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headers.py
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headers.py
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import pdb
from pydoc import pathdirs
from syslog import LOG_WARNING
import numpy as np;
import pandas as pd;
import sys
import numpy.polynomial.polynomial as poly
from astropy.io import fits as pyfits;
from astropy.time import Time;
from astropy.io import ascii;
from astropy.table import Table;
import matplotlib.pyplot as plt;
import matplotlib
matplotlib.use('TkAgg')
#from . import setup
import os, glob, pickle, datetime, re, csv, gc;
#import mircx_mystic as mrx;
from . import log
counters={'gpstime':0, 'etalon':0, 'sts':0}
# Global shortcut
# removing HIERARCH for 2.0
HM = 'MIRC ';
HMQ = 'MIRC QC ';
HMP = 'MIRC PRO ';
HMW = 'MIRC QC WIN ';
HC = 'CHARA ';
def str2bool (s):
if s == True or s == 'TRUE': return True;
if s == False or s == 'FALSE': return False;
raise ValueError('Invalid boolean string');
def getval (hdrs, key, default=np.nan):
'''
Return a numpy array with the values in header
'''
return np.array ([h.get(key,default) for h in hdrs]);
def summary (hdr):
'''
Return a short string to
summarize the header
'''
value = 'G%i-L%i-R%i %.4f %s'%(hdr.get('GAIN',0),hdr.get('NLOOPS',0),hdr.get('NREADS',0),
hdr.get('MJD-OBS',0.0),hdr.get('OBJECT','unknown'));
if 'MIRC PRO NCOHER' in hdr:
value += ' NCOHER=%i'%(hdr.get('MIRC PRO NCOHER',0));
return value;
# name conflicts with main library. I will comment out as not used it seems.
#def setup (hdr, params):
# '''
# Return the setup as string
# '''
# value = ' / '.join([str(hdr.get(p,'--')) for p in params]);
# return value;
def get_beam (hdr):
'''
Return the i of BEAMi
'''
n = hdr if type(hdr) is str else hdr['FILETYPE'];
for i in range(1,7):
if 'beam%i'%i in n: return i;
if 'BEAM%i'%i in n: return i;
return None;
def clean_date_obs (hdr):
'''
Clean DATE-OBS keyword to always match
ISO format YYYY-MM-DD
'''
if 'DATE-OBS' not in hdr:
return;
if hdr['DATE-OBS'][4] == '/':
# Reformat DATE-OBS YYYY/MM/DD -> YYYY-MM-DD
hdr['DATE-OBS'] = hdr['DATE-OBS'][0:4] + '-' + \
hdr['DATE-OBS'][5:7] + '-' + \
hdr['DATE-OBS'][8:10];
elif hdr['DATE-OBS'][2] == '/':
# Reformat DATE-OBS MM/DD/YYYY -> YYYY-MM-DD
hdr['DATE-OBS'] = hdr['DATE-OBS'][6:10] + '-' + \
hdr['DATE-OBS'][0:2] + '-' + \
hdr['DATE-OBS'][3:5];
def get_mjd (hdr, origin=['linux','gps','mjd'], check=2.0,Warning=True):
'''
Return the MJD-OBS as computed either by Linux time
TIME_S + 1e-9 * TIME_US (note than TIME_US is actually
nanosec) or by GPS time DATE-OBS + UTC-OBS, or by an
existing keyword 'MJD-OBS'.
'''
# Check input
if type(origin) is not list: origin = [origin];
# Read header silently
try:
mjdu = Time (hdr['DATE-OBS'] + 'T'+ hdr['UTC-OBS'], format='isot', scale='utc').mjd;
except:
mjdu = 0.0;
try:
mjdl = Time (hdr['TIME_S']+hdr['TIME_US']*1e-9,format='unix').mjd;
except:
mjdl = 0.0;
try:
mjd = hdr['MJD-OBS'];
except:
mjd = 0.0;
# Check the difference in [s]
delta = np.abs (mjdu-mjdl) * 24 * 3600;
if (delta > check) & (Warning == True):
log.warning ('IN %s :\n UTC-OBS and TIME differ %.1f s. Use Priority Origin: %s'%(hdr['ORIGNAME'],delta,origin[0]));
# Return the requested one
for o in origin: # if origin in array, then returns result in priority order.
