| blob | 5621894f165c72cecd4b705290763826dcc180de |
1 (ns lineage.identify
2 (:import
3 (lineage LineageClassifier)
4 (java.io InputStreamReader FileInputStream PushbackReader)
5 (javax.vecmath Point3d)
6 (javax.swing JTable JFrame JScrollPane JPanel JLabel BoxLayout JPopupMenu JMenuItem)
7 (javax.swing.table AbstractTableModel DefaultTableCellRenderer)
8 (java.awt.event MouseAdapter ActionListener)
9 (java.awt Color Dimension Component)
10 (java.util Map)
11 (mpicbg.models AffineModel3D)
12 (ij.measure Calibration)
13 (ini.trakem2.utils Utils)
14 (ini.trakem2.display Display Display3D LayerSet)
15 (ini.trakem2.analysis Compare)
16 (ini.trakem2.vector VectorString3D Editions))
17 (:use [clojure.set :only (intersection)]))
19 (defmacro report
20 [& args]
21 `(ij.IJ/log (str ~@args)))
23 (defn- as-VectorString3D
24 "Convert a map of {\"name\" {:x (...) :y (...) :z (...)}} into a map of {\"name\" (VectorString3D. ...)}"
25 [SATs]
26 (map
27 (fn [e]
28 {(key e)
29 (let [data (val e)]
30 (VectorString3D. (into-array Double/TYPE (data :x))
31 (into-array Double/TYPE (data :y))
32 (into-array Double/TYPE (data :z))
33 false))})
34 SATs))
36 (defn- load-SAT-lib-as-vs
37 "Returns the SATs library with VectorString3D instances"
38 [filepath]
39 (reduce
40 (fn [m e]
41 (let [label (key e)
42 data (val e)]
43 (assoc m
44 label
45 (assoc data :SATs (as-VectorString3D (data :SATs))))))
46 {}
47 (read
48 (PushbackReader.
49 (InputStreamReader. (FileInputStream. filepath))
50 4096))))
52 (defn- fids-as-Point3d
53 "Convert a map like {\"blva_joint\" [70.62114008906023 140.07819545137772 -78.72010436407604] ...}
54 into a sorted map of {\"blva_joint\" (Point3d ...)}"
55 [fids]
56 (reduce
57 (fn [m e]
58 (let [xyz (val e)]
59 (assoc m (key e) (Point3d. (double (get xyz 0))
60 (double (get xyz 1))
61 (double (get xyz 2))))))
62 {}
63 fids))
65 (defn- register-SATs
66 "Returns a map of SAT name vs VectorString3D,
67 where the VectorString3D is registered to the target fids."
68 [brain-label brain-data target-fids]
69 (let [source-fids (fids-as-Point3d (brain-data :fiducials))
70 SATs (into (sorted-map) (brain-data :SATs))
71 common-fid-keys (intersection (into #{} (keys source-fids)) (into #{} (keys target-fids)))
72 vs (Compare/transferVectorStrings (vals SATs)
73 (vals (into (sorted-map) (select-keys source-fids common-fid-keys)))
74 (vals (into (sorted-map) (select-keys target-fids common-fid-keys)))
75 AffineModel3D)]
76 (zipmap
77 (map #(str (.replaceAll % "\\[.*\\] " " [") \space brain-label \]) (keys SATs))
78 vs)))
80 (defn- load-mb
81 [SAT-lib reference-brain]
82 (let [r (re-pattern (str "peduncle . (dorsal|medial) lobe.*" reference-brain ".*"))]
83 (loop [sl SAT-lib
84 mb {}]
85 (if (= 2 (count mb))
86 mb
87 (if-let [[k v] (first sl)]
88 (recur (next sl)
89 (if (re-matches r k)
90 (into mb {k v})
91 mb)))))))
93 (def ^:dynamic *libs* (ref {}))
95 (defn- load-SAT-lib
96 "Load the named SAT-lib from filepath into *libs* and returns it.
97 Will setup the reference set of fiducial points and the mushroom body lobes from the entry named by reference brain,
98 as we as register all SATs to the reference brain."
