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annotate org/gabor.org @ 365:1727b68634ea

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add videos.
author Robert McIntyre <rlm@mit.edu>
date Thu, 07 Mar 2013 07:49:55 +0000
parents b599a189433b
children 871882350c83
rev   line source
rlm@356 1 #+title: Fun with Gabor Filters
rlm@356 2 #+author: Robert McIntyre
rlm@356 3 #+email: rlm@mit.edu
rlm@356 4 #+description: gabor filters in clojure with opencv
rlm@356 5 #+keywords: computer vision, jMonkeyEngine3, clojure, opencv
rlm@356 6 #+SETUPFILE: ../../aurellem/org/setup.org
rlm@356 7 #+INCLUDE: ../../aurellem/org/level-0.org
rlm@356 8 #+babel: :mkdirp yes :noweb yes :exports both
rlm@356 9
rlm@356 10
rlm@356 11
rlm@356 12 #+name: gabor
rlm@356 13 #+begin_src clojure
rlm@357 14 (ns cortex.gabor
rlm@357 15 (:import org.opencv.core.CvType)
rlm@357 16 (:import java.awt.image.BufferedImage)
rlm@357 17 (:import ij.ImagePlus)
rlm@358 18 (:import org.opencv.core.Mat)
rlm@364 19 (:use (cortex world sense util vision import))
rlm@363 20 (:import com.jme3.post.SceneProcessor)
rlm@363 21 (:import (com.jme3.util BufferUtils Screenshots))
rlm@363 22 (:import java.nio.ByteBuffer)
rlm@363 23 (:import java.awt.image.BufferedImage)
rlm@363 24 (:import (com.jme3.renderer ViewPort Camera))
rlm@363 25 (:import (com.jme3.math ColorRGBA Vector3f Matrix3f Vector2f))
rlm@363 26 (:import com.jme3.renderer.Renderer)
rlm@363 27 (:import com.jme3.app.Application)
rlm@363 28 (:import com.jme3.texture.FrameBuffer)
rlm@363 29 (:import (com.jme3.scene Node Spatial)))
rlm@363 30
rlm@363 31
rlm@363 32 (cortex.import/mega-import-jme3)
rlm@364 33 (use 'clojure.math.numeric-tower)
rlm@356 34 (defn load-opencv
rlm@356 35 "Load the opencv native library. Must be called before any OpenCV
rlm@356 36 stuff is used."
rlm@356 37 []
rlm@356 38 (clojure.lang.RT/loadLibrary "opencv_java249"))
rlm@356 39
rlm@364 40 (load-opencv)
rlm@364 41
rlm@364 42 (defn gabor-kernel
rlm@364 43 ([sigma wavelength theta]
rlm@364 44 (gabor-kernel sigma wavelength theta 1 0))
rlm@364 45 ([sigma wavelength]
rlm@364 46 (gabor-kernel sigma wavelength 0 1 0))
rlm@364 47 ([sigma wavelength theta aspect-ratio phase-offset]
rlm@359 48
rlm@359 49 ;; first, find the size of the kernel which is required
rlm@359 50 (let [square #(expt % 2)
rlm@359 51 rotated (fn [[x y]]
rlm@359 52 [(+ (* x (Math/cos theta)) (* y (Math/sin theta)))
rlm@359 53 (- (* y (Math/cos theta)) (* x (Math/sin theta)))])
rlm@359 54
rlm@359 55 gaussian (fn [[x y]]
rlm@359 56 (let [[x' y'] (rotated [x y])]
rlm@359 57 (Math/exp (- (/ (+ (square x')
rlm@359 58 (square (* aspect-ratio y')))
rlm@359 59 (* 2 (square sigma)))))))
rlm@359 60 sinusoid (fn [[x y]]
rlm@359 61 (let [[x' y'] (rotated [x y])]
rlm@359 62 (Math/cos
