From 73ef8b0db19d9bd5315299aed107596b2b00bf84 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Mon, 8 Jan 2024 12:53:02 +0100
Subject: [PATCH] remove gainCal_JF_Fit_sendDB_NBC after moving the code to
creat_gain_map NB
---
.../Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb | 302 ------------------
1 file changed, 302 deletions(-)
delete 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
deleted file mode 100755
index b0f3f6d30..000000000
--- a/notebooks/Jungfrau/gainCal_JF_Fit_sendDB_NBC.ipynb
+++ /dev/null
@@ -1,302 +0,0 @@
-{
- "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/exp/MID/202330/p900322/raw'\n",
- "g_map_old_dir = '/gpfs/exfel/data/user/mramilli/jungfrau/module_PSI_gainmaps/M302'\n",
- "gain_map_file = '/gainMaps_M109_Burst_Fix_20230523.h5' # path\n",
- "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/jf_ff/gain_maps\"\n",
- "metadata_folder = '' # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
- "\n",
- "g0_runs = [94]\n",
- "\n",
- "# Detector module parameters.\n",
- "karabo_id = 'MID_EXP_JF500K2'\n",
- "karabo_da = ['JNGFR02']\n",
- "\n",
- "# Parameter conditions\n",
- "bias_voltage = -1 # detector bias voltage\n",
- "integration_time = -1 # the detector acquisition rate, use 0 to try to auto-determine\n",
- "gain_setting = 0\n",
- "gain_mode = 0\n",
- "memory_cells = -1 # 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 = False\n",
- "send_bpix = False\n",
- "\n",
- "# CALCAT API parameters\n",
- "cal_db_interface = \"tcp://max-exfl-cal-001:8020\" # 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",
- "from pathlib import Path\n",
- "\n",
- "import dateutil.parser\n",
- "import matplotlib.pyplot as plt\n",
- "import numpy as np\n",
- "from h5py import File as h5file\n",
- "from iCalibrationDB import Conditions, Constants\n",
- "from XFELDetAna.plotting.heatmap import heatmapPlot\n",
- "\n",
- "from cal_tools.calcat_interface import CalCatApi\n",
- "from cal_tools.restful_config import calibration_client\n",
- "from cal_tools.tools import calcat_creation_time, get_report, send_to_db\n",
- "\n",
- "%matplotlib inline"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "if gain_setting == 1:\n",
- " gain_map_name = 'gain_map_hg0'\n",
- "da_name = karabo_da[0]\n",
- "g_map_old_dir = Path(g_map_old_dir)\n",
- "in_folder = Path(in_folder)\n",
- "out_folder = Path(out_folder)\n",
- "gain_file = g_map_old_dir / gain_map_file\n",
- "g0_run = g0_runs[0]\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",
- "calcat_client = calibration_client()\n",
- "calcat = CalCatApi(client=calcat_client)\n",
- "\n",
- "# Look up PDUs\n",
- "detector_id = calcat.detector(karabo_id)['id']\n",
- "pdus_by_da = calcat.physical_detector_units(\n",
- " detector_id, pdu_snapshot_at=creation_time)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Read constants from file\n",
- "constant_data = {}\n",
- "\n",
- "gain_map = None\n",
- "bad_pixel_ff = None\n",
- "pdu = pdus_by_da[da_name][\"physical_name\"]\n",
- "with h5file(out_folder / f\"const_RelativeGain_{pdu}.h5\", 'r') as f:\n",
- " gain_map = np.array(f[\"data\"])\n",
- " \n",
- " if memory_cells < 0:\n",
- " memory_cells = int(gain_map.shape[-2])\n",
- " # memory_cells = int(f[\"condition\"][\"Memory cells\"][\"value\"][()])\n",
- " print(f'Memory Cells: {memory_cells}')\n",
- "\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 < 0:\n",
- " integration_time = np.float32(f[\"condition\"][\"Integration Time\"][\"value\"][()])\n",
- " print(f'Integration time: {integration_time} us')\n",
- " else:\n",
- " print(f'Using manual set integration_time {integration_time} us')\n",
- "\n",
- " if bias_voltage < 0:\n",
- " bias_voltage = np.float32(f[\"condition\"][\"Sensor Bias Voltage\"][\"value\"][()])\n",
- " print(f'Bias voltage: {bias_voltage} V')\n",
- " else:\n",
- " print(f'Using manual set bias_voltage: {bias_voltage} V')\n",
- "\n",
- " if 'creation_time' in f.keys():\n",
- " creation_time = f['creation_time'][()].decode('utf-8')\n",
- " creation_time = dateutil.parser.isoparse(creation_time)\n",
- " print(f'Creation Time: {creation_time}')\n",
- " else:\n",
- " print(f'Using this date: {creation_time}')\n",
- "\n",
- " if 'file_loc' in f.keys():\n",
- " file_loc = f['file_loc'][()].decode('utf-8')\n",
- " print(f'file_loc: {file_loc}')\n",
- " else:\n",
- " proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
- " file_loc = f\"proposal:{proposal} runs:{g0_run}\"\n",
- " print(f'Using this file_loc: {file_loc}')\n",
- "\n",
- " if 'report_path' in f.keys():\n",
- " report_path = f['report_path'][()].decode('utf-8')\n",
- " print(f'report_path: {report_path}')\n",
- " else:\n",
- " report_path = get_report(metadata_folder)\n",
- " print(f'Using this report_path: {report_path}')\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 < 0:\n",
- " if \"gain_mode\" in f[\"condition\"].keys():\n",
- " gain_mode = np.int(f[\"condition\"][\"Gain Mode\"][\"value\"][()])\n",
- " else:\n",
- " gain_mode = 0\n",
- " print(f'Gain mode: {gain_mode}')\n",
- " else:\n",
- " print(f'Using manual set gain_mode {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=pdu,\n",
- " karabo_id=karabo_id, \n",
- " constant=gain, \n",
- " condition=condition, \n",
- " file_loc=file_loc, \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=pdu,\n",
- " karabo_id=karabo_id,\n",
- " constant=bpix_ff, \n",
- " condition=condition, \n",
- " file_loc=file_loc,\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
-}
--
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