From 874646bd4ee69447937a7edd213e4745b9571195 Mon Sep 17 00:00:00 2001
From: Steffen Hauf <xcal@max-exfl016.desy.de>
Date: Thu, 8 Aug 2019 17:06:11 +0200
Subject: [PATCH] Allow to query versions, fixes to AGIPD
---
cal_tools/cal_tools/agipdlib.py | 47 +-
cal_tools/cal_tools/tools.py | 27 +-
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 584 +++++++++++++++---
...Jungfrau_Gain_Correct_and_Verify_NBC.ipynb | 56 +-
...Jungfrau_dark_analysis_all_gains_NBC.ipynb | 33 +-
5 files changed, 595 insertions(+), 152 deletions(-)
diff --git a/cal_tools/cal_tools/agipdlib.py b/cal_tools/cal_tools/agipdlib.py
index 36d2d4044..dad5499d4 100644
--- a/cal_tools/cal_tools/agipdlib.py
+++ b/cal_tools/cal_tools/agipdlib.py
@@ -76,7 +76,8 @@ class AgipdCorrections:
cal_det_instance="AGIPD1M1", karabo_data_mode=False,
force_hg_if_below=None, force_mg_if_below=None,
mask_noisy_adc=False, adjust_mg_baseline=False,
- acquisition_rate=None):
+ acquisition_rate=None, dont_zero_nans=False,
+ dont_zero_orange=False):
"""
Initialize an AgipdCorrections Class
@@ -148,6 +149,9 @@ class AgipdCorrections:
self.adjust_mg_baseline = adjust_mg_baseline
self.mg_bl_adjust = 0
self.acquisition_rate = acquisition_rate
+ self.dont_zero_nans = dont_zero_nans
+ self.dont_zero_orange = dont_zero_orange
+ self.valid_indices = None
def get_iteration_range(self):
"""Returns a range expression over which to iterate in chunks
@@ -999,14 +1003,16 @@ class AgipdCorrections:
# create a bad pixel mask for the data
# we add any non-finite values to the mask
- bidx = ~np.isfinite(im)
- im[bidx] = 0
- msk[bidx] |= BadPixels.VALUE_IS_NAN.value
+ if not self.dont_zero_nans:
+ bidx = ~np.isfinite(im)
+ im[bidx] = 0
+ msk[bidx] |= BadPixels.VALUE_IS_NAN.value
# and such with have unrealistically high and low pixel values
- bidx = (im < -1e7) | (im > 1e7)
- im[bidx] = 0
- msk[bidx] |= BadPixels.VALUE_OUT_OF_RANGE.value
+ if not self.dont_zero_orange:
+ bidx = (im < -1e7) | (im > 1e7)
+ im[bidx] = 0
+ msk[bidx] |= BadPixels.VALUE_OUT_OF_RANGE.value
# include pixels with zero standard deviation in the dataset into
# the mask
@@ -1070,7 +1076,7 @@ class AgipdCorrections:
""" Return the indices of valid data
"""
agipd_base = self.idx_base
- print(agipd_base)
+
if self.index_v == 2:
count = np.squeeze(self.infile[agipd_base + "image/count"])
first = np.squeeze(self.infile[agipd_base + "image/first"])
@@ -1082,9 +1088,21 @@ class AgipdCorrections:
lowok = (idxtrains > medianTrain - 1e4)
highok = (idxtrains < medianTrain + 1e4)
valid &= lowok & highok
+
+ uq, fidxv, cntsv = np.unique(idxtrains,
+ return_index=True,
+ return_counts=True)
+ valid &= cntsv == 1 # filter out double trains
self.valid = valid
last_index = int(first[valid][-1] + count[valid][-1])
first_index = int(first[valid][0])
+
+ # do actual validity filtering:
+ validc, validf = count[valid], first[valid]
+ valid_indices = np.concatenate([np.arange(validf[i],
+ validf[i]+validc[i])
+ for i in range(validf.size)], axis=0)
+ self.valid_indices = np.squeeze(valid_indices).astype(np.int32)
elif self.index_v == 1:
status = np.squeeze(self.infile[agipd_base + "image/status"])
@@ -1119,8 +1137,11 @@ class AgipdCorrections:
last_index = self.last_index
max_cells = self.max_cells
agipd_base = self.agipd_base
- allcells = self.infile[agipd_base + "image/cellId"]
- allcells = np.squeeze(allcells[first_index:last_index, ...])
