diff --git a/notebooks/ePix/Correction_ePix_NBC.ipynb b/notebooks/ePix/Correction_ePix_NBC.ipynb
index 563a1af8e52885b5b1b17533919cc8dcbc44f161..fbf437b79267e09f108e48f2265ec70d0a09c354 100644
--- a/notebooks/ePix/Correction_ePix_NBC.ipynb
+++ b/notebooks/ePix/Correction_ePix_NBC.ipynb
@@ -18,13 +18,12 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:23.218849Z",
"start_time": "2018-12-06T15:54:23.166497Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
"in_folder = \"/gpfs/exfel/exp/MID/201930/p900071/raw\" # input folder, required\n",
- "out_folder = '/gpfs/exfel/data/user/xcal/test/' # output folder, required\n",
+ "out_folder = '/gpfs/exfel/data/scratch/karnem/test/' # output folder, required\n",
"path_template = 'RAW-R{:04d}-{}-S{{:05d}}.h5' # the template to use to access data\n",
"run = 466 # which run to read data from, required\n",
"h5path = '/INSTRUMENT/{}/DET/RECEIVER:daqOutput/data/image' # path in the HDF5 file to images\n",
@@ -50,6 +49,9 @@
"bias_voltage = 200 # bias voltage\n",
"in_vacuum = False # detector operated in vacuum\n",
"fix_temperature = 290. # fix temperature to this value\n",
+ "gain_photon_energy = 9.0 # Photon energy used for gain calibration\n",
+ "photon_energy = 8.0 # Photon energy to calibrate in number of photons, 0 for calibration in keV \n",
+ "no_relative_gain = False # do not do gain correction\n",
"split_evt_primary_threshold = 7. # primary threshold for split event correction\n",
"split_evt_secondary_threshold = 5. # secondary threshold for split event correction\n",
"split_evt_mip_threshold = 1000. # minimum ionizing particle threshold\n",
@@ -82,8 +84,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:23.455376Z",
"start_time": "2018-12-06T15:54:23.413579Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -129,7 +130,13 @@
"\n",
"h5path = h5path.format(instance)\n",
"h5path_t = h5path_t.format(instance)\n",
- "h5path_cntrl = h5path_cntrl.format(instance)"
+ "h5path_cntrl = h5path_cntrl.format(instance)\n",
+ "\n",
+ "plot_unit = 'ADU'\n",
+ "if not no_relative_gain:\n",
+ " plot_unit = 'keV'\n",
+ " if photon_energy>0:\n",
+ " plot_unit = '$\\gamma$'"
]
},
{
@@ -139,8 +146,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:23.679069Z",
"start_time": "2018-12-06T15:54:23.662821Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -173,7 +179,6 @@
"end_time": "2018-12-06T15:54:23.913269Z",
"start_time": "2018-12-06T15:54:23.868910Z"
},
- "collapsed": false,
"scrolled": true
},
"outputs": [],
@@ -213,8 +218,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:24.088948Z",
"start_time": "2018-12-06T15:54:24.059925Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -252,8 +256,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T18:43:39.776018Z",
"start_time": "2018-12-06T18:43:39.759185Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -283,8 +286,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:28.254544Z",
"start_time": "2018-12-06T15:54:24.709521Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -293,7 +295,7 @@
"offsetMap = None\n",
"temp_limits = 5.\n",
"\n",
- "## offset\n",
+ "# Offset\n",
"det = getattr(Detectors, db_module)\n",
"dconstants = getattr(Constants, dclass)\n",
"\n",
@@ -315,17 +317,52 @@
" None,\n",
" cal_db_interface,\n",
" creation_time=creation_time,\n",
+ " print_once=2,\n",
" timeout=cal_db_timeout)\n",
"\n",
- "\n",
+ "# Noise\n",
"const_name = \"Noise\"\n",
+ "condition = Conditions.Dark.ePix100(bias_voltage=bias_voltage,\n",
+ " integration_time=integration_time,\n",
+ " temperature=temperature_k,\n",
+ " in_vacuum=in_vacuum)\n",
+ "\n",
"noiseMap = get_constant_from_db(det,\n",
" getattr(dconstants, const_name)(),\n",
" condition,\n",
" None,\n",
" cal_db_interface,\n",
" creation_time=creation_time,\n",
- " timeout=cal_db_timeout)\n"
+ " print_once=2,\n",
+ " timeout=cal_db_timeout)\n",
+ "\n",
+ "# Gain\n",
+ "if not no_relative_gain:\n",
+ " const_name = \"RelativeGain\"\n",
+ " condition = Conditions.Illuminated.ePix100(photon_energy=gain_photon_energy,\n",
+ " bias_voltage=bias_voltage,\n",
+ " integration_time=integration_time,\n",
+ " temperature=temperature_k,\n",
