def update_html(update):
"""
check whether the update is needed and if so, run the update
input: update --- if it is 1, run the update without chekcing the file exist or not
output: none, but updated html pages (in <web_dir>)
"""
#
#--- find today's date
#
today = time.localtime()
year = today.tm_year
#
#--- if update is asked, just run the update
#
if update > 0:
run_update(year)
#
#--- otherwise, find the last update, and if needed, run the update
#
else:
cmd = 'ls ' + web_dir +'*.html > ' + zspace
os.system(cmd)
f = open(zspace, 'r')
out = f.read()
f.close()
#
#--- chekcing the file existance (looking for year in the file name)
#
mcf.rm_file(zspace)
mc = re.search(str(year), out)
if mc is None:
run_update(year)
def extract_data_and_combine(time_list,
detector,
level,
filetype,
name,
fcol_line=''):
"""
extract fits files in the time span(s) and combine all of them to one fits file
input: time_list --- a list of lists [[start_time>],[<stop_time>]]
detector --- detector name (e.g. hrc)
level --- level (e.g. 0, 1)
filetype --- file type (e.g. hrcss, hrchk)
name --- name of the resulted combined fits file
output: name --- resulted fits file
"""
#
#--- extreact files
#
fits_list = extract_fits_files(time_list, detector, level, filetype)
#
#--- combine fits file to one
#
hcf.combine_fits_files(fits_list, name, azip=0, fcol_line=fcol_line)
#
#--- remove indivisual fits files
#
for ent in fits_list:
mcf.rm_file(ent)
def extract_cron_file_name():
"""
extract cron error message file names for the current user/machine
output: cron_file_name: a list of cron file names (file names only no directory path)
"""
try:
cmd = 'crontab -l >' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
except:
exit(1)
cron_file_name = []
for ent in data:
m = re.search('Logs', ent)
if m is not None and ent[0] != '#':
atemp = re.split('Logs/', ent)
btemp = re.split('2>&1', atemp[1])
cron = btemp[0]
cron = cron.strip()
cron_file_name.append(cron)
#
#--- removing duplicated lines
#
cron_file_name = list(set(cron_file_name))
return cron_file_name
def combine_fits(flist, outname):
"""
combine fits files in the list
input: flist --- a list of fits file names
outname --- a outputfits file name
output: outname --- a combined fits file
"""
mcf.rm_file(outname)
cmd = 'mv ' + flist[0] + ' ' + outname
os.system(cmd)
for k in range(1, len(flist)):
try:
mfits.appendFitsTable(outname, flist[k], 'temp.fits')
except:
continue
cmd = 'mv temp.fits ' + outname
os.system(cmd)
cmd = 'rm -f ' + flist[k]
os.system(cmd)
cmd = 'rm -rf *fits.gz'
os.system(cmd)
return outname
def extract_data(start, stop):
"""
extract data to compute HRMA focus plots
input: start ---- start time in the foramt of mm/dd/yy (e.g. 05/01/15)
stio ---- stop time in the format of mm/dd/yy
output: acis*evt2.fits.gz, hrc*evt2.fits.gz
"""
#
#--- check whether previous fits files are still around, and if so, remove them
#
cmd = 'ls * > ' + zspace
os.system(cmd)
f = open(zspace, 'r')
chk = f.read(10000000)
f.close()
mcf.rm_file(zspace)
mc = re.search('fits', chk)
if mc is not None:
cmd = 'rm *fits*'
os.system(cmd)
#
#--- if time interval is not given, set for a month interval
#
if start == '':
[start, stop] = set_interval()
#
#--- extract acis and hrc evt2 files
#
inst = 'acis'
run_arc(inst, start, stop)
inst = 'hrc'
run_arc(inst, start, stop)
def test_combine_evt1_files(self):
#
#--- make a list of all evt1 file of the year
#
year = 2000
hdir = 'hrc_i_115'
e_list = get_evt1_list(year, hdir)
if len(e_list) == 0:
print "Something wrong in getting files"
#
#--- combined all evt1 files of the year
#
oname = 'test_combined_evt1.fits'
hcf.combine_fits_files(e_list, oname)
tstart = hcf.read_header_value(oname, 'tstart')
tstop = hcf.read_header_value(oname, 'tstop')
tstart = int(float(tstart))
tstop = int(float(tstop))
self.assertEquals(tstart, 65961070)
self.assertEquals(tstop, 93190294)
mcf.rm_file(oname)
def mv_old_file(dom):
dom -= 30
if dom > 0:
[year, ydate] = tcnv.DOMtoYdate(dom)
sydate = str(ydate)
if ydate < 10:
sydate = '00' + sydate
elif ydate < 100:
sydate = '0' + sydate
atime = str(year) + ':' + sydate + ':00:00:00'
stime = tcnv.axTimeMTA(atime)
cmd = 'ls ' + house_keeping + '/Defect/CCD*/* > ' + zspace
os.system(cmd)
fs = open(zspace, 'r')
ldata = [line.strip() for line in fs.readlines()]
fs.close()
mcf.rm_file(zspace)
for ent in ldata:
atemp = re.split('\/acis', ent)
btemp = re.split('_', atemp[1])
if int(btemp[0]) < stime:
out = ent
out = out.replace('Defect', 'Defect/Save')
