Created
August 4, 2010 16:41
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A clojure script for Fiji to help process the Diadem Neuromuscular data set
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| (import '(ij.io DirectoryChooser)) | |
| (import '(java.io File)) | |
| (import '(java.io FileWriter)) | |
| (import '(ij.plugin FolderOpener)) | |
| (import '(ij IJ)) | |
| (import '(ij.io FileSaver)) | |
| ;; d should be a java.io.File object | |
| (defn files-in-directory [d] | |
| (seq (. d (listFiles)))) | |
| ;; d should be a java.io.File object representing | |
| ;; a directory with a TIFF file for each slice, | |
| ;; starting at 000.tif | |
| (defn pack-to-single-tiff [d] | |
| (let [contents (files-in-directory d) | |
| n (count contents) | |
| first-file (.getAbsolutePath (new File d "000.tif")) | |
| o (str (.getAbsolutePath d) ".tif")] | |
| (if-not (.exists (new File o)) | |
| (do | |
| ;; Import the image sequence: | |
| (ij.IJ/run "Image Sequence..." (str "open=" first-file " number=" n " starting=1 increment=1 scale=100 file=[] or=[] sort")) | |
| ;; It's a bad idea to just convert 16-bit to 8-bit in this | |
| ;; way, of course, so don't do it: | |
| ;; (ij.IJ/run "8-bit") | |
| ;; Correct the Z separation according to the instructions: | |
| (let [i (IJ/getImage) | |
| c (.getCalibration i)] | |
| (set! (. c pixelDepth) (* 3.04 (.pixelWidth c))) | |
| (.setCalibration i c) | |
| ;; ... and save as a single stack: | |
| (let [saver (new FileSaver i)] | |
| (.saveAsTiffStack saver o) | |
| (.close i))))) | |
| o)) | |
| ;; These offsets are taken from: | |
| ;; http://www.diademchallenge.org/neuromuscular_projection_fibers_readme.html | |
| (def filename-to-offset | |
| { | |
| "001.tif" '(7694 0 0) | |
| "002.tif" '(9504 6 0) | |
| "003.tif" '(10410 10 0) | |
| "004.tif" '(13104 4 0) | |
| "005.tif" '(7686 922 0) | |
| "006.tif" '(8592 926 0) | |
| "007.tif" '(9496 930 0) | |
| "008.tif" '(10400 934 0) | |
| "009.tif" '(13120 940 0) | |
| "010.tif" '(14022 944 0) | |
| "011.tif" '(14926 946 0) | |
| "012.tif" '(2254 1866 0) | |
| "013.tif" '(3164 1998 0) | |
| "014.tif" '(4066 2106 0) | |
| "015.tif" '(4966 1834 0) | |
| "016.tif" '(5866 1838 0) | |
| "017.tif" '(8578 1846 0) | |
| "018.tif" '(9486 1852 0) | |
| "019.tif" '(10394 1854 0) | |
| "020.tif" '(13112 1864 0) | |
| "021.tif" '(14014 1866 0) | |
| "022.tif" '(14914 1868 0) | |
| "023.tif" '(4960 2756 0) | |
| "024.tif" '(4540 2456 0) | |
| "025.tif" '(5860 2758 0) | |
| "026.tif" '(6766 2714 0) | |
| "027.tif" '(7668 2820 0) | |
| "028.tif" '(8572 2730 0) | |
| "029.tif" '(9482 2794 0) | |
| "030.tif" '(10386 2766 0) | |
| "031.tif" '(12198 2778 0) | |
| "032.tif" '(13106 2780 0) | |
| "033.tif" '(14006 2782 0) | |
| "034.tif" '(14908 2784 0) | |
| "035.tif" '(4954 3670 0) | |
| "036.tif" '(5858 3674 0) | |
| "037.tif" '(6766 3676 0) | |
| "038.tif" '(7666 3678 0) | |
| "039.tif" '(8570 3680 0) | |
| "040.tif" '(9480 3684 0) | |
| "041.tif" '(10384 3686 0) | |
| "042.tif" '(11288 3690 0) | |
| "043.tif" '(12194 3692 0) | |
| "044.tif" '(13100 3694 0) | |
| "045.tif" '(14000 3696 0) | |
| "046.tif" '(14902 3698 0) | |
| "047.tif" '(6754 4586 0) | |
| "048.tif" '(8568 4592 0) | |
| "049.tif" '(9472 4596 0) | |
| "050.tif" '(10380 4600 0) | |
| "051.tif" '(11286 4602 0) | |
| "052.tif" '(13094 4606 0) | |
| "053.tif" '(13994 4608 0) | |
| "054.tif" '(14894 4610 0) | |
| "055.tif" '(15802 4616 0) | |
| "056.tif" '(6760 5520 0) | |
| "057.tif" '(9470 5510 0) | |
| "058.tif" '(10374 5512 0) | |
| "059.tif" '(11280 5516 0) | |
| "060.tif" '(11268 5508 0) | |
| "061.tif" '(12180 5518 0) | |
| "062.tif" '(13086 5520 0) | |
| "063.tif" '(13988 5520 0) | |
| "064.tif" '(14892 5524 0) | |
