diff --git a/cal_tools/cal_tools/agipdlib.py b/cal_tools/cal_tools/agipdlib.py
index 5650700d968c53f7094d4986a74face5dc089a68..3438769e6508db7ede72eb0188974431fffdca83 100644
--- a/cal_tools/cal_tools/agipdlib.py
+++ b/cal_tools/cal_tools/agipdlib.py
@@ -54,7 +54,8 @@ class AgipdCorrections:
h5_data_path="INSTRUMENT/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/",
h5_index_path="INDEX/SPB_DET_AGIPD1M-1/DET/{}CH0:xtdf/",
do_rel_gain=True, chunk_size_idim=512, il_mode=False,
- cal_det_instance="AGIPD1M1", karabo_data_mode=False):
+ cal_det_instance="AGIPD1M1", karabo_data_mode=False,
+ force_hg_if_below=None):
"""
Initialize an AgipdCorrections Class
@@ -80,6 +81,9 @@ class AgipdCorrections:
writing data out
:param il_mode: set to true if AGIPD data is interlaced (pre-Nov 2017 data)
:param karabo_data_mode: set to true to use data iterated with karabo data
+ :param force_hg_if_below: set to a value different to None/0 to force a pixels
+ gain to high, if the pixel value is below the given
+ value after high gain offset subtraction.
"""
self.agipd_base = h5_data_path.format(channel)
self.idx_base = h5_index_path.format(channel)
@@ -115,6 +119,7 @@ class AgipdCorrections:
self.il_mode = il_mode
self.cal_det_instance = cal_det_instance
self.karabo_data_mode = karabo_data_mode
+ self.force_hg_if_below = force_hg_if_below
def get_iteration_range(self):
"""Returns a range expression over which to iterate in chunks
@@ -794,6 +799,10 @@ class AgipdCorrections:
gain[ga > t0[cellid, ...]] = 1
# exceeding also second threshold means data is low gain
gain[ga > t1[cellid, ...]] = 2
+
+ # force into high gain if requested
+ if self.force_hg_if_below is not None and self.force_hg_if_below > 0:
+ gain[(im - self.offset[cellid, ...,0]) < self.force_hg_if_below] = 0
# check if any data has zero standard deviation, and mark this in
# the bad pixel maks
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index f53ea15e8fa88273bd4de502c14149f165deddbc..d0b696711733400fe8527095e00a2e6348d5d72a 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -13,22 +13,22 @@
},
{
"cell_type": "code",
- "execution_count": 9,
+ "execution_count": 1,
"metadata": {
"ExecuteTime": {
- "end_time": "2019-01-11T09:27:55.381275Z",
- "start_time": "2019-01-11T09:27:55.317063Z"
+ "end_time": "2019-02-12T14:30:10.801940Z",
+ "start_time": "2019-02-12T14:30:10.732217Z"
},
"collapsed": false
},
"outputs": [],
"source": [
"in_folder = \"/gpfs/exfel/exp/SPB/201801/p002108/raw/\" # the folder to read data from, required\n",
- "run = 410 # runs to process, required\n",
- "out_folder = \"/gpfs/exfel/data/scratch/haufs/test/\" # the folder to output to, required\n",
+ "run = 334 # runs to process, required\n",
+ "out_folder = \"/gpfs/exfel/exp/SPB/201801/p002108/proc/reproc/no_rel_gain_blc_fix_indices_forced_gain/\" # the folder to output to, required\n",
"calfile = \"/gpfs/exfel/data/scratch/haufs/agipd_on_demand/agipd_store.h5\" # path to calibration file. Leave empty if all data should come from DB\n",
"sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
- "mem_cells = 176 # memory cells in data\n",
+ "mem_cells = 128 # memory cells in data\n",
"interlaced = False # whether data is in interlaced layout\n",
"overwrite = True # set to True if existing data should be overwritten\n",
"no_relative_gain = True # do not do relative gain correction\n",
@@ -54,6 +54,7 @@
"chunk_size_idim = 32 # chunking size of imaging dimension, adjust if user software is sensitive to this.\n",
"creation_date_offset = \"00:00:00\" # add an offset to creation date, e.g. to get different constants\n",
"instrument = \"SPB\" # the instrument the detector is installed at, required\n",
+ "force_hg_if_below = 0 # set to a value other than 0 to force a pixel into high gain if it's high gain offset subtracted value is below this threshold\n",
"\n",
"def balance_sequences(in_folder, run, sequences, sequences_per_node):\n",
" import glob\n",
@@ -79,23 +80,31 @@
},
{
"cell_type": "code",
- "execution_count": 10,
+ "execution_count": 2,
