Speckled Bush Cricket Data Logger
Contents
1. a Linear Technology LTC1564 audio low pass filter LPF and amplifier the breakpoint and gain of which are digitally configured by the microcontroller based on user input parameters on the SD card The LPF which has a steep 8 order roll off at the specified break frequency can be adjusted to attenuate frequencies from above 10kHz to above 150kHz in 10kHz increments This stage is not only essential for the avoidance of aliasing when the analog audio is read by the microcontroller but also helps in the successful identification of the target insect song by effectively removing all frequencies above approximately 40kHz the audio signal is already much quieter which will help the software recognition algorithms to pick out the 40kHz spikes The gain stage which can be programmed to provide anything from 1 no amplification to 15 can be configured on the SD card This parameter is effectively directly adjusting the sensitivity of the microphone allowing it to hear quieter more distant insect calls Note however that whilst a higher sensitivity will allow the device to pick up quieter sounds it will be more susceptible to being overloaded or saturated by common but unwanted noises such as rustling leaves or nearby roads which greatly reduces the device s ability to detect SBCs University of York 12 Speckled Bush Cricket Data Logger Project Report 2 Field Trials and Results 2 1 Speckled Bush cricket i2. 13 2 0 0 0 0 9 5 2 9 24 45 40 29 0 0 5 12 4 3 8 24 47 39 65 26 16 18 34 01 12 13 13 2 0 0 0 11 10 5 2 9 24 44 40 46 0 0 7 13 3 3 8 24 47 39 65 3 2 Attaching amp Detaching Sensors The sensors are mated with a box by simply pressing the plug of a sensor firmly into a box socket ensuring that the white arrow of the plug aligns with the white arrow of the receiving socket An audible click indicates a secure locked in connection To disconnect the sensor gently pull the outer sheath of the connector marked with a white arrow away from the box which will disengage the lock and allow the plug to be removed from the socket To ensure the longevity and waterproofing of the plug and socket care should be taken to keep the rubber seals and contacts in both clear of debris and contaminants particular immediately following field use 3 3 Opening amp Closing the Lid University of York 23 Speckled Bush Cricket Data Logger Project Report To access the battery SD card fuse and other parts of the device the transparent lid should be unscrewed at each corner using a Phillips screwdriver Note that the screws needn t be fully removed from the lid as they are held in place by design for convenience The reverse procedure applies when attaching the lid use a reasonably firm force when doing up the screws to ensure a tight waterproof seal Always take a moment when re attaching the lid after field use to make sure debris suc
3. 5 Scatter Plot of BB y axis and NB Clicks x axis for University site 25 29 October 2013 1210 data points 100 hours Garden 1 2 11 2013 0 4 0 5 0 6 Normalised Clicks Figure 2 6 Scatter Plot of BB y axis and NB Clicks x axis for Garden Site 1 2 November 2013 277 data points 23 hours North Cave Wetlands 20 21 10 2013 Normalised Clicks Figure 2 7 Scatter Plot of BB y axis and NB Clicks x axis for North Cave Wetlands 24 25 October 2013 287 data points 23 9 hours University of York 16 Speckled Bush Cricket Data Logger Project Report North Cave Wetlands 25 28 10 2013 N 2 o co co 5 w 2 E o Oo zZ abs hy Tha 0 3 0 4 0 5 0 6 Normalised Clicks Figure 2 8 Scatter Plot of BB y axis and NB Clicks x axis for North Cave Wetlands 24 25 October 2013 557 data points 46 4 hours Count min 17 55 22 05 sd 03 00 04 00 Table 2 1 Summary of SBC counts for North Cave Wetlands on 24 25 October 2013 Logger set to 5 minute intervals University of York Speckled Bush Cricket Data Logger Project Report 24 25 10 2013 j T 0 7 tet ik ii fla 1 LA IMEERREARUTERESTERART NARS RASS TIN BETHE EET IET IE FEAE ELAR EAE EEEE SD PO DP PDS PT SS SS PL TEEN Bere ANRETT R IRE iR pad SHEMA a CULES EST OMIT Tee G Figure 2 2 9 Tee for North C Cave S Wetlands 2 24 25 TERET 2013 eT eer Tow dereaione based on algorithm 46 in 46 4 hours Lower graph sh
4. Device Operation section they are also summarized briefly here i SLEEP MODE In this mode the central processor is almost entirely shut down and all other peripherals such as the LCD screen and GPS module are set to low power modes to further reduce overall current draw SLEEP MODE is the default state of the device when the battery is plugged in ii STANDBY MODE This is the mode used when the device is started and being prepared for monitoring Entering this mode the device reads user configuration values from the SD card tests the sensors microphones GPS and other peripherals to ensure everything works Once these start up checks have been completed information from all peripherals is displayed on the LCD screen and messages are scrolled though using the CONTROL button University of York 7 Speckled Bush Cricket Data Logger Project Report iii MONITORING MODE This mode is the actual state in which the device listens to its surroundings collecting environmental data and periodically writing the collected information to the SD card The device will operate in this mode indefinitely until it is turned off by the user or until the battery falls beneath a certain user defined threshold at which point it will auto shutdown to help prevent battery damage IIT SD Card Capabilities There is an SD card slot on the device used to read from and save data to an SD card This is an essential part of the device s operatio