| "065.tif" '(15794 5526 0) | |
| "066.tif" '(16698 5528 0) | |
| "067.tif" '(6750 6438 0) | |
| "068.tif" '(7200 5942 0) | |
| "069.tif" '(7656 6440 0) | |
| "070.tif" '(10368 6430 0) | |
| "071.tif" '(11272 6438 0) | |
| "072.tif" '(12174 6442 0) | |
| "073.tif" '(13080 6444 0) | |
| "074.tif" '(13982 6442 0) | |
| "075.tif" '(14882 6444 0) | |
| "076.tif" '(15786 6448 0) | |
| "077.tif" '(16690 6450 0) | |
| "078.tif" '(17594 6452 0) | |
| "079.tif" '(18500 6454 0) | |
| "080.tif" '(7650 7362 0) | |
| "081.tif" '(9452 7348 0) | |
| "082.tif" '(10362 7350 0) | |
| "083.tif" '(11266 7358 0) | |
| "084.tif" '(12166 7362 0) | |
| "085.tif" '(13084 7374 0) | |
| "086.tif" '(13978 7360 0) | |
| "087.tif" '(14878 7362 0) | |
| "088.tif" '(15778 7368 0) | |
| "089.tif" '(16680 7370 0) | |
| "090.tif" '(17590 7372 0) | |
| "091.tif" '(18494 7374 0) | |
| "092.tif" '(5834 8286 0) | |
| "093.tif" '(6736 8288 0) | |
| "094.tif" '(7642 8288 0) | |
| "095.tif" '(8546 8290 0) | |
| "096.tif" '(9454 8292 0) | |
| "097.tif" '(10438 8354 0) | |
| "098.tif" '(13076 8306 0) | |
| "099.tif" '(13968 8290 0) | |
| "100.tif" '(14872 8292 0) | |
| "101.tif" '(15774 8294 0) | |
| "102.tif" '(16674 8300 0) | |
| "103.tif" '(17580 8302 0) | |
| "104.tif" '(17578 8264 0) | |
| "105.tif" '(5828 9206 0) | |
| "106.tif" '(6732 9202 0) | |
| "107.tif" '(7634 9206 0) | |
| "108.tif" '(8540 9210 0) | |
| "109.tif" '(9444 9210 0) | |
| "110.tif" '(13964 9208 0) | |
| "111.tif" '(14864 9212 0) | |
| "112.tif" '(15766 9212 0) | |
| "113.tif" '(16668 9214 0) | |
| "114.tif" '(6724 10122 0) | |
| "115.tif" '(7626 10126 0) | |
| "116.tif" '(7604 10116 0) | |
| "117.tif" '(8530 10130 0) | |
| "118.tif" '(8530 10104 0) | |
| "119.tif" '(9436 10132 0) | |
| "120.tif" '(14858 10132 0) | |
| "121.tif" '(15760 10134 0) | |
| "122.tif" '(16664 10136 0) | |
| "123.tif" '(17566 10138 0) | |
| "124.tif" '(17570 10122 0) | |
| "125.tif" '(18472 10140 0) | |
| "126.tif" '(6716 11046 0) | |
| "127.tif" '(7620 11048 0) | |
| "128.tif" '(8524 11052 0) | |
| "129.tif" '(9432 11056 0) | |
| "130.tif" '(10342 11060 0) | |
| "131.tif" '(14854 11056 0) | |
| "132.tif" '(15754 11058 0) | |
| "133.tif" '(7618 11964 0) | |
| "134.tif" '(8522 11968 0) | |
| "135.tif" '(9428 11970 0) | |
| "136.tif" '(10334 11976 0) | |
| "137.tif" '(15746 11974 0) | |
| "138.tif" '(16652 11976 0) | |
| "139.tif" '(8516 12878 0) | |
| "140.tif" '(9418 12880 0) | |
| "141.tif" '(9412 13796 0) | |
| "142.tif" '(2258 2754 0) | |
| "143.tif" '(1306 3682 0) | |
| "144.tif" '(800 4600 0) | |
| "145.tif" '(416 5524 0) | |
| "146.tif" '(252 6446 0) | |
| "147.tif" '(0 7382 0) | |
| "148.tif" '(1336 2772 0) | |
| "149.tif" '(19400 7378 0) | |
| "150.tif" '(20298 6886 0) | |
| "151.tif" '(21262 6876 0) | |
| "152.tif" '(12554 6636 0) } ) | |
| (let [dc (new DirectoryChooser "Open stacks directory") | |
| d (.getDirectory dc) | |
| df (new File d) | |
| ;; Only include directories made up of digits: | |
| directories (filter (fn [x] (and (.isDirectory x) | |
| (re-find #"^[0-9]+$" (.getName x)))) | |
| (seq (. df (listFiles)))) | |
| tiff-stacks (map pack-to-single-tiff directories) | |
| tile-configuration-output-file (new File df "TileConfiguration.txt")] | |
| (if (> (count directories) 0) | |
| (let [out (new FileWriter tile-configuration-output-file)] | |
| (.write out "dim = 3\n") | |
| (doall (map #(let [tf (new File %1) | |
| tfb (.getName tf) | |
| offset (get filename-to-offset tfb)] | |
| (.write out (str %1 "; ; (" (apply str (interpose ", " offset)) ")\n"))) tiff-stacks)) | |
| (.close out)) | |
| (ij.IJ/error "No directories found - you must select a directory that contains the directories 000, 001, etc."))) |
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