From af019974cf34f0e96cd91658879fc73b795c652d Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 25 Jan 2024 12:43:41 +0100
Subject: [PATCH] Remove unneeded parameters, read conditions the same, and
rename is_strixel to be used like the correction notebook
---
...ngfrau_Create_Fit_Spectra_Histos_NBC.ipynb | 39 +++++-------
.../Jungfrau_Create_Gain_maps_NBC.ipynb | 61 +++++++++----------
...ungfrau_gain_Spectra_Fit_Summary_NBC.ipynb | 1 -
.../Jungfrau_gain_map_Summary_NBC.ipynb | 3 +-
4 files changed, 45 insertions(+), 59 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
index be566bb2c..3e9b18eee 100644
--- a/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Create_Fit_Spectra_Histos_NBC.ipynb
@@ -8,7 +8,7 @@
"\n",
"Author: European XFEL Detector Group, Version: 1.0\n",
"\n",
- "Creates histograms from flat fields.\n",
+ "Creates histograms from flat fields and store it in HDF5 files then perform fitting based on the selecting `fit_func`.\n",
"\n",
"Histograms are on a pixel-by-pixel, memory cell by memory cell basis to save memory and space, histogram range are to be optimized around the desired peak."
]
@@ -27,35 +27,29 @@
"chunked_trains = 1000 # Number of trains per chunk.\n",
"gains = [0, 1, 2] # gain bit values\n",
"karabo_id = \"SPB_IRDA_JF4M\" # karabo prefix of Jungfrau devices\n",
- "karabo_da = [\"\"]\n",
+ "karabo_da = [\"\"] # Detector's data aggregators. Leave empty to derive from CALCAT.\n",
"creation_time = '' # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\"\n",
+ "\n",
+ "# Parameter conditions\n",
"bias_voltage = -1 # bias voltage - Set to -1 to derive from CONTROL file.\n",
"integration_time = -1. # integration time - Set to -1 to derive from CONTROL file.\n",
"gain_mode = 0 # number of memory cells - Set to -1 to derive from CONTROL file.\n",
- "gain_setting = 0\n",
+ "gain_setting = -1 # gain setting parameter conditions (High or low CDS) - Set to -1 to derive from CONTROL file.\n",
"memory_cells = -1 # number of memory cells - Set to -1 to derive from CONTROL file.\n",
- "sc_start = -1 # storage cell start value - should be derived from CONTROL file\n",
+ "sc_start = -1 # storage cell start value - should be derived from CONTROL file.\n",
+ "\n",
"h_bins_s = 2 # bin width in ADC units of the histogram\n",
"h_range = (-50, 450.) # histogram range in ADC units\n",
"block_size = [256, 64] # dimension of the chunks in 'row' and 'col'\n",
- "det_src_template = '{}/DET/{}:daqOutput'\n",
"control_src_template = '{}/DET/CONTROL'\n",
"extra_dims = ['cell', 'row', 'col'] # labels for the DataArray dims after the first\n",
"fit_func = 'CHARGE_SHARING' # function used to fit the single photon peak\n",
- "off_sub = True\n",
- "adc_fit = True\n",
- "is_strixel = False\n",
- "chunk_size = 10\n",
- "_h_range = (150, 350.) ## range of the histogram in x-axis units\n",
+ "fit_h_range = (150, 350.) # range of the histogram in x-axis units used in fitting\n",
"\n",
- "# CALCAT API parameters\n",
- "cal_db_interface = 'tcp://max-exfl-cal-001:8020' # the database interface to use\n",
- "cal_db_timeout = 180000\n",
- "\n",
- "rebin = 1\n",
"# parameters for the peak finder\n",
"n_sigma = 5. # n of sigma above pedestal threshold\n",
"ratio = 0.99 # ratio of the next peak amplitude in the peak_finder\n",
+ "rebin = 1\n",
"\n",
"\n",
"def find_das(in_folder, runs, karabo_da):\n",
@@ -162,16 +156,14 @@
"\n",
" if memory_cells < 0:\n",
" memory_cells, sc_start = ctrl_data.get_memory_cells()\n",
- "\n",
" if integration_time < 0:\n",
" integration_time = ctrl_data.get_integration_time()\n",
- "\n",
" if bias_voltage < 0:\n",
" bias_voltage = ctrl_data.get_bias_voltage()\n",
- "\n",
- " # gain_setting = ctrl_data.get_gain_setting() TODO: Where is the gain_setting?\n",
- " # if gain_mode < 0:\n",
- " # gain_mode = ctrl_data.get_gain_mode()\n",
+ " if gain_setting < 0:\n",
+ " gain_setting = ctrl_data.get_gain_setting()\n",
