nod2fits.py
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#!/usr/bin/env python
import sys, os
import struct
import scipy
import pyfits
import pylab as plt
import numpy as np
import datetime as DT
from fortranfile import FortranFile
RAD = np.pi/180.0
GRD = 180.0/np.pi
def nint(x):
if x > 0: return int(x+0.5)
else: return int(x-0.5)
def get_title(x, OS):
title = ""
for i in range(7, 17, 1):
if x[i] != 0.0:
if OS == "other":
if i == 8:
title += np.array(x[i]).tostring()[::-1].strip()
else:
title += np.array(x[i]).tostring()[::-1].strip() + "#"
elif OS == "unix":
title += np.array(x[i]).tostring().strip() + "#"
else:
title += " "
title = title.replace("#", "", 1)
title = title.replace("##", " ").replace("#", " ")
source = title.split()[0].strip().rstrip()
try:
scannum = np.array(x[10]).tostring()[::-1][:4]
except:
try:
scannum = title.split()[2].strip().rstrip()
except:
scannum = 0
try:
s = int(scannum)
except:
scannum = None
return title, source, scannum
def read_rawdata(filename, OS):
if OS == "other":
f = FortranFile(filename, endian=">")
elif OS == "unix":
f = FortranFile(filename, endian="<")
go = True
records = []
while go:
try: records.append(list(f.readReals('d')))
except: go = False
f.close()
title, source, scannum = get_title(records[0], OS)
if scannum != None:
outfile = "nod3_"+scannum.rstrip()+"_"+source.rstrip()+".fits"
else:
outfile = "nod3_"+source+".fits"
return outfile, records
def mapin(records, mapno, os='other'):
x = records[0]
if os in ('other', 'unix'):
title = get_title(x, os)
start = nint(x[1]) - 1
cols = nint(x[2])
rows = nint(x[3])
length = 0
n = 0
dat = []
while length < start+cols*rows:
length += len(records[n])
dat += records[n]
n += 1
for i in range(n):
records.pop(0)
header = dat[:start]
data = np.array(dat[start:start+cols*rows]).reshape((rows, cols))
return tuple(header), data
def rotmat(l, b, a):
cosl = np.cos(l*RAD)
sinl = np.sin(l*RAD)
cosb = np.cos(b*RAD)
sinb = np.sin(b*RAD)
cosa = np.cos(a*RAD)
sina = np.sin(a*RAD)
rotmat = []
rotmat.append(cosb*cosl)
rotmat.append(-sina*sinb*cosl - cosa*sinl)
rotmat.append(-cosa*sinb*cosl + sina*sinl)
rotmat.append(cosb*sinl)
rotmat.append(-sina*sinb*sinl + cosa*cosl)
rotmat.append(-cosa*sinb*sinl - sina*cosl)
rotmat.append(sinb)
rotmat.append(sina*cosb)
rotmat.append(cosa*cosb)
return np.reshape(rotmat, (3,3))
def create_fits(filename, header, data, keys, OS, mapno=1, sidpar=False):
m50 = [[ 0.9999257079524, -0.0111789381378, -0.0048590038154], \
[ 0.0111789381264, 0.9999375133500, -0.0000271625947], \
[ 0.0048590038415, -0.0000271579263, 0.9999881946024]]
hoff = {}
hoff[0] = [0.0, 0.0]
hoff[4850] = [242.5, -242.5]
dmax = np.nanmin(data)
dmin = np.nanmax(data)
data = np.where(data == header[5], np.nan, data)
title, source, scannum = get_title(header, OS)
hc = nint(header[30])
if hc < 0:
epoch = 2000.0
else:
epoch = 1950
if str(hc)[-1] == '0':
c1 = 'GLON-'
c2 = 'GLAT-'
sig = -1
elif str(hc)[-1] in ('1', '3'):
c1 = 'RA---'
c2 = 'DEC--'
sig = -1
elif str(hc)[-1] == '2':
c1 = 'ALON-'
c2 = 'ALAT-'
sig = 1
try: scdir = nint(header[52])
except: scdir = None
if scdir == 0:
SCANDIR = c1.replace("-", "")
ssig = -1
elif scdir == 1:
SCANDIR = c2.replace("-", "")
ssig = 1
