Add calculations for perimter and remove exg.

* src/manualRosetteDetect/analyzeImgRosette.m(analyzeImgRosette): Call
segmentRosette_mask method. It was the one that showed the most promise.
(analyzeImgRosette): calculate perimter by calling new method calc_perimeter.
(calc_perimeter): New method that counts the pixels in the perimeter image of
the rosette.
* src/manualRosetteDetect/rosettedetect_gui.m(populate_rosette_struct_from_lines):
Initialize area, perim, gcc and diam as matlab NaN.
(vector_Callback): Add perim to the vector generation logic.
Write to output file on every iteration.

* src/manualRosetteDetect/rosettedetect_gui.m(vector_Callback): Save the
accumulated vectors on every iteration. This will give us the chance to see
the progress.
Cleaning the project path

These files have not obvious general functionality.
* temp.m: Remove File.
* testROI.m: Likewise.
* workFlow.m: Likewise.
Remove files generated from source.

These files were generated as documentation from source.
* html/configProject.html: Remove File.
* html/createEachCamConfig.html: Likewise.
* html/workFlow.html: Likewise.
Put files in "helper functions" dir into matlib dir.

Directories should not have spaces. Additionally all files under what was
"helper functions" were ment to support matlab code. We keep them in library
directory called matlib for now.
*helper functions/addLines.m -> src/matlib/addLines.m
*helper functions/cleanDir.m -> src/matlib/cleanDir.m
*helper functions/colorCorrect.m -> src/matlib/colorCorrect.m
*helper functions/cropIm.m -> src/matlib/cropIm.m
*helper functions/cropPots.m -> src/matlib/cropPots.m
*helper functions/findObjectCenter.m -> src/matlib/findObjectCenter.m
*helper functions/fixColor.m -> src/matlib/fixColor.m
*helper functions/getColFromHead.m -> src/matlib/getColFromHead.m
*helper functions/getColorCheckerInfo.m -> src/matlib/getColorCheckerInfo.m
*helper functions/getColorROIs.m -> src/matlib/getColorROIs.m
*helper functions/getDataDrive.m -> src/matlib/getDataDrive.m
*helper functions/getDirList.m -> src/matlib/getDirList.m
*helper functions/getFileList.m -> src/matlib/getFileList.m
*helper functions/getGreen.m -> src/matlib/getGreen.m
*helper functions/getImageInfo.m -> src/matlib/getImageInfo.m
*helper functions/getPotNum.m -> src/matlib/getPotNum.m
*helper functions/getProjectInfo.m -> src/matlib/getProjectInfo.m
*helper functions/getROI.m -> src/matlib/getROI.m
*helper functions/graphRGB.m -> src/matlib/graphRGB.m
*helper functions/lensdistort.m -> src/matlib/lensdistort.m
*helper functions/loadFileList.m -> src/matlib/loadFileList.m
*helper functions/loadPlantDB.m -> src/matlib/loadPlantDB.m
*helper functions/loadSingleIm.m -> src/matlib/loadSingleIm.m
*helper functions/makeLab.m -> src/matlib/makeLab.m
*helper functions/padImage.m -> src/matlib/padImage.m
*helper functions/parseTSFilename.m -> src/matlib/parseTSFilename.m
*helper functions/pcName.m -> src/matlib/pcName.m
*helper functions/plotColors.m -> src/matlib/plotColors.m
*helper functions/quickMov.m -> src/matlib/quickMov.m
*helper functions/quickMovBAK.m -> src/matlib/quickMovBAK.m
*helper functions/reloadCamConfig.m -> src/matlib/reloadCamConfig.m
*helper functions/removeBackDSLR.m -> src/matlib/removeBackDSLR.m
*helper functions/removeBackIP.m -> src/matlib/removeBackIP.m
*helper functions/reportTime.m -> src/matlib/reportTime.m
*helper functions/saveCamSettings.m -> src/matlib/saveCamSettings.m
*helper functions/saveFullIms.m -> src/matlib/saveFullIms.m
*helper functions/savePotIms.m -> src/matlib/savePotIms.m
*helper functions/showPot.m -> src/matlib/showPot.m
*helper functions/smallestEnclosingCircle.m -> src/matlib/smallestEnclosingCircle.m
*helper functions/sortBySize.m -> src/matlib/sortBySize.m
*helper functions/summarizeData.m -> src/matlib/summarizeData.m
*helper functions/unwarp.m -> src/matlib/unwarp.m
Moved legacy code out of the way into src/legacy

