import ij.*; import ij.plugin.*; import java.io.*; // Plugin to handle file types which are not implemented // directly in ImageJ through io.Opener // NB: since there is no _ in the name it will not appear in Plugins menu // ----- // Can be user modified so that your own specialised file types // can be opened through File ... Open // OR by drag and drop onto the ImageJ main panel // OR by double clicking in the MacOS 9/X Finder // ----- // Go to the point marked MODIFY HERE and modify to // recognise and load your own file type // ----- // Gregory Jefferis - 030629 // jefferis@stanford.edu /* * Modified to handle more file types * Copyright (C) 2010-2014 - Andreas Maier * CONRAD is developed as an Open Source project under the GNU General Public License (GPL). */ /** * Plugin to handle file types which are not implemented * directly in ImageJ through io.Opener. */ public class HandleExtraFileTypes extends ImagePlus implements PlugIn { static final int IMAGE_OPENED = -1; static final int PLUGIN_NOT_FOUND = -2; /** Called from io/Opener.java. */ public void run(String path) { if (path.equals("")) return; File theFile = new File(path); String directory = theFile.getParent(); String fileName = theFile.getName(); if (directory == null) directory = ""; // Try and recognise file type and load the file if recognised ImagePlus imp = openImage(directory, fileName, path); if (imp==null) { IJ.showStatus(""); return; // failed to load file or plugin has opened and displayed it } ImageStack stack = imp.getStack(); // set the stack of this HandleExtraFileTypes object // to that attached to the ImagePlus object returned by openImage() setStack(fileName, stack); // copy over the calibration info since it doesn't come with the ImageProcessor setCalibration(imp.getCalibration()); // also copy the Show Info field over if it exists if (imp.getProperty("Info") != null) setProperty("Info", imp.getProperty("Info")); // copy the FileInfo setFileInfo(imp.getOriginalFileInfo()); // copy dimensions if (IJ.getVersion().compareTo("1.38s")>=0) setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames()); if (IJ.getVersion().compareTo("1.41o")>=0) setOpenAsHyperStack(imp.getOpenAsHyperStack()); } private Object tryOpen(String directory, String name, String path) { // set up a stream to read in 132 bytes from the file header // These can be checked for "magic" values which are diagnostic // of some image types InputStream is; byte[] buf = new byte[132]; try { if (0 == path.indexOf("http://")) is = new java.net.URL(path).openStream(); else is = new FileInputStream(path); is.read(buf, 0, 132); is.close(); } catch (IOException e) { // couldn't open the file for reading return null; } name = name.toLowerCase(); width = PLUGIN_NOT_FOUND; // Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed if (Menus.getCommands().get("Bio-Formats Importer")!=null && IJ.getVersion().compareTo("1.37u")>=0) IJ.suppressPluginNotFoundError(); // OK now we get to the interesting bit // GJ: added Biorad PIC confocal file handler // ------------------------------------------ // These make 12345 if you read them as the right kind of short // and should have this value in every Biorad PIC file if (buf[54]==57 && buf[55]==48) { return tryPlugIn("Biorad_Reader", path); } // GJ: added Gatan Digital Micrograph DM3 handler // ---------------------------------------------- // check if the file ends in .DM3 or .dm3, // and bytes make an int value of 3 which is the DM3 version number if (name.endsWith(".dm3") && buf[0]==0 && buf[1]==0 && buf[2]==0 && buf[3]==3) { return tryPlugIn("DM3_Reader", path); } // IPLab file handler // Little-endian IPLab files start with "iiii" or "mmmm". if (name.endsWith(".ipl") || (buf[0]==105 && buf[1]==105 && buf[2]==105 && buf[3]==105) || (buf[0]==109 && buf[1]==109 && buf[2]==109 && buf[3]==109)) { return tryPlugIn("IPLab_Reader", path); } // Packard InstantImager format (.img) handler -> check HERE // before Analyze check below! // Check extension and signature bytes KAJ_ if (name.endsWith(".img") && buf[0]==75 && buf[1]==65 && buf[2]==74 && buf[3]==0) { return tryPlugIn("InstantImager_Reader", path); } // Analyze format (.img/.hdr) handler // Opens the file using the Nifti_Reader if it is installed, // otherwise the Analyze_Reader is used. Note that // the Analyze_Reader plugin opens and displays the // image and does not implement the ImagePlus class. if (name.endsWith(".img") || name.endsWith(".hdr")) { if (Menus.getCommands().get("NIfTI-Analyze")!=null) return tryPlugIn("Nifti_Reader", path); else return tryPlugIn("Analyze_Reader", path); } // NIFTI format (.nii) handler if (name.endsWith(".nii")) { return tryPlugIn("Nifti_Reader", path); } // Image Cytometry Standard (.ics) handler // http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html if (name.endsWith(".ics")) { return tryPlugIn("Ics_Opener", path); } // Princeton Instruments SPE image file (.spe) handler // http://rsb.info.nih.gov/ij/plugins/spe.html if (name.endsWith(".spe")) { return tryPlugIn("OpenSPE_", path); } // Zeiss Confocal LSM 510 image file (.lsm) handler // http://rsb.info.nih.gov/ij/plugins/lsm-reader.html if (name.endsWith(".lsm")) { Object obj = tryPlugIn("LSM_Reader", path); if (obj==null && Menus.getCommands().get("Show LSMToolbox")!