CPA United States
/ V Environmental Protection Agency
EPA 600/R-12/010 | June 2012 | www.epa.gov/ord
$CANARY
d
CANARY Quick Start Guide
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Acknowledgements
The National Homeland Security Research Center would like to acknowledge the following
organizations and individuals for their support in the development of the CANARY Quick Start
Guide:
EPA Office of Research and Development - National Homeland Security Research Center
Jennifer Hagar
Terra Haxton
Regan Murray
EPA Office of Water - Water Security Division
Steve Allgeier
Katie Umberg
Sandia National Laboratories
David Hart
Sean Hollister
Katherine Klise
Sean McKenna
Questions concerning this document or its application should be addressed to:
Regan Murray
USEPA/NHSRC (NG 16)
26 W Martin Luther King Drive
Cincinnati OH 45268
(513) 569-7031
Murray.Regan@epa.gov
CANARY Quick Start Guide
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Disclaimer
The U.S. Environmental Protection Agency (EPA) through its Office of Research and
Development funded and collaborated in the research described here under Inter-Agency
Agreement # DW8992291401with the Department of Energy's Sandia National Laboratories.
This document has been subjected to the Agency's review and has been approved for
publication. EPA does not endorse the purchase or sale of any commercial products or services.
This report was prepared as an account of work sponsored by an agency of the United States
Government. Accordingly, the United States Government retains a nonexclusive, royalty free
license to publish or reproduce the published form of this contribution, or allow others to do so
for United States Government purposes.
Sandia Corporation, the United States Government, any agency thereof, and their employees do
not make any warranty, express or implied, or assume any legal liability or responsibility for the
accuracy, completeness, or usefulness of any information, apparatus, product, or process
disclosed, or represents that its use would not infringe privately-owned rights. Reference herein
to any specific commercial product, process, or service by trade name, trademark, manufacturer,
or otherwise does not necessarily constitute or imply its endorsement, recommendation, or
favoring by Sandia Corporation, the United States Government, or any agency thereof.
The views and opinions expressed herein do not necessarily state or reflect those of Sandia
Corporation, the United States Government or any agency thereof. Sandia is a multiprogram
laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States
Department of Energy's National Nuclear Security Administration under Contract DE-AC04-94-
AL85000.
CANARY Quick Start Guide
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Table of Contents
Acknowledgements 2
Disclaimer 3
Figures 5
1. Introduction 7
1.1 Purpose 7
2. CANARY Installation 8
2.1 Installing the CANARY Software 8
2.2 Updating the CANARY Software 25
2.3 Files and Associations 26
2.4 Running CANARY 29
2.5 Analysis of CANARY Output 32
3. Additional Resources 46
3.1 CANARY License Text 46
3.2 CANARY Directory Structure 55
3.3 MY CANARY Directory Structure 58
4. References 60
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Figures
Figure 1: Installation Startup Dialog Box 8
Figure 2: License Agreement Dialog Box 9
Figure 3: File Location Dialog Box 10
Figure 4: Select Components Dialog Box 11
Figure 5: Select Start Menu Folder Dialog Box 12
Figure 6: Select Additional Tasks Dialog Box 13
Figure 7: Installation Verification Dialog Box 14
Figure 8: Installation Progress Dialog Box 15
Figure 9: MATLAB Language Selection Screen 16
Figure 10: MATLAB Install Screen 16
Figure 11: MATLAB Compiler Runtime InstallShield Wizard 17
Figure 12: Customer Information Window 18
Figure 13: MATLAB Compiler Runtime Destination Folder Window 19
Figure 14: Begin Installation Window 20
Figure 15: MATLAB Installation Status Window 21
Figure 16: MATLAB InstallShield Wizard Complete 22
Figure 17: CANARY.exe System Error 23
Figure 18: MATLAB Compiler Modify, Repair, and Remove 23
Figure 19: CANARY Run Test DOS Window 24
Figure 20: CANARY Setup Complete 25
Figure 21: CANARY Directory 26
Figure 22: My CANARY Directory 27
Figure 23: My CANARY/examples Directory 27
Figure 24: Location of YML Configuration File 29
Figure 25: Location of CSV Data Source File 30
Figure 26: Selection of Configuration File 31
Figure 27: Initial CANARY Run File Creation 32
Figure 28: Directory Window Where EDSD File is Located 33
Figure 29: Selecting the Graph Data Option 34
Figure 30: Graph Result Type Window 34
Figure 31: Station Selection Window 35
Figure 32: Graph Scale Window 36
Figure 33: Output files from Graph Data 37
Figure 34: CANARY Output Graph 38
Figure 35: Selecting the Convert to CSV Option 39
Figure 36: Converting to CSV File Output 40
Figure 37: Example EDSD Naming Convention 41
Figure 38: Selecting Combine EDSD Files Option 42
Figure 39: First EDSD File to Combine 43
Figure 40: Last EDSD File to Combine 44
Figure 41: Combined EDSD File Created 45
Figure 42: CANARY\bin Folder 55
Figure 43: CANARY\doc Folder 56
Figure 44: CANARY\etc Folder 56
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Figure 45: CANARYMib Folder 57
Figure 46: My CANARY\examples\datasource_opts Folder 58
Figure 47: My CANARY\examples\sample_data Folder 59
CANARY Quick Start Guide Page 6
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1. Introduction
This document presents a step-by-step guide to downloading, installing, and running CANARY
on a PC with a Microsoft® Windows™ operating system. The steps described in this document
are the prerequisites for deploying CANARY as a water quality event detection tool.
Detailed information on CANARY can be found in the CANARY User's Manual (Hart and
McKenna 2011). Additional background on the motivation and theory behind CANARY can be
found in the EPA report, Water Quality Event Detection Systems for Drinking Water
Contamination Warning Systems: Development, Testing, and Application of CANARY(Murray
etal. 2010).
1.1 Purpose
This document provides step-by-step instructions on where to download the CANARY software,
how to install CANARY on a computer, how to obtain and install the latest update to the
software, how to run the software, and how to analyze output files. This document also
describes the folders and files that are installed on a PC when CANARY is installed.
More detailed information on CANARY, such as algorithm definitions and configuration file
format, can be found in the CANARY User's Manual (Hart and McKenna 2011).
Please note that the screen shots contained in this Quick Start Guide may appear slightly
different depending on the operating system of the computer on which CANARY is installed.
CANARY Quick Start Guide
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2. CANARY Installation
An automated CANARY installer is available that contains a set of executable files. Email Terra
Haxton at Haxton.Terra@epa.gov to receive a link and a password to an FTP site containing the
files. From this FTP site, download and save the files "setup.exe" and "update.exe" on the
computer that will be running CANARY.
When installing CANARY for the first time, both files are executed as described in Section 2.1.
If an older version of CANARY is already installed on the computer, only the "update.exe" file
needs to be executed to update the software to the latest available version. Updates are available
on the website: http://software.sandia.gov/trac/canary. In this case, skip ahead to Section 2.2.
2.1 Installing the CANARY Software
1. Double-click the "setup.exe" file to start the installation. Click "Next" on the CANARY
Setup Wizard dialog box (Figure 1).
% Setup - CANARY
Welcome to the CANARY Setup
Wizard
This will install CANARY 4.3.1 on your computer.
It is recommended that you close all other applications before
continuing.
~ick Next to continue, or Cancel to exit Setup.
Next >
Cancel
Figure 1: Installation Startup Dialog Box
CANARY Quick Start Guide Page
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2. After reading the license agreement, select "I accept the agreement" and click "Next" to
continue the installation (Figure 2). The license agreement must be accepted in order to
install and run CANARY. The full license agreement is included in Section 3.1 of this
document.
License Agreement
Please read the following important information before continuing.
Please read the following License Agreement. You must accept the terms of this
agreement before continuing with the installation.
This software is Copyright ® 2007-2D11 Sandia Corporation.
