From 7ed1506d68399f89edf474c45c8566bb577c0046 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Mon, 18 Mar 2024 13:01:44 +0100
Subject: [PATCH] Change calibration action from FF to GAIN_INJECT and update
out_folder in gain_map NBC to fit_data_folder
---
...ngfrau_Create_Fit_Spectra_Histos_NBC.ipynb | 3 +-
.../Jungfrau_Create_Gain_maps_NBC.ipynb | 35 ++++++++-----------
...ungfrau_gain_Spectra_Fit_Summary_NBC.ipynb | 3 --
src/xfel_calibrate/notebooks.py | 2 +-
4 files changed, 17 insertions(+), 26 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
index 241e80639..099bd0a81 100644
--- a/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
@@ -80,9 +80,8 @@
"\n",
"import numpy as np\n",
"import pasha as psh\n",
- "from extra_data import H5File, RunDirectory, open_run\n",
+ "from extra_data import RunDirectory\n",
"from h5py import File as h5file\n",
- "from XFELDetAna.detectors.jungfrau.util import count_n_files\n",
"\n",
"import cal_tools.restful_config as rest_cfg\n",
"from cal_tools.calcat_interface import JUNGFRAU_CalibrationData\n",
diff --git a/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
index 79f272704..163a9e96d 100755
--- a/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
@@ -25,7 +25,7 @@
"outputs": [],
"source": [
"in_folder = '/gpfs/exfel/exp/MID/202330/p900322/raw' # RAW data path, required\n",
- "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/jf_ff/gain_maps\" # Output path for gain data, required\n",
+ "fit_data_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/jf_ff/gain_maps\" # Output path for gain data, required\n",
"metadata_folder = '' # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"runs = [94] # Number of high gain\n",
"\n",
@@ -101,8 +101,12 @@
"from cal_tools.calcat_interface import JUNGFRAU_CalibrationData\n",
"from cal_tools.enums import BadPixels\n",
"from cal_tools.jungfrau.jfstrixel import from_strixel\n",
- "from cal_tools.jungfrau.jungfraulib import JungfrauCtrl\n",
- "from cal_tools.tools import calcat_creation_time, get_report, save_const_to_h5, send_to_db\n",
+ "from cal_tools.tools import (\n",
+ " calcat_creation_time,\n",
+ " get_report,\n",
+ " save_const_to_h5,\n",
+ " send_to_db,\n",
+ ")\n",
"\n",
"%matplotlib inline"
]
@@ -121,7 +125,7 @@
"outputs": [],
"source": [
"run = runs[0]\n",
- "out_folder = Path(out_folder)\n",
+ "fit_data_folder = Path(fit_data_folder)\n",
"proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
"file_loc = f\"proposal:{proposal} runs:{run}\"\n",
"report = get_report(metadata_folder)\n",
@@ -137,7 +141,7 @@
"g0_new = dict()\n",
"for da in karabo_da:\n",
" with h5file(\n",
- " out_folder / spectra_fit_temp.format(run, proposal.upper(), da, fit_func),\n",
+ " fit_data_folder / spectra_fit_temp.format(run, proposal.upper(), da, fit_func),\n",
" 'r'\n",
" ) as f:\n",
" if strixel_sensor:\n",
@@ -252,14 +256,9 @@
"for mod_info in jf_cal.physical_detector_units.values():\n",
" da_to_pdu[mod_info[\"karabo_da\"]] = mod_info[\"physical_name\"]\n",
"\n",
- "if g_map_old: # TODO: DECIDE WHAT TO DO IN THIS PART AS THE FILE IS PER MODULE\n",
- " with h5file(g_map_old, 'r') as f:\n",
- " gmap_old[da] = np.array(f[old_gain_dataset_name], dtype=np.float32)\n",
- "else:\n",
- " jf_metadata = jf_cal.metadata(calibrations=[\"RelativeGain10Hz\"])\n",
- " # TODO: display CCV timestamp\n",
- " const_data = jf_cal.ndarray_map(metadata=jf_metadata)\n",
- " jf_cal.display_markdown_retrieved_constants(metadata=jf_metadata)\n",
+ "jf_metadata = jf_cal.metadata(calibrations=[\"RelativeGain10Hz\"])\n",
+ "const_data = jf_cal.ndarray_map(metadata=jf_metadata)\n",
+ "jf_cal.display_markdown_retrieved_constants(metadata=jf_metadata)\n",
"\n",
"for da in karabo_da:\n",
" if const_data[da].get(\"RelativeGain10Hz\") is not None:\n",
@@ -338,7 +337,7 @@
" if correct_offset:\n",
" display(Markdown(\"#### Correct with better pedestal estimation\"))\n",
" with h5file(\n",
- " out_folder / spectra_fit_temp.format(run, proposal.upper(), da, fit_func),\n",
+ " fit_data_folder / spectra_fit_temp.format(run, proposal.upper(), da, fit_func),\n",
" 'r'\n",
" ) as fc:\n",
" corr = np.array(fc[g0_fit_dataset])\n",
@@ -533,10 +532,6 @@
"metadata": {},
"outputs": [],
"source": [
- "out_folder = Path(out_folder)\n",
- "out_folder.mkdir(parents=True, exist_ok=True)\n",
- "\n",
- "\n",
"for mode in [0, 1]:\n",
" # Inject constants for fixed and adaptive gain maps.\n",
" conditions = Conditions.Dark.jungfrau(\n",
@@ -599,9 +594,9 @@
" file_loc=file_loc,\n",
" report=report,\n",
" creation_time=creation_time,\n",
- " out_folder=out_folder,\n",
+ " out_folder=fit_data_folder,\n",
" )\n",
- " print(f\"Calibration constant {cname} is stored locally at {out_folder}.\\n\")"
+ " print(f\"Calibration constant {cname} is stored locally at {fit_data_folder}.\\n\")"
]
},
{
diff --git a/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb
index 78b78c9db..57e17f87d 100644
--- a/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb
@@ -37,7 +37,6 @@
"metadata": {},
"outputs": [],
"source": [
- "import math\n",
"import warnings\n",
"from pathlib import Path\n",
"\n",
@@ -47,13 +46,11 @@
"import matplotlib\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
- "from IPython.display import display\n",
"\n",
"matplotlib.use(\"agg\")\n",
"%matplotlib inline\n",
"\n",
"from cal_tools.plotting import init_jungfrau_geom\n",
- "from XFELDetAna.plotting.simpleplot import simplePlot\n",
"from cal_tools.restful_config import calibration_client\n",
"from cal_tools.calcat_interface import CalCatApi"
]
diff --git a/src/xfel_calibrate/notebooks.py b/src/xfel_calibrate/notebooks.py
index dbf72308b..fc12847b8 100644
--- a/src/xfel_calibrate/notebooks.py
+++ b/src/xfel_calibrate/notebooks.py
@@ -213,7 +213,7 @@ notebooks = {
"default concurrency": list(range(8)),
"cluster cores": 4},
},
- "FF": {
+ "GAIN_INJECT": {
"notebook":
"notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb",
"dep_notebooks": [
--
GitLab