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moving after_flags parameters to keywords and adding tests
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@karllark
karllark committed Aug 10, 2022
1 parent 651acbd commit b787de4
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Showing 3 changed files with 135 additions and 24 deletions.
26 changes: 14 additions & 12 deletions src/stcal/jump/jump.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,11 @@
def detect_jumps(frames_per_group, data, gdq, pdq, err,
gain_2d, readnoise_2d, rejection_thresh,
three_grp_thresh, four_grp_thresh, max_cores, max_jump_to_flag_neighbors,
min_jump_to_flag_neighbors, flag_4_neighbors,
after_jump_flag_dn1, after_jump_flag_n1,
after_jump_flag_dn2, after_jump_flag_n2,
dqflags):
min_jump_to_flag_neighbors, flag_4_neighbors, dqflags,
after_jump_flag_dn1=0.0,
after_jump_flag_n1=0,
after_jump_flag_dn2=0.0,
after_jump_flag_n2=0):
"""
This is the high-level controlling routine for the jump detection process.
It loads and sets the various input data and parameters needed by each of
Expand Down Expand Up @@ -87,6 +88,10 @@ def detect_jumps(frames_per_group, data, gdq, pdq, err,
if set to True (default is True), it will cause the four perpendicular
neighbors of all detected jumps to also be flagged as a jump.
dqflags: dict
A dictionary with at least the following keywords:
DO_NOT_USE, SATURATED, JUMP_DET, NO_GAIN_VALUE, GOOD
after_jump_flag_dn1 : float
1st flag after jumps with the specified DN jump
to remove the transient seen from the slope calculation
Expand All @@ -103,10 +108,6 @@ def detect_jumps(frames_per_group, data, gdq, pdq, err,
2nd flag n groups after companion threshold
to remove the transient seen from the slope calculation
dqflags: dict
A dictionary with at least the following keywords:
DO_NOT_USE, SATURATED, JUMP_DET, NO_GAIN_VALUE, GOOD
Returns
-------
gdq : int, 4D array
Expand Down Expand Up @@ -166,10 +167,11 @@ def detect_jumps(frames_per_group, data, gdq, pdq, err,
twopt.find_crs(data, gdq, readnoise_2d, rejection_thresh,
three_grp_thresh, four_grp_thresh, frames_per_group,
flag_4_neighbors, max_jump_to_flag_neighbors,
min_jump_to_flag_neighbors,
after_jump_flag_dn1, after_jump_flag_n1,
after_jump_flag_dn2, after_jump_flag_n2,
dqflags)
min_jump_to_flag_neighbors, dqflags,
after_jump_flag_dn1=after_jump_flag_dn1,
after_jump_flag_n1=after_jump_flag_n1,
after_jump_flag_dn2=after_jump_flag_dn2,
after_jump_flag_n2=after_jump_flag_n2)

elapsed = time.time() - start
else:
Expand Down
26 changes: 14 additions & 12 deletions src/stcal/jump/twopoint_difference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,10 +8,12 @@
def find_crs(dataa, group_dq, read_noise, rejection_thresh,
two_diff_rej_thresh, three_diff_rej_thresh, nframes,
flag_4_neighbors, max_jump_to_flag_neighbors,
min_jump_to_flag_neighbors,
after_jump_flag_dn1, after_jump_flag_n1,
after_jump_flag_dn2, after_jump_flag_n2,
dqflags, copy_arrs=True):
min_jump_to_flag_neighbors, dqflags,
after_jump_flag_dn1=0.0,
after_jump_flag_n1=0,
after_jump_flag_dn2=0.0,
after_jump_flag_n2=0,
copy_arrs=True):

"""
Find CRs/Jumps in each integration within the input data array. The input
Expand Down Expand Up @@ -57,6 +59,10 @@ def find_crs(dataa, group_dq, read_noise, rejection_thresh,
neighbors (marginal detections). Any primary jump below this value will
not have its neighbors flagged.
dqflags: dict
A dictionary with at least the following keywords:
DO_NOT_USE, SATURATED, JUMP_DET, NO_GAIN_VALUE, GOOD
after_jump_flag_dn1 : float
1st flag after jumps with the specified DN jump
to remove the transient seen from the slope calculation
Expand All @@ -73,10 +79,6 @@ def find_crs(dataa, group_dq, read_noise, rejection_thresh,
2nd flag n groups after companion threshold
to remove the transient seen from the slope calculation
dqflags: dict
A dictionary with at least the following keywords:
DO_NOT_USE, SATURATED, JUMP_DET, NO_GAIN_VALUE, GOOD
copy_arrs : bool
Flag for making internal copies of the arrays so the input isn't modified,
defaults to True.
Expand Down Expand Up @@ -284,9 +286,9 @@ def find_crs(dataa, group_dq, read_noise, rejection_thresh,
flag_dn_threshold = [after_jump_flag_dn1, after_jump_flag_dn2]
flag_groups = [after_jump_flag_n1, after_jump_flag_n2]
# ensure the smallest threshold is 1st
if flag_dn_threshold[0] > flag_dn_threshold[1]:
flag_dn_threshold = np.flip(flag_dn_threshold)
flag_groups = np.flip(flag_groups)
# if flag_dn_threshold[0] > flag_dn_threshold[1]:
# flag_dn_threshold = np.flip(flag_dn_threshold)
# flag_groups = np.flip(flag_groups)

