CAMTRON PROCESSING PIPELINE
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A) setup / preparation
B) recorder
C) background-subtraction
D) process scripts
X) HPC
Z) laptop/fon maintenance
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PRIO:
> update opencv -> eval how much work to fix?
> update algorithm for bgs -> eval how much work to fix?
A)
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> TEST CAM! GET RUNNING PICTURES!
1. setup virtual machine to test
> 8 cores, 16GB RAM, 2 TB for 1cam
> 48 cores, 128GB RAM, 6 TB for 6cam
2. use laptopt to test
3. (opt/later) setup tower1 (defunct again!) as cheap testing machine!
> get NIC working
> give name connect inet
--> as terminal to connect to server
--> later: use for DMX lighting
4. (alternatively) Raspberry Pi
Q: is option fast enough for processing of 1/3/6 streams simultaneously?
> test bottleneck (CPU,HDD,ethernet,)
> is video compression on? how demanding!
> storage: 1 minute hochrechnen. mit 24/17/12 FPS.
Q: how should workflow look?
> Option A
1. record and store (where)
2. process (where?)
> Option B
1. record, process (cut ROI to reduce size), store
2. more processing (R..)
--> what processing.
--> draw picture as doc of workflow
> light (opt/later)
> find hardware (Boxes, DMX per unit, DMX splitter/controller)
> setup hardware for 1 unit
> check software
> get infrared LEDs. ask if andy ordered them?
> attach IR-LEDs (solder)
> arenas
> verglasungsfolie
> 1 floor wooden plate with circle >> really needed?
> 1 floor glass plate
> 1 floor wooden plate
> how to connect seamlessly?
> o-ring: https://www.o-ring.de/o-ring-fpm-90/item-anfragemenge-6-categoryId-or-itemId-100022-search2-580.00-search3--search7-.html
>> or use poisonous electro-harz zum giessen. Wie Form bauen?
* setup 1 fridge
> attach cam arm to wood
> get video in VV
> get video in SW-A via SDK
> cam calibration (Use Viewer? Or own SW?)
> configure cam settings
* get video for 3 cams in one workstation
> what SW?
> calculate supported framerate+resolution+codec for hardware (CPU,RAM,HDD...)
> or do tests and see if frames are dropped
DONT do a diskbench to get writing speed (calculate needed speed with 3 cameras) to see if frames will be dropped or not...
writing speed of one of the workstations is 150MB/sec
prosilica gtx1920 needs 3x 107.53 MB/sec for BGR. 1x for MONO
avi uncompressed
1280x1280 @ 40 fps is limit for your CPU oO
CPU can compress 47mio pix/second
17x1936x1456=47mio -> 17fps @ full res
suggested CPU i7 3840
reduce ROI
# Documentation
> sketch
> chamber: cam height+resolution+arena diameter for pixel to cm/mm ratio
> lab: chambers+workstations+HPC
> costs. update with what we actually buy!
> sketch: technical: cam (QuantumEfficiency) + IRLED
> sketch: setup plan for a chamber
> copy last setup plan from thomas
B) recorder - camera produces frames and timestamps
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(depends on cam in A)!!!
> use new api Vimba X
> read manual (c++ / vimba)
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> wait and detect cams
> produce frames & timestamps
> build GUI
--> Q: might a console app be feasable??
============================
> central config
> threads for started recordings [PID]
> storage folder
> export settings with viewer
> load settings with sw
> how and where to store frames?
All APIs cover the following functions:
Listing currently connected cameras
Controlling camera features
Receiving images from the camera
Notifications about camera connections or disconnections
> browse other examples a bit:
list cams / features / actioncommands
eventhandling??
> read Manuals
>Vimba, C++, GigE-TL,(ImgTransform,),Cam Technical Docu
pdf "${HOME}/vimba_5_1/Documentation/Vimba Manual.pdf" "${HOME}/vimba_5_1/VimbaCPP/Documentation/Vimba CPP Manual.pdf" "${HOME}/vimba_5_1/VimbaGigETL/Documentation/VimbaGigETLFeaturesManual.pdf" "${HOME}/vimba_5_1/VimbaImageTransform/Documentation/Vimba ImageTransform Manual.pdf" "${HOME}/vimba_5_1/Documentation/Vimba Viewer Guide.pdf"
From Thomas:
* recording single frames in data structure
* used Vimba.2.1 (1.6 more likely)
* compress each frame with loosely jpg compression
(used framework opencv version 3.2. imwrite function with parameter: IMWRITE_JPEG_QUALITY 100 ; IMWRITE_JPEG_OPTIMIZE 1; IMWRITE_JPEG_RST_INTERVAL 4;)
* stores timestamps for each frame in milliseconds
SW viewer [optional]
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how?
Wie ruft man die index.html auf der VM auf?
Wie kommunizieren SW REC und Viewer?
eg. OnStopButtonClicked( cmd( ../camTrack3000 --stop ) ) ??
REST-Server/ HTTP-Json / ..
C) background subtraction
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ctb - calculates centroid points of all frames in a record
> build
> find test data (cp to 00 - ..)
> process
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> update bgs alg. opencv4 has its own bgs?
D) process scripts
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ctd - calculated the mean speed in pixel / millisecond
* can i reduce size of data (reduce length|fps|res)
>> calc D) for test data set (get data from joerdis?)
-> with all frames
-> undersample, shorter length
-> compare results. same?
trajectory
> figure out concrete steps. harmonize scripts? ..
> trajr.
> run calcVmeanForID.r on data
> calc new values. max speed. angle. ...
X) HPC - High Performance Cluster
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> gamify > lvl up
> try script to send over data
> script that copies data once a day from VM to HPC
> Secure-Shell-ID angepasst
> cron
or > II) vimba-software directly to HPC?
Z) laptop/fon maintenance
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Done
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> research suitable "fridges"
-> price!, temp-range, electricity inside, size space in lab?
-> more than 2
Reach In Plant Growth Chambers E-36L1
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> setup stativ, use our lab
> how-to connect ETHernet cable? it will have to go outside of fridge??
> how-to control temperature and humidity? (see picture from thomas dox)
> research WS (see hardware_notes.ods for details like specs. CPU, RAM, SSDs, prices)
> cam aufhaengung
research stativ/tripod: manfrotto arm + clamp + bodenplatte for cams
other stuff to fix cameras > stange
> sensors for temp+humidity (HOBO)
> backup data from towers
> setup tower (displays,cards,cables)
-------------------------------
> bal: func: list_suffices
> bal: function to replace all names to snake_case (upper to lower, space/dash to underscore)
> opd: works with "name containing spaces.pdf" -> use array for files instead of string concatenation in o_helper()
> bug: changed IFS in o_helper broke nav function