From 5a67eca9c24c03ac51691081f8c80cb1b9bb0e92 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas.kluyver@xfel.eu>
Date: Fri, 16 Dec 2022 16:57:31 +0100
Subject: [PATCH] Add helper function to get LPD memory cell order
---
notebooks/LPD/LPD_Correct_Fast.ipynb | 30 +++++++---------
...LPD_retrieve_constants_precorrection.ipynb | 36 +++++++++----------
2 files changed, 28 insertions(+), 38 deletions(-)
diff --git a/notebooks/LPD/LPD_Correct_Fast.ipynb b/notebooks/LPD/LPD_Correct_Fast.ipynb
index 3cfe25abd..443afdcdc 100644
--- a/notebooks/LPD/LPD_Correct_Fast.ipynb
+++ b/notebooks/LPD/LPD_Correct_Fast.ipynb
@@ -106,6 +106,7 @@
"from extra_data.components import LPD1M\n",
"\n",
"from cal_tools.lpdalgs import correct_lpd_frames\n",
+ "from cal_tools.lpdlib import get_mem_cell_order\n",
"from cal_tools.tools import CalibrationMetadata, calcat_creation_time\n",
"from cal_tools.files import DataFile\n",
"from cal_tools.restful_config import restful_config"
@@ -194,21 +195,6 @@
"# Obtain and prepare calibration constants"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Read the order of memory cells used\n",
- "raw_data = xd.DataCollection.from_paths([e[1] for e in data_to_process])\n",
- "\n",
- "cell_ids = raw_data[det_inp_sources[0], 'image.cellId'].drop_empty_trains()\n",
- "cell_ids_pattern = np.squeeze(cell_ids[0].ndarray())\n",
- "cell_ids_pattern_s = \",\".join([str(c) for c in cell_ids_pattern]) + \",\"\n",
- "print(\"Memory cells order:\", cell_ids_pattern_s)"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -277,9 +263,17 @@
" dict(parameter_id=13, value=256), # Pixels X\n",
" dict(parameter_id=14, value=256), # Pixels Y\n",
" ]\n",
- " dark_condition = base_condition + ([\n",
- " dict(parameter_id=142, value=cell_ids_pattern_s), # Memory cell order\n",
- " ] if use_cell_order else [])\n",
+ " if use_cell_order:\n",
+ " # Read the order of memory cells used\n",
+ " raw_data = xd.DataCollection.from_paths([e[1] for e in data_to_process])\n",
+ " cell_ids_pattern_s = get_mem_cell_order(raw_data, det_inp_sources)\n",
+ " print(\"Memory cells order:\", cell_ids_pattern_s)\n",
+ "\n",
+ " dark_condition = base_condition + [\n",
+ " dict(parameter_id=142, value=cell_ids_pattern_s), # Memory cell order\n",
+ " ]\n",
+ " else:\n",
+ " dark_condition = base_condition.copy()\n",
"\n",
" illuminated_calibrations = {\n",
" 20: 'BadPixelsFF', # np.uint32\n",
diff --git a/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb b/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
index 9066c3c46..5d2ef0579 100644
--- a/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
+++ b/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
@@ -56,6 +56,7 @@
"from calibration_client.modules import CalibrationConstantVersion\n",
"import extra_data as xd\n",
"\n",
+ "from cal_tools.lpdlib import get_mem_cell_order\n",
"from cal_tools.tools import (\n",
" CalibrationMetadata,\n",
" calcat_creation_time,\n",
@@ -85,23 +86,10 @@
" if not modules or modules == [-1]:\n",
" modules = list(range(16))\n",
"\n",
- " karabo_da = [f'LPD{i:02d}' for i in modules] "
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Read the order of memory cells used\n",
- "raw_data = xd.RunDirectory(Path(in_folder, f'r{run:04d}'))\n",
- "\n",
- "src = input_source.format(karabo_id=karabo_id, module_index=int(karabo_da[0][-2:]))\n",
- "cell_ids = raw_data[src, 'image.cellId'].drop_empty_trains()\n",
- "cell_ids_pattern = np.squeeze(cell_ids[0].ndarray())\n",
- "cell_ids_pattern_s = \",\".join([str(c) for c in cell_ids_pattern]) + \",\"\n",
- "print(\"Memory cells order:\", cell_ids_pattern_s)"
+ " karabo_da = [f'LPD{i:02d}' for i in modules]\n",
+ "\n",
+ "# List of detector sources.\n",
+ "det_inp_sources = [input_source.format(karabo_id=karabo_id, module_index=int(da[-2:])) for da in karabo_da]"
]
},
{
@@ -142,9 +130,17 @@
" dict(parameter_id=13, value=256), # Pixels X\n",
" dict(parameter_id=14, value=256), # Pixels Y\n",
"]\n",
- "dark_condition = base_condition + ([\n",
- " dict(parameter_id=142, value=cell_ids_pattern_s), # Memory cell order\n",
- "] if use_cell_order else [])\n",
+ "if use_cell_order:\n",
+ " # Read the order of memory cells used\n",
+ " raw_data = xd.RunDirectory(Path(in_folder, f'r{run:04d}'))\n",
+ " cell_ids_pattern_s = get_mem_cell_order(raw_data, det_inp_sources)\n",
+ " print(\"Memory cells order:\", cell_ids_pattern_s)\n",
+ "\n",
+ " dark_condition = base_condition + [\n",
+ " dict(parameter_id=142, value=cell_ids_pattern_s), # Memory cell order\n",
+ " ]\n",
+ "else:\n",
+ " dark_condition = base_condition.copy()\n",
"\n",
"illuminated_calibrations = {\n",
" 20: 'BadPixelsFF',\n",
--
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