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+#+OPTIONS: num:nil toc:nil reveal_single_file:t
+#+REVEAL_ROOT: ~/opt/reveal.js-3.9.2
+#+REVEAL_TRANS: none
+#+REVEAL_THEME: white
+#+REVEAL_MIN_SCALE: 1.0
+#+REVEAL_MAX_SCALE: 1.0
+#+REVEAL_TITLE_SLIDE: <h1>%t</h1><h3>%s</h3><p>%A %a</p><p><a href="%u">%u</a></p>
+
+#+Title: km3io
+#+Subtitle: Reading KM3NeT ROOT files without ROOT
+#+Author: Zineb Aly (CPPM) and Tamas Gal (ECAP)
+#+Email: zaly@km3et.de tgal@km3net.de
+#+REVEAL_TALK_URL: https://indico.cern.ch/event/878692/
+
+
+* Prerequisites
+#+BEGIN_SRC bash :results silent :async t
+python3 -m venv ~/tmp/km3io-premiere-venv
+. ~/tmp/km3io-permiere-venv/bin/activate
+pip install km3io==0.8.1
+#+END_SRC
+
+#+BEGIN_SRC elisp
+(setq org-babel-python-command "~/tmp/km3io-permiere-venv/bin/python")
+#+END_SRC
+
+#+RESULTS:
+: ~/tmp/km3io-permiere-venv/bin/python
+
+* km3io
+#+ATTR_REVEAL: :frag (appear)
+- [[https://git.km3net.de/km3py/km3io][km3io]] tiny Python package with minimal dependencies to read KM3NeT ROOT files
+- Uses the [[https://github.com/scikit-hep/uproot][uproot]] library to access ROOT data
+- Provides convenient wrapper classes
+- Maximum performance due to numpy and numba
+- Data are read lazily
+ - only loaded into memory when directly accessed
+ - apply several cut masks on huge datasets without reading them into the memory
+
+** Installation
+- Dependencies:
+ - Python 3.5+
+ - uproot (installed automatically)
+- Releases are published on the official Python package repository:
+ - ~pip install km3io~
+
+* Online (DAQ) Data
+** km3io supports the following DAQ datatypes
+#+ATTR_REVEAL: :frag (appear)
+- ~JDAQEvent~ (the event dataformat)
+ - header information
+ - snapshot hits
+ - triggered hits
+- ~JDAQSummaryslices~
+ - header information
+ - accessor methods for bit flags (HRV, FIFO, UDP status)
+- ~JDAQTimeslices~
+ - header information
+ - frame hits
+ - currently only L1, L2 and SN streams, the L0 stream is work in progress
+
+** Examples
+*** Opening a run file
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+import km3io
+f = km3io.DAQReader("KM3NeT_00000044_00006880.root")
+print(f.events)
+print(f.timeslices)
+print(f.summaryslices)
+#+END_SRC
+
+#+RESULTS:
+: Number of events: 115038
+: Available timeslice streams: SN, L1
+: <km3io.daq.SummmarySlices object at 0x7f8ee90cc970>
+
+*** Investigating timeslice frames
+
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+a_timeslice = f.timeslices.stream("L1", 23)
+print(a_timeslice.frames.keys())
+#+END_SRC
+
+#+RESULTS:
+: dict_keys([806451572, 806455814, 806465101, 806483369, 806487219, 806487226, 806487231, 808432835, 808435278, 808447180, 808447186, 808451904, 808451907, 808469129, 808472260, 808472265, 808488895, 808488990, 808489014, 808489117, 808493910, 808946818, 808949744, 808951460, 808956908, 808959411, 808961448, 808961480, 808961504, 808961655, 808964815, 808964852, 808964883, 808964908, 808969848, 808969857, 808972593, 808972598, 808972698, 808974758, 808974773, 808974811, 808974972, 808976377, 808979567, 808979721, 808979729, 808981510, 808981523, 808981672, 808981812, 808981864, 808982005, 808982018, 808982041, 808982066, 808982077, 808982547, 808984711, 808996773, 808997793, 809006037, 809007627, 809503416, 809521500, 809524432, 809526097, 809544058, 809544061])
+
+*** Reading the first 100 ToTs and channel IDs of a frame sent by the DOM 806451572
+
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+print(a_timeslice.frames[806451572].tot[:100])
+print(a_timeslice.frames[806451572].pmt[:100])
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+[33 16 22 24 7 27 4 31 31 15 5 26 30 24 7 26 26 26 27 15 7 3 63 28
+ 26 30 25 24 20 7 23 6 22 22 26 15 29 25 24 22 23 21 26 20 27 27 25 12