5. Note that once in MONITORING MODE the LED ring indicating device status green orange or red will be turned off to save power University of York 27 Speckled Bush Cricket Data Logger Project Report At this point the SD card is accessed again to find and or create a data directory and file on the SD card If any of the appropriate files and folders could not be created successfully on the SD card a warning message will display with an error ID and after a short pause the device will automatically shut down into SLEEP MODE If there were no problems the device will finish preparing peripherals for monitoring and enter MONITORING MODE indicated by a display of the NHM logo accompanied with the message MONITORING ENVIRONMENT During MONITORING MODE the LEDs play an important role in indicating the device s behaviour If a broad band click is detected the orange LED will flash briefly If a narrow band click is detected the green LED will flash briefly note that a green flash will always be accompanied by an orange one since all narrow band clicks will by design always register positively as broad band clicks too All four LEDs in the LED ring will flash together periodically approximately once every 7 seconds to indicate that the device is still operating successfully in MONITORING MODE In order for the user to easily keep track of current battery levels and monitor sensor performance clicking the CONTROL button during moni
6. a message describing a STRING CHAR ERROR Below is an explanation of all the configurable values in the current version of the device Note that for the sensor parameters sensor 1 and sensor 2 have the same format so only sensor 1 is explained i Update Interval Example update_int 2 This is the time interval between recorded readings on the SD card in minutes E g In this case an entry is made every two minutes Note that the microphones if enabled are continuously monitoring the environment for insect calls whereas the other environmental sensors temp light humidity will only take a reading at the end of each interval ii Low Battery Cutoff Level Example batt_cutout 10 8 This is the battery level in volts at which the battery is treated as 0 Note that at this percentage the device will automatically enter a low power state to avoid damage to the battery through over discharge Even in this state the current draw is still reasonable and the device should not be left connected to a flat battery for long over discharge may cause permanent damage to the battery University of York 20 Speckled Bush Cricket Data Logger Project Report iii Minimum Narrowband Detection figure Example c_val 10 This is the value of variable C in the Speckled Bush Cricket detection algorithm iv Detection Threshold Ratio Example t_val 0 9 This is the value of variable T in the Speckled Bush Crick
7. may cause irreversible corruption in these modules University of York 28 Speckled Bush Cricket Data Logger Project Report The device can be shutdown using the button hold at any time from STANDBY MODE and from MONITORING MODE Note that when shutting down from STANDBY mode it is necessary to keep holding the button when the RELEASE TO ENTER MONITORING MODE message appears After approximately five seconds the RELEASE TO POWER DOWN message will appear instead Note that whilst the device is powered i e the battery is connected and the power jumper is set to ON the device cannot be fully turned off in the conventional sense it can only put into Sleep mode Even in this mode it still draws about 30 milliamps of current from the battery which whilst lower power than normal running mode is still sufficient to drain a full battery in a couple of weeks As such the battery should always be left disconnected unless the device is or is shortly to be in use 3 9 Reset Procedure During normal operation a hard reset i e not using the CONTROL button shouldn t be required as all resetting can be done by powering down and powering up the device using the CONTROL button However in the unlikely event of a software crash where the device is otherwise unresponsive to user input a reset may be necessary A reset can be performed either by interrupting power to the device e g disconnecting the battery or by pressing t
8. mounted inside a custom designed 3D printed enclosure spray painted with a coat of highly visible UV protecting paint and then repeatedly lacquered this was necessary to ensure all sensors gained maximum exposure to the environment whilst simultaneously ensuring that they were thoroughly waterproofed against all weather conditions Each sensor unit operates three fully digital internal sensors operating on a single fully buffered 12C data bus and a fully analogue microphone circuit that sends an amplified audio signal back to the main device for processing The connecting cable has six conductive cores carrying audio data and power The sensors are connected to the main device via fully waterproofed IP67 rated connectors featuring gold plated connectors and a silicone rubber seal University of York 9 Speckled Bush Cricket Data Logger Project Report University of York 10 Speckled Bush Cricket Data Logger Project Report More detailed specifications of each sensor are provided in the following sections I Air Temperature amp Relative Humidity Despite being two very separate metrics both temperature and relative humidity are measured by a single chip within the sensor unit a Sensirion SHT21 The large apertures on each side of the sensor module allow good airflow through the device which in turn allow the SHT21 to make accurate measurements Nonetheless it should be kept in mind that there is a short delay between
9. EADY All desired peripherals appear to be working but have no finished starting The GPS may be trying to acquire a signal or one or more sensors may be still starting A solid orange LED will be lit exclusively on the board iii A PERIPHERAL HAS FAILED At least one peripheral has failed to function as expected This may happen for example if a sensor device has malfunctioned A solid red LED will be lit exclusively on the board University of York 25 Speckled Bush Cricket Data Logger Project Report ttt e e oo _ _ 7 e e _ _ _ _ oo el _ C m More information can be displayed about device parameters and about each sensor by tapping the CONTROL button to scroll through screens The order messages are displayed in is outlined below 1 Device Status Summary An instantaneous overview of the device status as described above Characteristically identifiable by the NHM logo on the left hand side 2 Device Configuration Summary A compact summary of the device s ID DEV the run instance number RUN and the user specified monitoring interval 1 3 RealTime Clock The current time and date note that this will only display correctly if the GPS is enabled and has found a signal at least once during runtime 4 Battery Level The current battery level both in volts and as a percentage The low threshold for 0 is specified in the user configurat
