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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| package fiji.plugin.DOM; | ||
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| import java.io.FileInputStream; | ||
| import java.io.InputStream; | ||
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| import javax.xml.stream.XMLInputFactory; | ||
| import javax.xml.stream.XMLStreamReader; | ||
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| import ij.IJ; | ||
| import ij.Prefs; | ||
| import ij.gui.GenericDialog; | ||
| import ij.plugin.PlugIn; | ||
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| public class Import_TrackMate implements PlugIn { | ||
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| SMLAnalysis sml_import = new SMLAnalysis(); | ||
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| @Override | ||
| public void run(String arg) { | ||
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| String sFilename; | ||
| long nPatNumber=0; | ||
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| IJ.register(Import_TrackMate.class); | ||
| sFilename=IJ.getFilePath("Open TrackMate XML file"); | ||
| if (sFilename==null) | ||
| return; | ||
| if(sFilename.endsWith(".xml")) | ||
| { | ||
| GenericDialog dgImportTM = new GenericDialog("Import of Trackmate results"); | ||
| dgImportTM.addNumericField("Pixel size of original image", Prefs.get("SiMoLoc.TMImportdPixelSize", 1.0), 2, 4, "units"); | ||
| dgImportTM.showDialog(); | ||
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| if (dgImportTM.wasCanceled()) | ||
| return; | ||
| double dPxSize = dgImportTM.getNextNumber(); | ||
| Prefs.set("SiMoLoc.TMImportdPixelSize", dPxSize); | ||
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| IJ.log(" --- DoM plugin version " + DOMConstants.DOMversion+ " --- "); | ||
| IJ.log("Loading TrackMate file:"+sFilename); | ||
| IJ.log("Original image pixel size:"+Double.toString(dPxSize)); | ||
| try | ||
| { | ||
| int nTrack = 0; | ||
| int nFrame; | ||
| XMLInputFactory inputFactory = XMLInputFactory.newInstance(); | ||
| InputStream in = new FileInputStream(sFilename); | ||
| XMLStreamReader streamReader = inputFactory.createXMLStreamReader(in); | ||
| int nPoint = 0; | ||
| while (streamReader.hasNext()) | ||
| { | ||
| if (streamReader.isStartElement()) | ||
| { | ||
| switch (streamReader.getLocalName()) | ||
| { | ||
| case "Tracks": | ||
| { | ||
| IJ.log("Loading total of: " + streamReader.getAttributeValue(0) + " tracks... "); | ||
| sml_import.ptable.reset(); | ||
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| break; | ||
| } | ||
| case "particle": | ||
| { | ||
| nPoint =1; | ||
| nTrack = nTrack + 1; | ||
| break; | ||
| } | ||
| case "detection": | ||
| { | ||
| nPatNumber++; | ||
| nFrame = Integer.parseInt(streamReader.getAttributeValue(0))+1; | ||
| sml_import.ptable.incrementCounter(); | ||
| sml_import.ptable.addValue("Abs_frame", nFrame); | ||
| sml_import.ptable.addValue("X_(px)", Float.parseFloat(streamReader.getAttributeValue(1))/dPxSize); | ||
| sml_import.ptable.addValue("Y_(px)", Float.parseFloat(streamReader.getAttributeValue(2))/dPxSize); | ||
| sml_import.ptable.addValue("Channel", 1); | ||
| sml_import.ptable.addValue("Slice", nFrame); | ||
| sml_import.ptable.addValue("Frame", nFrame); | ||
| sml_import.ptable.addValue("Track_ID", nTrack); | ||
| sml_import.ptable.addValue("Particle_ID", nPoint); | ||
| nPoint++; | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| streamReader.next(); | ||
| } | ||
| } | ||
| catch (Exception em) | ||
| { | ||
| IJ.log("Error reading "+sFilename); | ||
| IJ.log(em.getMessage()); | ||
| } | ||
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| Import_MTrackJ.add_Tracks_Lengths(sml_import,Import_MTrackJ.calculate_Tracks_Lengths(sml_import)); | ||
| sml_import.showTable(); | ||
| IJ.log("Done loading "+Long.toString(nPatNumber)+" particles."); | ||
| } | ||
| else | ||
| { | ||
| IJ.error("Not a TrackMate XML file"); | ||
| } | ||
| } | ||
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| } |
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