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annotate src/rlm/dna_melting.clj @ 0:78a630e650d2

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initial import
author Robert McIntyre <rlm@mit.edu>
date Tue, 18 Oct 2011 00:57:08 -0700
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rlm@0 1 (ns rlm.dna-melting
rlm@0 2 (:refer-clojure :only [])
rlm@0 3 (:require rlm.ns-rlm mobius.base))
rlm@0 4 (rlm.ns-rlm/ns-clone mobius.base)
rlm@0 5 (use :reload-all 'rlm.web-stuff)
rlm@0 6
rlm@0 7
rlm@0 8 (def pre "/home/r/MIT/6/6.122/DNA/samples/")
rlm@0 9
rlm@0 10
rlm@0 11
rlm@0 12 (defrecord dna-data [temp glow name temp-units glow-units]
rlm@0 13 clojure.lang.IFn
rlm@0 14 (invoke [this k] (get this k))
rlm@0 15 (invoke [this k not-found] (get this k not-found))
rlm@0 16 (toString [this] "whatever"))
rlm@0 17
rlm@0 18 (defmethod print-method dna-data [d w]
rlm@0 19 (.write w (.toString d)))
rlm@0 20
rlm@0 21 (defmethod print-dup dna-data [d w]
rlm@0 22 (print-method d w))
rlm@0 23
rlm@0 24 (defn load-data [source]
rlm@0 25 (let [data (read-dataset source :delim \tab)
rlm@0 26 temp (vec ($ :col0 data))
rlm@0 27 glow (vec ($ :col1 data))]
rlm@0 28 (dna-data. temp glow
rlm@0 29 (last (re-split #"/" source))
rlm@0 30 "Raw Temperature (Volts)"
rlm@0 31 "Raw Glow (Volts)")))
rlm@0 32
rlm@0 33
rlm@0 34 (def ?-1 (load-data (str pre "sample4-1.txt")))
rlm@0 35
rlm@0 36 ;; I accidentally removed the cuvette while it was still recording!
rlm@0 37 ;; drop last 5 seconds of invalid data!
rlm@0 38 (def ?-2* (load-data (str pre "sample4-2.txt")))
rlm@0 39 (def ?-2 (assoc ?-2*
rlm@0 40 :temp (drop-last 500 (:temp ?-2*))
rlm@0 41 :glow (drop-last 500 (:glow ?-2*))))
rlm@0 42
rlm@0 43 (def ?-3 (load-data (str pre "sample4-3.txt")))
rlm@0 44 (def A-1 (load-data (str pre "sampleA-1.txt")))
rlm@0 45 (def A-2 (load-data (str pre "sampleA-2.txt")))
rlm@0 46 (def A-3 (load-data (str pre "sampleA-3.txt")))
rlm@0 47 (def B-2 (load-data (str pre "sampleB-2.txt")))
rlm@0 48 (def B-3 (load-data (str pre "sampleB-3.txt")))
rlm@0 49 (def C-1 (load-data (str pre "sampleC-1.txt")))
rlm@0 50 (def C-2 (load-data (str pre "sampleC-2.txt")))
rlm@0 51 (def C-3 (load-data (str pre "sampleC-3.txt")))
rlm@0 52
rlm@0 53
rlm@0 54 (def pure-bleaching (load-data (str pre "sampleB-1(failed-to-heat).txt")))
rlm@0 55 (def double-cycle (load-data (str pre "sampleC-3(double).txt")))
rlm@0 56 (def triple-cycle (load-data (str pre "sampleC-3(triple).txt")))
rlm@0 57
rlm@0 58 (def all-samples
rlm@0 59 [?-1 ?-3 A-1 A-2 A-3 B-2 B-3 C-1 C-2 C-3])
rlm@0 60
rlm@0 61 (def everything
rlm@0 62 (concat [pure-bleaching double-cycle triple-cycle] all-samples))
rlm@0 63
rlm@0 64
rlm@0 65
rlm@0 66 (defn dna-plot [d]
rlm@0 67 (view
rlm@0 68 (->
rlm@0 69 (visual (:temp d))
rlm@0 70 (set-y-label (:temp-units d))
rlm@0 71 (set-x-label "Time (deci-seconds)")
rlm@0 72 (set-title (:name d))))
rlm@0 73 (view
rlm@0 74 (->
rlm@0 75 (visual (:glow d))
rlm@0 76 (set-y-label (:glow-units d))
rlm@0 77 (set-x-label "Time (deci-seconds)")
rlm@0 78 (set-title (:name d))))
rlm@0 79 d)
rlm@0 80
rlm@0 81 (defn dna-melting [d]
rlm@0 82
rlm@0 83 (->
rlm@0 84 (scatter-plot (:temp d) (:glow d))
rlm@0 85 (set-y-label (:glow-units d))
rlm@0 86 (set-x-label (:temp-units d))
rlm@0 87 (set-title (:name d))))
rlm@0 88
rlm@0 89
rlm@0 90 (defmethod visual clojure.lang.LazySeq [ls]
rlm@0 91 (visual (vec ls)))
rlm@0 92
rlm@0 93 (defmethod visual clojure.lang.PersistentVector [v]
rlm@0 94 (set-y-range (xy-plot (vec (range (count v))) v)
rlm@0 95 (apply min v) (apply max v)))
rlm@0 96
rlm@0 97 (defmethod visual dna-data [d]
rlm@0 98 (dna-plot d))
rlm@0 99
rlm@0 100
rlm@0 101
rlm@0 102
rlm@0 103
rlm@0 104
rlm@0 105 ;;; Filter V_RTD and V_F to reduce noise
rlm@0 106
rlm@0 107
rlm@0 108
rlm@0 109 ;(let [a (int 1.8e4) b (int 2.2e4)]
rlm@0 110 ; (visual (map (vec (temperature triple-cycle)) (range a b)))
rlm@0 111 ; (visual (map (vec (dna-fraction triple-cycle)) (range a b))))
rlm@0 112
rlm@0 113 ;; Differentiate the resulting function with respect to temperature.