+ " if gain_mode < 0:\n",
+ " gain_mode = ctrl_data.get_gain_mode()\n",
"\n",
" return (\n",
" bias_voltage,\n",
@@ -248,7 +240,6 @@
" modules=karabo_da,\n",
" memory_cells=memory_cells,\n",
" integration_time=integration_time,\n",
- " # TODO: No gain setting 1? I use 0 for now as I don't see gain_setting used anywhere for the 3 notebooks.\n",
" gain_setting=gain_setting,\n",
" gain_mode=gain_mode,\n",
" client=rest_cfg.calibration_client(),\n",
@@ -487,7 +478,7 @@
" _edges = np.array(edges[da])\n",
" x = (_edges[1:] + _edges[:-1]) / 2.0\n",
"\n",
- " x, _h_spectra = jungfrau_ff.set_histo_range(x, h_spectra[da], _h_range)\n",
+ " x, _h_spectra = jungfrau_ff.set_histo_range(x, h_spectra[da], fit_h_range)\n",
" print(f'adjusting histogram range: {x[0]} - {x[-1]}')\n",
" print(f'Histo shape updated from {h_spectra[da].shape} to {_h_spectra.shape}')\n",
" print(f'x-axis: {x.shape}')\n",
@@ -539,7 +530,7 @@
" dset_noi = fout.create_dataset(\n",
" \"noise_map\",\n",
" data=const_data[da][\"Noise10Hz\"])\n",
- " fout.attrs[\"memory_cells\"] = memory_cells # TODO: Why memory cells are not saved here. What about the other conditions??\n",
+ " fout.attrs[\"memory_cells\"] = memory_cells\n",
" fout.attrs[\"integration_time\"] = integration_time\n",
" fout.attrs[\"bias_voltage\"] = bias_voltage\n",
" fout.attrs[\"gain_setting\"] = gain_setting\n",
diff --git a/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
index b471f83bc..46eb9474a 100755
--- a/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Create_Gain_maps_NBC.ipynb
@@ -33,30 +33,30 @@
"karabo_da = ['']\n",
"fit_func = 'CHARGE_SHARING' # function used to fit the single photon peak\n",
"gains = [0, 1, 2]\n",
+ "\n",
"# Parameter conditions\n",
"bias_voltage = -1 # detector bias voltage\n",
"integration_time = -1. # the detector acquisition rate, use 0 to try to auto-determine\n",
- "gain_setting = 0\n",
+ "gain_setting = -1 # gain setting parameter conditions (High or low CDS) - Set to -1 to derive from CONTROL file.\n",
"gain_mode = 0\n",
- "memory_cells = -1\n",
- "adc_fit = True\n",
- "is_strixel = False\n",
+ "memory_cells = -1 # number of memory cells - Set to -1 to derive from CONTROL file.\n",
"# Condition limits\n",
"bias_voltage_lims = [0, 200]\n",
"integration_time_lims = [0.1, 1000]\n",
+ "\n",
+ "adc_fit = True\n",
+ "strixel_sensor = \"\" # reordering for strixel detector layout. Possible strixels to choose from are A0123 and A1256.\n",
"spectra_fit_temp = 'R{:04d}_{}_Gain_Spectra_{}_{}_Fit.h5' # 'R{:04d}_{proposal.upper()}_Gain_Spectra_{da}_{fit_func}_Fit.h5'\n",
"creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\"\n",
"g_map_old = '' # '/gpfs/exfel/data/user/mramilli/jungfrau/module_PSI_gainmaps/M302/gainMaps_M302_2022-02-23.h5' # old gain map file path to calculate gain ratios G0/G1 and G1/G2. Set to \"\" to get last gain constant from the database.\n",
"old_gain_dataset_name = 'gain_map_g0' # name of the data structure in the old gain map\n",
"correct_offset = False # correct the photon peak value with a pedestal fit position\n",
- "db_output = False\n",
- "local_output = True\n",
- "send_bpix = False # TODO: check why separate BPx from Gain.\n",
+ "db_output = False # A boolean to inject the gain maps to the database.\n",
+ "local_output = True # A boolean to store a local version of the constants in the out-folder\n",
"g0_fit_dataset = 'gainMap_fit' # name of the data structure in the fit files\n",
"E_ph = 8.048 # photon energy of the peak fitted\n",
"badpixel_threshold_sigma = 3. # number of std in gain distribution to mark bad pixels\n",
"roi = [0, 1024, 0, 256] # ROI to consider to evaluate gain distribution (for bad pixels evaluation)\n",
- "control_src_template = '{}/DET/CONTROL'\n",
"\n",
"# CALCAT API parameters\n",
"cal_db_interface = \"tcp://max-exfl-cal001:8020\" # the database interface to use\n",