cmd = 'mv ' + ent + ' ' + out
os.system(cmd)
def run_arc(inst, start, stop):
"""
run arc4gl and extract evt2 data for "inst"
input: inst --- instrument, acis or hrc
start --- interval start time in format of mm/dd/yy (e.g. 05/01/15)
stop --- interval stop time in format of mm/dd/yy
"""
line = 'operation=retrieve\n'
line = line + 'dataset=flight\n'
line = line + 'detector=' + inst + '\n'
line = line + 'level=2\n'
line = line + 'filetype=evt2\n'
line = line + 'tstart=' + start + '\n'
line = line + 'tstop=' + stop + '\n'
line = line + 'go\n'
f = open(zspace, 'w')
f.write(line)
f.close()
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' echo ' + hakama + ' |arc4gl -U' + dare + ' -Sarcocc -i' + zspace
cmd = cmd1 + cmd2
#
#--- run arc4gl
#
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
def selectTableData(file,
colname,
condition,
outname,
extension=1,
clobber='no'):
"""
select data for a given colname and the condition and create a new table fits file
Input: file --- input table fits file
colname --- column name
condition--- contidion of the data selection
if the selection is the interval, the format is in <start>:<stop>
if it is equal use: ==<value>
if it is not equal: !=<value>
outname --- output file name
clobber --- overwrite the file if exists. if not given, 'no'
"""
m1 = re.search('y', clobber)
m2 = re.search('Y', clobber)
if (m1 is not None) or (m2 is not None):
mcf.rm_file(outname)
t = fits.open(file)
tdata = t[extension].data
mc = re.search(':', condition)
mc1 = re.search('\!', condition)
chk = 0
if mc is not None:
atemp = re.split(':', condition)
start = float(atemp[0])
stop = float(atemp[1])
mask = tdata.field(colname) >= start
modt = tdata[mask]
mask = modt.field(colname) <= stop
modt2 = modt[mask]
elif mc1 is not None:
condition = condition.replace('!=', "")
mask = tdata.field(colname) != condition
modt2 = tdata[mask]
else:
condition = condition.replace('==', "")
if (isinstance(condition, float)) or (isinstance(condition, int)):
mask = tdata.field(colname) == condition
modt2 = tdata[mask]
else:
data = select_data_with_logical_mask(tbdata, colname, condition)
chk = 1
header = fits.getheader(file)
if chk == 0:
data = fits.BinTableHDU(modt2, header)
data.writeto(outname)
def fitsImgSection(file, x1, x2, y1, y2, outname, extension=0, clobber='no'):
"""
extract a x by y section of fits image file
Input: file --- input fits image file name
x1, x2 --- x range
y1, y2 --- y rnage
outname --- output fits image name
extension --- extension #. default = 0
clobber --- clobber or not. default = no
Output: outname --- fits image file of size x by y
"""
m1 = re.search('y', clobber)
m2 = re.search('Y', clobber)
if (m1 is not None) or (m2 is not None):
mcf.rm_file(outname)
t = fits.open(file)
data = t[extension].data
xsize = abs(x2 - x1)
ysize = abs(y2 - y1)
output = numpy.matrix(numpy.zeros([ysize, xsize]))
for x in range(x1, x2):
for y in range(y1, y2):
newx = x - x1
newy = y - y1
output[newy, newx] = data[y, x]
header = fits.getheader(file)
fits.writeto(outname, output, header)
t.close()
def run_arc4gl(start, stop, operation='retrieve', dataset='flight', detector='telem', level='raw'):
"""
extract data from archive using arc4gl
input: start --- starting time in the format of mm/dd/yy,hh/mm/ss. hh/mm/ss is optional
stop --- stoping time
operation --- operation command. default = retrieve
dataset --- dataset name. default = flight
detector --- detector name default = telem
level --- level defalut = raw
output: extracted data set
"""
#
#--- write arc4gl command
#
line = 'operation = ' + operation + '\n'
line = line + 'dataset = ' + dataset + '\n'
line = line + 'detector = ' + detector + '\n'
line = line + 'level = ' + level + '\n'
line = line + 'tstart=' + str(start) + '\n'
line = line + 'tstop=' + str(stop) + '\n'
line = line + 'go\n'
fo = open(zspace, 'w')
fo.write(line)
fo.close()
#
#--- run arc4gl
#
cmd1 = '/usr/bin/env PERL5LIB=""'
cmd2 = ' echo ' + hakama + '|arc4gl -U' + dare + ' -Sarcocc -i' + zspace
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
def get_dump_em_files(start, stop):
"""
extract Dump_EM files from archive
input: start --- start time in format of mm/dd/yy
stop --- stop time in format of mm/dd/yy
output: *Dump_EM* data in ./EM_data directory
data --- return data lists
"""
#
#--- get data from archive
#
run_arc4gl(start, stop)
#
#--- move the data to EM_Data directory and return the list of the data extracted
#
try:
cmd = 'mv *Dump_EM* ' + exc_dir + 'EM_Data/.'
