===== Fiji MVR (Multiview Reconstruction) =====

This software is for registering and fusing the datasets from two views.  It was originally developed for OpenSPIM-like setups but works well for diSPIM data as well.

See homepage at [[http://fiji.sc/Multiview-Reconstruction]].

As of April 2015 the MVR plugin allows for direct importing of Micro-Manager datasets.  Previously the Micro-Manager plugin's export function was used (it is still required for [[MIPAV GenerateFusion]]).


==== Fiji MVR scripts ====

This script was used during the 2018 EMBO Practical Course for Light sheet microscopy in Dresden to roughly align two views collected on the ct-dSPIM:

<code groovy>

#@File (label="Freshly loaded BDV XML File Location") xml_file

/** 
 *  Simple script to deskew, flip and move a DiSPIM dataset
 *  
 *  Olivier BURRI, Jon Daniels
 *  EMBO Lightsheet Course 2018
 *  
 *  INPUT: XML file which contains two angles named 0 and 90
 *  
 *  This will apply the transformations to the XML file and reopen the multiview applications
 *  
 *  Last modification: August 8 2018
 */
import groovy.util.XmlSlurper
import ij.IJ

def meta = new XmlSlurper().parse( xml_file )
//def size = meta.SpimData.SequenceDescription.ViewSetups.ViewSetup.sizexml_file
def size = meta.SequenceDescription.ViewSetups.ViewSetup.size[0] as String

def dimensions = size.tokenize(" ");
def width  = dimensions[0] as double
def height = dimensions[1] as double
def depth  = dimensions[2] as double

println("Width: "+width)
println("Height: "+height)
println("Depth: "+depth)

def deskew = "1.0, 0.0, -1.0, 0.0, "+
			 "0.0, 1.0, 0.0, 0.0, "+
			 "0.0, 0.0, 1.0, 0.0"

println(deskew)

def flip  =  "0.0, 0.0, -1.0, 0.0, "+
			 "0.0, -1.0, 0.0, 0.0, "+
			 "-1.0, 0.0, 0.0, 0.0"

def trans =  "1.0, 0.0, 0.0, "+(height/2)+", "+
			 "0.0, 1.0, 0.0, "+(width)+", "+
			 "0.0, 0.0, 1.0, "+depth

// Return to calibration only, if necessary
IJ.run("Apply Transformations", "select=["+xml_file.getAbsolutePath()+"] "+
							 "apply_to_angle=[All angles] apply_to_channel=[All channels] apply_to_illumination=[All illuminations] apply_to_tile=[All tiles] apply_to_timepoint=[All Timepoints] "+
							 "transformation=[Identity (no transformation)] "+
							 "apply=[Calibration (removes any existing transforms)] "+ 
							 "same_transformation_for_all_angles");

// Apply deskew to all angles
IJ.run("Apply Transformations", "select=["+xml_file.getAbsolutePath()+"] "+
							 "apply_to_angle=[All angles] apply_to_channel=[All channels] apply_to_illumination=[All illuminations] apply_to_tile=[All tiles] apply_to_timepoint=[All Timepoints] "+
							 "transformation=Affine apply=[Current view transformations (appends to current transforms)] "+
							 "same_transformation_for_all_angles "+
							 "timepoint_0_channel_0_illumination_0_all_angles=["+deskew+"]");

// Apply Flip to angle 90
IJ.run("Apply Transformations", "select=["+xml_file.getAbsolutePath()+"] "+
							 "apply_to_angle=[Single angle (Select from List)] apply_to_channel=[All channels] apply_to_illumination=[All illuminations] apply_to_tile=[All tiles] apply_to_timepoint=[All Timepoints] "+
							 "processing_angle=[angle 90] "+
							 "transformation=Affine apply=[Current view transformations (appends to current transforms)] "+
							 ""+
							 "timepoint_0_channel_0_illumination_0_angle_90=["+flip+"]");
							 
// Aplly Rough translation to angle 90
IJ.run("Apply Transformations", "select=["+xml_file.getAbsolutePath()+"] "+ 
							 "apply_to_angle=[Single angle (Select from List)] apply_to_channel=[All channels] apply_to_illumination=[All illuminations] apply_to_tile=[All tiles] apply_to_timepoint=[All Timepoints] "+
							 "processing_angle=[angle 90] "+
							 "transformation=Affine apply=[Current view transformations (appends to current transforms)] "+
							 ""+
							 "timepoint_0_channel_0_illumination_0_angle_90=["+trans+"]");

// Open MultiView Application
IJ.run("MultiView Reconstruction Application", "select_xml=["+xml_file.getAbsolutePath()+"]");

</code>

This script did some other pre-processing:

<code groovy>


#@File main_folder (label="Main Folder", style="directory")

// Iterate and find all files
import static groovy.io.FileType.FILES
import ij.IJ
import ij.plugin.ChannelSplitter
import ij.io.Opener

import groovyx.gpars.GParsPool


def save_folder = new File(main_folder, "exploded_channels_views")
save_folder.mkdir()


def opener = new Opener()
// Find all files.
def all_files = []
main_folder.eachFile(FILES) { file ->
    if(file.getName().endsWith(".tif") && !file.getName().contains("_1")) {
    	all_files.add(file)
    	//println(file)
    }
}

Collections.reverse(all_files)  // reverse order


//all_files = all_files.take(1)

//GParsPool.withPool(10) {
	//all_files.eachParallel{ file ->
	all_files.each { file ->
	    //def temp_image = opener.openTiff(file.getParent()+File.separator, file.getName())

		println("starting " + file)

	    def temp_image = IJ.openImage(file.getAbsolutePath())

	    def images = ChannelSplitter.split(temp_image)

	    // 0 is ch1 view 1
	    // 1 is ch1 view 2
	    // 2 is ch2 view 1
	    // 3 is ch2 view 2
	    
	    //resave all
	    def image_name = file.name.take(file.name.lastIndexOf('.'))
	    IJ.saveAsTiff(images[0], new File(save_folder, sprintf("%s_Ch%d_Angle%d.tif",image_name, 1, 0)).getAbsolutePath())
	    IJ.saveAsTiff(images[1], new File(save_folder, sprintf("%s_Ch%d_Angle%d.tif",image_name, 1, 90)).getAbsolutePath())
	    IJ.saveAsTiff(images[2], new File(save_folder, sprintf("%s_Ch%d_Angle%d.tif",image_name, 2, 0)).getAbsolutePath())
	    IJ.saveAsTiff(images[3], new File(save_folder, sprintf("%s_Ch%d_Angle%d.tif",image_name, 2, 90)).getAbsolutePath())
	    images.each{it.close()}
	    
	    temp_image.close()	

	    println("finished " + file)
	}
//}

</code>