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resolve_parser.py
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resolve_parser.py
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# -*- coding: utf-8 -*-
"""
parser.py
Written by Quirin Kronseder and Henrik Junklewitz.
Resolve.py defines the main function that runs RESOLVE on a measurement
set with radio interferometric data.
Copyright 2016 Henrik Junklewitz and Quirin Kronseder
RESOLVE is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
RESOLVE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with RESOLVE. If not, see <http://www.gnu.org/licenses/>.
"""
import sys
import csv
import numpy as np
import datetime
import pyfits
import utility_functions as utils
#---------------- Parsing runfile and parameters ------------------------------
def get_parameter_and_runscript_from_runfile(runfile):
actions = []
actions_buffer = []
parameter_file = []
parameter_file_buffer = []
parameter_changes = []
parameters = dict()
""" parse parameter file."""
path = './configuration'
# get Runfile
try:
reader = csv.reader(open(path+'/runfiles/'+runfile, 'rb'),\
delimiter=" ", skipinitialspace=True)
for row in reader:
if len(row) >= 3:
for i in range(2,len(row)):
row.remove(row[i])
if len(row) == 1:
actions_buffer.append(row[0])
parameter_file_buffer.append('')
if len(row) == 2:
actions_buffer.append(row[0])
parameter_file_buffer.append(row[1])
i = 0
stop = 0
go = 0
start = 0
times = 0
for i in range(len(actions_buffer)):
if str.isdigit(actions_buffer[i]):
start = min(i+1,len(actions_buffer)-1)#i + 1
for go in range(start,len(actions_buffer)):
if str.isdigit(actions_buffer[go]):
stop = go
break
elif go == len(actions_buffer)-1:
stop = go+1
break
for times in range(0,int(actions_buffer[start-1])):
if start == stop:
actions.append(actions_buffer[start])
parameter_file.append(parameter_file_buffer[start])
else:
for go in range(start,stop):
actions.append(actions_buffer[go])
parameter_file.append(parameter_file_buffer[go])
start = 0
stop = 0
# read parameter changes
for t in range(len(parameter_file)):
if parameter_file[t] != '':
reader = csv.reader(open(path+'/parameters/'\
+ parameter_file[t], 'rb'), delimiter=" ",\
skipinitialspace=True)
for row in reader:
if len(row) >= 4:
if row[1] == 'freq':
parameters[row[1]] = \
[int(row[2]),int(row[3])]
else:
for ii in range(3,len(row)):
row.remove(row[ii])
elif len(row) == 3:
if row[0].lower() == 'boolean':
parameters[row[1]] = utils.str2bool(row[2])
elif row[0].lower() == 'float':
parameters[row[1]] = float(row[2])
elif row[0].lower() == 'integer':
parameters[row[1]] = int(row[2])
elif row[0].lower() == 'string':
if row[2] == 'False':
parameters[row[1]] = ''
else:
parameters[row[1]] = str(row[2])
parameter_changes.append(parameters.copy())
else:
parameter_changes.append('')
print '#################################'
return actions, parameter_changes
except IOError, e:
print e.errno
print e
def load_default_parameters ():
param = dict()
try:
reader = csv.reader(open('./configuration/parameters/'\
+ 'default_parameters.cfg', 'rb'), delimiter=" ",\
skipinitialspace=True)
for row in reader:
if len(row) >= 4:
if row[1] == 'freq':
param[row[1]] = [int(row[2]),int(row[3])]
else:
for i in range(3,len(row)):
row.remove(row[i])
elif len(row) <= 2 and len(row) > 0:
print 'Default parameter file corupted!'
print './configuration/parameters/default_parameters.cfg'
# print row
break
elif len(row) == 3:
if row[0].lower() == 'boolean':
param[row[1]] = utils.str2bool(row[2])
elif row[0].lower() == 'float':
param[row[1]] = float(row[2])
elif row[0].lower() == 'integer':
param[row[1]] = int(row[2])
elif row[0].lower() == 'string':
if row[2] == 'False':
param[row[1]] = ''
else:
param[row[1]] = str(row[2])
return param
except IOError, e:
print e.errno
print e
#------------------------ Internal parameter class ----------------------------
def update_parameterclass(params, changep):
for key in changep:
if key in dir(params):
setattr(params,key,changep[key])
else:
raise IOError('Wrong parameter definition from config files')
return params
class parameters(object):
"""
Defines a parameter class for all parameters that are vital to controlling
basic functionality of the code. Some are even mandatory and given by
the user. Performs checks on default arguments with hard-coded default
values.
