Camera Trap Data Processing User Manual
Contents
1. Camera Trap Data Processing User Manual Supplement to Harris G R Thompson J L Childs and J G Sanderson 2010 Automatic storage and analysis of camera trap data Ecological Society of America Emerging Technologies July 2010 TABLE OF CONTENTS INTRODUCTION EE E E ee ee hs sitet tet te Seis te a stato Ay Aol E SAN cet 1 DATA RETRIEVAL RELABELING AND STORAGE wy oycs an ansevavcg sa waie wv lesaiciattaatanendea ne ha ane Bea ees SUMIMVAL e oie kata bese sas ha easy bn E Ube we SON aE Eaa CORSE Sha ONO ER Leta AEE aA LARA Ee Five Detatled Steps errari EENE nade kee bev taddaes dete EELEE tense eek eRe take DATA CREATION AND ANALYSIS cccccc cece cece eee n ene e eee eee e ene e tee e cents geeeeeeenenteseeeeen eee eeeeees 5 Creation of All FoldersFiles thtonnsiiiornsrcnerer nanan e a E D Edits Inp t titans yesen ks e aoa ya a E E EE EDE E NEEE e R 5 SPREADSHEET CAMERA TRAP DATA ssssssuussssserrsssscrrerssserresseessrresssrreessereeessseeeeres erre INTRODUCTION The following user manual contains the detailed steps necessary for generating a common format for labeling storing sharing and subsequently analyzing information gained from camera traps This document forms a supplement to the publication Harris G R Thompson J L Childs and J G Sanderson 2010 Automatic storage and analysis of camera trap data xxx This publication is the proper reference for citation purposes DATA RETRIEVAL RELABEL2. ING AND STORAGE Summary I Set up a file structure to hold the images II Visit a camera trap remove the memory card and store the images in a temporary folder II Relabel all the files in the temporary folder simultaneously with the date and time the image was recorded automated IV For each image file identify the species count the number of individuals of each species recorded and store the file in the proper location species number of individuals folder V Return to step II above until all camera traps have been visited and images processed Five Detailed Steps I Set up a file structure to hold the images Each image from a camera trap will ultimately be stored in a Site Location Species folder Figure 1 exemplifies such a file structure For example an image of 10 zebra would placed in the directory Site LocO1 zebra 10 Note that location directories can be copied pasted and relabeled Create or delete folders as needed More explicitly 1 Site refers to the general area where the camera traps are operating 2 Locations refer to places where a camera trap is was set Locations might be Loc01 Loc02 or have names like South Wash or Arroyo Seco or identified by UTM coordinates Location names are always unique in our program they are limited to 25 characters 3 For each location each species captured by the imagery is placed in a unique folder named by that species in our program names
3. are limited to 25 characters 4 Folders within each Species folder are labeled with the number of individuals in the image For example an image with 1 animal would be in folder name 01 An image with 5 animals of the same species would be in folder 05 Numbers need not be sequential and it does not matter if some folders are empty 5 Each Location folder can contain a folder Unknown for species with the number of individuals folder 99 where all unidentified images are stored Site ee ee LocO1 Loc02 ZI 74 Deer Puma Zebra Deer Peccary Rabbit MN AN AN 010203 01 071012 01020305 12 01 Figure 1 Example directory structure for storing and organizing imagery gained from camera traps II Visit a camera trap remove the memory card and store the images in a temporary folder Storing all the images from a memory card in a temporary location folder and then relabeling them in step III prevents subsequent loss of image files Image file counting resets to zero when images are moved from the memory card Subsequent file moves can over write existing files Relabeling the image files with their date and time makes the image files unique and prevents files from being over written IIIa Digital images Relabel all the files in the temporary folder simultaneously with the date and time the image was recorded The freeware program ReNamer is used to simultaneously relabel all images in the temporary lo
4. cation folder ReNamer is downloaded from http www snapfiles com downloads denrenamer dldenrenamer html Using ReNamer To begin make a copy of a file to use as a test case Perform the following steps on the test file When the file is properly relabeled save the steps in ReNamer These steps can then be automatically applied subsequently without the need to reenter them The following steps using ReNamer are visualized in Figure 2 1 Open ReNamer by double clicking on the icon 2 Drag and drop an image file group of image files or a folder of images into the lower frame of ReNamer The image files are listed 3 Click Add to add the first rule From the drop down list select Delete select Till the end skip extension Click Add Rule This deletes the name of the file leaving the extension Don t worry that it appears as if only one such file had the label deleted 4 Click Add to add the second rule Select Insert then click the yellow lightening bolt Insert Meta Tag and select from the drop down list EXIF_Date Then click the green check Insert Click Add Rule Now click on Preview at the top The new names of the files should appear with the date and time that the image was recorded 5 Click Add to add the third rule Select Replace In the Find box enter and in the Replace box enter a space or blank with the space bar on the keyboard Back in the Find b