elif scdir == 2:
SCANDIR = "ALON"
ssig = 1
elif scdir == 3:
SCANDIR = "ALAT"
ssig = 1
else:
SCANDIR = None
icode = str("%4.4i" % header[30])
if icode[-2] == '0':
proj = 'CAR'
elif icode[-2] == '1':
proj = 'DES'
elif icode[-2] == '2':
proj = 'DES'
freq = int(header[26])
if freq not in hoff.keys(): freq = 0
xoff = hoff[freq][0] / 3600
#rxpix = (header[2] + 1) / 2.0
#rypix = (header[3] + 1) / 2.0
rxpix = 1+(header[28] + xoff)/header[44]
rypix = 1-header[29]/header[45]
if proj == 'DES':
mat = np.array(header[31:40])
mat = mat.reshape(3,3)
vec = np.dot(mat, [1.0, 0.0, 0.0])
lon = np.arctan2(vec[1], vec[0]) * GRD
lat = np.arctan2(vec[2], np.sqrt(vec[1]**2 + vec[0]**2)) * GRD
if lon < 0.0: lon += 360.0
rot = np.dot(np.transpose(rotmat(lon, lat, 0.0)), mat)
rotx = np.arctan2(rot[2][1], rot[2][2]) * GRD
roty = rotx
else:
lon = header[28] + sig*rxpix*header[44]
lat = header[29] + rypix*header[45]
rotx = 0.0
roty = 0.0
try: sdir = int(header[52])
except: sdir = -1
cols = header[2]
rows = header[3]
if SCANDIR == "ALON":
data = np.fliplr(data)
hdu = pyfits.PrimaryHDU(data)
hdu.header.set('BSCALE', 1.0, 'data scaling factor')
hdu.header.set('BZERO', 0.0, 'data zero value')
#hdu.header.set('BLANK', header[5], 'data blank value (dummy)')
hdu.header.set('DATAMIN', dmin, 'minimum pixel value of image set')
hdu.header.set('DATAMAX', dmax, 'maximum pixel value of image set')
hdu.header.set('OBSLAT', header[27], 'latitude of observation')
if abs(header[27] - 50.525) < 0.025:
hdu.header.set('TELESCOP', 'Effelsberg', 'telescope used')
hdu.header.set('OBJECT', source, 'source name')
if scannum != None:
hdu.header.set('SCANNUM', scannum, 'SCAN NUMBER')
hdu.header.set('EPOCH', epoch, 'epoch of base system')
hdu.header.set('CTYPE1', c1+proj, 'projection type')
hdu.header.set('CRVAL1', lon, 'logitude of reference pixel')
hdu.header.set('CDELT1', sig*header[44], 'logitude of reference pixel')
hdu.header.set('CRPIX1', rxpix, 'reference pixel')
hdu.header.set('CROTA1', rotx, 'rotation angle of base system')
hdu.header.set('CTYPE2', c2+proj, 'projection type')
hdu.header.set('CRVAL2', lat, 'latitude of reference pixel')
hdu.header.set('CDELT2', header[45], 'latitude of reference pixel')
hdu.header.set('CRPIX2', rypix, 'reference pixel')
hdu.header.set('CROTA2', roty, 'rotation angle of base system')
hdu.header.set('CTYPE3', 'FREQ', 'projection type')
if SCANDIR != None:
hdu.header.set('SCANDIR', SCANDIR, 'Scanning direction')
hdu.header.set('SCANXVEL', header[53], 'Tracking rate along line')
isodate = convert_partial_year(header[25])
isodate = str(isodate).replace(" ", "T")
hdu.header.set('DATE_OBS', isodate, 'Epoch of Observation')
hdu.header.set('CRVAL3', header[26]*1e6, 'frequency [Hz]')
try: hdu.header.set('CDELT3', header[54]*1e6, 'band width [Hz]')
except: hdu.header.set('CDELT3', 10.0, 'band width [Hz]')
hdu.header.set('CRPIX3', 1, 'frequency step')
if sdir == 0: hdu.header.set('SCANDIR', 'ULON', 'Scanning direction')
if sdir == 1: hdu.header.set('SCANDIR', 'ULAT', 'Scanning direction')
hdu.header.set('BMAJ', header[42], 'Current longitude beamwidth')
hdu.header.set('BMIN', header[43], 'Current latitude beamwidth')
#hdu.header.set('BANDWID', header[54], 'Bandwidth in MHz')
