From 19d6fc3b9bd31a9b4cae53177a8e261cdbf20161 Mon Sep 17 00:00:00 2001
From: karnem <mikhail.karnevskiy@desy.de>
Date: Tue, 21 Jan 2020 13:28:05 +0100
Subject: [PATCH] Plot JF with 16 mem cells
---
cal_tools/cal_tools/ana_tools.py | 12 +++--
notebooks/generic/PlotFromCalDB_NBC.ipynb | 63 +++++++++++++----------
reportservice/report_conf.yaml | 28 ++++++++--
3 files changed, 68 insertions(+), 35 deletions(-)
diff --git a/cal_tools/cal_tools/ana_tools.py b/cal_tools/cal_tools/ana_tools.py
index a01475006..907c1682d 100644
--- a/cal_tools/cal_tools/ana_tools.py
+++ b/cal_tools/cal_tools/ana_tools.py
@@ -374,7 +374,7 @@ def get_range(data, scale, threshold = -1000):
return med - scale * mad, med + scale * mad
-def hm_combine(data, fname=None, htype=None, **kwargs):
+def hm_combine(data, mem_cells=32, fname=None, htype=None, **kwargs):
"""
Plot heatmap for calibration report
@@ -385,6 +385,7 @@ def hm_combine(data, fname=None, htype=None, **kwargs):
HMType.INSET_AXIS insets axis for memory cells
:param data: 2D numpy.array of data points to plot
+ :param mem_cells: number of memory cells shown in data
:param fname: file name of output file
:param htype: type of figure
:param kwargs: other keywords supported by pyDetLib heatmapPlot
@@ -490,9 +491,12 @@ def hm_combine(data, fname=None, htype=None, **kwargs):
use_axis=ax,
y_log=False)
if htype == HMType.INSET_AXIS:
-
- ax2 = plt.axes([pad_l, pad_b, w_frame, h_frame / 16.], frame_on=False,
- yticks=range(3), yticklabels=[32, 16, 0],
+ # Group y axis by pixels and memory cells
+ # Axis inset shows memory cells
+ nypix = data.shape[0] / mem_cells
+ ax2 = plt.axes([pad_l, pad_b, w_frame, h_frame / nypix],
+ frame_on=False, yticks=range(2),
+ yticklabels=[mem_cells, 0],
xticks=[], xticklabels=[]
)
ax2.yaxis.set_label_position("right")
diff --git a/notebooks/generic/PlotFromCalDB_NBC.ipynb b/notebooks/generic/PlotFromCalDB_NBC.ipynb
index 3e3ba7791..8240ddf2f 100644
--- a/notebooks/generic/PlotFromCalDB_NBC.ipynb
+++ b/notebooks/generic/PlotFromCalDB_NBC.ipynb
@@ -22,36 +22,36 @@
"outputs": [],
"source": [
"cluster_profile = \"noDB\" # The ipcluster profile to use\n",
- "start_date = \"2019-06-30\" # date to start investigation interval from\n",
+ "start_date = \"2019-01-01\" # date to start investigation interval from\n",
"end_date = \"NOW\" # date to end investigation interval at, can be \"now\"\n",
- "dclass=\"LPD\" # Detector class\n",
- "modules = [\"LPD1M1\"] # detector entry in the DB to investigate\n",
+ "dclass=\"jungfrau\" # Detector class\n",
+ "modules = [\"Jungfrau_M035\"] # detector entry in the DB to investigate\n",
"submodules = [2] # module index of a modular detector (1 for Q1M1 of AGIPD), range allowed \n",
- "constants = ['Noise'] # constants to plot\n",
- "nconstants = 7 # Number of time stamps to plot. If not 0, overcome start_date.\n",
+ "constants = ['RelativeGain'] # constants to plot\n",
+ "nconstants = 20 # Number of time stamps to plot. If not 0, overcome start_date.\n",
"max_time = 15 # max time margin in minutes to match bad pixels\n",
- "nMemToShow = 32 # Number of memory cells to be shown in plots\n",
+ "nMemToShow = 16 # Number of memory cells to be shown in plots\n",
"\n",
- "gain_setting = [0] # gain stages\n",
- "bias_voltage = [250, 500] # Bias voltage\n",
+ "gain_setting = [0,1,2] # gain stages\n",
+ "bias_voltage = [90, 180] # Bias voltage\n",
"temperature = [291] # Operation temperature\n",
- "integration_time = [250, 50] # Integration time\n",
+ "integration_time = [4.96, 10, 50, 250] # Integration time\n",
"pixels_x=[1024] # number of pixels along X axis\n",
- "pixels_y=[512, 1024] # number of pixels along Y axis\n",
+ "pixels_y=[512] # number of pixels along Y axis\n",