os.system(cmd)
cmd = 'gzip -d ' + exc_dir + 'EM_Data/*gz'
os.system(cmd)
cmd = 'ls ' + exc_dir + 'EM_Data/*Dump_EM*sto > ' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
except:
data = []
return data
def get_data(msid, start, stop):
"""
extract data for the given data period
input: msid --- msid
start --- starting time in seconds from 1998.1.1
stop --- stopping time in seconds from 1998.1.1
output: data --- a list of msid values
"""
#
#--- extract data with dataseeker
#
try:
ecf.data_seeker(start, stop, msid)
[col, tbdata] = ecf.read_fits_file('temp_out.fits')
mcf.rm_file('temp_out.fits')
except:
return []
time = tbdata.field('time')
#
#--- if the dataseeker's data is not filled for the given data period
#--- stop any farther data proccess
#
if time[-1] < 0.95 * stop:
data = []
else:
try:
name = msid + '_avg'
data = tbdata.field(name)
except:
data = []
return data
def find_tscpos_positive_period(start, stop):
"""
find time periods of tscpos is located in positive position
input: start --- starting time in mm/dd/yy,hh:mm:ss
stop --- stopping time in mm/dd/yy,hh:mm:ss
output: positive_period a list of lists containing a list of time of period starting
and a list of time of period ending. both in seconds from 1998.1.1
"""
#
#--- extract sim data
#
dlist = hcf.run_arc5gl('retrieve',
start,
stop,
detector='sim',
level='0',
filetype='sim')
#
#--- find time period when tscpos is in positive side
#
positive_periods = create_data_period(start,
stop,
dlist,
colname='TSCPOS',
lgc='>=',
val=0)
#
#-- clean the output directory
#
for ent in dlist:
mcf.rm_file(ent)
return positive_periods
def run_lephem(fname, time):
"""
run idl script lephem.pro which convert the data into ascii data
input: fname --- the name of the input file: DE<time>.EPH
time --- time stamp of the file copied
output: ascii data file -- DE<time>.EPH.dat0
"""
cmd = 'cp ' + fname + ' ' + eph_data + '/.'
os.system(cmd)
cname = 'DE' + str(time) + '.EPH'
try:
line = "lephem,'" + str(cname) + "'\n"
line = line + "exit\n"
fo = open('./eph_run.pro', 'w')
fo.write(line)
fo.close()
os.environ['IDL_PATH'] = idl_path
subprocess.call("idl eph_run.pro", shell=True)
mcf.rm_file('./eph_run.pro')
return 1
except:
return 0
def extract_acis_evt1(start, stop):
"""
extract acis evt1 files
input: start --- start time in the format of mm/dd/yy (e.g. 05/01/15)
stop --- sop time in the format of mm/dd/yy
output: acisf*evt1.fits.gz
"""
#
#--- write required arc4gl command
#
line = 'operation=retrieve\n'
line = line + 'dataset=flight\n'
line = line + 'detector=acis\n'
line = line + 'level=1\n'
# line = line + 'version=last\n'
line = line + 'filetype=evt1\n'
line = line + 'tstart=' + start + '\n'
line = line + 'tstop=' + stop + '\n'
line = line + 'go\n'
f = open(zspace, 'w')
f.write(line)
f.close()
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' echo ' + hakama + ' |arc4gl -U' + dare + ' -Sarcocc -i' + zspace
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
def get_data(msid, start, stop):
"""
extract data for the given data period
input: msid --- msid
start --- starting time in seconds from 1998.1.1
stop --- stopping time in seconds from 1998.1.1
output: data --- a list of msid values
"""
#
#--- extract data with dataseeker
#
try:
ecf.data_seeker(start, stop, msid)
[col, tbdata] = ecf.read_fits_file('temp_out.fits')
mcf.rm_file('temp_out.fits')
except:
return []
time = tbdata.field('time')
#
#--- if the dataseeker's data is not filled for the given data period
#--- stop any farther data proccess
#
if time[-1] < 0.95 * stop:
data = []
else:
try:
name = msid + '_avg'
data = tbdata.field(name)
except:
data = []
return data
def run_focal_temp_data(start, stop):
"""
run focal temp script and create a plot, read a table
input: start --- start time in seconds from 1998.1.1
stop --- stop time in seconds from 1998.1.1
output: fcnt --- number of peaks observed
fdata --- table input
"""
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' /usr/local/bin/perl ' + wdir + 'get_ftemp_data.perl ' + str(start) + ' ' + str(stop)
cmd = cmd1 + cmd2
#
#--- run the focal temp script to extract data
#
bash(cmd, env=ascdsenv)
mcf.rm_file('./test')
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' idl ./run_temp > out'
cmd = cmd1 + cmd2
#
#--- run the focal temp script to create a plot
#
bash(cmd, env=ascdsenv2)
cmd = 'rm -rf ./*fits '
os.system(cmd)
def mv_old_file(dom):
dom -= 30
if dom > 0:
[year, ydate] = tcnv.DOMtoYdate(dom)
sydate = str(ydate)
if ydate < 10:
sydate = '00' + sydate
elif ydate < 100:
sydate = '0' + sydate
atime = str(year) + ':' + sydate + ':00:00:00'
stime = tcnv.axTimeMTA(atime)
cmd = 'ls ' + house_keeping + '/Defect/CCD*/* > ' + zspace
os.system(cmd)
fs = open(zspace, 'r')
ldata = [line.strip() for line in fs.readlines()]
fs.close()
mcf.rm_file(zspace)
for ent in ldata:
atemp = re.split('\/acis', ent)
btemp = re.split('_', atemp[1])
if int(btemp[0]) < stime:
out = ent
out = out.replace('Defect', 'Defect/Save')
cmd = 'mv ' + ent + ' ' + out
os.system(cmd)
def find_entries(dir):
"""
create list of fies/directory under the "dir"
ipnt: dir --- directory name under /data/mta/www/mta_script_list/
output: data --- a list of files and directories
"""
try:
cmd = 'ls -d /data/mta/www/mta_script_list/' + dir + '/* >' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
except:
data = []
if len(data) > 0:
cleaned = []
for ent in data:
mc = re.search('\~', ent)
if mc is not None:
continue
else:
cleaned.append(ent)
data = cleaned
return data
def check_new_data(new_data, new_dict):
"""
check whether new observations are added to the list and send email to admin
input: new_data --- a list of updated new_obs_list
new_dict --- a dictionary of the previous new_obs_list info
output: email sent to adim
"""
save = []
for ent in new_data:
atemp = re.split('\s+', ent)
obsid = int(float(atemp[2]))
try:
test = new_dict[obsid]
except:
save.append(ent)
if len(save) > 0:
line = ''
for ent in save:
line = line + ent + '\n'
fo = open(zspace, 'w')
fo.write(line)
fo.close()
cmd = 'cat ' + zspace + '| mailx -s "Subject:TEST!! TEST !! New Observation(s)" [email protected]'
os.system(cmd)
mcf.rm_file(zspace)
def find_two_sigma_value(fits):
#
#-- make histgram
#
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' dmimghist infile=' + fits + ' outfile=outfile.fits hist=1::1 strict=yes clobber=yes'
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' dmlist infile=outfile.fits outfile=' + zspace + ' opt=data'
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
f= open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
#
#--- read bin # and its count rate
#
hbin = []
hcnt = []
vsum = 0
for ent in data:
atemp = re.split('\s+|\t+', ent)
if mcf.chkNumeric(atemp[0]):
hbin.append(float(atemp[1]))
val = int(atemp[4])
hcnt.append(val)
vsum += val
#
#--- checking one sigma and two sigma counts
#
if len(hbin) > 0:
v68= int(0.68 * vsum)
v95= int(0.95 * vsum)
v99= int(0.997 * vsum)
sigma1 = -999
sigma2 = -999
sigma3 = -999
acc= 0
for i in range(0, len(hbin)):
acc += hcnt[i]
if acc > v68 and sigma1 < 0:
sigma1 = hbin[i]
elif acc > v95 and sigma2 < 0:
sigma2 = hbin[i]
elif acc > v99 and sigma3 < 0:
sigma3 = hbin[i]
break
return (sigma1, sigma2, sigma3)
else:
return(0, 0, 0)
def acis_dose_test_run():
"""
test ska shell access
"""
start = '05/07/15,00:00:00'
stop = '05/15/15,00:00:00'
line = 'operation=browse\n'
line = line + 'dataset=flight\n'
line = line + 'detector=acis\n'
line = line + 'level=1\n'
line = line + 'filetype=evt1\n'
line = line + 'tstart=' + start + '\n'
line = line + 'tstop=' + stop + '\n'
line = line + 'go\n'
f = open('./zspace', 'w')
f.write(line)
f.close()
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' echo ' + hakama + ' |arc4gl -U' + dare + ' -Sarcocc -i./zspace > ./zout'
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
mtac.rm_file('./zspace')
f = open('./zout', 'r')
fitsList = [line.strip() for line in f.readlines()]
f.close()
mtac.rm_file('./zout')
for ent in fitsList:
print ent
def print_cti_results(out_type, elm, ccd, content):
"""
print out selected/corrected cti data to an appropriate file
Input: out_type --- directory name under <data_dir>
elm --- the name of element (al, mn, ti)
ccd --- ccd #
content --- a table list. each line is already terminated by "\n"
Output: <data_dir>/<out_type>/<elm>_ccd<ccd#>
"""
file = data_dir + '/' + out_type + '/' + elm + '_ccd' + str(ccd)
mcf.rm_file(file)
f = open(file, 'w')
for ent in content:
f.write(ent)
#
#--- just in a case, the line is not terminated by '\n', add it
#
chk = re.search('\n', ent)
if chk is None:
f.write('\n')
f.close()
def notify_new_gratings_obs():
"""
send email notification to admin when new gratings observations are found
input: none
output: email to admin
"""
ifile = data_dir + 'obslist~'
odata = mcf.read_data_file(ifile)
ifile = data_dir + 'obslist'
ndata = mcf.read_data_file(ifile)
diff = set(ndata) - set(odata)
if len(diff) > 0:
line = 'New Gratings Observations\n\n'
for ent in diff:
line = line + ent + '\n'
with open(zspace, 'w') as fo:
fo.write(line)
cmd = 'cat ' + zspace + '|mailx -s \"Subject: New Gratings Observations\n\" ' + admin
os.system(cmd)
mcf.rm_file(zspace)
def remove_old_data(fits, cols, cut):
"""
remove the data older the cut time
input: fits --- fits file name
cols --- a list of column names
cut --- cut time in seconds from 1998.1.1
output: updated fits file
"""
f = pyfits.open(fits)
data = f[1].data
f.close()
#
#--- find where the cut time
#
pos = 0
dtime = list(data['time'])
for k in range(0, len(dtime)):
if dtime[k] >= cut:
pos = k
break
#
#--- remove the data before the cut time
#
udata = []
for k in range(0, len(cols)):
udata.append(list(data[cols[k]][pos:]))
mcf.rm_file(fits)
create_fits_file(fits, cols, udata)
def update_fits_file(fits, cols, cdata):
"""
update fits file
input: fits--- fits file name
cols--- a list of column names
cdata --- a list of lists of data values
output: updated fits file
"""
#
#--- if the fits file exists, append the new data
#
if os.path.isfile(fits):
f = pyfits.open(fits)
data = f[1].data
f.close()
udata= []
for k in range(0, len(cols)):
nlist = list(data[cols[k]]) + list(cdata[k])
udata.append(nlist)
mcf.rm_file(fits)
#
#--- if the fits file does not exist, create one
#
else:
udata = cdata
create_fits_file(fits, cols, udata)
def send_email(address, subject, content, cc = '', submitter=''):
"""
sending out email
input: address --- email address. it can be multiple addresses, delimiated by ','.