rlm@359 63 (+ (* 2 Math/PI (/ x' wavelength))
rlm@359 64 phase-offset))))
rlm@359 65
rlm@361 66 half-width
rlm@361 67 (let [std-dev-capture 5]
rlm@361 68 (max
rlm@361 69 (int (* std-dev-capture (/ sigma aspect-ratio)))
rlm@361 70 (int (* std-dev-capture sigma))
rlm@361 71 (int (* std-dev-capture (/ aspect-ratio sigma)))))
rlm@359 72
rlm@359 73 grid (let [axis (range (- half-width) (inc half-width))]
rlm@359 74 (for [y (reverse axis) x axis] (vector x y)))
rlm@359 75
rlm@359 76 scale (reduce + (map gaussian grid))
rlm@359 77
rlm@359 78 gabor (fn [[x y :as coord]]
rlm@360 79 (* (sinusoid coord) (gaussian coord) (/ scale)))
rlm@359 80
rlm@359 81 mat-width (+ 1 (* 2 half-width))
rlm@359 82 mat (Mat. mat-width mat-width CvType/CV_32F)]
rlm@359 83
rlm@359 84 (.put mat 0 0 (float-array (map gabor grid)))
rlm@364 85 mat)))
rlm@359 86
rlm@359 87
rlm@361 88 (defn draw-kernel! [kernel img-path]
rlm@361 89 (let [output img-path
rlm@360 90 size (.size kernel)
rlm@360 91 width (int (.width size))
rlm@360 92 height (int (.height size))
rlm@360 93 tmp-array (float-array (* width height))]
rlm@360 94
rlm@360 95 ;; read values from matrix.
rlm@360 96 (.get kernel 0 0 tmp-array)
rlm@360 97
rlm@360 98 ;; find overall dynamic range of the filter
rlm@360 99 (let [vals (vec tmp-array)
rlm@360 100 low (apply min vals)
rlm@360 101 high (apply max vals)
rlm@360 102 scaled-vals (map #(* 255 (- % low) (/ (- high low))) vals)
rlm@360 103 new-mat (Mat. height width CvType/CV_32F)]
rlm@360 104 (.put new-mat 0 0 (float-array scaled-vals))
rlm@361 105 (org.opencv.highgui.Highgui/imwrite output new-mat))))
rlm@361 106
rlm@364 107 ;; some cool examples
rlm@364 108 #+end_src
rlm@364 109
rlm@364 110
rlm@364 111
rlm@364 112
rlm@364 113 [[../images/gabor-50-10.png]]
rlm@364 114
rlm@364 115 #+begin_src clojure
rlm@364 116 (def img-base "/home/r/proj/cortex/images/")
rlm@364 117
rlm@364 118 (draw-kernel! (gabor-kernel 50 10 0 1 0)
rlm@364 119 (str img-base "gabor-50-10.png"))
rlm@364 120 #+end_src
rlm@364 121
rlm@364 122
rlm@364 123 [[../images/gabor-50-10-pi-over-4.png]]
rlm@364 124
rlm@364 125 #+begin_src clojure
rlm@364 126 (draw-kernel! (gabor-kernel 50 10 (/ Math/PI 4) 1 0)
rlm@364 127 (str img-base "gabor-50-10-pi-over-4.png"))
rlm@364 128 #+end_src
rlm@364 129
rlm@364 130
rlm@364 131 [[../images/gabor-50-10-pi-over-2.png]]
rlm@364 132
rlm@364 133 #+begin_src clojure
rlm@364 134 (draw-kernel! (gabor-kernel 50 10 (/ Math/PI 2) 1 0)
rlm@364 135 (str img-base "gabor-50-10-pi-over-2.png"))
rlm@364 136 #+end_src
rlm@364 137
rlm@364 138
rlm@364 139 [[../images/gabor-50-50.png]]
rlm@364 140
rlm@364 141
rlm@364 142
rlm@364 143 #+begin_src clojure
rlm@364 144 (draw-kernel! (gabor-kernel 50 50 0 1 0)
rlm@364 145 (str img-base "gabor-50-50.png"))
rlm@364 146