rlm@0 114
rlm@0 115 (def test-temp-range (vec (range 260 380 0.1)))
rlm@0 116
rlm@0 117 (defn trans-print [& args] (apply println args) args)
rlm@0 118
rlm@0 119 ;; (def search
rlm@0 120 ;; #(for [x (range -1000 1000 100) y (range -1000 1000 100)]
rlm@0 121 ;; (do
rlm@0 122 ;; (print [x y])
rlm@0 123 ;; (try (trans-print (non-linear-model
rlm@0 124 ;; (ideal-dna-fraction 30e-6)
rlm@0 125 ;; test-dna-fraction test-temperature [x y]
rlm@0 126 ;; :method :newton-raphson))
rlm@0 127
rlm@0 128 ;; (catch Exception e (trans-print nil))))))
rlm@0 129
rlm@0 130
rlm@0 131 ;;(non-linear-model (ideal-dna-fraction 30e-6) test-dna-fraction test-temperature [-184 -71e3])
rlm@0 132
rlm@0 133 ;;(time (def answer (non-linear-model (ideal-dna-fraction 30e-6) test-dna-fraction test-temperature [-200 -90e3])))
rlm@0 134
rlm@0 135 ;;we're assuming that the SYBR Green 1 doesn't glow at all when there is only
rlm@0 136 ;;single stranded DNA, but it actually does. V_f only ever gets down to ~0.1 V
rlm@0 137 ;;even with everything melted.
rlm@0 138
rlm@0 139
rlm@0 140 ;;correct for thermal capacatance
rlm@0 141
rlm@0 142 (defn find-max [v]
rlm@0 143 (first (reduce (fn [a b] (if (> (last b) (last a)) b a)) (indexed v))))
rlm@0 144
rlm@0 145 (defn find-min [v]
rlm@0 146 (first (reduce (fn [a b] (if (< (last b) (last a)) b a)) (indexed v))))
rlm@0 147
rlm@0 148 (defn plot-thermal-delay []
rlm@0 149 (let [a (int 2.5e3) b (int 5e3)]
rlm@0 150 (dna-plot (assoc A-1
rlm@0 151 :temp (map (vec (:temp A-1)) (range a b))
rlm@0 152 :glow (map (vec (:glow A-1)) (range a b))))))
rlm@0 153
rlm@0 154 (defvar thermal-delay
rlm@0 155 (let [a (int 2.5e3) b (int 5e3)]
rlm@0 156 (-
rlm@0 157 (find-min (map (vec (:glow A-1)) (range a b)))
rlm@0 158 (find-max (map (vec (:temp A-1)) (range a b)))))
rlm@0 159 "There are two sources of thermal delay: thermal capacatance
rlm@0 160 of the cuvette holder and thermal capacatance from the time
rlm@0 161 it takes DNA to unwind.
rlm@0 162
rlm@0 163 Use A-1 to find the thermal delay. There was almost no delay
rlm@0 164 between heating and cooling for A-1, and thus the extremum of
rlm@0 165 temperature and glow should temporally coincide if there were
rlm@0 166 no delays. It turns out that there is about a 30 second lag!" )
rlm@0 167
rlm@0 168 (defn thermal-delay-correction*
rlm@0 169 "There is a certain delay between the RTD reporting changes in
rlm@0 170 temperature and the temperature of the DNA actually changing.
rlm@0 171 This shifts the temperature values so that the delay is eliminated."
rlm@0 172 [thermal-delay #^dna-data d]
rlm@0 173 (assoc d
rlm@0 174 :name (str (:name d) " |thermal-correction| ")
rlm@0 175 :temp (drop-last thermal-delay (:temp d))
rlm@0 176 :glow (drop thermal-delay (:glow d))))
rlm@0 177
rlm@0 178 (def thermal-delay-correction (partial thermal-delay-correction* thermal-delay))
rlm@0 179
rlm@0 180 ;;correct for photo-bleaching
rlm@0 181
rlm@0 182 (defn general-linear [[A B] x] (+ (* A x) B))
rlm@0 183
rlm@0 184 (defvar bleaching-coef nil
rlm@0 185 ;; (let [[A B]
rlm@0 186 ;; (:coefs
rlm@0 187 ;; (let [a (int 3e4) b (length (:glow pure-bleaching))]
rlm@0 188 ;; (non-linear-model
rlm@0 189 ;; general-linear
rlm@0 190 ;; (map (vec (:glow pure-bleaching)) (range a b))
rlm@0 191 ;; (range a b)
rlm@0 192 ;; [1 1])))]
rlm@0 193 ;; A)
rlm@0 194 "This function corrects V_f for photo-bleaching over a period of time.
rlm@0 195 Photo-bleaching was found to be linear(!) over quite a long period of time.
rlm@0 196 Data is taken from sample B-1, which I left in the holder for an hour
rlm@0 197 with no heating")
rlm@0 198
rlm@0 199 (defn bleaching-correction*
rlm@0 200 [bleaching-coef #^dna-data d]
rlm@0 201 ;;the correction is clibrated to apply to the raw data only
rlm@0 202 (assert (= (:glow-units d) "Raw Glow (Volts)"))
rlm@0 203 ;;we need to modulate this correction factor
rlm@0 204
rlm@0 205 (let [baseline (first (drop 3e4 (:temp pure-bleaching)))]
rlm@0 206 (assoc d
rlm@0 207 :name (str (:name d) " |bleaching-correction| ")
rlm@0 208 :glow (map (fn [[i n]] (- n (*
rlm@0 209 (/ n baseline)
rlm@0 210 ((partial general-linear [bleaching-coef 0]) i))))
rlm@0 211 (indexed (:glow d))))))
rlm@0 212
rlm@0 213 (def bleaching-correction (partial bleaching-correction* bleaching-coef))
rlm@0 214
rlm@0 215 ;; compensate for residual fluorescence when everything is melted
rlm@0 216
rlm@0 217 (defn residual-fluorescence
rlm@0 218 "the SYBR1 green dye doesn't completly stop glowing once everything
rlm@0 219 is melted."