10. Lev Cl iccccoccsstdicnctisinactcatesancardccsssinndauvendtiecsnbeeenindsnd soataiineoossanbddmebudendctenitoatnatessecauakeds 10 III Broadband Microphone Amplifier and Filter cccccccscssseccccceeseecceeeeeeeecesseeeeeeceeseeeeeeeeeeas 10 PROVE Tila lS ANG RESUIES alee crcuetemencvtiess E E A E E A 12 2 1 Speckled Bush cricket in Yorkshire sissiveisceiscvccdesssnnsescasendssaseedisunnsvaddenasessdevaddedsesdeetieanesvandbsevedsarsees 12 DoD WAG Vila OS a E E E E E A AAS E 12 Device Operation User Manual isrener nna E 19 Beds 9D Canc Morna ON esea E R 19 D eeri e A 19 D e 6 a A E E E eee ne 21 32 Attaching amp Detaching SENSOrS secscentececoeteacs cece o SEO 22 3 3 Opening amp Closing the Lid sosseessseesssrrresrresssrrresrrerssrrressrerssrrresererssreressrerssrereserersseeressreresseeeene 22 Bile BEN CEINE E panseesagaedgancnanssamacetvene eauassecenieennseaimaeeceticets 23 35 Bailery Mtaa O Ne E 23 3 6 Turn On Procedure s sse ssssseseesssseresssssssressssrrresssreresssserressssreeosssereessserressseereeeseeeressseeresesserressseene 24 Sift PVC rO Para O aa a E vebaadataenen betcemeiaeeiar Meee 24 D EANDEM ODE seerne A E E T O 24 H MONTORINO MODE irarri a E T E R NA 26 Io TOOP COUE eee E E E E 27 39 Reet ROC CN e E E E E 28 310 Flashing New TGR INN AVC sorore 28 University of York Speckled Bush Cricket Data Logger Project Report 1 Data Logger System Summary This report has been divided
11. UNIVERSITY OF YORK Speckled Bush Cricket Data Logger Project Report Project Summary and Device User Manual Wil Bennett David Chesmore Ed Baker 12 6 2013 This report summarises work carried out on the Speckled Bush Cricket data logger project by Wil Bennett and Dave Chesmore at the University of York and Ed Baker at the Natural History Museum who together designed and constructed at the time of writing a total of ten data logging devices to monitor the presence of Leptophyes punctatissima and other environmental variables such as temperature and humidity This document summarises the capabilities and functionality of these devices and comprehensively documents correct operational procedure for deploying the devices in the field University of York 2 Speckled Bush Cricket Data Logger Project Report Contents ile Data Logger System SUMMA ie nT erpuiserdtesivad encermaielatanctiadeateseuedat 3 Li OV NIEN ee A E E E E E E E E TSA 3 L2 MON E E E E E E S 4 H POWO oee E A bese teacececsdaasiescssadaietccoaaaacstossanasee acasiauisindoqnssaancosesancseuctias 6 II User Interaction amp Operational Behaviour cccccccccssssccccceeeseececceeeecccceeueeeeeeceseeeeeeeessaeneeeeeteas 6 W SDA TE AE e E A eo eee 7 W GPL PID a a E E 7 Lo ea IVC ACS a E E E E E E E E 8 I Air Temperature amp Relative Humidity ssseessssnssessrensesrrrrressrrrrsessrrrressrrrreussrtrresssrereressereressreeree 10 II Ambient Light
12. at an awkward angle as this will prevent the lid from being reattached With the battery in place attach the black lead to the black terminal first using a firm pressure and wiggling it on if necessary the connection is deliberately a tight fit Once the black lead is attached do the same for the red lead and the red terminal first ensuring that the POWER jumper is set to OFF see jumpers for further detail Always take great care to attach wires in the correct order and in the correct polarity Attaching a red lead to a black terminal or vice versa will result in irreparable device failure University of York 24 Speckled Bush Cricket Data Logger Project Report 3 6 Turn On Procedure Once a battery has been installed power to the device is regulated by jumpers these consist of two metal pins protruding from the circuit board and they work like an ordinary switch A connection is made by shorting both sides together using a plastic metal bridge known as a jumper Most of the jumpers have been set to a default configuration for normal use and should not be changed under normal circumstances The exception to this is the POWER jumper which is red and located in the very top left of the main circuit board which is used as an ON OFF switch when a battery is attached Set the red POWER jumper to ON to turn on the device Note that it will automatically boot into SLEEP MODE when power is supplied as indicated by
13. can send over email it s usually pretty small lt 1MB To upload to the STMicroelectronics ARM microprocessor you d usually need a separate uploading device called an ST LINK that you connect to the chip with a cable and upload code to it via USB Fortunately the board we re using already comes with an ST LINK in built so all that s needed to upload new software is a USB cable specifically a Mini B cable It s the slightly larger of the two USB sockets on the board the one on the opposite end from the headphone jack University of York Speckled Bush Cricket Data Logger Project Report You ll need to install the ST LINK UTILITY software Q i foo a A atan ooe onto a windows machine found at m izei Sep http www st com web en catalog tools PF258168 V gt f a gt IPEFF The installer includes all the drivers you ll need too For i a texeieeeee convenience this installer has also been included on all U SB ort the SD cards that have been shipped with the devices i along with an accompanying user manual from STMicroelectronics It s a lightweight program and once you ve got it installed it should look like the image here Open the update we ve sent the HEX file via FILE gt OPEN FILE Once it s loaded OK plug the device into the PC you ll need to disconnect and remove the battery when you do this and the device can take power from the USB so can still be tested as normal On