rlm@364 147 #+end_src
rlm@364 148
rlm@364 149 [[../images/gabor-50-10-0-3.png]]
rlm@364 150
rlm@364 151 #+begin_src clojure
rlm@364 152 (draw-kernel! (gabor-kernel 50 10 0 3 0)
rlm@364 153 (str img-base "gabor-50-10-0-3.png"))
rlm@364 154 #+end_src
rlm@364 155
rlm@364 156
rlm@364 157
rlm@364 158 [[../images/gabor-50-4-pi-over3-3.png]]
rlm@364 159 #+begin_src clojure
rlm@364 160 (draw-kernel! (gabor-kernel 50 4 (/ Math/PI 3) 3 0)
rlm@364 161 (str img-base "gabor-50-4-pi-over3-3.png"))
rlm@364 162 #+end_src
rlm@364 163
rlm@364 164
rlm@364 165
rlm@364 166
rlm@364 167
rlm@364 168 #:name gabor-tail
rlm@364 169 #+begin_src clojure
rlm@361 170 (defn show-kernel [kernel]
rlm@361 171 (let [img-path "/home/r/proj/cortex/tmp/kernel.png"]
rlm@362 172 (draw-kernel! kernel img-path)
rlm@364 173 (view (ImagePlus. img-path))))
rlm@359 174
rlm@359 175 (defn print-kernel [kernel]
rlm@359 176 (println (.dump kernel)))
rlm@359 177
rlm@363 178
rlm@363 179 (def brick-length 0.48)
rlm@363 180 (def brick-width 0.24)
rlm@363 181 (def brick-height 0.12)
rlm@363 182 (def gravity (Vector3f. 0 -9.81 0))
rlm@363 183
rlm@363 184
rlm@363 185 (defn brick* [position]
rlm@363 186 (println "get brick.")
rlm@363 187 (doto (box brick-length brick-height brick-width
rlm@363 188 :position position :name "brick"
rlm@363 189 :material "Common/MatDefs/Misc/Unshaded.j3md"
rlm@363 190 :texture "Textures/Terrain/BrickWall/BrickWall.jpg"
rlm@363 191 :mass 34)
rlm@363 192 (->
rlm@363 193 (.getMesh)
rlm@363 194 (.scaleTextureCoordinates (Vector2f. 1 0.5)))
rlm@363 195 (.setShadowMode RenderQueue$ShadowMode/CastAndReceive)
rlm@363 196 )
rlm@363 197 )
rlm@363 198
rlm@363 199
rlm@363 200 (defn floor*
rlm@363 201 "make a sturdy, unmovable physical floor"
rlm@363 202 []
rlm@363 203 (box 10 0.1 5 :name "floor" :mass 0 :color ColorRGBA/Gray :position (Vector3f. 0 0 0)))
rlm@363 204
rlm@363 205 (defn floor* []
rlm@363 206 (doto (box 10 0.1 5 :name "floor" ;10 0.1 5 ; 240 0.1 240
rlm@363 207 :material "Common/MatDefs/Misc/Unshaded.j3md"
rlm@363 208 :texture "Textures/BronzeCopper030.jpg"
rlm@363 209 :position (Vector3f. 0 0 0 )
rlm@363 210 :mass 0)
rlm@363 211 (->
rlm@363 212 (.getMesh)
rlm@363 213 (.scaleTextureCoordinates (Vector2f. 3 6)));64 64
rlm@363 214 (->
rlm@363 215 (.getMaterial)
rlm@363 216 (.getTextureParam "ColorMap")
rlm@363 217 (.getTextureValue)
rlm@363 218 (.setWrap Texture$WrapMode/Repeat))
rlm@363 219 (.setShadowMode RenderQueue$ShadowMode/Receive)
rlm@363 220 ))
rlm@363 221
rlm@363 222
rlm@363 223 (defn brick-wall* []
rlm@363 224 (let [node (Node. "brick-wall")]
rlm@363 225 (dorun
rlm@363 226 (map
rlm@363 227 (comp #(.attachChild node %) brick*)
rlm@363 228 (for [y (range 10)
rlm@363 229 x (range 4)
rlm@363 230 z (range 1)]
rlm@363 231 (Vector3f.
