From 74beb5c973aabb9c97ee36a9d74321988aafbae8 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Wed, 27 Dec 2023 10:57:34 +0100
Subject: [PATCH] send constant to database notebook
---
.../Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb | 276 ++++++++++++++++++
1 file changed, 276 insertions(+)
create mode 100755 notebooks/Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb
diff --git a/notebooks/Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb b/notebooks/Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb
new file mode 100755
index 000000000..2f5266eae
--- /dev/null
+++ b/notebooks/Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb
@@ -0,0 +1,276 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## Send constants from file to the DB"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "in_folder = '/gpfs/exfel/data/user/mramilli/jungfrau/module_PSI_gainmaps/M109'\n",
+ "raw_folder = '/gpfs/exfel/exp/SPB/202330/900322/raw'\n",
+ "gain_map_file = '/gainMaps_M109_Burst_Fix_20230523.h5' # path\n",
+ "g0_run = 94\n",
+ "\n",
+ "# Detector module parameters.\n",
+ "karabo_id = 'SPB_CFEL_JF1M'\n",
+ "da_name = 'JNGFR09'\n",
+ "db_module = \"Jungfrau_M109\" # ID of module in calibration database\n",
+ "\n",
+ "# Parameter conditions\n",
+ "bias_voltage = 180 # detector bias voltage\n",
+ "integration_time = 10 # the detector acquisition rate, use 0 to try to auto-determine\n",
+ "gain_setting = 0\n",
+ "gain_mode = 0\n",
+ "memory_cells = 0 # number of memory cells used, use 0 to auto-derive\n",
+ "\n",
+ "# Condition limits\n",
+ "bias_voltage_lims = [0, 200]\n",
+ "integration_time_lims = [0.1, 1000]\n",
+ "\n",
+ "gain_map_name = 'gain_map_g0'\n",
+ "db_output = True\n",
+ "send_bpix = False\n",
+ "\n",
+ "# CALCAT API parameters\n",
+ "cal_db_interface = \"tcp://max-exfl016:8020\" # the database interface to use\n",
+ "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\"\\\n",
+ "cal_db_timeout = 180000"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# imports, usually no need to change anything here\n",
+ "import os\n",
+ "from h5py import File as h5file\n",
+ "import numpy as np\n",
+ "import datetime\n",
+ "\n",
+ "import dateutil.parser\n",
+ "from iCalibrationDB import (\n",
+ " Constants,\n",
+ " Conditions,\n",
+ ")\n",
+ "from cal_tools.tools import (\n",
+ " send_to_db,\n",
+ " calcat_creation_time\n",
+ ")\n",
+ "from pathlib import Path\n",
+ "import matplotlib.pyplot as plt\n",
+ "from XFELDetAna.plotting.heatmap import heatmapPlot\n",
+ "%matplotlib inline"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if gain_setting == 1:\n",
+ " gain_map_name = 'gain_map_hg0'\n",
+ "\n",
+ "in_folder = Path(in_folder)\n",
+ "raw_folder = Path(raw_folder)\n",
+ "\n",
+ "in_file = in_folder / gain_map_file"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Read constants from file\n",
+ "constant_data = {}\n",
+ "\n",
+ "# Run's creation time:\n",
+ "creation_time = calcat_creation_time(in_folder, g0_run, creation_time)\n",
+ "print(f\"Creation time: {creation_time}\")\n",
+ "\n",
+ "gain_map = None\n",
+ "bad_pixel_ff = None\n",
+ "\n",
+ "with h5file(in_file, 'r') as f:\n",
+ " gain_map = np.array(f[gain_map_name])\n",
+ " \n",
+ " if memory_cells == 0:\n",
+ " memory_cells = int(gain_map.shape[-2])\n",
+ " print(f'Memory Cells: {memory_cells}')\n",
+ " if 'bad_pixel_fit' in f.keys():\n",
+ " bad_pixel_ff = np.array(f['bad_pixel_fit'])\n",
+ " print(bad_pixel_ff.shape)\n",
+ " else:\n",
+ " print('BadPixelsFF not found')\n",
+ " \n",
+ " if 'integration_time' in f.attrs.keys():\n",
+ " integration_time = np.float32(f.attrs['integration_time'])\n",
+ " print(f'Integration time: {integration_time} us')\n",
+ " else:\n",
+ " print('integration_time not found, using default {} us'.format(integration_time))\n",
+ " \n",
+ " if 'bias_voltage' in f.attrs.keys():\n",
+ " bias_voltage = np.float32(f.attrs['bias_voltage'])\n",