if title.upper().find("CH1") > 0:
hdu.header.set('MAPTYPE', "I1")
elif title.upper().find("CH2") > 0:
hdu.header.set('MAPTYPE', "I2")
elif title.upper().find("CH3") > 0:
hdu.header.set('MAPTYPE', "U")
elif title.upper().find("CH4") > 0:
hdu.header.set('MAPTYPE', "Q")
else:
hdu.header.set('MAPTYPE', "I")
if mapno < 5:
hdu.header.set('RXHORN', 0)
hdu.header.set('PATLONG', hoff[freq][0])
else:
hdu.header.set('RXHORN', 1)
hdu.header.set('PATLONG', hoff[freq][1])
hdu.header.set('EXTNAME', 'MAP-'+hdu.header['MAPTYPE']+'-H'+str(hdu.header['RXHORN']))
for key in keys:
val = str(keys[key])
if val.isdigit(): Val = int(val)
elif type(val) == type(" "): Val = val.split(",")
elif not val.isalpha(): Val = float(val)
if type(Val) == type([]):
val = Val[(mapno-1)%len(Val)].strip().upper()
else:
val = Val.upper()
if val.isdigit():
val = int(val)
elif val.isalnum():
val = val
else:
val = float(val)
hdu.header.set(key.upper(), val)
#for i in range(len(header)):
# print i, header[i]
#print hdu.header
#hdu.writeto(filename, clobber=True)
if sidpar:
sidmap, parmap = getsidpar(header)
hdu.header['OBJECT'] = 'Parallactic Angle Map'
hdu.header.set('EXTNAME', "PARMAP")
pyfits.append(filename, parmap, hdu.header)
hdu.header['OBJECT'] = 'Sidereal Time Map'
hdu.header.set('EXTNAME', "SIDMAP")
pyfits.append(filename, sidmap, hdu.header)
return
if mapno == 1:
if os.path.exists(filename): os.remove(filename)
pyfits.writeto(filename, hdu.data, hdu.header)
else:
pyfits.append(filename, hdu.data, hdu.header)
def getsidpar(header):
rows, cols = int(header[3]), int(header[2])
sidmap = np.zeros((rows, cols))
parmap = np.zeros((rows, cols))
off = len(header) - 4*rows
for j in range(rows):
i1 = off + j*4
i3 = off + j*4 + 2
ds = (header[i1+1] - header[i1])/float(cols-1)
dp = (header[i3+1] - header[i3])/float(cols-1)
for i in range(cols):
if ds > 0:
sidmap[j][i] = header[i1+1] - i*ds
else:
sidmap[j][i] = header[i1] + i*ds
if dp > 0:
parmap[j][i] = header[i3+1] - i*dp
else:
parmap[j][i] = header[i3] + i*dp
return sidmap, parmap
def convert_partial_year(atime):
"""
Convert atime (a float) to DT.datetime
This is the inverse of dt2t.
assert dt2t(t2dt(atime)) == atime
"""
year = int(atime)
remainder = atime - year
boy = DT.datetime(year, 1, 1)
eoy = DT.datetime(year + 1, 1, 1)
seconds = remainder * (eoy - boy).total_seconds()
return boy + DT.timedelta(seconds=seconds)
def main():
if len(sys.argv) < 2:
print "usage: ", sys.argv[0], " filename [os]"
sys.exit(0)
filename = sys.argv[1]
if len(sys.argv) >= 3:
if sys.argv[2].find("=") < 0:
OS = sys.argv[2]
else:
OS = 'other'
else:
OS = 'other'
keys = {}
keys['dx'] = -1
for arg in sys.argv:
ind = arg.find("=")
if ind > 0:
keys[arg[:ind].upper()] = arg[ind+1:].upper()
elif arg[:3] == "+dx":
keys['dx'] = 1
mapno = 1
outfile, raw = read_rawdata(filename, OS)
#try:
if 1:
while len(raw) > 0:
header, data = mapin(raw, mapno, os=OS)
create_fits(outfile, header, data, keys, OS, mapno=mapno)
mapno += 1
if len(header) - 4*header[3] > 40:
create_fits(outfile, header, data, keys, OS, mapno=mapno, sidpar=True)
print mapno-1, "maps converted to FITS"
#except:
else:
if mapno == 1:
print "unknown data type"
sys.exit(1)
if __name__ == '__main__':
main()