Changes for page Access data with ImageJ

Last modified by fwilde on 2018/12/18 12:01
From version 15.1
edited by fwilde
on 2018/12/18 12:01
Change comment: There is no comment for this version
To version 16.1
edited by fwilde
on 2018/12/18 12:01
Change comment: There is no comment for this version

Summary

Details

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2 2  {{layout-section ac:type="two_right_sidebar"}}
3 3  {{layout-cell}}
4 4  {{info}}
5 -As of 2017, all images are stored in TIFF format. These can be easily viewed with many image viewers including ImageJ.
5 +**As of 2017, all images are stored in TIFF format. These can be easily viewed with many image viewers including ImageJ.**
6 6  {{/info}}
7 7  
8 -\\
9 -
10 10  Until 2017 at P05 a generic data format was used to store raw and reconstructed data. This is a binary format in little endian byte order with different data types (uint16, real32, ...) and a header which describes the dataset (rows and columns, data format). This data can either be imported directly in ImageJ or loaded with our plugins.
11 11  
12 12  = {{id name="AccessdatawithImageJ-Readthefileheader"/}}Read the file header =
HandleExtraFileTypes.class
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HandleExtraFileTypes.jar
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HandleExtraFileTypes.java
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1 +import ij.*;
2 +import ij.plugin.*;
3 +import java.io.*;
4 +
5 +// Plugin to handle file types which are not implemented
6 +// directly in ImageJ through io.Opener
7 +// NB: since there is no _ in the name it will not appear in Plugins menu
8 +// -----
9 +// Can be user modified so that your own specialised file types
10 +// can be opened through File ... Open
11 +// OR by drag and drop onto the ImageJ main panel
12 +// OR by double clicking in the MacOS 9/X Finder
13 +// -----
14 +// Go to the point marked MODIFY HERE and modify to
15 +// recognise and load your own file type
16 +// -----
17 +// Gregory Jefferis - 030629
18 +// jefferis@stanford.edu
19 +
20 +/**
21 + * Plugin to handle file types which are not implemented
22 + * directly in ImageJ through io.Opener.
23 + */
24 +public class HandleExtraFileTypes extends ImagePlus implements PlugIn {
25 + static final int IMAGE_OPENED = -1;
26 + static final int PLUGIN_NOT_FOUND = -2;
27 +
28 + /** Called from io/Opener.java. */
29 + public void run(String path) {
30 + if (path.equals("")) return;
31 + File theFile = new File(path);
32 + String directory = theFile.getParent();
33 + String fileName = theFile.getName();
34 + if (directory == null) directory = "";
35 +
36 + // Try and recognise file type and load the file if recognised
37 + ImagePlus imp = openImage(directory, fileName, path);
38 + if (imp==null) {
39 + IJ.showStatus("");
40 + return; // failed to load file or plugin has opened and displayed it
41 + }
42 + ImageStack stack = imp.getStack();
43 + // get the title from the stack (falling back to the fileName)
44 + String title=imp.getTitle().equals("")?fileName:imp.getTitle();
45 + // set the stack of this HandleExtraFileTypes object
46 + // to that attached to the ImagePlus object returned by openImage()
47 + setStack(title, stack);
48 + // copy over the calibration info since it doesn't come with the ImageProcessor
49 + setCalibration(imp.getCalibration());
50 + // also copy the Show Info field over if it exists
51 + if (imp.getProperty("Info") != null)
52 + setProperty("Info", imp.getProperty("Info"));
53 + // copy the FileInfo
54 + setFileInfo(imp.getOriginalFileInfo());
55 + // copy dimensions
56 + if (IJ.getVersion().compareTo("1.38s")>=0)
57 + setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
58 + // copy the image subtitle field ("Label" property) if it exists
59 + if (imp.getProperty("Label")!=null)
60 + setProperty("Label", imp.getProperty("Label"));
61 + if (IJ.getVersion().compareTo("1.41o")>=0)
62 + setOpenAsHyperStack(imp.getOpenAsHyperStack());
63 + }
64 +
65 +
66 + private Object tryOpen(String directory, String name, String path) {
67 + // set up a stream to read in 132 bytes from the file header
68 + // These can be checked for "magic" values which are diagnostic