subject --- head line of the email
content --- email content
cc --- cc email address; default: <blank> (no cc address)
outout: email sent out
"""
#
#--- if this is a test, all email is sent to the submitter
#
if test == 'yes':
if submitter == '':
address = admin
else:
address = oda.get_email_address(submitter)
fo = open(zspace, 'w')
fo.write(content)
fo.close()
if cc == '':
#cmd = 'cat ' + zspace + ' |mailx -s "Subject: ' + subject + '" ' + ' -b ' + admin + ' ' + address
cmd = 'cat ' + zspace + ' |mailx -s "Subject (TEST!!): ' + subject + '" ' + address
else:
#cmd = 'cat ' + zspace + ' |mailx -s "Subject: ' + subject + '" ' + ' -c' + cc + ' -b ' + admin + ' ' + address
cmd = 'cat ' + zspace + ' |mailx -s "Subject (TEST!!): ' + subject + '" ' + ' -c' + cc + ' ' + address
os.system(cmd)
mcf.rm_file(zspace)
def find_last_entry(dir, tail):
"""
for a given file name (with a full path), extract date information
input: dir --- the name of directory where the data are kept
tail --- a suffix of the data file
output: [year, mon, day]
"""
#
#--- find the last file created
#
cmd = 'ls ' + dir + '/*' + tail + '| tail -1 > ' + zspace
os.system(cmd)
file = open(zspace, 'r').read()
mcf.rm_file(zspace)
#
#--- extract time part. assume that the file end <tail> and the time part is prepended to it
#
atemp = re.split('/', file)
for ent in atemp:
chk = re.search(tail, ent)
if chk is not None:
btemp = re.split('_', ent)
ldate = btemp[0]
break
#
#--- assume that the time is in the format of yyyymmdd, e.g. 20140515
#
year = int(float(ldate[0:4]))
mon = int(float(ldate[4:6]))
day = int(float(ldate[6:8]))
return [year, mon, day]
def run_bad_pix_and_photon(outdir):
"""
run bad pixel table script and photon table scrit
input: outdir --- output directory name
output: files in outdir: bad_pix_list, photons
"""
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = 'perl /data/mta4/MTA/bin/weekly_obs2html.pl 8 photons'
cmd = cmd1 + cmd2
#
#--- run the phonton script
#
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
cmd2 = 'perl ' + tdir + 'read_bad_pix_new.perl'
cmd = cmd1 + cmd2
#
#--- run the bad pixel script
#
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
cmd = 'mv photons bad_pix_list ' + outdir
os.system(cmd)
def find_the_last_data_created_date():
"""
find the data of the last created fits data file.
input: none
output: year --- year
mon --- momth
day --- day of the month
"""
cmd = 'ls /data/aschrc1/GENHRC/RAW/HRC_ENG/hrc_rates*fits* >' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
date = []
for ent in data:
atemp = re.split('hrc_rates_', ent)
btemp = re.split('\.fits', atemp[1])
date.append(btemp[0])
date.sort()
lent = str(date[-1])
year = lent[0] + lent[1] + lent[2] + lent[3]
year = int(float(year))
mon = lent[4] + lent[5]
mon = int(float(mon))
day = lent[6] + lent[7]
day = int(float(day))
return [year, mon, day]
def extract_cron_file_name():
"""
extract cron error message file names for the current user/machine
output: cron_file_name: a list of cron file names (file names only no directory path)
"""
try:
cmd = 'crontab -l >' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
except:
exit(1)
cron_file_name = []
for ent in data:
m = re.search('Logs', ent)
if m is not None and ent[0] != '#':
atemp = re.split('Logs/', ent)
btemp = re.split('2>&1', atemp[1])
cron = btemp[0]
cron = cron.strip()
cron_file_name.append(cron)
#
#--- removing duplicated lines
#
cron_file_name = list(set(cron_file_name))
return cron_file_name
def read_orbit_data(tstart, tstop):
"""
read altitude and sun angle data
input: tstart --- starting time in seconds from 1998.1.1
tstop --- stopping time in seconds from 1998.1.1
output: data --- a list of lists of [time alt, sun_angle]
"""
#
#--- set up the input for dataseeker and extract the data
#
fits = 'dataseek_avg.fits'
cmd = 'touch test'
os.system(cmd)
cmd1 = '/usr/bin/env PERL5LIB= '
cmd2 = " dataseeker.pl infile=test outfile=" + fits + " "
cmd2 = cmd2 + "search_crit='columns=pt_suncent_ang,sc_altitude timestart=" + str(
tstart)
cmd2 = cmd2 + " timestop=" + str(tstop) + "' loginFile=" + lfile
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
#
#--- read fits file and extract the data
