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software:fiji_mvr [2015/10/07 20:41]
Jon Daniels 		software:fiji_mvr [2019/07/27 18:19] (current)
Jon Daniels [Fiji MVR scripts]
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 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]]). 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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