99 [lib]
100 (let [SAT-lib (load-SAT-lib-as-vs (lib "filepath"))
101 reference (let [r (SAT-lib (lib "reference"))]
102 (if r
103 r
104 ; Else, use the first brain of the set as reference
105 (let [rr (first (keys SAT-lib))]
106 (println "Could not find reference brain '" (lib "reference") "'\n Instead, using as reference brain: " rr)
107 (SAT-lib rr))))
108 target-fids (fids-as-Point3d (reference :fiducials))
109 SATs (reduce
110 (fn [m e]
111 (conj m (register-SATs (key e) (val e) target-fids)))
112 {}
113 SAT-lib)]
114 (dosync
115 (commute *libs* (fn [libs]
116 (assoc libs (lib "title") {:filepath (lib "filepath")
117 :SATs SATs
118 :fids target-fids
119 :mb (load-mb SATs (lib "reference"))})))))
120 (@*libs* (lib "title")))
123 (defn forget-libs
124 []
125 (dosync
126 (commute *libs* (fn [_] {}))))
128 (defn- register-vs
129 "Register a singe VectorString3D from source-fids to target-fids."
130 [vs source-fids target-fids]
131 (let [common-fid-keys (intersection (into #{} (keys source-fids)) (into #{} (keys target-fids)))]
132 (if (empty? common-fid-keys)
133 nil
134 (first (Compare/transferVectorStrings [vs]
135 (vals (into (sorted-map) (select-keys source-fids common-fid-keys)))
136 (vals (into (sorted-map) (select-keys target-fids common-fid-keys)))
137 AffineModel3D)))))
139 (defn resample
140 "Returns a resampled copy of vs."
141 [vs delta]
142 (let [copy (.clone vs)]
143 (.resample copy delta)
144 copy))
146 (defn- match-all
147 "Returns a vector of two elements; the first element is the list of matches
148 of the query-vs against all SAT vs in the library sorted by mean euclidean distance,
149 and labeled as correct of incorrect matches according to the Random Forest classifier.
150 The second element is a list of corresponding SAT names for each match.
151 Assumes the query-vs is already registered to the corresponding SAT-lib reference fiducials."
152 [SATs query-vs delta direct substring]
153 (let [vs1 (resample query-vs delta) ; query-vs is already registered into FRT42-fids
154 matches (sort
155 #(int (- (%1 :med) (%2 :med)))
156 (doall (pmap
157 (fn [e]
158 (let [vs2 (let [copy (.clone (val e))]
159 (.resample copy delta)
160 copy)
161 c (Compare/findBestMatch vs1 vs2
162 (double delta) false (int 5) (float 0.5) Compare/AVG_PHYS_DIST
163 direct substring
164 (double 1.1) (double 1.1) (double 1))
165 stats (.getStatistics (get c 0) false (int 0) (float 0) false)]
166 {:SAT-name (key e)
167 :stats stats
168 :med (get stats 0)
169 :correct (LineageClassifier/classify stats)}))
170 SATs)))]
171 ; Cleanup thread table
172 (LineageClassifier/flush)
174 [matches
175 (map (fn [match]
176 (match :SAT-name))
177 matches)]))
179 (defn text-width
180 "Measure the width, in pixels, of the String text, by the Font and FontMetrics of component."
181 [#^String text #^Component component]
182 ; Get the int[] of widths of the first 256 chars
183 (let [#^ints ws (.getWidths (.getFontMetrics component (.getFont component)))]
184 (reduce (fn [sum c]
185 (if (< (int c) (int 256))
186 (+ sum (aget ws (int c)))
187 sum))
188 0
189 text)))
191 (defn- identify-SAT
192 "Takes a calibrated VectorString3D and a list of fiducial points, and checks against the library for identity.