69 + // of some image types
70 + InputStream is;
71 + byte[] buf = new byte[132];
72 + try {
73 + if (0 == path.indexOf("http://"))
74 + is = new java.net.URL(path).openStream();
75 + else
76 + is = new FileInputStream(path);
77 + is.read(buf, 0, 132);
78 + is.close();
79 + }
80 + catch (IOException e) {
81 + // couldn't open the file for reading
82 + return null;
83 + }
84 + name = name.toLowerCase();
85 + width = PLUGIN_NOT_FOUND;
86 +
87 + // Temporarily suppress "plugin not found" errors if LOCI Bio-Formats plugin is installed
88 + if (Menus.getCommands().get("Bio-Formats Importer")!=null && IJ.getVersion().compareTo("1.37u")>=0)
89 + IJ.suppressPluginNotFoundError();
90 +
91 + // OK now we get to the interesting bit
92 +
93 + // GJ: added Biorad PIC confocal file handler
94 + // ------------------------------------------
95 + // These make 12345 if you read them as the right kind of short
96 + // and should have this value in every Biorad PIC file
97 + if (buf[54]==57 && buf[55]==48) {
98 + return tryPlugIn("Biorad_Reader", path);
99 + }
100 + // GJ: added Gatan Digital Micrograph DM3 handler
101 + // ----------------------------------------------
102 + // check if the file ends in .DM3 or .dm3,
103 + // and bytes make an int value of 3 which is the DM3 version number
104 + if (name.endsWith(".dm3") && buf[0]==0 && buf[1]==0 && buf[2]==0 && buf[3]==3) {
105 + return tryPlugIn("DM3_Reader", path);
106 + }
107 +
108 + // IPLab file handler
109 + // Little-endian IPLab files start with "iiii" or "mmmm".
110 + if (name.endsWith(".ipl") ||
111 + (buf[0]==105 && buf[1]==105 && buf[2]==105 && buf[3]==105) ||
112 + (buf[0]==109 && buf[1]==109 && buf[2]==109 && buf[3]==109)) {
113 + return tryPlugIn("IPLab_Reader", path);
114 + }
115 +
116 + // Packard InstantImager format (.img) handler -> check HERE
117 + // before Analyze check below!
118 + // Check extension and signature bytes KAJ_
119 + //if (name.endsWith(".img") && buf[0]==75 && buf[1]==65 && buf[2]==74 && buf[3]==0) {
120 + // return tryPlugIn("InstantImager_Reader", path);
121 + //}
122 +
123 + // Analyze format (.img/.hdr) handler
124 + // Opens the file using the Nifti_Reader if it is installed,
125 + // otherwise the Analyze_Reader is used. Note that
126 + // the Analyze_Reader plugin opens and displays the
127 + // image and does not implement the ImagePlus class.
128 +
129 +
130 + // NIFTI format (.nii) handler
131 + if (name.endsWith(".nii") || name.endsWith( ".nii.gz" ) || name.endsWith( ".nii.z" ) ) {
132 + return tryPlugIn("Nifti_Reader", path);
133 + }
134 +
135 + // Image Cytometry Standard (.ics) handler
136 + // http://valelab.ucsf.edu/~nico/IJplugins/Ics_Opener.html
137 + if (name.endsWith(".ics")) {
138 + return tryPlugIn("Ics_Opener", path);
139 + }
140 +
141 + // Princeton Instruments SPE image file (.spe) handler
142 + // http://rsb.info.nih.gov/ij/plugins/spe.html
143 + if (name.endsWith(".spe")) {
144 + return tryPlugIn("OpenSPE_", path);
145 + }
146 +
147 + // Zeiss Confocal LSM 510 image file (.lsm) handler
148 + // http://rsb.info.nih.gov/ij/plugins/lsm-reader.html
149 + if (name.endsWith(".lsm")) {
150 + Object obj = tryPlugIn("LSM_Reader", path);
151 + if (obj==null && Menus.getCommands().get("Show LSMToolbox")!=null)
152 + obj = tryPlugIn("LSM_Toolbox", "file="+path);
153 + return obj;
154 + }
155 +
156 + // BM: added Bruker file handler 29.07.04
157 + if (name.equals("ser") || name.equals("fid") || name.equals("2rr") ||
158 + name.equals("2ii") || name.equals("3rrr") || name.equals("3iii") ||
159 + name.equals("2dseq")) {
160 + ij.IJ.showStatus("Opening Bruker " + name + " File");
161 + return tryPlugIn("BrukerOpener", name + "|" + path);
162 + }
163 +
164 + // AVI: open AVI files using AVI_Reader plugin
165 + if (name.endsWith(".avi")) {
166 + return tryPlugIn("AVI_Reader", path);
167 + }
168 +
169 + // QuickTime: open .mov and .pict files using QT_Movie_Opener plugin
170 + if (name.endsWith(".mov") || name.endsWith(".pict")) {
171 + return tryPlugIn("QT_Movie_Opener", path);
172 + }
173 +
174 + // ZVI file handler
175 + // Little-endian ZVI and Thumbs.db files start with d0 cf 11 e0
176 + // so we can only look at the extension.
