From 3f47771dfef96e7e7a3df748888887e3d7416cf9 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Wed, 19 Jul 2023 12:45:10 +0200
Subject: [PATCH] move back unneeded moved cell and error out for thresholds as
well
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 80 ++++++++++---------
src/cal_tools/agipdlib.py | 5 +-
2 files changed, 44 insertions(+), 41 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index dd59d0d1e..3717cc4e9 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -334,6 +334,37 @@
" print(f'Processing all valid trains')"
]
},
+ {
+ "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,
@@ -484,14 +515,6 @@
" print(f'Photon energy for rounding: {photon_energy:.3f} keV')"
]
},
- {
- "attachments": {},
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "## Retrieving constants"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -527,34 +550,11 @@
]
},
{
- "cell_type": "code",
- "execution_count": null,
+ "attachments": {},
+ "cell_type": "markdown",
"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:])"
+ "## Retrieving constants"
]
},
{
@@ -567,6 +567,7 @@
"agipd_corr.allocate_constants(modules, (3, mem_cells_db, 512, 128))\n",
"\n",
"step_timer.start()\n",
+ "# Instantiate agipd_cal with the read operating conditions.\n",
"agipd_cal = AGIPD_CalibrationData(\n",
" detector_name=karabo_id,\n",
" modules=karabo_da,\n",
@@ -582,10 +583,10 @@
" caldb_root=Path(cal_db_root),\n",
")\n",
"\n",
+ "# Prepare lists of expected calibrations\n",
"dark_constants = [\"Offset\", \"Noise\", \"BadPixelsDark\"]\n",
"if not gain_mode: # Adaptive gain\n",
" dark_constants.append(\"ThresholdsDark\")\n",
- "\n",
"gain_constants = []\n",
"if any(agipd_corr.pc_bools):\n",
" gain_constants += [\"SlopesPC\", \"BadPixelsPC\"]\n",
@@ -623,14 +624,19 @@
"# Validate constants availability and exclude modules with no offsets.\n",
"for da, calibrations in agipd_metadata.items():\n",
" mod = modules[karabo_da.index(da)]\n",
- " if {\"Offset\"} - set(calibrations):\n",
+ " # Constants to error out for when missing.\n",
+ " error_missing_constants = {\"Offset\"}\n",
+ " if gain_mode:\n",
+ " error_missing_constants |= {\"ThresholdsDark\"}\n",
+ "\n",
+ " if error_missing_constants - set(calibrations):\n",
" warning(f\"Offset constant is not available to correct {da}.\")\n",
" mapped_files.remove(module_index_to_qm(mod))\n",
" karabo_da.drop(da)\n",
" modules.drop(mod)\n",
"\n",
" warn_missing_constants = set(dark_constants + gain_constants)\n",
- " warn_missing_constants.remove(\"Offset\")\n",
+ " warn_missing_constants -= error_missing_constants\n",
" warn_missing_constants = warn_missing_constants - set(calibrations)\n",
" if warn_missing_constants:\n",
" warning(f\"Constants {warn_missing_constants} were not retrieved for {da}.\")\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 2e50df04d..60e245ab4 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -1180,10 +1180,7 @@ class AgipdCorrections:
calgs.transpose_constant(
self.noise[module_idx], cons_data["Noise"], **calgs_opts)
- if (
- self.gain_mode is AgipdGainMode.ADAPTIVE_GAIN and
- "ThresholdsDark" in cons_data
- ):
+ if self.gain_mode is AgipdGainMode.ADAPTIVE_GAIN:
calgs.transpose_constant(self.thresholds[module_idx],
cons_data["ThresholdsDark"][..., :3],
**calgs_opts)
--
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