+ allcells = np.squeeze(self.infile[agipd_base + "image/cellId"])
+ if self.valid_indices is not None:
+ allcells = allcells[self.valid_indices]
+ else:
+ allcells = allcells[first_index:last_index]
single_image = self.infile[agipd_base + "image/data"][first_index, ...]
single_image = np.array(single_image)
@@ -1129,7 +1150,10 @@ class AgipdCorrections:
if np.count_nonzero(can_calibrate) == 0:
return
allcells = allcells[can_calibrate]
- firange = np.arange(first_index, last_index)
+ if self.valid_indices is not None:
+ firange = np.arange(first_index, last_index)
+ else:
+ firange = self.valid_indices
firange = firange[can_calibrate]
self.oshape = (firange.size if not self.il_mode else firange.size // 2,
@@ -1152,6 +1176,7 @@ class AgipdCorrections:
if self.il_mode:
firange = firange[0::2]
alltrains = self.infile[agipd_base + "image/trainId"]
+
alltrains = np.squeeze(
alltrains[first_index:last_index, ...])
diff --git a/cal_tools/cal_tools/tools.py b/cal_tools/cal_tools/tools.py
index 363dd51c8..0e9c4be6e 100644
--- a/cal_tools/cal_tools/tools.py
+++ b/cal_tools/cal_tools/tools.py
@@ -297,9 +297,9 @@ def make_titlepage(sphinx_path, project, data_path, version):
title_tmp = Template(file_.read())
with open("{}/titlepage.tex.txt".format(sphinx_path), "w+") as mf:
- mf.write(dedent(title_tmp.render(project=project,
- data_path=data_path,
- version=version)))
+ mf.write(dedent(title_tmp.render(project=tex_escape(project),
+ data_path=tex_escape(data_path),
+ version=tex_escape(version))))
def finalize(joblist, finaljob, run_path, out_path, project, calibration,
@@ -454,7 +454,8 @@ already_printed = {}
def get_from_db(device, constant, condition, empty_constant,
cal_db_interface, creation_time=None,
- verbosity=1, timeout=30000, ntries=120, meta_only=True):
+ verbosity=1, timeout=30000, ntries=120, meta_only=True,
+ version_info=False):
"""
Return calibration constants and metadata requested from CalDB
@@ -474,6 +475,12 @@ def get_from_db(device, constant, condition, empty_constant,
from iCalibrationDB import ConstantMetaData, Versions
import zmq
+ meta_only=True
+ timeout=1200000
+
+ if version_info:
+ meta_only = False
+
if device:
metadata = ConstantMetaData()
metadata.calibration_constant = constant
@@ -486,17 +493,25 @@ def get_from_db(device, constant, condition, empty_constant,
start=creation_time)
while ntries > 0:
+
this_interface = get_random_db_interface(cal_db_interface)
try:
- metadata.retrieve(this_interface, timeout=timeout,
- meta_only=meta_only)
+ print("Retrieving from {} for {}".format(this_interface, device))
+
+ r = metadata.retrieve(this_interface, timeout=timeout,
+ meta_only=meta_only, version_info=version_info)
+
+ if version_info:
+ return r
break
except zmq.error.Again:
ntries -= 1
+ sleep(np.random.randint(30))
except Exception as e:
if verbosity > 0:
print(e)
ntries = 0
+ break
if ntries > 0:
if verbosity > 0:
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 5d6524115..051c37fd8 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -13,30 +13,29 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 1,
"metadata": {
"ExecuteTime": {
"end_time": "2019-02-21T11:30:06.730220Z",
"start_time": "2019-02-21T11:30:06.658286Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
- "in_folder = \"/gpfs/exfel/exp/SPB/201901/p002480/raw/\" # the folder to read data from, required\n",
- "run = 11 # runs to process, required\n",
- "out_folder = \"/gpfs/exfel/exp/SPB/201901/p002480/proc/\" # the folder to output to, required\n",
- "calfile = \"/gpfs/exfel/data/scratch/haufs/agipd_on_demand/agipd_store.h5\" # path to calibration file. Leave empty if all data should come from DB\n",
+ "in_folder = \"/gpfs/exfel/exp/MID/201931/p900090/raw/\" # the folder to read data from, required\n",
+ "run = 5 # runs to process, required\n",
+ "out_folder = \"/gpfs/exfel/exp/MID/201931/p900090/proc/\" # the folder to output to, required\n",
+ "calfile = \"/gpfs/exfel/data/scratch/haufs/agipd_on_demand/agipd_store_mid.h5\" # path to calibration file. Leave empty if all data should come from DB\n",
"sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
"mem_cells = 0 # number of memory cells used, set to 0 to automatically infer\n",
"interlaced = False # whether data is in interlaced layout\n",
"overwrite = True # set to True if existing data should be overwritten\n",
"no_relative_gain = False # do not do relative gain correction\n",
- "cluster_profile = \"noDB5\"\n",
+ "cluster_profile = \"noDB\"\n",
"max_pulses = 500\n",