#
cols = ['time', 'sc_altitude', 'pt_suncent_ang']
data = read_fits_data(fits, cols)
#
#--- clean up
#
mcf.rm_file(fits)
mcf.rm_file('test')
return data
def read_data_file(ifile, sep='', remove=0, c_len=0):
"""
read ascii data file
input: ifile --- file name
sep --- split indicator: default: '' --- not splitting
remove --- indicator whether to remove the file after reading: default: 0 --- no
c_len --- numbers of columns to be read. col=0 to col= c_len. default: 0 --- read all
output: data --- a list of lines or a list of lists
"""
data = mcf.read_data_file(ifile)
if remove > 0:
mcf.rm_file(ifile)
if sep != '':
atemp = re.split(sep, data[0])
if c_len == 0:
c_len = len(atemp)
save = []
for k in range(0, c_len):
save.append([])
for ent in data:
atemp = re.split(sep, ent)
for k in range(0, c_len):
try:
save[k].append(float(atemp[k]))
except:
save[k].append(atemp[k])
return save
else:
return data
def run_kplookup(time):
"""
run idl script kplookup.pro which adjusts the data for the solar wind influence
input: time --- time in the format of <yy><ydate>
output: DE<time>.EPH.dat0 updated for the soloar wind influence
"""
xxx = 999
if xxx == 999:
# try:
line = "kplookup,'/data/mta/Script/Ephem/EPH_Data/DE" + str(
time) + ".EPH.dat0'" + "\n"
line = line + "exit\n"
fo = open('./kp_run.pro', 'w')
fo.write(line)
fo.close()
os.environ['IDL_PATH'] = idl_path
subprocess.call("idl kp_run.pro", shell=True)
cmd = 'idl kp_run.pro'
os.system(cmd)
mcf.rm_file('./kp_run.pro')
return 1
def selectTableData(file, colname, interval, outname, extension = 1, clobber='no'):
"""
select data for a given colname and the condition and create a new table fits file
Input: file --- input table fits file
colname --- column name
interval --- the data interval inthe forma of <start>:<stop>
outname --- output file name
clobber --- overwrite the file if exists. if not given, 'no'
"""
m1 = re.search('y', clobber)
m2 = re.search('Y', clobber)
if (m1 is not None) or (m2 is not None):
mcf.rm_file(outname)
t = fits.open(file)
tdata = t[extension].data
atemp = re.split(':', interval)
start = float(atemp[0])
stop = float(atemp[1])
mask = tdata.field(colname) >= start
modt = tdata[mask]
mask = modt.field(colname) <= stop
modt2 = modt[mask]
header = fits.getheader(file)
data = fits.BinTableHDU(modt2, header)
data.writeto(outname)
def get_cti_data(test=''):
"""
get cti data
input: none
output: cti_data.txt
"""
#
#--- get all data
#
cmd = 'cat /data/mta/Script/ACIS/CTI/Data/Det_Data_adjust/mn_ccd* > ' + zspace
os.system(cmd)
#
#--- check the previous data file exists. if so, move to save.
#
if os.path.isfile('./cti_data.txt') and test == '':
cmd = 'mv -f cti_data.txt cti_data.txt~'
os.system(cmd)
#
#--- sort and select out data
#
cmd = 'sort -u -k 1,1 ' + zspace + ' -o cti_data.txt'
os.system(cmd)
mcf.rm_file(zspace)
#
#--- change the permission
#
cmd = 'chmod 755 cti_data.txt'
os.system(cmd)
cmd = 'mv -f ./cti_data.txt /data/mta4/www/DAILY/mta_rad/'
os.system(cmd)
def run_lephem(fname, time):
"""
run idl script lephem.pro which convert the data into ascii data
input: fname --- the name of the input file: DE<time>.EPH
time --- time stamp of the file copied
output: ascii data file -- DE<time>.EPH.dat0
"""
cmd = 'cp ' + fname + ' ' + eph_data + '/.'
os.system(cmd)
cname = 'DE' + str(time) + '.EPH'
try:
line = "lephem,'" + str(cname) + "'\n"
line = line + "exit\n"
fo = open('./eph_run.pro', 'w')
fo.write(line)
fo.close()
os.environ['IDL_PATH'] = idl_path
subprocess.call("idl eph_run.pro", shell=True)
mcf.rm_file('./eph_run.pro')
return 1
except:
return 0
def get_sca_data():
#
# NOTE: sca00 is not updated anymore and discoutinued.
#
"""
extract ephsca.fits data file from dataseeker
input: none
output: ephsca.fits
"""
#
#--- create an empty "test" file
#
mcf.rm_file('./test')
fo = open('./test', 'w')
fo.close()
#
#--- and run dataseeker
#
cmd1 = '/usr/bin/env PERL5LIB='
cmd2 = ' dataseeker.pl infile=test outfile=ephsca.fits search_crit="columns=_sca00_avg" '
cmd3 = 'clobber=yes loginFile=/home/mta/loginfile'
cmd = cmd1 + cmd2 + cmd3
bash(cmd, env=ascdsenv)
mcf.rm_file('./test')
cmd = 'mv -f ephsca.fits /data/mta4/www/DAILY/mta_rad/.'