Under the terms of Contract DE-AC04-94ALS5DDC1 with Sandia
Corporation, the U.S. Government retains certain rights
in this software.
Redistribution and use in source form, with or without
modification, and use in binary form, are permitted
provided that the following conditions are met:
1. Redistributions in source code must retain the above
copyright notice, this list of conditions, and the
o I accept the agreement
I do not accept the agreement
< Back
Next >
Cancel
Figure 2: License Agreement Dialog Box
CANARY Quick Start Guide
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3. Click "Browse" to choose the folder location where CANARY should be installed (Figure 3)
or use the default location and click "Next." Typically, software is installed in a new folder
under the Program Files folder. This new folder, in this case called CANARY, will be
created during the installation process.
Setup - CANARY
Select Destination Location
Where should CANARY be installed?
Setup will install CANARY into the following folder.
To continue, click Next. If you would like to select a different folder, click Browse.
C:\Program Files tx8G)\CANARY
Browse.
Pi least 278.3 MB of free disk space is required.
=: Back
Next >
Cance
Figure 3: File Location Dialog Box
CANARY Quick Start Guide
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4. Select "Example configuration and data files" (Figure 4), and click "Next." These files
contain example input data and CANARY configuration files which will be installed in a
folder called "My CANARY." With these files, users can practice running CANARY and
modifying configuration files.
Select Components
Which components should be installed?
Select the components you want to install; clear the components you do not want to
install. Click Next when you are ready to continue.
Full installation
~
0 Example configuration and data files
39.2 MB
Current selection requires at least 317.4 MB of disk space.
< Back Next >
Cancel
Figure 4: Select Components Dialog Box
CANARY Quick Start Guide
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5. Click "Browse" to choose the location in the Start Menu for a shortcut to CANARY (Figure
5) or use the default location and click "Next." This shortcut allows the user to access
CANARY from All Programs under the Start Menu.
Select Start Menu Folder
Where should Setup place the program's shortcuts?
Setup will create the program's shortcuts in the following Start Menu folder.
To continue, click Next. If you would like to select a different folder, click Browse.
mm
Browse...
< Back
Next
Cancel
Figure 5: Select Start Menu Folder Dialog Box
CANARY Quick Start Guide
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6. Select "Run Tests" to have CANARY nan a short example calculation as part of the
installation process (Figure 6) and click "Next." This will ensure CANARY has been
installed correctly.
Select Additional Tasks
Which additional tasks should be performed?
Select the additional tasks you would like Setup to perform while installing CANARY,
then click Next.
F7 Run Tests
< Back
Next >
Cancel
Figure 6: Select Additional Tasks Dialog Box
CANARY Quick Start Guide
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7.
Click "Install" if the information listed on the "Ready To Install" dialog box is accurate
(Figure 7). If this is the first time CANARY has been installed on the computer, the progress
bar will be shown (Figure 8).
Ready to Install
Setup is now ready to begin installing CANARY on your computer.
Click Install to continue with the installation, or click Back if you want to review or
change any settings.
Destination location:
C:\Program Files lx86)\CANARY
Setup type:
Full installation
Selected components:
Example configuration and data files
Start Menu folder:
CANARY
Additional tasks:
4
< Back
Install
Cancel
Figure 7: Installation Verification Dialog Box
CANARY Quick Start Guide
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Installing
Please wait while Setup installs CANARY on your computer.
Extracting files...
C:\Program Files fx86)SCANARY\MCR lnstaller.exe
Cancel
Figure 8: Installation Progress Dialog Box
CANARY Quick Start Guide
Page
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The setup application will automatically begin installing the MATLAB Compiler Runtime. This
library contains a number of functions that CANARY accesses when running.
8. Choose setup language or use the default option and click "OK" (Figure 9). Next, a progress
bar will be shown (Figure 10).
Choose Setup Language
0
Select the language for this installation from the choices below.
English (United States)
OK
Cancel
Figure 9: MATLAB Language Selection Screen
InstallShield Wizard
Preparing to Install...
MATLAB(R) Compiler Runtime 7.9 Setup is preparing the
InstallShield Wizard, which will guide you through the
program setup process. Please wait.
Configuring Windows Installer
Cancel
Figure 10: MATLAB Install Screen
CANARY Quick Start Guide
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9. Click "Next" (Figure 11) to begin installing the MATLAB Compiler Runtime.
J^jJ MATLAB{R) Compiler Runtime 7.9 - InstallShield Wizard
MATLAB
Compiler Runtime
Welcome to the InstallShield Wizard for
MATLAB(R) Compiler Runtime 7.9
The InstallShield (R) Wizard will install MATLAB(R) Compiler
Runtime 7,9 on your computer. To continue, dick Next,
MATLAB and Simulink are registered trademarks of The
MathWorks, Inc. Please see www.mathworks.com/trademarks
for a list of other trademarks owned by The MathWorks, Inc.
Other product or brand names are trademarks or registered
tradmarks of their respective owners,
WARNING: This program is protected by copyright law and
international treaties, Copyright 1934-2003, The MathWorks,
Inc.
J The MathWorks
< Back
Next >
Cancel
Figure 11: MATLAB Compiler Runtime InstallShield Wizard
CANARY Quick Start Guide
Page
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10. Type in the user's information (Figure 12) or use the default name and organization and click
"Next." This window is part of the MATLAB installer.
MATLAB(R) Compiler Runtime 7.9 - InstallShield Wizard
Customer Information
Please enter your information,
User Name:
Organization:
InstallShield
< Back
Next >
Cancel
Figure 12: Customer Information Window
CANARY Quick Start Guide
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11. Click "Change" to select another location other than the default to install the MATLAB
Compiler Runtime (Figure 13) and click "Next." Typically, the default location is selected.
MATLAB{R) Compiler Runtime 7,9 - InstallShieSd Wizard
Destination Folder
Click Next to install to this folder, or dick Change to install to a different folder.
/ Install MATLAB(R) Compiler Runtime 7.9 to:
J Cifrograrn Files [xSSJV^ATLAB'i/viATLAB Compiler Runtime\
Change.
InstallShield -
< Back
Next >
Cancel
Figure 13: MATLAB Compiler Runtime Destination Folder Window
CANARY Quick Start Guide
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12. Click "Install" (Figure 14) to begin installation of the MATLAB Compiler Runtime. As the
installation progresses, the status will be shown (Figure 15).
MATLAB(R) Compiler Runtime 7.9 - InstallShieid Wizard
Ready to Install the Program
The wizard is ready to begin installation,
Click Install to begin the installation.
If you want to review or change any of your installation settings, dick Back, Click Cancel to
exit the wizard,
InstallShield
< Back
Install
Cancel
Figure 14: Begin Installation Window
CANARY Quick Start Guide
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j^J MATLAB{R} Compiler Runtime 7.9 - InstallShieid Wizard
Installing MATLAB(R) Compiler Runtime 7.9
The program features you selected are being installed,
~ | Please wait while the InstallShieid Wizard installs MATLAB[R) Compiler
Runtime 7,9. This may take several minutes,
Status:
Validating install
InstallShieid
: Back
Next >
Cancel
Figure 15: MATLAB Installation Status Window
CANARY Quick Start Guide
Page
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13. Click "Finish" (Figure 16) and the MATLAB Compiler Runtime is now installed.
MATLAB{R) Compiler (Runtime 7,9 - InstallShield Wizard ¦
MATLAB
InstallShield Wizard Completed
Compiler Runtime
The InstallShield Wizard has successfully installed MATLABfR)
Compiler Runtime 7,9. Click Finish to exit the wizard.
J The MathWorks
< Back Finish Cancel
Figure 16: MATLAB Install Shield Wizard Complete
CANARY Quick Start Guide
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14. If an error message appears (Figure 17), click "OK" and then click "Finish." To fix this
problem, the installation needs to be repeated starting with step L During the process,
another error might occur stating that the UM is read only - click "Ignore." A dialog box
will show with the options to modify, repair, or remove the MATLAB Compiler Runtime
(Figure 18), choose "Repair" and click "Next."