if o == 'linux' and mjdl != 0.0:
return mjdl, (delta > check);
if o == 'gps' and mjdu != 0.0:
return mjdu, (delta > check);
if o == 'mjd' and mjd != 0.0:
return mjd, (delta > check);
return 0.0, None;
def loaddir (dirs, uselog=True):
'''
Load the headers of all files mircx*.fit* from
the input list of directory
'''
elog = log.trace ('loaddir');
# Ensure this is a list
if type(dirs) == str:
dirs = [dirs];
# Load all dirs
hdrs = [];
for dir in dirs:
if os.path.isdir (dir) is False:
log.info ('Skip directory (does not exist): '+dir);
continue;
log.info ('Load directory: '+dir);
files = glob.glob (dir+'/mircx*.fits');
files += glob.glob (dir+'/mystic*.fits');
files += glob.glob (dir+'/mircx*.fits.fz');
files += glob.glob (dir+'/mystic*.fits.fz');
files = [ x for x in files if "fibexpmap" not in x ] # remove non-data files.
# Check if any
if len(files) == 0:
log.warning ('No mircx or mystic data files in this directory');
continue;
# Sort them alphabetically
files = sorted (files);
# Load headers
hdrs_here = load (files);
# Append headers in case of multiple directories -- not used...
hdrs.extend (hdrs_here);
return hdrs;
def load (files):
'''
Load the headers of all input files. The following keywords
are added to each header: MJD-OBS, MJD-LOAD and ORIGNAME.
The following keywords are added if missing: MIRC HWP POS0-5.
This routine 'fixes' various issues with the headers that arose over the years, including reconciling times and
identifying use of etalon, etc.
The output is a list of FITS headers.
'''
hdrs = []
# Loop on files
log.info("Number of files to read: %i "%len(files))
log.info("First File: %s "%files[0])
log.info("Last File : %s"%files[-1])
for fn,f in enumerate (files):
try:
# Read compressed file
if f[-7:] == 'fits.fz':
#hdr = pyfits.getheader(f, 1);
hdulist=pyfits.open(f,memmap=False)
hdr=hdulist[1].header.copy()
del hdulist[1].header
hdulist.close()
del hdulist
fnum=int(f[-13:-8]) # might not always be true.
# Read normal file
else:
#hdr = pyfits.getheader(f, 0);
hdulist=pyfits.open(f,memmap=False)
hdr=hdulist[0].header.copy()
del hdulist[0].header # save a little memory along the way.
hdulist.close()
del hdulist
fnum=int(f[-10:-5])
# Add file name
hdr['ORIGNAME'] = f;
hdr['FILENUM'] = fnum;
# Test if FRAME_RATE is in header
if 'MIRC FRAME_RATE' not in hdr and 'EXPOSURE' in hdr:
log.warning ('Assume FRAME_RATE is 1/EXPOSURE');
hdr['MIRC FRAME_RATE'] = 1e3/hdr['EXPOSURE'];
# Test if NBIN is in header
if 'NBIN' not in hdr:
hdr['NBIN'] = 1;
if 'MIRC COMBINER_TYPE' not in hdr:
hdr['MIRC COMBINER_TYPE'] = 'ALL-IN-ONE' # default to all-in-one for old data
log.debug ('Old data with no MIRC COMBINER_TYPE (set to ALL-IN-ONE)');
if 'MIRC HWP0 POS' not in hdr:
hdr['MIRC HWP0 POS'] = 0.0
log.debug ('Header missing keyword MIRC HWP0 POS (set to 0.0)')
# Check change of card
if 'ENDFR' in hdr:
log.debug ('Old data with ENDFR');
hdr.rename_keyword ('ENDFR','LASTFR');
# Check NBIN
if 'NBIN' not in hdr and hdr['FILETYPE'] != 'FLAT_MAP': #JD What is FLAT_MAP
log.debug ('Old data with no NBIN (set to one)');
hdr['NBIN'] = 1;
# Rationalize the few fields when BIN != 1
hdr['STARTFR'] /= hdr['NBIN'];
hdr['LASTFR'] = (hdr['LASTFR']-(hdr['NBIN']-1))/hdr['NBIN'];
hdr['FRMPRST'] /= hdr['NBIN'];
# Reformat DATE-OBS
clean_date_obs (hdr);
if 'DPOL_ROW' in hdr:
if hdr['DPOL_ROW'] !=0:
# check if config ends with _WOLL and hdr['CONF_NA']
conf_na = hdr['CONF_NA'].strip()
if conf_na[-5:] != '_WOLL': hdr['CONF_NA']=conf_na+'_WOLL'
# Compute MJD from information in header
mjd, temp_flag = get_mjd (hdr, Warning = (counters["gpstime"] == 0));
#mjd, temp_flag = get_mjd (hdr, Warning = True);
if (counters["gpstime"] == 0) & temp_flag:
log.warning("Additional time discrepancy warnings suppressed.")