"metadata": {
"ExecuteTime": {
- "end_time": "2019-01-11T09:27:55.899528Z",
- "start_time": "2019-01-11T09:27:55.748845Z"
+ "end_time": "2019-02-12T14:30:12.069998Z",
+ "start_time": "2019-02-12T14:30:10.804460Z"
},
"collapsed": false
},
"outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "/home/haufs/calkarabo/karabo/extern/lib/python3.4/importlib/_bootstrap.py:321: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\n",
+ " return f(*args, **kwds)\n"
+ ]
+ },
{
"name": "stdout",
"output_type": "stream",
"text": [
"Connecting to profile noDB\n",
- "Using 2018-10-23 06:05:21.207336 as creation time\n",
- "Working in IL Mode: False. Actual cells in use are: 176\n",
- "Outputting to /gpfs/exfel/data/scratch/haufs/test//r0410\n",
+ "Using 2018-10-22 23:12:12.894488 as creation time\n",
+ "Working in IL Mode: False. Actual cells in use are: 128\n",
+ "Outputting to /gpfs/exfel/exp/SPB/201801/p002108/proc/reproc/no_rel_gain_blc_fix_indices_forced_gain//r0334\n",
"Detector in use is SPB_DET_AGIPD1M-1\n"
]
}
@@ -186,11 +195,11 @@
},
{
"cell_type": "code",
- "execution_count": 11,
+ "execution_count": 3,
"metadata": {
"ExecuteTime": {
- "end_time": "2019-01-11T09:27:56.435155Z",
- "start_time": "2019-01-11T09:27:56.388218Z"
+ "end_time": "2019-02-12T14:30:12.092645Z",
+ "start_time": "2019-02-12T14:30:12.071720Z"
},
"collapsed": true
},
@@ -246,11 +255,11 @@
},
{
"cell_type": "code",
- "execution_count": 12,
+ "execution_count": 4,
"metadata": {
"ExecuteTime": {
- "end_time": "2019-01-11T09:27:56.889297Z",
- "start_time": "2019-01-11T09:27:56.830345Z"
+ "end_time": "2019-02-12T14:30:12.132514Z",
+ "start_time": "2019-02-12T14:30:12.094044Z"
},
"collapsed": false
},
@@ -309,11 +318,10 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": null,
"metadata": {
"ExecuteTime": {
- "end_time": "2019-01-11T09:27:57.944770Z",
- "start_time": "2019-01-11T09:27:57.901437Z"
+ "start_time": "2019-02-12T13:30:10.738Z"
},
"collapsed": false
},
@@ -322,7 +330,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Processing a total of 32 sequence files in chunks of 32\n"
+ "Processing a total of 48 sequence files in chunks of 32\n"
]
},
{
@@ -330,40 +338,56 @@
"text/latex": [
"\\begin{tabular}{rlrl}\n",
"\\hline\n",
- " \\# & module & \\# module & file \\\\\n",
+ " \\# & module & \\# module & file \\\\\n",
"\\hline\n",
- " 0 & Q1M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD00-S00000.h5 \\\\\n",
- " 1 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD00-S00001.h5 \\\\\n",
- " 2 & Q1M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD01-S00000.h5 \\\\\n",
- " 3 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD01-S00001.h5 \\\\\n",
- " 4 & Q1M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD02-S00000.h5 \\\\\n",
- " 5 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD02-S00001.h5 \\\\\n",
- " 6 & Q1M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD03-S00000.h5 \\\\\n",
- " 7 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD03-S00001.h5 \\\\\n",
- " 8 & Q2M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD04-S00000.h5 \\\\\n",
- " 9 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD04-S00001.h5 \\\\\n",
- " 10 & Q2M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD05-S00000.h5 \\\\\n",
- " 11 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD05-S00001.h5 \\\\\n",
- " 12 & Q2M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD06-S00000.h5 \\\\\n",
- " 13 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD06-S00001.h5 \\\\\n",
- " 14 & Q2M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD07-S00000.h5 \\\\\n",
- " 15 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD07-S00001.h5 \\\\\n",
- " 16 & Q3M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD08-S00000.h5 \\\\\n",
- " 17 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD08-S00001.h5 \\\\\n",
- " 18 & Q3M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD09-S00000.h5 \\\\\n",
- " 19 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD09-S00001.h5 \\\\\n",