The program can't start because mclmcrrt79.dll is missing from your
computer. Try reinstalling the program to fix this problem.
OK
Figure 17: CANARY.exe System Error
MATLAB{R) Compiler Runtime 7,9 - InstallShield Wizard
A
Program Maintenance
Modify, repair, or remove the program.
Modify
Change which program features are installed. This option displays the
Custom Selection dialog in which you can change the way features are
installed,
Q Repair
Repair installation errors in the program. This option fixes missing or
corrupt files, shortcuts, and registry entries.
Remove
ffl
Remove MATLAB[R) Compiler Runtime 7.9 from your computer.
InstallShield
< Back
Next >
Cancel
Figure 18: MATLAB Compiler Modify, Repair, and Remove
CANARY Quick Start Guide
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15. If there were no errors, and if the "Run Tests" option was selected, a DOS window will show
and a test will be completed for a simple example (Figure 19). If the installation was
successful, this window will disappear once the run is complete.
C:\Program Files (x86)\CANARY\bin\canary.exe
1 B-|—S3-
CANARV 4.3.1 [MATLAB Compiler uersion: 4.9 libraries by end user
is NOT allowed per the deployment addendum of MCR license (see deploy.txt>
and the CANARV-binary license
[CANARV_Log]
Uersion: CANARV 4.3.1 [MATLAB Compiler versio
In: 4.9 ] on Win32
[Startup]
Timestamp: 20120131T165932
IntializeLocation: StationD
[BatchProcessing]
Timestamp: 20120131T165935
BatchStartDateTime: 2008-01-15 00:00:00
BatchStopDateTime: 2008-01-30 13:48:00
UpdateFromSource: ..\sample_data\test_station_d.csu
UpdateDuration: 20120131T165935 —> 20120131T165937
UpdateFromSource: output_CSU_File_Input.
UpdateDuration: 20120131T165937 —> 20120131T165937
Message:
timestamp:2012013IT165951
from: EDS
subject: Time to process day: 19.4 sec; est. remain: 4.7 min
content: 2008-01-15 23:58:00
McssciQ'e ¦
timestamp:20120131T170006
from: EDS
subject: Time to process day:
content: 2008-01-16 23:58:00
Message:
timestamp:20120131T170022
from: EDS
subject: Time to process day:
content: 2008-01-17 23:58:00
Message:
timestamp:2012013IT170037
from: EDS
subject: Time to process day:
content: 2008-01-18 23:58:00
Message:
timestamp:2012013IT170052
from: EDS
subject: Time to process day:
content: 2008-01-19 23:58:00
15.1 sec; est. remain: 3.9 min
15.3 sec; est. remain: 3.5 min
15.2 sec; est. remain: 3.1 min
15.1 sec; est. remain: 2.8 min
Message:
timestamp:2012013IT170107
from: EDS
subject: Time to process day: 15.0 sec; est. remain: 2.5 min
content: 2008-01-20 23:58:00
Figure 19: CANARY Run Test DOS Window
CANARY Quick Start Guide Page 24
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16. Click "Finish" (Figure 20). The installation is complete!
CANARY
Completing the CANARY Setup
Wizard
Setup has finished installing CANARY on your computer. The
application may be launched by selecting the installed icons.
Click Finish to exit Setup.
Finish
Figure 20: CANARY Setup Complete
2.2 Updating the CANARY Software
Double-click the "update.exe" file to start the installation. Follow steps 1-7 above. During the
process, an error might occur that says the UM is read only - click "Ignore." Then follow steps
15-16 above. The update is complete!
CANARY Quick Start Guide
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2.3 Files and Associations
A list of the main directories and files associated with the CANARY installation are described
below. The options under the CANARY shortcut are also described.
The "CANARY" folder under "Program Files" has four subfolders and three files (Figure 21).
The folders are listed below and should not be modified. Typically, a user might never access
these subfolders directly. Screen shots of each folder's contents are provided in Section 3.2.
• bin - contains the executables for running CANARY
• doc - contains documentation, including the CANARY User's Manual
• etc - contains icons and configuration files associated with databases
• lib - contains information the code needs to ran
0 L&U
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12/20/20119:35 AM
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12/20/20119:36 AM
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3 Libraries
[I license.txt
3/31/201110:35 AM
Text Document
23 KB
1 _"J Documents
[ , unins000.dat
12/20/20119:36 AM
DAT File
17 KB
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unins000.exe
12/20/20119:32 AM
Application
687 KB
B Pictures
3 Videos
(fli Computer
7 items
Figure 21: CANARY Directory
A "MY CANARY" folder is installed under "My Documents," which contains one subfolder and
four files (Figure 22). The four files are:
CANARY-UM.pdf- the CANARY User's Manual
DummyAlgorithm.java - an example custom algorithm written in java
EDDIES-Setup.txt - a help file for using the EDDIES SCADA interface
readme.txt - a help file for the MATLAB Runtime Compiler
CANARY Quick Start Guide Page 26
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~ Libraries ~ Documents ~ My CANARY ~
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Organize ~ Share with ~ Burn New folder
1
=' a #
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*
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by: Folder *
WL Desktop
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£ Downloads
A-
Name
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[M Recent Places
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10/19/2011 3:31 PM
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3 Libraries
® CANARY-UM.pdf
3/31/201110:35 AM
Adobe Acrobat D...
2,066 KB
[3 Documents
J
I 1 DummyAlgorithm.java
3/31/201110:35 AM
JAVA File
2KB
My Document!
[ 1 EDDIES-Setup.txt
3/31/201110:35 AM
Text Document
3 KB
Public Docume
j j readme.txt
3/31/201110:35 AM
Text Document
10 KB
J) Music
Ifel Pictures
H Videos
-
5 items
Figure 22: My CANARY Directory
If the example configuration and data files option was selected during installation, then a
subfolder called "examples" is located within the MY CANARY folder. The examples folder
contains four additional folders, in which two of the folders (algorithm opts and signal_opts) are
place holders for future CANARY releases (Figure 23). Screen shots of the contents for the two
folders listed below are provided in Section 3.3.
• datasource opts - contains example configuration files
• sample_data - contains example monitoring station data files
~ Libraries ~ Documents ~ My CANARY ~ examples ~
V *f I .
Organize ~ Share with ~
Favorites
H Desktop
4^. Downloads
'Mi Recent Places
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[Hi Documents
My Documents
, Public Documents
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examples
. algorithm_opts
datasource_opts
. sample_data
signal_opts
Date modified
Type
1/31/2012 4:20 PM File folder
1/31/2012 5:03 PM File folder
1/31/20124:21 PM File folder
1/31/2012 4:20 PM File folder
Figure 23: My CANARY/examples Directory
6e » EE «
Arrange by: Folder w
CANARY Quick Start Guide
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Under the Start Menu, click on "All Programs" and then "CANARY." Several options are
available:
• CANARY - option to run CANARY
• Uninstall CANARY - option to uninstall CANARY
• Cluster Pattern Editor - option to edit cluster patterns
• Graph Data Files - option to graph CANARY output
Four file types are associated with CANARY after running the software and are stored in the MY
CANARY folder. These files have the following endings:
• .EDSY - This is a CANARY configuration and settings file in the YML format. Double
click this type of file to run CANARY, or right-click and choose "Edit" to open the
configuration editor in a text editor (see Configuration Details section in the CANARY
User's Manual). Older configuration files were written in XML format and ended in EDSX.
These older files can still be read by CANARY.
• .EDSD - This is a CANARY output data file, which is graphed when double-clicked.
• .EDSC - This is a CANARY clustering-pattern library file.
• .log - This is a CANARY log file. It will open in a text editor if double-clicked.
CANARY Quick Start Guide
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2.4 Running CANARY
The process of running CANARY is demonstrated through an example. Readers can follow
along using their own installation of CANARY.
