3',width='100%')
page = page + html.hline(size='3', width='100')
else:
string = '''Unfortunately, no good regions for evaluating persistence were found.'''
page = page + html.paragraph(string)
page = page + html.hline(size='3', width='100')
page = page + html.end()
# Open the html file with the appropriate permissions, and then write it
g = per_list.open_file(html_filename)
g.write('%s' % page)
g.close()
return 'OK: subtract_html: %s' % html_filename
def doit(filename='foo.fits',mask_file='none',box=3,maxno=25,history_file='history.txt',local='no'):
'''
Main routine which handles finding of the peaks and creating plots which indicate
how well the persistence has been subtracted. It attemps to locate region with
a significant amount of persistence, but to avoid regions where the flux from
stars in the image under consideration is large.
The variables are as follows:
filename The persist model
mask_file The original science image which here is used to
identify regions which are contaminated by stars
box The size of the boxcar function used to smooth the persist
image.
maxno The maximum number of peaks to find
history_file The place to append history information
local The standard way in which to indicate where output files
should be stored.
The routine reads file name foo, and smooths it with boxcar function with kernal of size
box It also reads the mask_file, the original science image. This is used in find_peaks
to exclude regions of the image that have very high count rates, since it will be impossible
to see persistence agains a bright source. So that bad pixels pixels are also excluded
a large number is added to the mask when a pixel has bad data quality.
The routine also creates a plot for each of the peaks that indicates where
the peaks are. The individual subtractions are not evaluated here, see
subtract_eval instead.
111011 ksl Tried to clean this routine up and make it run a little better
130204 ksl Modified the data quality criterion to elimate the possibility
that the TDF had been set which causes all of the pixels to
be declared bad.
130913 ksl Restored the use of DQ flags to since the problem with loss of
lock, which in certain cases, particularly darks, caused all
pixels to have bad DQ.
'''
history=open(history_file,'a')
history.write('# Starting peaks on file %s using %s as mask \n' % (filename,mask_file))
# determine from the filename where we want
# to put the ouputs
work_dir=per_list.set_path(filename,'yes',local) # This will be the Persist directory for the dataset
fig_dir=work_dir+'/Figs/'
# Get a name for the root of any output files
try:
x=filename.split('/')
name=x[len(x)-1]
# print 'name',name
j=string.rindex(name,'.')
outroot=name[0:j]
# print 'OK got',outroot
except ValueError:
outroot=filename
print 'File had no extensions, using entire name'
# Read the persistence file
x=per_fits.get_image(filename,1)
if len(x)==0:
print 'Error: peaks: Nothing to do since no data returned for %s' % filename
history.write('Peaks: Nothing to do since no data returned for %s\n' % filename)
return 'NOK'
# Now read the flt file, which will be used to create a mask file in an attempt
# to remove from considerations regions of the image where there is persistence which
# would be overwhelmed by light in the current image.
# Read both the image and the data quality
# extension. The data quality extension is used to help assure that we are tracking
# persistence from light in earlier exp sures. For these pixels, we set the value
# in the persitence image to zero, before the persistence image is smoothed.
# Then smooth the persitence image so that peak finding is easier
if mask_file!='none':
mask=per_fits.get_image(mask_file,1,rescale='e/s')
xmask=smooth(mask,box)
dq=per_fits.get_image(mask_file,3,rescale='no')
z=numpy.select([dq>0],[0],default=x)
z=smooth(z,box)
history.write('Peaks: Using %s to mask exposure\n' % mask_file)
else:
history.write('Peaks: No mask from earlier undithered exposures\n')
z=smooth(x,box)
mask='none'
# After having set everything up call the routine that locates the peaks to use to see
# how well the subtraction works
sources=find_peaks(z,mask,maxno=maxno)
# Write out the results in a text file containing
# the x and y positions
outfile=work_dir+outroot+'.peaks.dat'
# print 'Error: Could not open %s' % outfile
g=per_list.open_file(outfile)
g.write('# peaks in %s\n' % filename)
for source in sources:
xflux=xmask[source[0],source[1]]
g.write('%5d %5d %6.3f %6.3f\n' % (source[1],source[0],source[2],xflux))
g.close()
# Write out a set of ds9 region files of the sources
make_reg(sources,work_dir+outroot+'.peaks.reg')