"local_input = False\n",
"bias_voltage = 300\n",
- "cal_db_interface = \"tcp://max-exfl016:8020#8025\" # the database interface to use\n",
+ "cal_db_interface = \"tcp://max-exfl016:8015#8045\" # the database interface to use\n",
"use_dir_creation_date = True # use the creation data of the input dir for database queries\n",
"sequences_per_node = 2 # number of sequence files per cluster node if run as slurm job, set to 0 to not run SLURM parallel\n",
"photon_energy = 9.2 # photon energy in keV\n",
@@ -53,12 +52,14 @@
"max_cells_db = 0 # set to a value different than 0 to use this value for DB queries\n",
"chunk_size_idim = 1 # chunking size of imaging dimension, adjust if user software is sensitive to this.\n",
"creation_date_offset = \"00:00:00\" # add an offset to creation date, e.g. to get different constants\n",
- "instrument = \"SPB\" # the instrument the detector is installed at, required\n",
+ "instrument = \"MID\" # the instrument the detector is installed at, required\n",
"force_hg_if_below = 1000 # set to a value other than 0 to force a pixel into high gain if it's high gain offset subtracted value is below this threshold\n",
"force_mg_if_below = 1000 # set to a value other than 0 to force a pixel into medium gain if it's medium gain offset subtracted value is below this threshold\n",
"mask_noisy_adc = 0.25 # set to a value other than 0 and below 1 to mask entire ADC if fraction of noisy pixels is above\n",
"adjust_mg_baseline = False # adjust medium gain baseline to match highest high gain value\n",
"acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
+ "dont_zero_nans = False # do not zero NaN values in corrected data\n",
+ "dont_zero_orange = False # do not zero very negative and very large values\n",
"\n",
"def balance_sequences(in_folder, run, sequences, sequences_per_node):\n",
" import glob\n",
@@ -84,15 +85,26 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 2,
"metadata": {
"ExecuteTime": {
"end_time": "2019-02-21T11:30:07.086286Z",
"start_time": "2019-02-21T11:30:06.929722Z"
- },
- "collapsed": false
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Connecting to profile noDB\n",
+ "Using 2019-07-19 08:16:33.773894 as creation time\n",
+ "Working in IL Mode: False. Actual cells in use are: 0\n",
+ "Outputting to /gpfs/exfel/exp/MID/201931/p900090/proc//r0005\n",
+ "Detector in use is MID_DET_AGIPD1M-1\n"
+ ]
+ }
+ ],
"source": [
"import sys\n",
"from collections import OrderedDict\n",
@@ -176,13 +188,12 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 3,
"metadata": {
"ExecuteTime": {
"end_time": "2019-02-21T11:30:07.263445Z",
"start_time": "2019-02-21T11:30:07.217070Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -236,13 +247,12 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 4,
"metadata": {
"ExecuteTime": {
"end_time": "2019-02-21T11:30:07.974174Z",
"start_time": "2019-02-21T11:30:07.914832Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -303,15 +313,407 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 5,
"metadata": {
"ExecuteTime": {
"end_time": "2019-02-21T11:30:08.870802Z",
"start_time": "2019-02-21T11:30:08.826285Z"
- },
- "collapsed": false
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Processing a total of 368 sequence files in chunks of 32\n"
+ ]
+ },
+ {
+ "data": {
+ "text/latex": [
+ "\\begin{tabular}{rlrl}\n",
+ "\\hline\n",
+ " \\# & module & \\# module & file \\\\\n",
+ "\\hline\n",
+ " 0 & Q1M1 & 0 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00000.h5 \\\\\n",
+ " 1 & & 1 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00001.h5 \\\\\n",
+ " 2 & & 2 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00002.h5 \\\\\n",
+ " 3 & & 3 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00003.h5 \\\\\n",
+ " 4 & & 4 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00004.h5 \\\\\n",
+ " 5 & & 5 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00005.h5 \\\\\n",
+ " 6 & & 6 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00006.h5 \\\\\n",
+ " 7 & & 7 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00007.h5 \\\\\n",
+ " 8 & & 8 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00008.h5 \\\\\n",
+ " 9 & & 9 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00009.h5 \\\\\n",
+ " 10 & & 10 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00010.h5 \\\\\n",
+ " 11 & & 11 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00011.h5 \\\\\n",
+ " 12 & & 12 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00012.h5 \\\\\n",
