def test_6grps_satat6_crat1(setup_cube):
ngroups = 6
#crmag = 1000
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=5 *
np.sqrt(2))
nframes = 1
data[0, 0, 100, 100] = 10000
data[0, 1, 100, 100] = 35000 #CR
data[0, 2, 100, 100] = 40005
data[0, 3, 100, 100] = 45029
data[0, 4, 100, 100] = 50014
data[0, 5, 100, 101] = 61000
data[0, 0, 100, 101] = 10000
data[0, 1, 100, 101] = 15001
data[0, 2, 100, 101] = 20003
data[0, 3, 100, 101] = 25006
data[0, 4, 100, 101] = 30010
data[0, 5, 100, 101] = 35015
gdq[0, 5, 100, 100] = dqflags.group['SATURATED']
find_crs(data, gdq, read_noise, rej_threshold, nframes)
# assert(4 == np.max(gdq)) # no CR was found
assert (np.array_equal(
[0, dqflags.group['JUMP_DET'], 0, 0, 0, dqflags.group['SATURATED']],
gdq[0, :, 100, 100]))
def test_6grps_satat6_crat1_flagadjpixels(setup_cube):
ngroups = 6
#crmag = 1000
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2))
nframes=1
data[0, 0, 100, 100] = 10000
data[0, 1, 100, 100] = 35000 #CR
data[0, 2, 100, 100] = 40005
data[0, 3, 100, 100] = 45029
data[0, 4, 100, 100] = 50014
data[0, 5, 100, 101] = 61000
data[0, 0, 100, 101] = 10000
data[0, 1, 100, 101] = 15001
data[0, 2, 100, 101] = 20003
data[0, 3, 100, 101] = 25006
data[0, 4, 100, 101] = 30010
data[0, 5, 100, 101] = 35015
gdq[0, 5, 100, 100] = dqflags.group['SATURATED']
find_crs(data, gdq, read_noise, rej_threshold, nframes)
# assert(4 == np.max(gdq)) # no CR was found
assert (np.array_equal([0, dqflags.group['JUMP_DET'], 0,0,0, dqflags.group['SATURATED']], gdq[0, :, 100, 100]))
assert (np.array_equal([0, dqflags.group['JUMP_DET'], 0, 0, 0, dqflags.group['SATURATED']], gdq[0, :, 99, 100]))
assert (np.array_equal([0, dqflags.group['JUMP_DET'], 0, 0, 0, dqflags.group['SATURATED']], gdq[0, :, 101, 100]))
assert (np.array_equal([0, dqflags.group['JUMP_DET'], 0, 0, 0, dqflags.group['SATURATED']], gdq[0, :, 100, 99]))
assert (np.array_equal([0, dqflags.group['JUMP_DET'], 0, 0, 0, dqflags.group['SATURATED']], gdq[0, :, 100, 101]))
def test_4grps_cr2_noflux(setup_cube):
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(gdq)) #a CR was found
assert(1 == np.argmax(gdq[0,:,100,100])) #find the CR in the expected group
def test_4grps_cr2_noflux(setup_cube):
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert (4 == np.max(gdq)) #a CR was found
assert (1 == np.argmax(gdq[0, :, 100,
100])) #find the CR in the expected group
def test_10grps_cr2_3sigma_2frames_nocr(setup_cube):
ngroups = 10
crmag=15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=5*np.sqrt(2))
nframes = 2
data[0, 0, 100, 100] = 0
data[0, 1:11, 100, 100] = crmag
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(0 == np.max(gdq)) # a CR was found
assert(np.array_equal([0, 0, 0, 0, 0, 0, 0, 0, 0, 0] , gdq[0, :, 100, 100]))
def test_10grps_cr2_gt3sigma(setup_cube):
ngroups = 10
crmag=16
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=5)
nframes = 1
data[0, 0, 100, 100] = 0
data[0, 1:11, 100, 100] = crmag
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(gdq)) # a CR was found
assert(np.array_equal([0, 4, 0, 0, 0,0,0,0,0,0] , gdq[0, :, 100, 100]))
def test_10grps_nocr_2pixels_sigma0(setup_cube):
ngroups = 10
crmag = 15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2))
nframes=1
data[0, 0, 100, 100] = crmag
data[0, 1:11, 100, 100] = crmag
read_noise[500, 500] = 0.0
read_noise[600, 600] = 0.0
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(0 == np.max(gdq)) # no CR was found
def test_10grps_cr2_3sigma_nocr(setup_cube):
ngroups = 10
crmag = 15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=5)
