From 796eb02c6b3833e1fd175c08663da913fbd7b8f2 Mon Sep 17 00:00:00 2001
From: Nuno Duarte <nuno.duarte@xfel.eu>
Date: Thu, 13 Jul 2023 14:31:59 +0200
Subject: [PATCH] solving merge conflicts
---
.../ePix100/Characterize_Darks_ePix100_NBC.ipynb | 9 +++------
notebooks/ePix100/Correction_ePix100_NBC.ipynb | 13 ++++++-------
src/cal_tools/epix100/epix100lib.py | 3 +--
3 files changed, 10 insertions(+), 15 deletions(-)
diff --git a/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb b/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
index 05fa93285..cfaf02206 100644
--- a/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
@@ -28,7 +28,7 @@
"outputs": [],
"source": [
"in_folder = '/gpfs/exfel/exp/MID/202330/p900329/raw' # input folder, required\n",
- "out_folder = ''\n",
+ "out_folder = '' # output folder, required\n",
"metadata_folder = '' # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"sequence = 0 # sequence file to use\n",
"run = 106 # which run to read data from, required\n",
@@ -76,7 +76,6 @@
"source": [
"import os\n",
"import warnings\n",
- "from datetime import datetime\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
@@ -181,7 +180,7 @@
"metadata": {},
"outputs": [],
"source": [
- " ctrl_data = epix100lib.epix100Ctrl(\n",
+ "ctrl_data = epix100lib.epix100Ctrl(\n",
" run_dc=run_dir,\n",
" instrument_src=instrument_src,\n",
" ctrl_src=f\"{karabo_id}/DET/CONTROL\",\n",
@@ -214,9 +213,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "tags": []
- },
+ "metadata": {},
"outputs": [],
"source": [
"# Passing repetitive code along the notebook to a function \n",
diff --git a/notebooks/ePix100/Correction_ePix100_NBC.ipynb b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
index b7559c7db..29ae0d4c5 100644
--- a/notebooks/ePix100/Correction_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
@@ -24,15 +24,15 @@
"metadata": {},
"outputs": [],
"source": [
- "in_folder = '/gpfs/exfel/exp/MID/202330/p900329/raw' # input folder, required\n",
- "out_folder = ''\n",
+ "in_folder = \"/gpfs/exfel/exp/MID/202330/p900329/raw\" # input folder, required\n",
+ "out_folder = \"\" # output folder, required\n",
"metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
"sequences_per_node = 1 # number of sequence files per cluster node if run as slurm job, set to 0 to not run SLURM parallel\n",
"run = 106 # which run to read data from, required\n",
"\n",
"# Parameters for accessing the raw data.\n",
- "karabo_id = \"MID_EXP_EPIX-1\" # karabo karabo_id\n",
+ "karabo_id = \"MID_EXP_EPIX-1\" # karabo karabo_id\n",
"karabo_da = \"EPIX01\" # data aggregators\n",
"db_module = \"\" # module id in the database\n",
"receiver_template = \"RECEIVER\" # detector receiver template for accessing raw data files\n",
@@ -89,7 +89,6 @@
"import h5py\n",
"import pasha as psh\n",
"import numpy as np\n",
- "from datetime import datetime\n",
"import matplotlib.pyplot as plt\n",
"from IPython.display import Latex, Markdown, display\n",
"from extra_data import RunDirectory, H5File\n",
@@ -538,7 +537,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "scrolled": false
+ },
"outputs": [],
"source": [
"empty_seq = 0\n",
@@ -580,7 +581,6 @@
" step_timer.start() # Correct data. \n",
"\n",
" # Overwrite seq_dc after eliminating empty trains or/and applying limited images.\n",
- " slow_data_dc = seq_dc.select(instrument_src,require_all=True).select_trains(np.s_[:corr_ntrains])\n",
" seq_dc = seq_dc.select(\n",
" instrument_src, \"*\", require_all=True).select_trains(np.s_[:corr_ntrains])\n",
"\n",
@@ -630,7 +630,6 @@
" \"data.trainId\", data=seq_dc.train_ids, chunks=min(50, len(seq_dc.train_ids)))\n",
" outp_source.create_key(\n",
" \"data.pulsenId\", data=list(seq_dc[instrument_src]['data.pulseId'].ndarray().squeeze()), chunks=min(50, len(seq_dc.train_ids)))\n",
- " \n",
" if pattern_classification:\n",
" # Add main corrected `data.image.pixels` dataset and store corrected data.\n",
" outp_source.create_key(\n",
diff --git a/src/cal_tools/epix100/epix100lib.py b/src/cal_tools/epix100/epix100lib.py
index b2a3a73ac..d2c71e1b9 100644
--- a/src/cal_tools/epix100/epix100lib.py
+++ b/src/cal_tools/epix100/epix100lib.py
@@ -43,5 +43,4 @@ class epix100Ctrl():
else:
return self.run_dc[
self.instrument_src.split(':daqOutput')[0], 'slowdata.backTemp.value'].as_single_value(
- reduce_by='mean', atol=1)
-
\ No newline at end of file
+ reduce_by='mean', atol=1)
\ No newline at end of file
--
GitLab