From 337549573fb9fb4ac11f638638e3964d288a4805 Mon Sep 17 00:00:00 2001
From: Nuno Duarte <nuno.duarte@xfel.eu>
Date: Mon, 26 Jun 2023 22:16:29 +0200
Subject: [PATCH] update paths of receiver slow data
---
.../Characterize_Darks_ePix100_NBC.ipynb | 33 ++++++++++---
.../ePix100/Correction_ePix100_NBC.ipynb | 46 +++++++++++++------
src/cal_tools/epix100/epix100lib.py | 30 +++++++-----
3 files changed, 79 insertions(+), 30 deletions(-)
diff --git a/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb b/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
index 7a174bdd7..8a2e065f8 100644
--- a/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
@@ -27,14 +27,14 @@
"metadata": {},
"outputs": [],
"source": [
- "in_folder = '/gpfs/exfel/exp/HED/202201/p002804/raw' # input folder, required\n",
- "out_folder = '' # output folder, required\n",
+ "in_folder = '/gpfs/exfel/exp/MID/202330/p900329/raw' # input folder, required\n",
+ "out_folder = ''\n",
"metadata_folder = '' # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"sequence = 0 # sequence file to use\n",
- "run = 281 # which run to read data from, required\n",
+ "run = 106 # which run to read data from, required\n",
"\n",
"# Parameters for accessing the raw data.\n",
- "karabo_id = \"HED_IA1_EPX100-1\" # karabo karabo_id\n",
+ "karabo_id = \"MID_EXP_EPIX-1\" # karabo karabo_id\n",
"karabo_da = [\"EPIX01\"] # data aggregators\n",
"receiver_template = \"RECEIVER\" # detector receiver template for accessing raw data files\n",
"path_template = 'RAW-R{:04d}-{}-S{{:05d}}.h5' # the template to use to access data\n",
@@ -75,6 +75,7 @@
"source": [
"import os\n",
"import warnings\n",
+ "from datetime import datetime\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
@@ -173,6 +174,24 @@
"print(f\"Number of dark images to analyze: {n_trains}\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Get timestamp of first train\n",
+ "train_time_stamp = run_dir.train_timestamps()[0].astype(datetime)/1e9\n",
+ "train_time_stamp = datetime.fromtimestamp(train_time_stamp)\n",
+ "\n",
+ "# Acessing receiver slow data through new device configuration\n",
+ "if train_time_stamp > datetime(2023,5,19): # date of device upgrade\n",
+ " rcvr_src = f\"{karabo_id}/DET/RECEIVER\"\n",
+ "# Acessing receiver slow data through old device configuration\n",
+ "else:\n",
+ " rcvr_src = f\"{karabo_id}/DET/RECEIVER:daqOutput\""
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -181,7 +200,7 @@
"source": [
"ctrl_data = epix100lib.epix100Ctrl(\n",
" run_dc=run_dir,\n",
- " instrument_src=instrument_src,\n",
+ " rcvr_src=rcvr_src,\n",
" ctrl_src=f\"{karabo_id}/DET/CONTROL\",\n",
" )\n",
"# Read integration time\n",
@@ -212,7 +231,9 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"outputs": [],
"source": [
"# Passing repetitive code along the notebook to a function \n",
diff --git a/notebooks/ePix100/Correction_ePix100_NBC.ipynb b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
index 57c48072c..ae2579f91 100644
--- a/notebooks/ePix100/Correction_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
@@ -24,15 +24,15 @@
"metadata": {},
"outputs": [],
"source": [
- "in_folder = \"/gpfs/exfel/exp/HED/202202/p003121/raw\" # input folder, required\n",
- "out_folder = \"\" # output folder, required\n",
+ "in_folder = '/gpfs/exfel/exp/MID/202330/p900329/raw' # input folder, required\n",
+ "out_folder = ''\n",
"metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
"sequences_per_node = 1 # number of sequence files per cluster node if run as slurm job, set to 0 to not run SLURM parallel\n",
- "run = 156 # which run to read data from, required\n",
+ "run = 106 # which run to read data from, required\n",
"\n",
"# Parameters for accessing the raw data.\n",
- "karabo_id = \"HED_IA1_EPX100-1\" # karabo karabo_id\n",
+ "karabo_id = \"MID_EXP_EPIX-1\" # karabo karabo_id\n",
"karabo_da = \"EPIX01\" # data aggregators\n",
"db_module = \"\" # module id in the database\n",
"receiver_template = \"RECEIVER\" # detector receiver template for accessing raw data files\n",
@@ -89,6 +89,7 @@
"import h5py\n",
"import pasha as psh\n",
"import numpy as np\n",
+ "from datetime import datetime\n",
"import matplotlib.pyplot as plt\n",
"from IPython.display import Latex, Markdown, display\n",
