From 5be8c9011913235f13aef17e25d2561daa888788 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 2 Jun 2022 11:28:19 +0200
Subject: [PATCH] add parameter conditions in the first cell
---
.../Gotthard2/Correction_Gotthard2_NBC.ipynb | 19 +++++++++----------
src/cal_tools/gotthard2algs.pyx | 6 ++----
src/xfel_calibrate/notebooks.py | 2 +-
3 files changed, 12 insertions(+), 15 deletions(-)
diff --git a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
index 166d77d04..ee4104f94 100644
--- a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
+++ b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
@@ -43,6 +43,13 @@
"relative_gain = True # do relative gain correction\n",
"constants_file = \"/gpfs/exfel/data/scratch/ahmedk/dont_remove/gotthard2/constants/calibration_constants_GH2.h5\"\n",
"\n",
+ "# Parameter conditions.\n",
+ "pulses = -1 # Number of detector pulses, -1 to use value in raw file.\n",
+ "bias_voltage = -1 # Detector bias voltage, -1 to use value in raw file.\n",
+ "integration_time = -1 # Detector integration time, -1 to use value in raw file.\n",
+ "acquisition_rate = -1 # Detector acquisition rate, -1 to use value in raw file.\n",
+ "gain_setting = -1 # Detector gain setting (High and Low CDS), -1 to use value in raw file.\n",
+ "\n",
"# Parameters for plotting\n",
"skip_plots = False # exit after writing corrected files\n",
"pulse_idx_preview = 3 # pulse index to preview. The following even/odd pulse index is used for preview. # TODO: update to pulseId preview.\n",
@@ -168,16 +175,8 @@
"metadata": {},
"outputs": [],
"source": [
- "# TODO: Retrieve calibration constants from CALCAT"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "531c12e6-1c02-45fc-a7a2-018a08eb7a2d",
- "metadata": {},
- "outputs": [],
- "source": [
+ "# TODO: Retrieve calibration constants from CALCAT\n",
+ "\n",
"# load constants temporarely using defined local paths.\n",
"with h5py.File(constants_file, 'r') as cfile:\n",
" offset_map = cfile[\"offset_map\"][()]\n",
diff --git a/src/cal_tools/gotthard2algs.pyx b/src/cal_tools/gotthard2algs.pyx
index 21d6daa4c..5a87ff564 100644
--- a/src/cal_tools/gotthard2algs.pyx
+++ b/src/cal_tools/gotthard2algs.pyx
@@ -1,7 +1,4 @@
-import numpy as np
-
-from cython cimport boundscheck, wraparound, cdivision
-cimport numpy as cnp
+from cython cimport boundscheck, cdivision, wraparound
@boundscheck(False)
@@ -39,6 +36,7 @@ def correct_train(
"""Correct Gotthard2 raw data.
1. Offset correction.
2. Gain correction.
+ 3. Mask badpixels.
"""
cdef:
diff --git a/src/xfel_calibrate/notebooks.py b/src/xfel_calibrate/notebooks.py
index 5a831031f..8d44b7cc5 100644
--- a/src/xfel_calibrate/notebooks.py
+++ b/src/xfel_calibrate/notebooks.py
@@ -194,7 +194,7 @@ notebooks = {
},
"EPIX100": {
"DARK": {
- "notebook": "notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb",
+ "notebook": "notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb", # noqa
"concurrency": {"parameter": None,
"default concurrency": None,
"cluster cores": 4},
--
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