+ " 13 & & 13 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00013.h5 \\\\\n",
+ " 14 & & 14 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00014.h5 \\\\\n",
+ " 15 & & 15 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00015.h5 \\\\\n",
+ " 16 & & 16 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00016.h5 \\\\\n",
+ " 17 & & 17 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00017.h5 \\\\\n",
+ " 18 & & 18 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00018.h5 \\\\\n",
+ " 19 & & 19 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00019.h5 \\\\\n",
+ " 20 & & 20 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00020.h5 \\\\\n",
+ " 21 & & 21 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00021.h5 \\\\\n",
+ " 22 & & 22 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD00-S00022.h5 \\\\\n",
+ " 23 & Q1M2 & 0 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00000.h5 \\\\\n",
+ " 24 & & 1 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00001.h5 \\\\\n",
+ " 25 & & 2 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00002.h5 \\\\\n",
+ " 26 & & 3 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00003.h5 \\\\\n",
+ " 27 & & 4 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00004.h5 \\\\\n",
+ " 28 & & 5 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00005.h5 \\\\\n",
+ " 29 & & 6 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00006.h5 \\\\\n",
+ " 30 & & 7 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00007.h5 \\\\\n",
+ " 31 & & 8 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00008.h5 \\\\\n",
+ " 32 & & 9 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00009.h5 \\\\\n",
+ " 33 & & 10 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00010.h5 \\\\\n",
+ " 34 & & 11 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00011.h5 \\\\\n",
+ " 35 & & 12 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00012.h5 \\\\\n",
+ " 36 & & 13 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00013.h5 \\\\\n",
+ " 37 & & 14 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00014.h5 \\\\\n",
+ " 38 & & 15 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00015.h5 \\\\\n",
+ " 39 & & 16 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00016.h5 \\\\\n",
+ " 40 & & 17 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00017.h5 \\\\\n",
+ " 41 & & 18 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00018.h5 \\\\\n",
+ " 42 & & 19 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00019.h5 \\\\\n",
+ " 43 & & 20 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00020.h5 \\\\\n",
+ " 44 & & 21 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00021.h5 \\\\\n",
+ " 45 & & 22 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD01-S00022.h5 \\\\\n",
+ " 46 & Q1M3 & 0 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00000.h5 \\\\\n",
+ " 47 & & 1 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00001.h5 \\\\\n",
+ " 48 & & 2 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00002.h5 \\\\\n",
+ " 49 & & 3 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00003.h5 \\\\\n",
+ " 50 & & 4 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00004.h5 \\\\\n",
+ " 51 & & 5 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00005.h5 \\\\\n",
+ " 52 & & 6 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00006.h5 \\\\\n",
+ " 53 & & 7 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00007.h5 \\\\\n",
+ " 54 & & 8 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00008.h5 \\\\\n",
+ " 55 & & 9 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00009.h5 \\\\\n",
+ " 56 & & 10 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00010.h5 \\\\\n",
+ " 57 & & 11 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00011.h5 \\\\\n",
+ " 58 & & 12 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00012.h5 \\\\\n",
+ " 59 & & 13 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00013.h5 \\\\\n",
+ " 60 & & 14 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00014.h5 \\\\\n",
+ " 61 & & 15 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00015.h5 \\\\\n",
+ " 62 & & 16 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD02-S00016.h5 \\\\\n",
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+ " 358 & & 13 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00013.h5 \\\\\n",
+ " 359 & & 14 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00014.h5 \\\\\n",
