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software:fiji_mvr [2015/06/09 22:01]
Jon Daniels 		software:fiji_mvr [2019/07/27 18:19] (current)
Jon Daniels [Fiji MVR scripts]
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 See homepage at [[http://fiji.sc/Multiview-Reconstruction]]. See homepage at [[http://fiji.sc/Multiview-Reconstruction]].
  
-As of April 2015 the MVR plugin allows for direct importing of Micro-Manager datasets, rendering the ASIdiSPIM plugin's export function obsolete for MVR analysis.+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>

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