5. m nput txt and so not included in camera trap data analysis For instance the species bobcat could be deleted and the number of species reduced from 6 to 5 The folder Unknown 99 is usually reserved for unidentifiable species recorded in poor images Unknown therefore appears in nput txt and can be deleted The second text file Al Pictures txt is a list of all image files that are labeled with the location name species name year month day hour minute second and number of individuals Note that location and species names are 25 characters left justified and blank filled LocO1 Deer 2009 11 27 13 55 45 O1 AllPictures txt can be imported and stored by a spreadsheet such as Excel AllPictures txt and Input txt contain all the information used by an analysis program to complete a full analysis of all camera trap data SPREADSHEET CAMERA TRAP DATA Much camera trap data is presently stored in spreadsheets In this case the spreadsheet functions can be used to produce the AllFolders Files txt that contains a list of images in the form above The type of naming formats can vastly differ so we do not give an example of how to produce the format above from existing spreadsheet data However we have not yet found an example of spreadsheet data that cannot be easily converted and stored in the text form identical to the above For Excel typical commands include Find Replace Text to Columns and amp The file Input txt is ea
6. mple below the site is known as Kofa Enter the command dir s Kofa gt AllFoldersFiles txt This creates a complex but structured text file list of all folder names and locations and the files within them The text file Al FoldersFiles txt is found in the folder that contains the Kofa folder Editing Input txt The data creation program reads AllFoldersFiles txt and produces two text files The first Input txt contains the site name the number of locations a list of locations the number of species and the list of species It defaults the camera trap start and stop times and also the UTM coordinates of each location This file can then be edited by the user An example with 2 sites and 4species including Unknown is as follows Note the start and stop year month and day YMD were defaulted and could be edited if any are known Fig 3 P Input Notepad File Edit Format Yiew Help KOFA TRAIL CAMERA DATA 3 Start ymd Stop ymd UTME W UTHN S Kofa0l 9999 99 99 0000 00 00 O00000 0000000 KofaO3 9999 99 99 0000 00 00 000000 90000000 Kofta0sd 9999 99 99 0000 00 00 000000 9000000 6 bobcat coyote bighorn sheep gray fox mountain lion mule deer Figure 3 The file nput txt is automatically produced by the data creation program The start and stop dates and UTM co ordinates appear as place holders for each location that can be edited or remain unchanged if they are unknown Any species and locations can be deleted fro
7. ox click on the sign to the right of the box and in the Find box enter and then in the Replace box enter another space Repeat this for all characters other than numbers This replaces all the non number characters with a space The names of all the files appear as yyyy mm dd hr mn sc jpg or JPG 6 Click on Preview on the upper right of the ReNamer box and the new names should appear If the file label does not appear as yyyy mm dd hr mn sc you might need to add a rule to delete a few more characters or add a space 7 To the right of Preview click on the green Rename right arrow and the files are relabeled and saved 8 From the top menu list select Presets save as and then give your rule set a name like MyRules You can then use the rules again without re entering them ei ReNamer by den4b File Settings Presets Help 2 Add Files 35 Add Folders gt SY Preview Hia Add Remove Up Down Rule Statement 1 Delete Delete from Position 1 until the End skip extension 2 Insert Insert SEXIF_Date as Prefix 3 Replace Replace all with with skip extension lt 2 oa ee E Files F Fiters Export Options State Name New Name vV IMG_1700 JPG 2010 04 04 14 18 19 JPG Figure 2 A file has been placed into ReNamer three rules have been added and the file successfully renamed with the date and time that the image was recorded IIIb Film images Relabel all the file
8. s in the temporary folder by hand with the date and time the image was recorded Unfortunately for film images this step must be done by hand since the year and month are inferred and the date and time are imprinted on the image Subsequent steps are the same IV For each image file identify the species count the number of individuals of each species recorded and store the file in the proper location species number of individuals folder Open each relabeled image file in the temporary folder identify the species recorded count the number of individuals and move the file to the proper location species number of individuals folder In the event that two or more species are recorded store a copy for each species in the proper species number of individuals folder VI Return to step II above until all camera traps have been visited and images processed Note that at no time was a user required to enter data by hand Also if a digital image was manipulated and subsequently saved it could have lost the original EXIF tag which indicates the date and time that the image was actually taken DATA CREATION AND ANALYSIS I Data creation Creation of AllFoldersFiles txt Open the command window the black window where commands are typed by going to Start Program Accessories Command Prompt Use the chdir command to change directories to the folder that contains all the location folders for example chdir C Site In the exa
9. sily created as well
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