14. ce you ve got it plugged in make sure the device stm3 TT a c y tee isn t in low power mode by pressing any button to wake it from low power mode and put it into STANDBY MODE You should now be able to connect to the device through the menu TARGET gt CONNECT in ST LINK UTILITY Once connected you can simply upload using TARGET gt PROGRAM amp VERIFY Reset the device once it s done uploading and you re done
15. d working correctly 11 Sensor 2 Temperature amp Humidity Readings 12 Sensor 2 Photodiode Readings 13 Sensor 2 Microphone Gain and Low Pass Filter Settings 14 Sensor 2 Microphone Detection Threshold Settings 15 Sensor 2 Microphone Real Time Broad and Narrow Band Clicks 16 GPS Signal Status This screen indicates if the GPS has acquired a signal lock and if so it displays the number of visible satellites it is reading SAT and the estimated accuracy of the given Latitude and Longitude coordinates ACC in meters 17 GPS Date amp Time Displays the last date and time reading from the GPS module Note that unlike the real time clock this clock does not tick each second It simply shows the timestamp of the latest data update which refreshes approximately once every five seconds When a signal is acquired it is this timestamp that is used the set the system s main real time clock 18 GPS Latitude amp Longitude Displays the system s last known Latitudinal and Longitudinal coordinates in the format DDD MM MMMM 19 LOOP BACK TO 1 II MONITORING MODE If all the desired sensors are attached and ready the device is ready for full deployment The user can enter MONITORING MODE by holding the CONTROL button for a short time until RELEASE TO START MONITORING is displayed on the screen This may be done at any point during STANDBY MODE from any screen Release the CONTROL button to send the device into MONITORING MODE
16. eceived signal strength varied considerably indicating that the insects were spread widely Approximate locations could be determined and this indicated that the majority of singing insects were well above 2m mainly in the tree canopy University of York 13 Speckled Bush Cricket Data Logger Project Report West Hull Old Moor a Yor North Cave Figure 2 1 Map of Yorkshire showing the Three known Colonies North Cave Wetlands Logger Location Figure 2 2 Map of North Cave Wetlands showing Location of Logger Photograph on right is of the main path Left Image credit http www northcavewetlands com University of York 14 Speckled Bush Cricket Data Logger Project Report Figure 2 3 Logger Deployed at North Cave Wetlands r r x 5 e AK U gt Hh n S AE iy gt a are T Gah a re 4 8 7 ae ae Se Fe J y y Sf gt gt TaN ar at EP d t cj Ro 50 tae NVR Via i a i ARS LOW EPU RN TL ee CN A NA K P A yee Y v i N ees N H gs KAE OETAN i ake E A 7 d a gt W c s af ra EEC r i 4 955 wt aoa amp E A gt gt yirt gt gt e Ta ES p s 7 Figure 2 4 Sensor Deployed at North Cave Wetlands at a Height of 2 5m above Ground University of York 15 Speckled Bush Cricket Data Logger Project Report 0 5 0 6 Normalised Clicks Figure 2
17. er than a lighter lithium ion alternative The system contains a high efficiency synchronous buck voltage regulator that converts the battery s 10 14 volts to a carefully maintained 5 volts used throughout most of the digital systems on the board During operation the regulator emits a faint very high pitched whine this is a normal phenomenon caused by the rapidly oscillating inductor and should not be mistaken for a device malfunction Each device contains a battery level monitor the reading can be displayed on the screen at any time and is also saved to the SD card alongside other collected data During field use the device monitors the battery voltage closely and automatically shuts down if the battery level falls below a user specified threshold to help prevent battery damage that can result from a so called deep discharge IT User Interaction amp Operational Behaviour During operation the device is controlled primarily through use of a single button on the side of the box referred to as the CONTROL button There is a backlit LCD screen in the center of the device that displays the status of the box at any given time and its various modes and menus are navigated intuitively using the CONTROL button Once a battery has been connected and the device is running it runs in one of three operational states as controlled by the user Whilst a full description of each operation and how it may be controlled is given in the
18. et detection algorithm v Broadband Detection Threshold Example s1_broadband_threshold 15 After the audio has been passed through a relatively broad band pass filter typically 30 50 KHz the maximum value in a given sample group is compared to this threshold level and is counted as a hit if it the measured value is greater than the threshold i e lower threshold value more sensitive Note that the units are arbitrary and some experimentation may be needed to find the optimal level for the environment vi Narrowband Detection Threshold Example si narrowband threshold 15 Similar to the above but after passing through a high precision 40KHz filter with an extremely narrow band typically 39 41 KHz This filter takes longer than the first filter but eliminates an enormous percentage of false positives picked up by the broadband filter vil Hardware Low Pass Filter Gain setting Example s1_hwlpf_gain 3 The incoming audio signal is amplified in hardware by a dedicated audio chip one for each of the two audio channels The chip can amplify the audio and also adds an all important low pass filter to prevent audio aliasing This parameter adjusts the audio gain much higher than 5 will likely to lead to a degree of audio clipping but once again some experimentation is required Values accepted are 1 15 viii Hardware Low Pass Filter Break Frequency Setting Example s1_hwlpf_brkpnt 40 Once again part o
