User`s Manual AGATHE software Flying Insect Counting
Contents
1. Height of the image cm distance from the object x 0 684 Example a distance of 1m from the camera will result in a shooting area of 90 6cm x 68 4cm At this distance one pixel will thus correspond to 0 34mm height and 0 35mm width 16 SUPPORT Support and additional information can be found at http beecam advansee com support en2. ADVANSE CADI NAIC i imhtc YCAKVIC A E SARL 2015 All rights reserved O LADVANS Embedded Electronics Figure 11 Concatenation of all the trajectories into a single jpg image The density of pixel represented in this image is a good indicator of the activity of insect for this particular area at this particular time 14 RECORDS When finished the software records several files in the ExportCSV directory 14 1 List of events compatible with Excel First is a text file containing a list of events with the same information as what is displayed in the event zone cf 11 The name of the file is composed of the root name of the video with an extension csv This file can be easily imported into any excel or similar software for further treatments 14 2 Concatenation image As indicated above cf the image of the all trajectories is recorded as root_name plus extension _hank jpg The density associated to all the trajectories is stored into a file named rootname plus the extension _hank txt 14 3 Series of masks The masks information are also recorder for further use with other videos Extensions are mask adv area adv and alg proprietary formats 1 all files created by the software are recorded in this ExportCSV directory a sub directory of the working directory Document ADV UM 9019 02 v1 0 ADVANSEE SARL 2015 All rights reserved page 11 A gt DVANS Embedded
3. Out Detected 4 Version 2 5 6 tT ADVANS gt Ci Ye Ctifl 11 COUNTS OF EVENTS Every detection that has been qualified as a count is both logged into a file and displayed in the list of events The information associated to this event are Number of the frame in the video The insect position X and Y in this frame at the time of the first detection Whether it is an entering IN or exiting OUT insect with reference to the area of counting At the end of the video processing you can click on one of the event The software will display the corresponding frame so you can check the insect 12 ZOOM AND RECORD OF IMAGES In case an image or a part of an image may present some interest you can zoom on the area by double clicking on the image This option is valid only for videos with resolution higher than VGA 640 x 480 Thus what is displayed the image or the zoom can be recorded by clicking on the Save Image button you must select the name and place where the file will be stored 13 DISPLAY TRAJECTORIES When selected the Display Trajectories button opens in an other window the traces of all the trajectories of the insects that have been counted This image is at the end of the video processing archived in the ExportCSV sub directory The name of the image is composed of the root name of the video combined with the extension _hank jpg Document ADV_UM_9019 02 v1 0
4. 4 MAH00434 video8 0 video9 video_20150704_1340_30_I 2 video_20150704_1350_30_I v Save image lt lt y gt gt gt In Detected 0 Out Detected 1 Version 2 5 6 ADVANS Figure 9 The red little box and number Illustrate the insect detection 10 THE VIRTUAL LINE For those who simply want a counting of individuals crossing a virtual line you can replace the counting box the green line by a straight line one starting point and one end point In this mode every line crossing detection will be both counted as IN and OUT Document ADV_UM_9019 02 v1 0 ADVANSEE SARL 2015 All rights reserved page 9 ASVANS Embedded Electronics I ce gt Agathe Working directory C Users tcorbiere Videos video_demo_agathe l ass fi Import mouse x 718 y 12 v Display trajectories C Users tcorbiere Videos video_demo_agathe P 1100759 MP4 File mask done Am1_22 juillet 15h25 Y Y MAH00433 Y Y MAH00433_1 N N MAH00434 N N 5 P1100759 N Y video3 Y Y videos Y Y 2 1 s 3 405 273 463 0 1 ceo of x 06 256 si7 1 lo la 4 F 5 434 263 49 1 0 ET Po i X 6 439 295 572 1 0 2 video_20150704 1340 301 Y Y alao a a o i 3 video_20150704 1350 301 Y Y alasi as lk e ia 9 513 165 jam o 1 Taj 10 598 606 507 1 0 laa as1 225 lsa li la Zi Save image lt lt lt Play gt gt gt 390 in Detected 8
