The COO module is designed to digitize landmarks, semilandmarks and outlines on 2D pictures - landmarks type I and II. - landmarks type III. For landmarks depending on other landmarks (which includes SEMILANDMARKS), COO (from CLIC_91) has a special feature allowing quick and accurate manual digitization. See hereunder. - pseudolandmarks for OUTLINES digitization (press the 'OUTLINES' blue button and select the word 'outlines'). ------------------------------------------------- INPUT FILE ------------------------------------------------- A digital picture, preferably in the .gif format. ------------------------------------------------- OUTPUT FILE ------------------------------------------------- 'coord_[date].txt' The 'coord_[date].txt' file is automatically located in the folder containing the digitized images. The complete name of the 'coo' output file always contains the date of the day (for instance 'coord_March14.txt'). The internal format looks like the (simplest) Rohlf's 'TPS' format (the TET module can convert it to the Rohlf's '.nts' format). ------------------------------------------------- MORE OUTPUT FILES ------------------------------------------------- After a digitizing session, when you hit the CANCEl button instead of OPENing another picture file, COO asks you whether you want to convert the 'coord_[date].txt' file into other formats: - 'coord_[date]_format.txt' for raw coordinates true landmarks data (vectorized matrix); - 'coord_[date]_OTL.txt', for coordinates of pseudolandmarks (outline) data; - 'coord_[date]_DB.txt' or 'coord_[date]_OTL_DB.txt': a copy-paste ready format for your database or spreadsheet application. In case of conversion error, close the module, edit the 'coord_[date].txt' output file, and use the TET module for the relevant conversions. Note that for pseudolandmarks, this conversion also creates the 'coord_..._OTL.DTA' file formatted for the EFAw script of J. Rohlf (http://life.bio.sunysb.edu/morph). After a digitizing session containing SEMILANDMARKS (type III landmarks), - 'coord_[date]_SL.txt' raw coordinates of semilandmarks - 'curvepts.txt', the data used by the R geomorph package to identify semilandamrks and flankink landmarks ------------------------------------------------- MORE about OUTPUT FILES - SCALING raw COORDINATES ------------------------------------------------- If you want your coordinates to be adjusted according to the correspondance "pixels / mm", or "pixels / cm", and provided you indicated (at least for the very first image) the correspondance "pixels" and either "mm" or "cm", please use the 'tet' module, calling the '..._DB.txt' file as INPUT. ------------------------------------------------- SEMILANDMARKS (SL) DIGITIZATION PROCEDURE ------------------------------------------------- The semilandmark (SL) digitization procedure requires the preparation of a guide (a kind of comb) - which can be contained in a code, the 'SL code' - that will apply to the image between successive landmarks (LM) and allow easy digitization of SL. See the sequence described below (steps II is performed only once, but has to be repeated when opening a new digitizing session) I. Open the COO module ------- --------- Please digitize the landmarks (NOT the semilandmarks) on your image ------- --------- --------- II Template preparation (three ways) ------- --------- --------- - A - click on the button at the top right, which is a half black, half white button symbolizing a SL (it is called the 'SL button'); - B - select YES, NO or CANCEL on the popup widget YES if you want to use an already existing SL code from within an SL file; just open an existing '..._SL.txt' file and confirm the SL code extracted from the file. Go to step III (note that the SL of your first image will be saved there, the next ones however will be saved in your working folder in the '..._SL.txt' file of the day <- it is a bug) NO if you want to write the SL code manually. This is the FASTEST WAY. You will be asked to enter the SL code. Write it which each symbol, for instance {2 5} {3 4} etc., which means: 5 SL after the LM 2, then 4 SL after the LM3, etc. Go to step III CANCEL and, if not exiting, follow the steps 1 to 7 hereunder: - 1 - keep the CONTROL key pressed and left-click on the starting LM; it is the LM after which you will digitize a set of SL located between the starting LM and the next one; - 2 - click on the "+" button next to the 'SL button' to increase the number of red lines (comb teeth); "-" to decrease it; - 3 - please digitize the set of SL, using the SHIFT button together with a mouse left-click. - 4 - When finished, hit the RETURN key to save the set of SL (semilandmarks) - 5 - Use the same sequence of steps 1to 4 above for the next set of SL, if any (thus, CONTROL CLICK on the starting LM of your choice, then SHIFT CLICK to digitize SL whose numbers have been adjusted in advance with the keys "+" and "-"). - 6 - Hit the DISK ICON button to save the complete template. - 7 - Go to III Note: Within the same digitizing session, step II does not need to be repeated each time you digitize SL according to this template. ------- --------- --------- III Then carry out the digitization session. ------- --------- --------- The procedure is as follows: (1) as for the template, first digitize the true LM (if the option above was "CANCEL", then please start with the image that was used to build the template) (2) hit the SL button, the first part of the template appears, with the relevant number of red lines (2) use SHIFT CLICK to digitize the SL (3) as soon as the last SL of the first part of the template has been collected, the next part of the templates appears (4) as for (2) and (3) Note: CLIC adjusts the shot if you are not exactly on the tooth of the comb. ------- --------- IV. Output files ------- --------- COO produces a file containing only the LM ('..._format.txt') and a file containing only the SL. ("... SL.txt") How to obtain the combined file of SL? - Please open the TET module, - request the LM file ('..._ format.txt'), - ask for the transformation called "INSERT SEMILANDMARKS" - open the file of SL (..._ SL.txt') corresponding to the landmark file ('..._format.txt') - a new, combined file is created ending by '..._SLformat.txt'; this file becomes the input file of MOG. ------- --------- ------------------------------------------------- Files format ------------------------------------------------- Both '..._format.txt' and '..._OTL.txt', as well as all the CLIC data files, have an internal format as follows: - The first row is a free comment, next rows are the data. - The first row is mandatory. - Data (next rows) are organized as a table without headers - Empty rows are allowed, except the first one (see above). - Columns are separated by a tabulation. Exceptions to this CLIC data format are 1. The 'coord_[date].txt' 'coo' output file, having an internal format close to the TPS format. 2. The 'coord_[date]_DB.txt', (or CLIC data base format): there are headers! 3. The 'coord_[date]_SL.txt' format containing the SL, with the name of the images and more than one row by image. 4. The CLIC distance matrix format ('..._MAHAphylip.txt', etc.): except for the first row (the comment), its format depends on the external software to which it is destinated.