rlm@0 220 [#^dna-data d]
rlm@0 221 (let [low (apply min (:glow d))
rlm@0 222 high (apply max (:glow d))]
rlm@0 223 (assoc d
rlm@0 224 :name (str (:name d) " |residual-fluorescence| ")
rlm@0 225 :glow (map (fn [f]
rlm@0 226 (- f (* (- 1 (/ f high)) low))) (:glow d)))))
rlm@0 227
rlm@0 228
rlm@0 229
rlm@0 230
rlm@0 231 ;; extract the cooling phase
rlm@0 232
rlm@0 233 (defn cooling-phase
rlm@0 234 "first stretch where the temperature is going down for a while
rlm@0 235 equivalent to where the f curve starts to recover"
rlm@0 236 [#^dna-data d]
rlm@0 237 (let [t (:temp d)
rlm@0 238 f (:glow d)
rlm@0 239 dividing-line (reduce (fn [a b] (if (< (a 1) (b 1)) a b)) (indexed f))
rlm@0 240 t-new (drop (dividing-line 0) t)
rlm@0 241 f-new (drop (dividing-line 0) f)]
rlm@0 242 (assoc d
rlm@0 243 :name (str (:name d) " |extract cooling| ")
rlm@0 244 :temp (vec t-new) :glow (vec f-new))))
rlm@0 245
rlm@0 246
rlm@0 247
rlm@0 248 ;; filter noise
rlm@0 249 ;;(http://clojure-log.n01se.net/date/2009-10-13.html by ambient
rlm@0 250 ;;this is such a cool transform!!!
rlm@0 251
rlm@0 252
rlm@0 253 (defn lo-pass
rlm@0 254 [d coll]
rlm@0 255 (reductions #(+ (* %2 d) (* %1 (- 1.0 d))) coll))
rlm@0 256
rlm@0 257
rlm@0 258 ;;)
rlm@0 259
rlm@0 260 (def reasonable-low-pass (partial lo-pass 1e-2))
rlm@0 261
rlm@0 262 (defn low-pass-correction
rlm@0 263 "filter the raw data through a low pass filter to remove
rlm@0 264 electronic noise"
rlm@0 265 [#^dna-data d]
rlm@0 266 (assert (= (:glow-units d) "Raw Glow (Volts)"))
rlm@0 267 (assert (= (:temp-units d) "Raw Temperature (Volts)"))
rlm@0 268 (assoc d
rlm@0 269 :name (str (:name d) " |low-pass| ")
rlm@0 270 :temp (reasonable-low-pass (:temp d))
rlm@0 271 :glow (reasonable-low-pass (:glow d))))
rlm@0 272
rlm@0 273
rlm@0 274
rlm@0 275
rlm@0 276
rlm@0 277 ;; correct for units
rlm@0 278
rlm@0 279 (defn RTD-voltage->temperature
rlm@0 280 "transform RTD voltage to temperature.
rlm@0 281 R_RTD = 1000 + 3.85 * (T - 273)
rlm@0 282 T = ((R_RTD - 1000) / 3.85 ) + 273
rlm@0 283 V_RTD = 15 * R_RTD / (R + R_RTD)
rlm@0 284 R_RTD = R / (15/V_RTD - 1)"
rlm@0 285 [coll]
rlm@0 286 (let [R 14.97e3
rlm@0 287 V 15]
rlm@0 288 (letfn [(T [R_RTD] (+ 273 (/ (- R_RTD 1000) 3.85))) ;; from lab notrd
rlm@0 289 (R_RTD [V_RTD] (/ R (- (/ V V_RTD) 1)))]
rlm@0 290 (map (comp T R_RTD) coll))))
rlm@0 291
rlm@0 292 (defn normalize
rlm@0 293 "Transform photodiode current to relative fluorescence."
rlm@0 294 [coll]
rlm@0 295 (let [low (apply min coll)
rlm@0 296 high (apply max coll)]
rlm@0 297 (map #(/ (- % low) (- high low)) coll)))
rlm@0 298
rlm@0 299 (defn unit-transform
rlm@0 300 "turn raw voltage into temperature and dna-concentration"
rlm@0 301 [#^dna-data d]
rlm@0 302 (assert (= (:glow-units d) "Raw Glow (Volts)"))
rlm@0 303 (assert (= (:temp-units d) "Raw Temperature (Volts)"))
rlm@0 304 (assoc d
rlm@0 305 :name (str (:name d) " |units| ")
rlm@0 306 :temp-units "Temperature (Kelvin)"
rlm@0 307 :glow-units "DNA-Fracton"
rlm@0 308 :temp (RTD-voltage->temperature (:temp d))
rlm@0 309 :glow (normalize (:glow d))))
rlm@0 310
rlm@0 311
rlm@0 312 (defn temp-unit-transform
rlm@0 313 "turn raw voltage into temperature and dna-concentration"
rlm@0 314 [#^dna-data d]
rlm@0 315 (assert (= (:temp-units d) "Raw Temperature (Volts)"))
rlm@0 316 (assoc d
rlm@0 317 :name (str (:name d) " |temp-units| ")
rlm@0 318 :temp-units "Temperature (Kelvin)"
rlm@0 319 :temp (RTD-voltage->temperature (:temp d))))
rlm@0 320
rlm@0 321 (defn glow-unit-transform
rlm@0 322 "turn raw voltage into temperature and dna-concentration"
rlm@0 323 [#^dna-data d]
rlm@0 324 (assert (= (:glow-units d) "Raw Glow (Volts)"))
rlm@0 325 (assoc d
rlm@0 326 :name (str (:name d) " |glow-units| ")
rlm@0 327 :glow-units "DNA-Fracton"
rlm@0 328 :glow (normalize (:glow d))))
rlm@0 329
rlm@0 330
rlm@0 331 (defn thermal-efficiency
rlm@0 332 [#^dna-data d]
rlm@0 333 (assert (= (:temp-units d) "Temperature (Kelvin)"))
rlm@0 334 (assert (= (:glow-units d) "Raw Glow (Volts)"))
rlm@0 335 (assoc d
rlm@0 336 :name (str (:name d) " |thermal-efficiency| ")
rlm@0 337 :glow nil))
rlm@0 338
rlm@0 339
rlm@0 340
rlm@0 341 (defn remove-first-values
rlm@0 342 "remove the first minute or so of data so that the initial temperature of
rlm@0 343 the cuvette itself doesn't matter"
rlm@0 344 [#^dna-data d]
rlm@0 345 (assoc d
rlm@0 346 :name (str (:name d) " |remove-first| ")