In order to run CANARY, a data source is needed (a data file or database) as well as a
configuration file. Typically, the data source is made up of data from water quality sensors
collected over a period of time. Configuration files contain information about how to run
CANARY on a specific data set. These files typically end in *.yml or *.edsy; see the
Configuration Details section in the CANARY User's Manual for more details.
In Figure 24, "test_station_B.yml," located in the datasource_opts folder, is the configuration file
that is used in this example. The data file used in this example, "test_station_b.csv," is located in
the sample_data folder and shown in Figure 25.
« Documents ~ My CANARY ~ ©camples ~ datasource_opts
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2/3/2012 3:34 PM
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7/1/201111:17 AM
EDSX File
8KB
[y) Documents
example_CSV_File_Input
2/3/2012 3:33 PM
EDSY File
7 KB
My Document:
example_MS_SQL_Server_2008
12/20/2010 4:25 PM
EDSX File
8 KB
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example_MS_SQL_Server_2008
8/1/201112:11 PM
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8KB
Jp Music
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12/20/2010 4:25 PM
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, DATAPART1 (DO
test_station_B
2/3/2012 3:42 PM
YML File
5 KB |
test_station_B Date modified: 2/3/2012 3:42 PM
Date created: 2/3/2012 3:33 PM
YML File
Size: 4.33 KB
Figure 24: Location of YML Configuration File
CANARY Quick Start Guide
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sH
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¦•'a] test station b
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
547 KB
test_station_c
test_station_d
a test_station_e
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12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM CANARY Cluster Pattern Library
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
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Date created: 1/31/20124:21 PM
Figure 25: Location of CSV Data Source File
CANARY Quick Start Guide Page 30
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If the default installation Start Menu shortcut was selected, CANARY can be accessed by going
to "All Programs," "CANARY," "CANARY." This will bring up a browser window in which a
CANARY configuration file should be selected (Figure 26). The user should browse to the
directory in which the correct YML file is located and select it. In this example, browse to the
directory shown in Figure 24 and select the "test_station_B.yml" configuration file
Select Configuration File
~ +~ III Search datasource_opts
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DATAPART1 (D:)
Network
File name: test station b
~ (*.edsx, \xml, *.edsy, \yaml.
Open ~
Cancel
Figure 26: Selection of Configuration File
CANARY Quick Start Guide
Page 31
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After the execution of the "test_station_B.yml" configuration file, the following files (Figure 27)
are created:
III Search data sou rce_opts
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EDSD File
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DAT File
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2/3/2012 3:44 PM
YML File
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2/3/20123:42 PM
YML File
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~
Figure 27: Initial CANARY Run File Creation
• test_station_B.log - Log file for every day that CANARY runs. This log is generated from
the information that prints out onto the DOS window.
• status.log - Status log that tracks when CANARY is running.
• CONTROL.msg - File which contains the messages passed between CANARY and Control.
• test_station_B.StationB.summary .text - Summary of the current CANARY run, which
explains the inputs and outputs of the YML (or EDSY) file and provides log information of
every event detected.
• test_station_b.edsd - Comprehensive output file.
• test_station_b.StationB.edsd - Output file just for the Station B sensor station. Note this file
will be created for every individual sensor station included in the configuration file.
• heartbeat.dat - File which states the specific date and time CANARY was run.
• test station b out.yml - A copy of the YML file which was run.
2.5 Analysis of CANARY Output
To visualize and utilize the output data contained in the EDSD files, four different automated
methods are available. The different methods are Graph Data, Convert to CSV, Create Cluster
Library, and Combine EDSD Files. All of these methods can be accessed by right-clicking on
the EDSD file. The following sections provide examples of each method.
CANARY Quick Start Guide
Page 32
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2.5.1 Graph Data
To visualize the results of the CANARY analysis, the Graph Data option can be utilized. The
process is demonstrated using the teststationB example files.
I. Open the datasource opts folder under the My CANARY examples folder to locate the
test_station_b EDSD files (Figure 28).
« Documents ~ My CANARY ~ examples ~ datasource_opts ~
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Organize •
Hi Graph Data ~
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j_j test_station_b
2/3/20123:45 PM
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32 KB
j j status
2/3/2012 3:45 PM
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2/3/2012 3:45 PM
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1 j test_station_b.StationB,summary
2/3/20123:45 PM
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[tt| test_station_b.StationB
2/3/2012 3:45 PM
EDSD File
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brrl test_station_b
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EDSD File
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heartbeat.dat
2/3/20123:45 PM
DAT File
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[3j test_station_b_out
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test_station_B
2/3/2012 3:42 PM
YML File
5 KB
ED
test_statio n_b. Stati o n B Date modified: 2/3/20123:45 PM
CANARY Data File Size: 134 KB
Date created: 2/3/20123:45 PM
Figure 28: Directory Window Where EDSD File is Located
CANARY Quick Start Guide
Page 33
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2. Right click on "test_station_b.StationB.edsd" and select "Graph Data" (Figure 29).
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E5I3 test_station_b.StationB
B test_station_b
[ heartbeat.dat
test_station_b_out
[ test_station_B
73/2012 3:45 PM EDSD File
| j test_station_b.StationB Date modified: 2/3/201
CANARY Data File Size: 134 KB
Graph Data
Convert To CSV
Create Cluster Library
Combine EDSD Files
Open with...
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Restore previous versions
Send to
Cut
Copy
Create shortcut
Delete
Rename
Open file location
Properties
PM
PM
PM
PM
:45 PM
EDSD File
DAT File
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YML File
Figure 29: Selecting the Graph Data Option
3. Select "Probability" (Figure 30) to graph the probability of an event.
r-i-uj1
~ Result type
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f Graph events with residuals or with probability of event?
Residuals
Probability
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Figure 30: Graph Result Type Window
CANARY Quick Start Guide
Page 34
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4. Select "StationB" (Figure 31) and Click "OK." Note that an EDSD file can contain results
from more than one sensor station.
D Graph data
Please select one or more
StationB
Select all
OK
Cancel
Figure 31: Station Selection Window
CANARY Quick Start Guide
Page 35
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5. Select "Weekly" to graph the data on a weekly basis (Figure 32) and click "OK."
Please select a time frame
[Daily
Weekly
Monthly
Quarterly
All
Events Only
Cancel
Figure 32: Graph Scale Window
CANARY Quick Start Guide
Page 36
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Once this process is completed, the graphs are created and added to the folder in which the
EDSD was located (Figure 33).
« Documents ~ My CANARY ~ examples ~ datasource_opts ~
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Dimensions: 1275x1350
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Date created: 1/3/2012 4:02 PM
3
S= - EH ®
Figure 33: Output files from Graph Data
After the graphs are created, they can be opened and viewed. Each graph contains the water
quality signals analyzed, any operational signals, and a probability of event plot for each
algorithm utilized. Water quality signal labels are in black, operational signal labels are green,
and operational signals that are ignored are labeled in purple. The probability of event plots are
at the bottom of the graph. A blue dot on the probability of event plot indicates an event. In
addition, a dot will be located on each water quality signal that contributed to the detection of the
event.
6. Double-click the "test station b.StationB.2006-02-21 .thru.2006-02-27.png" file to examine
the results.
Figure 34 shows the content of this file: the water quality signals are chlorine (CL2), pH (PH),
conductivity (COND), turbidity (TURB), and total organic carbon (TOC). The operational
signals in this example are the temperature (TEMP), plant pressure (PLNT OP PRES), and flow
CANARY Quick Start Guide
Page 37
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(PLNT OP FLOW). The probability of an event plot shows the probability that an event is
occurring at each time step as computed by CANARY using the LPCF algorithm. The first
event detected was caused by an unexpected change in the chlorine signal (CL2).