if (temp_flag):
counters["gpstime"]+=1
# Set in header
hdr['MJD-OBS'] = (mjd, '[mjd] Observing time');
# Add the loading time
hdr['MJD-LOAD'] = (Time.now().mjd, '[mjd] Last loading time (UTC)');
# Check if STS data
if hdr.get ('MIRC STS_IR_FOLD','OUT') == 'IN':
#log.info ('Set OBJECT = STS because STS_IR_FOLD is IN');
hdr['OBJECT'] = 'STS';
counters["sts"] +=1
# Check if ETALON
if hdr.get ('MIRC ARMADA','OUT') == 'IN':
counters["etalon"] +=1
#if hdr['OBJECT'][-1]=='E':
# #log.info ('ETALON is IN for OBJECT');
#else:
# #log.info ('Set OBJECT = OBJECT_E because ETALON is IN');
if hdr['OBJECT'][-1] != 'E':
hdr['OBJECT'] += '_E'; # JDM slightly preferes ETALON_OBJECT... but we will keep for now
# Append
hdrs.append (hdr);
except (KeyboardInterrupt, SystemExit):
raise;
except Exception as exc:
log.warning ('Cannot get header of '+f+' ('+str(exc)+')');
#progress bar
if fn == len(files)//4:
log.info("PROGRESS 25% Done")
if fn == len(files)//2:
log.info("PROGRESS 50% Done")
if fn == len(files)*3//4:
log.info("PROGRESS 75% Done")
log.info("PROGRESS 100% Done")
log.debug('Reconciling frames time to consistent frame rate.')
# JDM. Note that the reset time is currently about 1/10 of frametime. Frame rates are calculated
# based on first frame so the measured framerate is going to be off since this does not account for
# reset time. We could add complexity to the time calculation but it seems not worth it since we don't record
# all camera parameters in header so not sure how reset time changes with other parameters and over time, firmware
# #changes, etc.
# Specific Example:
# For a 8loops 6reads, 320x44 pixels, the true frame rate is 2.7294ms with reset time 0.26ms.
# The reported frametimes are 2.7346ms for 50 frames/reset and 2.7320 ms for 100 frames/reset.
# I had hoped to get ultra precise timing for removing the interference but this reset error will limit the preciison
# to timing error of +/- 1/20 frametime. This is phase error of ~5 degs for a 94Hz signal with typical frametime of 2.7ms.
# first group detector settings which should always have the same frame rate exactly.
keys = ['NREADS','NLOOPS','NBIN','CROPROWS','CROPCOLS','FRMPRST']
for h in hdrs: h['MJD-OBS0']=h['MJD-OBS'] # save original time
#JDM how does this work if NBIN=3?
gps = keygroup (hdrs, '.*', keys=keys,delta=1e20, Delta=1e20,continuous=False);
for gp in gps:
startfrs=np.array([gp0['STARTFR'] for gp0 in gp])
#lastfrs=np.array([gp0['LASTFR'] for gp0 in gp])
times=np.array([gp0['MJD-OBS'] for gp0 in gp])
dtimes=np.array([gp0['EXPOSURE'] for gp0 in gp]) # use zip?
restart_times = times-(np.median(dtimes)/1000./24./3600)*startfrs #all nums treated at double?
# find gaps of >10 seconds
gaps = restart_times-np.roll(restart_times,1)
gaptime=10. #Seconds
starts=np.concatenate( (np.array([0]), (np.where( gaps > gaptime/24./3600. ) )[0] ) )
lasts=np.roll(starts,-1)
lasts[-1]=len(times)
new_mjds=np.zeros(len(startfrs))
new_exposure=np.zeros(len(dtimes))
for in0,in1 in zip(starts,lasts):
#use a robust linear fit to each continuous chunk. TOTAL overkill but will handle any weird outlines well!!
xoffset=np.median(startfrs[in0:in1])
yoffset=np.median(times[in0:in1])
x=(startfrs[in0:in1]-xoffset)/1000000.
y=times[in0:in1] -yoffset
coefs = poly.polyfit(x, y, 1) # I'd have loved to use a robust estimator
new_y = poly.polyval(x, coefs)
new_mjds[in0:in1] = new_y+yoffset
new_exposure[in0:in1]=coefs[1]*24.*3600./1000. #update.