19. f the hardware audio chip this determines the breakpoint of the low pass filter in KHz Once implemented higher frequencies than this are attenuated as such this should typically be set to the frequency of interest Values between 10 to 150KHz are accepted but must be rounded to the nearest 10 ix ENABLE DISABLE FLAGS These all important flags control which sensors are enabled for use Possible values are 1 enabled or O disabled Note At the time of writing the software for the internal temperature measurement which uses a temperature sensor physically integrated inside the main processor is known to contain bugs and cause problems with the rest of the device s normal operations It should for now not be enabled University of York 21 Speckled Bush Cricket Data Logger Project Report gps_en 1 GPS Module batt_read_en 1 Battery Level Sensor intern_temp_en 0 Internal Processor Temperature s1_sensor_en 1 Light Temperature amp Humidity Sensor 1 s1_mic_en 1 Microphone Sensor 1 s2_sensor_en 1 Light Temperature amp Humidity Sensor 2 s2_mic_en 1 Microphone Sensor 2 II Data Output Data is written to the card in the form of a comma separated value CSV text file with a txt extension The data is stored inside a single DATA directory on the card and a new data file is created each time the device enters MONITORING MODE If there is no DATA folder on the card one is created with the nami
20. h as soil and dirt isn t present on the rubber seal and that the lid is correctly aligned to the box In our field tests we found dirt occasionally attached to the seal after being ina field for a time and it increased the risk of water leaking in 3 4 Battery Charging Charge the batteries using the provided Fully Automatic Battery Charger The procedure is very simple attach black and red terminal clips to their respective terminals with the charger turned off attaching the black terminal first Turn on the charger with the switch on the right hand side Depending on the level of discharge of the battery charging can take anywhere from 3 15 hours Because lead acid batteries are extremely robust there is no need to worry about over charging the charger will automatically stop charging when the batteries are full and will then float charge the batteries i e it will hold them at their full charge level without over charging them Charge levels are indicated by the LEDs in the chargers and all LEDs will flicker on and off rapidly when the battery is fully charged Turn off the charger before detaching the charging leads 3 5 Battery Installation To install a battery into a device remove the lid and gently drop the battery into place ensuring that the battery terminals are on the same side of the box as the SD card and GPS module Double check to make sure the battery is sitting flat on the bottom of the box and hasn t gone in
21. he black reset button approximately located in the center of the main circuit board After a battery disconnect reconnect the device will automatically enter sleep mode By contrast after a reset button reset the device will immediately attempt to turn on and enter standby mode Note that hard reset should only ever be used as a last resort as there is a risk of irreversible corruption of the SD card or the GPS module 3 10 Flashing new f a svsz stun uy e File Edit View Target ST UNK Externalloader Help firmware Be ytl as Although the software for the mane Address OxQ000000 Sane Date Width 8 bits device is complete it still has Device Memory Fie IS4MB_V2 hex room for expansion and further eT TE Address io ji j2 3 if 15 6 7 improvement to reduce the risk 0108000000 88 0 0x08000010 31 g SSSR 8 8S amp of software bugs and to improve the overall efficiency of the device At the time of writing a sie esieisisis gt SSSB B82 28 8 oo oo Oo 0 0 00 ioa 00 o0 SSB 8888 28838 ES R88 SEB ton om oe mt further improvements are still being made to the software so gt 10702718 SAMB V2 hex we have a system in place to send you firmware updates to load onto the device as and when they re ready and we d strongly recommend that you always update with the latest software that s available The update comes in the form of a single HEX file that we
22. ht spectrum there is still a reasonable level of light attenuation overall and as such the light level readings should not be interpreted as an exact reading of ambient light level in Lux but rather as relative Lux levels between different readings for example at different times of day HI Broadband Microphone Amplifier and Filter The microphone is the single more important aspect of the sensor unit and has been optimized to detect relatively quiet high frequency cricket songs The microphone used is a Knowles SPU0410LR5H QB which is an ultrasonic microphone with a rated frequency response of up to 80kHz approximately 4 5 times the frequency response of the human ear A SBC typically sings at 40kHz which is well within the available range of the system In fact the rest of the system has also been designed to perform well with audio at up to 80kHz so that only a software update would be required to adapt the system to listen to any insect or mammal with a song anywhere from 100Hz to 80kHz Immediately following the microphone stage is a high gain low noise amplification stage that has a fixed gain of 100 allowing the audio to be transmitted along the 5 meter cable back to the main University of York 11 Speckled Bush Cricket Data Logger Project Report device for processing whilst minimizing the introduction of electrical noise along the cable Once the signal reaches the main device it passes through a final hardware stage