os.system(cmd)
def convert_acistemp_into_c():
"""
convert all acistemp fits files in K into that of C
input: none, but read from <data_dir>/Acistemp/*fits
output: converted fits files in Compaciscent/*fits
"""
outdir = data_dir2 + '/Compaciscent/'
cmd = 'ls ' + data_dir + '/Acistemp/*fits* > ' + zspace
os.system(cmd)
fits_list = mcf.readFile(zspace)
mcf.rm_file(zspace)
for fits in fits_list:
atemp = re.split('\/', fits)
fname = atemp[-1]
btemp = re.split('_', fname)
msid = btemp[0]
cols = [msid] + bcols
flist = pyfits.open(fits)
fdata = flist[1].data
for col in cols:
odata = fdata[col] - 273.15 #--- this is a numpy object
fdata[col] = odata
flist[1].data = fdata
outfile = outdir + fname
mcf.rm_file(outfile)
flist.writeto(outfile)
def run_bad_pix_and_photon(outdir):
"""
run bad pixel table script and photon table scrit
input: outdir --- output directory name
output: files in outdir: bad_pix_list, photons
"""
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = 'perl /data/mta4/MTA/bin/weekly_obs2html.pl 8 photons'
cmd = cmd1 + cmd2
#
#--- run the phonton script
#
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
cmd2 = 'perl ' + tdir + 'read_bad_pix_new.perl'
cmd = cmd1 + cmd2
#
#--- run the bad pixel script
#
bash(cmd, env=ascdsenv)
mcf.rm_file(zspace)
cmd = 'mv photons bad_pix_list ' + outdir
os.system(cmd)
def run_ftp(tdir, dlist, ftp_address = ftp_site, outdir = './'):
"""
retrieve files from ftp site
input: tdir --- location of ftp file under "ftp_site"
dlist --- a list of file names you want to retrieve
ftp_address --- ftp address, default: ftp_site (see the top of this script)
outdir --- a directory name where you want to deposit files. default: './'
output: retrieved files in outdir
count --- the number of files retrieved
"""
#
#--- open ftp connection
#
ftp = FTP(ftp_address)
ftp.login('anonymous', '*****@*****.**')
ftp.cwd(tdir)
#
#--- check though the data
#
count = 0
for file in dlist:
local_file = os.path.join(outdir, file)
try:
ftp.retrbinary('RETR %s' %file, open(local_file, 'wb').write)
count += 1
except:
pass
#
#--- checking whether the retrieved file is empty, if so, just remove it
#
if os.stat(local_file)[6] == 0:
mcf.rm_file(local_file)
ftp.quit()
return count
def create_fp_list():
"""
create a focal plane temperature file list
Input: none, but read from /data/mta/Script/ACIS/Focal/Short_term/
Ooutput: fstart --- a list of start time of the files
fstop --- a list of stop time of the files
f_list --- a list of file names
"""
# temperature_file_list = mcf.create_list_from_dir('/data/mta/Script/ACIS/Focal/Short_term/*')
cmd = 'ls /data/mta/Script/ACIS/Focal/Short_term/data_* > ' + zspace
os.system(cmd)
f = open(zspace, 'r')
temperature_file_list = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
fstart = []
fstop = []
f_list = []
for tfile in temperature_file_list:
#
#--- tfile has a format of "data_2012_285_0003_285_1130"
#
chk = re.search('data_', tfile)
if chk is not None:
atemp = re.split('data_', tfile)
if len(atemp) > 0:
btemp = re.split('_', atemp[1])
year = int(btemp[0])
year2 = year
ydate = int(btemp[1])
ydate2 = int(btemp[3])
if ydate > ydate2:
year2 += 1
ttemp = btemp[2]
ttemp = list(ttemp)
if len(ttemp) == 4:
hour = ttemp[0] + ttemp[1]
minutes = ttemp[2] + ttemp[3]
line = btemp[0] + ':' + btemp[
1] + ':' + hour + ':' + minutes + ':00'
begin = tcnv.axTimeMTA(line)
ttemp = btemp[4]
ttemp = list(ttemp)
hour = ttemp[0] + ttemp[1]
minutes = ttemp[2] + ttemp[3]
line = str(year2) + ':' + btemp[
3] + ':' + hour + ':' + minutes + ':00'
end = tcnv.axTimeMTA(line)
fstart.append(begin)
fstop.append(end)
f_list.append(tfile)
return (fstart, fstop, f_list)
def find_observation(start, stop, lev):
"""
find information about observations in the time period
input: start --- starting time in the format of <yyyy>-<mm>-<dd>T<hh>:<mm>:<ss>
stop --- stoping time in the format of <yyyy>-<mm>-<dd>T<hh>:<mm>:<ss>
lev --- data level
output: acis_obs --- a list of the observation infromation
"""
#
#--- run arc5gl to get observation list
#
run_arc5gl_browse(start, stop,lev, zspace)
#
#--- create obsid list
#
data = read_file(zspace, remove=1)
obsid_list = []
for ent in data:
mc = re.search('acisf', ent)
if mc is not None:
atemp = re.split('acisf', ent)
btemp = re.split('_', atemp[1])
obsid = btemp[0]
mc = re.search('N', obsid)
if mc is not None:
ctemp = re.split('N', obsid)
obsid = ctemp[0]
obsid_list.append(obsid)
#
#--- remove duplicate
#
o_set = set(obsid_list)
obsid_list = list(o_set)
#
#--- open database and extract data for each obsid
#
save = {}
tlist = []
for obsid in obsid_list:
out = get_data_from_db(obsid)
if out != NULL:
[tsec, line] = out
tlist.append(tsec)
save[tsec] = line
tlist.sort()
mcf.rm_file('./acis_obs')
fo = open('./acis_obs', 'w')
for ent in tlist:
fo.write(save[ent])
fo.close()
def read_data(infile, remove=0):
try:
f = open(infile, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
except:
data = []
if remove == 1:
mcf.rm_file(infile)
return data
def extract_stat_result(file):