nframes = 1
data[0, 0, 100, 100] = 0
data[0, 1:11, 100, 100] = crmag
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert (0 == np.max(gdq)) # a CR was found
assert (np.array_equal([0, 0, 0, 0, 0, 0, 0, 0, 0, 0], gdq[0, :, 100,
100]))
def test_6grps_twocrs_2nd_5th_nframes2(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=10*np.sqrt(2))
nframes=2
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 60
data[0, 4, 100, 100] = 115
data[0, 5, 100, 100] = 115
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(gdq)) #a CR was found
assert(np.array_equal([0,4,0,0,4,0] , gdq[0, :, 100, 100]) )
def test_10grps_cr2_gt3sigma_2frames(setup_cube):
ngroups = 10
crmag = 16
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=5 *
np.sqrt(2))
nframes = 2
data[0, 0, 100, 100] = 0
data[0, 1:11, 100, 100] = crmag
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert (4 == np.max(gdq)) # a CR was found
assert (np.array_equal([0, 4, 0, 0, 0, 0, 0, 0, 0, 0], gdq[0, :, 100,
100]))
def test_10grps_nocr_2pixels_sigma0(setup_cube):
ngroups = 10
crmag = 15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=5 *
np.sqrt(2))
nframes = 1
data[0, 0, 100, 100] = crmag
data[0, 1:11, 100, 100] = crmag
read_noise[500, 500] = 0.0
read_noise[600, 600] = 0.0
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert (0 == np.max(gdq)) # no CR was found
def test_6grps_twocrs_2nd_5th_nframes2(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=10 *
np.sqrt(2))
nframes = 2
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 60
data[0, 4, 100, 100] = 115
data[0, 5, 100, 100] = 115
find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert (4 == np.max(gdq)) #a CR was found
assert (np.array_equal([0, 4, 0, 0, 4, 0], gdq[0, :, 100, 100]))
def test_5grps_satat4_crat3(setup_cube):
ngroups = 5
#crmag = 1000
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2))
nframes=1
data[0, 0, 100, 100] = 10000
data[0, 1, 100, 100] = 30000
data[0, 2, 100, 100] = 60000
data[0, 3, 100, 100] = 61000
data[0, 4, 100, 100] = 61000
gdq[0, 3, 100, 100] = dqflags.group['SATURATED']
gdq[0, 4, 100, 100] = dqflags.group['SATURATED']
find_crs(data, gdq, read_noise, rej_threshold, nframes)
# assert(4 == np.max(gdq)) # no CR was found
assert (np.array_equal([0, 0, dqflags.group['JUMP_DET'],dqflags.group['SATURATED'], dqflags.group['SATURATED']], gdq[0, :, 100, 100]))
def test_nocrs_noflux(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise,
rej_threshold, nframes,
False, 200, 10)
assert 0 == np.max(out_gdq) # no CR found
def test_10grps_satat8_crsat3and6(setup_cube):
ngroups = 10
# crmag = 1000
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=5 *
np.sqrt(2))
nframes = 1
data[0, 0, 100, 100] = 0
data[0, 1, 100, 100] = 5000
data[0, 2, 100, 100] = 15000 # CR
data[0, 3, 100, 100] = 20000
data[0, 4, 100, 100] = 25000
data[0, 5, 100, 100] = 40000 # CR
data[0, 6, 100, 100] = 45000
data[0, 7:11, 100, 100] = 61000
gdq[0, 7:11, 100, 100] = dqflags.group['SATURATED']
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise,
rej_threshold, nframes,
False, 200, 10)
# assert(4 == np.max(out_gdq)) # no CR was found
assert np.array_equal([
0, 0, dqflags.group['JUMP_DET'], 0, 0, dqflags.group['JUMP_DET'], 0,
dqflags.group['SATURATED'], dqflags.group['SATURATED'],
dqflags.group['SATURATED']
], out_gdq[0, :, 100, 100])
def test_first_last_group(setup_cube):
ngroups = 7
nframes = 1
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=25.0)
