From da25e17d72cabe52ec8ce3a1b36665262ddc20f0 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Fri, 16 Aug 2024 18:50:06 +0200
Subject: [PATCH] doc: improve first markdown cell notebooks descriptions
---
...ngfrau_Create_Fit_Spectra_Histos_NBC.ipynb | 17 +++++++++--
.../Jungfrau_Create_Gain_maps_NBC.ipynb | 29 ++++++++++++++-----
2 files changed, 35 insertions(+), 11 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
index 1f5f10fa5..9cbc44689 100644
--- a/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
@@ -4,13 +4,24 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Histogram of single photon spectra\n",
+ "# Jungfrau Detector Flatfield Gain Calibration - Part 1: Histogram Creation and Fitting\n",
"\n",
"Author: European XFEL Detector Group, Version: 1.0\n",
"\n",
- "Creates histograms from flat fields and store it in HDF5 files then perform fitting based on the selecting `fit_func`.\n",
+ "This notebook performs the first part of the Jungfrau detector flatfield gain calibration process.\n",
"\n",
- "Histograms are on a pixel-by-pixel, memory cell by memory cell basis to save memory and space, histogram range are to be optimized around the desired peak."
+ "#### Overview\n",
+ "\n",
+ "1. Load Raw Data: Read detector data for specified run. Currently works for only one run.\n",
+ "2. Initialize Histograms: Create empty histograms for each module and memory cell\n",
+ "3. Offset Correction: Apply offset subtraction to raw data\n",
+ "4. Histogram Population: Fill histograms with offset-corrected data\n",
+ "5. Histogram Fitting: Apply specified function (Charge Sharing, Double Charge Sharing, or Gaussian)\n",
+ "6. Save Intermediate Results:\n",
+ " - Store histogram data as HDF5 files\n",
+ " - Save fit results (gain map, sigma map, chi-square map, alpha map) as HDF5 files\n",
+ "\n",
+ "Note: Results from this notebook are used later for Gain Map and BadPixelsFF Generation."
]
},
{
diff --git a/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
index 18b9c29c8..96f17e552 100755
--- a/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
@@ -4,17 +4,30 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Create Gain Map\n",
+ "# Jungfrau Detector Flatfield Gain Calibration - Part 2: Gain Map Generation\n",
"\n",
"Author: European XFEL Detector Group, Version: 1.0\n",
"\n",
- "Converts the map with fit value of the photon peak into a gain conversion factor map.\n",
- "\n",
- "Calculates the bad pixels map according to:\n",
- "\n",
- "- Failed fit\n",
- "- Not enough entries in the fit\n",
- "- Gain value deviation too high"
+ "This notebook performs the final steps in the Jungfrau detector flatfield gain calibration process, focusing on gain map creation and refinement.\n",
+ "\n",
+ "#### Overview\n",
+ "\n",
+ "1. Load Fit Results: Import photon peak fit data from previous processing step (Histogram creation and Fitting)\n",
+ "2. Retrieve Old Gain Map: Access previous gain calibration from database or file\n",
+ "3. Calculate New Gain Map:\n",
+ " - Use fit results for high gain (G0)\n",
+ " - Apply gain ratios for medium (G1) and low (G2) gains\n",
+ "4. Evaluate Bad Pixels:\n",
+ " - Identify pixels with failed fits\n",
+ " - Flag pixels with insufficient data\n",
+ " - Detect pixels with high gain deviation\n",
+ "5. Correct Bad Pixels: Replace identified bad pixels with median values\n",
+ "6. Generate Bad Pixel Map: Create a map of all identified bad pixels\n",
+ "7. Save:\n",
+ " - Store new gain maps for all gain levels\n",
+ " - Save bad pixel map\n",
+ " - Optionally inject new calibration maps into database\n",
+ "8. Visualize Results: Plot gain maps and bad pixel distributions"
]
},
{
--
GitLab