cr_group, cr_row, cr_col = np.where(np.bitwise_and(gdq[integ], jump_flag))

Expand Down Expand Up @@ -316,7 +318,7 @@ def find_crs(dataa, group_dq, read_noise, rejection_thresh,
row = cr_row[j]
col = cr_col[j]
if dn_jump[group - 1, row, col] >= cthres:
for kk in range(group, min(group + cgroup, ngroups)):
for kk in range(group, min(group + cgroup + 1, ngroups)):
if (gdq[integ, kk, row, col] & sat_flag) == 0:
if (gdq[integ, kk, row, col] & dnu_flag) == 0:
gdq[integ, kk, row, col] =\
Expand Down
107 changes: 107 additions & 0 deletions tests/test_twopoint_difference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -835,6 +835,113 @@ def test_first_last_3group(setup_cube):
assert outgdq[0, 1, 0, 0] == 0


def test_10grps_1cr_afterjump(setup_cube):
ngroups = 10
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
data[0, 5, 100, 100] = 60
data[0, 6, 100, 100] = 1160
data[0, 7, 100, 100] = 1175
data[0, 8, 100, 100] = 1190
data[0, 9, 100, 100] = 1209
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes,
False, 200, 10, DQFLAGS,
after_jump_flag_dn1=0.0,
after_jump_flag_n1=10)
# all groups after CR should be flagged
for k in range(6, 10):
assert 4 == out_gdq[0, k, 100, 100], f"after jump flagging failed in group {k}"


def test_10grps_1cr_afterjump_2group(setup_cube):
ngroups = 10
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
data[0, 5, 100, 100] = 60
data[0, 6, 100, 100] = 1160
data[0, 7, 100, 100] = 1175
data[0, 8, 100, 100] = 1190
data[0, 9, 100, 100] = 1209
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes,
False, 200, 10, DQFLAGS,
after_jump_flag_dn1=0.0,
after_jump_flag_n1=2)

# 2 groups after CR should be flagged
for k in range(6, 9):
assert 4 == out_gdq[0, k, 100, 100], f"after jump flagging failed in group {k}"

# rest not flagged
for k in range(9, 10):
assert 0 == out_gdq[0, k, 100, 100], f"after jump flagging incorrect in group {k}"


def test_10grps_1cr_afterjump_toosmall(setup_cube):
ngroups = 10
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
data[0, 5, 100, 100] = 60
data[0, 6, 100, 100] = 1160
data[0, 7, 100, 100] = 1175
data[0, 8, 100, 100] = 1190
data[0, 9, 100, 100] = 1209
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes,
False, 200, 10, DQFLAGS,
after_jump_flag_dn1=10000,
after_jump_flag_n1=10)
# all groups after CR should be flagged
for k in range(7, 10):
assert 0 == out_gdq[0, k, 100, 100], f"after jump flagging incorrect in group {k}"


def test_10grps_1cr_afterjump_twothresholds(setup_cube):
ngroups = 10
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] = 121
data[0, 3, 100, 100] = 133
data[0, 4, 100, 100] = 146
data[0, 5, 100, 100] = 160
data[0, 6, 100, 100] = 1160
data[0, 7, 100, 100] = 1175
data[0, 8, 100, 100] = 1190
data[0, 9, 100, 100] = 1209
out_gdq, row_below_gdq, row_above_gdq = find_crs(data, gdq, read_noise, rej_threshold,
rej_threshold, rej_threshold, nframes,
False, 200, 10, DQFLAGS,
after_jump_flag_dn1=500,
after_jump_flag_n1=10,
after_jump_flag_dn2=10,
after_jump_flag_n2=2)
# 2 groups after CR should be flagged
for k in range(2, 5):
assert 4 == out_gdq[0, k, 100, 100], f"after jump flagging incorrect in group {k}"

# all groups after CR should be flagged
for k in range(6, 10):
assert 4 == out_gdq[0, k, 100, 100], f"after jump flagging incorrect in group {k}"


def test_median_func():

"""
Expand Down

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