# set up the data so that if the first and last group are used in jump
# detection it would cause a jump to be detected between group 1-2
# and group 6-7. Add a jump between 3 and 4 just to make sure jump detection is working
# set group 1 to be 10,000
data[0, 0, 100, 100] = 10000.0
# set groups 1, 2 - to be around 30,000
data[0, 1, 100, 100] = 30000.0
data[0, 2, 100, 100] = 30020.0
# set up a jump to make sure it is detected
data[0, 3, 100, 100] = 40000.0
data[0, 4, 100, 100] = 40020.0
data[0, 5, 100, 100] = 40040.0
# set group 6 to be 50,000
data[0, 6, 100, 100] = 50000.0
gdq[0, 0, 100, 100] = dqflags.group['DO_NOT_USE']
gdq[0, 6, 100, 100] = dqflags.group['DO_NOT_USE']
outgdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert outgdq[0, 0, 100, 100] == dqflags.group['DO_NOT_USE']
assert outgdq[0, 6, 100, 100] == dqflags.group['DO_NOT_USE']
assert outgdq[0, 3, 100, 100] == dqflags.group['JUMP_DET']
def test_6grps_different_valid_grps_each_pixel(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2), nrows=3, ncols=2)
nframes = 1
# pixel 0, 0 no crs
data[0, 0, 0, 0] = 0
data[0, 1, 0, 0] = 10
data[0, 2, 0, 0] = 20
data[0, 3, 0, 0] = 25
data[0, 4, 0, 0] = 35
data[0, 5, 0, 0] = 42
# pixel 0, 1 one crs grp 3
data[0, 0, 0, 1] = 0
data[0, 1, 0, 1] = 10
data[0, 2, 0, 1] = 20
data[0, 3, 0, 1] = 2500
data[0, 4, 0, 1] = 2510
data[0, 5, 0, 1] = 2522
# pixel 1, 0 one cr, two last grps saturated
data[0, 0, 1, 0] = 0
data[0, 1, 1, 0] = 10
data[0, 2, 1, 0] = 20
data[0, 3, 1, 0] = 2500
data[0, 4, 1, 0] = 2510
data[0, 5, 1, 0] = 1522
gdq[0, 4, 1, 0] = dqflags.group['SATURATED']
gdq[0, 5, 1, 0] = dqflags.group['SATURATED']
# pixel 1, 1 two crs
data[0, 0, 1, 1] = 0
data[0, 1, 1, 1] = 1000
data[0, 2, 1, 1] = 1100
data[0, 3, 1, 1] = 10000
data[0, 4, 1, 1] = 10102
data[0, 5, 1, 1] = 10208
# pixel 2, 0 one cr, three last groups saturated
data[0, 0, 2, 0] = 0
data[0, 1, 2, 0] = 1000
data[0, 2, 2, 0] = 10100
data[0, 3, 2, 0] = 10000
data[0, 4, 2, 0] = 10102
data[0, 5, 2, 0] = 10208
gdq[0, 3, 2, 0] = dqflags.group['SATURATED']
gdq[0, 4, 2, 0] = dqflags.group['SATURATED']
gdq[0, 5, 2, 0] = dqflags.group['SATURATED']
# pixel 2, 1 two crs, last group saturated
data[0, 0, 2, 1] = 0
data[0, 1, 2, 1] = 10000
data[0, 2, 2, 1] = 20100
data[0, 3, 2, 1] = 20200
data[0, 4, 2, 1] = 20302
data[0, 5, 2, 1] = 10208
gdq[0, 5, 2, 1] = dqflags.group['SATURATED']
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes, False, 200, 10)
assert np.array_equal([0, 0, 0, 0, 0, 0], out_gdq[0, :, 0, 0])
assert np.array_equal([0, 0, 0, 4, 0, 0], out_gdq[0, :, 0, 1])
assert np.array_equal([0, 0, 0, 4, 2, 2], out_gdq[0, :, 1, 0])
assert np.array_equal([0, 4, 0, 4, 0, 0], out_gdq[0, :, 1, 1])
assert np.array_equal([0, 0, 4, 2, 2, 2], out_gdq[0, :, 2, 0])
assert np.array_equal([0, 4, 4, 0, 0, 2], out_gdq[0, :, 2, 1])
def test_10grps_satat8_crsat3and6(setup_cube):
ngroups = 10
#crmag = 1000
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2))
nframes=1
data[0, 0, 100, 100] = 0
data[0, 1, 100, 100] = 5000
data[0, 2, 100, 100] = 15000 #CR
data[0, 3, 100, 100] = 20000
data[0, 4, 100, 100] = 25000
data[0, 5, 100, 100] = 40000 #CR
data[0, 6, 100, 100] = 45000
data[0, 7:11, 100, 100] = 61000
gdq[0, 7:11, 100, 100] = dqflags.group['SATURATED']
find_crs(data, gdq, read_noise, rej_threshold, nframes)
# assert(4 == np.max(gdq)) # no CR was found
assert (np.array_equal([0, 0, dqflags.group['JUMP_DET'], 0, 0, dqflags.group['JUMP_DET'],
0,dqflags.group['SATURATED'],dqflags.group['SATURATED'],dqflags.group['SATURATED']], gdq[0, :, 100, 100]))
def test_5grps_cr2_negjumpflux(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 1000.0
data[0, 1:6, 100, 100] = 10