5. Electronics 15 TROUBLE SHOOTING 15 1 Over counting As indicated above the software is based on movement tracking As indicated in chapter 8 it is important to leave a margin between the flowers or the vegetation and the counting box the green border If not large enough any movement of the plants caused by the wind or anything else will provoke an erroneous count This is illustrated by Fig 12 where the green line gets too close to the large white portion of the flower which because of the wind blends and crosses the line generating false counts 15 2 Shadow To eliminate the double count of an insect due to the projection of its shadow onto the background colored wall orient the scene so that the sun does not project to much light in the direction of the panel 15 3 Respect the distance The regular BEECAM is equipped with a 5Mega Pixel image sensor The lens of the sensor is fixed and not accessible The focal plane is managed to get correct images from 60cm to infinity For a full resolution image the lens gives Horizontal field of view 53 Vertical field of view 40 With these numbers one can calculate the area that an image will correspond using the following equation full resolution of 2591 x 1944 Width of the image cm distance from the object x 0 906 Document ADV_UM_9019 02 v1 0 ADVANSEE SARL 2015 All rights reserved page 12 ADVANS Embedded Electronics
6. Windows 7 8 10 64 bits e CPU quad core or hexa core Intel i7 Xeon e 16 GB RAM 2 3 Software installation Execute the launcher setup Agathe 2 5 6 exe with appropriate administrator rights Select the directory where you want the AGATHE software be installed Answer the questions By default answers are recommended Once installed you can run the AGATHE software by either click the AGATHE icon or run Agathe exe from the installation directory you have selected ADVANS Embedded Electronics 3 AGATHE FIRST SCREEN At first use the AGATHE software will display the screen as per Fig 1 The zones illustrate different information that are either provided by the software or by the operator ADVANS Figure 1 AGATHE screen at first use Zone 1 The directory where video files are available This will be the working directory Zone 2 The list of videos available in the working directory Zone 3 The 90 image of the video selected in zone 2 will be displayed here Zone 4 Resolution and frame rate of the selected video are displayed Zone 5 User will draw areas of interest using these buttons Zone 6 This area is designed to display events one insect has been detected when the video is being processed Zone 7 Standard buttons to play with the selected video Zone 8 The process button and some selections to be used when ready to process Zone 9 The number of the current frame the one
7. Y 6 video4 Y d B video Y Y Y lt lt lt lt lt 2 lt lt l2lzlz EE 11 video_20150704 1340_30 I 12 video_20150704 1350_30 lt lt lt toons ASVANS ctifl aa www emmramm 90 In Detected 0 Out Detected 0 Figure 5 Drawing the Tracking box red lines Document ADV_UM_9019 02 v1 0 ADVANSEE SARL 2015 All rights reserved page 6 ADVANS Embedded Electronics 7 2 Apply these boxes to several videos at once These boxes might be defined only once and applied for several videos In case the videos are small shoots repeated regularly over the day the same two boxes are applicable In this case select in the list of videos the one of reference and follow the instruction 7 1 to draw the two boxes When ready to process the videos select in the appropriate list of zone 8 cf Fig 1 either the option only unprocessed files or all files When you will press the button Process all the videos of the working directory will be processed sequentially IMPORTANT NOTICE The software is using movement detection As such processing videos captured in outdoor natural environment justifies some constraints associated to the parasitic effects of moving plants or leaves 8 1 Optimizing the scene To obtain correct detection rate it is highly recommended to adapt the zone of the shooting with a
8. colorized panel to mask the background 8 2 Dimension of the back panel One constraint is due to the algorithm used to detect insects one insect is positively detected if and only if its trace is found in two successive images and if its trajectory crosses the counting area as designed by the operator cf 7 1 Therefore the drawing of the two areas counting and tracking is of very high importance Video properties Width 640 Fps Height 480 Frame C Users tcorbiere Videos video_demo_agathe Am1_22 juillet_15h25 mp4 Counting box f Start Save Cancel Tracking box orking directory C Users tcorbiere Videos video_demo_agathe r Import mouse x 618 y 363 Display trajectories File Am1_22 juillet_15h25 start Save Cancel Shift mask MAH00433 MAH00433_1 e Start Cancel 4 MAH00434 video3 G video4 video5 B video D video 1 video_20150704 1340 _30 I h N N N N N N N Y Y Y Y N Y Y Y Y Y Y Y 12 video_20150704_1350_30_I zj Save image lt In Detected 0 Out Detected 0 Version 2 5 6 Ctifl Figure 6 Resulting counting area in violet as the intersection of Counting and Tracking boxes Document ADV UM 9019 02 v1 0 ADVANSEE SARL 2015 All rights reserved page 7 ADVANS Embedded Electronics In Fig 6 the area colorized in violet is the area where the tra
