iTag User Manual
Contents
1. 7 KEY REFERENCES Note A sign indicates that both keys mouse strokes have to be performed simultaneously LMB RMB indicates a left right mouse button click 7 1 SESSION SETUP Key Control N F1 Control O Control Q 7 2 MAIN INTERFACE Key Control S F9 LMB Control Q 1 through 9 RMB Shift RMB Alt RMB Ctrl RMB x LMB drag mouse w or lt arrow key left Function Start a new session Display help page Load session resume previously saved session Exit iTag Function Save the current session Switch general panel on off On panel image navigate image End session Select category number of categories depends on session setup Increase tag size display size Decrease tag size display size Add tag Add modified tag shift modifier Add modified tag a t modifier Add modified tag c r modifier Enter eraser mode right click near tag to remove tag In main interface image Navigate image Go to previous image q or gt arrow key right m FT 7 2 1 MAGNIFIER MODE Key g u S Mouse Wheel up down Go to next image Switch magnifier mode on off Display help page Function Switch solarized mode on off Switch equalized histogram on off Switch inverted image on off Switch auto contrast on off Switch posterize filter on off Switch unsharp filter on off Switch smart sharpen filter on off Zoom in out 8 FAQ Q Is there2. Added output per image Added options to modify number of categories and modifier names Added overview panel displaying session summary All basic functions adding and removing tags present 5 RESTRICTIONS e iTag uses Tkinter for all GUI elements a graphical window manager not at all suited for image display and modification A possible port to more potent environments such as WinAPI may improve performance in future releases e While we regard the user interface to be ok that sentiment may not necessarily apply to all users We encourage you to submit any suggestions to the authors e The manual constitutes awork in progress andis far from being comprehensive e Tag will read all EXIF data stored within the image files it will also replace any unavailable field with None values If your camera saves EXIF info in a version non compliant to EXIF 2 1 or below please contact the authors e Image display in python is using up a lot of memory you will encounter problems when trying to load images that exceed 10000 x 10000 pixels Reduce image size if possible 6 USING THE SOFTWARE 6 1 PREPARING YOUR IMAGES In orderto get the most out of iTag youshould organize your files in folders Since it is very difficult to implement Unicode file browsing in Tag pathnames may only contain ASCII characters i e a pathname like C users Sacha Surveys 2014_09_11 Fifth Leg would be ok whereas C users Sacha Surveys 2014_09_11 ftinfte Ru
3. ITAG Image tagging Software Version 0 6 0 5 Authors Sacha Viquerat amp Abbo van Neer Source code written by Sacha Viquerat Maintainer Sacha Viquerat Maintainer email itag biology at yahoo com Lizenz GPL Document Save Date 02 01 2015 15 32 Word Count 3936 1 CONTENTS 2 Ambitions OF ITAG ci AA AAA AAA A Es 3 LICENSE and COpynght NOti CO ii a A a 4 Version History Major releases oooccccccoocnnncnnonnnononononononannnnnoncnnnnnonnnnonnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnonnnos 5 RESTACHON Silla it liada 6 Using the Oi a 6 1 PREPARING YOUR IMAGES oocccccncnnicicicininininininononononononononononononononononononononononononononinininanininenes 8 6 2 SAMPLE SESSION sissscccsoiver eacsscepenvetedacdesvccccesevapevavsiscselesvagetarsugenvcyedavedah e 9 6 2 1 SETTING UP A NEW SESSION coooococococoncnonononononononcnnononononononononono no nono nono no nananananananananas 9 6 2 2 RESUMING A PREVIOUSLY SAVED SESSION ooocccccncconononononononininnnnnnnnnnnnnnncnnnnnonononos 10 A A CE A O aa ca sda AEEA LEA EAE OERE EA snes tedeasaeceaneeaa 11 6 3 1 MOVING AROUND THE IMAGE cccccececececeeeceeeecececececececececececeeeceeesecaeaeasanaeaeas 13 6 3 2 TAGGING OBJECTS AA ai 13 6 3 3 TAG MODIFIERS ii ia iia wa Kaa AE at 14 6 3 4 REMOVINGA TAG E kaniki cases c ecs hig casdeaeth cdeteca ecscebanecenacacees 14 6 3 5 MAGNIFIER MODE cave iii swa tetr KIKE caveds sedan eshacedeeadeneibaeardiacabaceoreateneuecoacess 15