193 For consistency in the usage of the Random Forest classifier, the registration is done into the FRT42D-BP106 brain."
194 [pipe SAT-lib query-vs fids delta direct substring]
195 (let [SATs (SAT-lib :SATs)
196 vs1 (register-vs query-vs fids (SAT-lib :fids))
197 [matches names] (match-all SATs vs1 delta direct substring)
198 SAT-names (vec names)
199 indexed (vec matches)
200 column-names ["SAT" "Match" "Seq sim %" "Lev Dist" "Med Dist" "Avg Dist" "Cum Dist" "Std Dev" "Prop Mut" "Prop Lengths" "Proximity" "Prox Mut" "Tortuosity"]
201 worker (agent nil) ; for event dispatch
202 table (JTable. (proxy [AbstractTableModel] []
203 (getColumnName [col]
204 (get column-names col))
205 (getRowCount []
206 (count matches))
207 (getColumnCount []
208 (count column-names))
209 (getValueAt [row col]
210 (let [match (get indexed row)
211 stats (match :stats)]
212 (cond
213 (= col 0) (get SAT-names row)
214 (= col 1) (str (match :correct)) ; Whether the classifier considered it correct or not
215 true (Utils/cutNumber
216 (cond
217 (= col 2) (* 100 (get stats 6)) ; Similarity
218 (= col 3) (get stats 5) ; Levenshtein
219 (= col 4) (get stats 3) ; Median Physical Distance
220 (= col 5) (get stats 0) ; Average Physical Distance
221 (= col 6) (get stats 1) ; Cummulative Physical Distance
222 (= col 7) (get stats 2) ; Std Dev
223 (= col 8) (get stats 4) ; Prop Mut
224 (= col 9) (get stats 9) ; Prop Lengths
225 (= col 10) (get stats 7) ; Proximity
226 (= col 11) (get stats 8) ; Prox Mut
227 (= col 12) (get stats 10)) ; Tortuosity
228 2))))
229 (isCellEditable [row col]
230 false)
231 (setValueAt [ob row col] nil)))
232 frame (JFrame. (str "Matches for " pipe))
233 dummy-ls (LayerSet. (.. Display getFront getProject) (long -1) "Dummy" (double 0) (double 0) (double 0) (double 0) (double 0) (double 512) (double 512) false (int 0) (java.awt.geom.AffineTransform.))]
234 (.setCellRenderer (.getColumn table "Match")
235 (proxy [DefaultTableCellRenderer] []
236 (getTableCellRendererComponent [t v sel foc row col]
237 (proxy-super setText (str v))
238 (proxy-super setBackground
239 (if (Boolean/parseBoolean v)
240 (Color. 166 255 166)
241 (if sel
242 (Color. 184 207 229)
243 Color/white)))
245 this)))
246 (.add frame (JScrollPane. table))
247 (.setSize frame (int 950) (int 550))
248 (.addMouseListener table
249 (proxy [MouseAdapter] []
250 (mousePressed [ev]
251 (try
252 (clear-agent-errors worker) ; I don't care what it was
253 (catch Exception e))
254 (send-off worker
255 (fn [_]
256 (let [match (indexed (.rowAtPoint table (.getPoint ev)))
257 show-match (fn []
258 (Display3D/addMesh dummy-ls
259 (resample (.clone vs1) delta)
260 "Query"
261 Color/yellow)
262 (Display3D/addMesh dummy-ls
263 (resample (SATs (match :SAT-name)) delta)
264 (match :SAT-name)
265 (if (match :correct)
266 Color/red
267 Color/blue)))]
268 (cond
269 ; On double-click, show 3D view of the match:
270 (= 2 (.getClickCount ev))
271 (show-match)
272 ; On right-click, show menu
273 (Utils/isPopupTrigger ev)
274 (let [popup (JPopupMenu.)
275 new-command (fn [title action]
276 (let [item (JMenuItem. title)]
277 (.addActionListener item (proxy [ActionListener] []
278 (actionPerformed [evt]
279 (send-off worker (fn [_] (action))))))
280 item))]
281 (doto popup
282 (.add (new-command "Show match in 3D"
283 show-match))
284 (.add (new-command "Show Mushroom body"
285 #(doseq [[k v] (SAT-lib :mb)]
286 (Display3D/addMesh dummy-ls v k Color/gray))))
287 (.add (new-command "Show interpolated"
288 #(Display3D/addMesh dummy-ls
289 (VectorString3D/createInterpolatedPoints
290 (Editions. (SATs (match :SAT-name)) (.clone vs1) delta false (double 1.1) (double 1.1) (double 1)) (float 0.5))
291 (str "Interpolated with " (match :SAT-name)) Color/magenta)))
292 (.add (new-command "Show stdDev plot"
293 #(let [cp (ini.trakem2.analysis.Compare$CATAParameters.)]