rlm@0 347 :temp (drop 600 (:temp d))
rlm@0 348 :glow (drop 600 (:glow d))))
rlm@0 349
rlm@0 350 (defn diff [coll] (map - (rest coll) coll ))
rlm@0 351 (defn temp-transform
rlm@0 352 "my assumption will be that at the very end of the temperature data, the
rlm@0 353 cuvette is exactly the same temperature as the RTD. Then, I use newton's
rlm@0 354 heat transfer and numerical integration to derive the heat of the cuvette
rlm@0 355 for previous times"
rlm@0 356 [k-value temperature-data]
rlm@0 357 (let [T1 (vec (reverse temperature-data))
rlm@0 358 ;; want fast indexed access, and instead of doing the problem in reverse
rlm@0 359 ;; just reverse the vector at the start, treat it normally, and
rlm@0 360 ;; then reverse at the end
rlm@0 361 initial-cuvette-temp (first T1)
rlm@0 362 initial-RTD-temp (first T1)
rlm@0 363 step (fn [prev-T2 current-T1]
rlm@0 364 (let [new-T2 (+ prev-T2 (* k-value (- current-T1 prev-T2)))]
rlm@0 365 new-T2))]
rlm@0 366 (reverse (reductions step initial-cuvette-temp T1))))
rlm@0 367
rlm@0 368 (def k-value 0.1)
rlm@0 369
rlm@0 370 (defn temp-corr-2 [k-value T1*]
rlm@0 371 (let [T1 (reverse T1*)]
rlm@0 372 (reverse (cons (first T1) (map + (map (partial * k-value) (diff T1)) (rest T1))))))
rlm@0 373
rlm@0 374 (defn temp-corr-3 [initial-cuvette-temp k-value T1]
rlm@0 375 (let [step
rlm@0 376 (fn [prev-T2 current-T1]
rlm@0 377 (+ prev-T2 (* k-value (- current-T1 prev-T2))))]
rlm@0 378 (rest (reductions step initial-cuvette-temp T1))))
rlm@0 379
rlm@0 380 (defn newton-temp-correction* [k-value #^dna-data d]
rlm@0 381 (assoc d
rlm@0 382 :name (str (:name d) " |newton-temp| ")
rlm@0 383 :temp (temp-transform k-value (:temp d))))
rlm@0 384 (defn newton-temp-correction2* [k-value #^dna-data d]
rlm@0 385 (assoc d
rlm@0 386 :name (str (:name d) " |newton-temp-reverse| ")
rlm@0 387 :temp (temp-corr-2 k-value (:temp d))))
rlm@0 388 (defn newton-temp-correction3* [init-temp k-value #^dna-data d]
rlm@0 389 (assoc d
rlm@0 390 :name (str (:name d) " |newton-temp-reverse| ")
rlm@0 391 :temp (temp-corr-3 init-temp k-value (:temp d))))
rlm@0 392
rlm@0 393 (defn turn-e [n] (format "%5.2e" n))
rlm@0 394
rlm@0 395 (defn newton-temp-correction4*
rlm@0 396 "now with AIR!!!"
rlm@0 397 [k-block-sample k-sample-air initial-sample-temp room-temp #^dna-data d]
rlm@0 398 (let [old-temp (:temp d)
rlm@0 399 step (fn [prev-T2 current-T1]
rlm@0 400 (+ prev-T2
rlm@0 401 (* k-block-sample (- current-T1 prev-T2))
rlm@0 402 (* k-sample-air (- room-temp prev-T2))))
rlm@0 403 new-temp (rest (reductions step initial-sample-temp old-temp))]
rlm@0 404 (assoc d
rlm@0 405 :name (str (:name d)
rlm@0 406 " |temp-adjusted {"
rlm@0 407 "initial-sample:" (turn initial-sample-temp) " "
rlm@0 408 "room-temp:" (turn room-temp) " "
rlm@0 409 "k-block-sample:" (turn-e k-block-sample) " "
rlm@0 410 "k-sample-air:" (turn-e k-sample-air) "}")
rlm@0 411 :temp new-temp)))
rlm@0 412
rlm@0 413 (defn plot-adjusted-temp
rlm@0 414 "visualize the temperature correction"
rlm@0 415 [adjuster #^dna-data d]
rlm@0 416 (view
rlm@0 417 (add-lines
rlm@0 418 (visual (:temp d))
rlm@0 419 (vec (range (count (:temp d))))
rlm@0 420 (vec (:temp (adjuster d))))))
rlm@0 421
rlm@0 422
rlm@0 423
rlm@0 424
rlm@0 425
rlm@0 426 ;; process data
rlm@0 427
rlm@0 428 (defn process [#^dna-data d]
rlm@0 429 (cooling-phase
rlm@0 430 (unit-transform
rlm@0 431 (residual-fluorescence
rlm@0 432 (bleaching-correction
rlm@0 433 (low-pass-correction
rlm@0 434 ;(thermal-delay-correction
rlm@0 435 d))))))
rlm@0 436
rlm@0 437
rlm@0 438 (defn first-pass
rlm@0 439 "after this, the only thing stopping the melting curve from
rlm@0 440 being a straight line is thermal capacatance"
rlm@0 441 [#^dna-data data]
rlm@0 442 (low-pass-correction
rlm@0 443 ;(remove-first-values
rlm@0 444 (bleaching-correction
rlm@0 445 data)))
rlm@0 446
rlm@0 447
rlm@0 448
rlm@0 449 (defn explore [k-value]
rlm@0 450 (dna-melting (newton-temp-correction* k-value (first-pass A-2))))
rlm@0 451
rlm@0 452
rlm@0 453 (defn explore2 [k-value]
rlm@0 454 (dna-melting (newton-temp-correction2* k-value (first-pass A-2))))
rlm@0 455
rlm@0 456
rlm@0 457 (defn explore3 [init-temp k-value]
rlm@0 458 (dna-melting (newton-temp-correction3* init-temp k-value (unit-transform (first-pass A-2)))))
rlm@0 459
rlm@0 460
rlm@0 461
rlm@0 462 ;; get the three characteristic values we want.
