########################################################################3
# imcontsub_test.py
#
#
# Copyright (C) 2008, 2009
# Associated Universities, Inc. Washington DC, USA.
#
# This scripts free software; you can redistribute it and/or modify it
# under the terms of the GNU Library General Public License as published by
# the Free Software Foundation; either version 2 of the License, or (at your
# option) any later version.
#
# This library 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 Library General Public
# License for more details.
#
# You should have received a copy of the GNU Library General Public License
# along with this library; if not, write to the Free Software Foundation,
# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
#
# Correspondence concerning AIPS++ should be adressed as follows:
# Internet email: aips2-request@nrao.edu.
# Postal address: AIPS++ Project Office
# National Radio Astronomy Observatory
# 520 Edgemont Road
# Charlottesville, VA 22903-2475 USA
#
# <author>
# Shannon Jaeger (University of Calgary)
# </author>
#
# <summary>
# Test suite for the CASA imcontsub Task
# </summary>
#
# <reviewed reviwer="" date="" tests="" demos="">
# </reviewed
#
# <etymology>
# imcontsub_test stands for image momemnts test
# </etymology>
#
# <synopsis>
# imcontsub_test.py is a Python script that tests the correctness
# of the imcontsub task in CASA.
#
# The tests include:
# 1. Incorrect input for each paramter. Incorrect input includes
# one input of the incorrect data type, out-of-bounds (where
# applicable, and correct data type but non-sensical.
# 2. A set of sample continuum subtractions with expected
# output
# 3. Calculating one example for each allowed fitorder
# 4. Continuum subtraction with region selection on the sky,
# channels, and stokes values, as well as using an input
# region file.
#
# In the imcontsub task a specified continuum channel is subtracted
# from spectral line data.
#
# The expected input is a spectral line image. Both a continuum
# image and a continuum-subtracted spectral line are created as
# output, as long as the user has provided filenames for them.
#
# By default the continuum subtraction is applied to the whole
# image, however, if a region file is given and/or the user specifies
# a box range, channels, or stokes values then the subtraction is
# performed on this portion of the image only.
#
# </synopsis>
#
# <example>
# # This test was designed to run in the CASA unit test system.
# # This example shows who to run it manually from outside casapy.
# casapy -c runUnitTest test_imcontsub
#
# or
#
# # This example shows who to run it manually from with casapy.
# runUnitTest.main(['imcontsub_test'])
#
# </example>
#
# <motivation>
# To provide a test standard to the imcontsub task to try and ensure
# coding changes do not break the
# </motivation>
#
# <todo>
# Almost everything!
#
# imcontsub doesn't return anything currently on success or failure.
# If this changes the tests will need to change to check for this.
# The basic design of the tests is based on the immoments test which
# returns an image tool upon success.
# </todo>
#import random
from __future__ import absolute_import
import os
import shutil
import unittest
from casatasks.private.casa_transition import is_CASA6
if is_CASA6:
from casatools import ctsys, image
from casatasks import casalog, imcontsub, immath
_ia = image( )
datapath = ctsys.resolve('unittest/imcontsub/')
else:
import casac
from tasks import *
from taskinit import *
_ia = iatool( )
datapath = os.environ.get('CASAPATH').split()[0]+'/casatestdata/unittest/imcontsub/'
# Input files
mylist = ['g192_a2.image', 'g192_a2.image-2.rgn',
'g192_a2.contfree', 'g192_a2.cont',
'g192_a2.contfree.order1', 'g192_a2.cont.order1',
'g192_a2.contfree.order2', 'g192_a2.cont.order2',
'boxychans_cont.im', 'boxychans_line.im']
