//LINESCANPANEL loads linescan images acquired with PrairieView and creates linescan profiles with IGOR PRO.
//
//INSTALLATION:
//Copy the Linescanpanel.ipf file in Igor Procedure folder in the Wavemetrics folder. Restrat Igor Pro. The Linescan panel can be launched
//from the Macro menu
//
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//It is recommended to load each linescan folder in a separate data folder, then to merge folders as needed once profiles have been calculated
//The Load images box in the LineScan Analysis panel calls the function Loadlinescanimages()
//Select the prairieview xml config file and load tiffs images of corresponding channel. Rename and splits in groups depending similar to neuromatic groups
// Loaded tiff are renamed as: list_group_filesuffix_Channel_index. Then creates a stack of each tiff and group, named Stack_channel_filesuffix_group
//The Analyze images box in the LineScan Analysis panel calls the function CalcLSprofiles()
// this allows to select the position of the vertical profile to create (using Igor Imagelineprofile function)
//output waves are named profile_channel_filesuffix_indexofprofile_group_indexofwave
// to display position of calculated profile on image select image and appendtograph lineprofy vs lineprofx in subfolder infoprof...
//-------------
//By Alex Tran-Van-Minh (alexandra.tran.van.minh@gmail.com)
//-------------

//02-JAN-2013: Current PV version (4.3.2.13) does already includes zoom in pixel size. Other versions (e.g. 4.2.1.17) required
//dividing by optical zoom to get real pixel size
//Background subtraction checkbox for subtraction from user-entered value or profile.
//Output wave (background subtracted) is named c_profile_channel_filesuffix_indexofprofile_group_indexofwave and is the one plotted

//13-MAR-2013:
//1. Corrected image loading to load and display images properly even when there are no repetitions
//2. All loaded waves are now scaled (including unclassified waves "ls_...")
//3. All profile waves called "profile_Chx_profilenumber_groupnumber_..." or "c_profile_Chx_profilenumber_groupnumber_..." are now INDIVIDUAL waves,
// the stack of these waves are now contained in "st_Chx_profilenumber_groupnumber" or "c_st_Chx_profilenumber_groupnumber"
//4. Fixed "rename error" bug that was appearing when creating multiple profiles with background subtraction:
//now unique names are created for background waves each time the "calculate" button is used. Background waves are named bg_channel_indexofprofile_group_indexofwave,
//the average value of each of these background waves is used to subtract from the corresponding profile from the same image.

//27-APR-2013:
//Add option for 4 channels selection and addition of profiles from 2 channels.

//06-MAY-2013:
//Add option for adding images and making a deltaF/F image from one of the 2d image in current folder.

//08-MAY-2013:
//Add background subtraction when making a deltaF/F image and filtering of deltaF/F image.

//22-JAN-2014:
//Fixed Make error when using user-entered value for background subtraction.

//05-MAR-2014:
//Fixed Background subtraction error from profile when only one image is in the stack
//Background profiles are now scaled like loaded image

//11-APR-2014:
//1/ Added Button "profile from all images" : calls function calcall2d()
//this calculates (using values from the panel) profiles (and background subtracts) for ALL 2d images contained
//in current data folder, even if they were not loaded with the panel
//the calculated profiles are 1d waves named as "prof_+name of wave+index"
//if applicable the background corrected profiles are named as "c_prof+name of wave+index"
//2/ Redesigned panel
//3/ added dropped-down menu to do 4 basic operations on profiles

//05-JUN-2014:
//From version 5.1 on PrairieView includes ".ome" suffix in their file names. Modified loading procedure accordingly.

//13-AUG-2014:
//Adjusted reading of PrairieView .xml  file in Loadlinescanimages() as order and name of some parameters changed in 5.2 version