From f011e93184d2a28da9abf5af8896ff0aeaf5e3c9 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Thu, 25 Jan 2024 11:01:41 -0500
Subject: [PATCH 01/19] Update jump.py

---
 src/stcal/jump/jump.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index 6139d103..ac58b886 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -427,6 +427,13 @@ def detect_jumps(
             # save the neighbors to be flagged that will be in the next slice
             previous_row_above_gdq = row_above_gdq.copy()
             k += 1
+            # remove redundant bits in pixels that have jump flagged but were
+            # already flagged as do_not_use or saturated.
+            gdq[gdq == np.bitwise_or(dqflags['DO_NOT_USE'], dqflags['JUMP_DET'])] = \
+                dqflags['DO_NOT_USE']
+            gdq[gdq == np.bitwise_or(dqflags['SATURATED'], dqflags['JUMP_DET'])] = \
+                dqflags['SATURATED']
+
         #  This is the flag that controls the flagging of snowballs.
         if expand_large_events:
             total_snowballs = flag_large_events(

From 623934a70eb651e8ce36c3af176629efc036c5ec Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Thu, 25 Jan 2024 11:03:32 -0500
Subject: [PATCH 02/19] Update jump.py

---
 src/stcal/jump/jump.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index ac58b886..59c25936 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -314,7 +314,7 @@ def detect_jumps(
             log.info("Total showers= %i", num_showers)
             number_extended_events = num_showers
     else:
-        yinc = int(n_rows / n_slices)
+        yinc = int(n_rows // n_slices)
         slices = []
         # Slice up data, gdq, readnoise_2d into slices
         # Each element of slices is a tuple of

From c0ff94a090534b847137f3b36f43397b58cc7a11 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Thu, 25 Jan 2024 14:17:00 -0500
Subject: [PATCH 03/19] Update CHANGES.rst

---
 CHANGES.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHANGES.rst b/CHANGES.rst
index b22ce3e2..7976861e 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -86,6 +86,9 @@ jump
 - Added more allowable selections for the number of cores to use for
   multiprocessing [#183].
 
+- Fixed the numer of rows per slice in multiprocessing that lead to
+  different results when running the step with multiprocess [#239]
+
 ramp_fitting
 ~~~~~~~~~~~~
 

From c5c0248dde98cd2d0005fe6f4c706b78d5ea7b53 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Thu, 25 Jan 2024 14:53:35 -0500
Subject: [PATCH 04/19] Update CHANGES.rst

---
 CHANGES.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGES.rst b/CHANGES.rst
index 7976861e..48d9eda8 100644
--- a/CHANGES.rst
+++ b/CHANGES.rst
@@ -86,8 +86,8 @@ jump
 - Added more allowable selections for the number of cores to use for
   multiprocessing [#183].
 
-- Fixed the numer of rows per slice in multiprocessing that lead to
-  different results when running the step with multiprocess [#239]
+- Fixed the computation of the number of rows per slice for multiprocessing,
+  which caused different results when running the step with multiprocess [#239]
 
 ramp_fitting
 ~~~~~~~~~~~~

From 8f30516d93302bdd04226ff21de018e0fa657e03 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Fri, 26 Jan 2024 14:53:55 -0500
Subject: [PATCH 05/19] Add unit test for the double flagging of pixels

---
 src/stcal/jump/jump.py |  8 +++----
 tests/test_jump.py     | 48 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 52 insertions(+), 4 deletions(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index 59c25936..eea6ce43 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -427,11 +427,11 @@ def detect_jumps(
             # save the neighbors to be flagged that will be in the next slice
             previous_row_above_gdq = row_above_gdq.copy()
             k += 1
-            # remove redundant bits in pixels that have jump flagged but were
-            # already flagged as do_not_use or saturated.
-            gdq[gdq == np.bitwise_or(dqflags['DO_NOT_USE'], dqflags['JUMP_DET'])] = \
+        # remove redundant bits in pixels that have jump flagged but were
+        # already flagged as do_not_use or saturated.
+        gdq[gdq == np.bitwise_or(dqflags['DO_NOT_USE'], dqflags['JUMP_DET'])] = \
                 dqflags['DO_NOT_USE']
-            gdq[gdq == np.bitwise_or(dqflags['SATURATED'], dqflags['JUMP_DET'])] = \
+        gdq[gdq == np.bitwise_or(dqflags['SATURATED'], dqflags['JUMP_DET'])] = \
                 dqflags['SATURATED']
 
