PME Cyclops-7 User manual

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Precision Measurement Engineering, Inc. • www.Turner Designs.com
USB Cyclops-7 Logger User’s Manual
(Interchangeable and Fixed Sensors)
2018

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(INTENTIONALLY BLANK)

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Warranty
1-YEAR LIMITED WARRANTY
Precision Measurement Engineering, Inc. warrant that the Logger shall be free of
defects in workmanship and materials, under normal use, for a period of one year
from the date of shipment. This warranty is made only to the original purchaser. In the
event a Logger covered by this warranty fails to operate according to our published
specifications, then return it freight pre-paid to Precision Measurement Engineering or
an authorized Service Provider. Precision Measurement Engineering (PME) will
repair the unit at no charge to the customer and bear the cost of return shipment to
customer. Carefully pack all components, as the customer is responsible for any
freight damage.
This warranty does not apply to services or consumable / expendable items (such as
batteries, fuses and ropes) required for general maintenance. The Cyclops-7
sensor, manufactured by Turner Designs, is warranted only to the limit of the
warranties provided by their original manufacturer.
PME makes no warranty, either expressed or implied, that the sensors will be
operable after they are exposed to adverse environmental conditions, such as bio-
fouling, oil fouling, freezing temperatures or others.
This warranty is void if, in our opinion, the Logger has been damaged by accident,
mishandled, altered, or repaired by the customer, where such treatment has affected
its performance or reliability. In the event of such treatment by the customer, costs for
repairs plus two-way freight costs (no COD shipments will be accepted) will be borne
by the customer. In such cases, an estimate will be submitted for approval before
repair work is started. Items found to be defective should be returned to PME
carefully packed, as the customer will be responsible for freight damage.
Incidental or consequential damages or costs incurred as a result of the product
malfunction are not the responsibility of PME.
For all warranty or non-warranty returns please obtain, complete, and submit a RMA
to PME. This RMA form may be obtained at
http://www.pme.com/HTML%20Docs/RMAform.html
After submission of this form, then PME will respond with a RMA number. Please
place this number on all shipments and related communications.

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Safety Information
BURSTING HAZARD
Should water enter the Cyclops-7 Logger and come into contact with the enclosed
batteries, then the batteries may generate gas causing the internal pressure to
increase. This gas will likely exit via the same location where the water entered, but
not necessarily. The Cyclops-7 Logger is designed to release internal pressure as
the end cap is unscrewed, prior to the disengagement of the end cap threads. If
internal pressure is suspected, then treat the Cyclops-7 Logger with extreme caution.
Revision History
Date Revision Description
2015FEB24 Copied from RS232 C7 manual
2015APR16 Added Android device instructions
2015APR28 Updated wording
2015MAY08 Inserted pictures in Chapter 3
2015MAY25 Released for distribution to customer
2015JUN25 Added evaluation of calibration result
2015NOV09 Added Notes section
2016MAR03 Modified autorange description
2017AUG03 Clarified battery orientation, added warnings
2018MAY02 Added information on silicon spray

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CONTENTS
Chapter 1 Quick Start
1.1 Calibrate and Go
1.2 A Few Details
Chapter 2 Software
2.1 Overview and Software Installation
2.2 Cyc7Control
2.3 Cyc7Plot
2.4 Cyc7Concatenate
Chapter 3 Cyclops-7 Logger
3.1 Overview
3.2 Opening and Closing the Logger
3.3 Electrical Connections and Controls
3.4 Battery Replacement
3.5 Interchangeable Sensor Installation
3.6 Notes

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Chapter 1: Quick Start
1.1 Calibrate and Go
PME produces two types of loggers, a logger with the sensor permanently installed
and a logger with a connector that you will use to plug in your own sensor. Even if
the sensor is already installed, the logger/sensor are provided to you in an un-
calibrated state. The logger itself is set to measure temperature and concentration
once every 10 minutes and record 1 file of measurements daily. However, you must
calibrate the sensor before the system can be used. At one measurement every 10
minutes the Cyclops-7 Logger will operate for roughly a half year before the internal
battery is expended.
At the end of the deployment period you need only to open the logger and connect it
to a host device via USB. The Cyclops-7 Logger will appear as a ‘thumb drive’. Your
temperature and sensor measurements, together with a time stamp indicating the
time the measurement was made, are recorded in text files in the folder having the
serial number of your Cyclops-7 Logger. These files can be copied onto any
Windows or Mac host computer.
This Manual and other software is supplied in files on the Cyclops-7 Logger:
 Cyc7Control allows you to see the state of the logger as well as set the recording
interval.
 Cyc7Plot allows you to see plots of the recorded measurements.
 C7Concatenate gathers all the daily files into one CAT.txt file.
When not connected to USB, your Cyclops-7 Logger will record measurements if the
Recording Control Switch is in the Record position. If you wish to stop recording,
switch the Recording Control Switch to the Halt position.
You may switch the Recording Control Switch at any time.
Follow these steps to start the deployment, logging Cyclops-7 output and
Temperature once each 10 minutes:
1) Install your sensor onto the logger if required as described in Chapter 3.
2) Calibrate the sensor/logger as described in Chapter 2, Cyc7Control program.
3) Open the Cyclops-7 Logger (if not already open from calibration) as described in
Chapter 3.
4) Switch the Recording Control Switch to the Record position. The LED will flash
green 5 times. The Cyclops-7 Logger will now record a measurement of time,