+ 27 15 21 9 17 27 21 30 29 5 25 24 22 27 34 10 13 17 25 10 15 28 15 20
+ 29 24 24 5 16 26 25 33 26 26 26 14 30 6 27 10 18 24 26 49 59 25 31 30
+ 23 25 28 11]
+[ 0 9 4 12 13 2 10 10 8 9 27 27 28 18 27 2 6 15 4 2 2 12 27 3
+ 15 10 23 14 19 9 9 24 24 6 7 20 7 20 27 22 24 25 22 14 18 27 30 29
+ 29 11 28 1 1 11 12 18 29 20 20 19 10 23 21 2 2 16 1 3 3 24 26 9
+ 13 10 29 30 30 10 22 0 22 30 6 19 21 25 25 27 27 26 27 25 29 9 10 5
+ 13 6 13 11]
+#+end_example
+
+*** Checking the number of UDP packets in summary slices
+
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+f = km3io.DAQReader("KM3NeT_00000044_00006880.root")
+sumslice = f.summaryslices.slices[23]
+print(sumslice.dom_id)
+print(km3io.daq.get_number_udp_packets(sumslice.dq_status))
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+[806451572 806483369 806487231 808435278 808447180 808451907 808472265
+ 808488895 808489014 808489117 808493910 808946818 808949744 808951460
+ 808956908 808959411 808961448 808961504 808961655 808964815 808964883
+ 808964908 808969848 808969857 808972593 808972598 808972698 808974972
+ 808976377 808979721 808979729 808981510 808981523 808981672 808981812
+ 808981864 808982005 808982018 808982041 808982066 808982547 808984711
+ 808996773 808997793 809006037 809007627 809521500 809524432 809544058]
+[17 17 16 16 25 16 27 17 18 17 21 16 16 16 34 18 18 18 17 18 16 18 15 17
+ 20 18 15 17 17 19 16 18 16 17 17 16 18 18 17 27 18 20 16 17 15 18 17 17
+ 17]
+#+end_example
+
+* Offline (MC/reco) Data
+** Reading offline files (aka aanet-ROOT files)
+#+ATTR_REVEAL: :frag (appear)
+- Events
+ - header information
+ - hits
+ - tracks (from reconstruction)
+ - MC tracks
+- MC information
+- Reco information
+
+** Opening a reconstructed MUPAGE file
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+f = km3io.OfflineReader("mc.root")
+print(f)
+#+END_SRC
+
+#+RESULTS:
+: <km3io.offline.OfflineReader object at 0x7f8eeb436e20>
+
+** Investigating events and tracks
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+print(f.events)
+#+END_SRC
+
+#+RESULTS:
+: Number of events: 10
+
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+print(f.tracks.lik)
+print(f.tracks.dir_z)
+#+END_SRC
+
+#+RESULTS:
+: [[294.6407542676734 294.6407542676734 294.6407542676734 ... 67.81221253265059 67.7756405143316 67.77250505700384] [96.75133289411137 96.75133289411137 96.75133289411137 ... 39.21916536442286 39.184645826013806 38.870325146341884] [560.2775306614813 560.2775306614813 560.2775306614813 ... 118.88577278801066 118.72271313687405 117.80785995187605] ... [71.03251451148226 71.03251451148226 71.03251451148226 ... 16.714140573909347 16.444395245214945 16.34639241716669] [326.440133294878 326.440133294878 326.440133294878 ... 87.79818671079849 87.75488082571873 87.74839444768625] [159.77779654216795 159.77779654216795 159.77779654216795 ... 33.8669134999348 33.821631538334984 33.77240735670646]]
+: [[-0.872885221293917 -0.872885221293917 -0.872885221293917 ... -0.6631226836266504 -0.5680647731737454 -0.5680647731737454] [-0.8351996698137462 -0.8351996698137462 -0.8351996698137462 ... -0.7485107718446855 -0.8229838871876581 -0.239315690284641] [-0.989148723802379 -0.989148723802379 -0.989148723802379 ... -0.9350162572437829 -0.88545604390297 -0.88545604390297] ... [-0.5704611045902105 -0.5704611045902105 -0.5704611045902105 ... -0.9350162572437829 -0.4647231989130516 -0.4647231989130516] [-0.9779941383490359 -0.9779941383490359 -0.9779941383490359 ... -0.88545604390297 -0.88545604390297 -0.8229838871876581] [-0.7396916780974963 -0.7396916780974963 -0.7396916780974963 ... -0.6631226836266504 -0.7485107718446855 -0.7485107718446855]]
+
+** Some pretty print features for single objects
+*** Hits
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+print(f[0].hits[1])