         #  This is the flag that controls the flagging of snowballs.
diff --git a/tests/test_jump.py b/tests/test_jump.py
index 0ddbefb1..ccd450c8 100644
--- a/tests/test_jump.py
+++ b/tests/test_jump.py
@@ -8,6 +8,7 @@
     find_faint_extended,
     flag_large_events,
     point_inside_ellipse,
+    detect_jumps,
 )
 
 DQFLAGS = {"JUMP_DET": 4, "SATURATED": 2, "DO_NOT_USE": 1, "GOOD": 0, "NO_GAIN_VALUE": 8}
@@ -30,6 +31,53 @@ def _cube(ngroups, readnoise=10):
     return _cube
 
 
+def test_multiprocessing():
+    nints = 1
+    nrows = 13
+    ncols = 2
+    ngroups = 13
+    readnoise = 10
+    frames_per_group = 1
+
+    data = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.float32)
+    readnoise_2d = np.ones((nrows, ncols), dtype=np.float32) * readnoise
+    gain_2d = np.ones((nrows, ncols), dtype=np.float32) * 4
+    gdq = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.uint32)
+    pdq = np.zeros(shape=(nrows, ncols), dtype=np.uint32)
+    err = np.zeros(shape=(nrows, ncols), dtype=np.float32)
+    num_cores = "1"
+    data[0, 4:, 5, 1] = 2000
+    gdq[0, 4:, 6, 1] = DQFLAGS['DO_NOT_USE']
+    gdq, pdq, total_primary_crs, number_extended_events, stddev = detect_jumps(
+        frames_per_group, data, gdq, pdq, err, gain_2d, readnoise_2d, rejection_thresh=5, three_grp_thresh=6,
+        four_grp_thresh=7, max_cores=num_cores, max_jump_to_flag_neighbors=10000, min_jump_to_flag_neighbors=100,
+        flag_4_neighbors=True, dqflags=DQFLAGS)
+    print(data[0, 4, :, :])
+    print(gdq[0, 4, :, :])
+    assert gdq[0, 4, 5, 1] == DQFLAGS['JUMP_DET']
+    assert gdq[0, 4, 6, 1] == DQFLAGS['DO_NOT_USE']
+
+    # This section of code will fail without the fixes for PR #239 that prevent
+    # the double flagging pixels with jump which already have do_not_use or saturation set.
+    num_cores = "5"
+    data = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.float32)
+    gdq = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.uint32)
+    pdq = np.zeros(shape=(nrows, ncols), dtype=np.uint32)
+    readnoise_2d = np.ones((nrows, ncols), dtype=np.float32) * readnoise
+    gain_2d = np.ones((nrows, ncols), dtype=np.float32) * 3
+    err = np.zeros(shape=(nrows, ncols), dtype=np.float32)
+    data[0, 4:, 5, 1] = 2000
+    gdq[0, 4:, 6, 1] = DQFLAGS['DO_NOT_USE']
+    gdq, pdq, total_primary_crs, number_extended_events, stddev = detect_jumps(
+        frames_per_group, data, gdq, pdq, err, gain_2d, readnoise_2d, rejection_thresh=5, three_grp_thresh=6,
+        four_grp_thresh=7, max_cores=num_cores, max_jump_to_flag_neighbors=10000, min_jump_to_flag_neighbors=100,
+        flag_4_neighbors=True, dqflags=DQFLAGS)
+    assert gdq[0, 4, 5, 1] == DQFLAGS['JUMP_DET']
+    assert gdq[0, 4, 6, 1] == DQFLAGS['DO_NOT_USE'] #This value would have been 5 without the fix.
+
+
+
+
 def test_find_simple_ellipse():
     plane = np.zeros(shape=(5, 5), dtype=np.uint8)
     plane[2, 2] = DQFLAGS["JUMP_DET"]