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battery voltage, temperature, and sensor output every 10 minutes (or at some
other interval you may have set using Cyc7Control).
5) Inspect the o-ring seal for debris.
6) Close the Cyclops-7 Logger by screwing the white housing back onto the black
end cap.
7) Deploy the Cyclops-7 Logger.
Follow these steps to end the deployment
1) Recover the Cyclops-7 Logger
2) Clean and dry all accessible surfaces.
3) Open the Cyclops-7 as described in Chapter 3.
4) Connect to a Windows host computer via USB. The Cyclops-7 Logger will appear
as a ‘thumb drive’.
5) Copy the folder having the same serial number as the Cyclops-7 Logger (example
7377-191770) to the host computer.
6) (Suggested, but optional) Delete the measurement folder, but NOT Cyc7Control
or the other .jar programs or manual.
7) (Optionally) run the Cyc7Plot program to see a plot of measurements.
8) (Optionally) Run the C7Concatenate program to gather together all the daily files
of measurements into one CAT.txt file.
9) If no more recording is desired, switch the Recording Control Switch to Halt,
otherwise leave it set to Record to begin recording after USB disconnection.
10) Disconnect the Cyclops-7 Logger from the USB connection.
11) Inspect the o-ring seal for debris.
12) Close the Cyclops-7 Logger by screwing the white housing back onto the black
end cap.
Remove the batteries if storing the Cyclops-7 Logger for extended periods.
1.2 A Few Details
The previous section gives instructions for sampling at 10-minute intervals. However
there are a few additional details that will enhance use of the Cyclops-7 Logger.
Sensor guard – The sensor guard is the long tube having slots in the end that covers
the Turner C7 sensor. This guard not only protects the sensor but also establishes a
consistent field of view for the sensor. The guard must be used when the sensor is
calibrated and also when it is used for measurements in the field.
Sampling rate – The Cyclops-7 Logger records measurements at equal time
intervals. The default time interval is 10 minutes. However, it is also possible to
instruct the Cyclops-7 Logger to record at different intervals. This is accomplished by
connecting a Windows computer to the logger and using the Cyc7Control program
supplied for this purpose. Recording intervals must be 1 or more minutes and must
be less than or equal to 60 minutes. Intervals outside this range will be rejected by
Cyc7Control. (Contact PME for other recording intervals.)

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Please refer to Chapter 2 for instructions on operating the Cyc7Control program.
Time – All Cyclops-7 Logger times are UTC (formerly known as Greenwich mean
time (GMT)). The Cyclops-7 Logger internal clock will drift in the < 10 ppm range
(<about 30 secnds/month) so you should plan to connect it occasionally to a host
having an internet connection. The Cyc7Control program will automatically set time
based on an internet time server.
Please refer to Chapter 2 for instructions on operating the Cyc7Control program.
File Information – The Cyclops-7 Logger software creates 1 file daily on the
Cyclops-7 Logger’s internal SD card.. The number of measurements in each file will
depend upon the sample interval. Files are named by the time of the first
measurement within the file based on the logger’s internal clock and expressed in
YYYY-MM-DD HHMMSSZ.txt format. For example a file having the first
measurement on September 9, 2014 at 17:39:00 UTC will be named
2014-09-09 173900Z.txt
Files can be uploaded from the Cyclops-7 Logger by connecting the Logger to a host
computer and by using the host computer to copy/past the files from Logger to some
host computer storage.
Each measurement within files has a time stamp. The time stamp format is Unix
Epoch 1970, the number of seconds that have passed since the first moment of
1970. This may be inconvenient in some cases. If so, the C7Concatenate software
not only concatenates all the measurement files but also adds more readable
statements of the time stamp.
Please refer to Chapter 2 for instructions on operating the C7Concatenate program.
The Cyclops-7 Logger requires time and battery energy to work through the file
directory on SD card to allocate new file space. A few hundred files on SD is not a
problem, but as the number of files grows large into the thousands the Logger may
suffer decreased battery life or other performance problems. Please, at the earliest
convenient time, copy recorded files to a host computer and delete them from the
Logger. Also, do not use the Logger to store files unrelated to Logger operation.
Cleaning the Sensor – The sensor may be cleaned by unscrewing the black sensor
guard and gently wiping the optical face.
Battery Life – The Cyclops-7 Logger consumes battery power mostly from the
Cyclops-7 sensor, but also slightly from simply keeping track of time, writing files,
sleeping, and other activities. The Cyclops-7 Logger will record approximately
30,000 total samples and will operate for up to a year (depending on sample interval)
when powered by the battery pack (2 X alkaline ‘C’ cells) supplied by PME.

