diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index 95bb91ef5f09434db26126aeed0bd6772059d668..d0d89969be4e5d3abb1c89da958069a1e277b808 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -44,8 +44,8 @@
"limit_trains = 0 # ONLY FOR TESTING. process only first N trains, Use 0 to process all.\n",
"chunks_ids = 32 # HDF chunk size for memoryCell and frameNumber.\n",
"chunks_data = 1 # HDF chunk size for pixel data in number of frames.\n",
- "replace_wrong_gain_value = -1 # Force gain value into the chosen gain [0, 1, or 2] for pixels marked with WRONG_GAIN_VALUE badpixel. Default -1 for not changing the gain values.\n",
- "wrong_gain_pixels = [-1] # List with groups of 5 values (e.g. [4, 0, 255, 896, 1024]) defining the module number (4 for JNGFR04). And using the indexes of the FEM row [pixel_x_0:pixel_x_1] and column [pixel_y_0:pixel_y_1]. Set to -1 to not pick pixels for gain replacement.\n",
+ "wrong_gain_pixels = [-1] # List of 5 values (e.g. [4, 0, 255, 896, 1024]) defining the module number (4 for JNGFR04). And using the indexes of the FEM row [pixel_x_0:pixel_x_1] and column [pixel_y_0:pixel_y_1]. Set to -1 to not pick pixels for gain replacement.\n",
+ "replace_wrong_gain_value = 0 # Force gain value into the chosen gain [0, 1, or 2] for pixels specified in `wrong_gain_pixels`. This has no effect if wrong_gain_pixels = [-1]\n",
"\n",
"# Parameters for retrieving calibration constants\n",
"integration_time = -1 # integration time in us. set to -1 to overwrite by value in file.\n",
@@ -95,7 +95,7 @@
"from cal_tools.calcat_interface import JUNGFRAU_CalibrationData\n",
"from cal_tools.enums import BadPixels\n",
"from cal_tools.files import DataFile\n",
- "from cal_tools.jungfraulib import JungfrauCtrl, replace_pixels_gain_values\n",
+ "from cal_tools.jungfraulib import JungfrauCtrl\n",
"from cal_tools.plotting import init_jungfrau_geom\n",
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
@@ -402,13 +402,17 @@
" # Change low gain to 2 for indexing purposes.\n",
" g[g==3] = 2\n",
"\n",
- " if replace_wrong_gain_value > -1:\n",
- " g = replace_pixels_gain_values(\n",
- " g,\n",
- " replace_wrong_gain_value,\n",
- " wrong_gain_pixels,\n",
- " local_karabo_da,\n",
- " )\n",
+ " # A fix for a module hardware problem (e.g. Jungfrau_M302)\n",
+ " # of chip being stuck on the wrong gain bit.\n",
+ " if (\n",
+ " wrong_gain_pixels[0] > -1 and\n",
+ " wrong_gain_pixels[0] == int(local_karabo_da[-2:])\n",
+ " ):\n",
+ " x1 = wrong_gain_pixels[1]\n",
+ " x2 = wrong_gain_pixels[2]\n",
+ " y1 = wrong_gain_pixels[3]\n",
+ " y2 = wrong_gain_pixels[4]\n",
+ " g[:, x1:x2, y1:y2] = replace_wrong_gain_value\n",
"\n",
" # Select memory cells\n",
" if memory_cells > 1:\n",
diff --git a/src/cal_tools/jungfraulib.py b/src/cal_tools/jungfraulib.py
index c27352e432b0b0cc03fa574be8a97b05b8f6db3a..bb1fcbcfa14439eb965d84cae47785a09725ffb0 100644
--- a/src/cal_tools/jungfraulib.py
+++ b/src/cal_tools/jungfraulib.py
@@ -209,36 +209,3 @@ def sort_runs_by_gain(
"Please verify the selected 3 dark runs to process.")
return runs
-
-
-def replace_pixels_gain_values(
- gain_arr,
- new_gain_value,
- wrong_gain_pixels,
- karabo_da,
-):
- """Replace gain values with the chosen new gain value
- for a single module.
