diff --git a/.gitignore b/.gitignore
index ed97aeba7b1917852b45e1498fa0a364e02968e3..d4acccc40c48fb2183901bcb00260a82f5810f71 100755
--- a/.gitignore
+++ b/.gitignore
@@ -13,3 +13,4 @@ annot_distrib.pdf
annot_distrib.tex
humpback/annot
humpback_CARIMAM/
+dolphin/zips
diff --git a/dolphin/dolphin.csv b/dolphin/dolphin.csv
new file mode 100644
index 0000000000000000000000000000000000000000..685db9f8bde3e2410c2e75ffeb6d13fb5e5e6efb
--- /dev/null
+++ b/dolphin/dolphin.csv
@@ -0,0 +1,401 @@
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diff --git a/good_species.txt b/good_species.txt
index 8a826fa8c6abd7aed183ecfb5ec506fc9f05dc24..f9c520f1bc980636b8d3972671be55130e9aaae7 100755
--- a/good_species.txt
+++ b/good_species.txt
@@ -4,4 +4,5 @@ california_thrashers
cassin_vireo
black-headed_grosbeaks
humpback
-zebra_finch
+dolphin
+otter
diff --git a/humpback/humpback.csv b/humpback/humpback.csv
old mode 100644
new mode 100755
index 2702688ac455bc5283dd3ec49a9d66e2b2bf5241..a51ca89175a90804d17d2bb34a9fbc37cd2f1a29
--- a/humpback/humpback.csv
+++ b/humpback/humpback.csv
@@ -14,7 +14,7 @@ pos,fn,label,label_prefilter
13.121459746,RSL20000908_T10_144502.aif,L,L
13.5318341885,RSL20000908_T10_144502.aif,Q,Q
14.478852133,RSL20000908_T10_144502.aif,D,D
-15.6784081965,RSL20000908_T10_144502.aif,K,K
+15.678408196500001,RSL20000908_T10_144502.aif,K,K
16.015125688,RSL20000908_T10_144502.aif,J,J
16.457067395499998,RSL20000908_T10_144502.aif,L,L
16.888486681499998,RSL20000908_T10_144502.aif,K,K
@@ -22,8 +22,8 @@ pos,fn,label,label_prefilter
18.992971003,RSL20000908_T10_144502.aif,K,K
19.2770763865,RSL20000908_T10_144502.aif,J,J
19.645361143,RSL20000908_T10_144502.aif,L,L
-22.686340988,RSL20000908_T10_144502.aif,D,D
-27.4815324835,RSL20000908_T10_144502.aif,D,D
+22.686340987999998,RSL20000908_T10_144502.aif,D,D
+27.481532483499997,RSL20000908_T10_144502.aif,D,D
28.7547454985,RSL20000908_T10_144502.aif,K,K
29.0388508815,RSL20000908_T10_144502.aif,J,J
29.3522756415,RSL20000908_T10_144502.aif,L,L
@@ -36,20 +36,20 @@ pos,fn,label,label_prefilter
33.708558186999994,RSL20000908_T10_144502.aif,Q,Q
34.227189356,RSL20000908_T10_144502.aif,K,K
35.1742073005,RSL20000908_T10_144502.aif,D,D
-36.236971883,RSL20000908_T10_144502.aif,K,K
+36.236971882999995,RSL20000908_T10_144502.aif,K,K
36.531599688,RSL20000908_T10_144502.aif,J,J
36.8758070915,RSL20000908_T10_144502.aif,L,L
37.4124505935,RSL20000908_T10_144502.aif,L,L
37.741678173,RSL20000908_T10_144502.aif,K,K
38.7728754905,RSL20000908_T10_144502.aif,D,D
-39.9194441805,RSL20000908_T10_144502.aif,K,K
+39.919444180499994,RSL20000908_T10_144502.aif,K,K
40.203549564,RSL20000908_T10_144502.aif,J,J
40.537609811500005,RSL20000908_T10_144502.aif,L,L
-41.084775735,RSL20000908_T10_144502.aif,Q,Q
+41.084775734999994,RSL20000908_T10_144502.aif,Q,Q
41.571464373,RSL20000908_T10_144502.aif,K,K
42.4316457005,RSL20000908_T10_144502.aif,L,L
42.873587408,RSL20000908_T10_144502.aif,Q,Q
-43.252394586,RSL20000908_T10_144502.aif,L,L