9. displayed Zone 10 This button validates the display of an image with accumulation of all insects trajectories Zone 11 The software version number ADVANS Embedded Electronics 4 THE WORKING DIRECTORY 4 1 Selection of the working directory The selection of the working directory is the very first operation to make when using AGATHE In this directory must be placed the videos to be treated 4 2 Results in sub directory As far as the software has been ran once an ExportCSV sub directory is created that will contain the results of the counting and some additional information related to the masks that have been defined by the operator cf 4 2 The files generated in this sub directory have the root name of the initial video with different extensions 5 THE LIST OF VIDEO FILES Once the working directory has been selected the list of available videos is displayed In relation with each video file the software displays whether the file has been already processed and if the masks have been defined cf example in Fig 2 Working directory C Users tcorbiere Videos video_demo_ac File mask done arking directory C Users tcorbiere Wideos video_demo_agathe l Ami_22 juillet 15h25 N N C Users toc 2 MAHO00433 N N File mask done a A 7 juille 2 Ge B MAHO00433 1 N N Amd 22 juillet 15h35 Delete Result WLAHOO4 33 4 MAH00434 N N j Ee isk MAHOO433 1 N N 5 video3 T Y MAHO0434 M M 6 video4 Y Y vi
10. 9 13 Display WA SCO aca ea da ates a anise pede nine nee bev ecieentareemenic 9 VT GCOS oes erent eters a eae ested Se nce te een te sd on ented E E eee eee 10 14 1 List of events compatible with Excel 10 14 2 Concatenation MARS 2 des cesse anne tee es nec lente 10 145 Series of ASKS ne EARR RAEN 10 19 Trouble SNOON cicis aene EEEE EET E EA ORN ESENE EEEN 11 15 1 Over COUNTING iecnn2eeiccna00c0snacsoisceseasseseendssensadehacesnemsmentadadhotinneliondacadecseasvsseqsesdeaudens 11 oL A OWN e E E ocd eee sa ectoee ete eae oee aed eee eeueoee 11 15 3 Respect the distance ss 11 16 DO ee 12 1 ADVANS Embedded Electronics INTRODUCTION This document is the user s manual for the AGATHE software This software is aimed at extracting insect numbers out from MP4 videos the footage collected using the BEEcam in indoor or outdoor conditions DESCRIPTION 2 1 Product references Commercial name AGATHE Current version 2 5 3 Product number none 2 2 Product usage The software must be used to count insect flying all over a bunch of flowers or the vegetation in open conditions The footage must have been collected by the BEEcam from Advansee The current version 2 5 3 accepts MP4 videos Minimum configuration The following description shows the minimum and recommended Hardware and Software requirements Minimum e Windows 7 8 10 e Any CPU Intel i5 i7 Xeon recommended e 4 GB RAM Recommended e
11. ADVANS Embedded Electronics User s Manual AGATHE software Flying Insect Counting Reference Document ADV_UM_9019 02 Revision 1 0 Date 27 10 2015 ADVANSEE 2 rue Alfred Kastler CS30750 44307 Nantes cedex 3 France T l 33 0 2 4050 2173 Email contact advansee com www advansee com SARL au capital de 40 200 510 580 814 RCS Nantes SIRET 510 580 814 00042 TVAI FR 31 510 580 814 ADVANS Embedded Electronics Table of content OO a E LE A EE 3 PADE SCH DUI OM sa ae a A E 3 2 l POOUIC ROIS a en eee en code 3 2 2 POUCES AS nn Esee E EA Ea EEEE ONERE REEERE 3 2 0 DOM WAN HS CAN ON sn E E 3 SAGE FIAS TOC ae ne eee 4 A TAS Working CUS CUO tec ce n E aE da oc 5 4 1 Selection of the working directory 5 4 2 Results in SUD AITOCIOTV 22e s nn ee dec neuee sense ete ccm ent ees chrome 5 5 Thelist of video files sssusa EAEE KE EPRA Eidi 5 6 Display of the video 90th image Re 5 7 Drawing of the areas of interest 6 7 1 Drawing the two boxes 6 7 2 Apply these boxes to several videos at once T o importan NOCE sssi E ERE E T 9 Processing the video iii T 9 1 Processing ModE assassini Eaa aE E EEEE TTEA 8 9 2 Start the image processing sisi 8 10 THS WUC el EG ea E 8 WA GUIS OT EVENS ose cts r A E E sereea nedeasoscsacerees TEO 9 12 Zoom and record OF IMAGES scsi icsccuccnsnzsuencsuscadaneneucasvecdueddewseatgaesstesewnderencecdedawbaaacuiene