median_diff, out_gdq =find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(out_gdq)) #a CR was found
assert(1 == np.argmax(out_gdq[0,:,100,100])) #find the CR in the expected group
def test_3grps_cr2_noflux(setup_cube):
ngroups = 3
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 4 == np.max(out_gdq) # a CR was found
assert np.array_equal([0, 4, 0], out_gdq[0, :, 100, 100])
def test_3grps_cr2_noflux(setup_cube):
ngroups = 3
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
median_diff, out_gdq = find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(out_gdq)) # a CR was found
# assert(1,np.argmax(out_gdq[0,:,100,100])) #find the CR in the expected group
assert(np.array_equal([0, 4, 0], out_gdq[0, :, 100, 100]))
def test_10grps_cr2_3sigma_2frames_nocr(setup_cube):
ngroups = 10
crmag = 15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=5*np.sqrt(2))
nframes = 2
data[0, 0, 100, 100] = 0
data[0, 1:11, 100, 100] = crmag
median_diff, out_gdq = find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(0 == np.max(out_gdq)) # a CR was found
assert(np.array_equal([0, 0, 0, 0, 0, 0, 0, 0, 0, 0] , out_gdq[0, :, 100, 100]))
def test_5grps_cr2_negjumpflux(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 1000.0
data[0, 1:6, 100, 100] = 10
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 4 == np.max(out_gdq) # a CR was found
assert 1 == np.argmax(out_gdq[0, :, 100, 100]) # find the CR in the expected group
def test_4grps_cr2_noflux(setup_cube):
# This test should fail because with 2 CRs and only 4 groups we cannot detect the jump
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 4 == np.max(out_gdq) # a CR was found
assert 1 == np.argmax(out_gdq[0, :, 100, 100]) # find the CR in the expected group
def test_4grps_twocrs_2nd_4th(setup_cube):
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes=1
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 115
median_diff, out_gdq = find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(out_gdq)) #a CR was found
assert(np.array_equal([0,4,0,4] , out_gdq[0, :, 100, 100]) )
def test_10grps_cr2_3sigma_2frames_nocr(setup_cube):
ngroups = 10
crmag = 15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2))
nframes = 2
data[0, 0, 100, 100] = 0
data[0, 1:11, 100, 100] = crmag
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 0 == np.max(out_gdq) # a CR was found
assert np.array_equal([0, 0, 0, 0, 0, 0, 0, 0, 0, 0], out_gdq[0, :, 100, 100])
def test_5grps_nocr(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=10)
nframes = 1
data[0, 0, 100, 100] = 0
data[0, 1, 100, 100] = 10
data[0, 2, 100, 100] = 21
data[0, 3, 100, 100] = 33
data[0, 4, 100, 100] = 46
median_diff, out_gdq = find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(11 == median_diff[0, 100, 100])
def test_5grps_satat4_crat3(setup_cube):
ngroups = 5
#crmag = 1000
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,
readnoise=5 *
np.sqrt(2))
nframes = 1
data[0, 0, 100, 100] = 10000
data[0, 1, 100, 100] = 30000
data[0, 2, 100, 100] = 60000
data[0, 3, 100, 100] = 61000
data[0, 4, 100, 100] = 61000
gdq[0, 3, 100, 100] = dqflags.group['SATURATED']
gdq[0, 4, 100, 100] = dqflags.group['SATURATED']
find_crs(data, gdq, read_noise, rej_threshold, nframes)
# assert(4 == np.max(gdq)) # no CR was found
assert (np.array_equal([
0, 0, dqflags.group['JUMP_DET'], dqflags.group['SATURATED'],
dqflags.group['SATURATED']
], gdq[0, :, 100, 100]))
def test_5grps_nocr(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=10)
nframes = 1
data[0, 0, 100, 100] = 0
data[0, 1, 100, 100] = 10