rlm@0 463
rlm@0 464 (defn ideal-dna-fraction* [concentration [delta-S delta-H] temperature]
rlm@0 465 (let [R 8.31447215
rlm@0 466 t temperature
rlm@0 467 Ct concentration
rlm@0 468 K_eq (exp (- (/ delta-S R) (/ delta-H (* R t))))
rlm@0 469 f (/
rlm@0 470 (+ 1 (* Ct K_eq)
rlm@0 471 (- (sqrt (+ 1 (* 2 Ct K_eq)))))
rlm@0 472 (* Ct K_eq))]
rlm@0 473 f))
rlm@0 474
rlm@0 475 (def ideal-dna-fraction (partial ideal-dna-fraction* 30e-6))
rlm@0 476
rlm@0 477 (defvar starting-values
rlm@0 478 ;; [-184 -71e3]
rlm@0 479 [-904 -32e4]
rlm@0 480 "chosen from theoritical estimation")
rlm@0 481
rlm@0 482
rlm@0 483 (defn analyze* [iterations #^dna-data d]
rlm@0 484 (let [best-fit-results
rlm@0 485 (non-linear-model
rlm@0 486 ideal-dna-fraction
rlm@0 487 (:glow d)
rlm@0 488 (:temp d)
rlm@0 489 starting-values
rlm@0 490 :max-iter iterations)]
rlm@0 491 best-fit-results))
rlm@0 492
rlm@0 493
rlm@0 494 (def analyze (partial analyze* 200))
rlm@0 495
rlm@0 496 (defn plot-results [d]
rlm@0 497 (let [ans (analyze d)]
rlm@0 498 (view (doto (xy-plot (:x ans) (:y ans))
rlm@0 499 (set-title (:name d))
rlm@0 500 (add-lines (:x ans) (:fitted ans))))
rlm@0 501 ans))
rlm@0 502
rlm@0 503 (defn zzz [d [A B]]
rlm@0 504 (let [gar (vec (map (partial ideal-dna-fraction [A B]) (:temp d)))]
rlm@0 505 (view (doto (xy-plot (:temp d) (:glow d))
rlm@0 506 (set-title (:name d))
rlm@0 507 (add-lines (:temp d) gar)))))
rlm@0 508
rlm@0 509
rlm@0 510
rlm@0 511
rlm@0 512 (defn index-filter [pred coll]
rlm@0 513 (when pred
rlm@0 514 (for [[idx elt] (indexed coll) :when (pred elt)] idx)))
rlm@0 515
rlm@0 516
rlm@0 517
rlm@0 518
rlm@0 519 ;; we're going to estimate two correction factors,
rlm@0 520 ;; a constant capacative temperature delay,
rlm@0 521 ;; and a linear decrease in brightness. We'll do this
rlm@0 522 ;; before unit-transforms.
rlm@0 523
rlm@0 524 (defn zipmap-collect
rlm@0 525 "Returns a map with the keys mapped to the corresponding vals.
rlm@0 526 adds extra values to a list"
rlm@0 527 [keys vals]
rlm@0 528 (loop [map {}
rlm@0 529 ks (seq keys)
rlm@0 530 vs (seq vals)]
rlm@0 531 (if (and ks vs)
rlm@0 532 (recur (if (contains? map (first ks))
rlm@0 533 (assoc map (first ks) (cons (first vs) (map (first ks))))
rlm@0 534 (assoc map (first ks) (list (first vs))))
rlm@0 535 (next ks)
rlm@0 536 (next vs))
rlm@0 537 map)))
rlm@0 538
rlm@0 539
rlm@0 540 (defn little-process [thermal-cap bleaching #^dna-data d]
rlm@0 541 ((partial thermal-delay-correction thermal-cap)
rlm@0 542 ((partial bleaching-correction bleaching) d)))
rlm@0 543
rlm@0 544 (def little-process (memoize little-process))
rlm@0 545
rlm@0 546 ;(defn lookup-map [#^dna-data d]
rlm@0 547
rlm@0 548
rlm@0 549 (defn converge-function
rlm@0 550 "this is the vertical discrepancy after applying the two transforms"
rlm@0 551 [#^dna-data d [thermal-cap bleaching] x]
rlm@0 552 (let [new-d (little-process thermal-cap bleaching d)
rlm@0 553 spreads
rlm@0 554 (map (vec (:glow new-d))
rlm@0 555 (index-filter (partial = x) (vec (:temp new-d))))
rlm@0 556 spread (- (apply max spreads) (apply min spreads))]
rlm@0 557 spread))
rlm@0 558
rlm@0 559
rlm@0 560
rlm@0 561
rlm@0 562
rlm@0 563
rlm@0 564
rlm@0 565
rlm@0 566
rlm@0 567
rlm@0 568 (defn blah [k] (comp
rlm@0 569 ( partial newton-temp-correction3* 280 k ) temp-unit-transform first-pass))
rlm@0 570
rlm@0 571 ;(def ggg (comp
rlm@0 572 ; dna-melting ( partial thermal-delay-correction* 120 ) (blah 0.0018)))
rlm@0 573
rlm@0 574
rlm@0 575
rlm@0 576
rlm@0 577
rlm@0 578 ;; Ensure that the melting function is uniquely valued by
rlm@0 579 ;; combining samples with identical temperature values.
rlm@0 580 (defn cooling-function
rlm@0 581 "just put it in a map for this!"
rlm@0 582 [source]
rlm@0 583 (let [data (cooling-phase source)
rlm@0 584 lookup (apply sorted-map
rlm@0 585 (interleave
rlm@0 586 (:temperature data) (:dna-fraction data)))]
rlm@0 587 {:temperature (vec (keys lookup))
rlm@0 588 :dna-fraction (vec (map lookup (keys lookup)))}))
rlm@0 589
rlm@0 590
rlm@0 591 (defn turn [n]
rlm@0 592 (format "%5.2f" n))
rlm@0 593
rlm@0 594 (defn bleach-correction-2 [bleaching-constant #^dna-data d]
rlm@0 595 (assert (= (:glow-units d) "Raw Glow (Volts)"))
rlm@0 596 (let [old-glow (vec (:glow d))
rlm@0 597 integral-old-glow (vec (reductions + old-glow))
rlm@0 598 correction (fn [t] (+
rlm@0 599 (old-glow t)
rlm@0 600 (* bleaching-constant (integral-old-glow t))))
rlm@0 601 new-glow (map + (map correction (range 0 (count old-glow))) old-glow)]
rlm@0 602 ;;glow is related to the number of particles,
rlm@0 603 ;;and the number destroyed is some fraction of
rlm@0 604 ;;the number present and glowing.
