JP-3448: Always flag at least one group when showers are detected (#237)

* test * fix conflicts * Update jump.py * Update jump.py * Update jump.py * tests2 * Update jump.py * changes * Update jump.py * tests * fixes * changes * Update jump.py * Update jump.py * Update jump.py * Update jump.py * Update jump.py * Update jump.py * add tests * Update test_jump.py * clean up * Update test_jump.py * Update test_twopoint_difference.py * Update CHANGES.rst * Update jump.py * Update CHANGES.rst based on suggestion Co-authored-by: Howard Bushouse <bushouse@stsci.edu> * Update CHANGES.rst uses suggestion Co-authored-by: Howard Bushouse <bushouse@stsci.edu> * Update jump.py addressed comments in PR * Update src/stcal/jump/jump.py * Update tests/test_jump.py * Update tests/test_jump.py * Update src/stcal/jump/jump.py * Update src/stcal/jump/jump.py * Update src/stcal/jump/jump.py * Update test_jump.py * fixes * Update test_jump.py * Update jump.py * Update test_jump.py * fix num_grps_masked for snowballs --------- Co-authored-by: Howard Bushouse <bushouse@stsci.edu>
spacetelescope · Feb 7, 2024 · fd2d6ce · fd2d6ce
1 parent dfa9a50
commit fd2d6ce
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diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,7 +1,10 @@
 1.5.3 (unreleased)
 ==================
 
-- 
+jump
+----
+- Fix the code to at least always flag the group with the shower and the requested
+  groups after the primary shower. [#237]
 
 1.5.2 (2023-12-13)
 ==================

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
@@ -1,11 +1,13 @@
 import logging
 import multiprocessing
 import time
-
-import cv2 as cv
 import numpy as np
-from astropy import stats
-from astropy.convolution import Ring2DKernel, convolve
+import cv2 as cv
+import astropy.stats as stats
+
+from astropy.convolution import Ring2DKernel
+from astropy.convolution import convolve
+
 
 from . import constants
 from . import twopoint_difference as twopt
@@ -285,7 +287,7 @@ def detect_jumps(
             dqflags['SATURATED']
         #  This is the flag that controls the flagging of snowballs.
         if expand_large_events:
-            total_snowballs = flag_large_events(
+            gdq, total_snowballs = flag_large_events(
                 gdq,
                 jump_flag,
                 sat_flag,
@@ -443,7 +445,7 @@ def detect_jumps(
 
         #  This is the flag that controls the flagging of snowballs.
         if expand_large_events:
-            total_snowballs = flag_large_events(
+            gdq, total_snowballs = flag_large_events(
                 gdq,
                 jump_flag,
                 sat_flag,
@@ -485,7 +487,6 @@ def detect_jumps(
     data /= gain_2d
     err /= gain_2d
     readnoise_2d /= gain_2d
-
     # Return the updated data quality arrays
     return gdq, pdq, total_primary_crs, number_extended_events, stddev
 
@@ -592,9 +593,10 @@ def flag_large_events(
                 sat_flag,
                 jump_flag,
                 expansion=expand_factor,
+                num_grps_masked=0,
                 max_extended_radius=max_extended_radius,
             )
-    return total_snowballs
+    return gdq, total_snowballs
 
