Feat/dss cimprove master rebasing

notebooks/DSSC/Characterize_DSSC_Darks_NBC.ipynb

@@ -27,40 +27,40 @@
    "source": [
     "cluster_profile = \"noDB\" # The ipcluster profile to use\n",
     "in_folder = \"/gpfs/exfel/exp/SCS/202030/p900125/raw\" # path to input data, required\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/DSSC\" # path to output to, required\n",
-    "=======",
+    "=======\n",
     "out_folder = \"/gpfs/exfel/data/scratch/samartse/test/\" # path to output to, required\n",
-    ">>>>>>> modified notebook for DSSC specifics",
+    ">>>>>>> modified notebook for DSSC specifics\n",
     "sequences = [0] # sequence files to evaluate.\n",
     "modules = [-1]  # modules to run for\n",
     "run = 222 # run numbr in which data was recorded, required\n",
     "\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "karabo_id = \"SCS_DET_DSSC1M-1\" # karabo karabo_id\n",
     "karabo_da = ['-1']  # a list of data aggregators names, Default [-1] for selecting all data aggregators\n",
     "receiver_id = \"{}CH0\" # inset for receiver devices\n",
     "path_template = 'RAW-R{:04d}-{}-S{:05d}.h5' # the template to use to access data\n",
     "h5path = '/INSTRUMENT/{}/DET/{}:xtdf/image' # path in the HDF5 file to images\n",
     "h5path_idx = '/INDEX/{}/DET/{}:xtdf/image' # path in the HDF5 file to images\n",
-    "=======",
+    "=======\n",
     "run = 203 # run number in which data was recorded, required\n",
-    ">>>>>>> modified notebook for DSSC specifics",
+    ">>>>>>> modified notebook for DSSC specifics\n",
     "\n",
     "use_dir_creation_date = True # use the dir creation date for determining the creation time\n",
     "cal_db_interface = \"tcp://max-exfl016:8020\" # the database interface to use\n",
     "cal_db_timeout = 3000000 # timeout on caldb requests\"\n",
     "local_output = True # output constants locally\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "db_output = False # output constants to database\n",
     "\n",
     "mem_cells = 0 # number of memory cells used, set to 0 to automatically infer\n",
     "bias_voltage = 300 # detector bias voltage\n",
-    "=======",
+    "=======\n",
     "db_output = True # output constants to database\n",
     "bias_voltage = 100 # detector bias voltage\n",
     "cal_db_interface = \"tcp://max-exfl016:8020\" # the database interface to use\n",
-    ">>>>>>> modified notebook for DSSC specifics",
+    ">>>>>>> modified notebook for DSSC specifics\n",
     "rawversion = 2 # RAW file format version\n",
     "\n",
     "thresholds_offset_sigma = 3. # thresholds in terms of n sigma noise for offset deduced bad pixels\n",
@@ -71,14 +71,14 @@
     "offset_numpy_algorithm = \"mean\"\n",
     "\n",
     "instrument = \"SCS\" # the instrument\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "high_res_badpix_3d = False # set this to True if you need high-resolution 3d bad pixel plots. Runtime: ~ 1h",
-    "=======",
+    "=======\n",
     "high_res_badpix_3d = False # set this to True if you need high-resolution 3d bad pixel plots. Runtime: ~ 1h\n",
     "modules = [i for i in range(16)]  # modules to run for\n",
     "slow_data_pattern = 'RAW-R{}-DA{}-S[0-9]+\\.h5'\n",
     "slow_data_aggregators = {1:1,2:2,3:3,4:4} #quadrant/aggregator",
-    ">>>>>>> modified notebook for DSSC specifics"
+    ">>>>>>> modified notebook for DSSC specifics\n"
    ]
   },
   {
@@ -108,13 +108,13 @@
     "import re\n",
     "from os import listdir\n",
     "\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "from cal_tools.tools import (map_gain_stages, parse_runs, run_prop_seq_from_path, \n",