+43.252394585999994,RSL20000908_T10_144502.aif,L,L
43.9573968335,RSL20000908_T10_144502.aif,K,K
44.8412802485,RSL20000908_T10_144502.aif,L,L
45.7488657515,RSL20000908_T10_144502.aif,D,D
@@ -64,9 +64,9 @@ pos,fn,label,label_prefilter
57.36595585,RSL20000908_T10_144502.aif,K,K
57.713195763,RSL20000908_T10_144502.aif,D,D
58.070958098000006,RSL20000908_T10_144502.aif,L,L
-58.5023773835,RSL20000908_T10_144502.aif,P,P
+58.502377383500004,RSL20000908_T10_144502.aif,P,P
58.818050032,RSL20000908_T10_144502.aif,P,P
-60.354323587,RSL20000908_T10_144502.aif,D,D
+60.354323586999996,RSL20000908_T10_144502.aif,D,D
61.638059023,RSL20000908_T10_144502.aif,K,K
62.016866201,RSL20000908_T10_144502.aif,J,J
62.3430612705,RSL20000908_T10_144502.aif,L,L
@@ -76,37 +76,37 @@ pos,fn,label,label_prefilter
65.2156823695,RSL20000908_T10_144502.aif,L,L
65.583967126,RSL20000908_T10_144502.aif,Q,Q
66.5941196005,RSL20000908_T10_144502.aif,P,P
-67.36225637800001,RSL20000908_T10_144502.aif,,M
-72.560332652,RSL20000908_T10_144502.aif,,M
+67.36225637800001,RSL20000908_T10_144502.aif,M,M
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75.369039218,RSL20000908_T10_144502.aif,P,P
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@@ -114,7 +114,7 @@ pos,fn,label,label_prefilter
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@@ -137,7 +137,7 @@ pos,fn,label,label_prefilter
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@@ -149,7 +149,7 @@ pos,fn,label,label_prefilter
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@@ -188,9 +188,9 @@ pos,fn,label,label_prefilter
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130.4405557955,RSL20000930B_T19_111606.aif,G,G
134.6965078815,RSL20000930B_T19_111606.aif,I,I
140.94581968900002,RSL20000930B_T19_111606.aif,E,E
@@ -7213,7 +7297,7 @@ pos,fn,label,label_prefilter
149.68093813000002,RSL20000930B_T19_111606.aif,G,G
154.1556014915,RSL20000930B_T19_111606.aif,I,I
156.68536322,RSL20000930B_T19_111606.aif,I,I
-160.8817915005,RSL20000930B_T19_111606.aif,E,E
+160.88179150050001,RSL20000930B_T19_111606.aif,E,E
164.3936960185,RSL20000930B_T19_111606.aif,G,G
167.0425053585,RSL20000930B_T19_111606.aif,E,E
170.63932813,RSL20000930B_T19_111606.aif,G,G
@@ -7225,27 +7309,27 @@ pos,fn,label,label_prefilter
190.553583415,RSL20000930B_T19_111606.aif,G,G
194.883940257,RSL20000930B_T19_111606.aif,I,I
197.45834484,RSL20000930B_T19_111606.aif,I,I
-201.440842429,RSL20000930B_T19_111606.aif,E,E
+201.44084242899999,RSL20000930B_T19_111606.aif,E,E
204.3575088925,RSL20000930B_T19_111606.aif,G,G
206.902151573,RSL20000930B_T19_111606.aif,E,E
209.3128656915,RSL20000930B_T19_111606.aif,F,F
212.0509607395,RSL20000930B_T19_111606.aif,E,E
-214.297984393,RSL20000930B_T19_111606.aif,F,F
-217.882396108,RSL20000930B_T19_111606.aif,I,I
+214.29798439299998,RSL20000930B_T19_111606.aif,F,F
+217.88239610800002,RSL20000930B_T19_111606.aif,I,I
220.0698959565,RSL20000930B_T19_111606.aif,I,I
224.011159307,RSL20000930B_T19_111606.aif,E,E
