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--- biac:analysis:roi_et [2011/04/25 20:06] – petty
+++ biac:analysis:roi_et [2011/04/25 20:32] – [PupilOmetry in Matlab] petty
@@ Line 317: / Line 317: @@
 ET_filename = '11436_run4_pre.txt';
-%%Path to your actual images
+%%Path to your actual images, an array if multiple locations possible
-imgPath = '/home/petty/net/hill/data/Dichter/AutReg.01/Stimuli/AutReg.01/';
+imgPath = {'//hill/data/Dichter/AutReg.01/Stimuli/AutReg.01/','//hill/data/Dichter/AutReg.01/Notes/SubjectPics/PS06'};
 %%Image attribute name from behavioral XML [value=name"THIS"]
@@ Line 342: / Line 342: @@
 </file>
+The output will look like this:
+{{:biac:analysis:plotter_example.png?800|}}
+Hits are green circles inside the ROI, misses are red Xs outside.  Since **linesOn** was turned on, there is a yellow gaze path from one point to the next.  If **withPause** was turned on, there would be a slight pause between each point.
+Currently, to move to the next image in the XML, just close the current figure.  If you want to stop the redrawing, "ctrl + c" inside matlab to kill the loop.  There are some updates planned to the controls.
+Also, if you just have the behavioral XML and preprocessed ET data, you can run the function **ET_plot** instead.  This will look at all images and ignore any ROIs, otherwise and ROI must be present for the image to get plotted.
+===== PupilOmetry in Matlab =====
+A matlab script based on pupilometry steps from {{:biac:analysis:2006_urry_neuro.pdf|Urry et al}} can be run to denoise pupil dilation data found in the preprocessed viewpoint WKS or cigal eyetracking files.
+The result will be a pupilchange element added to your behavioral+ROI XML.
+This example node has all previous steps run, pupil gotten smaller by 2.9% :
+<HTML>
+   <event type="image" units="sec">
+      <onset>17.141</onset>
+      <duration>4</duration>
+      <value name="imgName">HAI_21.bmp</value>
+      <value name="regType">look</value>
+      <value name="trialType">HAI</value>
+      <value name="response">2</value>
+      <value name="RT">1212</value>
+      <roi type="block">
+         <name>object</name>
+         <origin>260 258</origin>
+         <size>500 205</size>
+         <units>pixels</units>
+         <value name="hits">10</value>
+         <value name="hit_percent">8.47</value>
+      </roi>
+      <value name="samples">118</value>
+      <value name="pupilChange">-0.029751</value>
+   </event>
+</HTML>
+The pupilOmetry function can be found: \\Munin\Data\Programs\Users_Scripts\petty\matlab\ or just added to your path.
+This example script will run pupilOmetry on preprocessed eyetracking data and create the new XML with the added element:
+<file matlab run_pupilOmetry_sample.m>
+%% add BIAC tools if needed
+%run /usr/local/packages/MATLAB/BIAC/startup.m
+%% add path to pupilOmetry function
+%addpath /home/petty/net/munin/data/Programs/User_Scripts/petty/matlab/
+%addpath \\Munin\Data\Programs\User_Scripts\petty\matlab\
+%%input XML ( merged behavioral + ROI )
+xmlName = '/home/petty/eyetracking/autreg/11436_run04_roiHits.xml';
+%%preprocessed eyetracking output
+ET_filename = '/home/petty/net/hill/data/Dichter/AutReg.01/Data/Eyetracking/subj1234_run1_pre.wks';
+%%the attribute to match images with from the inputXML
+imgAttr = 'imgName';
+%%output name of the XML with added pupilOmetry data. will be everything from input + pupilchange
+outName = '/home/petty/eyetracking/autreg/11436_cigal_pupil2.xml';
+%%show the denoising plots
+plot = 0; %1 to show, 0 to skip
+%%run the actual function
+pupilOmetry(xmlName,ET_filename,imgAttr,outName,plot);
+</file>