294 (if (.setup cp false nil true true)
295 (let [condensed (VectorString3D/createInterpolatedPoints
296 (let [v1 (.clone vs1)
297 v2 (SATs (match :SAT-name))]
298 (.resample v1 delta true)
299 (.resample v2 delta true)
300 (Editions. v1 v2 delta false (double 1.1) (double 1.1) (double 1)))
301 (float 0.5))
302 _ (let [c1 (Calibration.); Dummy default calibration but with same units as the pipe.
303 ; VectorString3D instances are already calibrated.
304 c2 (.. pipe getLayerSet getCalibrationCopy)]
305 (.setUnit c1 (.getUnit c2))
306 (.calibrate condensed c1))
307 _ (set! (. cp plot_max_x) (.length condensed))
308 plot (Compare/makePlot cp (str "Query versus " (match :SAT-name)) condensed)]
309 ; There are lazy evaluations ... that need to be promoted: lets print some data:
310 (println "plot is" plot " and condensed has " (.getStdDevAtEachPoint condensed))
311 (if plot
312 (.show plot)
313 (report "ERROR: could not make a plot!")))))))
314 (.show table (.getX ev) (.getY ev)))))))))))
316 ; Enlarge the cell width of the first column
317 (.setMinWidth (.. table getColumnModel (getColumn 0)) (int 250))
318 (doto frame
319 ;(.pack)
320 (.setVisible true))))
322 (defn fetch-lib
323 "Returns the SAT lib for the given name, loading it if not there yet. Nil otherwise."
324 [lib]
325 (if-let [cached (@*libs* (lib "title"))]
326 cached
327 (try
328 (load-SAT-lib lib)
329 (catch Exception e
330 (do
331 (report "An error ocurred while loading the SAT library '" (lib "title") ": " e "\nCheck the terminal output.")
332 (.printStackTrace e))))))
335 (defn extract-fiducial-points
336 "Find a set of fiducial points in the project.
337 Will find the first node of type 'fiducial_points' and recursively inspect
338 its children nodes for nodes of type 'ball'. To each found 'ball', it will
339 assign the name of the ball node itself or the first superior node that
340 has a name different that this type.
341 Returns nil if none found."
342 [project]
343 (if-let [fp-node (.. project getRootProjectThing (findChildrenOfTypeR "fiducial_points"))]
344 (if-let [ball-nodes (.findChildrenOfTypeR (first fp-node) "ball")]
345 (let [fids (reduce
346 (fn [fids pt-ball]
347 (let [title (.. pt-ball getObject getTitle) ; the title of the Ball ob itself, if any
348 b (.. pt-ball getObject getWorldBalls)]
349 (if (= 0 (count b))
350 (do
351 (println "WARNING: empty ball object" (.getObject pt-ball))
352 fids)
353 (do
354 (if (> (count b) 1)
355 (println "WARNING: ball object with more than one ball:" (.getObject pt-ball)))
356 (assoc fids
357 (-> (if (not (= title (.getType pt-ball)))
358 title
359 (.. pt-ball getParent getTitle))
360 (.toLowerCase)
361 (.replace \space \_))
362 (let [b0 (get b 0)]
363 (Point3d. (get b0 0) (get b0 1) (get b0 2))))))))
364 {}
365 ball-nodes)]
366 (println "Found" (count fids) "fiducial points:\n" fids)
367 fids)
368 (println "No ball objects found for" fp-node))
369 (println "No fiducial points found")))
371 (defn identify
372 "Identify a Pipe or Polyline (which implement Line3D) that represent a SAT."
