diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 49bbda86a0f183555114769a7f9167df77f913f1..9a2da6a73ab0a5cf6a0f62143cfaae6fcd047d51 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -137,6 +137,7 @@
"import math\n",
"import multiprocessing\n",
"import os\n",
+ "import sys\n",
"import warnings\n",
"from datetime import timedelta\n",
"from logging import warning\n",
@@ -182,6 +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",
@@ -326,6 +328,29 @@
"print(f\"Instrument {instrument}\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "train_available = False\n",
+ "\n",
+ "for m in modules:\n",
+ " try:\n",
+ " # Attempt to select the module. If no trains are available, ValueError might be raised\n",
+ " if len(dc[instrument_src.format(m), 'image.data'].drop_empty_trains().train_ids) > 0:\n",
+ " train_available = True\n",
+ " break # Found a module with available trains.\n",
+ " except ValueError as e:\n",
+ " warning(f\"Missing module {m} from data: {e}\")\n",
+ "\n",
+ "if not train_available:\n",
+ " # Execute this block if no modules with trains were found.\n",
+ " latex_warning(\"No trains available to correct for selected modules.\")\n",
+ " sys.exit(0)"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -519,15 +544,21 @@
" get_data = {'auto': litfrm.read_or_process, 'offline': litfrm.process, 'online': litfrm.read}\n",
" r = get_data[use_litframe_finder]()\n",
" cell_sel = LitFrameSelection(r, train_ids, max_pulses, energy_threshold, use_super_selection)\n",
+ " print(f\"{cell_sel.msg()}\\n\")\n",
" cell_sel.print_report()\n",
+ " if np.count_nonzero(r.nLitFrame.value) == 0: # No lit frames.\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",
" # Use range selection\n",
" cell_sel = CellRange(max_pulses, max_cells=mem_cells)\n",
- "\n",
- "print(cell_sel.msg())"
+ " print(cell_sel.msg())"
]
},
{
@@ -881,8 +912,6 @@
"\n",
" Yields (file data slot, start index, stop index)\n",
" \"\"\"\n",
- " \n",
- " \n",
" for i_proc, n_img in enumerate(img_counts):\n",
" n_chunks = math.ceil(n_img / chunk_size)\n",
" for i in range(n_chunks):\n",
@@ -896,6 +925,7 @@
"outputs": [],
"source": [
"step_timer.start()\n",
+ "all_imgs_counts = []\n",
"if max_tasks_per_worker == -1:\n",
" max_tasks_per_worker = None\n",
"with multiprocessing.Pool(maxtasksperchild=max_tasks_per_worker) as pool:\n",
@@ -911,7 +941,8 @@
" )\n",
" step_timer.done_step(f'Loading data from files')\n",
"\n",
- " if img_counts == 0:\n",
+ " all_imgs_counts += img_counts\n",
+ " if not np.any(img_counts):\n",
" # Skip any further processing and output if there are no images to\n",
" # correct in this file.\n",
" continue\n",
@@ -984,8 +1015,10 @@
"outputs": [],
"source": [
"if skip_plots:\n",
- " print('Skipping plots')\n",
- " import sys\n",
+ " print(\"Skipping plots as configured.\")\n",
+ " sys.exit(0)\n",
+ "elif not np.any(all_imgs_counts):\n",
+ " latex_warning(f\"All sequence files contain no data for correction.\")\n",
" sys.exit(0)"
]
},
@@ -1030,7 +1063,6 @@
" run_data = RunDirectory(data_folder, include)\n",
" except FileNotFoundError:\n",
" warning(f'No corrected files for {include}. Skipping plots.')\n",
- " import sys\n",
" sys.exit(0)\n",
" if tid is not None:\n",
" tid, data = run_data.select(\n",
diff --git a/notebooks/test/test-cli.ipynb b/notebooks/test/test-cli.ipynb
index daacfb22315d6a9edadd4991c31937751e721e74..3636da9d1da1bed89988f4a7f15d027f04d22001 100644
--- a/notebooks/test/test-cli.ipynb
+++ b/notebooks/test/test-cli.ipynb
@@ -43,7 +43,9 @@
"metadata": {},
"outputs": [],
"source": [
- "from pathlib import Path"
+ "from pathlib import Path\n",
+ "\n",
+ "from cal_tools.tools import latex_warning"
]
},
{
@@ -72,6 +74,28 @@
"source": [
"print(\"🥼\")"
]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "Test `latex_warning` output which uses a custom `warningbox` latex command"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "latex_warning(\"This is a warning test message.\")\n",
+ "\n",
+ "# empty message\n",
+ "latex_warning(\"\")\n",
+ "\n",
+ "# special characters\n",
+ "latex_warning(\"$x < y$\")"
+ ]
}
],
"metadata": {
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 66128cc39383201018b9be85e3e141f9416c40ff..cacbfde83b069758e304c3486e180e9a26d0dae8 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -1719,11 +1719,13 @@ class LitFrameSelection(CellSelection):
t0, tN, st = (rec['train_range'] + (1,))[:3]
ntrain = max((int(tN) - int(t0)) // int(st), 1)
trsintf = ':'.join([str(n) for n in rec['train_range']])
- print(("{pattern_no:2d} {trsintf:25s} {ntrain:5d} "
- "{nmissed_trains:4d} {npulse_exposed:4d} {ndataframe:3d} "
- "{nframe_total:3d} [{frmintf}]"
- ).format(frmintf=frmintf, ntrain=ntrain,
- trsintf=trsintf, **rec))
+ frmintf_display = f"[{frmintf}]" if frmintf else "No lit frames to correct!"
+ print(
+ f"{rec['pattern_no']:2d} {trsintf:25s} {ntrain:5d} "
+ f"{rec['nmissed_trains']:4d} {rec['npulse_exposed']:4d} "
+ f"{rec['ndataframe']:3d} {rec['nframe_total']:3d} "
+ f"{frmintf_display}"
+ )
if nrec > max_lines:
print(f"... {nrec - max_lines + 1} more lines skipped")
diff --git a/src/cal_tools/tools.py b/src/cal_tools/tools.py
index 81be77efff25b2b34e54142f764373af14689ca8..0161fb8922db89a638ac1c8e70ca27e88da2882d 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
@@ -21,7 +22,7 @@ import numpy as np
import requests
import yaml
import zmq
-from extra_data import H5File, RunDirectory
+from extra_data import H5File, PropertyNameError, RunDirectory
from iCalibrationDB import ConstantMetaData, Versions
from jupyter_server.serverapp import list_running_servers
@@ -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 82f6235c8afa9c03ed165f776092dbe83f8258cd..c2c46b513dc150dbc98a9495de2a2fd11ee9c0d4 100644
--- a/src/xfel_calibrate/finalize.py
+++ b/src/xfel_calibrate/finalize.py
@@ -245,6 +245,19 @@ 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%
+ }%
+ }
+ }
+ '''
+
+ latex_elements['preamble'] += custom_latex_preamble
mf.write("latex_elements = {}\n".format(latex_elements))
mf.write("latex_logo = '{}/{}'\n".format(module_path,
logo_path))