+ " print(f'Bias voltage: {bias_voltage} V')\n",
+ " else:\n",
+ " print('bias_voltage not found, using default {} V'.format(bias_voltage))\n",
+ "\n",
+ " if 'dir_date_iso' in f.attrs.keys():\n",
+ " dir_date_iso = str(f.attrs['dir_date_iso'])\n",
+ " creation_time = dateutil.parser.isoparse(dir_date_iso)\n",
+ " print(f'Acquisition Time: {creation_time}')\n",
+ " else:\n",
+ " print(f'Acquisition date not found!\\nUsing this date: {creation_time}')\n",
+ "\n",
+ " if 'karabo_id' in f.attrs.keys():\n",
+ " if isinstance(f.attrs['karabo_id'], str):\n",
+ " karabo_id = str(f.attrs['karabo_id'])\n",
+ " print(f'Karabo ID: {karabo_id}')\n",
+ " else:\n",
+ " print(f'karabo id not a string, using {karabo_id}')\n",
+ " else:\n",
+ " print(f'karabo id not found, using {karabo_id}')\n",
+ " \n",
+ " if 'da_name' in f.attrs.keys():\n",
+ " if isinstance(f.attrs['da_name'], str):\n",
+ " da_name = str(f.attrs['da_name'])\n",
+ " print(f'DA name: {da_name}')\n",
+ " else:\n",
+ " print(f'DA name not a string, using {da_name}')\n",
+ " else:\n",
+ " print(f'DA name not found, using {da_name}')\n",
+ "\n",
+ " if 'gain_mode' in f.attrs.keys():\n",
+ " gain_mode = np.int(f.attrs['gain_mode'])\n",
+ " print(f'Gain mode: {gain_mode}')\n",
+ " else:\n",
+ " print(f'gain mode not found, using default {gain_mode}')\\\n",
+ "\n",
+ " f.close()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "gain = Constants.jungfrau.RelativeGain()\n",
+ "gain.data = gain_map\n",
+ "\n",
+ "condition = Conditions.Dark.jungfrau(\n",
+ " memory_cells=memory_cells, \n",
+ " bias_voltage=bias_voltage,\n",
+ " integration_time=integration_time,\n",
+ " gain_mode=gain_mode,\n",
+ " gain_setting=gain_setting)\n",
+ "\n",
+ "for parm in condition.parameters:\n",
+ " if parm.name == \"Integration Time\":\n",
+ " print('setting integration time limits')\n",
+ " parm.lower_deviation = integration_time - integration_time_lims[0]\n",
+ " parm.upper_deviation = integration_time_lims[1] - integration_time\n",
+ "\n",
+ "for parm in condition.parameters:\n",
+ " if parm.name == \"Sensor Bias Voltage\":\n",
+ " print('setting bias voltage limits')\n",
+ " parm.lower_deviation = bias_voltage - bias_voltage_lims[0]\n",
+ " parm.upper_deviation = bias_voltage_lims[1] - bias_voltage"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "print('Creating time: ', creation_time)\n",
+ "\n",
+ "if db_output:\n",
+ " send_to_db(\n",
+ " db_module=db_module,\n",
+ " karabo_id=karabo_id, \n",
+ " constant=gain, \n",
+ " condition=condition, \n",
+ " file_loc=in_file, \n",
+ " report_path='',\n",
+ " cal_db_interface=cal_db_interface,\n",
+ " creation_time=creation_time,\n",
+ " )\n",
+ "\n",
+ "if bad_pixel_ff is not None and send_bpix:\n",
+ " bpix_ff = Constants.jungfrau.BadPixelsFF()\n",
+ " # WHY CONDITION DEVIATIONS ARE NOT CONSIDERED FOR THE BADPIXELS\n",
+ " condition = Conditions.Dark.jungfrau(\n",
+ " memory_cells=memory_cells, \n",
+ " bias_voltage=bias_voltage,\n",
+ " integration_time=integration_time,\n",
+ " gain_setting=gain_setting,\n",
+ " )\n",
+ "\n",
+ " bpix_ff.data = bad_pixel_ff\n",
+ " send_to_db(\n",
+ " db_module=db_module,\n",
+ " karabo_id=karabo_id,\n",
+ " constant=bpix_ff, \n",
+ " condition=condition, \n",
+ " file_loc=in_file,\n",
+ " report_path='',\n",
+ " cal_db_interface=cal_db_interface,\n",
+ " creation_time=creation_time,\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "for g in range(0, gain_map.shape[3]):\n",
+ " f_im = heatmapPlot(\n",
+ " np.swapaxes(gain_map[..., 0, g], 0, 1), \n",
+ " y_label=\"Row\",\n",
+ " x_label=\"Column\",\n",
+ " lut_label=\"G{:01d}[ADCu/keV]\".format(g),\n",
+ " aspect=1.,\n",
+ " vmin=np.min(gain_map[..., 0, g].ravel()),\n",
+ " vmax=np.max(gain_map[..., 0, g].ravel()),\n",
+ " )\n",
+ " plt.show()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.11"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
--
GitLab