4. 6 3 6 THE GENERAL PANEL iisi 15 6 3 7 SAVING THESESSI Ni aug ien Erener EAE oR E enia Eei KE Eaa ANART 15 6 4 ENDING THE SESSION isis 16 6 4 1 COLUMNS TO PROCESS naiean nea eaoaai cita 16 6 4 2 PROCESS IMAGES iii de 16 6 4 3 CREATE ESVIFILES 00 tds E E 16 6 4 4 CREATE GOOGLE EARTH KML FILES e ecceccceeeeeeeeeeennecececeeeeeeeesnaeeeseeseneeeees 16 6 4 5 CREATE SO FALE ii aay a ra eraan Ra ia 16 6 5 THE DOWNLOADABLE SAMPLE SESSION ccececeeecececeeeceeececececececececececececeeeeecesaeaeananaeaeas 17 7 KEV felere nEs Css io A O seats 18 Lal SESSION SETUP A din cde aah akali 18 732 MAINI NE RA CE cee an ara O ai 18 7 2 1 MAGNIFIER MODE wi idad a 19 8 Alia Aia 2 AMBITIONS OFITAG iTag has been designed at the nstitute for Terrestrialand Aquatic Wildlife Research ITAW Werftstr 6 in 25761 B sum Germany for researchers that rely on photographic census techniques of animals that are hard to detect via image recognition algorithms and was originally developed for counting grey seals in the German Wadden Sea during March 2013 It has since then been further expanded and has now reached beta status Tag allows users to define up to 9 different categories and name them accordingly In addition 4 modifiers are available to further increase the options during a tagging session Option files can be saved to accommodateto different survey setups Users are able to load a series of images into a session and add
5. Maps e Info panel Toggles display of an additional panel containing the summary of the session 6 3 7 SAVING THE SESSION At any time you can select Save Session Ctrl S by clicking File gt Save Session Ctrl S or simply hit ctrl S In orderto save your current session in asingle file named using your username and the lt TiD suffix You can resume from this file any time you want to 6 4 ENDING THE SESSION Once you have tagged all the animals and are satisfied with the tags you can click on End Session Ctrl Q or press control Q to display a save dialog and trigger the processing of the tagged images As when saving in during a session a single file ending on TiD will be generated allowing you to resume review your choices anytime Within the Output Options window you will then be presented with various output options described in detail below 6 4 1 COLUMNS TO PROCESS Youcan select the categories modifiers combinations you want to see in the summary by either clicking on the corresponding check button to select or deselect a modifier category combination or by simply clicking on the modifier name to unselect select a complete modifier Note This only applies to the summary table The detailed table and the sqlite database will not be affected by this decision 6 4 2 PROCESS IMAGES By checking this value tagged images will be produced within the images subfolder ofthe output directory Pe
6. tags on objects on these images within previously defined categories and modifiers Upon ending the session result files are produced including if provided by the EXIF data the GPS information for each picture the number of objects in each category and a detailed result file that describes each individual object In addition youcan optto haveall images that were tagged saved as well as a legend in a graphical and in a spreadsheet format A sqlite compatible file that includes all the spreadsheet data and can be viewed with SQLite browsers is produced All outputis written into a folder named after the user created below the image directory The user can also save the current session and resume later on 3 LICENSE AND COPYRIGHT NOTICE Tag is open source under LGPL due to the PIL Library Copyright 1997 2011 by Secret Labs AB and Copyright 1995 2011 by Fredrik Lundh and may be freely distributed as longas the authors of the program are properly cited information on howto cite will be made available as soon as possible iTag may not be changed in parts or as a whole without previous acknowledgement by the authors themselves 4 VERSION HISTORY MAJOR RELEASES 0 6 0 5 0 4 0 3 0 2 0 1 Complete UI overhaul Added output Options Added new Panel SQLite backend replaces old storage engine thus improving speed and flexibility Options can now be saved and restored Added new magnifier function and graphics filter
7. figure out When have found out what causes this flicker will have it fixed Q Where is full screen mode A For reasons that cannot disclose without losing my sanity fullscreen just doesn t seem to work when there is a menu Maximizing the window offers basically the samespace for the main window Q would like to see some features that find useful where are they A Well as long as they are only living inside of your head there will be no change contact me through sourceforge or itag biology yahoo com and make your suggestions and ideas heard
8. UP A NEW SESSION Upon openingiTag you will encounter the start page If you wish to setting up a new session you ll need to go to New Session Ctrl N first by either clicking on File gt NewSession Ctrl N or by pressing ctrl N was Tag 0 6 File View About x A newsession wizard will open which will guide you through your session setup The session wizard loads the default settings from disk however you can always specify a previously saved option file and later define this as your new default file On the first slide you will be prompted to enter your username Characters that are not allowed will not be displayed The usernamein combination with the information from the photographs will then be used to organize the output on your computer Additionally you can enter up to 9 generic parameters that could describe the specifics of your survey e g the type of vessel you used the weather conditions etc Note while theses parameters will be saved upon ending the session they will not appear in any table The export of a session table containing these info is still under construction The next slide will prompt you to specify the image directory You can click on Choose Directory and select the folder that contains your images Note you should create a folder such as one folder per survey day and put all the images as JPG files or BMP into that folder iTag will not parse subfolders and will not identify dupli