#median_frame = np.median(startfrs[in0:in1])
#median_time0 = np.median(times[in0:in1] - (np.median(dtimes)/1000./24./3600)*(startfrs[in0:in1]-median_frame))
#new_mjds[in0:in1]=median_time0+(np.median(dtimes)/1000./24./3600)*(startfrs[in0:in1]-median_frame)
#check
diffs=new_mjds-times
log.debug('Maximum time change in cam setting: %f milliseconds'%(24*3600*1000.*np.max(np.abs(new_mjds-times))))
#plt.plot(diffs*24*3600*1000.)
#plt.show()
#Update the original headers with the median EXPOSURE (detimes) for each camera mode
quickref=[gp0['ORIGNAME'] for gp0 in gp]
for hdr in hdrs:
if hdr['ORIGNAME'] in quickref:
index= list.index(quickref,hdr['ORIGNAME'])
#log.info('Found %s'%hdr['ORIGNAME'])
hdr['EXPOSURE']=new_exposure[index] # unify
hdr['MIRC FRAME_RATE']=1000./hdr['EXPOSURE']
hdr['MJD-OBS']=new_mjds[index] #save original MJD-OBS before overwriting!
hdr['RESTART0']= hdr['MJD-OBS']-(hdr['EXPOSURE']/1000./24./3600)*hdr['STARTFR'] #make perfect
check_diffs=np.array([g['MJD-OBS']-g['MJD-OBS0'] for g in hdrs])
alltimes=np.array([g['MJD-OBS'] for g in hdrs])
exposures = np.array([g['EXPOSURE'] for g in hdrs])
restarts=np.array([g['RESTART0'] for g in hdrs])
log.info('MJD-OBS corrected for jitter (max change %f mS)'%(24.*3600.*1000.*np.max(np.abs(check_diffs))))
#breakpoint()
# Identify camera restarts by either startfrs going down with time (typical case) or rarely if the the restart_times difference is large,
# say
gc.collect()
log.info('Number of files with time discrepancy: %i '%counters['gpstime'])
log.info('Number of files with STS: %i '%counters['sts'])
log.info('Number of files with Etalon: %i '%counters['etalon'])
log.info ('%i headers loaded'%len(hdrs));
return hdrs;
def frame_mjd (hdr):
'''
Compute MJD time for each frame from STARTFR to LASTFR.
Assumig STARTFR has the MJD-OBS and the time between
frame is given by HIERARCH MIRC FRAME_RATE.
'''
# Check consistency
if hdr['LASTFR'] < hdr['STARTFR']:
raise ValueError ('LASTFR is smaller than STARTFR');
# Number of frame since start
nframe = hdr['LASTFR'] - hdr['STARTFR'] + 1;
# Build counter
counter = np.arange(0,nframe)
# Time step between frames in [d]
# with new headers, the HIERRACH is removed from dictionary.
#delta = 1./hdr['MIRC FRAME_RATE'] / 24/3600;
delta = hdr['EXPOSURE'] / 24./3600/1000; # should be more accurate.
# Compute assuming MJD-OBS is time of first frame
mjd = hdr['MJD-OBS'] + delta * counter;
return mjd;
def match (h1,h2,keys,delta):
'''
Return True fs all keys are the same in header h1
and header h2, and if the time difference is less
than delta (s). The keys shall be a list of string.
'''
# Check all keywords are the same
answer = True;
for k in keys:
answer *= (h1.get(k,None) == h2.get(k,None));
# Check time is close-by
answer *= (np.abs(h1.get('MJD-OBS',0.0) - h2.get('MJD-OBS',0.0))*24.*3600 < delta);
# Ensure binary output
return True if answer else False;
def group (hdrs, mtype, delta=300.0, Delta=300.0, continuous=True, keys=[]):
'''
Group the input headers into list of compatible files.
A new group is started if:
- a file of different type is interleaved,
- the detector or instrument setup is different,
- the time distance between consecutive is larger than delta.
- the total integration is larger than Delta
The output is a list of list.