StationB 2006-02-21 00:00:00 to 2006-02-27 23:40:00
BCL2 3
CL2 (Mg/L) 2
21-Feb
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
¦Feb
28-Feb
B PH 7.4
PH (pH) 7 2
Operational
Signal:
Ignore All
Changes
21-Feb
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
27-Feb
28-Feb
B TEMP
TEMP (°F)
21-Feb
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
27-Feb
28-Feb
BCOND 238
COND (jiS/cm)
232
^ 230
Water
Quality
Signal Plots
21-Feb
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
27-Feb
28-Feb
BTURB 0 6
TURB(NTU) Q4
Detected
Fvpnt
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
27-Feb
28-Feb
B PLNT OP 75
PRES (PSI) ?0
Operational
Signal Plots
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
28-Feb
B PLNT OP 14
FLOW (gpm) 13 5
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
28-Feb
10.32
B TOC
TOC(ppb) 1Q31
10.3
21-Feb
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
28-Feb
Probability
of Event
yT7 0.5
21-Feb
22-Feb
23-Feb
24-Feb
25-Feb
26-Feb
27-Feb
28-Feb
Figure 34: CANARY Output Graph
2.5.2 Converting to CSV Files
To view the contents of the EDSD file, it is recommended that the "Convert to CSV" option be
utilized. This converts the contents of the file to a comma separated values (CSV) file that can
be opened in Microsoft Excel. Two types of CSV are created, a summary file and a details file.
The summary file provides the probability of an event and the CANARY status at every time
step. The details file provides extensive details on CANARY results for every time step,
including the CANARY status, the probability of an event, and the residuals for each active
CANARY Quick Start Guide
Page 38
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water quality signal. A details CSV file is written for each active algorithm in the configuration
file. The process is demonstrated below using the previous example files.
1. Open the datasourceopts folder under the My CANARY examples folder to locate the
"test_station_b.StationB.edsd" (Figure 28).
2. Right click on "test_station_b.StationB.edsd" file and select "Convert to CSV" to convert the
format of the results data (Figure 35).
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2/3/20123:45 PM
2/3/2012 3:45 PM
2/3/2012 3:45 PM
2/3/2012 3:45 PM
Type
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Text Document
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EDSD File
Size
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Convert To CSV
Create Cluster Library
Combine EDSD Files
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~
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32KB
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Figure 35: Selecting the Convert to CSV Option
The converted CSV files are added to the folder (Figure 36). The new files are
"test_station_b.StationB-summary.csv" and "test_station_b.StationB-details-alg_l.csv."
CANARY Quick Start Guide
Page 39
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« Documents ~ My CANARY ~ examples ~ datasource_opts ~
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2/3/20124:15 PM
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2/3/2012 4:15 PM
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2/3/2012 4:14 PM
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Date modified: 2/3/2012 4:53 PM
Size: 939 KB
Date created: 2/3/2012 4:53 PM
Figure 36: Converting to CSV File Output
2.5.3 Create Cluster Library
Another option available by right-clicking on the EDSD file is "Create Cluster Library." This is
an advanced option for CANARY users; for details, please refer to the CANARY User's Manual
section on Water Quality Pattern Matching (Hart and McKenna 2011).
2.5.4 Combine EDSD Files
This option is most often needed for long-term CANARY runs in online mode (i.e., connected to
a database) when a separate EDSD file is created eveiy day. This option allows multiple EDSD
files to be combined into a single EDSD file. Note that CANARY expects the EDSD file names
being joined to have a particular naming convention, see Figure 37. This is the same naming
convention used for the daily EDSD files created during an online ran. This convention is also
followed for intermediate files created in offline mode (i.e., running from a CSV file). At the
CANARY Quick Start Guide
Page 40
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end of an offline run, CANARY automatically deletes the intermediate files and combines them
into the final EDSD file. The process is demonstrated below through an example.
1. Open the folder where the EDSD files are located (Figure 37).
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2/3/2012 4:07 PM
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-
YML File
Size: 4.33 KB
Figure 37: Example EDSD Naming Convention
CANARY Quick Start Guide
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2. Right click on any of these intermediate EDSD files and select "Combine EDSD Files'
(Figure 38)
I
~ Libraries ~ Documents ~ My CANARY ~ examples ~ datasource_opts ~
Search dataso
l= - rn
Graph Data ~
Share with ~
Organize ~
Favorites
B Desktop
jfc. Downloads
'Mi Recent Places
Libraries
_H Documents
J) Musk
B Pictures
H Videos
j*P Computer
& OS (CO
tj, DATAPART1 (D:)
Network
Documents library
datasource_opts
I 1 heartbeat.dat
test_station_b .2006-03-15.th ru.2006 -03-16
^ test_station_b.2006-03-14 .th ru .2006 -03-15
test_station_b.2006-03-13 .th ru .2006-03-14
^test_station_b.2006-03-12.thru.2006-03-13
(§¦] test_station_b.2006-03-11 .th ru .2006-03-12
fjii test_station_b.2006-03-10 .th ru .2006-03-11
test_statio n_b.2006-03-09.th ru .2006-03-10
^ test_station_b .2006-03-08.th ru .2006-03-09
liU test_station_b .2006-03-07 .th ru .2006-03-Oi
^ test_stati on_b.2006-03-06.th ru .2006-03-07
Q test_stati on_b.2006-03-05.th ru .2006-03-06
|§3 test_stati on_b.2006-03-04.th ru .2006-03-05
test_station_b.2006-03-03 .th ru .2006-03-04
test.stati on_b.2006-03-02.th ru .2006-03-03
^ test_stati o n_b.2006-03-01 .thru .2006-03-02
fjw] test_stati on_b.2006-02-28 .th ru .2006-03-01
Q test_station_b.2006-02-27.thru.2006-02-28
test_station_b-2006-02-26.thru.2006-02-27
gtest_station_b.2006-02-25.thru.2006-02-26
|§j test_station_b.2006-02-24.thru.2006-02-25
§§ test_stati o n_b .2006-02-23 .th ru .2006 -02-24
^test_station_b.2006-02-22.thru.2006-02-23
test_5tation_b,2006-02-21 .thru.2006-02-22
Fif 1 test_station_b.2006-02-21.thru.2006-02-22 Date modified: 21
CANARY Data File Size; It
Arrange by: Name "
Date modified
Type
Size
2/3/2012 6:41 PM
DAT File
1KB
2/3/2012 6:41 PM
EDSD File
84 KB
2/3/2012 6:41 PM
EDSD File
84 KB
2/3/2012 6:41 PM
EDSD File
83 KB
2/3/2012 6:41 PM
EDSD File
83 KB
2/3/2012 6:41 PM
EDSD File
83 KB
2/3/2012 6:41 PM
EDSD File
82 KB
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EDSD File
82 KB
2/3/20126:41 PM
EDSD File
82 KB
2/3/20126:41 PM
EDSD File
82 KB
2/3/2012 6:41 PM
EDSD File
82 KB
2/3/20126:41 PM
EDSD File
83 KB
2/3/20126:41 PM
EDSD File
83 KB
2/3/20126:41 PM
EDSD File
82 KB
2/3/20126:41 PM
EDSD File
82 KB
2/3/20126:41 PM
EDSD File
81 KB
2/3/20126:41 PM
EDSD File
81 KB
2/3/20126:41 PM
EDSD File
81 KB
Graph Data
ile
81 KB
Convert To CSV
ile
81KB
Create Cluster Library
ile
80 KB
Combine EDSD Files
ile
80 KB
Open with...
ile
79 KB
Share with
~
ile
77 KB
Restore previous versions
>012 6:41PM
Send to
~
Cut
Copy
Create shortcut
Delete
Rename
Open file location
Properties
Figure 38: Selecting Combine EDSD Files Option
CANARY Quick Start Guide
Page 42
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3. Select the "test_station_b.2006-02-21.thai.2006-02-22.edsd" file as the first EDSD file to be
included in the combined file (Figure 39).