373 ([p
374 ^Map lib]
375 (identify p lib 1.0 true false))
376 ([p
377 ^Map lib
378 delta direct substring]
379 (if p
380 (if-let [SAT-lib (fetch-lib (into {} lib))]
381 (if-let [fids (extract-fiducial-points (.getProject p))]
382 (identify-SAT
383 p
384 SAT-lib
385 (let [vs (.asVectorString3D p)]
386 (.calibrate vs (.. p getLayerSet getCalibrationCopy))
387 vs)
388 fids
389 delta
390 direct
391 substring)
392 (report "Cannot find fiducial points for project" (.getProject p)))
393 (report "Cannot find or parse SAT library at " (.get lib "title") " at " (.get lib "filepath")))
394 (report "Cannot identify a null pipe or polyline!"))))
397 (defn identify-without-gui
398 "Identify a Pipe or Polyline (which implement Line3D) that represent a SAT.
399 No GUI is shown. Returns the vector containing the list of matches and the list of names."
400 ([p
401 ^Map lib]
402 (identify-without-gui p lib 1.0 true false))
403 ([p
404 ^Map lib
405 delta direct substring]
406 (if p
407 (if-let [SAT-lib (fetch-lib (into {} lib))]
408 (let [SATs (SAT-lib :SATs)
409 query-vs (let [vs (.asVectorString3D p)]
410 (.calibrate vs (.. p getLayerSet getCalibrationCopy))
411 vs)
412 fids (extract-fiducial-points (.getProject p)) ; (first (.. p getProject getRootProjectThing (findChildrenOfTypeR "fiducial_points"))))
413 vs1 (register-vs query-vs fids (SAT-lib :fids))]
414 (match-all SATs vs1 delta direct substring)))
415 (report "Cannot identify a null pipe or polyline!"))))
418 ;(defn lib-stats
419 ; "Returns a map with the number of SATs in the library, a list of names vs. sorted sequence lengths, the median length, the average length."
420 ; [lib-name delta]
421 ; (if-let [lib (fetch-lib lib-name)]
422 ; (let [SATs (SAT-lib :SATs)
423 ; lengths (reduce
424 ; (sorted-map-by
425 ; #(<
426 ;
427 ;
428 ; {:n (count SATs)
429 ; :
430 ; (report (str "Unknown library " lib-name))))
432 (defn- ready-vs
433 "Return a calibrate and registered VectorString3D from a chain."
434 [chain source-fids target-fids]
435 (let [vs (.clone (.vs chain))]
436 (.calibrate vs (.. chain getRoot getLayerSet getCalibrationCopy))
437 (register-vs vs source-fids target-fids)))
439 (defn quantify-all
440 "Take all pipes in project and score/classify them.
441 Returns a sorted map of name vs. a vector with:
442 - if the top 1,2,3,4,5 have a homonymous
443 - the number of positives: 'true' and homonymous
444 - the number of false positives: 'true' and not homonymous
445 - the number of false negatives: 'false' and homonymous
446 - the number of true negatives: 'false' and not homonymous
447 - the FPR: false positive rate: false positives / ( false positives + true negatives )
448 - the FNR: false negative rate: false negatives / ( false negatives + true positives )
449 - the TPR: true positive rate: 1 - FNR
450 - the length of the sequence queried"
451 [project lib regex-exclude delta direct substring]
452 (let [fids (extract-fiducial-points (first (.. project getRootProjectThing (findChildrenOfTypeR "fiducial_points"))))
453 tops (int 5)
454 SAT-lib (fetch-lib lib)]
455 (if SAT-lib
456 (reduce
457 (fn [m chain]
458 (let [vs (resample (ready-vs chain fids (SAT-lib :fids)) delta)
459 [matches names] (match-all (SAT-lib :SATs) vs delta direct substring)
460 names (vec (take tops names))
461 #^String SAT-name (let [t (.getCellTitle chain)]
462 (.substring t (int 0) (.indexOf t (int \space))))
463 ;has-top-match (fn [n] (some #(.startsWith % SAT-name) (take names n)))
464 dummy (println "###\nSAT-name: " SAT-name "\ntop 5 names: " names "\ntop 5 meds: " (map #(% :med) (take 5 matches)))