"""
def __init__(self, params_dict, datafn, imsize, cellsize, save,
python_casacore, verbosity):
# mandatory parameters
self.datafn = datafn
self.imsize = int(imsize)
self.cellsize = float(cellsize)
self.save = save
self.python_casacore = python_casacore
self.verbosity = verbosity
# read dict into parameter class
for key in params_dict:
setattr(self,key,params_dict[key])
#----------------------- Code I/O ---------------------------------------------
def write_output_to_fits(m, params, notifier='',mode='I',u=None):
"""
"""
hdu_main = pyfits.PrimaryHDU(utils.convert_RES_to_CASA(m,FITS=True))
try:
generate_fitsheader(hdu_main, params)
except:
print "Warning: There was a problem generating the FITS header, no " + \
"header information stored!"
print "Unexpected error:", sys.exc_info()[0]
hdu_list = pyfits.HDUList([hdu_main])
if mode == 'I':
hdu_list.writeto('resolve_output_' + str(params.save) +\
'/' + str(params.save) + '_' + 'expm' + str(notifier) + '.fits', clobber=True)
elif mode == 'I_u':
hdu_list.writeto('resolve_output_' + str(params.save) +\
'/' + str(params.save) + '_' + 'expu' + str(notifier) + '.fits', clobber=True)
elif mode == 'I_mu':
hdu_list.writeto('resolve_output_' + str(params.save) +\
'/' + str(params.save) + '_' + 'expmu' + str(notifier) + '.fits', clobber=True)
else:
hdu_list.writeto('resolve_output_' + str(params.save) +\
'/' + str(params.save) + '_' + 'a' + str(notifier) + '.fits', clobber=True)
def generate_fitsheader(hdu, params):
"""
"""
today = datetime.datetime.today()
#hdu.header = inhead.copy()
hdu.header.set('ORIGIN', 'resolve.py', 'Origin of the data set')
hdu.header.set('DATE', str(today), 'Date when the file was created')
# hdu.header.set('OBJECT', params.summary['name'], 'Name of object')
hdu.header.set('NAXIS', 3,
'Number of axes in the data array, must be 2')
hdu.header.set('BUNIT','JY/PIXEL')
hdu.header.set('BTYPE','Intensity')
hdu.header.set('NAXIS1', params.imsize,
'Length of the RA axis')
hdu.header.set('CTYPE1', 'RA---SIN', 'Axis type')
hdu.header.set('CUNIT1', 'deg', 'Axis units')
# In FITS, the first pixel is 1, not 0!!!
hdu.header.set('CRPIX1', params.imsize/2, 'Reference pixel')
hdu.header.set('CRVAL1', params.summary['field_0']['direction']\
['m0']['value'] * 57.2958, 'Reference value')
hdu.header.set('CDELT1', -1 * params.cellsize * 57.2958, 'Size of pixel bin')
hdu.header.set('NAXIS2', params.imsize,
'Length of the RA axis')
hdu.header.set('CTYPE2', 'DEC--SIN', 'Axis type')
hdu.header.set('CUNIT2', 'deg', 'Axis units')
# In FITS, the first pixel is 1, not 0!!!
hdu.header.set('CRPIX2', params.imsize/2, 'Reference pixel')
hdu.header.set('CRVAL2', params.summary['field_0']['direction']\
['m1']['value'] * 57.2958, 'Reference value')
hdu.header.set('CDELT2', params.cellsize * 57.2958, 'Size of pixel bin')
if (params.summary['field_0']['direction']['refer'] == '1950' or \
params.summary['field_0']['direction']['refer'] == '1950_VLA'or \
params.summary['field_0']['direction']['refer'] == 'B1950' or \
params.summary['field_0']['direction']['refer'] == 'B1950_VLA'):
hdu.header.set('EQUINOX', 1950)
hdhdu.header.set('RADESYS', 'FK4')
elif (params.summary['field_0']['direction']['refer'] == '2000' or \
params.summary['field_0']['direction']['refer'] == 'J2000'):
hdu.header.set('EQUINOX', 2000)
hdhdu.header.set('RADESYS', 'FK5')
if params.freq == 'wideband':
raise NotImplementedError('No widefield FITS-cube output yet.')
else:
hdu.header.set('NAXIS3', 1, 'Length of frequency axis')
hdu.header.set('CTYPE3', 'FREQ', 'Axis type')
hdu.header.set('CRVAL3', params.freqs[params.freq[0],params.freq[1]]\
, 'Frequency Reference value')
hdu.header.add_history('RESOLVE: Reconstruction performed by ' +
'resolve.py.')
hdu.header.__delitem__('NAXIS4')
hdu.header.__delitem__('CTYPE4')
hdu.header.__delitem__('CRVAL4')
hdu.header.__delitem__('CRPIX4')
hdu.header.__delitem__('CDELT4')
hdu.header.__delitem__('CUNIT4')