Select the FIRST raw data file to combine
« My Documents ~ My CANARY ~ examples ~ datasource_opts
~ Search datasource_opts
Organize '
New folder
/ Favorites
H Desktop
4- Downloads
H Recent Places
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ij-j Documents
^ Music
B Pictures
0 Videos
fj®|' Computer
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w Removable Disk (HO
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Name
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Type
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H test_station_b,2006-02-21.thru .2006-02-22 2/3/2012 4:14 PM CANARY Data File
¦ test_5tation_b.2006-02-22.thru.2006-02-23 2/3/2012 4:14 PM
H te5t_station_b.2006-02-23.thru.2006-02-24 2/3/20124:14 PM
H test_station_b.2006-02-24.thru.2006-02-25 2/3/2012 4:14 PM
!3 test station_b,2006-02-25.thru.2006-02-26 2/3/20124:14 PM
M test_station_b.2006-02-26.thru.2006-02-27 2/3/2012 4:14 PM
H test_station_b.2006-02-27.thru.2006-02-28 2/3/20124:14 PM
H test_station_b.2006-02-28.thru.2006-03-01 2/3/2012 4:14 PM
H test.station_b.2006-03-01.thru.2006-03-02 2/3/2012 4:14 PM
S3 test station_b.2006-03-02.thru.2006-03-03 2/3/20124:14 PM
H test_station_b,2006-03-03.thru.2006-03-04 2/3/2012 4:14 PM
H test_station_b.2006-03-04.thru.2006-03-05 2/3/2012 4:15 PM
H test_station_b,2006-03-05.thru.2006-03-06 2/3/2012 4:15 PM
H test_station_b.2006-03-06.thru.2006-03-07 2/3/20124:15 PM
H test.stati on_b .2006-03-07.th ru.2006 -03-08 2/3/2012 4:15 PM
H test.station_b.2006-03-08.thru.2006-03-09 2/3/2012 4:15 PM
H test_station_b.2006-03-09.thru.2006-03-10 2/3/2012 4:15 PM
H test_station_b.2006-03-10.thru.2006-03-11 2/3/2012 4:15 PM
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
CANARY
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
Data File
l. -inns nD n +-Ur.. mnz nD 1 t mnmi i.it nM
r/iM/iDv c;u
File name: test station b.2006-02-21,thru.2006-02-22
(*.edsd, *.mat)
Open m
77 KB
79 KB
80 KB
80 KB
81 KB
81 KB
81 KB
81 KB
81 KB
82 KB
82 KB
83 KB
83 KB
82 KB
82 KB
82 KB
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82 KB
Cancel
Figure 39: First EDSD File to Combine
CANARY Quick Start Guide
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4. Select the "test_station_b.2006-03-09.thru.2006-03-10.edsd" file as the last EDSD file to be
included in the combined file (Figure 40).
Select the LAST raw data file to combine
EXE
Search datosource_opts
Organize
New folder
; Favorites
Name
Date modified
Type
Size
W Desktop
H te5t_stati on_b .2006 -02-21 .th r u .2006-02 -22
2/3/2012 4:14 PM
CANARY Data File
77 KB
& Downloads
Htest_station_b-2006-02-22.thru.2006-02-23
2/3/2012 4:14 PM
CANARY Data File
79 KB
'Mi Recent Places
[§r| test_stati o n_b .2006 -02-23 .th ru .2006 -02-24
2/3/20124:14 PM
CANARY Data File
80 KB
H t est_stati o n_b .2006 -02-24 .th r u .2006-02 -25
2/3/20124:14 PM
CANARY Data File
80 KB
Libraries
H te5t_stati on_b.2006-02-25 .thru.2006 -02-26
2/3/20124:14 PM
CANARY Data File
81 KB
H Documents
H t est_st ati o n_b .2006 -02-26 .th r u .2006 -02-27
2/3/20124:14 PM
CANARY Data File
81 KB
Music
H test_stati on_b.2006-02-27 .th ru .2006 -02 -28
2/3/2012 4:14 PM
CANARY Data File
81 KB
B Pictures
H test_stati o n_b .2006 -02-28 .th ru .2006 -03 -01
2/3/20124:14 PM
CANARY Data File
81 KB
0 Videos
H test_stati o n_b.2006-03 -01 .th ru .2006-03 -02
2/3/2012 4:14 PM
CANARY Data File
81 KB
H test_station_b.2006-03-02.thru.2006-03-03
2/3/20124:14 PM
CANARY Data File
82 KB
0» Computer
H te5t_statio n_b.2006 -03 -03 .th ru.2006-03 -04
2/3/20124:14 PM
CANARY Data File
82 KB
& OS (CO
H test_station_b.2006-03-04.th ru.2006-03 -05
2/3/2012 4:15 PM
CANARY Data File
83 KB
u DATAPART1 (D:)
H te5t_stati o n_b .2006 -03 -05 .th r u .2006 -03 -06
2/3/20124:15 PM
CANARY Data File
83 KB
^ Removable Disk (H:)
H test_stati o n_b .2006 -03 -06.th ru .2006-03 -07
2/3/2012 4:15 PM
CANARY Data File
82 KB
ftsrl test_station_b.2006 -03-07.thru .2006 -03 -08
2/3/20124:15 PM
CANARY Data File
82 KB
Op Network
H test_stati o n_b .2006 -03 -08 .th ru .2006 -03 -09
2!3/2012 4:15 PM
CANARY Data File
82 KB
ffrH test_stati on_b .2006 -03 -09 .th ru .2006 -03 -10
2/3/20124:15 PM
CANARY Data File
82 KB
hrrl test_station_b.2006 -03-10 .thru.2006-03 -11
2/3/2012 4:15 PM
CANARY Data File
82 KB
Lk_J 4.-^4- — u innz nj 11 i-i mnc nj n
m /mi t a.k nh a
r m a dv n-.*-. c;i~
03 l'"D
File name: test station b.2006-03-09.thru.2006-03-10
(*,edsd, *.mat)
Open ~
Cancel
Figure 40: Last EDSD File to Combine
CANARY Quick Start Guide
Page 44
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Once the last EDSD file is selected, CANARY creates a combined EDSD file,
"test_station_b.2006-02-21.combined.2006-03-10.edsd," containing the first, the last, and all the
intermediate files (Figure 41).
?l « Dc
Documents ~ My CANARY ~ ©camples ~ datasource_opts ~
III Search data sou rce_opts
Organize ~ js) Graph Data
Favorites
S Desktop
^ Downloads
a Recent Places
^§1 Libraries
3 Documents
J5j My Documents
Public Documents
Music
fa 1 Pictures
Q Videos
flip Computer
lit OS(G)
tj DATAPART1 (D:)
^ Removable Disk (H:)
Share with
Print
Burn
m
a ®
Documents library
datasource_opts
Arrange by:
Name T
Name
Date modified
Type Size
j | test_station_b
2/3/2012 4:15 PM
Text Document
16KB
i j status
2/3/2012 4:15 PM
Text Document
1KB
|3 CONTROL.msg
2/3/20124:15 PM
Text Document
2KB
j | test_station_b,StationB,summary
2/3/2012 4:15 PM
Text Document
3 KB
test_station_b,StationB
2/3/2012 4:15 PM
EDSD File
125 KB
H test_station_b
2/3/2012 4:15 PM
EDSD File
125 KB
heartbeat.dat
2/3/20124:15 PM
DAT File
1 KB
hrd test_5tation_b2006-02-21.combined,2006-03-10
2/3/2012 415 PM
EDSD File
38 KB
test_station_b_out
2/3/2012 4:14 PM
YML File
5 KB
[ j test_station_B
2/3/2012 4:14 PM
YML File
5KB
example
2/3/20123:34 PM
YML File
7KB
example_CSV_FileJnput
2/3/2012 3:33 PM
EDSY File
7 KB
example_0racle_Datab ase_10g_XE
8/1/20113:12 PM
EDSY File
8KB
example_MySQL_Server_5
8A/20113:12 PM
EDSY File
8 KB
example_SQLServer_2008_by_rows
8./1/201112:11 PM
EDSY File
8 KB
example_SQLServer_2008_by_cols
8/1/201112:11 PM
EDSY File
8 KB
example_MS_SQL_Server_2008
8/1/201112:11 PM
EDSY File
8KB
example_CSV_File_Input
7A/201111:17 AM
EDSX File
8 KB
exam pie_Oracle_Database_10g_XE
12/20/2010 4:25 PM
EDSX File
8 KB
^ Network
hr I test_Station_b,2006-02-21,combired.2006... Date modified: 2/3/2012 4:15 PM
CANARY Data File Size: 37.4 KB
Date created: 2/3/20124:15 PM
Figure 41: Combined EDSD File Created
CANARY Quick Start Guide
Page 45
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3. Additional Resources
In this section, the CANARY license text, an example YAML configuration file, and screen
captures of CANARY related directories are provided.