465 top-matches (loop [i (int 0)
466 r []]
467 (if (>= i tops)
468 r
469 (if (.startsWith (names i) SAT-name)
470 (into r (repeat (- tops i) true)) ; the rest are all true
471 (recur (inc i) (into [false] r)))))
472 true-positives (filter #(and
473 (% :correct)
474 (.startsWith (% :SAT-name) SAT-name))
475 matches)
476 true-negatives (filter #(and
477 (not (% :correct))
478 (not (.startsWith (% :SAT-name) SAT-name)))
479 matches)
480 false-positives (filter #(and
481 (% :correct)
482 (not (.startsWith (% :SAT-name) SAT-name)))
483 matches)
484 false-negatives (filter #(and
485 (not (% :correct))
486 (.startsWith (% :SAT-name) SAT-name))
487 matches)]
488 (println "top matches for " SAT-name " : " (count top-matches) top-matches)
489 (assoc m
490 SAT-name
491 [(top-matches 0)
492 (top-matches 1)
493 (top-matches 2)
494 (top-matches 3)
495 (top-matches 4)
496 (count true-positives)
497 (count false-positives)
498 (count true-negatives)
499 (count false-negatives)
500 (/ (count false-positives) (+ (count false-positives) (count true-negatives))) ; False positive rate
501 (let [divisor (+ (count false-negatives) (count true-positives))]
502 (if (= 0 divisor)
503 Double/MAX_VALUE
504 (/ (count false-negatives) divisor))) ; False negative rate
505 (let [divisor (+ (count false-negatives) (count true-positives))]
506 (if (= 0 divisor)
507 Double/MAX_VALUE
508 (- 1 (/ (count false-negatives) divisor)))) ; True positive rate
509 (.length vs)])))
510 (sorted-map)
511 (Compare/createPipeChains (.getRootProjectThing project) (.getRootLayerSet project) regex-exclude)))))
513 (defn summarize-as-confusion-matrix
514 "Takes the results of quantify-all and returns the confusion matrix as a map."
515 [qa]
516 (reduce
517 (fn [m results]
518 (merge-with + m {:true-positives (results 5)
519 :false-positives (results 6)
520 :true-negatives (results 7)
521 :false-negatives (results 8)}))
522 {:true-positives 0
523 :false-positives 0
524 :true-negatives 0
525 :false-negatives 0}
526 (vals qa)))
528 (defn summarize-as-distributions
529 "Takes the results of quantify-all and returns four vectors representing four histograms,
530 one for each distribution of true-positives, false-positives, true-negatives and false-negatives."
531 [qa]
532 (reduce
533 (fn [m results]
534 (merge-with (fn [m1 m2]
535 (merge-with + m1 m2))
536 m
537 {:true-positives {(results 5) 1}
538 :false-positives {(results 6) 1}
539 :true-negatives {(results 7) 1}
540 :false-negatives {(results 8) 1}}))
541 {:true-positives (sorted-map)
542 :false-positives (sorted-map)
543 :true-negatives (sorted-map)
544 :false-negatives (sorted-map)}
545 (vals qa)))
547 (defn summarize-quantify-all
548 "Takes the results of quantify-all and returns a map of two maps,
549 one with the confusion matrix and one with the distribution of true/false-positive/negative matches."
550 [project lib regex-exclude delta direct substring]
551 (let [qa (quantify-all project lib regex-exclude delta direct substring)]
552 {:confusion-matrix (summarize-as-confusion-matrix qa)
553 :distributions (summarize-as-distributions)}))
556 (defn print-quantify-all [t]
557 (doseq [[k v] t]
558 (print k \tab)
559 (doseq [x (take 5 v)] (print x \tab))
560 (doseq [x (nthnext v 5)] (print (float x) \tab))
561 (print \newline)))
564 (defn find-rev-match
565 "Take a set of non-homonymous VectorString3D.
566 Do pairwise comparisons, in this fashion:
567 1. reverse vs2
568 2. substring length SL = 0.5 * max(len(vs1), len(vs2))
569 3. for all substrings of len SL of vs1, match against all of vs2.