It will eventually be removed. I put it there just in case someone misses it.
This is the log of all the movements that were made.
*config.mat -> src/legacy/config.mat
*config/16-Jul-2013-14H07_BVZ0012-expInfo-settings.mat -> src/legacy/config/16-Jul-2013-14H07_BVZ0012-expInfo-settings.mat
*config/16-Sep-2013-15H09_BVZ0018-expInfo-settings.mat -> src/legacy/config/16-Sep-2013-15H09_BVZ0018-expInfo-settings.mat
*config/16-Sept-2013-15H09_BVZ0018-CAN04-settings.mat -> src/legacy/config/16-Sept-2013-15H09_BVZ0018-CAN04-settings.mat
*config/19-Sep-2013-21H09_BVZ0012-expInfo-settings.mat -> src/legacy/config/19-Sep-2013-21H09_BVZ0012-expInfo-settings.mat
*config/19-Sep-2013-22H09_BVZ0012-expInfo-settings.mat -> src/legacy/config/19-Sep-2013-22H09_BVZ0012-expInfo-settings.mat
*config/23-Sep-2013-19H09_BVZ0018-CAN05-settings.mat -> src/legacy/config/23-Sep-2013-19H09_BVZ0018-CAN05-settings.mat
*config/23-Sep-2013-19H09_BVZ0018-expInfo-settings.mat -> src/legacy/config/23-Sep-2013-19H09_BVZ0018-expInfo-settings.mat
*config/24-Sep-2013-20H09_BVZ0018-CAN05-settings.mat -> src/legacy/config/24-Sep-2013-20H09_BVZ0018-CAN05-settings.mat
*config/24-Sep-2013-20H09_BVZ0018-expInfo-settings.mat -> src/legacy/config/24-Sep-2013-20H09_BVZ0018-expInfo-settings.mat
*config/27-Jun-2013-17H06-BVZ0012-camSettings.mat -> src/legacy/config/27-Jun-2013-17H06-BVZ0012-camSettings.mat
*config/BVZ0012-CAN01-settings.mat -> src/legacy/config/BVZ0012-CAN01-settings.mat
*config/BVZ0012-CAN02-settings.mat -> src/legacy/config/BVZ0012-CAN02-settings.mat
*config/BVZ0012-CAN03-settings.mat -> src/legacy/config/BVZ0012-CAN03-settings.mat
*config/BVZ0012-CAN05-settings.mat -> src/legacy/config/BVZ0012-CAN05-settings.mat
*config/BVZ0012-CAN06-settings.mat -> src/legacy/config/BVZ0012-CAN06-settings.mat
*config/BVZ0018-CAN05-settings.mat -> src/legacy/config/BVZ0018-CAN05-settings.mat
*config/backup/11-Jul-2013-22H07_BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/11-Jul-2013-22H07_BVZ0012-expInfo-settings.mat
*config/backup/12-Jul-2013-10H07_BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/12-Jul-2013-10H07_BVZ0012-expInfo-settings.mat
*config/backup/12-Jul-2013-11H07_BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/12-Jul-2013-11H07_BVZ0012-expInfo-settings.mat
*config/backup/12-Jul-2013-12H07_BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/12-Jul-2013-12H07_BVZ0012-expInfo-settings.mat
*config/backup/19-Jun-2013-19H06-BVZ0012-camSettings.mat -> src/legacy/config/backup/19-Jun-2013-19H06-BVZ0012-camSettings.mat
*config/backup/19-Jun-2013-20H06-BVZ0012-camSettings.mat -> src/legacy/config/backup/19-Jun-2013-20H06-BVZ0012-camSettings.mat
*config/backup/27-Jun-2013-13H06-BVZ0012-camSettings.mat -> src/legacy/config/backup/27-Jun-2013-13H06-BVZ0012-camSettings.mat
*config/backup/27-Jun-2013-15H06-BVZ0012-camSettings.mat -> src/legacy/config/backup/27-Jun-2013-15H06-BVZ0012-camSettings.mat
*config/backup/27-Jun-2013-15H06_BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/27-Jun-2013-15H06_BVZ0012-expInfo-settings.mat
*config/backup/27-Jun-2013-17H06_BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/27-Jun-2013-17H06_BVZ0012-expInfo-settings.mat
*config/backup/BVZ0012-CAN01-settings.mat -> src/legacy/config/backup/BVZ0012-CAN01-settings.mat
*config/backup/BVZ0012-CAN02-settings.mat -> src/legacy/config/backup/BVZ0012-CAN02-settings.mat
*config/backup/BVZ0012-CAN03-settings.mat -> src/legacy/config/backup/BVZ0012-CAN03-settings.mat
*config/backup/BVZ0012-CAN05-settings.mat -> src/legacy/config/backup/BVZ0012-CAN05-settings.mat
*config/backup/BVZ0012-CAN06-settings.mat -> src/legacy/config/backup/BVZ0012-CAN06-settings.mat
*config/backup/BVZ0012-expInfo-settings.mat -> src/legacy/config/backup/BVZ0012-expInfo-settings.mat
*config/expInfo with noon images/12-Jul-2013-13H07_BVZ0012-expInfo-settings.mat -> src/legacy/config/expInfo with noon images/12-Jul-2013-13H07_BVZ0012-expInfo-settings.mat
*configProject.m -> src/legacy/configProject.m
*createEachCamConfig.m -> src/legacy/createEachCamConfig.m
*processAll.m -> src/legacy/processAll.m
*setPathVars.m -> src/legacy/setPathVars.m
Test directory will house automatic tests.