- " 20 & Q3M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD10-S00000.h5 \\\\\n",
- " 21 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD10-S00001.h5 \\\\\n",
- " 22 & Q3M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD11-S00000.h5 \\\\\n",
- " 23 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD11-S00001.h5 \\\\\n",
- " 24 & Q4M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD12-S00000.h5 \\\\\n",
- " 25 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD12-S00001.h5 \\\\\n",
- " 26 & Q4M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD13-S00000.h5 \\\\\n",
- " 27 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD13-S00001.h5 \\\\\n",
- " 28 & Q4M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD14-S00000.h5 \\\\\n",
- " 29 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD14-S00001.h5 \\\\\n",
- " 30 & Q4M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD15-S00000.h5 \\\\\n",
- " 31 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw/r0410/RAW-R0410-AGIPD15-S00001.h5 \\\\\n",
+ " 0 & Q1M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD00-S00000.h5 \\\\\n",
+ " 1 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD00-S00001.h5 \\\\\n",
+ " 2 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD00-S00002.h5 \\\\\n",
+ " 3 & Q1M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD01-S00000.h5 \\\\\n",
+ " 4 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD01-S00001.h5 \\\\\n",
+ " 5 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD01-S00002.h5 \\\\\n",
+ " 6 & Q1M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD02-S00000.h5 \\\\\n",
+ " 7 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD02-S00001.h5 \\\\\n",
+ " 8 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD02-S00002.h5 \\\\\n",
+ " 9 & Q1M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD03-S00000.h5 \\\\\n",
+ " 10 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD03-S00001.h5 \\\\\n",
+ " 11 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD03-S00002.h5 \\\\\n",
+ " 12 & Q2M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD04-S00000.h5 \\\\\n",
+ " 13 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD04-S00001.h5 \\\\\n",
+ " 14 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD04-S00002.h5 \\\\\n",
+ " 15 & Q2M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD05-S00000.h5 \\\\\n",
+ " 16 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD05-S00001.h5 \\\\\n",
+ " 17 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD05-S00002.h5 \\\\\n",
+ " 18 & Q2M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD06-S00000.h5 \\\\\n",
+ " 19 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD06-S00001.h5 \\\\\n",
+ " 20 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD06-S00002.h5 \\\\\n",
+ " 21 & Q2M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD07-S00000.h5 \\\\\n",
+ " 22 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD07-S00001.h5 \\\\\n",
+ " 23 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD07-S00002.h5 \\\\\n",
+ " 24 & Q3M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD08-S00000.h5 \\\\\n",
+ " 25 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD08-S00001.h5 \\\\\n",
+ " 26 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD08-S00002.h5 \\\\\n",
+ " 27 & Q3M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD09-S00000.h5 \\\\\n",
+ " 28 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD09-S00001.h5 \\\\\n",
+ " 29 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD09-S00002.h5 \\\\\n",
+ " 30 & Q3M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD10-S00000.h5 \\\\\n",
+ " 31 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD10-S00001.h5 \\\\\n",
+ " 32 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD10-S00002.h5 \\\\\n",
+ " 33 & Q3M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD11-S00000.h5 \\\\\n",
+ " 34 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD11-S00001.h5 \\\\\n",