+ " 360 & & 15 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00015.h5 \\\\\n",
+ " 361 & & 16 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00016.h5 \\\\\n",
+ " 362 & & 17 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00017.h5 \\\\\n",
+ " 363 & & 18 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00018.h5 \\\\\n",
+ " 364 & & 19 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00019.h5 \\\\\n",
+ " 365 & & 20 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00020.h5 \\\\\n",
+ " 366 & & 21 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00021.h5 \\\\\n",
+ " 367 & & 22 & /gpfs/exfel/exp/MID/201931/p900090/raw//r0005/RAW-R0005-AGIPD15-S00022.h5 \\\\\n",
+ "\\hline\n",
+ "\\end{tabular}"
+ ],
+ "text/plain": [
+ "<IPython.core.display.Latex object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"import copy\n",
"from IPython.display import HTML, display, Markdown, Latex\n",
@@ -337,15 +739,63 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 6,
"metadata": {
"ExecuteTime": {
"end_time": "2019-02-21T11:30:16.057429Z",
"start_time": "2019-02-21T11:30:10.082114Z"
- },
- "collapsed": false
+ }
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Running 32 tasks parallel\n",
+ "foo\n",
+ "Have input\n",
+ "Set memory cells to 250\n",
+ "Set acquistion rate cells to 4.5 MHz\n",
+ "Retrieving from tcp://max-exfl016:8022 for AGIPD_SIV1_AGIPDV11_M337: 00303000100000\n",
+ "Offset was injected on: 2019-07-19 01:14:42+02:00\n",
+ "Retrieving from tcp://max-exfl016:8034 for AGIPD_SIV1_AGIPDV11_M337: 00303000100000\n",
+ "Noise was injected on: 2019-07-19 01:14:42+02:00\n",
+ "Retrieving from tcp://max-exfl016:8034 for AGIPD_SIV1_AGIPDV11_M337: 00303000100000\n",
+ "BadPixelsDark was injected on: 2019-07-19 01:14:42+02:00\n",
+ "Retrieving from tcp://max-exfl016:8034 for AGIPD_SIV1_AGIPDV11_M337: 00303000100000\n",
+ "ThresholdsDark was injected on: 2019-07-19 01:14:42+02:00\n",
+ "Offet medians are [4844. 7332. 7579.]\n",
+ "Threshold medians are [6455.25 7125. 5848. 7053. 7196. ]\n",
+ "2019-07-19 01:14:42+02:00\n",
+ "After reading from file: \n",
+ "Offet medians are [4844. 7122.10742188 7579. ]\n",
+ "Gain medians are [ 0.99791807 35.87737 160.88506 ]\n",
+ "Threshold medians are [6455.25 7125. 5848. 7053. 7196. ]\n",
+ "Initialized constants\n",
+ "Iterated\n",
+ "Iterated\n",
+ "Iterated\n",
+ "Iterated\n",
+ "Iterated\n",
+ "Iterated\n"
+ ]
+ },
+ {
+ "ename": "KeyboardInterrupt",
+ "evalue": "",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-6-ef2b971fe04b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 199\u001b[0m \u001b[0;31m#r = view.map_sync(p, inp)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 200\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 201\u001b[0;31m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0minp\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 202\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 203\u001b[0m \u001b[0minp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m<ipython-input-6-ef2b971fe04b>\u001b[0m in \u001b[0;36mcorrect_module\u001b[0;34m(max_cells, do_rel_gain, index_v, CHUNK_SIZE, total_sequences, sequences_qm, bins_gain_vs_signal, bins_signal_low_range, bins_signal_high_range, bins_dig_gain_vs_signal, max_pulses, dbparms, fileparms, nodb, chunk_size_idim, special_opts, il_mode, loc, dinstance, force_hg_if_below, force_mg_if_below, mask_noisy_adc, adjust_mg_baseline, acq_rate, dont_zero_nans, dont_zero_orange, inp)\u001b[0m\n\u001b[1;32m 121\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mirange\u001b[0m \u001b[0;32min\u001b[0m \u001b[0magipd_corr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_iteration_range\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 122\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 123\u001b[0;31m \u001b[0magipd_corr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcorrect_agipd\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mirange\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 124\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Iterated\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 125\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m~/calibration_webservice_deployed/cal_tools/cal_tools/agipdlib.py\u001b[0m in \u001b[0;36mcorrect_agipd\u001b[0;34m(self, irange)\u001b[0m\n\u001b[1;32m 931\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 932\u001b[0m \u001b[0;31m# also choose the correct bad pixel mask\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 933\u001b[0;31m \u001b[0mmsk\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchoose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgain\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mtmask\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m...