23. ility The main board is mounted securely to a two tiered laser cut plywood chassis that not only supports the board but also keeps the 4kg Lead Acid battery securely in place On the side of the device is a robust pushbutton used for all user control during field operations There are also two adjacent waterproof sockets for the sensors to attach securely to eera Waterproof o O interface Enclosure a Conio Button University of York Speckled Bush Cricket Data Logger Project Report g C ed _ i i Tal gt stmS260 dacovery a AUG t a a D 3 gidh 59 ET e ee Iyi s 5 st com cut j9 ui aaa aaaae a TERETE EN 7 Fieno ij g Sd D 2 jrco S _ aa x GNO tap oo S ieta ee amp aS nis 9 ue O THE UNIVERSITY FJOR University of York 6 Speckled Bush Cricket Data Logger Project Report I Power Power to the device is controlled through use of a simple electrical jumper as described in the Device Operation section Each device is powered from a 12 volt 12 ampere hour lead acid battery At the tradeoff of its relatively large size and weight the battery provides enough energy for the system to run at full power for a number of weeks on a single charge lead acid batteries are also affordable and well suited to extreme variations in temperature and full discharge charge cycle s so should operate bett
24. into two main sections The first section is an overview of the data logger device detailing what it is capable of what it contains and its exact specifications The second section functions as a user manual with a full comprehensive guide to use of the device 1 1 Overview The Speckled Bush Cricket Data Logger is a fully custom built device capable of being deployed ina field and operating independently for weeks at a time The device itself consists of a central unit inside a waterproof box with two smaller environmental sensor units attached to the box and broken out onto five meter cables The central box contains a battery processor SD card LCD screen GPS unit and a number of other peripherals supporting the device s operation Each sensor unit contains a high sensitivity broadband microphone light sensor temperature sensor and a Ce ntral Hub w fried iia a Beem Processing Core Power User Interaction Sensors Other Circuitry E ARM Cortex m4 gt d Software Configurable Lo Pass Audio Filter amp Amplifier GPS Time amp Internal Location Temp Sensor Sensor Humidity Sensor EEEE EANNAN eee Oy CATO a Bhue ie 2C Buffer Controller High Gai per Ultrasonic Microphone High Gain Audio Ultrasonic Amplifier L Microphone Amplifier humidity sensor An overview of the system is displayed below The device uses two microphones to constantly lis
25. ion file on the SD card Recall also that the device will shut down automatically if it reaches 0 in MONITORING MODE 5 Core Processor Temperature Temperature reading from the processors internal temperature sensor 6 Sensor 1 Temperature amp Humidity Readings Displays the current temperature reading in centigrade and relative humidity as a percentage Note that all sensor readings will update approximately every 3 5 seconds 7 Sensor 1 Photodiode Readings Displays the current light level reading in Lux Normal mode N and Infrared Mode IR are both displayed 8 Sensor 1 Microphone Gain and Low Pass Filter Settings The user assigned values for microphone gain and LPF breakpoint are displayed on this University of York 26 Speckled Bush Cricket Data Logger Project Report screen for the user to confirm that they have loaded correctly 9 Sensor 1 Microphone Detection Threshold Settings The user assigned values for microphone broad and narrow band noise level thresholds are displayed on this screen for the user to confirm that they have loaded correctly 10 Sensor 1 Microphone Real Time Broad and Narrow Band Clicks When this screen is viewed the system starts running the audio recognition algorithms for the microphone in real time The system increments a count of broad and narrow band clicks each time they are detected and displays both on the screen This tool is invaluable for testing that the microphone is setup an
26. n there is a configuration file stored on the SD card that may be edited by the user and is read by the device on start up to determine some aspects of its operational behavior These include but are not limited to microphone gain settings sensor enable disable flags and parameters to allow fine tuning of the insect recognition algorithms The device will not run without an SD card containing this parameter file As well as providing operational parameters the SD card is used to log all data to Data is saved in the form of a plain text file with a txt extension Further details are provided in the Device Operation section IV GPS Capabilties Each device is fitted with a Maestro A2035H GPS module which when activated can obtain millisecond accurate time and date information as well as a latitude longitude location typically accurate to within a few meters The device usually takes less than a minute to acquire a signal when used outdoors It performs with varying reliability indoors in cases where a signal is found it invariable takes much longer than when used outdoors University of York 8 Speckled Bush Cricket Data Logger Project Report 1 3 Sensor Modules There are two sensor units supplied with each device that are used to monitor the local environment The devices themselves each consist of a small densely populated circuit board fabricated to a high standard to ensure durability during outdoor use The circuit board is
27. n Yorkshire SBC has been recorded in Yorkshire for more than 100 years but only sporadically usually with single records There has been no evidence of the species breeding in the county until recent years when three colonies have been found these are indicated in Figure 2 1 Itis interesting to note that the two sites in East Yorkshire North Cave Wetlands and West Hull appear to have been colonised for a number of years given the large number of crickets recorded even though the first records were in 2011 and 2010 respectively 2 2 The Trial Sites A number of short and extended trials were carried out at York University gardens at North Cave Wetlands NCW a Yorkshire Wildlife Trust nature reserve in East Yorkshire where the target species is known to exist NCW is 40ha in size and is an old sand and gravel extraction site http www northcavewetlands com Figure 2 2 is a map of NCW indicating where the logger was located This was amongst trees of various deciduous species including Sorbus aucuparia Acer campestre A pseudoplatanus Betula pendula Salix spp and a sparse undergrowth Figures 2 3 and 2 4 are photographs of the logger and one sensor respectively deployed on 25 October 2013 Manual recording of the activity of the species at this location was undertaken using a bat detector Magenta Bat4 tuned to 40kHz Results for 20 October 2013 between 10 11am and 10 39am ranged from 23 49 calls per minute N 28 mean 32 9 SD 7 64 The r
