From d55d3db6ddfa8022154b9b7999c5e128a0af3a5b Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Sun, 23 Oct 2022 15:41:57 +0200
Subject: [PATCH] Build intensity histograms before and after AGIPD
photonization
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 30 +++++++++++++++++++
src/cal_tools/agipdlib.py | 22 ++++++++++++++
2 files changed, 52 insertions(+)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 9ceff41ac..018dc4445 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -1270,6 +1270,36 @@
"geom.plot_data_fast(np.log2(mask[cell_idx_preview]), ax=ax, vmin=0, vmax=32, cmap=\"jet\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if round_photons:\n",
+ " display(Markdown('### Photonization histograms ###'))\n",
+ " \n",
+ " x_preround = (agipd_corr.hist_bins_preround[1:] + agipd_corr.hist_bins_preround[:-1]) / 2\n",
+ " x_postround = (agipd_corr.hist_bins_postround[1:] + agipd_corr.hist_bins_postround[:-1]) / 2\n",
+ " x_photons = np.arange(0, (x_postround[-1] + 1) / photon_energy)\n",
+ "\n",
+ " fig, ax = plt.subplots(ncols=1, nrows=1, clear=True)\n",
+ " ax.plot(x_preround, agipd_corr.shared_hist_preround, '.-', color='C0')\n",
+ " ax.bar(x_postround, agipd_corr.shared_hist_postround, photon_energy, color='C1', alpha=0.5)\n",
+ " ax.set_yscale('log')\n",
+ " ax.set_ylim(0, max(agipd_corr.shared_hist_preround.max(), agipd_corr.shared_hist_postround.max())*3)\n",
+ " ax.set_xlim(x_postround[0], x_postround[-1]+1)\n",
+ " ax.set_xlabel('Photon energy / keV')\n",
+ " ax.set_ylabel('Intensity')\n",
+ " ax.vlines(x_photons * photon_energy, *ax.get_ylim(), color='k', linestyle='dashed')\n",
+ "\n",
+ " phx = ax.twiny()\n",
+ " phx.set_xlim(x_postround[0] / photon_energy, (x_postround[-1]+1)/photon_energy)\n",
+ " phx.set_xticks(x_photons)\n",
+ " phx.set_xlabel('# Photons')\n",
+ " pass"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 535eef0db..03f9680d7 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -2,6 +2,7 @@ import os
import posixpath
import zlib
from datetime import datetime
+from multiprocessing import Manager
from multiprocessing.pool import ThreadPool
from typing import Any, Dict, List, Optional, Tuple
@@ -416,6 +417,14 @@ class AgipdCorrections:
self.mask = {}
self.xray_cor = {}
+ if corr_bools.get('round_photons'):
+ # Variables related to histogramming.
+ self.shared_hist_preround = None
+ self.shared_hist_postround = None
+ self.hist_bins_preround = np.linspace(-5.0, 60.0, 200)
+ self.hist_bins_postround = np.arange(-5.5, 60.1)
+ self.hist_lock = Manager().Lock()
+
# check if given corr_bools are correct
tot_corr_bools = ['only_offset', 'adjust_mg_baseline', 'rel_gain',
'xray_corr', 'blc_noise', 'blc_hmatch',
@@ -909,6 +918,8 @@ class AgipdCorrections:
# Round keV-normalized intensity to photons.
if self.corr_bools.get("round_photons"):
+ data_hist_preround, _ = np.histogram(data, bins=self.hist_bins_preround)
+
data /= self.photon_energy
np.round(data, out=data)
@@ -919,6 +930,13 @@ class AgipdCorrections:
msk[bidx] |= BadPixels.VALUE_OUT_OF_RANGE
del bidx
+ data_hist_postround, _ = np.histogram(data * self.photon_energy,
+ bins=self.hist_bins_postround)
+
+ with self.hist_lock:
+ self.shared_hist_preround += data_hist_preround
+ self.shared_hist_postround += data_hist_postround
+
if np.issubdtype(self.recast_image_fields.get('image'), np.integer):
# If the image data is meant to be recast to an integer
# type, make sure its values are within its bounds.
@@ -1497,6 +1515,10 @@ class AgipdCorrections:
self.shared_dict[i]["n_valid_trains"] = sharedmem.empty(1, dtype="i4") # noqa
self.shared_dict[i]["valid_trains"] = sharedmem.empty(1024, dtype="u8") # noqa
+ if self.corr_bools.get("round_photons"):
+ self.shared_hist_preround = sharedmem.empty(len(self.hist_bins_preround) - 1, dtype="i8")
+ self.shared_hist_postround = sharedmem.empty(len(self.hist_bins_postround) - 1, dtype="i8")
+
def validate_selected_pulses(
max_pulses: List[int], max_cells: int
--
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