 
 def extend_saturation(
@@ -645,7 +647,8 @@ def extend_ellipses(
     # For a given DQ plane it will use the list of ellipses to create
     #  expanded ellipses of pixels with
     # the jump flag set.
-    plane = gdq_cube[intg, grp, :, :]
+    out_gdq_cube = gdq_cube.copy()
+    plane = gdq_cube[intg, grp, :, :].copy()
     ncols = plane.shape[1]
     nrows = plane.shape[0]
     image = np.zeros(shape=(nrows, ncols, 3), dtype=np.uint8)
@@ -685,15 +688,38 @@ def extend_ellipses(
         )
         jump_ellipse = image[:, :, 2]
         ngrps = gdq_cube.shape[1]
-        last_grp = min(grp + num_grps_masked, ngrps)
+        last_grp = find_last_grp(grp, ngrps, num_grps_masked)
         #  This loop will flag the number of groups
         for flg_grp in range(grp, last_grp):
             sat_pix = np.bitwise_and(gdq_cube[intg, flg_grp, :, :], sat_flag)
             saty, satx = np.where(sat_pix == sat_flag)
             jump_ellipse[saty, satx] = 0
-            gdq_cube[intg, flg_grp, :, :] = np.bitwise_or(gdq_cube[intg, flg_grp, :, :], jump_ellipse)
-    return gdq_cube, num_ellipses
+            out_gdq_cube[intg, flg_grp, :, :] = np.bitwise_or(gdq_cube[intg, flg_grp, :, :], jump_ellipse)
+    diff_cube = out_gdq_cube - gdq_cube
+    return out_gdq_cube, num_ellipses
+
+def find_last_grp(grp, ngrps, num_grps_masked):
+    """
+    Parameters
+    ----------
+    grp : int
+        The location of the shower
+    
+    ngrps : int
+        The number of groups in the integration
+    
+    num_grps_masked : int
+        The requested number of groups to be flagged after the shower
 
+    Returns
+    -------
+    last_grp : int
+        The index of the last group to flag for the shower
+
+    """
+    num_grps_masked += 1
+    last_grp = min(grp + num_grps_masked, ngrps)
+    return last_grp
 
 def find_circles(dqplane, bitmask, min_area):
     # Using an input DQ plane this routine will find the groups of pixels with at least the minimum
@@ -848,7 +874,7 @@ def find_faint_extended(
     Total number of showers detected.
 
     """
-    read_noise_2 = readnoise_2d**2
+    read_noise_2d_sqr = readnoise_2d**2
     data = indata.copy()
     data[gdq == sat_flag] = np.nan
     data[gdq == 1] = np.nan
@@ -863,12 +889,11 @@ def find_faint_extended(
         # calculate sigma for each pixel
         if nints <= minimum_sigclip_groups:
             median_diffs = np.nanmedian(first_diffs_masked[intg], axis=0)
-            sigma = np.sqrt(np.abs(median_diffs) + read_noise_2 / nframes)
+            sigma = np.sqrt(np.abs(median_diffs) + read_noise_2d_sqr / nframes)
             # The difference from the median difference for each group
             e_jump = first_diffs_masked[intg] - median_diffs[np.newaxis, :, :]
             # SNR ratio of each diff.
             ratio = np.abs(e_jump) / sigma[np.newaxis, :, :]
-
         #  The convolution kernel creation
         ring_2D_kernel = Ring2DKernel(inner, outer)
         ngrps = data.shape[1]
@@ -895,14 +920,14 @@ def find_faint_extended(
             extended_emission = np.zeros(shape=(nrows, ncols), dtype=np.uint8)
             exty, extx = np.where(masked_smoothed_ratio > snr_threshold)
             extended_emission[exty, extx] = 1
+
             #  find the contours of the extended emission
             contours, hierarchy = cv.findContours(extended_emission, cv.RETR_EXTERNAL, cv.CHAIN_APPROX_SIMPLE)
             #  get the contours that are above the minimum size
             bigcontours = [con for con in contours if cv.contourArea(con) > min_shower_area]
             #  get the minimum enclosing rectangle which is the same as the
             # minimum enclosing ellipse
             ellipses = [cv.minAreaRect(con) for con in bigcontours]
-
             expand_by_ratio = True
             expansion = 1.0
             plane = gdq[intg, grp, :, :]
@@ -947,6 +972,7 @@ def find_faint_extended(
             if len(ellipses) > 0:
                 # add all the showers for this integration to the list
                 all_ellipses.append([intg, grp, ellipses])
+    total_showers = 0
     if all_ellipses:
         #  Now we actually do the flagging of the pixels inside showers.
         # This is deferred until all showers are detected. because the showers
@@ -956,6 +982,7 @@ def find_faint_extended(
             intg = showers[0]
             grp = showers[1]
             ellipses = showers[2]
+            total_showers += len(ellipses)
             gdq, num = extend_ellipses(
                 gdq,
                 intg,
@@ -966,9 +993,9 @@ def find_faint_extended(
                 expansion=ellipse_expand,
                 expand_by_ratio=True,
                 num_grps_masked=num_grps_masked,
-                max_extended_radius=max_extended_radius,
+                max_extended_radius=max_extended_radius
             )
-    return gdq, len(all_ellipses)
+    return gdq, total_showers
 