-226.674849598,RSL20000930B_T19_111606.aif,F,F
+226.67484959799998,RSL20000930B_T19_111606.aif,F,F
228.981397057,RSL20000930B_T19_111606.aif,E,E
-231.377230224,RSL20000930B_T19_111606.aif,F,F
-233.520087218,RSL20000930B_T19_111606.aif,E,E
-235.692706115,RSL20000930B_T19_111606.aif,F,F
-239.4687780025,RSL20000930B_T19_111606.aif,I,I
-241.6562778505,RSL20000930B_T19_111606.aif,I,I
+231.37723022400002,RSL20000930B_T19_111606.aif,F,F
+233.52008721800001,RSL20000930B_T19_111606.aif,E,E
+235.69270611500002,RSL20000930B_T19_111606.aif,F,F
+239.46877800250002,RSL20000930B_T19_111606.aif,I,I
+241.65627785049998,RSL20000930B_T19_111606.aif,I,I
245.540206152,RSL20000930B_T19_111606.aif,E,E
248.144372638,RSL20000930B_T19_111606.aif,F,F
-250.70389627,RSL20000930B_T19_111606.aif,E,E
+250.70389626999997,RSL20000930B_T19_111606.aif,E,E
252.7872294585,RSL20000930B_T19_111606.aif,F,F
-254.9179346435,RSL20000930B_T19_111606.aif,E,E
+254.91793464350002,RSL20000930B_T19_111606.aif,E,E
257.209601151,RSL20000930B_T19_111606.aif,F,F
260.691743766,RSL20000930B_T19_111606.aif,I,I
262.83460076,RSL20000930B_T19_111606.aif,I,I
@@ -7256,7 +7340,7 @@ pos,fn,label,label_prefilter
275.9090986005,RSL20000930B_T19_111606.aif,E,E
278.1710032055,RSL20000930B_T19_111606.aif,F,F
281.7275505775,RSL20000930B_T19_111606.aif,I,I
-284.1382646955,RSL20000930B_T19_111606.aif,I,I
+284.13826469549997,RSL20000930B_T19_111606.aif,I,I
288.260288219,RSL20000930B_T19_111606.aif,E,E
290.8346928025,RSL20000930B_T19_111606.aif,F,F
293.394216434,RSL20000930B_T19_111606.aif,E,E
@@ -7271,12 +7355,12 @@ pos,fn,label,label_prefilter
29.6455396845,RSL20000930B_T19_112606.aif,B,B
32.875923118,RSL20000930B_T19_112606.aif,B,B
36.7060845835,RSL20000930B_T19_112606.aif,B,B
-40.7060533255,RSL20000930B_T19_112606.aif,A,A
+40.706053325499994,RSL20000930B_T19_112606.aif,A,A
45.0953516675,RSL20000930B_T19_112606.aif,A,A
-50.863578932,RSL20000930B_T19_112606.aif,B,B
+50.863578931999996,RSL20000930B_T19_112606.aif,B,B
54.0939623655,RSL20000930B_T19_112606.aif,B,B
58.092482577,RSL20000930B_T19_112606.aif,B,B
-61.7016731885,RSL20000930B_T19_112606.aif,A,A
+61.701673188499996,RSL20000930B_T19_112606.aif,A,A
65.64758129200001,RSL20000930B_T19_112606.aif,A,A
71.484492527,RSL20000930B_T19_112606.aif,B,B
74.820100177,RSL20000930B_T19_112606.aif,B,B
@@ -7288,30 +7372,30 @@ pos,fn,label,label_prefilter
106.548190348,RSL20000930B_T19_112606.aif,D,D
109.780279052,RSL20000930B_T19_112606.aif,F,F
112.210958443,RSL20000930B_T19_112606.aif,E,E
-114.8205190025,RSL20000930B_T19_112606.aif,F,F
-118.8400840565,RSL20000930B_T19_112606.aif,I,I
+114.82051900249999,RSL20000930B_T19_112606.aif,F,F
+118.84008405649999,RSL20000930B_T19_112606.aif,I,I
121.060315016,RSL20000930B_T19_112606.aif,I,I
-125.22062471,RSL20000930B_T19_112606.aif,E,E
-127.924887064,RSL20000930B_T19_112606.aif,F,F
+125.22062471000001,RSL20000930B_T19_112606.aif,E,E
+127.92488706399999,RSL20000930B_T19_112606.aif,F,F
130.7343736335,RSL20000930B_T19_112606.aif,E,E