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Keep a general record of Cyclops-7 Logger number of samples. It is not possible to
accurately determine the charge state of the battery pack from measurements of its
terminal voltage. If you have a general idea of the number of samples already
obtained on a battery, then you can make a guess as to how many more samples
remain. Err on the side of caution.
The 2 X ‘C’ battery pack holds the batteries very tightly. The holder itself is glued to
the aluminum chassis. Take care when changing batteries that the glue joint is not
broken. Always use the paper tube supplied with the Cyclops-7 to contain the
batteries. Use only new batteries as replacements.
Coin Cell Battery Life – The Cyclops-7 Logger uses a coin cell for backup of the
clock when the power is switched off. This coin cell will supply roughly 2 years of
clock operation, but this is only required if the main power is off. Should the coin cell
discharge it must be replaced. Coin cells are not user-replaceable.
O-Ring and Seal – When the cover is screwed on, it passes along the o-ring located
in the end cap several revolutions. Keep this o-ring lightly lubricated with silicone
grease or oil compatible with buna-N o-ring material.
When the Cyclops-7 Logger is opened after deployment, a small number of water
drops are deposited on the inner surface of the o-ring. When the pressure housing is
screwed back on, these drops become trapped inside the Cyclops-7 Logger. Be sure
to carefully dry the o-ring and adjacent surfaces (especially underneath) prior to
closing the Cyclops-7. Re-lube the o-ring at this time. Remove any debris from the
drying process.
Closing the Logger – The logger is much more difficult to open than to close. Screw
the white logger housing onto the black cap until the housing touches the cap. No
further tightening is necessary.
LED Indications – The Cyclops-7 Logger performs various tests as it begins logging
operations. If any test fails the software flashes the LED light and re-conducts the
test. In general if a test fails once it will continue to fail and the LED light will
continue to flash. The following table gives the number of flashes and the reason
these flashes appear.

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LED Reason
1 Green
Flash
Normal. Presented immediately after new batteries are
installed. Indicates that the CPU has started its program.
1 Green
Flash
Occurs at the time of sampling for sample intervals of 1 minute
or less.
5 Green
Flashes
Normal. Indicates that miniDOT is beginning to record
measurements. This indication appears in response to
switching the Recording Control Switch to Record.
5 Red
Flashes
Normal. Indicates the miniDOT is ending recording of
measurements. This indication appears in response to
switching the Recording Control Switch to Halt.
Continuously
Green
Normal. Indicates the miniDOT is connected to a host device
via USB.
Continuously
Flashing Red
SD card write error. Try removing/reinstalling batteries.
Contact PME.
AutoRanging – The Cyclops-7 sensor has three output ranges: 1X, 10X and 100X.
The best of these ranges is automatically selected by the logger based on the voltage
measured of the sensor. The logger software remembers the best range and, at
each sample time, first measures sensor output voltage using this range. Software
then reviews this voltage to determine if the range was appropriate. In most cases
the range will be appropriate and the measurement is recorded. However sometimes
software determines that a different range would yield a better measurement. In this
case software selects a new “best range” and re-measures the sensor output voltage
using this range. This new best range becomes the range selected at the next
sample time. The best range is determined as follows:
Sensor Voltage (Gain = 1) Best Range
0.00 to 0.04 100X
0.04 to 0.4 10X
0.4 and higher 1X
Should the first voltage measurement be unacceptably close to the sensor maximum
output voltage (an over-range condition) the first voltage is re-measured using range
of 1X and the best range calculated. This range becomes the best range and
software proceeds as above.
Calculation of Engineering Units – Engineering units are calculated from voltage
measurements of the sensor and from information gained during calibration (see
Chapter 4). The result of calibration is the following information:
Name Definition
Vz1 Voltage output of sensor in zero solution on
range 1X
Vz10 Voltage output of sensor in zero solution on
range 10X

