From 7ab1903024b587689fdebc0138a5d825e5112989 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Fri, 15 Mar 2024 11:48:49 +0100
Subject: [PATCH] Custom warning command extra check if there are any trains
to correct
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 21 +++++++++++++++++--
src/cal_tools/tools.py | 7 +++++++
src/xfel_calibrate/finalize.py | 14 +++++++++++++
3 files changed, 40 insertions(+), 2 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 166257f9e..fdd307e5e 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -183,6 +183,7 @@
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
" calcat_creation_time,\n",
+ " latex_warning,\n",
" map_modules_from_folder,\n",
" module_index_to_qm,\n",
" write_constants_fragment,\n",
@@ -327,6 +328,21 @@
"print(f\"Instrument {instrument}\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Before going further check if there are any trains\n",
+ "# to correction in AGIPD detector modules INSTRUMENT sources.\n",
+ "channels_to_correct = [instrument_src.format(m) for m in modules]\n",
+ "total_trains = len(dc.select(channels_to_correct, require_all=True).train_ids)\n",
+ "if total_trains == 0:\n",
+ " latex_warning(f\"No trains available to correct in: {channels_to_correct}\")\n",
+ " sys.exit(0)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -523,11 +539,12 @@
" print(f\"{cell_sel.msg()}\\n\")\n",
" cell_sel.print_report()\n",
" if np.count_nonzero(r.nLitFrame.value) == 0: # No lit frames.\n",
- " warning(\n",
- " \"Warning: No lit frames identified using AGIPD LitFrameFinder.\"\n",
+ " latex_warning(\n",
+ " \"No lit frames identified using AGIPD LitFrameFinder.\"\n",
" \" Offline correction will not be performed.\")\n",
" sys.exit(0)\n",
" except LitFrameFinderError as err:\n",
+ " print(cell_sel.msg())\n",
" warning(f\"Cannot use AgipdLitFrameFinder due to:\\n{err}\")\n",
" cell_sel = CellRange(max_pulses, max_cells=mem_cells)\n",
"else:\n",
diff --git a/src/cal_tools/tools.py b/src/cal_tools/tools.py
index cc81c81a4..0161fb892 100644
--- a/src/cal_tools/tools.py
+++ b/src/cal_tools/tools.py
@@ -3,6 +3,7 @@ import json
import os
import re
import zlib
+from IPython.display import Latex, display
from collections import OrderedDict
from glob import glob
from multiprocessing.pool import ThreadPool
@@ -1151,3 +1152,9 @@ def exit_notebook(message):
import sys
print(message)
sys.exit(0)
+
+
+def latex_warning(message):
+ """Show latex warning custom command parsed correctly
+ when reports are generated."""
+ display(Latex("\warningbox{" + message + "}"))
diff --git a/src/xfel_calibrate/finalize.py b/src/xfel_calibrate/finalize.py
index 82f6235c8..78efb19b0 100644
--- a/src/xfel_calibrate/finalize.py
+++ b/src/xfel_calibrate/finalize.py
@@ -245,6 +245,20 @@ def make_report(run_path: Path, cal_work_dir: Path, project: str,
latex_elements = {'extraclassoptions': ',openany, oneside',
'preamble': r'\usepackage{longtable}',
'maketitle': r'\input{titlepage.tex.txt}'}
+
+ # Define a new LaTeX command for warning boxes within the preamble
+ custom_latex_preamble = r'''
+ \newcommand{\warningbox}[1]{%
+ \noindent\fcolorbox{orange}{yellow}{%
+ \parbox{\textwidth}{%
+ \textbf{Warning:} #1%
+ }%
+ }
+ }
+ '''
+
+ # Append the custom preamble
+ latex_elements['preamble'] += custom_latex_preamble
mf.write("latex_elements = {}\n".format(latex_elements))
mf.write("latex_logo = '{}/{}'\n".format(module_path,
logo_path))
--
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