From 320dde542d468335ee1b1ccf534ea0c29639c99d Mon Sep 17 00:00:00 2001
From: Karim Ahmed <karim.ahmed@xfel.eu>
Date: Wed, 6 May 2020 00:25:50 +0200
Subject: [PATCH] get memory cells and acquistion rate from file
---
...aracterize_AGIPD_Gain_FlatFields_NBC.ipynb | 80 +++++++++++--------
1 file changed, 47 insertions(+), 33 deletions(-)
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
index 89bb40836..a72c2e167 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
@@ -38,10 +38,10 @@
"sequences = [0,1,2,3]#,4,5,6,7,8] #,5,6,7,8,9,10] # sequences files to use, range allowed\n",
"cluster_profile = \"noDB\" # The ipcluster profile to use\n",
"local_output = True # output constants locally\n",
- "db_output = True # output constants to database\n",
+ "db_output = False # output constants to database\n",
"bias_voltage = 300 # detector bias voltage\n",
"cal_db_interface = \"tcp://max-exfl016:8026#8035\" # the database interface to use\n",
- "mem_cells = 250 # number of memory cells used\n",
+ "mem_cells = 0 # number of memory cells used\n",
"interlaced = False # assume interlaced data format, for data prior to Dec. 2017\n",
"fit_hook = True # fit a hook function to medium gain slope\n",
"rawversion = 2 # RAW file format version\n",
@@ -51,7 +51,7 @@
"high_res_badpix_3d = False # set this to True if you need high-resolution 3d bad pixel plots. Runtime: ~ 1h\n",
"db_input = True # retreive data from calibration database, setting offset-store will overwrite this\n",
"deviation_threshold = 0.75 # peaks with an absolute location deviation larger than the medium are are considere bad\n",
- "acqrate = 2.2 # acquisition rate\n",
+ "acqrate = 0. # acquisition rate\n",
"use_dir_creation_date = True\n",
"creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC.ms e.g. 2019-07-04 11:02:41.00\n",
"gain_setting = 0.1 # gain setting can have value 0 or 1, Default=0.1 for no (None) gain-setting\n",
@@ -61,12 +61,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "ExecuteTime": {
- "end_time": "2019-09-13T07:34:24.830847Z",
- "start_time": "2019-09-13T07:34:24.745094Z"
- }
- },
+ "metadata": {},
"outputs": [],
"source": [
"# std library imports\n",
@@ -101,13 +96,24 @@
"profile = cluster_profile\n",
"\n",
"from iCalibrationDB import ConstantMetaData, Constants, Conditions, Detectors, Versions\n",
- "from cal_tools.agipdlib import get_gain_setting\n",
+ "from cal_tools.agipdlib import get_num_cells, get_acq_rate, get_gain_setting\n",
"from cal_tools.enums import BadPixels\n",
"from cal_tools.influx import InfluxLogger\n",
"from cal_tools.plotting import show_overview, plot_badpix_3d\n",
- "from cal_tools.tools import gain_map_files, parse_runs, run_prop_seq_from_path, get_notebook_name, get_dir_creation_date, get_random_db_interface\n",
- "\n",
- "\n",
+ "from cal_tools.tools import gain_map_files, parse_runs, run_prop_seq_from_path, get_notebook_name, get_dir_creation_date, get_random_db_interface\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2019-09-13T07:34:24.830847Z",
+ "start_time": "2019-09-13T07:34:24.745094Z"
+ }
+ },
+ "outputs": [],
+ "source": [
"# usually no need to change these lines\n",
"sensor_size = [128, 512]\n",
"block_size = [128, 512]\n",
@@ -115,13 +121,6 @@
"MODULES_PER_QUAD = 4\n",
"DET_FILE_INSET = \"AGIPD\"\n",
"\n",
- "IL_MODE = interlaced\n",
- "max_cells = mem_cells if not interlaced else mem_cells*2\n",
- "memory_cells = mem_cells\n",
- "\n",
- "\n",
- "\n",
- "\n",
"# Define constant creation time.\n",
"if creation_time:\n",
" try:\n",
@@ -156,36 +155,51 @@
"limit_trains = 20\n",
"limit_trains_eval = None\n",
"\n",
- "\n",
"print(\"Parameters are:\")\n",
- "print(\"Memory cells: {}/{}\".format(memory_cells, max_cells))\n",
+ "\n",
"print(\"Runs: {}\".format(runs))\n",
"print(\"Modules: {}\".format(modules))\n",
"print(\"Sequences: {}\".format(sequences))\n",
- "print(\"Interlaced mode: {}\".format(IL_MODE))\n",
"print(\"Using DB: {}\".format(db_output))\n",
"\n",
+ "\n",
+ "if instrument == \"SPB\":\n",
+ " loc = \"SPB_DET_AGIPD1M-1\"\n",
+ " dinstance = \"AGIPD1M1\"\n",
+ "else:\n",
+ " loc = \"MID_DET_AGIPD1M-1\"\n",
+ " dinstance = \"AGIPD1M2\"\n",
+ "\n",
+ "cal_db_interface = get_random_db_interface(cal_db_interface)\n",
+ "\n",
"# these lines can usually stay as is\n",
"fbase = \"{}/{{}}/RAW-{{}}-AGIPD{{:02d}}-S{{:05d}}.h5\".format(in_folder)\n",
"gains = np.arange(3)\n",
- "cells = np.arange(max_cells)\n",
- "\n",
"\n",
"\n",
"run, prop, seq = run_prop_seq_from_path(in_folder)\n",
"logger = InfluxLogger(detector=\"AGIPD\", instrument=instrument, mem_cells=mem_cells,\n",
" notebook=get_notebook_name(), proposal=prop)\n",
- "\n",
- "if acqrate == 0:\n",
- " acqrate = None\n",
+ "channel = 0\n",
+ "fname = fbase.format(runs[0], runs[0].upper(), channel, 0)\n",
+ "if acqrate == 0.:\n",
+ " acqrate = get_acq_rate(fname, loc, channel)\n",
" \n",
- "if instrument == \"SPB\":\n",
- " dinstance = \"AGIPD1M1\"\n",
- "else:\n",
- " dinstance = \"AGIPD1M2\"\n",
+ "\n",
+ "if mem_cells == 0:\n",
+ " cells = get_num_cells(fname, loc, channel)\n",
+ " mem_cells = cells # avoid setting twice\n",
" \n",
"\n",
- "cal_db_interface = get_random_db_interface(cal_db_interface)"
+ "IL_MODE = interlaced\n",
+ "max_cells = mem_cells if not interlaced else mem_cells*2\n",
+ "memory_cells = mem_cells\n",
+ "print(\"Interlaced mode: {}\".format(IL_MODE))\n",
+ "\n",
+ "cells = np.arange(max_cells)\n",
+ "\n",
+ "print(f\"Acquisition rate and memory cells set from file {fname} are \" \n",
+ " f\"{acqrate} MHz and {max_cells}, respectively\")"
]
},
{
--
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