From 714a2eea50db95cbccd3d5585d047b01737de7a4 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas.kluyver@xfel.eu>
Date: Thu, 29 Jun 2023 17:39:07 +0200
Subject: [PATCH] Rework LPD Mini cell order condition to match LPD-1M again
---
.../LPDMini/LPD_Mini_Char_Darks_NBC.ipynb | 23 +++++-------
notebooks/LPDMini/LPD_Mini_Correct.ipynb | 35 ++++++++++---------
2 files changed, 27 insertions(+), 31 deletions(-)
diff --git a/notebooks/LPDMini/LPD_Mini_Char_Darks_NBC.ipynb b/notebooks/LPDMini/LPD_Mini_Char_Darks_NBC.ipynb
index a375fe263..38706bbff 100644
--- a/notebooks/LPDMini/LPD_Mini_Char_Darks_NBC.ipynb
+++ b/notebooks/LPDMini/LPD_Mini_Char_Darks_NBC.ipynb
@@ -22,12 +22,12 @@
"metadata": {},
"outputs": [],
"source": [
- "in_folder = \"/gpfs/exfel/exp/FXE/202231/p900316/raw/\" # path to input data, required\n",
+ "in_folder = \"/gpfs/exfel/exp/FXE/202330/p900319/raw/\" # path to input data, required\n",
"out_folder = \"/gpfs/exfel/data/scratch/kluyvert/darks-lpdmini\" # path to output to, required\n",
"metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
- "run_high = 10 # run number in which high gain data was recorded, required\n",
- "run_med = 11 # run number in which medium gain data was recorded, required\n",
- "run_low = 12 # run number in which low gain data was recorded, required\n",
+ "run_high = 3 # run number in which high gain data was recorded, required\n",
+ "run_med = 4 # run number in which medium gain data was recorded, required\n",
+ "run_low = 5 # run number in which low gain data was recorded, required\n",
"\n",
"karabo_id = \"FXE_DET_LPD_MINI\" # karabo karabo_id\n",
"karabo_da = [''] # a list of data aggregators names with module number, e.g. 'LPDMINI00/2', Default [''] for selecting all data aggregators\n",
@@ -53,7 +53,7 @@
"min_trains = 370 # minimum number of trains needed for each gain stage\n",
"high_res_badpix_3d = False # plot bad-pixel summary in high resolution\n",
"test_for_normality = False # permorm normality test\n",
- "inject_cell_order = False # Include memory cell order as part of the detector condition\n",
+ "inject_cell_order = 'auto' # Include memory cell order as part of the detector condition (auto = only if cells wrap around)\n",
"operation_mode = \"\" # This in given as a default input argument through the webservice in production. Don't remove!"
]
},
@@ -88,6 +88,7 @@
"\n",
"from cal_tools.calcat_interface import CalCatApi\n",
"from cal_tools.enums import BadPixels\n",
+ "from cal_tools.lpdlib import make_cell_order_condition\n",
"from cal_tools.plotting import plot_badpix_3d\n",
"from cal_tools.restful_config import calibration_client\n",
"from cal_tools.tools import (\n",
@@ -207,7 +208,7 @@
" cell_ids = cell_ids[skip_first_ntrains : skip_first_ntrains + ntrains]\n",
" \n",
" if len(data.train_ids) < min_trains:\n",
- " raise Exception(f\"Run {run_path} only contains {len(data.train_ids)} trains, but {min_ntrains} required\")\n",
+ " raise Exception(f\"Run {run_path} only contains {len(data.train_ids)} trains, but {min_trains} required\")\n",
"\n",
" im = data.ndarray()\n",
" if im.ndim > 3:\n",
@@ -354,10 +355,7 @@
" old_const[mod_num] = {}\n",
" old_mdata[mod_num] = {}\n",
"\n",
- " if inject_cell_order:\n",
- " mem_cell_order = \",\".join([str(c) for c in cellid_pattern]) + \",\"\n",
- " else:\n",
- " mem_cell_order = None\n",
+ " mem_cell_order = make_cell_order_condition(inject_cell_order, cellid_pattern)\n",
"\n",
" # mod_num is from 1 to 8, so b_v_0 applies to odd numbers\n",
" bias_voltage = bias_voltage_0 if (mod_num % 2 == 1) else bias_voltage_1\n",
@@ -432,10 +430,7 @@
" db_module = pdu_name_by_da[karabo_da_m]\n",
" print(f\"Storing constants for PDU {db_module}\")\n",
"\n",
- " if inject_cell_order:\n",
- " mem_cell_order = \",\".join([str(c) for c in cellid_pattern]) + \",\"\n",