"in_vacuum = [0] # 0 if detector is operated in room pressure\n",
- "memory_cells = [1, 512] # number of memory cells\n",
+ "memory_cells = [1, 16] # number of memory cells\n",
"acquisition_rate = [1.1] # aquisition rate\n",
- "parameter_names = ['bias_voltage', 'memory_cells'] # names of parameters\n",
+ "parameter_names = ['bias_voltage', 'integration_time', 'pixels_x', 'pixels_y', 'temperature', 'memory_cells'] # names of parameters\n",
"\n",
- "separate_plot = ['gain_setting'] # Plot on separate plots\n",
+ "separate_plot = ['gain_setting', 'memory_cells', 'integration_time'] # Plot on separate plots\n",
"x_labels = ['Sensor Temperature', 'Integration Time'] # parameters to be shown on X axis: Acquisition rate, Memory cells, Sensor Temperature, Integration Time\n",
"photon_energy = 9.2 # Photon energy of the beam\n",
- "out_folder = \"/gpfs/exfel/data/scratch/karnem/test_bla3/\" # output folder\n",
+ "out_folder = \"/gpfs/exfel/data/scratch/karnem/test_bla4/\" # output folder\n",
"use_existing = \"\" # If not empty, constants stored in given folder will be used\n",
"cal_db_interface = \"tcp://max-exfl016:8016\" # the database interface to use\n",
"cal_db_timeout = 180000 # timeout on caldb requests\",\n",
"plot_range = 3 # range for plotting in units of median absolute deviations\n",
- "spShape = [64, 64] # Shape of superpixel\n",
+ "spShape = [256, 64] # Shape of superpixel\n",
"sp_name = 'ASIC IDs' # name of superpixel\n",
"gain_titles = ['High gain', 'Medium gain', 'Low gain'] # Title inset related to gain"
]
@@ -96,7 +96,7 @@
" submodules = ['']\n",
"\n",
"# 0 is considered as None.\n",
- "acquisition_rate = [x if x>0 else None for x in acquisition_rate]\n",
+ "acquisition_rate = [x if x > 0 else None for x in acquisition_rate]\n",
"\n",
"nMem = max(memory_cells) # Number of mem Cells to store\n",
"\n",
@@ -106,7 +106,7 @@
"if separate_plot == ['']:\n",
" separate_plot = []\n",
"\n",
- "# Mapping between consatnts and their bad pixel maps \n",
+ "# Mapping between consatnts and their bad pixel maps\n",
"constantsDark = {\"SlopesFF\": 'BadPixelsFF',\n",
" 'SlopesPC': 'BadPixelsPC',\n",
" 'SlopesCI': 'BadPixelsCI',\n",
@@ -134,7 +134,7 @@
"metadata": {},
"outputs": [],
"source": [
- "parameter_list = combine_lists(*parameters, names = parameter_names)\n",
+ "parameter_list = combine_lists(*parameters, names=parameter_names)\n",
"print(parameter_list)"
]
},
@@ -172,7 +172,7 @@
" # Loop over parameters\n",
" for pars in parameter_list:\n",
"\n",
- " if (const in [\"Offset\", \"Noise\", \"SlopesPC\", \"SlopesCI\"] or \"DARK\" in const.upper()):\n",
+ " if (const in [\"Offset\", \"Noise\", \"SlopesPC\", \"SlopesCI\", \"RelativeGain\"] or \"DARK\" in const.upper()):\n",
" dcond = Conditions.Dark\n",
" mcond = getattr(dcond, dclass)(**pars)\n",
" else:\n",
@@ -708,10 +708,17 @@
" for key, item in keys.items():\n",
" if item[0] in data:\n",
" rdata[key] = np.array(data[item[0]])[sort_ind]\n",
+ " \n",
+ " # Limit number of memory cells to show\n",
+ " # with respect to one available in data\n",
+ " if len(rdata['Mean'].shape)==4:\n",
+ " nMem = min(nMemToShow, rdata['Mean'].shape[3])\n",
+ " if len(rdata['Mean'].shape)<4:\n",
+ " nMem = 1\n",
"\n",
" nTimes = rdata['Mean'].shape[0]\n",
" nPixels = rdata['Mean'].shape[1] * rdata['Mean'].shape[2]\n",
- " nBins = nMemToShow * nPixels\n",
+ " nBins = nMem * nPixels\n",
"\n",
" # Avoid too low values\n",
" if const[0] in [\"Noise10Hz\", \"Offset10Hz\"]:\n",
@@ -728,16 +735,18 @@
" for key in rdata:\n",
" if len(rdata[key].shape)<3:\n",
" continue\n",
- " if dclass in ['AGIPD', 'LPD']:\n",
- " pdata[key] = rdata[key][:, :, :, :nMemToShow].reshape(\n",
+ " if len(rdata[key].shape)==4:\n",