12. cking of the insects is done Since we need two successive detections to qualify an insect of interest the maximum the violet area the best the results If the bunch of flowers can not be adapted only the back panel can 8 3 Dimensions and speed of the insects We would like to know what insect are visiting this lovely flower of Fig 8 We suppose to put a colorized gray panel to suppress parasitic movements created by the vegetation at the background The formula in 1 gives the minimum dimension Delta that allows the detection of insects traveling at a particular speed CR Figure 8 Original Figure 7 Instrumented area Delta 2x Vmax x Lp LrxF with 1 Delta in pixels Vmax in cm sec Lr Horizontal or vertical length of the scene in cm Lp Horizontal or vertical resolution of the video Example An insect traveling at a speed of 120cm sec 4 3km hour would need 28 pixels to be surely detected 8 4 Other parasites removal The bottom of the Fig 5 page 6 gives an illustration of the overlapped areas where the stems of the flowers might move with the wind The red border goes into the green area With such a trick no counting nor detection will be made in this particular zone This will definitively prevent the software to over count erratic movements caused by the vegetation The resulting counting area is presented in violet in Fig 6 PROCESSING THE VIDEO 9 1 Processing mode When all the parameters hav
13. deo3 Y Y 7 video5 Y N video Y Y video v video5 YO N D videos Y Y video Y Y 10 video9 YY Figure 3 You can reset the status of every file 11 video _ 20150704 1340 30 I Y Y 2 video_20150704_1350_30 1I Y Y Figure 2 List of files present in the working directory and their status It is possible to reset the status of each file cf Fig 3 Select the video in the list click the right button and choose the option you want to reset mask and or processed 6 DISPLAY OF THE VIDEO 90TH IMAGE Once one video has been selected in the list of files the software displays the image number ADVANS Embedded Electronics 90 of the video DRAWING OF THE AREAS OF INTEREST Before starting drawing the two boxes please read carefully the note in 8 To run the AGATHE software needs the operator to declare two main areas The counting box all insects going through this area will be counted It is displayed in green color The tracking box if an insect is detected in this area and provided the green area remains inside the red area then its trajectory is examined so as it is counted only if it crosses the borders of the area of interest It is displayed in red color 7 1 Drawing the two boxes To draw the box select the appropriate button in zone 5 of the screen Draw small adjacent segments and finish your drawing by a double click Click on save to record your box Repeat this operation for the ot
14. e been correctly set up select the processing mode in the list of zone 8 Several options are possible only unprocessed files all files with Done as N will be processed They will use the masks setup of the selected file Document ADV_UM_9019 02 v1 0 ADVANSEE SARL 2015 All rights reserved page 8 ASVANS Embedded Electronics only one file the selected file will be processed and only this one It will use its own masks ll files all files will be processed They will use the masks setup of the selected file 9 2 Start the image processing Press the Process button to start processing the video The images of the video will be displayed and the software will indicate when a movement has been detected with a red rectangle overlay An actual count will be qualified only if the trajectory of the insect crosses the red border of the counting area see limitations above The event is logged and displayed in the list of event zone 6 Once started the Process button is changed to a Cancel button that you can use to cancel the image processing Video properties Width 640 Fps Height 480 Frame C Users tcorbiere Videos video_demo_agathe Am1_22 juillet_15h25 mp4 Counting box mask done Start Save Cance Tracking box orking directory C Users tcorbiere Videos video_demo_agathe Import mouse x 301 y 403 _ Display trajectories 2 MAHO00433 f Start Shift mask 3 MAH00433_1 Start
15. her box Fig 4 and Fig 5 illustrate the process of drawing the two boxes It is important to notice that only the insects going through the counting box will be included in the total counting Therefore and because of their speed it is highly recommended to leave as much as possible space between green and red lines Video properties Width 640 Fps 25 t 480 Frame 54737 C Users tcorbiere Videos video_demo_agathe Am1_22 juillet_15h25 mp4 Counting box start J save Cancel Tracking box start _ _ save cancel Shift mask lorking directory C Users tcorbiere Videos video_demo_agathe an Import Display trajectories 1 video_20150704_1340_30_I lt lt lt lt lt lt lt z z z 2 video_20150704_1350_30_1 Play gt gt only unprocessed files Y lt i lt lt Advans O AY cue 0 jes Width 640 Fps 25 Height 480 Frame 54737 C Users tcorbiere Videos video_demo_agathe Am1_22 juillet_15h25 mp4 Counting box Car J sove Je Tracking box start save cancel forking directory C Users tcorbiere Videos fvideo_demo_agathe sun Import mouse x 618 y 363 E Display trajectories Am1_22 juillet_15h25 Figure 4 Drawing the Counting box green lines MAH00433 MAH00433_1 4 MAHO0434 5 video3 video5 Y N N N
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