9. a limitation to the number of Images can load the number of tags can create A In theory there is However the number depends on the amount of ram you possess and will exceed a couple million tags a hundred million images on any PC with 2 gb or more RAM The speed when deleting items may be reduced significantly after a couple hundred thousand tags orso Q have an old save but the images are gone Do have to redo everything A Usually iTag will ask for a new directory when encountering missing files Even though there is no clear indication onscreen iTag is basically in Recovery mode when no new file location is supplied would recommend ending the session and unchecking the export images option that way you should get the database file as long as your tag data is present Version 0 6 1 will clearly identify Recovery mode as such on the main window and lead the user to possible repair solutions untilthen use the hack described above Q Tag fails to load images even though know that have provided the right location A You should check for bad characters in your directory and filenames Bad characters are special characters like 6 or This is usually the most common reason why any file load operation may fail However in 0 6 1 this will hopefully have been fixed Q Sometimes there is a smaller widow visible before another window with content opens Is something wrong A No It s just something can t
10. ame TiD Dateiname no Dateityp all files 7 7 bd The default file ending for Tag session files is TiD as shown in the image above Once you have selected the session file Tag will load the session and you will be able to resume the session In case thatyou load up a Save from a previous Version before 0 6 Tag will attemptto automatically recover that session transfer the save data into the new format and create a backup of the old save adding a bu tothe file suffix e g sam TiD_bu in aboveimageis the backup of the old version save In case that the folder saved within the save file does not exist anymore Tag will prompt you to select the new location of the folder If then found iTag will compare the content of that folder with the images previously saved and warn you in case of missing images As long as at least one image in the saved file was found in the new folder Tag will open the session If any file is missing Tag will warn you about the number of missing files and their respective filenames If none of the previous files can be found iTag will ask you if you would like to try a data dump of the tag data if available In this case Tag will try to export the tag data into a sqlite file within the save file s folder and if desired the samecsv tables as during the end of a session see also 6 4 3 experimental feature 6 3 MAIN INTERFACE Upon loading the first image you
11. are presented with the main interface window showing the first image File View About RE a Category filename P1020867 Large JPG 118 Objects 0 Username Sacha The display of the Menu bar has now changed The view Menu is nowaccessible which includes the options e ShowGeneralPanel F9 toggles a panel displaying various information on the current image see 6 3 6 Also the Options Menu is now accessible offering the following settings e hide all tags toggles the display of all tags currently visible on the image on off Note You cannot add or remove tags while tags are hidden from view e suppress warnings toggles warnings for duplicate tags on or off The warnings get reset when you change images e increase tagsize increases the displayed tag size e decrease tagsize decreases the displayed tag size Within the file menu the following items are available e Save Session Ctr S Save your current session in order to have a well earned break from clicking e End Session A t Q Ends the current session and if any tags had been placed asks the user whether the session should be saved The next part of the window displays a status bar which shows the currently selected category any message produced by the software the current filename of the image in square brackets the file number total number of files the objects tagged so far and the current user name There are also cont