177 + if (name.endsWith(".zvi")) {
178 + return tryPlugIn("ZVI_Reader", path);
179 + }
180 +
181 + // University of North Carolina (UNC) file format handler
182 + // 'magic' numbers are (int) offsets to data structures and
183 + // may change in future releases.
184 + if (name.endsWith(".unc") || (buf[3]==117 && buf[7]==-127 && buf[11]==36 && buf[14]==32 && buf[15]==-127)) {
185 + return tryPlugIn("UNC_Reader", path);
186 + }
187 +
188 + // Amira file handler
189 + // http://wbgn013.biozentrum.uni-wuerzburg.de/ImageJ/amira-io.html
190 + if (buf[0]==0x23 && buf[1]==0x20 && buf[2]==0x41
191 + && buf[3]==0x6d && buf[4]==0x69 && buf[5]==0x72
192 + && buf[6]==0x61 && buf[7]==0x4d && buf[8]==0x65
193 + && buf[9]==0x73&&buf[10]==0x68 && buf[11]==0x20) {
194 + return tryPlugIn("AmiraMeshReader_", path);
195 + }
196 +
197 + // Deltavision file handler
198 + // Open DV files generated on Applied Precision DeltaVision systems
199 + if (name.endsWith(".dv") || name.endsWith(".r3d")) {
200 + return tryPlugIn("Deltavision_Opener", path);
201 + }
202 +
203 + // Albert Cardona: read .mrc files (little endian).
204 + // Documentation at: http://ami.scripps.edu/prtl_data/mrc_specification.htm.
205 + // The parsing of the header is a bare minimum of what could be done.
206 + if (name.endsWith(".mrc")) {
207 + return tryPlugIn("Open_MRC_Leginon", path);
208 + }
209 +
210 + // Albert Cardona: read .dat files from the EMMENU software
211 + if (name.endsWith(".dat") && 1 == buf[1] && 0 == buf[2]) { // 'new format' only
212 + return tryPlugIn("Open_DAT_EMMENU", path);
213 + }
214 +
215 + // Timo Rantalainen and Michael Doube: read Stratec pQCT files.
216 + // File name is IDDDDDDD.MHH, where D is decimal and H is hex.
217 + if (name.matches("[iI]\\d{7}\\.[mM]\\p{XDigit}{2}")) {
218 + return tryPlugIn("org.doube.bonej.pqct.Read_Stratec_File", path);
219 + }
220 +
221 + //Michael Doube: read Scanco ISQ files
222 + //File name is ADDDDDDD.ISQ;D where D is a decimal and A is a letter
223 + try {
224 + String isqMagic=new String(buf,0,16,"UTF-8");
225 + if (name.matches("[a-z]\\d{7}.isq;\\d+") || isqMagic.equals("CTDATA-HEADER_V1"))
226 + return tryPlugIn("org.bonej.io.ISQReader", path);
227 + }
228 + catch (Exception e) {}
229 +
230 + // Jerome Parent : read .bin from the LynceeTec's software Koala
231 + if (name.endsWith(".bin")) {
232 + return tryPlugIn("Koala_Bin_Reader", path);
233 + }
234 +
235 + //HZG-Tomo file format
236 + if (name.endsWith(".img") || name.endsWith(".ref") || name.endsWith(".dar") || name.endsWith(".sin") || name.endsWith(".sis") || name.endsWith(".sli") || name.endsWith(".comp")) {
237 + return tryPlugIn("read_dat", path);
238 + }
239 +
240 +
241 + // ****************** MODIFY HERE ******************
242 + // do what ever you have to do to recognise your own file type
243 + // and then call appropriate plugin using the above as models
244 + // e.g.:
245 +
246 + /*
247 + // A. Dent: Added XYZ handler
248 + // ----------------------------------------------
249 + // check if the file ends in .xyz, and bytes 0 and 1 equal 42
250 + if (name.endsWith(".xyz") && buf[0]==42 && buf[1]==42) {
251 + // Ok we've identified the file type - now load it
252 + return tryPlugIn("XYZ_Reader", path);
253 + }
254 + */
255 +
256 + return null;
257 + }
258 +
259 + private ImagePlus openImage(String directory, String name, String path) {
260 + Object o = tryOpen(directory, name, path);
261 + // if an image was returned, assume success
262 + if (o instanceof ImagePlus) return (ImagePlus)o;
263 +
264 + // try opening the file with LOCI Bio-Formats plugin - always check this last!