     "                             get_notebook_name, get_dir_creation_date,\n",
     "                             get_random_db_interface, get_from_db, save_const_to_h5)\n",
-    "=======",
+    "=======\n",
     "from cal_tools.tools import gain_map_files, parse_runs, run_prop_seq_from_path, get_notebook_name, get_dir_creation_date\n",
-    ">>>>>>> modified notebook for DSSC specifics",
+    ">>>>>>> modified notebook for DSSC specifics\n",
     "from cal_tools.influx import InfluxLogger\n",
     "from cal_tools.enums import BadPixels\n",
     "from cal_tools.plotting import (show_overview, plot_badpix_3d,\n",
@@ -151,24 +151,24 @@
     "creation_time=None\n",
     "if use_dir_creation_date:\n",
     "    creation_time = get_dir_creation_date(in_folder, run)\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "    print(f\"Using {creation_time} as creation time of constant.\")\n",
     "\n",
-    "=======",
+    "=======\n",
     "\n",
     "run_number = run\n",
-    ">>>>>>> modified notebook for DSSC specifics",
+    ">>>>>>> modified notebook for DSSC specifics\n",
     "run, prop, seq = run_prop_seq_from_path(in_folder)\n",
     "logger = InfluxLogger(detector=\"DSSC\", instrument=instrument, mem_cells=mem_cells,\n",
     "                      notebook=get_notebook_name(), proposal=prop)\n",
     "\n",
     "dinstance = \"DSSC1M1\"\n",
     "\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "print(f\"Detector in use is {karabo_id}\")    \n",
     "\n",
     "cal_db_interface = get_random_db_interface(cal_db_interface)",
-    "=======",
+    "=======\n",
     "loc = None\n",
     "ctrlloc = None\n",
     "if instrument == \"SCS\":\n",
@@ -176,7 +176,7 @@
     "    dinstance = \"DSSC1M1\"\n",
     "\n",
     "print(\"Detector in use is {}\".format(loc))",
-    ">>>>>>> modified notebook for DSSC specifics"
+    ">>>>>>> modified notebook for DSSC specifics\n"
    ]
   },
   {
@@ -341,13 +341,13 @@
     "    if cells == 0:\n",
     "        cells = get_num_cells(filename, h5path)\n",
     "\n",
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "    print(f\"Using {cells} memory cells\")\n",
     "    \n",
     "    pulseid_checksum = None\n",
-    "=======",
+    "=======\n",
     "    pulseid_checksum = None    \n",
-    ">>>>>>> modified notebook for DSSC specifics",
+    ">>>>>>> modified notebook for DSSC specifics\n",
     "\n",
     "    thresholds_offset_hard, thresholds_offset_sigma, thresholds_noise_hard, thresholds_noise_sigma = bp_thresh \n",
     "\n",
@@ -549,7 +549,7 @@
    },
    "outputs": [],
    "source": [
-    "<<<<<<< HEAD",
+    "<<<<<<< HEAD\n",
     "# Push the same constant two different times.\n",
     "# One with the generated pulseID check sum setting for the offline calibration.\n",
     "# And another for the online calibration as it doesn't have this pulseID checksum, yet.\n",
@@ -595,7 +595,7 @@
     "            print(\"Generated constants with conditions:\\n\")\n",
     "            print(f\"• memory_cells: {max_cells}\\n• bias_voltage: {bias_voltage}\\n\"\n",
     "                  f\"• pulseid_checksum: {pidsum}\\n• creation_time: {creation_time}\\n\")",
-    "=======",
+    "=======\n",
     "if db_output:\n",
     "    for dont_use_pulseIds in [True, False]:\n",
     "        for qm in offset_g.keys():\n",
@@ -664,7 +664,7 @@
     "                metadata.send(cal_db_interface, timeout=3000000)\n",
     "            except Exception as e:\n",
     "                print(e)",
-    ">>>>>>> modified notebook for DSSC specifics"
+    ">>>>>>> modified notebook for DSSC specifics\n"
    ]
   },
   {