From be254e7dfe5f63f00dde0f96cc8d59e34936e632 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Mon, 29 Jan 2024 16:33:41 -0500
Subject: [PATCH 06/19] fixes

---
 src/stcal/jump/twopoint_difference.py |  2 +-
 tests/test_jump.py                    | 46 +++++++++++++++++++++++++++
 2 files changed, 47 insertions(+), 1 deletion(-)

diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index 62d44b1a..970be369 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -411,7 +411,7 @@ def find_crs(
                 row = cr_row[j]
                 col = cr_col[j]
                 if e_jump_4d[intg, group - 1, row, col] >= cthres[row, col]:
-                    for kk in range(group, min(group + cgroup + 1, ngroups)):
+                    for kk in range(group + 1, min(group + cgroup + 1, ngroups)):
                         if (gdq[intg, kk, row, col] & sat_flag) == 0 and (
                             gdq[intg, kk, row, col] & dnu_flag
                         ) == 0:
diff --git a/tests/test_jump.py b/tests/test_jump.py
index ccd450c8..a85eef51 100644
--- a/tests/test_jump.py
+++ b/tests/test_jump.py
@@ -76,6 +76,52 @@ def test_multiprocessing():
     assert gdq[0, 4, 6, 1] == DQFLAGS['DO_NOT_USE'] #This value would have been 5 without the fix.
 
 
+def test_multiprocessing_big():
+    nints = 1
+    nrows = 2048
+    ncols = 7
+    ngroups = 13
+    readnoise = 10
+    frames_per_group = 1
+
+    data = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.float32)
+    readnoise_2d = np.ones((nrows, ncols), dtype=np.float32) * readnoise
+    gain_2d = np.ones((nrows, ncols), dtype=np.float32) * 4
+    gdq = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.uint32)
+    pdq = np.zeros(shape=(nrows, ncols), dtype=np.uint32)
+    err = np.zeros(shape=(nrows, ncols), dtype=np.float32)
+    num_cores = "1"
+    data[0, 4:, 204, 5] = 2000
+    gdq[0, 4:, 204, 6] = DQFLAGS['DO_NOT_USE']
+    gdq, pdq, total_primary_crs, number_extended_events, stddev = detect_jumps(
+        frames_per_group, data, gdq, pdq, err, gain_2d, readnoise_2d, rejection_thresh=5, three_grp_thresh=6,
+        four_grp_thresh=7, max_cores=num_cores, max_jump_to_flag_neighbors=10000, min_jump_to_flag_neighbors=100,
+        flag_4_neighbors=True, dqflags=DQFLAGS)
+    print(data[0, 4, :, :])
+    print(gdq[0, 4, :, :])
+    assert gdq[0, 4, 204, 5] == DQFLAGS['JUMP_DET']
+    assert gdq[0, 4, 205, 5] == DQFLAGS['JUMP_DET']
+    assert gdq[0, 4, 204, 6] == DQFLAGS['DO_NOT_USE']
+
+    # This section of code will fail without the fixes for PR #239 that prevent
+    # the double flagging pixels with jump which already have do_not_use or saturation set.
+    num_cores = "10"
+    data = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.float32)
+    gdq = np.zeros(shape=(nints, ngroups, nrows, ncols), dtype=np.uint32)
+    pdq = np.zeros(shape=(nrows, ncols), dtype=np.uint32)
+    readnoise_2d = np.ones((nrows, ncols), dtype=np.float32) * readnoise
+    gain_2d = np.ones((nrows, ncols), dtype=np.float32) * 3
+    err = np.zeros(shape=(nrows, ncols), dtype=np.float32)
+    data[0, 4:, 204, 5] = 2000
+    gdq[0, 4:, 204, 6] = DQFLAGS['DO_NOT_USE']
+    gdq, pdq, total_primary_crs, number_extended_events, stddev = detect_jumps(
+        frames_per_group, data, gdq, pdq, err, gain_2d, readnoise_2d, rejection_thresh=5, three_grp_thresh=6,
+        four_grp_thresh=7, max_cores=num_cores, max_jump_to_flag_neighbors=10000, min_jump_to_flag_neighbors=100,
+        flag_4_neighbors=True, dqflags=DQFLAGS)
+    assert gdq[0, 4, 204, 5] == DQFLAGS['JUMP_DET']
+    assert gdq[0, 4, 205, 5] == DQFLAGS['JUMP_DET']
+    assert gdq[0, 4, 204, 6] == DQFLAGS['DO_NOT_USE'] #This value would have been 5 without the fix.
+
 