What was in testfiles were local tests. We will replace these with automated
verification tests for our code. We add images that will serve this purpose.
*testfiles/loadSomeIms.m: Removed file and directory.
*testfiles/test.m: Likewise.
*testfiles/test2.m: Likewise.
*testfiles/testing.m: Likewise.
*README: New file explaining vision of project
Add logic to handle directories recursively

* src/manualRosetteDetect/rosettedetect_gui.m(imgseries_Callback): Use new
rdir function to get all the jpeg files from directory structure. When we
don't find a directory in the destination, we create it.
* src/manualRosetteDetect/rosettedetect_gui.m(vector_Callback): Likewise, but
there is no need to create a directory.
* src/manualRosetteDetect/rdir.m: new file containing logic for recursively
accessing directories. Downloaded from
http://www.mathworks.com/matlabcentral/fileexchange/32226-recursive-directory-listing-enhanced-rdir
Skip the files that are too small.

* src/manualRosetteDetect/rosettedetect_gui.m(imgseries_Callback): Continue in
the loop when the number of bytes is too small.
* src/manualRosetteDetect/rosettedetect_gui.m(imgseries_Vector): Likewise.
Return image mask instead of different hue.

* src/manualRosetteDetect/analyzeImgRosette.m(analyzeImgRosette): Get the size
from original image and return a mask with the detected rosettes.
Create the feature matrix and the image masks.

* src/manualRosetteDetect/rosettedetect_gui.m(vector_Callback): For the Vector
button, create mask series as well as the feature matrix.
Remove execute permissions for rdir.m