# Tests the correctness of the imcontsub task in CASA including:
# 1. Incorrect input for each paramter. Incorrect input includes
# one input of the incorrect data type, out-of-bounds (where
# applicable, and correct data type but non-sensical.
# 2. Doing a couple continuum subtractions checking the
# results with previous results.
# 3. Doing continuum subtraction with fitorder from 1 to ??
# and verifying the results.
# 4. Doing continuum subtraiong with region selection on the sky,
# channels, and stokes values, as well as using an input
# region file.
#
# Data used for this test includes:
# 1. g192_a2.image
class imcontsub_test(unittest.TestCase):
def try_imcs(self, *args, **kwargs):
passes = False
# CASA6 tasks throw exceptions, CASA5 tasks return False
# this test is used for expected errors
try:
results = imcontsub(*args, **kwargs)
if not results:
passes = True
except:
passes = True
self.assertTrue(passes)
def setUp(self):
if(os.path.exists(mylist[0])):
for f in mylist:
os.system('rm -rf ' +f)
for f in mylist:
os.system('cp -RH '+os.path.join(datapath,f)+' '+f)
def tearDown(self):
for f in mylist:
os.system('rm -rf ' +f)
os.system('rm -rf cont_*')
os.system('rm -rf input_test*')
os.system('rm -rf fit_test*')
os.system('rm -rf line_*')
if os.path.exists( 'garbage.rgn' ):
os.remove('garbage.rgn')
####################################################################
# Incorrect inputs to parameters. The parameters are:
# imagename
# linefile
# contfile
# fitorder
# region
# box
# chans
# stokes
#
# Returns True if successful, and False if it has failed.
####################################################################
def test_bad_imagename(self):
"""Test bad image name throws exception"""
self.try_imcs( 'g192', contfile='input_test_cont1', linefile='input_test_line1' )
def test_bad_linefile(self):
""" Test bad line file name fails"""
# FIXME shouldn't a bad linefile name throw an exception?
filename = 'input_test_line1'
myfile = open(filename, mode="w")
myfile.write("x")
myfile.close()
with self.assertRaises(ValueError):
imcontsub( 'g192_a2.image', linefile=filename )
def test_bad_contfile(self):
""" Test bad continuum file name fails"""
# FIXME shouldn't a bad linefile name throw an exception?
filename = 'input_test_cont'
myfile = open(filename, mode="w")
myfile.write("x")
myfile.close()
with self.assertRaises(ValueError):
imcontsub( 'g192_a2.image', contfile=filename )
def test_bad_fitorder(self):
"""Test bad fitorder fails"""
self.try_imcs( 'g192_a2.image', fitorder=-1, contfile='moment_test' )
self.try_imcs( 'g192_a2.image', fitorder=-2.3, contfile='moment_test' )
def test_bad_region(self):
""" Test bad region parameter fails"""
self.try_imcs( 'g192_a2.image', region=7 )
filename = os.getcwd()+'/garbage.rgn'
self.try_imcs( 'g192_a2.image', region=filename)
fp=open( filename, 'w' )
fp.writelines('This file does NOT contain a valid CASA region specification\n')
fp.close()
self.try_imcs( 'g192_a2.image', region=filename)
def test_bad_chans(self):
"""Test bad chans parameter causes failure"""
self.try_imcs( 'g192_a2.image', chans='-5' )
self.try_imcs( 'g192_a2.image', chans='-2' )
self.try_imcs( 'g192_a2.image', chans='-18' )
self.try_imcs( 'g192_a2.image', chans='45' )
self.try_imcs( 'g192_a2.image', chans='40' )
def test_bad_box(self):
"""Test bad box parameter causes failure"""
self.try_imcs( 'g192_a2.image', box='-3,0,511,511' )
self.try_imcs( 'g192_a2.image', box='0,-3,511,511' )
self.try_imcs( 'g192_a2.image', box='-2,0,511,511' )
self.try_imcs( 'g192_a2.image', box='0,-2,511,511' )
self.try_imcs( 'g192_a2.image', box='0,0,512,511' )
self.try_imcs( 'g192_a2.image', box='0,0,511,512' )
self.try_imcs( 'g192_a2.image', box='0, 0,525,511' )
self.try_imcs( 'g192_a2.image', box='0,0,511,525' )
def test_bad_stokes(self):
"""Test bad stokes parameter causes failure"""
self.try_imcs( 'g192_a2.image', stokes='Q' )
self.try_imcs( 'g192_a2.image', stokes='yellow' )