133.638561997,RSL20000930B_T19_112606.aif,F,F
137.7949185325,RSL20000930B_T19_112606.aif,I,I
140.0467167565,RSL20000930B_T19_112606.aif,I,I
144.243971186,RSL20000930B_T19_112606.aif,E,E
147.379003652,RSL20000930B_T19_112606.aif,G,G
-150.1148332705,RSL20000930B_T19_112606.aif,E,E
+150.11483327050001,RSL20000930B_T19_112606.aif,E,E
153.1137234285,RSL20000930B_T19_112606.aif,G,G
157.1432585555,RSL20000930B_T19_112606.aif,I,I
159.626550055,RSL20000930B_T19_112606.aif,I,I
163.81447385500002,RSL20000930B_T19_112606.aif,E,E
166.613438003,RSL20000930B_T19_112606.aif,G,G
-169.73859722050005,RSL20000930B_T19_112606.aif,E,E
+169.73859722050003,RSL20000930B_T19_112606.aif,E,E
172.55860621149998,RSL20000930B_T19_112606.aif,G,G
177.137564882,RSL20000930B_T19_112606.aif,I,I
179.526154587,RSL20000930B_T19_112606.aif,I,I
183.64394821,RSL20000930B_T19_112606.aif,E,E
186.8322419575,RSL20000930B_T19_112606.aif,G,G
-189.2734437705,RSL20000930B_T19_112606.aif,E,E
+189.27344377050002,RSL20000930B_T19_112606.aif,E,E
191.8514370645,RSL20000930B_T19_112606.aif,F,F
196.1111963125,RSL20000930B_T19_112606.aif,I,I
198.552398125,RSL20000930B_T19_112606.aif,I,I
@@ -7327,7 +7411,7 @@ pos,fn,label,label_prefilter
229.51038978,RSL20000930B_T19_112606.aif,F,F
231.720211055,RSL20000930B_T19_112606.aif,E,E
233.9225918545,RSL20000930B_T19_112606.aif,F,F
-237.9740251795,RSL20000930B_T19_112606.aif,I,I
+237.97402517950002,RSL20000930B_T19_112606.aif,I,I
240.198727406,RSL20000930B_T19_112606.aif,I,I
243.9784890485,RSL20000930B_T19_112606.aif,E,E
246.270155556,RSL20000930B_T19_112606.aif,F,F
@@ -7337,22 +7421,22 @@ pos,fn,label,label_prefilter
255.221470027,RSL20000930B_T19_112606.aif,F,F
258.5000237195,RSL20000930B_T19_112606.aif,I,I
260.4717497725,RSL20000930B_T19_112606.aif,I,I
-264.515071995,RSL20000930B_T19_112606.aif,E,E
+264.51507199499997,RSL20000930B_T19_112606.aif,E,E
267.0522742,RSL20000930B_T19_112606.aif,F,F
269.3662621345,RSL20000930B_T19_112606.aif,E,E
271.46447627450004,RSL20000930B_T19_112606.aif,F,F
273.4287618525,RSL20000930B_T19_112606.aif,E,E
275.390092735,RSL20000930B_T19_112606.aif,F,F
-278.8596100975,RSL20000930B_T19_112606.aif,I,I
+278.85961009749997,RSL20000930B_T19_112606.aif,I,I
280.950383762,RSL20000930B_T19_112606.aif,I,I
284.80455016099995,RSL20000930B_T19_112606.aif,E,E
287.245026182,RSL20000930B_T19_112606.aif,F,F
-289.7786060755,RSL20000930B_T19_112606.aif,E,E
+289.77860607549997,RSL20000930B_T19_112606.aif,E,E
292.025629729,RSL20000930B_T19_112606.aif,E,E
293.98991530700005,RSL20000930B_T19_112606.aif,E,E
296.073248496,RSL20000930B_T19_112606.aif,F,F
299.614914916,RSL20000930B_T19_112606.aif,I,I
-3.6309521285,RSL20000930B_T19_104606.aif,E,E
+3.6309521284999997,RSL20000930B_T19_104606.aif,E,E
6.5624995445,RSL20000930B_T19_104606.aif,F,F
17.380951174,RSL20000930B_T19_104606.aif,E,E
20.550593811,RSL20000930B_T19_104606.aif,G,G
@@ -7362,7 +7446,7 @@ pos,fn,label,label_prefilter
39.9804739645,RSL20000930B_T19_104606.aif,G,G