=null) obj = tryPlugIn("LSM_Toolbox", "file="+path); return obj; } // BM: added Bruker file handler 29.07.04 if (name.equals("ser") || name.equals("fid") || name.equals("2rr") || name.equals("2ii") || name.equals("3rrr") || name.equals("3iii") || name.equals("2dseq")) { ij.IJ.showStatus("Opening Bruker " + name + " File"); return tryPlugIn("BrukerOpener", name + "|" + path); } // AVI: open AVI files using AVI_Reader plugin if (name.endsWith(".avi")) { return tryPlugIn("AVI_Reader", path); } // QuickTime: open .mov and .pict files using QT_Movie_Opener plugin if (name.endsWith(".mov") || name.endsWith(".pict")) { return tryPlugIn("QT_Movie_Opener", path); } // ZVI file handler // Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0 // so we can only look at the extension. if (name.endsWith(".zvi")) { return tryPlugIn("ZVI_Reader", path); } // University of North Carolina (UNC) file format handler // 'magic' numbers are (int) offsets to data structures and // may change in future releases. if (name.endsWith(".unc") || (buf[3]==117 && buf[7]==-127 && buf[11]==36 && buf[14]==32 && buf[15]==-127)) { return tryPlugIn("UNC_Reader", path); } // Amira file handler // http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html if (buf[0]==0x23 && buf[1]==0x20 && buf[2]==0x41 && buf[3]==0x6d && buf[4]==0x69 && buf[5]==0x72 && buf[6]==0x61 && buf[7]==0x4d && buf[8]==0x65 && buf[9]==0x73&&buf[10]==0x68 && buf[11]==0x20) { return tryPlugIn("AmiraMeshReader_", path); } // Deltavision file handler // Open DV files generated on Applied Precision DeltaVision systems if (name.endsWith(".dv") || name.endsWith(".r3d")) { return tryPlugIn("Deltavision_Opener", path); } // Albert Cardona: read .mrc files (little endian). // Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm. // The parsing of the header is a bare minimum of what could be done. if (name.endsWith(".mrc")) { return tryPlugIn("Open_MRC_Leginon", path); } // Albert Cardona: read .dat files from the EMMENU software if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only return tryPlugIn("Open_DAT_EMMENU", path); } // ****************** MODIFY HERE ****************** // do what ever you have to do to recognise your own file type // and then call appropriate plugin using the above as models // e.g.: // Bio formats NRRD Reads // Open NRRD files if (name.endsWith(".nrrd") || name.endsWith(".nhdr")) { return tryPlugIn("Nrrd_Reader", path); } // Viva file handler if (name.endsWith(".viv") || name.endsWith(".seq")) { return tryPlugIn("Viva_Reader", path); } // Viva file handler if (name.endsWith(".mkt")) { return tryPlugIn("MKT_Reader", path); } // Dennerlein file handler if (name.endsWith(".bin")) { if (name.matches(".*\\dx\\d.*")){ return tryPlugIn("RCL_Reader", path); } return tryPlugIn("Dennerlein_Reader", path); } // Nurbs Reader for XCat's nrb format if (name.endsWith(".nrb")) { return tryPlugIn("Nurbs_Reader", path); } // Nurbs Reader for XCat's nrb format if (name.endsWith(".zip")) { return tryPlugIn("ZIP_Reader", path); } /* // A. Dent: Added XYZ handler // ---------------------------------------------- // check if the file ends in .xyz, and bytes 0 and 1 equal 42 if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) { // Ok we've identified the file type - now load it return tryPlugIn("XYZ_Reader", path); } */ return null; } private ImagePlus openImage(String directory, String name, String path) { Object o = tryOpen(directory, name, path); // if an image was returned, assume success if (o instanceof ImagePlus) return (ImagePlus)o; // try opening the file with LOCI Bio-Formats plugin - always check this last! // Do not call Bio-Formats if File>Import>Image Sequence is opening this file. if (o==null && (IJ.getVersion().compareTo("1.38j")<0||!IJ.redirectingErrorMessages()) && (new File(path).exists())) { Object loci = IJ.runPlugIn("loci.plugins.LociImporter", path); if (loci!=null) { // plugin exists and was launched try { // check whether plugin was successful Class<? extends Object> c = loci.getClass(); boolean success = c.getField("success").getBoolean(loci); boolean canceled = c.getField("canceled").getBoolean(loci); if (success || canceled) { width = IMAGE_OPENED; return null; } } catch (Exception exc) { } } } return null; } // openImage /** * Attempts to open the specified path with the given plugin. If the * plugin extends the ImagePlus class (e.g., BioRad_Reader), set * extendsImagePlus to true, otherwise (e.g., LSM_Reader) set it to false. * * @return A reference to the plugin, if it was successful. */ private Object tryPlugIn(String className, String path) { Object o = IJ.runPlugIn(className, path); if (o instanceof ImagePlus) { // plugin extends ImagePlus class ImagePlus imp = (ImagePlus)o; if (imp.getWidth()==0) o = null; // invalid image else width = IMAGE_OPENED; // success } else { // plugin does not extend ImagePlus; assume success width = IMAGE_OPENED; } return o; } }