rlm@363 232 (+ (* 2 x brick-length)
rlm@363 233 (if (even? (+ y z))
rlm@363 234 (/ brick-length 4) (/ brick-length -4)))
rlm@363 235 (+ (* brick-height (inc (* 2 y))))
rlm@363 236 (* 2 z brick-width) ))))
rlm@363 237 (.setShadowMode node RenderQueue$ShadowMode/CastAndReceive)
rlm@363 238 node))
rlm@363 239
rlm@363 240 (import com.aurellem.capture.Capture)
rlm@363 241
rlm@363 242 (import java.io.File)
rlm@363 243
rlm@364 244 (def base "/home/r/proj/cortex/render/gabor-1/")
rlm@363 245
rlm@363 246 (defn brick-wall-game-run [record?]
rlm@364 247 (let [capture-dir (File. base "main")]
rlm@364 248
rlm@364 249 (.mkdir (File. base "main"))
rlm@364 250 (doto
rlm@364 251 (world
rlm@364 252 (doto (Node.) (.attachChild (floor*))
rlm@364 253 (.attachChild (brick-wall*))
rlm@364 254 )
rlm@364 255 {"key-f" (fn [game value]
rlm@364 256 (if (not value) (add-element game (brick-wall*))))
rlm@364 257 "key-space" (fire-cannon-ball )}
rlm@364 258 (fn [world]
rlm@364 259 (position-camera world
rlm@364 260 (Vector3f. 1.382548, 4.0383573, 5.994235)
rlm@364 261 (Quaternion. 0.0013082094, 0.98581666, -0.1676442, 0.0076932586))
rlm@363 262
rlm@364 263 ;;(speed-up world)
rlm@364 264
rlm@364 265 (if record?
rlm@364 266 (Capture/captureVideo
rlm@364 267 world capture-dir))
rlm@364 268
rlm@363 269 (add-camera! world (.getCamera world) no-op))
rlm@364 270 (fn [& _]))
rlm@364 271 (.start))))
rlm@363 272
rlm@364 273 (defn convolve-preview [kernel]
rlm@363 274 (let [input "/home/r/proj/cortex/render/gabor-1/main/0000032.png"
rlm@357 275
rlm@357 276
rlm@357 277 output "/home/r/ppp.png"
rlm@356 278
rlm@357 279 i (org.opencv.highgui.Highgui/imread input)
rlm@358 280
rlm@364 281 ;;kernel (gabor-kernel 10 1 (/ Math/PI 2) 10 0)
rlm@358 282
rlm@358 283 new-mat (Mat.)
rlm@358 284
rlm@357 285 ]
rlm@356 286
rlm@360 287 (org.opencv.imgproc.Imgproc/filter2D i new-mat CvType/CV_32F kernel)
rlm@358 288
rlm@358 289 (org.opencv.highgui.Highgui/imwrite "/home/r/ppp.png" new-mat)
rlm@358 290
rlm@357 291 (view (ImagePlus. input))
rlm@361 292 (view (ImagePlus. output))))
rlm@357 293
rlm@364 294 (use 'clojure.java.shell)
rlm@363 295
rlm@363 296
rlm@364 297 (defn apply-gabor [kernel source dest]
rlm@364 298 (let [i (org.opencv.highgui.Highgui/imread source)
rlm@364 299 new-mat (Mat.)]