rlm@0 605 (assoc d
rlm@0 606 :name (str (:name d) " |bleaching-corrected constant = " (turn bleaching-constant) "| ")
rlm@0 607 :glow new-glow)))
rlm@0 608
rlm@0 609
rlm@0 610
rlm@0 611 (defn ultimate-correction
rlm@0 612 ([k-block-sample k-sample-air initial-sample-temp room-temp bleach-constant
rlm@0 613 #^dna-data d
rlm@0 614 ]
rlm@0 615 ((comp
rlm@0 616 (partial newton-temp-correction4*
rlm@0 617 k-block-sample k-sample-air initial-sample-temp room-temp)
rlm@0 618
rlm@0 619 temp-unit-transform
rlm@0 620 (partial bleach-correction-2 bleach-constant)
rlm@0 621 low-pass-correction) d))
rlm@0 622
rlm@0 623 ([{:keys [test-k-sample-air
rlm@0 624 test-k-block-sample
rlm@0 625 test-sample-temp
rlm@0 626 test-room-temp
rlm@0 627 test-bleach]}
rlm@0 628 #^dna-data d]
rlm@0 629 (ultimate-correction
rlm@0 630 (mean test-k-block-sample) (mean test-k-sample-air)
rlm@0 631 (mean test-sample-temp) (mean test-room-temp) (mean test-bleach) d)))
rlm@0 632
rlm@0 633
rlm@0 634 ;;((uui 0.0020 0.0001 280 293) (bleach-correction-2 1.1e-5 ?-3))
rlm@0 635
rlm@0 636
rlm@0 637 ;;; this is for ?-3 after 35 iterations
rlm@0 638 (def opt {:test-k-sample-air '(9.375630358472117E-4 9.375630359053611E-4), :test-k-block-sample '(0.0010343754438043107 0.0010343754455447197), :test-room-temp '(294.9804782861611 294.98047828674316), :test-sample-temp '(293.36120605294127 293.3612060546875), :test-bleach '(1.771081481128931E-5 1.7710814863094127E-5), :align 1.5796052678842228E-4})
rlm@0 639
rlm@0 640
rlm@0 641 ;;; C-1 after 20 iterations
rlm@0 642 (def opt2
rlm@0 643 {:test-k-sample-air '(9.936472587585448E-4 9.936491641998292E-4), :test-k-block-sample '(2.9390106201171873E-4 2.939580917358398E-4), :test-room-temp '(294.76531982421875 294.7653388977051), :test-sample-temp '(294.765625 294.765682220459), :test-bleach '(2.39045524597168E-5 2.3906250000000002E-5), :align 1.7562642331021098E-4})
rlm@0 644
rlm@0 645
rlm@0 646 ;;(time (def result-?-3 (doall (take 10 (iterate (partial improve ?-3) start-values-overestimates)))))
rlm@0 647
rlm@0 648
rlm@0 649 ;;(doall (map (comp dna-melting #(ultimate-correction % ?-3)) result-?-3))
rlm@0 650
rlm@0 651
rlm@0 652 (defn subsample
rlm@0 653 "subsample v every n points"
rlm@0 654 [n v]
rlm@0 655
rlm@0 656 (vec (map (vec v) (vec (range 0 (count (vec v)) n)))))
rlm@0 657
rlm@0 658
rlm@0 659 (defn max-difference [v] (- (apply max v) (apply min v)))
rlm@0 660
rlm@0 661 (defn alignment [#^dna-data d]
rlm@0 662 (let [distribution (vec (vals
rlm@0 663 (apply sorted-map
rlm@0 664 (interleave (:temp d) (:glow d)))))]
rlm@0 665 (mean (map variance (partition 10 distribution)))))
rlm@0 666
rlm@0 667 (defn garigh [d]
rlm@0 668 (let [distribution (vec (vals
rlm@0 669 (apply sorted-map
rlm@0 670 (interleave (:temp d) (:glow d)))))]
rlm@0 671 (view (visual (vec (map max-difference (partition 100 distribution)))))))
rlm@0 672
rlm@0 673
rlm@0 674 (defn alignment-4 [#^dna-data d]
rlm@0 675 (let [distribution (vec (vals
rlm@0 676 (apply sorted-map
rlm@0 677 (interleave (:temp d) (:glow d)))))]
rlm@0 678 (reduce + (map sq (map max-difference (partition 100 distribution))))))
rlm@0 679
rlm@0 680
rlm@0 681 (defn alignment-2 [#^dna-data d]
rlm@0 682 (let [distribution
rlm@0 683 (vec
rlm@0 684 (vals
rlm@0 685 (apply sorted-map
rlm@0 686 (interleave (subsample 2 (:temp d)) (subsample 2(:glow d))))))]
rlm@0 687 (reduce + (map max-difference (partition 30 distribution)))))
rlm@0 688 (defn alignment-3 [#^dna-data d]
rlm@0 689 (let [distribution
rlm@0 690 (vec
rlm@0 691 (vals
rlm@0 692 (apply sorted-map
rlm@0 693 (interleave (subsample 2 (:temp d)) (subsample 2(:glow d))))))]
rlm@0 694 (reduce max (map max-difference (partition 30 distribution)))))
rlm@0 695
rlm@0 696
rlm@0 697 (comment
rlm@0 698 ;; this takes a while
rlm@0 699 (def opts (zipmap all-samples (map #(last (take 20 (iterate (partial improve %) start-values))) all-samples))))
rlm@0 700
rlm@0 701 ;(def opts (zipmap all-samples opts-vals))
rlm@0 702
rlm@0 703 (defn mean-map [v s]
rlm@0 704 (map mean (map (partial vector v) s)))
rlm@0 705
rlm@0 706
rlm@0 707 (def start-values
rlm@0 708 {:test-k-sample-air [0.000001 0.001]
rlm@0 709 :test-k-block-sample [0.001 0.03]
rlm@0 710 :test-room-temp [290 300]
rlm@0 711 :test-sample-temp [285 310]
rlm@0 712 :test-bleach [0.00001 0.0009]})
rlm@0 713
rlm@0 714 (def start-values-2
rlm@0 715 {:test-k-sample-air [1e-15 0.0005]
rlm@0 716 :test-k-block-sample [0.001 0.002]
rlm@0 717 :test-room-temp [290 300]
rlm@0 718 :test-sample-temp [290 300]
rlm@0 719 :test-bleach [1e-7 0.0005]})
rlm@0 720
rlm@0 721
rlm@0 722
rlm@0 723 (def start-values-3
rlm@0 724 {:test-k-block-sample [0.0005 0.00125 0.002]
rlm@0 725 :test-k-sample-air [0.0000001 0.000001 0.0000019]
rlm@0 726 :test-sample-temp [280 300]
rlm@0 727 :test-room-temp [300 306]
rlm@0 728 :test-bleach [0.000001 0.00001]})
rlm@0 729
rlm@0 730 (defn condense [[a b :as v]]
rlm@0 731 (if (< (/ (abs (- (apply max v) (apply min v))) (apply max v)) 1e-2) (vector (mean v)) v))
rlm@0 732
rlm@0 733 (defn mass-shift
rlm@0 734 [value v]
rlm@0 735 (let [frac 2/3]
rlm@0 736 (cond (>= (count v) 2)
rlm@0 737 (let [[a b] v]
rlm@0 738 (condense (vec (map #(float (+ (* frac %) (* (- 1 frac) value))) v))))
rlm@0 739 (= (count v) 1)
rlm@0 740 v)))
rlm@0 741
rlm@0 742
rlm@0 743 (defn improve* [#^dna-data d
rlm@0 744 {:keys [test-k-sample-air
rlm@0 745 test-k-block-sample
rlm@0 746 test-room-temp
rlm@0 747 test-sample-temp
rlm@0 748 test-bleach] :as domain}]
rlm@0 749 (do (print \newline)
rlm@0 750 (reduce (fn [m1 m2] (if (< (:align m1) (:align m2)) m1 m2))
rlm@0 751
rlm@0 752
rlm@0 753 (for [k-sample-air (condense test-k-sample-air)
rlm@0 754 k-block-sample (condense test-k-block-sample)
rlm@0 755 room-temp (condense test-room-temp)
rlm@0 756 initial-sample-temp (condense test-sample-temp)
rlm@0 757 bleach-constant (condense test-bleach)]
rlm@0 758
rlm@0 759 (do
rlm@0 760 (print ".")