+ " # take first nMem memory cells\n",
+ " pdata[key] = rdata[key][:, :, :, :nMem].reshape(\n",
" nTimes, nBins).swapaxes(0, 1)\n",
" else:\n",
+ " # case of no memory cells\n",
" pdata[key] = rdata[key].reshape(nTimes, nBins).swapaxes(0, 1)\n",
"\n",
" # Summary over ASICs\n",
" adata = {}\n",
" for key in rdata:\n",
- " if len(rdata[key].shape)<3 or nMemToShow==1:\n",
+ " if len(rdata[key].shape)<3 or nMem==1:\n",
" continue\n",
" adata[key] = np.nanmean(rdata[key], axis=(1, 2)).swapaxes(0, 1)\n",
"\n",
@@ -780,13 +789,15 @@
" fname = '{}_{}'.format(fname, item)\n",
" fname = '{}_ASIC_{}.png'.format(fname, key)\n",
"\n",
- " if nMemToShow>1:\n",
+ " if nMem>1:\n",
" htype=HMType.INSET_AXIS\n",
" else: \n",
" htype=HMType.mro\n",
"\n",
- " hm_combine(pdata[key][::-1].astype(float), htype=htype,\n",
+ " hm_combine(pdata[key][::-1].astype(float), htype=htype, mem_cells=nMem,\n",
" x_label='Creation Time', y_label=sp_name,\n",
+ " y_ticks=np.arange(0, nBins+1, nBins//16),\n",
+ " y_ticklabels=np.arange(0, nPixels+1, nPixels//16),\n",
" x_ticklabels=ctimes_ticks,\n",
" x_ticks=np.arange(len(ctimes_ticks))+0.3,\n",
" title=title, cb_label=cb_label,\n",
@@ -794,7 +805,7 @@
" fname=fname,\n",
" pad=[0.125, 0.125, 0.12, 0.185])\n",
"\n",
- " if nMemToShow>1:\n",
+ " if nMem>1:\n",
" vmin,vmax = get_range(adata[key][::-1].flatten(), plot_range)\n",
" hm_combine(adata[key].astype(float), htype=HMType.mro,\n",
" x_label='Creation Time', y_label='Memory cell ID',\n",
diff --git a/reportservice/report_conf.yaml b/reportservice/report_conf.yaml
index c272c6755..4a6ade68e 100644
--- a/reportservice/report_conf.yaml
+++ b/reportservice/report_conf.yaml
@@ -81,17 +81,22 @@ SPB:
constants:
- "Noise"
- "Offset"
+ - "RelativeGain"
dclass: "jungfrau"
- nMemToShow: 1
+ nMemToShow: 16
modules:
- "Jungfrau_M035"
- "Jungfrau_M203"
- "Jungfrau_M221"
+ - "Jungfrau_M275"
+ - "Jungfrau_M273"
+ - "Jungfrau_M267"
bias-voltage:
- 90
- 180
memory-cells:
- 1
+ - 16
pixels-x:
- 1024
pixels-y:
@@ -100,19 +105,22 @@ SPB:
temperature:
- 291
integration-time:
+ - 4.96
- 50
- 250
gain-setting:
- 0
+ - 1
+ - 2
separate-plot:
- "integration_time"
- "gain_setting"
+ - "memory_cells"
parameter-names:
- "bias_voltage"
- "integration_time"
- "pixels_x"
- "pixels_y"
- - "gain_setting"
- "temperature"
- "memory_cells"
spShape:
@@ -291,6 +299,7 @@ FXE:
constants:
- "Noise"
- "Offset"
+ - "RelativeGain"
dclass: "jungfrau"
modules:
- "Jungfrau_M233"
@@ -301,6 +310,7 @@ FXE:
- 180
memory-cells:
- 1
+ - 16
pixels-x:
- 1024
pixels-y:
@@ -309,19 +319,22 @@ FXE:
temperature:
- 291
integration-time:
+ - 4.96
- 50
- 250
gain-setting:
- 0
+ - 1
+ - 2
separate-plot:
- "integration_time"
- "gain_setting"
+ - "memory_cells"
parameter-names:
- "bias_voltage"
- "integration_time"
- "pixels_x"
- "pixels_y"
- - "gain_setting"
- "temperature"
- "memory_cells"
spShape:
@@ -511,7 +524,7 @@ SQS:
x-labels:
- "Sensor Temperature"
- "Integration Time"
- sp-name: "ASICs id"
+ sp-name: "Supercolumn 256*256"
photon-energy: 9.2
use-existing: "''"
out-folder: "/gpfs/exfel/data/scratch/xcal/report_service/tmp/{instrument}/{detector}/"
@@ -571,6 +584,7 @@ HED:
constants:
- "Noise"
- "Offset"
+ - "RelativeGain"
dclass: "jungfrau"
nMemToShow: 1
modules:
@@ -581,6 +595,7 @@ HED:
- 180
memory-cells:
- 1
+ - 16
pixels-x:
- 1024
pixels-y:
@@ -589,19 +604,22 @@ HED:
temperature:
- 291
integration-time:
+ - 4.96
- 50
- 250
gain-setting:
- 0
+ - 1
+ - 2
separate-plot:
- "integration_time"
- "gain_setting"
+ - "memory_cells"
parameter-names:
- "bias_voltage"
- "integration_time"
- "pixels_x"
- "pixels_y"
- - "gain_setting"
- "temperature"
- "memory_cells"
spShape:
--
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