3.1 CANARY License Text
This software is Copyright © 2007-2011 Sandia Corporation. Under the terms of Contract DE-
AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this
software.
Redistribution and use in source form, with or without modification, and use in binary form, are
permitted provided that the following conditions are met:
1. Redistributions in source code must retain the above copyright notice, this list of conditions,
and the following disclaimer.
2. The binary form of this software was created using MATLAB [C] 1984-2009, The
MathWorks, Inc., and was created and distributed according to a limited license agreement
between the authors and the MathWorks; the use of this software in BINARY form is subject
to the disclaimer and the following additional conditions:
3. The user must accept the MATLAB Compiler Runtime (MCR) Libraries License prior to
installing or running this software.
4. In accordance with the MCR Libraries License, the binary form of this software may not be
modified, decompiled or redistributed without prior written permission from the copyright
holders.
5. There is no grant of any license rights to the user to any MathWorks products or to support or
warranty in any form from the MathWorks beyond those expressly specified in the MCR
Libraries License.
6. If any source files originating from Sandia Corporation are modified, you must cause the
modified files to carry prominent notices stating that you changed the files and the date of
any change.
DISCLAIMER:
THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESSED OR IMPLIED
WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
CANARY Quick Start Guide
Page 46
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DISCLAIMED. IN NO EVENT SHALL THE UNITED STATES GOVERNMENT, NOR THE
UNITED STATES DEPARTMENT OF ENERGY, NOR SANDIA CORPORATION, NOR
THE MATHWORKS, NOR ANY OF THEIR EMPLOYEES OR THEIR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
ANY LICENSEE OF THIS SOFTWARE HAS THE OBLIGATION AND RESPONSIBILITY
TO ABIDE BY THE APPLICABLE EXPORT CONTROL LAWS, REGULATIONS, AND
GENERAL PROHIBITIONS RELATING TO THE EXPORT OF TECHNICAL DATA.
FAILURE TO OBTAIN AN EXPORT CONTROL LICENSE OR OTHER AUTHORITY
FROM THE GOVERNMENT MAY RESULT IN CRIMINAL LIABILITY UNDER U.S.
LAWS.
License for Apache Commons Math JAR File:
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Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
7. Definitions.
"License" shall mean the terms and conditions for use, reproduction, and distribution as
defined by Sections 1 through 9 of this document.
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"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted
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"Source" form shall mean the preferred form for making modifications, including but not
limited to software source code, documentation source, and configuration files.
CANARY Quick Start Guide
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"Object" form shall mean any form resulting from mechanical transformation or translation
of a Source form, including but not limited to compiled object code, generated
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"Work" shall mean the work of authorship, whether in Source or Object form, made available
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CANARY Quick Start Guide
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CANARY Quick Start Guide
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service marks, or product names of the Licensor, except as required for reasonable and
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END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following boilerplate notice, with the
fields enclosed by brackets "[]" replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate comment syntax for the file format.
We also recommend that a file or class name and description of purpose be included on the same
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CANARY Quick Start Guide
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Copyright [yyyy] [name of copyright owner]
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
in compliance with the License. You may obtain a copy of the License at
http ://www. apache. org/licenses/LICEN SE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License
is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
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APACHE COMMONS MATH DERIVATIVE WORKS:
The Apache commons-math library includes a number of subcomponents whose implementation
is derived from original sources written in C or Fortran. License terms of the original sources are
reproduced below.
For the lmder, lmpar and qrsolv Fortran routine from minpack and translated in the
LevenbergMarquardtOptimizer class in package org.apache.commons.math.optimization.general
Original source copyright and license statement:
Minpack Copyright Notice (1999) University of Chicago. All rights reserved
Redistribution and use in source and binary forms, with or without modification, are permitted
provided that the following conditions are met:
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Argonne National Laboratory.
Alternately, this acknowledgment may appear in the software itself, if and wherever such
third-party acknowledgments normally appear.
CANARY Quick Start Guide
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23. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS" WITHOUT
WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE UNITED STATES,
THE UNITED STATES DEPARTMENT OF ENERGY, AND THEIR EMPLOYEES: (1)
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THAT USE OF THE SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED
RIGHTS, (4) DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION
UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL BE
CORRECTED.
24. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT HOLDER, THE
UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, OR THEIR
EMPLOYEES: BE LIABLE FOR ANY INDIRECT, INCIDENTAL, CONSEQUENTIAL,
SPECIAL OR PUNITIVE DAMAGES OF ANY KIND OR NATURE, INCLUDING BUT
NOT LIMITED TO LOSS OF PROFITS OR LOSS OF DATA, FOR ANY REASON
WHATSOEVER, WHETHER SUCH LIABILITY IS ASSERTED ON THE BASIS OF
CONTRACT, TORT (INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR
OTHERWISE, EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE
POSSIBILITY OF SUCH LOSS OR DAMAGES.
Copyright and license statement for the odex Fortran routine developed by E. Hairer and G.
Wanner and translated in GraggBulirschStoerlntegrator class in package
org. apache. commons. math. ode. non stiff:
Copyright (c) 2004, Ernst Hairer
Redistribution and use in source and binary forms, with or without modification, are permitted
provided that the following conditions are met:
- Redistributions of source code must retain the above copyright notice, this list of conditions and
the following disclaimer.
- Redistributions in binary form must reproduce the above copyright notice, this list of conditions
and the following disclaimer in the documentation and/or other materials provided with the
distribution.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
CANARY Quick Start Guide
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CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Copyright and license statement for the original lapack fortran routines translated in
EigenDecompositionlmpl class in package org.apache.commons.math.linear:
Copyright (c) 1992-2008 The University of Tennessee. All rights reserved.
$COPYRIGHT$
Additional copyrights may follow
$HEADER$
Redistribution and use in source and binary forms, with or without modification, are permitted
provided that the following conditions are met:
- Redistributions of source code must retain the above copyright notice, this list of conditions and
the following disclaimer.
- Redistributions in binary form must reproduce the above copyright notice, this list of conditions
and the following disclaimer listed in this license in the documentation and/or other materials
provided with the distribution.
- Neither the name of the copyright holders nor the names of its contributors may be used to
endorse or promote products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
CANARY Quick Start Guide
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OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Copyright and license statement for the original Mersenne twister C routines translated in
MersenneTwister class in package org.apache.commons.math.random:
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted
provided that the following conditions are met:
25. Redistributions of source code must retain the above copyright notice, this list of conditions
and the following disclaimer.
26. Redistributions in binary form must reproduce the above copyright notice, this list of
conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
27. The names of its contributors may not be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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3.2 CANARY Directory Structure
This section provides screen captures of the subfolders and files contained in the CANARY
directory under Program Files once the software is installed on a computer.
Figure 42 shows the files contained within the "bin" folder of the "CANARY" directory found
under Program Files.