## ####################################################################
## # Continuum subtraction correctness test.
## #
## # This test subtacts the continuum from the g192 data file
## # and compares the results (both continuum and spectral line
## # with subtracted continuum files) with pervious results.
## #
## # Random values are selected in the files and compared.
## # FIXME compare the entire arrays, not bloody random values
## # FIXED - replacing it with the equivalent but better test_fitorder(0)
## # sped the suite up from 1847s to 1194s on faraday.cv.nrao.edu.
## #
## # Returns True if successful, and False if it has failed.
## ####################################################################
## def test_continuum(self):
## '''Imcontsub: Testing continuum sub correctness'''
## retValue = {'success': True, 'msgs': "", 'error_msgs': '' }
## casalog.post( "Starting imcontsub CONTINUUM SUB CORRECTNESS tests.", 'NORMAL2' )
## try:
## results=imcontsub( 'g192_a2.image', fitorder=0, contfile='cont_test_cont1', linefile='cont_test_line1' )
## except Exception, err:
## retValue['success']=False
## retValue['error_msgs']=retValue['error_msgs']\
## +"\nError: Unable to subtract continuum with a fit order of 0 "\
## +"\n\t REULTS: "+str(results)
## else:
## if ( not os.path.exists( 'cont_test_cont1' ) or not os.path.exists( 'cont_test_line1' ) or not results ):
## retValue['success']=False
## retValue['error_msgs']=retValue['error_msgs']\
## +"\nError: continuum 3 output files were NOT created."
## else:
## # Now that we know something has been done lets check some values
## # with previously created files to see if the values are the same.
## # We randomly pick 50 points (almost 10%)
## # FIXME lovely, yes let's pick random values to make sure any failures
## # cannot easily be reproduced, ugh
## for count in range(0,50):
## x = random.randint(0,511)
## y = random.randint(0,511)
## box=str(x)+','+str(y)+','+str(x)+','+str(y)
## chan = str(random.randint(0,39))
## line_prev_value={}
## line_cur_value={'empty':''}
## try:
## line_prev_value = imval( 'g192_a2.contfree', box=box, chans=chan, stokes='I' )
## line_cur_value = imval( 'cont_test_line1', box=box, chans=chan, stokes='I' )
## except:
## retValue['success']=False
## retValue['error_msgs']=retValue['error_msgs']\
## +"\nError: Unable to compare spectral line files."
## else:
## #print "Spec line prev value: ", line_prev_value
## #print "spec line current value: ", line_cur_value
## casalog.post( "*** line_prev_value " + str(line_prev_value), 'WARN')
## casalog.post( "*** line_cur_value " + str(line_cur_value), 'WARN')
## if ( (line_prev_value['data'] != line_cur_value['data']).any() ):
## retValue['success'] = False
## retValue['error_msgs'] = '\nError: spectral line value differs with '\
## + "previously calculated value at: "\
## + "\t["+str(x)+','+str(y)+','+chan+',I].'\
## + "\tvalues are "+str(line_prev_value)+" and "+str(line_cur_value)
## try:
## cont_prev_value = imval( 'g192_a2.cont', box=box, chans=chan, stokes='I' )
## cont_cur_value = imval( 'cont_test_cont1', box=box, chans=chan, stokes='I' )
## except:
## retValue['success']=False
## retValue['error_msgs']=retValue['error_msgs']\
## +"\nError: Unable to compare continuum files."
## else:
## #print "Continuum prev value: ", cont_prev_value
## #print "Continuum current value: ", cont_cur_value
## if ( (cont_prev_value['data'] != cont_cur_value['data']).any() ):
## retValue['success'] = False
## retValue['error_msgs'] = '\nError: continuum value differs with '\
## + "previously calculated value at: "\
## + "\t["+str(x)+','+str(y)+','+chan+',I].'
## #+ "\tvalues are "+str(cont_prev_value)+" and "+str(cont_cur_value)
## self.assertTrue(retValue['success'],retValue['error_msgs'])
####################################################################
# Region selection correction test.
#
# This test selects a region for continuum subtraction. Checks
# are done to make sure only the data in the selected region
# changes.
#
# Returns True if successful, and False if it has failed.
####################################################################
# def test_region(self):
# '''Imcontsub: Testing region parameters'''
# retValue = {'success': True, 'msgs': "", 'error_msgs': '' }
# casalog.post( "Starting imcontsub REGION tests.", 'NORMAL2' )
#
# # First step get rid of all the old test files!
# for file in os.listdir( '.' ):
# if file.startswith( 'rgn_test_' ):
# shutil.rmtree( file )
#
#
#
# self.assertTrue(retValue['success'],retValue['error_msgs'])
####################################################################