\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtmask\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m...\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtmask\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m...\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 934\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 935\u001b[0m \u001b[0;31m# scale raw gain for use in the identifying snowy pixels\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/software/anaconda3/5.2/lib/python3.6/site-packages/numpy/core/fromnumeric.py\u001b[0m in \u001b[0;36mchoose\u001b[0;34m(a, choices, out, mode)\u001b[0m\n\u001b[1;32m 377\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 378\u001b[0m \"\"\"\n\u001b[0;32m--> 379\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0m_wrapfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'choose'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mchoices\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mout\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mout\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmode\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 380\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 381\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/software/anaconda3/5.2/lib/python3.6/site-packages/numpy/core/fromnumeric.py\u001b[0m in \u001b[0;36m_wrapfunc\u001b[0;34m(obj, method, *args, **kwds)\u001b[0m\n\u001b[1;32m 50\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m_wrapfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmethod\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 51\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 52\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmethod\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 53\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0;31m# An AttributeError occurs if the object does not have\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
+ ]
+ }
+ ],
"source": [
"import copy\n",
"from functools import partial\n",
@@ -353,7 +803,8 @@
" bins_gain_vs_signal, bins_signal_low_range, bins_signal_high_range,\n",
" bins_dig_gain_vs_signal, max_pulses, dbparms, fileparms, nodb, chunk_size_idim,\n",
" special_opts, il_mode, loc, dinstance, force_hg_if_below, force_mg_if_below,\n",
- " mask_noisy_adc, adjust_mg_baseline, acq_rate, inp):\n",
+ " mask_noisy_adc, adjust_mg_baseline, acq_rate, dont_zero_nans, dont_zero_orange,\n",
+ " inp):\n",
" print(\"foo\")\n",
" import numpy as np\n",
" import copy\n",
@@ -445,7 +896,8 @@
" h5_index_path=\"INDEX/{}/DET/{{}}CH0:xtdf/\".format(loc),\n",
" cal_det_instance=dinstance, force_hg_if_below=force_hg_if_below,\n",
" force_mg_if_below=force_mg_if_below, mask_noisy_adc=mask_noisy_adc,\n",
- " adjust_mg_baseline=adjust_mg_baseline, acquisition_rate=acq_rate)\n",
+ " adjust_mg_baseline=adjust_mg_baseline, acquisition_rate=acq_rate,\n",
+ " dont_zero_nans=dont_zero_nans, dont_zero_orange=dont_zero_orange)\n",
" \n",
" blc_noise, blc_noise_threshold, blc_hist, match_asics, corr_asic_diag, melt_snow = special_opts\n",
" agipd_corr.baseline_corr_using_noise = blc_noise\n",
@@ -466,7 +918,7 @@
" print(\"Initialized constants\")\n",
" \n",
" for irange in agipd_corr.get_iteration_range():\n",
- " \n",
+ " \n",
" agipd_corr.correct_agipd(irange)\n",
" print(\"Iterated\")\n",
" \n",
@@ -541,7 +993,7 @@
" sequences_qm, bins_gain_vs_signal, bins_signal_low_range, bins_signal_high_range,\n",
" bins_dig_gain_vs_signal, max_pulses, dbparms, fileparms, nodb, chunk_size_idim,\n",
" special_opts, il_mode, loc, dinstance, force_hg_if_below, force_mg_if_below,\n",
- " mask_noisy_adc, adjust_mg_baseline, acq_rate)\n",
+ " mask_noisy_adc, adjust_mg_baseline, acq_rate, dont_zero_nans, dont_zero_orange)\n",
" \n",
" r = view.map_sync(p, inp)\n",
" \n",
@@ -571,9 +1023,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"\n",
@@ -590,8 +1040,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:28:51.765030Z",
"start_time": "2019-02-18T17:28:51.714783Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -636,8 +1085,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:28:52.857960Z",