12. atabase that uses the SQL standard feature is currently deactivated 6 5 THE DOWNLOADABLE SAMPLE SESSION Youcan obtain a sample Session from the current version s sourceforge directory Instead of going through the whole session setup you can simply load up the sample session provided within the extracted folder by choosing Resume Session Ctri O or by clicking File gt Resume Session Ctrl 0 or by simply hitting ctrl O after Tag has started Selecting the extracted folder you should see a folder called Sample Images Click on the file called Example TiD and confirm by clicking Ok Since this file has been removed from its original folder you will be prompted to specify the new location of the folder If you want to save the new path simply save the session by either ending it or pressing Save Session Ctrl S or by pressing ctrl S After a short intermission the session will be resumed and you can review my session progress As you can see have set up 4 categories my user name is Example and have reassigned the modifier keys from default swimming to flying When you browse through the images by using q w lt left arrow key or gt right arrow key you can see the different images that have been already assigned Feel free to use all the tools at your disposalto review my tagging Note deliberately made some obvious mistakes such as classifying a guy on a bike as unknown bird
13. be removed and then right click near the tag you want to remove iTag will never remove a tag from a category different from the currently selected one 6 3 5 MAGNIFIER MODE As an additional tool you can activate the magnifier tool by pressing the m key This will display a cropped version of the image next to your mouse pointer that you can zoom into using the mouse wheel Note existing tags will NOT be displayed within the magnifying tool In addition youcan add various image filters to the magnifying tool by pressing the appropriate button e g switches on off solarised filter e h switch on off the equalised histogram filter e j switches invert filter on off e k switch on off the autocontrast filter e switches on off posterised filter e u switches on off unsharp filter e s switches on off smart sharpen filter experimental feature 6 3 6 THE GENERAL PANEL Aftertoggling the general panel you willsee a floating window displaying a scaled down version of the current picture Upon left clicking on the panel picture you will quickly panto the selected areaas indicated by the rectangle There are two additional buttons belowthe panel image e Gps panel Toggles display of an additional panel containing the spatial metadata of the current image file if availablein green else displayed in red If the coordinates are displayedin green and you click on the coordinates a browser window will open and display the position on Google
14. cates Upon successfully loading the images from the directory a small summary of the files is displayed within the wizard In the next Wizard slide you can further set up the categories and modifiers that will be available during your session You can define up to 9 different categories and modify the text that is associated with the modifier keys Note If you don t wantto use some of the modifiers just keep them as they are but avoid duplicate modifier names By clicking on the coloured button next to each category you can then pick a colour for the category Tag will warn you if you pick a colour that is very similar to another existing colour but you will still be able to use duplicate colours The last slide will then give you a short summary of your setup and offer you to savethis specific setup as the default session setup excluding the directory name Upon clicking Done your session will start immediately 6 2 2 RESUMINGA PREVIOUSLY SAVED SESSION Once you have a saved session on yourcomputer you can resume at any time by clicking Resume Session Ctrl OY or by clicking File gt Resume Session Ctrl O or by simply pressing ctrl O A file browsing dialog asks you to select a previously saved session Suchen in m7 Tag_Testpics es El L ay Zuletzt besucht 0 Bibliotheken P1020867 Large JPG P1020872b Large P1020910 Large JPG da 9 9 sam TiD sam TiD_bu Usern
15. nde raises an error dueto the umlaut Tag works with jpeg amp bmp Images Tag is case insensitive so any file ending with jpg bmpor any upper lower case version of jpg or bmp will be found Since Tag will need to create Subfolders and write to that particular directory you should also have full read write access to that folder Don t put your image folder anywhere that you don t have access to Tag will create a subfolder with the name of the user and store all results inside that folder including copies of all tagged images iTag will never touch or modify your raw data Ifyour data complies with the EXIF 2 1 or earlier Standard and has geographical data stored these will be read otherwise the corresponding fields default to None It is generally a good idea to sort your data by survey date or whatever is applicable for your specific design Once you have putall yourimages into one folder you can then open up Tag and continue with setting up the session As Python is not very good at handling large images there is a built in limit to the maximum allowed width or height of an image The default maximum image size set to a limit of 10 000 pixels You can override that setting by supplying Tag with start up options Right Click on your shortcut and change the target from itag exe to itag exe m5000 setting the maximum side of images to 5 000 pixels for example 6 2 SAMPLE SESSION 6 2 1 SETTING