# Fitorder tests correctness test.
#
# This test subtacts the continuum from the g192 data file
# for fitorder =1 and fitorder=2, note that fitorder=0 is
# tested in the continuum test and valid/invalid inputs to
# the fitorder paramter are tested in the input test.
#
# The results, image file contents, are compared with previously
# created image files.
#
# Returns True if successful, and False if it has failed.
####################################################################
def test_fitorder(self):
'''Imcontsub: testing fitorder correctness'''
retValue = {'success': True, 'msgs': "", 'error_msgs': '' }
casalog.post( "Starting imcontsub INPUT/OUTPUT tests.", 'NORMAL2' )
# First step get rid of all the old test files!
for file in os.listdir( '.' ):
if file.startswith( 'fit_test_' ):
shutil.rmtree( file )
# TODO I'm just fixing the tests here to do something more reasonable since they were broken
# and in bad need of rewriting (see the diff with the previous version before I made these
# edits). This whole test file probably needs to be reviewed but of course time is tight so
# I cannot do that now.
for order in range(2):
contfile='fit_test_cont'+str(order)
linefile='fit_test_line'+str(order)
if order > 0:
oldcontfile='g192_a2.cont.order'+str(order)
oldlinefile='g192_a2.contfree.order'+str(order)
else:
oldcontfile = 'g192_a2.cont'
oldlinefile = 'g192_a2.contfree'
try:
imcontsub('g192_a2.image', fitorder=order, contfile=contfile, linefile=linefile)
except Exception as exc:
retValue['success']=False
retValue['error_msgs']=retValue['error_msgs']\
+"\nError: Unable to subtract continuum with a fit order="+str(order)\
+"\n\t Exception: "+str(exc)
else:
if os.path.isdir(contfile) and os.path.isdir(linefile):
retValue = self.cmp_images(linefile, oldlinefile,
"Order " + str(order) + " line image",
retValue)
retValue = self.cmp_images(contfile, oldcontfile,
"Order " + str(order) + " continuum image",
retValue)
else:
retValue['success']=False
retValue['error_msgs']=retValue['error_msgs']\
+"\nError: output files were NOT created for fitorder="\
+str(order)+" test."
self.assertTrue(retValue['success'], retValue['error_msgs'])
def cmp_images(self, newimg, oldimg, errmsg, retval, tol=1.0e-8):
"""
Check that newimg matches oldimg to within tol.
errmsg is a descriptive label in case there is an error.
retval is updated with the results and returned.
"""
try:
subtract_expr = '(\"' + newimg + '\"-\"' + oldimg + '\")'
output_image = newimg + '.diff'
immath(mode='evalexpr', expr=subtract_expr, outfile=output_image)
_ia.open(output_image)
stats = _ia.statistics()
_ia.close()
absmax = max(abs(stats['min']), abs(stats['max']))
# in an infinite precision utopia, the difference image would be 0, but
# alas, we do not live in such a world yet.
if (absmax > tol):
retval['success'] = False
retval['error_msgs'] += errmsg + ' error: Max residual is ' + str(absmax)
except Exception as err:
retval['success'] = False
retval['error_msgs'] += errmsg + " error: Exception thrown: " + str(err)
return retval
def test_box_and_chans(self):
'''Imcontsub: Testing box and chans'''
retValue = {'success': True, 'msgs': "", 'error_msgs': '' }
#casalog.post("Starting imcontsub box and chans tests.", 'NORMAL2')
oldcfil = 'boxychans_cont.im'
cfil = 'test_' + oldcfil
oldlfil = 'boxychans_line.im'
lfil = 'test_' + oldlfil
bx = [400, 420, 490, 470]
try:
imcontsub('g192_a2.image', fitorder=0, contfile=cfil,
linefile=lfil, box=bx,
chans='32~37') # Purposely one-sided.
except Exception as exc:
retValue['success']=False
retValue['error_msgs'] += "\nError: Unable to subtract continuum with box and chans "\
+"\n\t Exception:: "+str(exc)
else:
if os.path.isdir(cfil) and os.path.isdir(lfil):
retValue = self.cmp_images(lfil, oldlfil,
"box and chans line image", retValue)
retValue = self.cmp_images(cfil, oldcfil,
"box and chans continuum image",
retValue)
else:
retValue['success']=False
retValue['error_msgs'] += "\nError: box and chans output files were NOT created."
self.assertTrue(retValue['success'], retValue['error_msgs'])
def suite():
return [imcontsub_test]
if is_CASA6:
if __name__ == '__main__':
unittest.main()