"start_time": "2019-02-18T17:28:51.767217Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -651,8 +1099,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:28:53.690522Z",
"start_time": "2019-02-18T17:28:52.860143Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -687,8 +1134,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:28:54.370559Z",
"start_time": "2019-02-18T17:28:53.691959Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -702,8 +1148,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:31:51.668096Z",
"start_time": "2019-02-18T17:31:51.529158Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -730,7 +1175,6 @@
"end_time": "2019-02-18T17:28:57.327702Z",
"start_time": "2019-02-18T17:28:54.377061Z"
},
- "collapsed": false,
"scrolled": false
},
"outputs": [],
@@ -748,8 +1192,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:20.634480Z",
"start_time": "2019-02-18T17:28:57.329231Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -802,8 +1245,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:27.025667Z",
"start_time": "2019-02-18T17:29:20.642029Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -835,8 +1277,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:33.226396Z",
"start_time": "2019-02-18T17:29:27.027758Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -866,8 +1307,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:33.761015Z",
"start_time": "2019-02-18T17:29:33.227922Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -887,8 +1327,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:35.903487Z",
"start_time": "2019-02-18T17:29:33.762568Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -913,8 +1352,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:39.369686Z",
"start_time": "2019-02-18T17:29:35.905152Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -934,8 +1372,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:49.217848Z",
"start_time": "2019-02-18T17:29:39.371232Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -952,8 +1389,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:49.222484Z",
"start_time": "2019-02-18T17:29:49.219933Z"
- },
- "collapsed": true
+ }
},
"outputs": [],
"source": [
@@ -976,8 +1412,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:49.641675Z",
"start_time": "2019-02-18T17:29:49.224167Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -1006,8 +1441,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:49.651913Z",
"start_time": "2019-02-18T17:29:49.643556Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -1036,8 +1470,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:50.086169Z",
"start_time": "2019-02-18T17:29:49.653391Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -1064,8 +1497,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:51.686562Z",
"start_time": "2019-02-18T17:29:50.088883Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -1090,8 +1522,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:53.662423Z",
"start_time": "2019-02-18T17:29:51.688376Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -1109,8 +1540,7 @@
"ExecuteTime": {
"end_time": "2019-02-18T17:29:55.483270Z",
"start_time": "2019-02-18T17:29:53.664226Z"
- },
- "collapsed": false
+ }
},
"outputs": [],
"source": [
@@ -1127,9 +1557,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": true
- },
+ "metadata": {},
"outputs": [],
"source": []
}
@@ -1150,7 +1578,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
}
},
"nbformat": 4,
diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index f3e593039..018361629 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -14,9 +14,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"in_folder = \"/gpfs/exfel/exp/FXE/201802/p002271/ra\" # the folder to read data from, required\n",
@@ -42,6 +40,7 @@
"gmapfile = \"/gpfs/exfel/data/scratch/xcal/jfgain/gainMaps_M233.h5\" #temporary gain calibration file, not in the DB; leave empty if using DB\n",
"memcells = 1 # number of memory cells\n",
"karabo_id = \"FXE_XAD_JF1M\" # karabo prefix of Jungfrau devices\n",
+ "karabo_id_control = \"\" # if control is on a different ID, set to empty string for using the same as for data\n",
"receiver_id = \"RECEIVER\" # inset for receiver devices\n",
"control_id = \"CONTROL\" # inset for control devices\n",
"db_module = \"Jungfrau_M233\" # ID of module in calibration database\n",
@@ -158,22 +157,23 @@
" creation_time = get_dir_creation_date(in_folder, run)\n",