42.837616623,RSL20000930B_T19_104606.aif,E,E
45.8882116495,RSL20000930B_T19_104606.aif,F,F
-56.8565641395,RSL20000930B_T19_104606.aif,E,E
+56.856564139499994,RSL20000930B_T19_104606.aif,E,E
60.055968679,RSL20000930B_T19_104606.aif,G,G
62.838706581,RSL20000930B_T19_104606.aif,E,E
65.3089445045,RSL20000930B_T19_104606.aif,G,G
@@ -7370,19 +7454,19 @@ pos,fn,label,label_prefilter
78.86904362300001,RSL20000930B_T19_104606.aif,G,G
81.6498688775,RSL20000930B_T19_104606.aif,E,E
84.2540353635,RSL20000930B_T19_104606.aif,G,G
-94.8492727225,RSL20000930B_T19_104606.aif,E,E
-97.9488813125,RSL20000930B_T19_104606.aif,G,G
-100.627452555,RSL20000930B_T19_104606.aif,E,E
+94.84927272249999,RSL20000930B_T19_104606.aif,E,E
+97.94888131249999,RSL20000930B_T19_104606.aif,G,G
+100.62745255499999,RSL20000930B_T19_104606.aif,E,E
103.350666652,RSL20000930B_T19_104606.aif,G,G
-114.169118281,RSL20000930B_T19_104606.aif,E,E
+114.16911828100001,RSL20000930B_T19_104606.aif,E,E
117.1982811745,RSL20000930B_T19_104606.aif,G,G
-120.040542882,RSL20000930B_T19_104606.aif,E,E
+120.04054288200001,RSL20000930B_T19_104606.aif,E,E
122.793518881,RSL20000930B_T19_104606.aif,G,G
132.838161041,RSL20000930B_T19_104606.aif,E,E
135.963160824,RSL20000930B_T19_104606.aif,G,G
138.5398879295,RSL20000930B_T19_104606.aif,E,E
141.48631629599998,RSL20000930B_T19_104606.aif,G,G
-151.382148942,RSL20000930B_T19_104606.aif,E,E
+151.38214894200001,RSL20000930B_T19_104606.aif,E,E
154.060720185,RSL20000930B_T19_104606.aif,G,G
156.8104130495,RSL20000930B_T19_104606.aif,E,E
159.459222389,RSL20000930B_T19_104606.aif,F,F
@@ -7399,14 +7483,14 @@ pos,fn,label,label_prefilter
200.454594981,RSL20000930B_T19_104606.aif,E,E
202.418880559,RSL20000930B_T19_104606.aif,F,F
204.7998327745,RSL20000930B_T19_104606.aif,E,E
-206.523844433,RSL20000930B_T19_104606.aif,G,G
-216.698338897,RSL20000930B_T19_104606.aif,E,E
+206.52384443300002,RSL20000930B_T19_104606.aif,G,G
+216.69833889699999,RSL20000930B_T19_104606.aif,E,E
219.615005361,RSL20000930B_T19_104606.aif,G,G
-221.8988774555,RSL20000930B_T19_104606.aif,E,E
+221.89887745549998,RSL20000930B_T19_104606.aif,E,E
224.0119725465,RSL20000930B_T19_104606.aif,F,F
234.9767738535,RSL20000930B_T19_104606.aif,E,E
237.4618927285,RSL20000930B_T19_104606.aif,F,F
-243.238576592,RSL20000930B_T19_104606.aif,G,G
-255.3963138425,RSL20000930B_T19_104606.aif,F,F
+243.23857659200002,RSL20000930B_T19_104606.aif,G,G
+255.39631384249998,RSL20000930B_T19_104606.aif,F,F
258.140265511,RSL20000930B_T19_104606.aif,E,E
260.104551089,RSL20000930B_T19_104606.aif,F,F
diff --git a/models.py b/models.py
index 597b8963823088dff7861fbcb3bb884f976f48fa..bc0c65e312f366c09f812d3105e321c5d6879adb 100755
--- a/models.py
+++ b/models.py
@@ -41,12 +41,12 @@ meta = {
'sampleDur': 2
},
'humpback':{
- 'nfft': 512,
+ 'nfft': 1024,
'sr': 11025,
'sampleDur': 2
},
'humpback2':{
- 'nfft': 512,
+ 'nfft': 2048,
'sr': 11025,
'sampleDur': 2
},
@@ -57,12 +57,17 @@ meta = {
},
'otter':{
'nfft':2048,