data[0, 2, 100, 100] = 21
data[0, 3, 100, 100] = 33
data[0, 4, 100, 100] = 46
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
assert(11 == median_diff[0, 100, 100])
def test_5grps_2crs(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2), nrows=2, ncols=2)
nframes = 1
data[0, 0, 1, 1] = 0
data[0, 1, 1, 1] = 1000
data[0, 2, 1, 1] = 1100
data[0, 3, 1, 1] = 10000
data[0, 4, 1, 1] = 10102
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes, False, 200, 10)
assert np.array_equal([0, 4, 0, 4, 0], out_gdq[0, :, 1, 1])
def test_5grps_twocrs_2nd_5thbig_nframes2(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=10*np.sqrt(2))
nframes=2
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 60
data[0, 4, 100, 100] = 2115
median_diff, out_gdq = find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(out_gdq)) #a CR was found
assert(np.array_equal([0,4,0,0,4] , out_gdq[0, :, 100, 100]) )
def test_4grps_twocrs_2nd_4th(setup_cube):
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes = 1
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 115
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise,
rej_threshold, nframes,
False, 200, 10)
assert np.max(out_gdq) == 4 # a CR was found
def test_3grps_cr2_noflux(setup_cube):
ngroups = 3
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
print("test data "+repr(data[0,:,100,100]))
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print(repr(gdq[0, :, 100, 100]))
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
assert(4 == np.max(gdq)) #a CR was found
# assert(1,np.argmax(gdq[0,:,100,100])) #find the CR in the expected group
assert(np.array_equal([0, 4, 0], gdq[0, :, 100, 100]))
def test_4grps_twocrs_2nd_4th(setup_cube):
# This test should fail because two jumps with four groups we cannot find the second jump.
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes = 1
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 115
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert np.max(out_gdq) == 4 # a CR was found
def test_5grps_cr2_nframe2(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes=2
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 500
data[0, 2, 100, 100] = 1002
data[0, 3, 100, 100] = 1001
data[0, 4, 100, 100] = 1005
median_diff, out_gdq = find_crs(data, gdq, read_noise, rej_threshold, nframes)
assert(4 == np.max(out_gdq)) #a CR was found
assert(np.array_equal([0,4,4,0,0], out_gdq[0, :, 100, 100]) )
def test_3grps_cr2_noflux(setup_cube):
ngroups = 3
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 10.0
data[0, 1:4, 100, 100] = 1000
print("test data " + repr(data[0, :, 100, 100]))
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print(repr(gdq[0, :, 100, 100]))
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
assert (4 == np.max(gdq)) #a CR was found
# assert(1,np.argmax(gdq[0,:,100,100])) #find the CR in the expected group
assert (np.array_equal([0, 4, 0], gdq[0, :, 100, 100]))
def test_10grps_nocr_2pixels_sigma0(setup_cube):
ngroups = 10
crmag = 15
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2))
nframes = 1
data[0, 0, 100, 100] = crmag
data[0, 1:11, 100, 100] = crmag
read_noise[50, 50] = 0.0
read_noise[60, 60] = 0.0
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 0 == np.max(out_gdq) # no CR was found
def test_5grps_cr2_negslope(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes = 1
data[0, 0, 100, 100] = 100.0
data[0, 1, 100, 100] = 0
data[0, 2, 100, 100] = -200
data[0, 3, 100, 100] = -260
data[0, 4, 100, 100] = -360
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
