diff --git a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
index 3401a39b86ab21ce34ab066d60202ba0cb5051bc..50a7b7559a2bcf9f979cfc143207b9e9b1114c9e 100644
--- a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
@@ -13,28 +13,28 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"cluster_profile = 'noDB' # the ipcluster profile name\n",
- "in_folder = '/gpfs/exfel/exp/FXE/201931/p900089/raw/' # folder under which runs are located, required\n",
- "out_folder = '/gpfs/exfel/data/scratch/karnem/test_dark/' # path to place reports at, required\n",
+ "in_folder = '/gpfs/exfel/exp/FXE/202030/p900121/raw/' # folder under which runs are located, required\n",
+ "out_folder = '/gpfs/exfel/exp/HSLAB/201831/p900053/proc/proc_data/FXE/p900121/test_dark/' # path to place reports at, required\n",
"sequences = 1 # number of sequence files in that run\n",
- "run_high = 86 # run number for G0 dark run, required\n",
- "run_med = 87 # run number for G1 dark run, required\n",
- "run_low = 88 # run number for G2 dark run, required\n",
+ "run_high = 130 # run number for G0 dark run, required\n",
+ "run_med = 131 # run number for G1 dark run, required\n",
+ "run_low = 132 # run number for G2 dark run, required\n",
"\n",
- "karabo_da = ['JNGFR01'] # list of data aggregators, which corresponds to different JF modules\n",
- "karabo_id = \"FXE_XAD_JF1M\" # bla karabo prefix of Jungfrau devices\n",
+ "karabo_da = ['JNGFR03'] # list of data aggregators, which corresponds to different JF modules\n",
+ "karabo_id = \"FXE_XAD_JF500K\" # bla karabo prefix of Jungfrau devices\n",
"karabo_id_control = \"\" # if control is on a different ID, set to empty string if it is the same a karabo-id\n",
- "receiver_id = 'RECEIVER-{}' # inset for receiver devices\n",
+ "receiver_id = 'JNGFR{:02d}' # inset for receiver devices\n",
"receiver_control_id = \"CONTROL\" # inset for control devices\n",
"path_template = 'RAW-R{:04d}-{}-S{{:05d}}.h5' # template to use for file name, double escape sequence number\n",
"h5path = '/INSTRUMENT/{}/DET/{}:daqOutput/data' # path in H5 file under which images are located\n",
"h5path_run = '/RUN/{}/DET/{}' # path to run data\n",
"h5path_cntrl = '/CONTROL/{}/DET/{}' # path to control data\n",
- "karabo_da_control = \"JNGFR01\" # file inset for control data\n",
+ "karabo_da_control = \"JNGFRCTRL00\" # file inset for control data\n",
"\n",
"use_dir_creation_date = True # use dir creation date\n",
"cal_db_interface = 'tcp://max-exfl016:8016' # calibrate db interface to connect to\n",
@@ -44,7 +44,7 @@
"\n",
"integration_time = 1000 # integration time in us, will be overwritten by value in file\n",
"bias_voltage = 90 # sensor bias voltage in V, will be overwritten by value in file\n",
- "badpixel_threshold_sigma = 20. # bad pixels defined by values outside n times this std from median\n",
+ "badpixel_threshold_sigma = 5. # bad pixels defined by values outside n times this std from median\n",
"offset_abs_threshold_low = [1000, 10000, 10000] # absolute bad pixel threshold in terms of offset, lower values\n",
"offset_abs_threshold_high = [8000, 15000, 15000] # absolute bad pixel threshold in terms of offset, upper values\n",
"chunkSize = 10 # iteration chunk size, needs to match or be less than number of images in a sequence file\n",
@@ -57,7 +57,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"metadata": {
"code_folding": []
},
@@ -83,7 +83,7 @@
"from XFELDetAna.detectors.jungfrau import readerPSI as jfreaderPSI\n",
"from XFELDetAna.detectors.jungfrau import reader as jfreader\n",
"from XFELDetAna.detectors.jungfrau.jf_chunk_reader import JFChunkReader\n",
- "from XFELDetAna.detectors.jungfrau.util import non_empty_trains, count_n_files, rollout_data, sanitize_data_cellid\n",
+ "from XFELDetAna.detectors.jungfrau.util import count_n_files, rollout_data, sanitize_data_cellid\n",
"import glob\n",
"import matplotlib.pyplot as plt\n",
"%matplotlib inline\n",
@@ -97,9 +97,20 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 3,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Using 2020-03-04 11:22:16.791550 as creation time\n",
+ "Calibration database interface: tcp://max-exfl016:8016\n",
+ "Path inset JNGFR03\n",
+ "Receiver Id JNGFR03\n"
+ ]
+ }
+ ],
"source": [
"path_inset = karabo_da[0] # karabo_da is a concurrency parameter\n",
"receiver_id = receiver_id.format(int(path_inset[-2:]))\n",
@@ -141,7 +152,7 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
@@ -160,9 +171,35 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 5,
"metadata": {},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Gain stage 0, run 126\n",
+ "Integration time is 250.00001525878906 us\n",
+ "Bias voltage is 90 V\n",
+ "Dark runs in single cell mode\n",
+ " storage cell start: 15\n",
+ "Reading data from /gpfs/exfel/exp/FXE/202030/p900121/raw//r0126//RAW-R0126-JNGFR03-S{:05d}.h5\n",
+ "Run is: 126\n",
+ "HDF5 path: /INSTRUMENT/FXE_XAD_JF500K/DET/JNGFR03:daqOutput/data\n"
+ ]
+ },
+ {
+ "ename": "KeyboardInterrupt",
+ "evalue": "",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-5-2cdbfae5a631>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 72\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 73\u001b[0m \u001b[0midxs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnonzero\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtrainId\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 74\u001b[0;31m \u001b[0mimages\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mimages\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m...\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midxs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 75\u001b[0m \u001b[0mgainmaps\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgainmaps\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m...\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midxs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 76\u001b[0m \u001b[0mfr_num\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfr_num\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m...\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midxs\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
+ ]
+ }
+ ],
"source": [
"chunkSize = 100\n",
"filep_size = 1000\n",
@@ -236,7 +273,7 @@
" \n",
" \n",
" \n",
- " idxs = non_empty_trains(trainId)\n",
+ " idxs = np.nonzero(trainId)[0]\n",
" images = images[..., idxs]\n",
" gainmaps = gainmaps[..., idxs]\n",
" fr_num = fr_num[..., idxs]\n",
@@ -516,7 +553,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.7.6"
+ "version": "3.6.7"
}
},
"nbformat": 4,