'''
elog = log.trace ('group_headers');
groups = [[]];
mjd = -10e9;
# Key used to define setup
keys = ['FILETYPE'] + keys;
# Define the regular expression to match file type
regex = re.compile ('^'+mtype+'$');
# Sort by time
hdrs = sorted (hdrs,key=lambda h: h['MJD-OBS']);
# Assume hdrs is sorted
for h in hdrs:
fileinfo = h['ORIGNAME'] + ' (' +h['FILETYPE']+')';
# if different type, start new group and continue
if bool (re.match (regex, h['FILETYPE'])) is False:
if groups[-1] != [] and str2bool (continuous):
groups.append([]);
continue;
# If no previous
if groups[-1] == []:
log.debug('New group %s'%fileinfo);
groups[-1].append(h);
continue;
# If no match with last, we start new group
if match (h,groups[-1][-1],keys,delta) is False:
log.debug('New group (gap) %s'%fileinfo);
groups.append([h]);
continue;
# If no match with first, we start new group
if match (h,groups[-1][0],keys,Delta) is False:
log.debug('New group (integration) %s'%fileinfo);
groups.append([h]);
continue;
# Else, add to current group
log.debug('Add file %s'%fileinfo);
groups[-1].append(h);
# Clean from void groups
groups = [g for g in groups if g != []];
# For the BACKGROUND, remove the first file if there is more than 3 files
# because it is often contaminated with light (slow shutter)
# This needs to be more robust for all kinds of shutters. will be done later.
#if mtype == 'BACKGROUND':
# for i in range(np.shape(groups)[0]):
# if np.shape(groups[i])[0] > 3:
# groups[i] = groups[i][1:];
# log.debug ('Ignore the first BACKGROUND files (more than 3)');
return groups;
def keygroup (hdrs, mtype, delta=300.0, Delta=300.0, continuous=True, keys=[]):
'''
Group the input headers into list of compatible files.
A new group is started if:
- keys change
- the time distance between consecutive is larger than delta.
- the total integration is larger than Delta
The output is a list of list.
'''
#elog = log.trace ('keygroup_headers');
groups = [[]];
mjd = -10e9;
# Define the regular expression to match file type
regex = re.compile ('^'+mtype+'$');
# Sort by time
hdrs = sorted (hdrs,key=lambda h: h['MJD-OBS']);
# Assume hdrs is sorted
for h in hdrs:
fileinfo = h['ORIGNAME'] + ' (' +h['FILETYPE']+')';
# if different type, start new group and continue
if bool (re.match (regex, h['FILETYPE'])) is False:
if groups[-1] != [] and str2bool (continuous):
groups.append([]);
continue;
# If no previous
if groups[-1] == []:
log.debug('New group %s'%fileinfo);
groups[-1].append(h);
continue;
# If no match with last, we start new group
if match (h,groups[-1][-1],keys,delta) is False:
log.debug('New group (gap) %s'%fileinfo);
groups.append([h]);
continue;
# If no match with first, we start new group
if match (h,groups[-1][0],keys,Delta) is False:
log.debug('New group (integration) %s'%fileinfo);
groups.append([h]);
continue;
# Else, add to current group
log.debug('Add file %s'%fileinfo);
groups[-1].append(h);
# Clean from void groups
groups = [g for g in groups if g != []];
# For the BACKGROUND, remove the first file if there is more than 3 files
# because it is often contaminated with light (slow shutter)
# This needs to be more robust for all kinds of shutters. will be done later.
#if mtype == 'BACKGROUND':
# for i in range(np.shape(groups)[0]):
# if np.shape(groups[i])[0] > 3:
# groups[i] = groups[i][1:];
# log.debug ('Ignore the first BACKGROUND files (more than 3)');
return groups;
def assoc (h, allh, tag, keys=[], which='closest', required=0, quality=None):
'''
Search for headers with tag and matching criteria
'''
# Keep only the requested tag
atag = [a for a in allh if a['FILETYPE']==tag]
# Keep only the requested criteria
out = [];
for a in atag:
tmp = True;
for k in keys:
tmp *= (h.get(k,None) == a.get(k,None));
if tmp:
out.append(a);
# Keep only the requested quality
l1 = len (out);
if quality is not None:
out = [o for o in out if o.get (HMQ+'QUALITY', 0.0) > quality];
# Check closest
if len (out) > required and which=='closest':
if required < 2:
time_diffs = np.array([o['MJD-OBS'] - h['MJD-OBS'] for o in out])
out = [out[np.abs(time_diffs).argmin()]]
else:
raise NotImplementedError('Not supported yet');
# Check best quality
if len (out) > required and which=='best':
if required < 2:
quality = np.array([o[HMQ+'QUALITY'] for o in out]);
out = [out[np.argmax (quality)]];
else:
raise NotImplementedError('Not supported yet');
# Check required
if len (out) < required:
log.warning ('Cannot find %i %s (%i rejected for quality)'%(required,tag,l1-len(out)))
elif required > 0:
log.info ('Find %i %s (%s ...)'%(len(out),tag,out[0]['ORIGNAME']));
return out
def assoc_flat (h, allh):
'''
Return the best FLAT for a given file. Note that the flat header is return
as a list of one to match the output of 'assoc' function.