"""
extract stat informaiton:
Input: file --- image fits file
Output: avg
minp
maxp
devp
"""
cmd1 = "/usr/bin/env PERL5LIB="
cmd2 = ' dmstat infile=' + file + ' centroid=no >' + zspace
cmd = cmd1 + cmd2
bash(cmd, env=ascdsenv)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
#
#--- extract mean, dev, min, and max
#
for ent in data:
atemp = re.split('\s+|\t+', ent)
m1 = re.search('mean', ent)
m2 = re.search('min', ent)
m3 = re.search('max', ent)
m4 = re.search('sigma',ent)
if m1 is not None:
avg = atemp[1]
if m2 is not None:
minv = atemp[1]
btemp = re.split('\(', ent)
ctemp = re.split('\s+|\t+', btemp[1])
minp = '(' + ctemp[1] + ',' + ctemp[2] + ')'
if m3 is not None:
maxv = atemp[1]
btemp = re.split('\(', ent)
ctemp = re.split('\s+|\t+', btemp[1])
maxp = '(' + ctemp[1] + ',' + ctemp[2] + ')'
if m4 is not None:
dev = atemp[1]
return [avg, minv, minp, maxv, maxp, dev]
def find_entries(dir):
"""
create list of fies/directory under the "dir"
ipnt: dir --- directory name under /data/mta/www/mta_script_list/
output: data --- a list of files and directories
"""
cmd = 'ls -d /data/mta/www/mta_script_list/' + dir + '/* >' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
return data
def test_run_ftp(self):
tdir = '/pub/lists/costello'
dlist = ['ace_pkp_15m.txt']
run_ftp(tdir, dlist)
if os.path.isfile('ace_pkp_15m.txt'):
if os.stat('ace_pkp_15m.txt')[6] == 0:
yes = 0
else:
yes = 1
mcf.rm_file('ace_pkp_15m.txt')
else:
yes = 0
self.assertEquals(yes, 1)
def check_dataseeker_entry(msid):
"""
check msid is listed in dataseeker database
input: msid --- msid
output: True/False
"""
cmd = 'grep -i ' + msid + ' ' + house_keeping + 'dataseeker_entry_list >' + zspace
os.system(cmd)
if os.stat(zspace).st_size == 0:
mcf.rm_file(zspace)
return False
else:
mcf.rm_file(zspace)
return True
def read_file_data(infile, remove=0):
"""
read the content of the file and return it
input: infile --- file name
remove --- if 1, remove the input file after read it, default: 0
output: out --- output
"""
f = open(infile, 'r')
out = [line.strip() for line in f.readlines()]
f.close()
if remove == 1:
mcf.rm_file(infile)
return out
def read_file(file, remove=0):
"""
read a file
input: file --- a file to be read
remove --- indicator whether to remove the file after it was read default=0 (no)
output: data --- a list of the data
"""
f = open(file, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
if remove > 0:
mcf.rm_file(file)
return data
def test_get_cti_data(self):
get_cti_data(test = 'test')
cmd = 'ls > ' + zspace
os.system(cmd)
f = open(zspace, 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file(zspace)
yes = 0
for ent in data:
if ent == 'cti_data.txt':
yes = 1
break
self.assertEquals(yes, 1)
def find_available_deph_data():
"""
create a list of potential new data file name
input: none, but read from /dsops/GOT/aux/DEPH.dir/
output: cdata --- a list of the data file names
"""
#
#--- find current time
#
ttemp = tcnv.currentTime()
year = int(ttemp[0])
ydate = int(ttemp[7])
syear = str(year)
tyear = syear[2] + syear[3]
#
#--- first 20 days of the year, we also check the last year input data
#
if ydate < 20:
lyear = year -1
slyear = str(lyear)
ltyear = slyear[2] + slyear[3]
cmd = 'ls /dsops/GOT/aux/DEPH.dir/DE' + ltyear + '*.EPH > ' + zspace
os.system(cmd)
cmd = 'ls /dsops/GOT/aux/DEPH.dir/DE' + tyear + '*.EPH >> ' + zspace
try:
os.system(cmd)
except:
pass
else:
cmd = 'ls /dsops/GOT/aux/DEPH.dir/DE' + tyear + '*.EPH > ' + zspace
try:
os.system(cmd)
except:
pass
try:
f = open(zspace, 'r')
cdata = [line.strip() for line in f.readlines()]
f.close()
except:
cdata = []
mcf.rm_file(zspace)
return cdata
def extract_hrc_evt2(obsid):
"""
extract hrc evt2 file
Input: obsid --- obsid of the data
Output: hrcf<obsid>*evt2.fits.gz
file name if the data is extracted. if not 'na'
"""
#
#--- write required arc5gl command
#
line = 'operation=retrieve\n'
line = line + 'dataset=flight\n'
line = line + 'detector=hrc\n'
line = line + 'level=2\n'
line = line + 'filetype=evt2\n'
line = line + 'obsid=' + str(obsid) + '\n'
line = line + 'go\n'
f = open(zspace, 'w')
f.write(line)
f.close()
cmd = ' /proj/sot/ska/bin/arc5gl -user isobe -script ' + zspace + ' > fits_list'
#
#--- run arc5gl
#
os.system(cmd)
mcf.rm_file(zspace)
#
#--- check the data is actually extracted
#
f = open('fits_list', 'r')
data = [line.strip() for line in f.readlines()]
f.close()
mcf.rm_file('fits_list')
for ent in data:
mc = re.search('fits.gz', ent)
if mc is not None:
cmd = 'gzip -d ' + ent
fits = ent.replace('\.gz', '')
return fits
break
else:
return 'na'
def send_mail(tag, email_list):
"""
sending email out
Input: tag --- user and machine name in the form of c3po-v_mat
email_list --- a string of name in the from of 'tisobecfa.harvard.edu,[email protected]'
Output: email sent out
"""
chk = mcf.isFileEmpty(zspace)
if chk > 0:
atemp = re.split('_', tag)
cmd = 'cat ' + zspace + ' | mailx -s "Subject: Cron Error : ' + atemp[1] + ' on ' + atemp[0] + '" ' + email_list
os.system(cmd)
mcf.rm_file(zspace)