rlm@364 300
rlm@364 301 (println dest)
rlm@364 302 (if (not (.exists (File. dest)))
rlm@364 303 (do
rlm@364 304 (org.opencv.imgproc.Imgproc/filter2D i new-mat CvType/CV_32F kernel)
rlm@364 305 (org.opencv.highgui.Highgui/imwrite dest new-mat)
rlm@364 306 (println "mogrify" "-modulate" "1000%" dest)
rlm@364 307 (sh "mogrify" "-modulate" "1000%" dest)))))
rlm@363 308
rlm@363 309
rlm@364 310 (import java.io.File)
rlm@363 311
rlm@364 312 (defn images [path]
rlm@364 313 (sort (rest (file-seq (File. path)))))
rlm@364 314
rlm@364 315
rlm@364 316
rlm@364 317 (defn pics [file]
rlm@364 318 (images (str base file)))
rlm@364 319
rlm@364 320 (defn generate-gabor-images [kernel name]
rlm@364 321 (draw-kernel! kernel (str base name ".png"))
rlm@364 322
rlm@364 323 (.mkdir (File. (str base name)))
rlm@364 324
rlm@364 325 (let [main (map #(.getCanonicalPath %) (pics "main"))
rlm@364 326 targets (map #(str base name "/" (format "%07d.png" %))
rlm@364 327 (range 0 (count main)))]
rlm@364 328 (dorun (pmap (partial apply-gabor kernel) main targets))))
rlm@364 329
rlm@364 330
rlm@364 331 (def banks
rlm@364 332 [[(gabor-kernel 2.8 3.5) "bank-1-1"]
rlm@364 333 [(gabor-kernel 2.8 3.5 (/ Math/PI 2)) "bank-1-1-rot"]
rlm@364 334
rlm@364 335 ;; [(gabor-kernel 3.6 4.6) "bank-1-2"]
rlm@364 336 ;; [(gabor-kernel 4.5 5.6) "bank-2-1"]
rlm@364 337 ;; [(gabor-kernel 6.3 7.9) "bank-3-1"]
rlm@364 338 ;; [(gabor-kernel 7.3 9.1) "bank-3-2"]
rlm@364 339
rlm@364 340 [(gabor-kernel 12.3 15.4) "bank-6-1"]
rlm@364 341
rlm@364 342
rlm@364 343 ;; [(gabor-kernel 17 21.2) "bank-8-1"]
rlm@364 344 ;; [(gabor-kernel 18.2 22.8) "bank-8-2"]
rlm@364 345 ])
rlm@364 346
rlm@364 347
rlm@364 348 (defn make-all-images []
rlm@364 349 (dorun (map (partial apply generate-gabor-images) banks)))
rlm@364 350
rlm@364 351
rlm@364 352
rlm@364 353 (defn compile-left-right []
rlm@364 354 (.mkdir (File. (str base "left-right")))
rlm@364 355 (let [main (pics "main")
rlm@364 356 left (pics "bank-1-1")
rlm@364 357 right (pics "bank-1-1-rot")
rlm@364 358 left-kernel (repeat 20000 (File. (str base "bank-1-1.png")))
rlm@364 359 right-kernel (repeat 20000 (File. (str base "bank-1-1-rot.png")))
rlm@364 360 targets (map
rlm@364 361 #(File. (str base "left-right/" (format "%07d.png" %)))
rlm@364 362 (range 0 (count main)))]
rlm@364 363
rlm@364 364 (dorun
rlm@364 365 (pmap
rlm@364 366 (comp
rlm@364 367 (fn [[main left right left-kernel right-kernel target]]
rlm@364 368 (println target)
rlm@364 369 (if (not (.exists (File. target)))
rlm@364 370 (sh "convert"
rlm@364 371 "-size" "1940x515" "xc:white"
rlm@364 372 main "-geometry" "+0+0" "-composite"
rlm@364 373 left "-geometry" "+650+0" "-composite"
rlm@364 374 right "-geometry" "+1300+0" "-composite"
rlm@364 375 left-kernel "-geometry" "+960+485" "-composite"
rlm@364 376 right-kernel "-geometry" "+1610+485" "-composite"
rlm@364 377 target)))
rlm@364 378 (fn [& args] (map #(.getCanonicalPath %) args)))
rlm@364 379 main left right left-kernel right-kernel targets))))
rlm@364 380
rlm@364 381
rlm@364 382 (defn compile-big-small []
rlm@364 383 (.mkdir (File. (str base "big-small")))
rlm@364 384 (let [main (pics "main")
rlm@364 385 left (pics "bank-1-1")
rlm@364 386 right (pics "bank-6-1")