0 MM
v/L
Organize ~ Include in library
$ Downloads
- Recent Places
^ Libraries
IS Documents
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0 Videos
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i= - a #
*¦
Name
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Type
Size
ra
kl canary.exe
10/27/20114:05 PM
Application
795 KB
H canary-debugging.bat
3/31/201110:35 AM
Windows Batch File
1KB
fel canary-eddies.bat
3/31/201110:35 AM
Windows Batch File
1KB
configure-canary.bat
3/31/201110:35 AM
Windows Batch File
1KB
S] graph-outputs.bat
3/31/201110:35 AM
Windows Batch File
1KB
Figure 42: CANARY\bin Folder
CANARY Quick Start Guide Page 55
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Figure 43 shows the files contained within the "doc" folder of the "CANARY" directory found
under Program Files.
a lka.1
« DriveC (CO ~ Program Files (x86) ~ CANARY ~ doc
~\*t
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Organize ~ Include in library ~ Share with ~
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' EH ®
$ Downloads
-
A,
Name
Date modified
Type
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"S CANARY-UM.pdf
3/31/201110:35 AM
Adobe Acrobat D...
2,066 KB
Libraries
[H EDDIES-Setup.txt
3/31/201110:35 AM
Text Document
3 KB
Documents
Music
£
B Pictures
B Videos
Computer
& DriveC (CO
r-a DriveC (D:)
2 items
Figure 43: CANARY\doc Folder
Figure 44 shows the files contained within the "etc" folder of the "CANARY" directory found
under Program Files.
, « DriveC (CO ~ Program Files (x86) ~ CANARY ~ etc
Organize ~ Include in library ~ Share with w Burn New folder
Downloads
- ; Recent Places
^ Libraries
J Documents
J) Music
B Pictures
Q Videos
Computer
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t aj DriveC (D:)
5 items
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0 II.&m
1=
a #
Name
Date modified
Type
Size
canary.ico
3/31/201110:35 AM
Icon
1 KB
H graphResidsWith Data.ico
3/31/201110:35 AM
Icon
1 KB
Ql mysql.cfg
3/31/201110:35 AM
CFG File
1 KB
! , oracle.cfg
3/31/201110:35 AM
CFG File
1 KB
j j sql server, cfg
3/31/201110:35 AM
CFG File
1 KB
Figure 44: CANARY\etc Folder
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Figure 45 shows the files contained within the "lib" folder of the "CANARY" directory found
under Program Files.
[I Search
~ Computer ~ OS (C:) ~ Program Files (x86) ~ CANARY ~ lib ~
Organize ~ Include in library ~ Share with ~ Burn New folder §~ ~ Qj]
* X Favorites
Name
Date modified
Type
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H Desktop
0 CanarysCore
1/4/2012 2:02 PM
Executable Jar File
81 KB
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[uu] commons-math-2.0
12/20/2010 4:24 PM
Executable Jar File
742 KB
^ Recent Places
commons-math-2.0
12/20/2010 4:24 PM
Compressed (zipp...
10,484 KB
1 1 commons-math-2.0.zip.asc
12/20/2010 4:24 PM
ASC File
1 KB
^ i^j Libraries
j "| commons-math-2.0.zip.md5
12/20/2010 4:24 PM
MD5 File
1 KB
t> HI) Documents
i commons-math-2.0-javadoc
12/20/2010 4:24 PM
Executable Jar File
4,454 KB
[> J"- Music
M commons-math-2.0-sources
12/20/2010 4:24 PM
Executable Jar File
952 KB
~ S Pictures
§J LICENSE
12/20/2010 4:25 PM
Text Document
19 KB
Q Videos
0 NOTICE
12/20/2010 4:24 PM
Text Document
3 KB
snakeyaml
1/3/201211:18 AM
Executable Jar File
248 KB
* J®' Computer
1^1 snakeyaml-1.7
12/20/2010 4:25 PM
Executable Jar File
248 KB
os (co
> 0 DATAPARTl (D:)
Network
Figure 45: CANARWlib Folder
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3.3 MY CANARY Directory Structure
This section provides screen captures of the subfolders and files contained in the examples folder
under the My CANARY directory after the software is installed on a computer.
Figure 46 shows the files contained within the "datasource_opt" folder of the "examples"
directory.
imSm
« Documents ~ My CANARY ~ examples ~ datasource_opts ~
- +~
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Organize »
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Burn
it Favorites
H Desktop
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^ k Recent Places
^ Libraries
_^| Documents
111 My Documents
Public Docume
,J' Music
B Pictures
Q Videos
m Computer
& OS (CO
, „ DATAPART1 (DO
12 items
Documents library
datasource_opts
Arrange by: Name T
Name
Date modified
Type
Size
example
2/3/2012 3:34 PM
YML File
7 KB
example_CSV_File_Input
7/1/201111:17 AM
EDSX File
8 KB
example_CSV_File_Input
2/3/2012 3:33 PM
EDSY File
7 KB
example_MS_SQL_Server_2008
12/20/2010 4:25 PM
EDSX File
8 KB
example_MS_SQl__Server_2008
8/1/201112:11 PM
EDSY File
8KB
example_MySQL_Server_5
12/20/2010 4:25 PM
EDSX File
8 KB
example_MySQL_Sen/er_5
8/1/20113:12 PM
EDSY File
8 KB
exa m pie_0 ra cl e_Database_10g_XE
12/20/2010 4:25 PM
EDSX File
8 KB
exa mpi e_Orac 1 e_Datab a se_10g_XE
8/1/20113:12 PM
EDSY File
8 KB
example_SQLServer_2008_by_col5
8/1/201112:11 PM
EDSY File
8 KB
^ example_SQLServer_2008_by_rows
8/1/201112:11 PM
EDSY File
8KB
test_station_B
2/3/2012 3:42 PM
YML File
5 KB
Figure 46: My C A IN A RY\exam ples\datasou rce opts Folder
CANARY Quick Start Guide Page 58
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Figure 47 shows the files contained within the "sample_data" folder of the "examples" directory.
« Documents
My CANARY ~ examples ~ sample_data
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Organize •
|§ci Open ~ Share with ~
Print
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H Desktop
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n Recent Places
^ Libraries
I! Documents
My Documents
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qfr Music
B Pictures
Q Videos
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SL 05(G)
|i* j "1 test_station_b
Ci.A Microsoft Office
Documents
sample_data
Name
test_station_a
library
Date modified
New folder
Type
H ' Oil
Arrange by: Folder '
Size
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
IK.
test_station b
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
test_station_c
test_station_d
test_station_e
ffiil test_station_f
test_station_g
^ TSTl_Jan_Aug
STST2
_Jan_Aug_
08
08
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
12/20/2010 4:25 PM CANARY Cluster Pattern Library
12/20/2010 4:25 PM Microsoft Office Excel Comma Separated Values File
Date modified: 12/20/2010 4:25 PM
Excel Comma Separated VaL. Size: 546 KB
Date created: 1/31/20124:21 PM
I KB
547 KB
4,499 KB
7,559 KB
3,584 KB
4,386 KB
4,776 KB
5,764 KB
125 KB
5,716 KB
Figure 47: My CAN A RY\exanipies\sampledata Folder
CANARY Quick Start Guide
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4. References
Hart, D. B. and McKenna, S. A. (2011). CANARY user's manual, version 4.3.1, U.S.
Environmental Protection Agency, Office of Research and Development, National Homeland
Security Research Center, Cincinnati, OH.
Murray, R., Haxton, T., McKenna, S. A., Hart, D. B., Klise, K. A., Koch, M. W., Vugrin, E.,
Martin, S., Wilson, M., Cruz, V., and Cutler, L. (2010). Water quality event detection systems for
drinking water contamination warning systems: Development, testing, and application of
CANARY, U.S. Environmental Protection Agency, Office of Research and Development,
National Homeland Security Research Center, Cincinnati, OH.
CANARY Quick Start Guide
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