Changes for page Access data with ImageJ

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

Summary

Details

Page properties
Content
... ... @@ -2,9 +2,11 @@
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 +
8 8  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.
9 9  
10 10  = {{id name="AccessdatawithImageJ-Readthefileheader"/}}Read the file header =
HandleExtraFileTypes.class
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fwilde
Size
... ... @@ -1,1 +1,0 @@
1 -5.8 KB
Content
HandleExtraFileTypes.jar
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fwilde
Size
... ... @@ -1,1 +1,0 @@
1 -9.7 KB
Content
HandleExtraFileTypes.java
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fwilde
Size
... ... @@ -1,1 +1,0 @@
1 -10.8 KB
Content
... ... @@ -1,313 +1,0 @@
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
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fwilde
Size
... ... @@ -1,1 +1,0 @@
1 -11.9 KB
Content
read_dat.class
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fwilde
Size
... ... @@ -1,1 +1,0 @@
1 -5.0 KB
Content
read_dat.java
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fwilde
Size
... ... @@ -1,1 +1,0 @@
1 -5.2 KB
Content
... ... @@ -1,147 +1,0 @@
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
... ... @@ -1,1 +1,1 @@
1 -34870216
1 +116602069
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/P5I/pages/34870216/Access data with ImageJ
1 +https://confluence.desy.de/spaces/P5I/pages/116602069/Access data with ImageJ