-
- Args:
- gain_arr (ndarray): The raw gain array to be updated.
- new_gain_value (int): _description_
- wrong_gain_pixels (list): [module_index, row1, row12, col1, col2].
- e.g. [4, 0, 255, 896, 1024] for JNGFR04 slicing module [0:255, 896:1024].
- karabo_da (str): _description_
- memory_cells (int): Number of memory cells.
-
- Returns:
- (ndarray): The update gain_arr.
-
- """
- if wrong_gain_pixels[0] > -1:
- if wrong_gain_pixels[0] == int(karabo_da[-2:]):
- x1 = wrong_gain_pixels[1]
- x2 = wrong_gain_pixels[2]
- y1 = wrong_gain_pixels[3]
- y2 = wrong_gain_pixels[4]
- gain_arr[:, x1:x2, y1:y2] = new_gain_value
- return gain_arr
- else: # No gain replacement
- return gain_arr
\ No newline at end of file
diff --git a/tests/test_jungfraulib.py b/tests/test_jungfraulib.py
index c8ce1a35eba4b646219305e801499347d109a182..c7fb5258ba2c0035cbad2668e4bdc35131866855 100644
--- a/tests/test_jungfraulib.py
+++ b/tests/test_jungfraulib.py
@@ -1,13 +1,7 @@
-import numpy as np
import pytest
from extra_data import RunDirectory
-from cal_tools.enums import BadPixels
-from cal_tools.jungfraulib import (
- JungfrauCtrl,
- replace_pixels_gain_values,
- sort_runs_by_gain,
-)
+from cal_tools.jungfraulib import JungfrauCtrl, sort_runs_by_gain
# TODO: replace with mocked RAW data as in tests/test_agipdlib.py
JF = JungfrauCtrl(
@@ -70,46 +64,3 @@ def test_sort_runs_by_gain(original_runs, sorted_runs):
runs=original_runs,
ctrl_src="FXE_XAD_JF1M/DET/CONTROL")
assert validated_runs == sorted_runs
-
-
-GAIN = np.zeros((1, 512, 1024), dtype=np.uint8)
-NEW_GAIN = GAIN.copy() # all pixels in high gain.
-GAIN[:, 0:255, 896:1024] = 3 # subsection of a chip is stuck in gain bit = 3
-BP = np.zeros((512, 1024, 3), dtype=np.uint32)
-for i in range(3):
- BP[0:255, 896:1024, i] = BadPixels.WRONG_GAIN_VALUE.value
-
-MEM_CELLS = 1
-KARABO_DA = "JNGFR04"
-REPLACE_WRONG_GAIN_VALUE = 0
-WRONG_GAIN_PIXELS = [4, 0, 255, 896, 1024]
-
-
-def test_replace_pixels_gain_values():
- assert np.allclose(
- NEW_GAIN,
- replace_pixels_gain_values(
- gain_arr=GAIN,
- new_gain_value=REPLACE_WRONG_GAIN_VALUE,
- wrong_gain_pixels=WRONG_GAIN_PIXELS,
- karabo_da=KARABO_DA,
- )
- )
- assert np.allclose(
- NEW_GAIN,
- replace_pixels_gain_values(
- gain_arr=GAIN,
- new_gain_value=REPLACE_WRONG_GAIN_VALUE,
- wrong_gain_pixels=WRONG_GAIN_PIXELS,
- karabo_da=KARABO_DA,
- )
- )
- assert np.allclose(
- GAIN, # No replacement for non-selected module.
- replace_pixels_gain_values(
- gain_arr=GAIN,
- new_gain_value=REPLACE_WRONG_GAIN_VALUE,
- wrong_gain_pixels=WRONG_GAIN_PIXELS,
- karabo_da="JNGFR01",
- )
- )