- " else:\n",
- " mem_cell_order = None\n",
+ " mem_cell_order = make_cell_order_condition(inject_cell_order, cellid_pattern)\n",
"\n",
" # Do not store empty constants\n",
" # In case of 0 trains data_g is initiated with nans and never refilled.\n",
diff --git a/notebooks/LPDMini/LPD_Mini_Correct.ipynb b/notebooks/LPDMini/LPD_Mini_Correct.ipynb
index efc8fca0c..769e5121b 100644
--- a/notebooks/LPDMini/LPD_Mini_Correct.ipynb
+++ b/notebooks/LPDMini/LPD_Mini_Correct.ipynb
@@ -45,7 +45,7 @@
"bias_voltage_1 = -1 # bias voltage for minis 2, 4, 6, 8; Setting -1 will read the value from files\n",
"capacitor = '5pF' # Capacitor setting: 5pF or 50pF\n",
"photon_energy = 9.3 # Photon energy in keV.\n",
- "use_cell_order = False # Whether to use memory cell order as a detector condition (not stored for older constants)\n",
+ "use_cell_order = 'auto' # Whether to use memory cell order as a detector condition (auto = used only when memory cells wrap around)\n",
"\n",
"# Correction parameters\n",
"offset_corr = True # Offset correction.\n",
@@ -101,7 +101,7 @@
"\n",
"from cal_tools.calcat_interface import CalCatApi\n",
"from cal_tools.lpdalgs import correct_lpd_frames\n",
- "from cal_tools.lpdlib import get_mem_cell_order\n",
+ "from cal_tools.lpdlib import get_mem_cell_pattern, make_cell_order_condition\n",
"from cal_tools.tools import CalibrationMetadata, calcat_creation_time\n",
"from cal_tools.files import DataFile\n",
"from cal_tools.restful_config import calibration_client"
@@ -247,22 +247,23 @@
"\n",
"base_condition = [\n",
" # Bias voltage added below as it differs by module\n",
- " dict(parameter_id=15, value=capacitor), # Feedback capacitor\n",
- " dict(parameter_id=7, value=mem_cells), # Memory cells\n",
- " dict(parameter_id=13, value=256), # Pixels X\n",
- " dict(parameter_id=14, value=32), # Pixels Y\n",
+ " dict(parameter_name='Feedback capacitor', value=capacitor),\n",
+ " dict(parameter_name='Memory cells', value=mem_cells),\n",
+ " dict(parameter_name='Pixels X', value=256),\n",
+ " dict(parameter_name='Pixels Y', value=32),\n",
"]\n",
- "if use_cell_order:\n",
+ "dark_condition = base_condition.copy()\n",
+ "if use_cell_order != 'never':\n",
" # Read the order of memory cells used\n",
" raw_data = xd.DataCollection.from_paths([e[0] 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=30, value=cell_ids_pattern_s), # Memory cell order\n",
- " ]\n",
- "else:\n",
- " dark_condition = base_condition.copy()\n",
+ " cell_ids_pattern_s = make_cell_order_condition(\n",
+ " use_cell_order, get_mem_cell_pattern(raw_data, det_inp_sources)\n",
+ " )\n",
+ " if cell_ids_pattern_s is not None: \n",
+ " print(\"Memory cells order:\", cell_ids_pattern_s)\n",
+ " dark_condition.append(\n",
+ " dict(parameter_name='Memory cell order', value=cell_ids_pattern_s),\n",
+ " )\n",
"\n",
"illuminated_calibrations = {}\n",
"if rel_gain:\n",
@@ -274,7 +275,7 @@
" illuminated_calibrations[42] = 'GainAmpMap' # np.float32\n",
"\n",
"illuminated_condition = base_condition + [\n",
- " dict(parameter_id=3, value=photon_energy), # Source energy\n",
+ " dict(parameter_name='Source Energy', value=photon_energy),\n",
"]"
]
},
@@ -298,7 +299,7 @@
" mod_num = int(karabo_da_m.split('/')[-1])\n",
" # mod_num is from 1 to 8, so b_v_0 applies to odd numbers\n",
" bias_voltage = bias_voltage_0 if mod_num % 2 == 1 else bias_voltage_1\n",
- " condition_w_voltage = [dict(parameter_id=1, value=bias_voltage)] + condition\n",
+ " condition_w_voltage = [dict(parameter_name='Sensor Bias Voltage', value=bias_voltage)] + condition\n",
" \n",
" resp = CalibrationConstantVersion.get_closest_by_time_by_detector_conditions(\n",
" calcat_client, karabo_id, list(calibrations.keys()),\n",
--
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