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+offline hit:
+ id : 0
+ dom_id : 806451572
+ channel_id : 9
+ tdc : 0
+ tot : 30
+ trig : 1
+ pmt_id : 0
+ t : 70104016.0
+ a : 0.0
+ pos_x : 0.0
+ pos_y : 0.0
+ pos_z : 0.0
+ dir_x : 0.0
+ dir_y : 0.0
+ dir_z : 0.0
+ pure_t : 0.0
+ pure_a : 0.0
+ type : 0
+ origin : 0
+ pattern_flags : 0
+#+end_example
+
+*** Tracks
+
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+print(f[0].tracks[0])
+#+END_SRC
+
+#+RESULTS:
+#+begin_example
+offline track:
+ fUniqueID : 0
+ fBits : 33554432
+ id : 1
+ pos_x : 445.835395997812
+ pos_y : 615.1089636184813
+ pos_z : 125.1448339836911
+ dir_x : 0.0368711082700674
+ dir_y : -0.48653048395923415
+ dir_z : -0.872885221293917
+ t : 70311446.46401498
+ E : 99.10458562488608
+ len : 0.0
+ lik : 294.6407542676734
+ type : 0
+ rec_type : 4000
+ rec_stages : [1, 3, 5, 4]
+ status : 0
+ mother_id : -1
+ hit_ids : []
+ error_matrix : []
+ comment : 0
+ JGANDALF_BETA0_RAD : 0.004957442219414389
+ JGANDALF_BETA1_RAD : 0.003417848024252858
+ JGANDALF_CHI2 : -294.6407542676734
+ JGANDALF_NUMBER_OF_HITS : 142.0
+ JENERGY_ENERGY : 99.10458562488608
+ JENERGY_CHI2 : 1.7976931348623157e+308
+ JGANDALF_LAMBDA : 4.2409761837248484e-12
+ JGANDALF_NUMBER_OF_ITERATIONS : 10.0
+ JSTART_NPE_MIP : 24.88469697331908
+ JSTART_NPE_MIP_TOTAL : 55.88169412579765
+ JSTART_LENGTH_METRES : 98.89582506402911
+ JVETO_NPE : 0.0
+ JVETO_NUMBER_OF_HITS : 0.0
+ JENERGY_MUON_RANGE_METRES : 344.9767431592819
+ JENERGY_NOISE_LIKELIHOOD : -333.87773581129136
+ JENERGY_NDF : 1471.0
+ JENERGY_NUMBER_OF_HITS : 101.0
+#+end_example
+
+** Extracting the energy of every first reco track in each event
+
+#+BEGIN_SRC python :results output replace :session km3io :exports both
+f = km3io.OfflineReader("mupage.root")
+print(f.mc_tracks)
+print(f.mc_tracks.id.counts)
+mask = f.mc_tracks.id.counts > 0
+print(f.mc_tracks.E[mask, 0])
+#+END_SRC
+
+#+RESULTS:
+: Number of tracks: 12236
+: [11 2 3 ... 10 1 4]
+: [17.72 73.213 10884.78 1694.332 1221.061 22945.123 11019.418 ...]
+
+* ORCA DU4 RBR Analysis Example
+** A tiny function to extract track attributes from a list of files
+
+#+BEGIN_SRC python
+def extract_features(files, features):
+ """Return a dict with the features from every best reco track"""
+ data = defaultdict(list)
+ for f in tqdm(files):
+ tracks = km3io.OfflineReader(f).tracks
+ mask = tracks.len.counts > 0
+ for feature in features:
+ data[feature].append(getattr(tracks, feature)[mask, 0])
+ return {k: np.hstack(v) for k, v in data.items()}
+#+END_SRC
+
+** Extracting ~E~, ~lik~, ~pos[xyz]~ and ~dir[xyz]~
+- Only takes a few seconds per file
+- Results are numpy arrays
+
+#+BEGIN_SRC python
+sea_files = glob("data/reco-sea/*aanet*.root")
+features = ['E', 'lik', *[e + '_' + q for q in 'xyz' for e in ['pos', 'dir']]]
+sea_data = extract_features(sea_files, features)
+#+END_SRC
+
+** Plotting some data with ~matplotlib~
+#+BEGIN_SRC python
+fig, ax = plt.subplots()
+plot_options = {
+ 'histtype': 'step',
+ 'bins': 100,
+ 'log': True,
+ 'linewidth': 2
+}
+ax.hist(sea_data['E'], label="sea data", **plot_options)
+ax.hist(mc_data['E'], label="atm. muons MC (JSirene)", **plot_options)
+ax.set_xlabel("energy / GeV")
+ax.legend(); ax.grid();
+#+END_SRC
+
+#+REVEAL: split
+
+[[file:./images/orca-du4.png]]
+
+* Command line tool(s)
+- We are working on some counter parts to the Jpp tools
+ - ~KPrintTree -f FILENAME~: similar to ~JPrintTree~
+ - more to come (feel free to request or contribute)
+
+* Thanks
+- Zineb Aly (CPPM)
+- Tamas Gal (ECAP)
+- Johannes Schumann (ECAP)
+
+** Important links
+- Docs: [[https://km3py.pages.km3net.de/km3io]]
+- Source: [[https://git.km3net.de/km3py/km3io]]
+- uproot: [[https://github.com/scikit-hep/uproot]]