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Vz100 Voltage output of sensor in zero solution on
range 100X
S Sensitivity of sensor
Vz1, Vz10, and Vz100 are measured with the sensor in a solution of zero
concentration. S is determined from the voltage output of the sensor using the “best
range”, described above, with the sensor in a reference solution of known
concentration. The user must enter the concentration value of this solution, given the
name C. The sensor voltage is measured in this solution and given the name Vs.
The following table shows how S is determined.
Range S
1X S = C / (Vs – Vz1)
10X S = 10.0 * C / (Vs – Vz10)
100X S = 100 * C / (Vs – Vz100)
Note that since only one calibration concentration is actually measured, there is only
one S determined. However this S is used to compute engineering units from the
other ranges should these be implemented by the logger during the measurement of
samples.
Engineering units are computed as shown in the following table:
Range EU
1X EU = S * (Vs – Vz1)
10X EU = S * (Vs– Vz10) / 10.0
100X EU = S * (Vs– Vz100) / 100.0
Engineering units computed using the same range that was used to determine S will
be more accurate than engineering units computed using other ranges since the
sensor may not exactly implement ranges. For example the 100X range may
actually be implemented by circuitry as 100.1X but the calculations would use 100X.
Closing and Opening – Close and open Cyclops-7 Logger like you would a
flashlight: open by unscrewing the white cylinder from the black end cap. Close by
screwing the white cylinder on. When closing, do not tighten the white cylinder. Just
screw it on until it makes contact with the black end cap. See Chapter 3 for more
instructions.
Storage When Not in Use – Remove the batteries.
Java – miniDOT programs depend on Java and require Java 1.7 or higher. Update
Java at
https://java.com/en/download/index.jsp

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Upload Files to an Android device – It is possible to transfer your measurement
files from your logger to an android device. This operation has 3 prerequisites.
1. An Android device equipped with USB On-The-Go (OTG). OTG is a feature on
most modern Android devices that allows them to act as a USB host. OTG was
introduced with Android version 3.1 and should be a useable feature on most
devices. It is still possible that your device doesn't support OTG. Please test your
device with a logger prior to attempting to upload while in the field.
2. A USB OTG cable. This is essentially an adapter with a micro USB connector on
one end that connects to your Android device and a standard A type USB plug on
the other. The cable supplied with the logger connects to this end.
3. A "File Explorer" app downloaded on your Android device. These types of apps
assist with being able to view and move files from device to device. "ES File
Explorer" is a free app available on the Google app store and is recommended for
use with the logger.
If the 3 requirements are met, then connect the logger to your device. You should
see the logger green connection light come on and your device display a message
about "preparing USB storage". When "USB storage ready" is shown, use your "file
explorer" program to move your data from the logger onto you device.
Again, it is highly recommended that you try this operation at your work station prior
to depending upon this in the field.
Currently the associated logger programs, Control, Plot, and Concatenate, are not
supported by Android devices.

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Chapter 2: Software
2.1 Overview and Software Installation
The miniDOT arrives with these files:
 Cyc7Control.jar allows you to see the state of the logger as well as set the
recording interval.
 Cyc7Plot.jar allows you to see plots of the recorded measurements.
 C7Concatenate.jar gathers all the daily files into one CAT.txt file.
 Manual.pdf this manual.
These files are located on the root directory of the Cyclops-7 Logger.
PME suggests you leave these programs where they are on the Logger, but you may
copy them to any folder on your computer’s hard drive.
Cyc7Control, Cyc7Plot, and C7Concatenate are Java language programs that require
the host computer to have the Java Runtime Engine V1.7 (JRE) or later installed.
This engine is commonly required for internet applications and will likely already be
installed on the host computer. You can test this by running Cyc7Plot. If this
program displays its graphical user interface then the JRE is installed. If not then the
JRE can be downloaded via internet from
http://www.java.com/en/download/windows_xpi.jsp
At this time Cyclops-7 Logger software is supported on Windows operating systems,
but may also operate on Macintosh and perhaps Linux.
2.1 Cyc7Control
The Cyc7Control program provides these services:
 It enables time setting (based on internet timeserver clock).
 It enables sample interval setting.
 It enables calibration of the sensor.
Turner C7 sensors, are not factory calibrated. Calibration must be physically
performed by the customer. Calibration consists of an experiment where the sensor
is exposed to two solutions, the first having 0 concentration of the sensed material
(chl-a, rhodamine… whatever the C7 sensor senses) and a second solution having a
known concentration created by the customer. Cyc7Control software records sensor
output in each solution and creates a linear fit to these two points. After calibration
the Cyclops 7 Logger will measure sensor output and record it in engineering units
using this linear fit.

