From 8e4cd0ef5380f8e4df2d8eb7dae888582cf0d9ff Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Tue, 13 Dec 2022 13:42:49 +0100
Subject: [PATCH] warning instead of warn and some refactors
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 42 +++++++++----------
...IPD_Retrieve_Constants_Precorrection.ipynb | 23 ++--------
2 files changed, 24 insertions(+), 41 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index c746b776b..e38e3245e 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -122,12 +122,13 @@
"outputs": [],
"source": [
"import itertools\n",
+ "import os\n",
"import math\n",
"import multiprocessing\n",
+ "import re\n",
"import warnings\n",
- "import os\n",
"from datetime import timedelta\n",
- "from logging import warn\n",
+ "from logging import warning\n",
"from pathlib import Path\n",
"from time import perf_counter\n",
"\n",
@@ -439,7 +440,7 @@
"if gain_mode:\n",
" for to_disable in disable_for_fixed_gain:\n",
" if corr_bools.get(to_disable, False):\n",
- " warn(f\"{to_disable} correction was requested, but does not apply to fixed gain mode\")\n",
+ " warning(f\"{to_disable} correction was requested, but does not apply to fixed gain mode\")\n",
" corr_bools[to_disable] = False"
]
},
@@ -463,7 +464,7 @@
" cell_sel = LitFrameSelection(r, train_ids, max_pulses, energy_threshold, use_super_selection)\n",
" cell_sel.print_report()\n",
" except LitFrameFinderError as err:\n",
- " warn(f\"Cannot use AgipdLitFrameFinder due to:\\n{err}\")\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",
@@ -490,11 +491,11 @@
" photon_energy = (h * c / e) / (wavelength_data.as_single_value(rtol=1e-2) * 1e-6)\n",
" print(f'Obtained photon energy {photon_energy:.3f} keV from {use_xgm_device}')\n",
" except ValueError:\n",
- " warn('XGM source available but photon energy varies greater than 1%, '\n",
+ " warning('XGM source available but photon energy varies greater than 1%, '\n",
" 'photon rounding disabled!')\n",
" round_photons = False\n",
" else:\n",
- " warn('Neither explicit photon energy nor XGM device configured, photon rounding disabled!')\n",
+ " warning('Neither explicit photon energy nor XGM device configured, photon rounding disabled!')\n",
" round_photons = False\n",
"elif round_photons:\n",
" print(f'Photon energy for rounding: {photon_energy:.3f} keV')"
@@ -559,6 +560,9 @@
"# Retrieve calibration constants to RAM\n",
"agipd_corr.allocate_constants(modules, (3, mem_cells_db, 512, 128))\n",
"\n",
+ "metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
+ "# NOTE: this notebook will not overwrite calibration metadata file\n",
+ "const_yaml = metadata.get(\"retrieved-constants\", {})\n",
"\n",
"def retrieve_constants(mod):\n",
" \"\"\"\n",
@@ -567,12 +571,12 @@
" Metadata for constants is taken from yml file or retrieved from the DB\n",
" \"\"\"\n",
" k_da = module_index_to_karabo_da[mod]\n",
- " try:\n",
- " # check if there is a yaml file in out_folder that has the device constants.\n",
- " if k_da in const_yaml:\n",
- " when = agipd_corr.initialize_from_yaml(k_da, const_yaml, mod)\n",
- " print(f\"Found constants for {k_da} in calibration_metadata.yml\")\n",
- " else:\n",
+ " # check if there is a yaml file in out_folder that has the device constants.\n",
+ " if k_da in const_yaml:\n",
+ " when = agipd_corr.initialize_from_yaml(k_da, const_yaml, mod)\n",
+ " print(f\"Found constants for {k_da} in calibration_metadata.yml\")\n",
+ " else:\n",
+ " try:\n",
" # TODO: replace with proper retrieval (as done in pre-correction)\n",
" when = agipd_corr.initialize_from_db(\n",
" karabo_id=karabo_id,\n",
@@ -589,10 +593,10 @@
" only_dark=False,\n",
" )\n",
" print(f\"Queried CalCat for {k_da}\")\n",
- " except Exception as e:\n",
- " err = f\"Error: {e}\\nError traceback: {traceback.format_exc()}\"\n",
- " when = None\n",
- " return err, mod, when, k_da\n",
+ " except Exception as e:\n",
+ " warning(f\"Module: {k_da}, {e}\")\n",
+ " when = None\n",
+ " return mod, when, k_da\n",
"\n",
"\n",
"print(f'Preparing constants (FF: {agipd_corr.corr_bools.get(\"xray_corr\", False)}, PC: {any(agipd_corr.pc_bools)}, '\n",
@@ -612,11 +616,7 @@
"# allocate memory for images and hists\n",
"n_images_max = mem_cells * 256\n",
"data_shape = (n_images_max, 512, 128)\n",
- "agipd_corr.allocate_images(data_shape, n_cores_files)\n",
- "\n",
- "metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
- "# NOTE: this notebook will not overwrite calibration metadata file\n",
- "const_yaml = metadata.get(\"retrieved-constants\", {})"
+ "agipd_corr.allocate_images(data_shape, n_cores_files)"
]
},
{
diff --git a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
index 8137e875e..bbb32e928 100644
--- a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
+++ b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
@@ -335,7 +335,9 @@
" mdata_dict[\"physical-detector-unit\"] = mdata_const.device_name\n",
" else:\n",
" const_mdata[\"file-path\"] = const_dict[const_name][:2]\n",
- " const_mdata[\"creation-time\"] = None"
+ " const_mdata[\"creation-time\"] = None\n",
+ "\n",
+ " return mdata_dict, k_da, local_acq_rate, local_mem_cells"
]
},
{
@@ -436,25 +438,6 @@
"\n",
"metadata.save()"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "print(\"\\nRetrieved constants for modules:\",\n",
- " ', '.join([module_index_to_qm(x) for x in modules]))\n",
- "print(f\"Operating conditions are:\")\n",
- "print(f\"• Bias voltage: {bias_voltage}\")\n",
- "print(f\"• Memory cells: {mem_cells}\")\n",
- "print(f\"• Acquisition rate: {acq_rate}\")\n",
- "print(f\"• Gain mode: {gain_mode.name}\")\n",
- "print(f\"• Gain setting: {gain_setting}\")\n",
- "print(f\"• Integration time: {integration_time}\")\n",
- "print(f\"• Photon Energy: 9.2\")\n",
- "step_timer.done_step(f\"Constant metadata is saved under \\\"retrieved-constants\\\" in {metadata.filename}\")"
- ]
}
],
"metadata": {
--
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