" print(\"Using {} as creation time\".format(creation_time))\n",
" \n",
- "cal_timeout = 600000 #ms"
+ "cal_timeout = 600000 #ms\n",
+ "\n",
+ "if karabo_id_control == \"\":\n",
+ " karabo_id_control = karabo_id"
]
},
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"import h5py\n",
"if not manual_slow_data:\n",
" with h5py.File(fp_path_contr.format(0), 'r') as f:\n",
- " integration_time = int(f['/RUN/{}/DET/{}/exposureTime/value'.format(karabo_id, control_id)][()]*1e6)\n",
- " bias_voltage = int(np.squeeze(f['/RUN/{}/DET/{}/vHighVoltage/value'.format(karabo_id, control_id)])[0])\n",
+ " integration_time = int(f['/RUN/{}/DET/{}/exposureTime/value'.format(karabo_id_control, control_id)][()]*1e6)\n",
+ " bias_voltage = int(np.squeeze(f['/RUN/{}/DET/{}/vHighVoltage/value'.format(karabo_id_control, control_id)])[0])\n",
"print(\"Integration time is {} us\".format(integration_time))\n",
"print(\"Bias voltage is {} V\".format(bias_voltage))"
]
@@ -214,9 +214,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"import copy\n",
@@ -459,9 +457,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"h, ex, ey = np.histogram2d(rim_data.flatten(), gim_data.flatten(),\n",
@@ -481,9 +477,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize=(20,10))\n",
@@ -506,9 +500,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize=(20,10))\n",
@@ -531,9 +523,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize=(20,10))\n",
@@ -554,9 +544,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize=(20,10))\n",
@@ -583,9 +571,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize=(20,10))\n",
@@ -606,9 +592,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"from cal_tools.enums import BadPixels\n",
@@ -632,9 +616,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"fig = plt.figure(figsize=(20,10))\n",
@@ -669,7 +651,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
}
},
"nbformat": 4,
diff --git a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_NBC.ipynb
index a79590ee1..b54e489e5 100644
--- a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_NBC.ipynb
@@ -40,6 +40,7 @@
"run_med = 0 # run number for G1 dark run, required\n",
"run_low = 0 # run number for G2 dark run, required\n",
"karabo_id = \"FXE_XAD_JF500K\" # karabo prefix of Jungfrau devices\n",
+ "karabo_id_control = \"\" # if control is on a different ID, set to empty string for using the same as for data\n",
"receiver_id = \"RECEIVER\" # inset for receiver devices\n",
"control_id = \"CONTROL\" # inset for control devices\n",
"db_module = \"Jungfrau_M233\" # ID of module in calibration database\n",
@@ -50,9 +51,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"import warnings\n",
@@ -92,7 +91,10 @@
" creation_time = get_dir_creation_date(in_folder, run_high)\n",
" print(\"Using {} as creation time\".format(creation_time))\n",
" \n",
- "offset_abs_threshold = [offset_abs_threshold_low, offset_abs_threshold_high]"
+ "offset_abs_threshold = [offset_abs_threshold_low, offset_abs_threshold_high]\n",
+ "\n",
+ "if karabo_id_control == \"\":\n",
+ " karabo_id_control = karabo_id"
]
},
{
@@ -110,9 +112,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"import h5py\n",
@@ -126,8 +126,8 @@
"\n",
" if not manual_slow_data:\n",
" with h5py.File(fp_path.format(0), 'r') as f:\n",
- " integration_time = int(f['/RUN/{}/DET/{}/exposureTime/value'.format(karabo_id, control_id)][()]*1e6)\n",
- " bias_voltage = int(np.squeeze(f['/RUN/{}/DET/{}/vHighVoltage/value'.format(karabo_id, control_id)])[0])\n",
+ " integration_time = int(f['/RUN/{}/DET/{}/exposureTime/value'.format(karabo_id_control, control_id)][()]*1e6)\n",
+ " bias_voltage = int(np.squeeze(f['/RUN/{}/DET/{}/vHighVoltage/value'.format(karabo_id_control, control_id)])[0])\n",
" print(\"Integration time is {} us\".format(integration_time))\n",
" print(\"Bias voltage is {} V\".format(bias_voltage))\n",
"\n",
@@ -176,7 +176,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
- "collapsed": false,
"scrolled": false
},
"outputs": [],
@@ -257,9 +256,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"def print_bp_entry(bp):\n",
@@ -273,9 +270,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"bad_pixels_map = np.zeros(noise_map.shape, np.uint32)\n",
@@ -441,9 +436,7 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {
- "collapsed": false
- },
+ "metadata": {},
"outputs": [],
"source": [
"is_log = True\n",
@@ -481,7 +474,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.6.6"
+ "version": "3.6.7"
}
},
"nbformat": 4,
--
GitLab