'''
# Associate best FLAT based in gain
flats = [a for a in allh if a['FILETYPE']=='FLAT_MAP'];
# Check
if len (flats) < 1:
log.warning ('Cannot find FLAT');
return [];
# Get closest gain
m = np.argmin ([np.abs (h['GAIN'] - f['GAIN']) for f in flats]);
flat = flats[m];
# Return
log.info ('Find 1 FLAT (%s)'%os.path.basename(flat['ORIGNAME']));
return [flat];
def clean_option (opt):
'''
Check options
'''
if opt == 'FALSE': return False;
if opt == 'TRUE': return True;
def check_input (hdrs, required=1, maximum=100000):
'''
Check the input when provided as hdrs
'''
breakpoint()
# Ensure a list
if type (hdrs) is not list:
hdrs = [hdrs];
# Check inputs are headers
# JDM. in new version this is just a plain dict not a pyfits object... problem?
hdrs = [h for h in hdrs if type(h) is pyfits.header.Header or \
type(h) is pyfits.hdu.compressed.CompImageHeader];
if len(hdrs) < required:
raise ValueError ('Missing mandatory input');
if len(hdrs) > maximum:
raise ValueError ('Too many input');
def rep_nan (val,*rep):
''' Replace nan by value'''
rep = 0.0 if not rep else rep[0];
return val if np.isfinite (val) else rep;
def parse_argopt_catalog (input):
'''
Parse the syntax 'NAME1,d1,e1,NAME2,d2,e2,...'
and return an astropy Table with column NAME,
ISCAL, MODEL_NAME, PARAM1 and PARAM2.
'''
if input == 'name1,diam,err,name2,diam,err':
raise (ValueError('No calibrators specified'));
# Catalog is a list
if input[-5:] == '.list':
log.info ('Calibrators given as list');
catalog = ascii.read (input);
return catalog;
# Check it is a multiple of 3
values = input.split(',');
if float(len (values) / 3).is_integer() is False:
raise (ValueError('Wrong syntax for calibrators'));
# Parse each star
names = np.array (values[0::3]);
diam = np.array (values[1::3]).astype(float);
ediam = np.array (values[2::3]).astype(float);
# Create catalog
catalog = Table ();
catalog['NAME'] = names;
catalog['ISCAL'] = 'CAL';
catalog['MODEL_NAME'] = 'UD_H';
catalog['PARAM1'] = diam;
catalog['PARAM2'] = ediam;
return catalog;
def update_diam_from_jmmc (catalog):
'''
For all stars with diam=0 and err=0 in the catalog, we try
to get the information from the JMMC SearchCal.
FIXME: this is not working anymore, need to deal with the new
format for catalog based on astropy Table.
'''
# Init
searchCal = 'http://apps.jmmc.fr/~sclws/getstar/sclwsGetStarProxy.php';
voTableToTsv = os.path.dirname (log.__file__) + '/sclguiVOTableToTSV.xsl';
# Loop on stars in catalog, query for the one
# with err = 0 and diam = 0
for c in catalog:
if c[1] == 0 and c[2] == 0:
try:
# Call online SearchCal
log.info ('Query JMMC SearchCal for star '+c[0]);
os.system ('wget '+searchCal+'?star='+c[0]+' -O mircx_searchcal.vot -o mircx_searchcal.log');
# Not found
if 'has not been found' in open('mircx_searchcal.vot').read():
log.warning (c[0]+' has not been found');
continue;
# Convert and parse
os.system ('xsltproc '+voTableToTsv+' mircx_searchcal.vot > mircx_searchcal.tsv');
answer = [l for l in csv.reader(open('mircx_searchcal.tsv'),delimiter='\t') if l[0][0] != '#'];
c[1] = float (answer[1][answer[0].index('UD_H')]);
c[2] = float (answer[1][answer[0].index('e_LDD')]);
log.info ('%s found %.4f +- %.4f mas'%(c[0],c[1],c[2]));
except:
log.error ('Cannot reach JMMC SearchCal or parse answer');
def get_sci_cal (hdrs, catalog):
'''
Spread the headers from SCI and CAL according to the
entries defined in catalog. Catalog should be an astropy
Table with the columns NAME, ISCAL, PARAM1 and PARAM2.