 
 def test_find_simple_ellipse():

From 35d808624030c56e17b82a1bc14588f08b321ff4 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Mon, 29 Jan 2024 17:20:51 -0500
Subject: [PATCH 07/19] Update jump.py

---
 src/stcal/jump/jump.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index eea6ce43..eca264a4 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -333,7 +333,7 @@ def detect_jumps(
                 i,
                 (
                     data[:, :, i * yinc : (i + 1) * yinc, :],
-                    gdq[:, :, i * yinc : (i + 1) * yinc, :],
+                    gdq[:, :, i * yinc : (i + 1) * yinc, :].copy(),
                     readnoise_2d[i * yinc : (i + 1) * yinc, :],
                     rejection_thresh,
                     three_grp_thresh,
@@ -359,7 +359,7 @@ def detect_jumps(
             n_slices - 1,
             (
                 data[:, :, (n_slices - 1) * yinc : n_rows, :],
-                gdq[:, :, (n_slices - 1) * yinc : n_rows, :],
+                gdq[:, :, (n_slices - 1) * yinc : n_rows, :].copy(),
                 readnoise_2d[(n_slices - 1) * yinc : n_rows, :],
                 rejection_thresh,
                 three_grp_thresh,

From d4d36402820f6374542ca781e338dcf484a1066e Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Mon, 29 Jan 2024 17:23:10 -0500
Subject: [PATCH 08/19] Update jump.py

---
 src/stcal/jump/jump.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index eca264a4..923c766b 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -359,7 +359,7 @@ def detect_jumps(
             n_slices - 1,
             (
                 data[:, :, (n_slices - 1) * yinc : n_rows, :],
-                gdq[:, :, (n_slices - 1) * yinc : n_rows, :].copy(),
+                gdq[:, :, (n_slices - 1) * yinc : n_rows, :].copy() ,
                 readnoise_2d[(n_slices - 1) * yinc : n_rows, :],
                 rejection_thresh,
                 three_grp_thresh,

From 8f9c6eded668183d576b64f766925314211467c1 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Mon, 29 Jan 2024 17:24:32 -0500
Subject: [PATCH 09/19] Update jump.py

---
 src/stcal/jump/jump.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index 923c766b..ce07cb59 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -323,11 +323,11 @@ def detect_jumps(
 
         # must copy arrays here, find_crs will make copies but if slices
         # are being passed in for multiprocessing then the original gdq will be
-        # modified unless copied beforehand
+        # modified unless copied beforehand.
         gdq = gdq.copy()
         data = data.copy()
         copy_arrs = False  # we don't need to copy arrays again in find_crs
-
+        print("this is a test")
         for i in range(n_slices - 1):
             slices.insert(
                 i,