@@ -128,23 +128,6 @@
"in_folder = Path(in_folder)"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "run_folder = in_folder / f'r{run:04d}'\n",
- "control_src = control_src_template.format(karabo_id, karabo_da[0])\n",
- "\n",
- "ctrl_data = JungfrauCtrl(RunDirectory(run_folder), control_src)\n",
- "\n",
- "if memory_cells < 0:\n",
- " memory_cells, _ = ctrl_data.get_memory_cells()\n",
- "\n",
- "print(f'Memory cells: {memory_cells}')"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -157,9 +140,10 @@
" out_folder / spectra_fit_temp.format(run, proposal.upper(), da, fit_func),\n",
" 'r'\n",
" ) as f:\n",
- " if is_strixel:\n",
+ " if strixel_sensor:\n",
" g0_new[da] = np.transpose(\n",
- " from_strixel(np.transpose(f[g0_fit_dataset][()])))\n",
+ " from_strixel(np.transpose(f[g0_fit_dataset][()])),\n",
+ " kind=strixel_sensor)\n",
" else:\n",
" g0_new[da] = f[g0_fit_dataset][()]\n",
"\n",
@@ -173,9 +157,21 @@
"\n",
" if bias_voltage < 0 and 'bias_voltage' in f.attrs.keys():\n",
" bias_voltage = np.float32(f.attrs['bias_voltage'])\n",
- " print(f'bias voltage: {bias_voltage}')\n",
+ " print(f'Bias voltage: {bias_voltage}')\n",
+ " else:\n",
+ " print(f'Bias voltage not found!\\nUsing default value {bias_voltage}')\n",
+ "\n",
+ " if gain_setting < 0 and 'gain_setting' in f.attrs.keys():\n",
+ " gain_setting = np.bool(f.attrs['gain_setting'])\n",
+ " print(f'Gain setting: {gain_setting}')\n",
+ " else:\n",
+ " print(f'Gain setting not found!\\nUsing default value {gain_setting}')\n",
+ "\n",
+ " if memory_cells < 0 and 'memory_cells' in f.attrs.keys():\n",
+ " memory_cells = np.bool(f.attrs['memory_cells'])\n",
+ " print(f'Memory cells: {memory_cells}')\n",
" else:\n",
- " print(f'bias voltage not found!\\nUsing default value {bias_voltage}')\n",
+ " print(f'Memory cells not found!\\nUsing default value {memory_cells}')\n",
"\n",
" # Run's creation time:\n",
" creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
@@ -239,7 +235,7 @@
" modules=karabo_da,\n",
" memory_cells=memory_cells,\n",
" integration_time=integration_time,\n",
- " gain_setting=gain_setting, # TODO: No gain setting 1? I use 0 for now as I don't see gain_setting used anywhere for the 3 notebooks.\n",
+ " gain_setting=gain_setting,\n",
" gain_mode=gain_mode,\n",
" client=rest_cfg.calibration_client(),\n",
")\n",
@@ -341,8 +337,9 @@
" 'r'\n",
" ) as fc:\n",
" corr = np.array(fc[g0_fit_dataset])\n",
- " if is_strixel:\n",
- " corr = np.transpose(from_strixel(np.transpose(corr)))\n",
+ " if strixel_sensor:\n",
+ " corr = np.transpose(\n",
+ " from_strixel(np.transpose(corr)), kind=strixel_sensor)\n",
"\n",
" g0_new[da] -= corr\n",
"\n",
diff --git a/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb
index 21e94d626..178fbd031 100644
--- a/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_gain_Spectra_Fit_Summary_NBC.ipynb
@@ -52,7 +52,6 @@
"%matplotlib inline\n",
"\n",
"from cal_tools.plotting import init_jungfrau_geom\n",
- "from cal_tools.tools import CalibrationMetadata\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/notebooks/Jungfrau/Jungfrau_gain_map_Summary_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_gain_map_Summary_NBC.ipynb
index 3f70fcc90..aabbc5147 100644
--- a/notebooks/Jungfrau/Jungfrau_gain_map_Summary_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_gain_map_Summary_NBC.ipynb
@@ -24,8 +24,7 @@
"# Parameters used to access raw data.\n",
"karabo_da = [] # list of data aggregators, which corresponds to different JF modules. This is only needed for the detectors of one module.\n",
"karabo_id = \"SPB_IRDA_JF4M\" # detector identifier.\n",
- "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\"\n",
- "g0_fit_dataset = 'gainMap_fit' # name of the data structure in the fit files"
+ "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\""
]
},
{
--
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