570 4. Record best result in a set sorted by mean euclidean distance of the best match.
571 Assumes chains are registered and resampled.
572 Will ignore cases where the shorter chain is shorter than half the longer chain."
573 [chains delta]
574 (reduce
575 (fn [s chain1]
576 (let [rvs1 (let [v (.clone (.vs chain1))]
577 (.reverse v)
578 (.resample v delta)
579 v)
580 len1 (.length rvs1)]
581 (conj s (reduce
582 ; Find best reverse submatch for chain1 in chains
583 (fn [best chain2]
584 (println "Processing " (.getShortCellTitle chain1) " versus " (.getShortCellTitle chain2))
585 (let [vs2 (.vs chain2)
586 len2 (.length vs2)
587 SL (int (/ (max len1 len2) 2))]
588 (if (or (= chain1 chain2) (< len1 SL) (< len2 SL))
589 best ; A chain has to be longer than half the length of the other to be worth looking at
590 (let [b (reduce
591 ; Find best reverse submatch between chain1 and chain2
592 (fn [best-rsub start]
593 (let [bm (Compare/findBestMatch (.substring rvs1 start (+ start SL))
594 vs2
595 delta
596 false 0 0
597 Compare/AVG_PHYS_DIST ; Also known as mean euclidean distance
598 true true
599 1.1 1.1 1.0)]
600 (if (and
601 best-rsub
602 (< (best-rsub :med) (get bm 1)))
603 best-rsub
604 {:chain1 chain1 :chain2 chain2 :med (get bm 1)})))
605 {:med Double/MAX_VALUE}
606 (range (- len1 SL)))]
607 (if (and
608 best
609 (< (best :med) (b :med)))
610 best
611 b)))))
612 {:med Double/MAX_VALUE} ; bogus initial element
613 chains))))
614 (sorted-set-by
615 #(int (- (%1 :med) (%2 :med)))
616 {:med Double/MAX_VALUE}) ; adding a bogus initial element
617 chains))
620 (defn find-reverse-match
621 "Takes all the chains of a project and compares them all-to-all pairwise with one of the two reversed.
622 Will calibrate the chains and resample them to delta."
623 [project delta regex-exclude]
624 (let [cal (.. project getRootLayerSet getCalibrationCopy)]
625 (find-rev-match (map
626 (fn [chain]
627 (.calibrate (.vs chain) cal)
628 (.resample (.vs chain) delta)
629 chain)
630 (Compare/createPipeChains (.getRootProjectThing project) (.getRootLayerSet project) regex-exclude))
631 delta)))
633 (defn print-reversed-match
634 "Prints the sorted set returned by find-reversed-similar"
635 [s]
636 (doseq [m s]
637 (let [c1 (m :chain1)
638 c2 (m :chain2)]
639 (if c1
640 (println (.getShortCellTitle c1) (.getShortCellTitle c2) (m :med))))))
643 (defn print-stats
644 "Prints the number of unique SATs and the number of unique lineages in a library of SATs.
645 Returns the two sets in a map."
646 [lib]
647 (let [lib (fetch-lib lib)
648 unique-sats (reduce
649 (fn [unique clone]
650 (if (> (.indexOf clone (int \space)) -1)
651 (conj unique (.substring clone 0 (.indexOf clone (int \space))))
652 unique))
653 (sorted-set)
654 (keys (lib :SATs)))
655 unique-lineages (reduce
656 (fn [unique clone]
657 (if (> (.indexOf clone (int \:)) -1)
658 (conj unique (.substring clone 0 (.indexOf clone (int \:))))
659 unique))
660 (sorted-set)
661 unique-sats)]
662 (println "Unique SATs: " (count unique-sats) \newline "Unique lineages: " (count unique-lineages))
663 {:unique-sats unique-sats
664 :unique-lineages unique-lineages}))
666 (defn- test
667 []
668 (identify (first (ini.trakem2.display.Display/getSelected))
669 {"title" "3rd instar"
670 "reference" "FRT42 new"
671 "filepath" "/home/albert/Programming/fiji/plugins/SAT-lib-Drosophila-3rd-instar.clj"}))