rlm@0 761 (let [align
rlm@0 762 (alignment-2
rlm@0 763 (ultimate-correction
rlm@0 764 k-block-sample k-sample-air initial-sample-temp room-temp
rlm@0 765 bleach-constant d))
rlm@0 766 align (if (Double/isNaN align) Double/POSITIVE_INFINITY align)]
rlm@0 767 {:test-k-sample-air (mass-shift k-sample-air test-k-sample-air)
rlm@0 768 :test-k-block-sample(mass-shift k-block-sample test-k-block-sample)
rlm@0 769 :test-room-temp (mass-shift room-temp test-room-temp)
rlm@0 770 :test-sample-temp (mass-shift initial-sample-temp test-sample-temp)
rlm@0 771 :test-bleach (mass-shift bleach-constant test-bleach)
rlm@0 772 :align align}))))))
rlm@0 773
rlm@0 774
rlm@0 775
rlm@0 776 (def println-repl (bound-fn [& args] (apply println args)))
rlm@0 777 (def print-repl (bound-fn [& args] (apply print args)))
rlm@0 778
rlm@0 779
rlm@0 780
rlm@0 781 (defn improve [#^dna-data d
rlm@0 782 {:keys [test-k-block-sample
rlm@0 783 test-k-sample-air
rlm@0 784 test-sample-temp
rlm@0 785 test-room-temp
rlm@0 786 test-bleach] :as domain}]
rlm@0 787 (reduce
rlm@0 788 (fn [m1 m2] (if (< (:align m1) (:align m2)) m1 m2))
rlm@0 789 (let [return-hash
rlm@0 790 (fn
rlm@0 791 [[k-block-sample k-sample-air initial-sample-temp
rlm@0 792 room-temp bleach-constant]]
rlm@0 793 (do
rlm@0 794 (print-repl ".")
rlm@0 795 (let [align
rlm@0 796 (alignment-4
rlm@0 797 (ultimate-correction
rlm@0 798 k-block-sample k-sample-air initial-sample-temp room-temp
rlm@0 799 bleach-constant d))
rlm@0 800 align (if (Double/isNaN align) Double/POSITIVE_INFINITY align)]
rlm@0 801 {:test-k-sample-air (mass-shift k-sample-air test-k-sample-air)
rlm@0 802 :test-k-block-sample(mass-shift k-block-sample test-k-block-sample)
rlm@0 803 :test-room-temp (mass-shift room-temp test-room-temp)
rlm@0 804 :test-sample-temp (mass-shift initial-sample-temp test-sample-temp)
rlm@0 805 :test-bleach (mass-shift bleach-constant test-bleach)
rlm@0 806 :align align})))]
rlm@0 807 (pmap return-hash
rlm@0 808 (cartesian-product
rlm@0 809 test-k-block-sample
rlm@0 810 test-k-sample-air
rlm@0 811 test-sample-temp
rlm@0 812 test-room-temp
rlm@0 813 test-bleach)))))
rlm@0 814
rlm@0 815 (def improve (memoize improve))
rlm@0 816
rlm@0 817 (defn iterate-test [n #^dna-data d]
rlm@0 818 (last (take n (iterate (partial improve d) start-values-3))))
rlm@0 819
rlm@0 820
rlm@0 821 (defn nested-vals [key coll]
rlm@0 822 (for [x (tree-seq coll? seq coll) :when (contains? x key)]
rlm@0 823 (get x key)))
rlm@0 824
rlm@0 825
rlm@0 826 (defn quantum-efficiency* [q-constant #^dna-data d]
rlm@0 827 ;; 0.8 at room temperature
rlm@0 828 ;; quantum efficiency is somehow
rlm@0 829 ;; inversely proportional to temperature
rlm@0 830 (let [correction
rlm@0 831
rlm@0 832
rlm@0 833
rlm@0 834 (fn [t g] (/ g (* 0.8 (exp (* q-constant (- 292 t))))))]
rlm@0 835 (assoc d
rlm@0 836 :name (str (:name d) " |quantum-correction| ")
rlm@0 837 :glow (map correction (:temp d) (:glow d)))))
rlm@0 838
rlm@0 839 (def quantum-efficiency (partial quantum-efficiency* 1.2e-2))
rlm@0 840
rlm@0 841 (defn exp-decay [[A] x]
rlm@0 842 (* 0.8 (exp (* A (- 298 x)))))
rlm@0 843
rlm@0 844 ;(defn final-join [#^dna-data d]
rlm@0 845
rlm@0 846
rlm@0 847
rlm@0 848 (def join-opts
rlm@0 849 {
rlm@0 850 A-1 {:test-k-sample-air [1.760184242508937E-6], :test-k-block-sample [0.0012930832259977858], :test-room-temp [304.41977945963544], :test-sample-temp [281.31689453125], :test-bleach [9.956068424799014E-6], :align 0.800815268639094}
rlm@0 851 A-2 {:test-k-sample-air [3.017639376897326E-7], :test-k-block-sample [0.0011550507430608075], :test-room-temp [304.6666717529297], :test-sample-temp [282.6337890625], :test-bleach [9.5610075732111E-6], :align 0.8530570499185829}
rlm@0 852 A-3 {:test-k-sample-air [2.6829059556281816E-6], :test-k-block-sample [0.002413294818252325], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6]}
rlm@0 853
rlm@0 854 B-2 {:test-k-sample-air [1.6274943088016396E-6], :test-k-block-sample [0.0013714926317334175], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6], :align 0.7631166194402621}
rlm@0 855 B-3
rlm@0 856 {:test-k-sample-air [1.455345833771086E-6], :test-k-block-sample [0.0014841814991086721], :test-room-temp [304.6666717529297], :test-sample-temp [287.9835662841797], :test-bleach [9.965317076421343E-6], :align 0.5358800697386289}