28. ng convention D _DATA where is the Device ID A file is then created inside the data folder for writing data to with the naming convention D _RUN XXxX txt where is the Device ID and XXX is the Run Instance If the GPS is enabled and was able to establish a signal lock the newly created data file will have a correct date created timestamp that may be viewed in the file s properties in most operating systems This may be useful when organising data files at a later data Note that if the GPS is disabled or could not establish a signal lock the date created field will be empty Data files should be loaded into a data management program such as Microsoft Excel using a CSV importer With this importer Excel asks about the nature of the file the data is in the delimited format with tabs and commas both being used as the delimiters When importing into Excel using the CSV importer ensure that the treat consecutive delimiters as one checkbox is un ticked t The GPS doesn t need to have a signal at the point MONITORING MODE is started only at some point during STANDBY MODE so that the real time clock can be set at a note made of the location University of York 22 Speckled Bush Cricket Data Logger Project Report An example data import is shown below D5_RUN 023 txt Update interval 2 Minutes Start date 01 12 13 Start time 15 52 34 Latitude N 53 56 7429 Longitude W 001 03 2154 Sensor 1 LPF Gain 3 LPF Roll
29. off 40 kHz Photodiode Mode 1 Sensor 2 LPF Gain 3 LPF Rolloff 40 kHz Photodiode Mode 1 Enable flags GPS device 1 Battery Sensor 1 Internal Temperature O S1 Sensors 1 S1 Microphone 1 S2 Sensors 1 S2 Microphone 1 INT S1CLICK S1 S1BRDBND S1 S1IR S1 S1 S2 CLICK S2 S2BRDBND S2 S2 IR S2 S2 RUNTIME mins TIME DATE BATT V TEMP C DETECT CLICKS CLICKS LIGHT Lux LIGHT Lux TEMP C HUMID DETECT CLICKS CLICKS LIGHT Lux LIGHT Lux TEMP C HUMID O 15 52 34 01 12 13 13 1 0 0 0 0 13 3 2 9 24 48 40 36 0 0 0 14 3 3 8 24 53 39 62 2 15 54 34 01 12 13 13 2 0 0 0 0 13 3 2 9 24 48 40 33 0 0 1 14 3 3 8 24 53 39 59 4 15 56 34 01 12 13 13 2 0 0 5 127 13 3 2 9 24 47 40 29 0 4 203 14 3 3 8 24 44 39 78 6 15 58 34 01 12 13 13 2 0 0 12 244 13 3 2 9 24 46 40 29 0 12 158 14 3 3 8 24 43 39 72 8 16 00 34 01 12 13 13 2 0 0 7 154 13 3 2 9 24 45 40 29 0 2 185 14 3 3 8 24 43 39 72 10 16 02 34 01 12 13 13 2 0 0 1 11 13 3 2 9 24 46 40 29 0 1 21 14 3 3 8 24 43 39 68 12 16 04 34 01 12 13 13 2 0 0 0 2 12 4 2 9 24 46 40 33 0 0 0 14 3 3 8 24 45 39 72 14 16 06 34 01 12 13 13 2 0 0 0 0 13 3 2 9 24 46 40 29 0 0 1 14 3 3 8 24 46 39 68 16 16 08 34 01 12 13 13 2 0 0 0 3 13 3 2 9 24 46 40 29 0 0 0 14 3 3 8 24 47 39 65 18 16 10 34 01 12 13 13 2 0 0 0 0 13 3 2 9 24 46 40 29 0 0 0 14 3 3 8 24 47 39 62 20 16 12 34 01 12 13 13 2 0 0 0 0 12 4 2 9 24 46 40 29 0 0 2 14 3 3 8 24 46 39 62 22 16 14 34 01 12 13 13 2 0 0 0 1 11 4 2 9 24 46 40 33 0 0 0 13 3 2 9 24 47 39 59 24 16 16 34 01 12 13
30. ows NB clicks green BB clicks 50 red temperature light green relative humidity orange and light 100 pink Black bar indicates night 25 28 10 2013 detect T 0 7 24 min 22 6 min pocimin im ft i i k ET H l iF hy iis ten LS eA aN nla eee ji a Ad MA Le i omit ite R S W uM 4 Figure 2 10 Recording for North Cave e Wetlands 25 28 October 2013 Upper eraph shows 19 detections based on algorithm Lower graph shows NB clicks green BB clicks 50 red temperature light green relative humidity lilac and light 100 pink Black bars indicate night University of York 18 Speckled Bush Cricket Data Logger Project Report i aint Teer te ee h npepe i h i FE SRG eae ee Fe eee Ee eae eae ee ee cs Figure 2 11 Recording for York University 25 29 October 2013 Graph shows NB clicks green BB clicks 100 red temperature light green relative humidity lilac and light 100 pink University of York 19 Speckled Bush Cricket Data Logger Project Report 3 Device Operation User Manual This section of the report is designed to be a comprehensive guide to use of the data logger from battery charging to data retrieval 3 1 SD Card Information The SD card is central to the operation of the device Collected data is stored to the card and configurable device parameters are saved onto the card by the user for the
31. sudden environmental changes and a corresponding change in the measured value e g if stored ina heated car and suddenly exposed to a cold winters day it could take up to 10 minutes for the device to adjust to the new ambient temperature and humidity i Temperature The SHT21 is programmed to resolve the current temperature to the nearest 0 01 C It has a typical accuracy of 0 3 C ii Humidity Relative humidity is resolved to the nearest 0 04 It has a typical accuracy of 2 II Ambient Light Level The light level sensor used is an Intersil ISL29003 This device features two photodiodes respectively capable of measuring both full spectrum light levels and light levels of the infrared spectrum only The ISL29003 is capable of measuring an ambient light level of up to 64 000 Lux with a resolution of 1 Lux or a light level of up to 1000 Lux with a resolution of 001 Lux At the time of writing the device has been programmed to work in the maximum range mode capable of measuring up to 64 000 Lux to the nearest 1 Lux Every time a reading is taken both the full spectrum measurement and the infra red measurement are recorded to the SD card Note that the photodiode chip is placed directly beneath a light diffusing panel on the sensor enclosure Its purpose is both to diffuse incident light and to protect the electronics from rainwater Though the diffuser has been carefully selected for relatively flat attenuation across the lig