+ " in_vacuum=in_vacuum)\n",
+ "\n",
+ " gainMap = get_constant_from_db(det,\n",
+ " getattr(dconstants, const_name)(),\n",
+ " condition,\n",
+ " None,\n",
+ " cal_db_interface,\n",
+ " creation_time=creation_time,\n",
+ " print_once=2,\n",
+ " timeout=cal_db_timeout)\n",
+ " \n",
+ " if gainMap is None:\n",
+ " print(\"Gain map requisted, but not found\")\n",
+ " print(\"No gain correction will be applied\")\n",
+ " no_relative_gain = True\n",
+ " plot_unit = 'ADU'\n",
+ " gainMap = np.ones(sensorSize, np.float32)\n",
+ "\n",
+ "else:\n",
+ " gainMap = np.ones(sensorSize, np.float32)\n"
]
},
{
@@ -335,8 +372,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T15:54:28.771629Z",
"start_time": "2018-12-06T15:54:28.346051Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -347,7 +383,17 @@
" nCells = memoryCells, \n",
" cores=cpuCores, gains=None,\n",
" blockSize=blockSize,\n",
- " parallel=run_parallel)\n"
+ " parallel=run_parallel)\n",
+ "\n",
+ "gainCorrection = xcal.RelativeGainCorrection(\n",
+ " sensorSize, \n",
+ " 1. / gainMap[..., None],\n",
+ " nCells=memoryCells,\n",
+ " parallel=run_parallel,\n",
+ " cores=cpuCores,\n",
+ " blockSize=blockSize,\n",
+ " gains=None)\n",
+ "\n"
]
},
{
@@ -357,8 +403,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:51.886343Z",
"start_time": "2018-12-06T16:08:51.842837Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -386,21 +431,19 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:53.042555Z",
"start_time": "2018-12-06T16:08:53.034522Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
"histCalOffsetCor.debug()\n",
- "offsetCorrection.debug()"
+ "offsetCorrection.debug()\n",
+ "gainCorrection.debug()"
]
},
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"#************************Calculators************************#\n",
@@ -446,9 +489,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": [
"cmCorrection.debug()\n",
@@ -464,8 +505,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:08:53.551111Z",
"start_time": "2018-12-06T16:08:53.531064Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -498,8 +538,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:10:55.917179Z",
"start_time": "2018-12-06T16:09:01.603633Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -525,6 +564,11 @@
" dtype=np.float32)\n",
"\n",
" data = offsetCorrection.correct(data.astype(np.float32)) #correct for the offset\n",
+ " if not no_relative_gain:\n",
+ " data = gainCorrection.correct(data.astype(np.float32)) #correct for the gain\n",
+ " if photon_energy>0:\n",
+ " data /= photon_energy\n",
+ " \n",
" histCalOffsetCor.fill(data)\n",
" ddset[...] = np.moveaxis(data, 2, 0)\n",
" except Exception as e:\n",
@@ -575,8 +619,7 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:13:12.889583Z",
"start_time": "2018-12-06T16:13:11.122653Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -614,7 +657,7 @@
" })\n",
"\n",
"\n",
- "fig = xana.simplePlot(d, aspect=1, x_label='Energy(ADU)', \n",
+ "fig = xana.simplePlot(d, aspect=1, x_label='Energy({})'.format(plot_unit), \n",
" y_label='Number of occurrences', figsize='2col',\n",
" y_log=True, x_range=(-50,500),\n",
" legend='top-center-frame-2col')"
@@ -634,14 +677,13 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:11:08.317130Z",
"start_time": "2018-12-06T16:11:05.788655Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
"fig = xana.heatmapPlot(np.nanmedian(data, axis=2),\n",
" x_label='Columns', y_label='Rows',\n",
- " lut_label='Signal (ADU)',\n",
+ " lut_label='Signal ({})'.format(plot_unit),\n",
" x_range=(0,y),\n",
" y_range=(0,x), vmin=-50, vmax=50)"
]
@@ -662,14 +704,13 @@
"ExecuteTime": {
"end_time": "2018-12-06T16:11:10.908912Z",
"start_time": "2018-12-06T16:11:08.318486Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
"fig = xana.heatmapPlot(data[...,0],\n",
" x_label='Columns', y_label='Rows',\n",
- " lut_label='Signal (ADU)',\n",
+ " lut_label='Signal ({})'.format(plot_unit),\n",
" x_range=(0,y),\n",
" y_range=(0,x), vmin=-50, vmax=50)"
]
@@ -677,9 +718,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": []
}
@@ -700,7 +739,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,