'''
# Check format of catalog
try:
t = catalog['NAME'];
t = catalog['ISCAL'];
t = catalog['PARAM1'];
t = catalog['PARAM2'];
except:
log.error ('Calibrators not specified correclty');
raise (ValueError);
# Check if enought
if len (catalog) == 0:
log.error ('No valid calibrators');
raise (ValueError);
# Get values
name,iscal = catalog['NAME'], catalog['ISCAL'];
# Loop on input headers
scis, cals = [], [];
for h in hdrs:
if h['FILETYPE'] != 'OIFITS':
continue;
# Find where in catalog
idx = np.where (name == h['OBJECT'])[0];
if len(idx) > 0 and iscal[idx[0]] == 'CAL':
idx = idx[0];
log.info ('%s (%s) -> OIFITS_CAL (%s, %f,%f)'%(h['ORIGNAME'],h['OBJECT'], \
catalog[idx]['MODEL_NAME'],catalog[idx]['PARAM1'],catalog[idx]['PARAM2']));
h['FILETYPE'] += '_CAL';
h[HMP+'CALIB MODEL_NAME'] = (catalog[idx]['MODEL_NAME']);
h[HMP+'CALIB PARAM1'] = (catalog[idx]['PARAM1']);
h[HMP+'CALIB PARAM2'] = (catalog[idx]['PARAM2']);
cals.append (h);
else:
log.info ('%s (%s) -> OIFITS_SCI'%(h['ORIGNAME'],h['OBJECT']));
h['FILETYPE'] += '_SCI';
scis.append (h);
return scis,cals;
def p2h (phdrs): # convert panda frame to our standard header list of dictionaries
hdr0=[]
allh=phdrs.transpose().to_dict()
keylist=list(allh.keys())
for key in keylist:
temp=allh[key]
hdr0.append(temp)
return hdr0;
def updatehdrs(hdrs,blocks):
#Information in the block file takes precedence of the header information.
#loop over the blocks then modify hdrs based on the numbers and add new block field.
#remove hdrs entries not explicitly included in blocks.
for hdr in hdrs:
for block in blocks:
if hdr['FILENUM'] >= block['START'] and hdr['FILENUM'] <= block['END']:
hdr['BLOCK']=block['BLOCK']
inkeys=['BLOCK','OBJECT','COMBINER_TYPE','CONFIG','GAIN','FILETYPE']
outkeys=['BLOCK','OBJECT','MIRC COMBINER_TYPE','CONF_NA','GAIN','FILETYPE']
#JDM detail. Since HWP angles are all 6 beams, we cant use blocks to over-ride. you will need to set
#the header csv tables to the correct values if not correct.
for inkey,outkey in zip(inkeys,outkeys):
if hdr[outkey] != block[inkey]:
hdr[outkey]=block[inkey]
log.info('Updated Header %i %s from %s to %s'%(hdr['FILENUM'],outkey,hdr[outkey],block[inkey]))
if 'BLOCK' not in hdr.keys():
hdr['BLOCK']=''
log.info('Removed Header %i from hdrs since not referenced in block csv'%(hdr['FILENUM']))
#hdrs=[hdr if hdr['BLOCK'] != '' for hdr in hdrs]
hdrs=[hdr for hdr in hdrs if hdr['BLOCK'] !='' ]
# remove hdrs with
return hdrs
#def keyupdatehdrs(hdrs,idkey=[],idval=[], newkey=[],newval=[]):
#Information in the blocks precedence of the header information.
#loop over the blocks then modify hdrs based on the numbers and add new block field.
#remove hdrs entries not explicitly included in blocks.
# for hdr in hdrs:
# if hdr[idkey] = idval:
# hdr[newkey]=newval; # fancy way to do this?
#log.info('Updated Header %i %s from %s to %s'%(hdr['FILENUM'],outkey,hdr[outkey],block[inkey]))
# return hdrs