From 58b86651013c9c41f16a8cffddebc4bf5ac0eae3 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 25 Apr 2024 10:07:42 +0200
Subject: [PATCH] Remove warning from agipdlib and test PRINT statement
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 11 +++++--
src/cal_tools/agipdlib.py | 30 ++++++++-----------
2 files changed, 22 insertions(+), 19 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index e32d7f16a..9ffa2487e 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -238,9 +238,16 @@
"\n",
"# Dont apply any corrections if only_offset is requested\n",
"if not only_offset:\n",
- " corr_bools[\"adjust_mg_baseline\"] = adjust_mg_baseline\n",
- " corr_bools[\"cs_corr\"] = cs_corr \n",
+ " corr_bools[\"cs_corr\"] = cs_corr\n",
" corr_bools[\"pc_corr\"] = pc_corr\n",
+ " if cs_corr:\n",
+ " corr_bools[\"adjust_mg_baseline\"] = False\n",
+ " warning(\n",
+ " \"Currently, `adjust_mg_baseline` correction\"\n",
+ " \" is not allowed with Current Source gain correction.\"\n",
+ " \" Skipping `adjust_mg_baseline` correction step.\")\n",
+ " else:\n",
+ " corr_bools[\"adjust_mg_baseline\"] = adjust_mg_baseline\n",
" corr_bools[\"xray_corr\"] = xray_gain\n",
" corr_bools[\"blc_noise\"] = blc_noise\n",
" corr_bools[\"blc_stripes\"] = blc_stripes\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index d28b8021b..522ee4695 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -1056,12 +1056,6 @@ class AgipdCorrections:
# Adjust medium gain baseline to match highest high gain value
# This correction is disabled in case CS gain correction is selected.
if self.corr_bools.get("adjust_mg_baseline"):
- if self.corr_bools.get("cs_corr"):
- warning(
- "Currently, `adjust_mg_baseline` correction"
- " is not allowed with Current Source gain correction."
- " Skipping `adjust_mg_baseline` correction step.")
- else:
mgbc = self.md_additional_offset[module_idx][cellid, ...]
data[gain == 1] += mgbc[gain == 1]
del mgbc
@@ -1437,20 +1431,22 @@ class AgipdCorrections:
# it is not expected to have SlopesCS and SlopesPC at the sametime.
if "SlopesCS" in cons_data:
- rel_gain[..., 1] = rel_gain[..., 0] * cons_data["SlopesCS"][..., self.max_cells, 6] # noqa
- rel_gain[..., 2] = rel_gain[..., 1] * cons_data["SlopesCS"][..., self.max_cells, 7] # noqa
- # TODO: Decide between:
+ # TODO consider updating the SlopesCS shape instead of doing this here.
+ cons_data["SlopesCS"] = np.transpose(cons_data["SlopesCS"], (2, 3, 1, 0))
+ rel_gain[..., 1] = rel_gain[..., 0] * cons_data["SlopesCS"][..., :self.max_cells, 6] # noqa
+ rel_gain[..., 2] = rel_gain[..., 1] * cons_data["SlopesCS"][..., :self.max_cells, 7] # noqa
+ # TODO: Decide between: BTW both medium fractions are not the equal after testing!
# - Median of ratio of high gain and medium gain slope
# - Ratio of medians of high gain slope and medium gain slope
- frac_high_med_ofratio = np.median(
- cons_data["SlopesCS"][..., self.max_cells, 6])
+ # frac_high_med_ofratio = np.median(
+ # cons_data["SlopesCS"][..., :self.max_cells, 6])
frac_high_med = (
- np.median(cons_data["SlopesCS"][..., self.max_cells, 0]) /
- np.median(cons_data["SlopesCS"][..., self.max_cells, 1]))
- # TODO: DECIDE AND REMOVE THIS PRINT AFTER TESTING
- print(
- "CHECK IF BOTH MEDIAN FRACTIONS ARE THE SAME:",
- np.allclose(frac_high_med, frac_high_med_ofratio))
+ np.median(cons_data["SlopesCS"][..., :self.max_cells, 0]) /
+ np.median(cons_data["SlopesCS"][..., :self.max_cells, 1]))
+ # Currently, `adjust_mg_baseline` correction
+ # is not allowed with Current Source gain correction.
+ # Skipping `adjust_mg_baseline` correction step."
+ md_additional_offset = np.zeros((128, 512, self.max_cells), np.float32)
elif "SlopesPC" in cons_data:
slopesPC = cons_data["SlopesPC"].astype(np.float32, copy=False)
--
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