32. system to read and act on I User Input There are a number of operational parameters that may be specified by the user through the configuration file located in the SYSTEM directory of the SD card the file is called config txt The other file in this directory sys isamb is a system file for the device that keeps track of the device ID and run instance This file must not be deleted moved or modified under any circumstances During tests we found that even the most basic word editors on an Apple computer running OSX seem to do slightly odd things to the format of this txt file when modified saving it in more advanced text formats than the one it s natively saved in and thus making it unreadable to the device Hence we strongly recommend only editing the file in Notepad on the Windows OS If attempting to modify the file in a different environment be sure to take a copy of the file somewhere first so you ve got a backup Inside the file each variable has a name and an associated value typically a number or a binary flag 0 or 1 The value must always be within a pair of single quotations Always use the apostrophe character not grave accent character If in doubt just don t delete the quotations already in there The device will only be able to read numbers in this very specific format and will throw an error during load up displayed on the LCD screen if this formatting has not been adhered to typically with
33. ten to the local environment and processes all audio in real time Using a series of audio processing techniques and carefully designed algorithms it is able to identify the song of the song of any nearby Leptophyes punctatissima also known as the Speckled Bush Cricket SBC with a high level of accuracy When an SBC is detected the device University of York 4 Speckled Bush Cricket Data Logger Project Report increments an internal counter of the number of clicks that have been heard and this data is periodically saved to an SD card alongside temperature humidity ambient light level date time of day and the system s current battery level 1 2 Main Unit At the heart of the device is an STM32F4DISCOVERY board an affordable commercially available breakout board that contains an ARM Cortex M4 microcontroller The M4 uses a 32 bit architecture and is capable of running at up to 168MHz making it suitably powerful for the data heavy task of ongoing real time audio processing The STM32F4DISCOVERY board also includes an integrated ST LINK programmer allowing full software updates to be carried out easily by anyone with access to a Windows PC and a USB cable The STM32F4DISCOVERY board is them mounted to a large custom circuit board referred to as the main board that accommodates all the peripherals necessary to support the device s operation This includes power regulation user interactivity and GPS capab
34. the familiar NHM logo displayed in the center of the LCD screen Press the CONTROL button to wake the device from SLEEP MODE and begin normal use 3 7 Device Operation I STANDBY MODE When the device is started it will first attempt to read the configuration files on the SD card to establish parameters such as its Device ID Run and a list of user configuration values such as which sensors to use If the read is OK it will run through a series of start up checks to establish communication with the desired sensors e g GPS and then enter STANDBY MODE Observe any warning messages and comments that appear on the screen during start up if the SD card is not inserted the syntax of parameters within the configuration file is wrong or the system cannot find a configuration file in the correct directory it will report that there has been an SD related failure and display the associated error ID It will them automatically re enter SLEEP MODE At the completion of the start up checks a home screen message will be displayed denoted by the NHM logo on the left hand side of the display indicating the overall status of the device The status is also indicated on the LEDs as depicted below i PERIPHERALS ALL READY All desired peripherals have started OK If GPS is active it has a signal lock If sensors are active they re established as working and OK A solid green LED will be lit exclusively on the board ii PERIPHERALS NOT R
35. toring mode will pause monitoring and make the device display a series of consecutive status messages pausing on each for approximately 2 seconds in the following order Real Time Clock Battery Level Sensor 1 Temperature amp Humidity Readings Sensor 1 Photodiode Readings Sensor 2 Temperature amp Humidity Readings ow ee i E Sensor 2 Photodiode Readings Finally the device also features an in built low power shutdown feature When the battery level drops to the user specified threshold stored in the configuration file on the SD card the system will automatically finish monitoring and enter SLEEP MODE to prevent over discharging the battery which can cause damage Note that whilst this does help reduce current consumption the device will still draw a fair amount of current in SLEEP MODE and should not be allowed to stay in this mode for more than a few days when the battery is low 3 8 Turn Off Procedure At the end of use the device may be put into Sleep mode turned off by holding down the CONTROL button until the LCD shows RELEASE TO POWER DOWN from STANDBY MODE or RELEASE TO END MONITORING from MONITORING MODE Release the button to place the device into Sleep mode It is essential to always shut down the device in this way before removing power doing so ensures that the SD card and GPS modules are shut down correctly before their power is removed The abrupt removal of power during STANDBY or MONITORING MODE
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