265 + // Do not call Bio-Formats if File>Import>Image Sequence is opening this file.
266 + if (o==null && (IJ.getVersion().compareTo("1.38j")<0||!IJ.redirectingErrorMessages()) && (new File(path).exists())) {
267 + Object loci = IJ.runPlugIn("loci.plugins.LociImporter", path);
268 + if (loci!=null) {
269 + // plugin exists and was launched
270 + try {
271 + // check whether plugin was successful
272 + Class c = loci.getClass();
273 + boolean success = c.getField("success").getBoolean(loci);
274 + boolean canceled = c.getField("canceled").getBoolean(loci);
275 + if (success || canceled) {
276 + width = IMAGE_OPENED;
277 + return null;
278 + }
279 + }
280 + catch (Exception exc) { }
281 + }
282 + }
283 +
284 + return null;
285 +
286 + } // openImage
287 +
288 + /**
289 + * Attempts to open the specified path with the given plugin. If the
290 + * plugin extends the ImagePlus class (e.g., BioRad_Reader), set
291 + * extendsImagePlus to true, otherwise (e.g., LSM_Reader) set it to false.
292 + *
293 + * @return A reference to the plugin, if it was successful.
294 + */
295 + private Object tryPlugIn(String className, String path) {
296 + Object o = IJ.runPlugIn(className, path);
297 + if (o instanceof ImagePlus) {
298 + // plugin extends ImagePlus class
299 + ImagePlus imp = (ImagePlus)o;
300 + if (imp.getWidth()==0)
301 + o = null; // invalid image
302 + else
303 + width = IMAGE_OPENED; // success
304 + } else {
305 + // plugin does not extend ImagePlus; assume success
306 + width = IMAGE_OPENED;
307 + }
308 + return o;
309 + }
310 +
311 +
312 +}
313 +
imagej_raw_import.png
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read_dat.class
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read_dat.java
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1 +import ij.IJ;
2 +import ij.ImagePlus;
3 +
4 +import ij.io.FileInfo;
5 +import ij.io.FileOpener;
6 +import ij.io.OpenDialog;
7 +
8 +import ij.plugin.PlugIn;
9 +
10 +import ij.process.ByteProcessor;
11 +
12 +import java.io.DataInputStream;
13 +import java.io.InputStream;
14 +import java.io.File;
15 +import java.io.FileInputStream;
16 +import java.io.IOException;
17 +import java.util.Arrays;
18 +import java.util.HashMap;
19 +import java.util.Map;
20 +
21 +public class read_dat extends ImagePlus implements PlugIn {
22 +
23 + public void run(String arg) {
24 + String path = getPath(arg);
25 + if (null == path) return;
26 + if (!parse(path)) return;
27 + if (null == arg || 0 == arg.trim().length()) this.show(); // was opened by direct call to the plugin
28 + // not via HandleExtraFileTypes which would
29 + // have given a non-null arg.