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Begin program operation by clicking on Cyc7Control.jar. Software presents the
screen shown below:
The Cyclops-7 Logger must be connected to USB at this time. When correctly
connected the Logger will display a constant green light.

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Click the Connect button. The software will contact the logger. If the connection is
successful the button will turn green and display “Connected”. The Serial Number
and other parameters will be filled in from information take from the Logger.
If the host computer is connected to the internet, the current difference between an
internet time server’s time and the Logger internal clock will be displayed. And, if
more than a week has passed since time was last set, the Logger clock will be set
and check mark icon will appear. If the host computer is not connected to the internet
no time services will occur.
The current Logger sample interval will be displayed next to the Set Sample Interval
button. If this interval is acceptable the interval need not be set.
To set the interval, enter a interval not less than 1 minute and not greater than 60
minutes. Click the Set Sample Interval button. Shorter and faster intervals are
available. Contact PME.
Turner C7 sensors are optical devices that operate by sending colored light into the
water and observing how much light returns. The field of view available to these
sensors is quite important in establishing their response. PME’s Cyclops 7 Logger is
supplied with a sensor cover that not only protects the sensor from damage but also
establishes the field of view. This cover has slots near where it covers the sensor so
that exterior water can enter and be sensed.
The sensor cover must be in position when the sensor is calibrated and must be in
the same position when the sensor is used.
A small amount of light can exit through the sensor cover slots, be reflected by the
container holding the calibration solution, and return. Calibrate the sensor in black
containers.
Exterior light such as room lighting or sunlight can enter through the slots and cause
a very small measurement effect. Attempt to calibrate in the same lighting as the
system will experience in field use.
Be sure that there are no bubbles trapped in the cover or stuck on the sensor.
Calibration proceeds by dipping the system in one solution and then the next. Take
care not to transport one solution to the next. Mix two 0 solutions and two solutions
of the sensed material. Label one each as the “calibration” and one each as the
“wash” When moving the sensor back and forth first dip the sensor in the wash then
into the calibration. The most noticeable effect is when the 0 solution is contaminated
prior to calibration. If the 0 solution is contaminated and is actually 1, and if this is not
noticed and the value 0 is entered into Cyc7Control, then later in a truly 0 solution the
Cyclops 7 Logger will be indicated as a concentration of –1. A negative
concentration can not exist and so the sensor is suspected of poor measurement
when the problem is that it was poorly calibrated.

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Cyc7Control requires that the host computer be connected to the Cyclops 7 Logger at
the time the calibration is performed. The logger must be open at this time. Take
care that no calibrating solutions splash onto logger circuits.
When calibration is completed, use the sensor to log measurements in each
calibration solution. Do this right away using the same solutions that were used for
calibration. The values 0 and the known concentration should be recorded by the
logger. This gives a check on the results of calibration.
Cyclops-7 Loggers support various Turner Cyclops-7 sensors. The sensor type is
shown on a small tag inside the logger.
Sensors are calibrated in response to the Calibrate button, after both the Unit of
Measure and the Calibration Value are entered.
Enter the unit of measure that is appropriate for the Cyclops 7 sensor mounted on the
logger.
Enter the calibration value for the solution.
Click on the Calibrate button. The adjacent scroll bar shows how far the program has
progress through the calibration procedure.

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A dialog window appears instructing you to place the sensor in the zero solution.
This will most likely simply be clear water contained in a bucket. Whatever the
solution, the sensor after calibration will report 0 when returned to this solution. Click
OK when the sensor is suitably positioned. If this solution is NOT 0 and the sensor is
later placed into a solution that IS 0 the sensor will report a negative concentration!
Negative concentration values can also result if the reflected light in a later solution is
less.

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At this time the software reads information from the sensor, selecting all three ranges
of the sensor sensitivity.
When this is completed a Zeroing of sensor completed dialog appears. Click OK.

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A “Please place sensor in calibration standard of <Calibration Value> (<Unit of
Measure>)” dialog appears. In the screen shot above the value of 400 (ppb) is
displayed. This information is taken from the Unit of Measure and Calibration Value
text boxes and will be whatever is entered in the boxes.
Place the sensor in the calibration solution. Whatever the solution, the sensor after
calibration will report the calibration value (400 ppb in the above example) when

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returned to this solution. The same considerations about solution accuracy and
reflected light apply in a similar way to those a zeroing.
Click OK. At this time the software reads information from the sensor, selecting the
best sensitivity range.
When this is completed a “Calibration completed” dialog window appears along with
the actual calibration results.