 
 def calc_num_slices(n_rows, max_cores, max_available):

diff --git a/tests/test_jump.py b/tests/test_jump.py
@@ -9,6 +9,7 @@
     flag_large_events,
     point_inside_ellipse,
     detect_jumps,
+    find_last_grp
 )
 
 DQFLAGS = {"JUMP_DET": 4, "SATURATED": 2, "DO_NOT_USE": 1, "GOOD": 0, "NO_GAIN_VALUE": 8}
@@ -220,7 +221,7 @@ def test_flag_large_events_withsnowball():
     cube[0, 2, 5, 1:6] = DQFLAGS["JUMP_DET"]
     cube[0, 2, 1:6, 1] = DQFLAGS["JUMP_DET"]
     cube[0, 2, 1:6, 5] = DQFLAGS["JUMP_DET"]
-    flag_large_events(
+    cube, total_snowballs = flag_large_events(
         cube,
         DQFLAGS["JUMP_DET"],
         DQFLAGS["SATURATED"],
@@ -253,7 +254,7 @@ def test_flag_large_events_groupedsnowball():
     cube[0, 2, 5, 1:6] = DQFLAGS["JUMP_DET"]
     cube[0, 2, 1:6, 1] = DQFLAGS["JUMP_DET"]
     cube[0, 2, 1:6, 5] = DQFLAGS["JUMP_DET"]
-    flag_large_events(
+    cube, total_snowballs = flag_large_events(
         cube,
         DQFLAGS["JUMP_DET"],
         DQFLAGS["SATURATED"],
@@ -284,7 +285,7 @@ def test_flag_large_events_withsnowball_noextension():
     cube[0, 2, 5, 1:6] = DQFLAGS["JUMP_DET"]
     cube[0, 2, 1:6, 1] = DQFLAGS["JUMP_DET"]
     cube[0, 2, 1:6, 5] = DQFLAGS["JUMP_DET"]
-    flag_large_events(
+    cube, num_snowballs = flag_large_events(
         cube,
         DQFLAGS["JUMP_DET"],
         DQFLAGS["SATURATED"],
@@ -446,3 +447,15 @@ def test_calc_num_slices():
     assert calc_num_slices(n_rows, "3/4", max_available_cores) == 1
     n_rows = 9
     assert calc_num_slices(n_rows, "21", max_available_cores) == 9
+
+
+def test_find_last_grp():
+    assert (find_last_grp(grp=5, ngrps=7, num_grps_masked=0) == 6)
+    assert (find_last_grp(grp=5, ngrps=7, num_grps_masked=2) == 7)
+    assert (find_last_grp(grp=5, ngrps=7, num_grps_masked=3) == 7)
+    assert (find_last_grp(grp=5, ngrps=6, num_grps_masked=1) == 6)
+    assert (find_last_grp(grp=5, ngrps=6, num_grps_masked=0) == 6)
+    assert (find_last_grp(grp=5, ngrps=6, num_grps_masked=2) == 6)
+    assert (find_last_grp(grp=5, ngrps=8, num_grps_masked=0) == 6)
+    assert (find_last_grp(grp=5, ngrps=8, num_grps_masked=1) == 7)
+    assert (find_last_grp(grp=5, ngrps=8, num_grps_masked=2) == 8)