rlm@364 387 small-kernel (repeat 20000 (File. (str base "bank-1-1.png")))
rlm@364 388 big-kernel (repeat 20000 (File. (str base "bank-6-1.png")))
rlm@364 389 targets (map
rlm@364 390 #(File. (str base "big-small/" (format "%07d.png" %)))
rlm@364 391 (range 0 (count main)))]
rlm@364 392
rlm@364 393 (dorun
rlm@364 394 (pmap
rlm@364 395 (comp
rlm@364 396 (fn [[main left right small-kernel big-kernel target]]
rlm@364 397 (println target)
rlm@364 398 (if (not (.exists (File. target)))
rlm@364 399 (sh "convert"
rlm@364 400 "-size" "1940x610" "xc:white"
rlm@364 401 main "-geometry" "+0+0" "-composite"
rlm@364 402 left "-geometry" "+650+0" "-composite"
rlm@364 403 right "-geometry" "+1300+0" "-composite"
rlm@364 404 small-kernel "-geometry" "+960+485" "-composite"
rlm@364 405 big-kernel "-geometry" "+1560+485" "-composite"
rlm@364 406 target)))
rlm@364 407 (fn [& args] (map #(.getCanonicalPath %) args)))
rlm@364 408 main left right small-kernel big-kernel targets))))
rlm@364 409
rlm@364 410
rlm@364 411 (defn regen-everything []
rlm@364 412 (make-all-images)
rlm@364 413 (compile-left-right)
rlm@364 414 (compile-big-small))
rlm@364 415
rlm@364 416
rlm@364 417 #+end_src
rlm@364 418
rlm@364 419 #+name: make-left-right
rlm@364 420 #+begin_src sh
rlm@364 421 #!/bin/sh
rlm@364 422
rlm@364 423 ffmpeg -framerate 60 -i ./left-right/%07d.png -b:v 9000k\
rlm@365 424 -c:v mpeg4 -r 60 gabor-rotation.mp4
rlm@364 425
rlm@364 426 #+end_src
rlm@364 427
rlm@364 428
rlm@364 429 #+name: make-big-small
rlm@364 430 #+begin_src sh
rlm@364 431 #!/bin/sh
rlm@364 432
rlm@364 433 ffmpeg -framerate 60 -i ./big-small/%07d.png -b:v 9000k\
rlm@365 434 -c:v mpeg4 -r 60 gabor-big-small.mp4
rlm@363 435
rlm@356 436 #+end_src
rlm@356 437
rlm@365 438 #+begin_html
rlm@365 439 <div class="figure">
rlm@365 440 <video controls="controls" width="755">
rlm@365 441 <source src="../video/gabor-rotation.mp4" type="video/mp4"
rlm@365 442 preload="none" poster="../images/aurellem-1280x480.png" />
rlm@365 443 </video>
rlm@365 444 <br> <a href="http://youtu.be/r5Bn2aG7MO0"> YouTube </a>
rlm@365 445 <p>Two gabor filters with different values of theta are compared. The
rlm@365 446 horizontally aligned one does better in this example.</p>
rlm@365 447 </div>
rlm@365 448 #+end_html
rlm@365 449
rlm@365 450
rlm@365 451
rlm@365 452 #+begin_html
rlm@365 453 <div class="figure">
rlm@365 454 <video controls="controls" width="755">
rlm@365 455 <source src="../video/gabor-big-small.mp4" type="video/mp4"
rlm@365 456 preload="none" poster="../images/aurellem-1280x480.png" />
rlm@365 457 </video>
rlm@365 458 <br> <a href="http://youtu.be/r5Bn2aG7MO0"> YouTube </a>
rlm@365 459 <p>Here we compare a gabor filter from bank 1 with one from bank 6.</p>
rlm@365 460 </div>
rlm@365 461 #+end_html
rlm@365 462
rlm@365 463
rlm@356 464
rlm@356 465
rlm@356 466 * COMMENT Generate Source
rlm@356 467 #+begin_src clojure :tangle ../src/cortex/gabor.clj
rlm@356 468 <<gabor>>
rlm@364 469 <<gabor-tail>>
rlm@356 470 #+end_src
rlm@364 471
rlm@364 472 #+begin_src clojure :tangle ../render/gabor-1/make-rotation.sh
rlm@364 473 <<make-left-right>>
rlm@364 474 #+end_src
rlm@364 475
rlm@364 476 #+begin_src clojure :tangle ../render/gabor-1/make-big-small.sh
rlm@364 477 <<make-big-small>>
rlm@364 478 #+end_src