From c2bcca944f5df623176bb3f212eb8e3d26b987a5 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 09:52:04 -0500
Subject: [PATCH 10/19] Update twopoint_difference.py

---
 src/stcal/jump/twopoint_difference.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index 970be369..b07c5f2d 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -412,10 +412,7 @@ def find_crs(
                 col = cr_col[j]
                 if e_jump_4d[intg, group - 1, row, col] >= cthres[row, col]:
                     for kk in range(group + 1, min(group + cgroup + 1, ngroups)):
-                        if (gdq[intg, kk, row, col] & sat_flag) == 0 and (
-                            gdq[intg, kk, row, col] & dnu_flag
-                        ) == 0:
-                            gdq[intg, kk, row, col] = np.bitwise_or(gdq[integ, kk, row, col], jump_flag)
+                       gdq[intg, kk, row, col] = np.bitwise_or(gdq[integ, kk, row, col], jump_flag)
     if "stddev" in locals():
         return gdq, row_below_gdq, row_above_gdq, num_primary_crs, stddev
 

From f0e856ae73b4990a2371016f392b2338bbe87d09 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 10:14:12 -0500
Subject: [PATCH 11/19] Update jump.py

---
 src/stcal/jump/jump.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index ce07cb59..274ccac6 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -380,7 +380,9 @@ def detect_jumps(
             ),
         )
         log.info("Creating %d processes for jump detection ", n_slices)
-        pool = multiprocessing.Pool(processes=n_slices)
+#        pool = multiprocessing.Pool(processes=n_slices)
+######### JUST FOR DEBUGGING #########################
+        pool = multiprocessing.Pool(processes=1)
         # Starts each slice in its own process. Starmap allows more than one
         # parameter to be passed.
         real_result = pool.starmap(twopt.find_crs, slices)

From 907e25ad45b2cb15d0059764848820fbe9c557da Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 10:19:21 -0500
Subject: [PATCH 12/19] Update twopoint_difference.py

---
 src/stcal/jump/twopoint_difference.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index b07c5f2d..b394832f 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -401,7 +401,7 @@ def find_crs(
     # the transient seen after ramp jumps
     flag_e_threshold = [after_jump_flag_e1, after_jump_flag_e2]
     flag_groups = [after_jump_flag_n1, after_jump_flag_n2]
-
+    print("starting flagging after jump")
     for cthres, cgroup in zip(flag_e_threshold, flag_groups):
         if cgroup > 0:
             cr_intg, cr_group, cr_row, cr_col = np.where(np.bitwise_and(gdq, jump_flag))

From 9c7d6147ae74c2c1f7804a60f208d978f7012740 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 10:32:48 -0500
Subject: [PATCH 13/19] Update twopoint_difference.py

---
 src/stcal/jump/twopoint_difference.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index b394832f..af950a10 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -412,7 +412,7 @@ def find_crs(
                 col = cr_col[j]
                 if e_jump_4d[intg, group - 1, row, col] >= cthres[row, col]:
                     for kk in range(group + 1, min(group + cgroup + 1, ngroups)):
-                       gdq[intg, kk, row, col] = np.bitwise_or(gdq[integ, kk, row, col], jump_flag)
+                       gdq[intg, kk, row, col] = np.bitwise_or(gdq[intg, kk, row, col], jump_flag)
     if "stddev" in locals():
         return gdq, row_below_gdq, row_above_gdq, num_primary_crs, stddev
 

From 2c8d36003d62228f3c7072f4af71c440e09097d6 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 10:33:50 -0500
Subject: [PATCH 14/19] Update jump.py