# Plot the results. This creates two images, one with the regions selectd for detailed
# anaylsis superposed.
xmed=numpy.median(x)
pylab.figure(1,(8,12))
pylab.clf()
pylab.subplot(211)
pylab.imshow(x,origin='lower',cmap=pylab.cm.gray,vmin=xmed-0.05,vmax=xmed+0.05)
plothandle=pylab.subplot(212)
ysize,xsize=x.shape
pylab.imshow(z,origin='lower',extent=[0,xsize,0,ysize],cmap=pylab.cm.gray,vmin=xmed-0.05,vmax=xmed+0.05)
# For reasons I don't quit understand, one needs to add 1 to both axes
# To get the circles to line up, as if the elements were being counted
# from one as in IRAF.
for source in sources:
circle(source[1]+1,source[0]+1,plothandle)
# Note that this really needs to be in the Figs subdirectory
figure_name=fig_dir+outroot+'.peaks.png'
if os.path.isfile(figure_name):
os.remove(figure_name)
pylab.savefig(figure_name)
os.chmod(figure_name,0770)
# Generation of this summary plot is now complete.
# 110325 - This next line was generating errors with the backend I was using. The desired behavior
# is that there be no window created when the program is run from the command line.
# The error seems to occur # when you try to close the figure without first drawing it. For now
# I have deleted the next line. The behaviou I am currently seeing is taht the window
# appears as if one had issued a draw command, i.e. the window stays up, but the program
# continues ulike show()
# pylab.close('all')
history.write('# Finished peaks on file %s\n' % filename)
return 'OK'
def steer(argv):
'''
This is a steering routine for subtract persist so that options can be exercised from the
command line. See the top level documentaion for details
100907 ksl Added to begin to automate the subtraction process
101215 ksl Moved to a separate routine so that one would be able to split various portions
of persistence subtraction and evaluation of the results into multiple files
111114 ksl Added a command.log to keep track of all of the run_persist commands
140924 ksl Updated to allow for varioua model types
160103 ksl Begin implemenation of multiprocessing
'''
log('# Start run_persist %s\n' % date.get_gmt())
xstart=time.clock()
cur_time=date.get_gmt()
i=1
dataset_list='none'
model_type=1
norm=0.3
alpha=0.174
gamma=1.0
e_fermi=90000
kT=20000
fileroot='observations'
words=[]
mjd_start=0.0 # A amall number for mjd
mjd_stop=1.e6 # A large number for mjd
dryrun='no'
clean='no'
ds9='no'
local='no'
pffile='persist.pf'
lookback_time=16
switch='single'
np=1
while i<len(argv):
if argv[i]=='-h':
print __doc__
return
elif argv[i]=='-model':
i=i+1
model_type=int(argv[i])
elif argv[i]=='-n':
i=i+1
norm=eval(argv[i])
elif argv[i]=='-e':
i=i+1
e_fermi=eval(argv[i])
elif argv[i]=='-kT':
i=i+1
kT=eval(argv[i])
elif argv[i]=='-alpha':
i=i+1
alpha=eval(argv[i])
elif argv[i]=='-gamma':
i=i+1
gamma=eval(argv[i])
elif argv[i]=='-obslist':
i=i+1
fileroot=eval(argv[i])
elif argv[i]=='-many':
i=i+1
dataset_list=argv[i]
switch='many'
print 'OK you want to evaluate a number of datasets in file %s', dataset_list
elif argv[i]=='-all':
switch='all'
print 'OK you want to evaluate all the records in the obslist'
elif argv[i] =='-prog_id':
i=i+1
prog_id=int(argv[i])
switch='prog_id'
print 'OK, you want to evaluate all the records for program %d' % prog_id
elif argv[i]=='-start':
i=i+1
z=argv[i]
try:
mjd_start=float(z)
except ValueError:
mjd_start=date.iso2mjd(z)
if switch !='prog_id':
switch='all'
elif argv[i]=='-stop':
i=i+1
z=argv[i]
try:
mjd_stop=float(z)
except ValueError:
mjd_stop=date.iso2mjd(z)
if switch !='prog_id':
switch='all'
elif argv[i]=='-dryrun':
dryrun='yes'
print 'OK, This will be a dry run!'