rlm@0 857
rlm@0 858 C-1
rlm@0 859 {:test-k-sample-air [1.6907095717518434E-6], :test-k-block-sample [0.001278722076676786], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6], :align 0.7249279378017799}
rlm@0 860 C-2
rlm@0 861 {:test-k-sample-air [1.77524979487013E-6], :test-k-block-sample [0.001278722076676786], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6], :align 2.0474987460209793}
rlm@0 862 C-3
rlm@0 863 {:test-k-sample-air [1.010541116860016E-6], :test-k-block-sample [0.001601272417853276], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6], :align 0.7191738524207253}
rlm@0 864
rlm@0 865 ?-1
rlm@0 866 {:test-k-sample-air [1.5533593114014366E-6], :test-k-block-sample [0.0013761443551629782], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6], :align 1.3838506291264723}
rlm@0 867 ?-3
rlm@0 868 {:test-k-sample-air [2.940294715851148E-7], :test-k-block-sample [0.0018434864080821474], :test-room-temp [304.6666717529297], :test-sample-temp [281.31689453125], :test-bleach [9.965317076421343E-6], :align 0.48549623932134006}
rlm@0 869
rlm@0 870 })
rlm@0 871
rlm@0 872
rlm@0 873 (defn final-join [#^dna-data d]
rlm@0 874
rlm@0 875 (let [
rlm@0 876 m (apply sorted-map (interleave (:temp d) (:glow d)))
rlm@0 877 distribution (vec (vals m))
rlm@0 878 ordinates (vec (keys m))
rlm@0 879 ]
rlm@0 880 (assoc d
rlm@0 881 :name (str (:name d) " |joined| ")
rlm@0 882 :temp (map (fn [region] (mean [(apply min region) (apply max region)]))
rlm@0 883 (partition 30 ordinates))
rlm@0 884
rlm@0 885 :glow (map (fn [region] (mean [(apply min region) (apply max region)]))
rlm@0 886 (partition 30 distribution)))))
rlm@0 887
rlm@0 888
rlm@0 889 (defn melting-point [#^dna-data d]
rlm@0 890 (let [t (drop 150 (:temp d))
rlm@0 891 g (drop 150 (:glow d))]
rlm@0 892 (nth t (find-min (map / (diff g) (diff t) )))))
rlm@0 893
rlm@0 894
rlm@0 895 (def target-dir (file-str "/home/r/MIT/6/6.122/DNA/output"))
rlm@0 896
rlm@0 897 (defn x-form-dna [#^dna-data d]
rlm@0 898 (final-join (ultimate-correction (join-opts d) d)))
rlm@0 899
rlm@0 900 (defn save-raw-dna-curve [#^dna-data d]
rlm@0 901 (save (dna-melting d) (str target-dir File/separator (:name d) ".png")))
rlm@0 902
rlm@0 903 (defn save-dna-curve-with-temp [#^dna-data d*]
rlm@0 904 (let [
rlm@0 905
rlm@0 906 melt (melting-point d*)
rlm@0 907 d (assoc d* :name (str (:name d*) " |M.P. = " (turn melt) " |"))
rlm@0 908 ]
rlm@0 909 (save (add-lines (dna-melting d) (repeat (count (:glow d)) melt) (:glow d))
rlm@0 910 (str target-dir File/separator (:name d) ".png"))))
rlm@0 911
rlm@0 912
rlm@0 913
rlm@0 914 (defn process-all []
rlm@0 915 (doall (pmap save-dna-curve all-samples))
rlm@0 916 (doall (pmap (comp save-dna-curve-with-temp x-form-dna) all-samples)))
rlm@0 917
rlm@0 918
rlm@0 919 (def ?-temps (vec (map (comp melting-point x-form-dna) [?-1 ?-3])))
rlm@0 920 (def A-temps (vec (map (comp melting-point x-form-dna) [A-1 A-2 A-3])))
rlm@0 921 (def B-temps (vec (map (comp melting-point x-form-dna) [B-2 B-3])))
rlm@0 922 (def C-temps (vec (map (comp melting-point x-form-dna) [C-1 C-2 C-3])))
rlm@0 923
rlm@0 924 (defn report [temps]
rlm@0 925
rlm@0 926 (sorted-map :data temps :std (sqrt (variance temps)) :mean (mean temps)))
rlm@0 927
rlm@0 928
rlm@0 929 ;;; now it's time to start data reporting
rlm@0 930
rlm@0 931 ;(defn process [#^dna-data d]
rlm@0 932 ; (ultimate-correction (opts d) d)
rlm@0 933
rlm@0 934
rlm@0 935
rlm@0 936 (report A-temps)
rlm@0 937 {:data [348.8771481779248 349.3989434763391 348.76079920968573],
rlm@0 938 :mean 349.0122969546499,
rlm@0 939 :std 0.33986161910548834}
rlm@0 940
rlm@0 941 (report B-temps)
rlm@0 942 {:data [349.0655539116902 349.92155530431506],
rlm@0 943 :mean 349.4935546080026,
rlm@0 944 :std 0.6052843894485812}
rlm@0 945
rlm@0 946 (report C-temps)
rlm@0 947 {:data [349.92341967511976 349.68832687337056 348.2872189461977],
rlm@0 948 :mean 349.299655164896,
rlm@0 949 :std 0.884639745344559}
rlm@0 950
rlm@0 951 (report ?-temps)
rlm@0 952 {:data [350.4525305192239 349.87377093318975],
rlm@0 953 :mean 350.1631507262068,
rlm@0 954 :std 0.4092448279511269}
rlm@0 955
rlm@0 956