---
 src/stcal/jump/jump.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index 274ccac6..016017b4 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -380,9 +380,9 @@ def detect_jumps(
             ),
         )
         log.info("Creating %d processes for jump detection ", n_slices)
-#        pool = multiprocessing.Pool(processes=n_slices)
+        pool = multiprocessing.Pool(processes=n_slices)
 ######### JUST FOR DEBUGGING #########################
-        pool = multiprocessing.Pool(processes=1)
+#        pool = multiprocessing.Pool(processes=1)
         # Starts each slice in its own process. Starmap allows more than one
         # parameter to be passed.
         real_result = pool.starmap(twopt.find_crs, slices)

From efd4abcae2face69d00a8860cf8e45579bf48243 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 12:05:07 -0500
Subject: [PATCH 15/19] fixes

---
 src/stcal/jump/jump.py                | 4 ++--
 src/stcal/jump/twopoint_difference.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index 016017b4..1c3dfdc6 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -235,8 +235,8 @@ def detect_jumps(
     err *= gain_2d
     readnoise_2d *= gain_2d
     # also apply to the after_jump thresholds
-    after_jump_flag_e1 = after_jump_flag_dn1 * gain_2d
-    after_jump_flag_e2 = after_jump_flag_dn2 * gain_2d
+    after_jump_flag_e1 = after_jump_flag_dn1 * np.nanmedian(gain_2d)
+    after_jump_flag_e2 = after_jump_flag_dn2 * np.nanmedian(gain_2d)
 
     # Apply the 2-point difference method as a first pass
     log.info("Executing two-point difference method")
diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index af950a10..39a54fc0 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -403,7 +403,7 @@ def find_crs(
     flag_groups = [after_jump_flag_n1, after_jump_flag_n2]
     print("starting flagging after jump")
     for cthres, cgroup in zip(flag_e_threshold, flag_groups):
-        if cgroup > 0:
+        if cgroup > 0 and cthres > 0:
             cr_intg, cr_group, cr_row, cr_col = np.where(np.bitwise_and(gdq, jump_flag))
             for j in range(len(cr_group)):
                 intg = cr_intg[j]

From 38d617e88ac781b961813cd392a3347a47a51cfc Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 12:16:36 -0500
Subject: [PATCH 16/19] Update twopoint_difference.py

---
 src/stcal/jump/twopoint_difference.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index 39a54fc0..5e118a1f 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -410,7 +410,7 @@ def find_crs(
                 group = cr_group[j]
                 row = cr_row[j]
                 col = cr_col[j]
-                if e_jump_4d[intg, group - 1, row, col] >= cthres[row, col]:
+                if e_jump_4d[intg, group - 1, row, col] >= cthres:
                     for kk in range(group + 1, min(group + cgroup + 1, ngroups)):
                        gdq[intg, kk, row, col] = np.bitwise_or(gdq[intg, kk, row, col], jump_flag)
     if "stddev" in locals():

From e5c15e2b6305d3634d01e5c46bcd040373e5c110 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 12:35:16 -0500
Subject: [PATCH 17/19] Update jump.py

---
 src/stcal/jump/jump.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index 1c3dfdc6..d49e3b56 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -277,6 +277,12 @@ def detect_jumps(
             minimum_sigclip_groups=minimum_sigclip_groups,
             only_use_ints=only_use_ints,
         )
+        # remove redundant bits in pixels that have jump flagged but were
+        # already flagged as do_not_use or saturated.
+        gdq[gdq == np.bitwise_or(dqflags['DO_NOT_USE'], dqflags['JUMP_DET'])] = \
+            dqflags['DO_NOT_USE']
+        gdq[gdq == np.bitwise_or(dqflags['SATURATED'], dqflags['JUMP_DET'])] = \
+            dqflags['SATURATED']
         #  This is the flag that controls the flagging of snowballs.
         if expand_large_events:
             total_snowballs = flag_large_events(

From 9701831129de722175bf3cba899ab1e53dae8599 Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 13:13:45 -0500
Subject: [PATCH 18/19] delete jumps