+ " 35 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD11-S00002.h5 \\\\\n",
+ " 36 & Q4M1 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD12-S00000.h5 \\\\\n",
+ " 37 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD12-S00001.h5 \\\\\n",
+ " 38 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD12-S00002.h5 \\\\\n",
+ " 39 & Q4M2 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD13-S00000.h5 \\\\\n",
+ " 40 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD13-S00001.h5 \\\\\n",
+ " 41 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD13-S00002.h5 \\\\\n",
+ " 42 & Q4M3 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD14-S00000.h5 \\\\\n",
+ " 43 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD14-S00001.h5 \\\\\n",
+ " 44 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD14-S00002.h5 \\\\\n",
+ " 45 & Q4M4 & 0 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD15-S00000.h5 \\\\\n",
+ " 46 & & 1 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD15-S00001.h5 \\\\\n",
+ " 47 & & 2 & /gpfs/exfel/exp/SPB/201801/p002108/raw//r0334/RAW-R0334-AGIPD15-S00002.h5 \\\\\n",
"\\hline\n",
"\\end{tabular}"
],
@@ -403,7 +427,7 @@
"execution_count": null,
"metadata": {
"ExecuteTime": {
- "start_time": "2019-01-11T08:28:49.990Z"
+ "start_time": "2019-02-12T13:30:10.746Z"
},
"collapsed": false
},
@@ -414,27 +438,18 @@
"text": [
"Running 32 tasks parallel\n",
"INDEX/SPB_DET_AGIPD1M-1/DET/0CH0:xtdf/\n",
- "Offset was injected on: 2018-10-21 20:55:02+02:00\n",
- "Noise was injected on: 2018-10-21 20:55:02+02:00\n",
- "BadPixelsDark was injected on: 2018-10-21 20:55:02+02:00\n",
- "ThresholdsDark was injected on: 2018-10-21 20:55:02+02:00\n",
- "(27776,) 27775\n",
- "Offet medians are [4957. 7500. 7724.]\n",
- "Threshold medians are [6268.75 7083.5 ]\n",
+ "Offset was injected on: 2018-10-22 22:24:16+02:00\n",
+ "Noise was injected on: 2018-10-22 22:24:16+02:00\n",
+ "BadPixelsDark was injected on: 2018-10-22 22:24:16+02:00\n",
+ "ThresholdsDark was injected on: 2018-10-22 22:24:16+02:00\n",
+ "(28544,) 28543\n",
+ "Offet medians are [5094. 7641. 7866.]\n",
+ "Threshold medians are [6414.5 7233.75]\n",
"After reading from file: \n",
- "Offet medians are [4957. 7397.23876953 7724. ]\n",
- "Gain medians are [ 0.9968053 33.925804 152.13365 ]\n",
- "Threshold medians are [6268.75 7083.5 ]\n",
- "Initialized constants\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n",
- "Iterated\n"
+ "Offet medians are [5094. 7529.09924316 7866. ]\n",
+ "Gain medians are [ 0.9956078 33.962654 152.29889 ]\n",
+ "Threshold medians are [6414.5 7233.75]\n",
+ "Initialized constants\n"
]
}
],
@@ -444,7 +459,7 @@
"def correct_module(max_cells, do_rel_gain, index_v, CHUNK_SIZE, total_sequences, sequences_qm, \n",
" bins_gain_vs_signal, bins_signal_low_range, bins_signal_high_range,\n",
" bins_dig_gain_vs_signal, max_pulses, dbparms, fileparms, nodb, chunk_size_idim,\n",
- " special_opts, il_mode, loc, dinstance, inp):\n",
+ " special_opts, il_mode, loc, dinstance, force_hg_if_below, inp):\n",
" import numpy as np\n",
" import copy\n",
" import h5py\n",
@@ -510,7 +525,7 @@
" il_mode=il_mode, raw_fmt_version=index_v, \n",
" h5_data_path=\"INSTRUMENT/{}/DET/{{}}CH0:xtdf/\".format(loc),\n",
" h5_index_path=\"INDEX/{}/DET/{{}}CH0:xtdf/\".format(loc),\n",
- " cal_det_instance=dinstance)\n",
+ " cal_det_instance=dinstance, force_hg_if_below=force_hg_if_below)\n",
" \n",
" blc_noise, blc_noise_threshold, blc_hist, match_asics, corr_asic_diag, melt_snow = special_opts\n",
" agipd_corr.baseline_corr_using_noise = blc_noise\n",
@@ -599,7 +614,7 @@
" p = partial(correct_module, max_cells, do_rel_gain, index_v, CHUNK_SIZE, total_sequences,\n",
" sequences_qm, bins_gain_vs_signal, bins_signal_low_range, bins_signal_high_range,\n",
" bins_dig_gain_vs_signal, max_pulses, dbparms, fileparms, nodb, chunk_size_idim,\n",
- " special_opts, il_mode, loc, dinstance)\n",
+ " special_opts, il_mode, loc, dinstance, force_hg_if_below)\n",
" \n",
" r = view.map_sync(p, inp)\n",
" \n",