"from extra_data import RunDirectory, H5File\n",
@@ -189,6 +190,27 @@
"step_timer = StepTimer()"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Get timestamp of first train\n",
+ "train_time_stamp = run_dc.train_timestamps()[0].astype(datetime)/1e9\n",
+ "train_time_stamp = datetime.fromtimestamp(train_time_stamp)\n",
+ "\n",
+ "# Acessing receiver slow data through new device configuration\n",
+ "if train_time_stamp > datetime(2023,5,19): # date of device upgrade\n",
+ " rcvr_src = f\"{karabo_id}/DET/RECEIVER\"\n",
+ " key_prefix = 'slowdata'\n",
+ "# Acessing receiver slow data through old device configuration\n",
+ "else:\n",
+ " rcvr_src = f\"{karabo_id}/DET/RECEIVER:daqOutput\"\n",
+ " key_prefix = 'data'\n",
+ " "
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -207,7 +229,7 @@
"# Read control data.\n",
"ctrl_data = epix100lib.epix100Ctrl(\n",
" run_dc=run_dc,\n",
- " instrument_src=instrument_src,\n",
+ " rcvr_src=rcvr_src,\n",
" ctrl_src=f\"{karabo_id}/DET/CONTROL\",\n",
" )\n",
"\n",
@@ -250,7 +272,6 @@
]
},
{
- "attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
@@ -602,9 +623,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "scrolled": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"empty_seq = 0\n",
@@ -646,6 +665,7 @@
" step_timer.start() # Correct data. \n",
"\n",
" # Overwrite seq_dc after eliminating empty trains or/and applying limited images.\n",
+ " slow_data_dc = seq_dc.select(rcvr_src,require_all=True).select_trains(np.s_[:corr_ntrains])\n",
" seq_dc = seq_dc.select(\n",
" instrument_src, \"*\", require_all=True).select_trains(np.s_[:corr_ntrains])\n",
"\n",
@@ -684,7 +704,7 @@
" \"digitalInputVolt\", \"guardCurr\", \"relHumidity\", \"digitalCurr\"\n",
" ]\n",
" for field in data_raw_fields:\n",
- " field_arr = seq_dc[instrument_src, f\"data.{field}\"].ndarray()\n",
+ " field_arr = slow_data_dc[rcvr_src, f\"{key_prefix}.{field}\"].ndarray()\n",
"\n",
" outp_source.create_key(\n",
" f\"data.{field}\", data=field_arr,\n",
@@ -902,9 +922,9 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "cal_venv",
"language": "python",
- "name": "python3"
+ "name": "cal_venv"
},
"language_info": {
"codemirror_mode": {
@@ -916,7 +936,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.12"
+ "version": "3.8.11"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
diff --git a/src/cal_tools/epix100/epix100lib.py b/src/cal_tools/epix100/epix100lib.py
index 9cea56634..c54002a44 100644
--- a/src/cal_tools/epix100/epix100lib.py
+++ b/src/cal_tools/epix100/epix100lib.py
@@ -6,16 +6,16 @@ class epix100Ctrl():
self,
run_dc: extra_data.DataCollection,
ctrl_src: str,
- instrument_src: str,
+ rcvr_src: str,
):
"""Read epix100 parameters to use later while quering CALCAT.
:param run_dir: EXtra-data RunDirectory DataCollection object.
- :param ctrl_src: CONTROL source for accessing slow data.
- :param instrument_src: INSTRUMENT source for accessing fast data.
+ :param ctrl_src: CONTROL/*/DET/CONTROL source for accessing slow data from controler.
+ :param rcvr_src: CONTROL/*/DET/RECEIVER source for accessing slow data from receiver.
"""
self.run_dc = run_dc
self.ctrl_src = ctrl_src
- self.instrument_src = instrument_src
+ self.rcvr_src = rcvr_src
def get_integration_time(self):
return self.run_dc[
@@ -23,12 +23,20 @@ class epix100Ctrl():
def get_temprature(self):
"""Get temperature value from CONTROL.
- Temprature is stored in Celsius/100 units.
- Therefore, we are dividing by 100 and
- there is an absolute tolerance of 100.
- atol=100 is a 1 degree variation tolerance.
+ Temprature is stored in Celsius
+ atol is degree variation tolerance.
"""
- # data.backTemp shape evolved from (n_trains,) to (n_trains, 1)
+
+ # older device configuration
+ if self.rcvr_src.find('daqOutput') > 0:
+ atol = 100 # temperature was in C/100
+ data_key = 'data.backTemp'
+ # new device configuration
+ else:
+ atol = 1
+ data_key = 'slowdata.backTemp'
+
+ # data.backTemp shape evolved from (n_trains,) to (n_trains, 1)
return self.run_dc[
- self.instrument_src, 'data.backTemp'].as_single_value(
- reduce_by='mean', atol=100).item() / 100
+ self.rcvr_src, data_key].as_single_value(
+ reduce_by='mean', atol=atol).item() / atol
\ No newline at end of file
--
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