assert(4 == np.max(gdq)) # a CR was found
assert(np.array_equal([0, 0, 4, 0, 0] , gdq[0, :, 100, 100]))
def test_3grps_1cr(setup_cube):
""""
A test of a three group integration that has a jump in the third group of pixel 1, 1
"""
ngroups = 3
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups, readnoise=5 * np.sqrt(2), nrows=2, ncols=2)
nframes = 1
data[0, 0, 1, 1] = 0
data[0, 1, 1, 1] = 40000
data[0, 2, 1, 1] = 44500
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes, False, 200, 10)
assert np.array_equal([0, 4, 0], out_gdq[0, :, 1, 1])
def test_4grps_twocrs_2nd_4th(setup_cube):
ngroups = 4
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes=1
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 115
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
print(repr(gdq[0, :, 100, 100]))
assert(4 == np.max(gdq)) #a CR was found
assert(np.array_equal([0,4,0,4] , gdq[0, :, 100, 100]) )
def test_5grps_twocrs_2nd_5thbig_nframes2(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups,readnoise=10*np.sqrt(2))
nframes=2
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 60
data[0, 2, 100, 100] = 60
data[0, 3, 100, 100] = 60
data[0, 4, 100, 100] = 2115
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
assert(4 == np.max(gdq)) #a CR was found
assert(np.array_equal([0,4,0,0,4] , gdq[0, :, 100, 100]) )
def test_6grps_negative_differences_zeromedian(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 100
data[0, 1, 100, 100] = 90
data[0, 2, 100, 100] = 95
data[0, 3, 100, 100] = 105
data[0, 4, 100, 100] = 100
data[0, 5, 100, 100] = 100
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 0 == np.max(out_gdq) # no CR was found
def test_5grps_cr2_nframe2(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes = 2
data[0, 0, 100, 100] = 10.0
data[0, 1, 100, 100] = 500
data[0, 2, 100, 100] = 1002
data[0, 3, 100, 100] = 1001
data[0, 4, 100, 100] = 1005
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold, rej_threshold, rej_threshold,
nframes, False, 200, 10)
assert 4 == np.max(out_gdq) # a CR was found
assert np.array_equal([0, 4, 4, 0, 0], out_gdq[0, :, 100, 100])
def test_6grps_negative_differences_zeromedian(setup_cube):
ngroups = 6
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
data[0, 0, 100, 100] = 100
data[0, 1, 100, 100] = 90
data[0, 2, 100, 100] = 95
data[0, 3, 100, 100] = 105
data[0, 4, 100, 100] = 100
data[0, 5, 100, 100] = 100
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print('shape '+str(median_diff.shape))
print('median differences of 100,100 '+str(median_diff[0,100,100]))
assert(0 == np.max(gdq)) #no CR was found
assert(0 == median_diff[0,100,100]) #Median difference is zero
def test_10grps_twocrs_10percenthit(setup_cube):
ngroups = 10
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
nframes=2
data[0:200, 0, 100, 100] = 10.0
data[0:200, 1, 100, 100] = 60
data[0:200, 2, 100, 100] = 60
data[0:200, 3, 100, 100] = 60
data[0:200, 4, 100, 100] = 60
data[0:200, 5, 100, 100] = 60
data[0:200, 6, 100, 100] = 60
data[0:200, 7, 100, 100] = 2115
data[0:200, 8, 100, 100] = 2115
data[0:200, 9, 100, 100] = 2115
median_diff = find_crs(data, gdq, read_noise, rej_threshold, nframes)
print("calculated median diff of pixel is ", median_diff[0, 100, 100])
assert(4 == np.max(gdq)) #a CR was found
assert(np.array_equal([0,4,0,0,0,0,0,4,0,0] , gdq[0, :, 100, 100]) )
def test_nocrs_noflux(setup_cube):
ngroups = 5
data, gdq, nframes, read_noise, rej_threshold = setup_cube(ngroups)
assert(0 == np.max(find_crs(data, gdq, read_noise, rej_threshold, nframes))) # no CR found
