From 0b8e7598ec95b611c2f2a6e33b03c7e03bb4aab6 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 30 May 2024 11:27:48 +0200
Subject: [PATCH] fix(AGIPD)(CORRECT): Account for a modified file list if
skipping correcting any modules.
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 69 ++++++++++---------
1 file changed, 36 insertions(+), 33 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index e401e18e0..8172dcbd0 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -414,37 +414,6 @@
" train_ids = None"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# set everything up filewise\n",
- "mapped_files, _, total_sequences, _, _ = map_modules_from_folder(\n",
- " str(in_folder), run, path_template, karabo_da, sequences\n",
- ")\n",
- "file_list = []\n",
- "\n",
- "# ToDo: Split table over pages\n",
- "print(f\"Processing a total of {total_sequences} sequence files in chunks of {n_cores_files}\")\n",
- "table = []\n",
- "ti = 0\n",
- "for k, files in mapped_files.items():\n",
- " i = 0\n",
- " for f in list(files.queue):\n",
- " file_list.append(f)\n",
- " if i == 0:\n",
- " table.append((ti, k, i, f))\n",
- " else:\n",
- " table.append((ti, \"\", i, f))\n",
- " i += 1\n",
- " ti += 1\n",
- "md = display(Latex(tabulate.tabulate(table, tablefmt='latex',\n",
- " headers=[\"#\", \"module\", \"# module\", \"file\"])))\n",
- "file_list = sorted(file_list, key=lambda name: name[-10:])"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -786,7 +755,6 @@
" if error_missing_constants:\n",
" warning(f\"Offset constant is not available to correct {da}.\")\n",
" # Remove module from files to process.\n",
- " del mapped_files[module_index_to_qm(mod)]\n",
" karabo_da.remove(da)\n",
" modules.remove(mod)\n",
"\n",
@@ -796,7 +764,9 @@
" if warn_missing_constants:\n",
" warning(f\"Constants {warn_missing_constants} were not retrieved for {da}.\")\n",
"\n",
- "if not mapped_files: # Offsets are missing for all modules.\n",
+ "# Skip das not available in CALCAT and with no constants.\n",
+ "karabo_da = [da for da in karabo_da if da in agipd_metadata.keys()]\n",
+ "if not da: # Offsets are missing for all modules.\n",
" raise Exception(\"Could not find offset constants for any modules, will not correct data.\")"
]
},
@@ -813,6 +783,39 @@
" caldb_root=agipd_cal.caldb_root)"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Set everything up filewise\n",
+ "# This cell needs to be after getting and validating CCVs and\n",
+ "# after modifying `karabo_da` in case of missing required constants.\n",
+ "mapped_files, _, total_sequences, _, _ = map_modules_from_folder(\n",
+ " str(in_folder), run, path_template, karabo_da, sequences\n",
+ ")\n",
+ "file_list = []\n",
+ "\n",
+ "# ToDo: Split table over pages\n",
+ "print(f\"Processing a total of {total_sequences} sequence files in chunks of {n_cores_files}\")\n",
+ "table = []\n",
+ "ti = 0\n",
+ "for k, files in mapped_files.items():\n",
+ " i = 0\n",
+ " for f in list(files.queue):\n",
+ " file_list.append(f)\n",
+ " if i == 0:\n",
+ " table.append((ti, k, i, f))\n",
+ " else:\n",
+ " table.append((ti, \"\", i, f))\n",
+ " i += 1\n",
+ " ti += 1\n",
+ "md = display(Latex(tabulate.tabulate(table, tablefmt='latex',\n",
+ " headers=[\"#\", \"module\", \"# module\", \"file\"])))\n",
+ "file_list = sorted(file_list, key=lambda name: name[-10:])"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
--
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