16. r default Tag will create scaled down jpg image files for each image containing the tags you ve placed for future reference and archival Also a legend image is produced 6 4 3 CREATE CSV FILES A databasefile will always be produced However you can also create spreadsheets of each databasetable Per default Tag will create multiple colon separated files in a subfolder called Tables using a point decimal separator If enabled Tag will producea detailed table that contains info on each individual tag and an aggregated summary table that collates tags on each image You can choose the column separator via the dropdown Menu Note The summary file will only contain the previously selected combinations of modifiers and categories 6 4 4 CREATE GOOGLE EARTH KML FILES You can toggle the creation of a KML Layer that you can display within Google Earth If you choseto export your tagged images all images that had been tagged and that included spatial information are displayed upon loading the KML file into Google Earth Note The KML file does not include the Images it s just referencing them As long as the images are within the Images subfolder the images will be displayed correctly If you share the KML file without providing the images the images will not display properly within Google Earth 6 4 5 CREATE SQL FILE Tag will try to create a native SQL dump of the database You can import this file into any existing d
17. rols that allow the user to quickly access pictures by either browsing to the beginning of pictures lt lt the previous picture lt the next picture gt or the last picture gt gt In addition youcan simply providethe image number you want to see and click Goto The largest portion of the screen is reserved for the actual image display To the bottom and the right of the image are rulers in case the images are larger than the available screen space The bottom gives youa short overview of the available categories in ascending order 1 through 9 and their respective colours 6 3 1 MOVING AROUND THE IMAGE Panning the image is straightforward simply left click and hold the mouse button then move the mouse around Additionally to displaying various info on the current session the General Panel activated by either clicking the button Show Genera Panel F9 or by hitting the F9 key you can simply left click anywhere in the preview picture to jump straight to that position 6 3 2 TAGGING OBJECTS Tagging objects is as straightforward as selecting a category by pressing 1 through 9 depending onthe number of categories you have defined or clicking the category buttons at the bottom of the screen positioning the mouse abovethe target object and right clicking the mouse Tag will display a warning window when you place a new tag very close to an existing one however the tag will still be placed By clicking View gt
18. supress warnings allsuch warnings are suppress until the image changes ilename 0104 DSC 3042 Large JPG 418 Objects 1 Username Sacha 6 3 3 TAG MODIFIERS When right clicking youcan use modifiers with each tag as defined in the session options at the beginning Per default these are e Nomodifier adult e shift Key juvenile e ctri Key swimming e alt Key dead In the example below you can see that we have tagged an adult grey seal y e yellow being the colour for grey seals and the circle being the symbol for adult animals Additionally by holding down the shift key while right clicking the animal we ve also tagged a juvenile harbour seal green square green the colour for harbour seals and square as symbol for juvenile animals The use of these symbols is strict and is as follows e circles adults no modifier e squares juveniles shift modifier e hollow squares swimming ctr modifier e horizontal bar dead alt modifier cha filename _DS File View About Category MEE filename _DSC5705 JPG 618 Objects 3 Username Sacha lt lt lt cele gt gt gt Halichoerus Grvpus ieee Jueni S 6 3 4 REMOVING ATAG If you want to remove a tag press x and you will enter erase mode This is also indicated by a red ERASE notification in front of the category identifier within the status bar In order to erase a tag you llhaveto select the same category as the tag to
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