---
 src/stcal/jump/jump.py                | 1 -
 src/stcal/jump/twopoint_difference.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/src/stcal/jump/jump.py b/src/stcal/jump/jump.py
index d49e3b56..d6aeb3ad 100644
--- a/src/stcal/jump/jump.py
+++ b/src/stcal/jump/jump.py
@@ -333,7 +333,6 @@ def detect_jumps(
         gdq = gdq.copy()
         data = data.copy()
         copy_arrs = False  # we don't need to copy arrays again in find_crs
-        print("this is a test")
         for i in range(n_slices - 1):
             slices.insert(
                 i,
diff --git a/src/stcal/jump/twopoint_difference.py b/src/stcal/jump/twopoint_difference.py
index 5e118a1f..b9111870 100644
--- a/src/stcal/jump/twopoint_difference.py
+++ b/src/stcal/jump/twopoint_difference.py
@@ -401,7 +401,6 @@ def find_crs(
     # the transient seen after ramp jumps
     flag_e_threshold = [after_jump_flag_e1, after_jump_flag_e2]
     flag_groups = [after_jump_flag_n1, after_jump_flag_n2]
-    print("starting flagging after jump")
     for cthres, cgroup in zip(flag_e_threshold, flag_groups):
         if cgroup > 0 and cthres > 0:
             cr_intg, cr_group, cr_row, cr_col = np.where(np.bitwise_and(gdq, jump_flag))

From a061bdd2f95405f92394236f9c2d08a1eba3373b Mon Sep 17 00:00:00 2001
From: Mike Regan <mregan@stsci.edu>
Date: Tue, 30 Jan 2024 14:05:15 -0500
Subject: [PATCH 19/19] Update test_twopoint_difference.py

---
 tests/test_twopoint_difference.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/test_twopoint_difference.py b/tests/test_twopoint_difference.py
index c6443bc7..f066b4b1 100644
--- a/tests/test_twopoint_difference.py
+++ b/tests/test_twopoint_difference.py
@@ -855,7 +855,7 @@ def test_10grps_1cr_afterjump(setup_cube):
     data[0, 8, 100, 100] = 1190
     data[0, 9, 100, 100] = 1209
 
-    after_jump_flag_e1 = np.full(data.shape[2:4], 1.0) * 0.0
+    after_jump_flag_e1 = 1.0
     out_gdq, row_below_gdq, rows_above_gdq, total_crs, stddev = find_crs(
         data,
         gdq,
@@ -891,7 +891,7 @@ def test_10grps_1cr_afterjump_2group(setup_cube):
     data[0, 8, 100, 100] = 1190
     data[0, 9, 100, 100] = 1209
 
-    after_jump_flag_e1 = np.full(data.shape[2:4], 1.0) * 0.0
+    after_jump_flag_e1 = 1.0
     out_gdq, row_below_gdq, rows_above_gdq, total_crs, stddev = find_crs(
         data,
         gdq,
@@ -932,7 +932,7 @@ def test_10grps_1cr_afterjump_toosmall(setup_cube):
     data[0, 8, 100, 100] = 1190
     data[0, 9, 100, 100] = 1209
 
-    after_jump_flag_e1 = np.full(data.shape[2:4], 1.0) * 10000.0
+    after_jump_flag_e1 = 10000.0
     out_gdq, row_below_gdq, rows_above_gdq, total_crs, stddev = find_crs(
         data,
         gdq,
@@ -968,8 +968,8 @@ def test_10grps_1cr_afterjump_twothresholds(setup_cube):
     data[0, 8, 100, 100] = 1190
     data[0, 9, 100, 100] = 1209
 
-    after_jump_flag_e1 = np.full(data.shape[2:4], 1.0) * 500.0
-    after_jump_flag_e2 = np.full(data.shape[2:4], 1.0) * 10.0
+    after_jump_flag_e1 = 500.0
+    after_jump_flag_e2 = 10.0
     out_gdq, row_below_gdq, rows_above_gdq, total_crs, stddev = find_crs(
         data,
         gdq,