elif argv[i]=='-clean':
dryrun='yes'
clean='yes'
print 'OK. This run will clean out various Persist directories, and revise the .sum file'
elif argv[i]=='-ds9':
ds9='yes'
elif argv[i]=='-local':
local='yes'
elif argv[i]=='-pf':
i=i+1
pffile=argv[i]
elif argv[i]=='-lookback':
i=i+1
lookback_time=eval(argv[i])
elif argv[i]=='-np':
i=i+1
np=int(argv[i])
elif argv[i][0]=='-':
print 'Error: Unknown switch --- %s' % argv[i]
return
else:
words.append(argv[i])
i=i+1
# At this point all of the options have been processed and we can
# begin the processing of individual datasets
# Check that the listfile actually exists, and if not exit with a stern warning
listfile=fileroot+'.ls'
if os.path.exists(listfile)==False:
print 'Error: run_persist.steer - No %s file in run directory. EXITING!!!' % listfile
return
# At this point, we are able to determine exactly what datasets to process
log('# Starting at %s\n' % (cur_time),'command.log')
log('# Starting at %s\n' % (cur_time))
string=''
for one in argv:
string=string+'%s ' % one
log('Command: %s\n' % string,'command.log')
log('Command: %s\n' % string)
datasets=[]
if switch=='single': # Then we are processing a single file
datasets.append(words[0])
elif switch=='all': # Then we are working from the obslist
records=per_list.read_ordered_list_mjd(fileroot,mjd_start,mjd_stop)
for record in records:
datasets.append(record[1])
elif switch=='many': # Then we are reading a file with rootnames of the files we want to process
f=open(dataset_list,'r')
lines=f.readlines()
f.close()
for line in lines:
x=line.strip()
if len(x)>0 and x[0]!='#':
xx=x.split() # Take the first word to be the dataset name
datasets.append(xx[0])
elif switch=='prog_id':
records=per_list.read_ordered_list_progid(fileroot,prog_id,mjd_start,mjd_stop)
for record in records:
datasets.append(record[1])
else:
print 'Error: run_persist: Unknown switch %s'% switch
# Ok, now, unless this is a dryrun we actually process the data
ntot=len(datasets)
print 'There are %d datasets to process' % ntot
dry=[]
if dryrun=='yes':
for one in datasets:
record=per_list.read_ordered_list_one(fileroot,one)
dry.append(record)
per_list.write_ordered_list('dryrun',dry)
if clean=='yes':
# xclean=open('CleanFiles','w')
# os.chmod('CleanFiles',0770)
xclean=per_list.open_file(Cleanfiles)
for one in dry:
xxx=per_list.set_path(one[0])
xclean.write('rm -r -f %s\n' % xxx)
xclean.close()
# return
elif np==1 or len(datasets)==1:
n=1
for one in datasets:
do_dataset(one,model_type,norm,alpha,gamma,e_fermi,kT,fileroot,ds9,local,pffile,lookback_time)
print '# Completed dataset %d of %d. Elapsed time is %0.1f s' % (n,ntot,time.clock()-xstart)
n=n+1
else:
print 'There will be %d processes running simultaneously' % np
jobs=[]
for one in datasets:
p=multiprocessing.Process(target=do_dataset,args=(one,model_type,norm,alpha,gamma,e_fermi,kT,fileroot,ds9,local,pffile,lookback_time,))
jobs.append(p)
i=0
while i<np and i<len(jobs):
print '!Starting %s' % datasets[i]
one=jobs[i]
one.start()
i=i+1
njobs=get_no_jobs(jobs)
while i<len(jobs):
time.sleep(2)
njobs=get_no_jobs(jobs)
print 'Running %d jobs,including job %d (%s) of %d total' % (njobs,i,datasets[i-1],len(datasets))
if njobs<np:
print 'Starting: ',datasets[i]
one=jobs[i]
one.start()
i=i+1
p.join()
print 'Completed multiprocessing'
per_list.fixup_summary_file(datasets)
print 'xxx',xstart,time.clock()
dtime=time.clock()-xstart
cur_time=date.get_gmt()
log('# End %s (Elapsed time for %d datasets was %.1f (or %.1f per dataset)\n' % (date.get_gmt(),ntot,dtime,dtime/ntot))
cur_time=date.get_gmt()
log('# End %s (Elapsed time for %d datasets was %.1f (or %.1f per dataset)\n' % (date.get_gmt(),ntot,dtime,dtime/ntot),'command.log')
log('# Finished at %s\n' % (cur_time))
log('# Finished at %s\n' % (cur_time),'command.log')
return