30 + }
31 +
32 + /** Accepts URLs as well. */
33 + private String getPath(String arg) {
34 + if (null != arg) {
35 + if (0 == arg.indexOf("http://")
36 + || new File(arg).exists()) return arg;
37 + }
38 + // else, ask:
39 + OpenDialog od = new OpenDialog("Choose a file", null);
40 + String dir = od.getDirectory();
41 + if (null == dir) return null; // dialog was canceled
42 + dir = dir.replace('\\', '/'); // Windows safe
43 + if (!dir.endsWith("/")) dir += "/";
44 + return dir + od.getFileName();
45 + }
46 +
47 + /** Opens URLs as well. */
48 + private InputStream open(String path) throws Exception {
49 + if (0 == path.indexOf("http://"))
50 + return new java.net.URL(path).openStream();
51 + return new FileInputStream(path);
52 + }
53 +
54 + private boolean parse(String path) {
55 + // Open file and read header
56 + byte[] buf = new byte[136];
57 + try {
58 + InputStream is = open(path);
59 + is.read(buf, 0, 136);
60 + is.close();
61 + } catch (Exception e) {
62 + e.printStackTrace();
63 + return false;
64 + }
65 + // Analyze image header
66 + // split off first 40 characters of the file and convert them to String
67 + byte[] subarray_buf = Arrays.copyOfRange(buf, 0, 40);
68 + String firstchars = new String(subarray_buf);
69 + // split the first character at the newline
70 + String[] splitted_chars = firstchars.split("\\r\\n");
71 + // read the actual header
72 + String header = splitted_chars[0];
73 + // get the header length
74 + int header_length = header.length();
75 + // split the header for individual information
76 + String[] header_atoms = header.split("_");
77 + // header: computer information
78 + String hdr_comp = header_atoms[0];
79 + // header: number of dimensions
80 + int hdr_arrdim = Integer.parseInt(header_atoms[1]);
81 + // header: IDL data type
82 + String hdr_idltype = header_atoms[2];
83 + // header: (variable length) array with the dimension sizes
84 + String[] hdr_dimsize = Arrays.copyOfRange(header_atoms, 3, header_atoms.length);
85 +
86 + Map<String, Integer> idlToImagej = new HashMap<String, Integer>();
87 + idlToImagej.put("B", 0); // "GRAY8"
88 + idlToImagej.put("I", 1); // "GRAY16_SIGNED"
89 + idlToImagej.put("U", 2); // "GRAY16_UNSIGNED"
90 + idlToImagej.put("L", 3); // "GRAY32_INT"
91 + idlToImagej.put("F", 4); // "GRAY32_FLOAT"
92 +
93 + // Read width,height,slices ... from the header
94 + /* THIS IS AN EXAMPLE */
95 + int n_slices = 1;
96 + int height = 1;
97 + int width = Integer.parseInt(hdr_dimsize[0]);
98 + if (hdr_dimsize.length >= 2) {
99 + height = Integer.parseInt(hdr_dimsize[1]);
100 + }
101 + if (hdr_dimsize.length >= 3) {
102 + n_slices = Integer.parseInt(hdr_dimsize[2]);
103 + }
104 + int type = idlToImagej.get(hdr_idltype);
105 +
106 +
107 + // Build a new FileInfo object with all file format parameters and file data
108 + FileInfo fi = new FileInfo();
109 + fi.fileType = type;
110 + fi.fileFormat = fi.RAW;
111 + int islash = path.lastIndexOf('/');
112 + if (0 == path.indexOf("http://")) {
113 + fi.url = path;
114 + } else {
115 + fi.directory = path.substring(0, islash+1);
116 + }
117 + fi.fileName = path.substring(islash+1);
118 + fi.width = width;
119 + fi.height = height;
120 + fi.nImages = n_slices;
121 + fi.gapBetweenImages = 0;
122 + fi.intelByteOrder = true; // little endian
123 + fi.whiteIsZero = false; // no inverted LUT
124 + fi.longOffset = fi.offset = (header_length + 2); // header size in bytes +2 for newline
125 +
126 + // Now make a new ImagePlus out of the FileInfo
127 + // and integrate its data into this PlugIn, which is also an ImagePlus
128 + try {
129 + FileOpener fo = new FileOpener(fi);
130 + ImagePlus imp = fo.open(false);
131 + this.setStack(imp.getTitle(), imp.getStack());
132 + this.setCalibration(imp.getCalibration());
133 + Object obinfo = imp.getProperty("Info");
134 + if (null != obinfo) this.setProperty("Info", obinfo);
135 + this.setFileInfo(imp.getOriginalFileInfo());
136 + } catch (Exception e) {
137 + e.printStackTrace();
138 + return false;
139 + }
140 + return true;
141 + }
142 +
143 + //private final int readIntLittleEndian(byte[] buf, int start) {
144 + // return (buf[start]) + (buf[start+1]<<8) + (buf[start+2]<<16) + (buf[start+3]<<24);
145 + //}
146 +}
147 +
Confluence.Code.ConfluencePageClass[0]
Id
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1 -116602069
1 +34870216
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/116602069/Access data with ImageJ
1 +https://confluence.desy.de/spaces/P5I/pages/34870216/Access data with ImageJ