- 'sr':48000,
- 'sampleDur':0.5
+ 'sr':96000,
+ 'sampleDur':1
+ },
+ 'dolphin':{
+ 'nfft':512,
+ 'sr':96000,
+ 'sampleDur':2
}
}
-vgg16 = torchmodels.vgg16(pretrained=True) # weights=torchmodels.VGG16_Weights.DEFAULT)
+vgg16 = torchmodels.vgg16(weights=torchmodels.VGG16_Weights.DEFAULT)
vgg16 = vgg16.features[:13]
for nm, mod in vgg16.named_modules():
if isinstance(mod, nn.MaxPool2d):
@@ -82,6 +87,13 @@ frontend = {
nn.InstanceNorm2d(1),
u.Croper2D(n_mel, 128)
),
+ 'logMel_vggish': lambda sr, nfft, sampleDur, n_mel : nn.Sequential(
+ STFT(nfft, int((sampleDur*sr - nfft)/96)),
+ MelFilter(sr, nfft, n_mel, 0, sr//2),
+ Log1p(7, trainable=False),
+ nn.InstanceNorm2d(1),
+ u.Croper2D(n_mel, 128)
+ ),
'logSTFT': lambda sr, nfft, sampleDur, n_mel : nn.Sequential(
STFT(nfft, int((sampleDur*sr - nfft)/128)),
Log1p(7, trainable=False),
@@ -117,8 +129,28 @@ sparrow_VQ_encoder = lambda nfeat, shape : nn.Sequential(
u.Reshape(nfeat * shape[0] * shape[1])
)
+sparrow_encoder_maxPool = lambda nfeat, shape : nn.Sequential(
+ nn.Conv2d(1, 32, 3, bias=False, padding=1),
+ nn.BatchNorm2d(32),
+ nn.ReLU(True),
+ nn.Conv2d(32, 32, 3, bias=False, padding=1),
+ nn.BatchNorm2d(32),
+ nn.MaxPool2d((4, 4)),
+ nn.ReLU(True),
+ nn.Conv2d(32, 32, 3, bias=False, padding=1),
+ nn.BatchNorm2d(32),
+ nn.ReLU(True),
+ nn.Conv2d(32, 32, 3, bias=False, padding=1),
+ nn.BatchNorm2d(32),
+ nn.ReLU(True),
+ nn.Conv2d(32, nfeat, 3, bias=False, padding=1),
+ nn.MaxPool2d((4, 4)),
+ u.Reshape(nfeat * shape[0] * shape[1])
+)
+
+
sparrow_encoder = lambda nfeat, shape : nn.Sequential(
- nn.Conv2d(1, 32, 3, stride=2, bias=False, padding=(1)),
+ nn.Conv2d(1, 32, 3, stride=2, bias=False, padding=1),
nn.BatchNorm2d(32),
nn.ReLU(True),
nn.Conv2d(32, 64, 3, stride=2, bias=False, padding=1),
@@ -177,7 +209,7 @@ sparrow_decoder = lambda nfeat, shape : nn.Sequential(
nn.Conv2d(32, 1, (3, 3), bias=False, padding=1),
nn.BatchNorm2d(1),
nn.ReLU(True),
- nn.Conv2d(1, 1, (3, 3), bias=False, padding=1),
+ nn.Conv2d(1, 1, (3, 3), bias=False, padding=1)
)
sparrow_decoder_old = lambda nfeat, shape : nn.Sequential(
diff --git a/plot_annot_distrib.py b/plot_annot_distrib.py
index 6b5e5c975989b816828d58c7f63bd568f2d9b9ac..3a6ac5c0a5758a8827b9d04518761104980696b2 100755
--- a/plot_annot_distrib.py
+++ b/plot_annot_distrib.py
@@ -2,6 +2,15 @@ import matplotlib.pyplot as plt
import pandas as pd, numpy as np
species = np.loadtxt('good_species.txt', dtype=str)
+info = {
+ 'bengalese_finch1': ['bengalese finch', 'nicholson2017bengalese', 'bird'],
+ 'bengalese_finch2': ['bengalese finch', 'koumura2016birdsongrecognition', 'bird'],
+ 'california_thrashers': ['california trashers', 'arriaga2015bird', 'bird'],
+ 'cassin_vireo': ['cassin vireo', 'arriaga2015bird', 'bird'],
+ 'black-headed_grosbeaks': ['black-headed grosbeaks', 'arriaga2015bird', 'bird'],
+ 'zebra_finch': ['zebra finch', 'elie2018zebra', 'bird'],
+ 'humpback': ['humpback whale', 'malige2021use', 'cetacean'],
+}
fig, ax = plt.subplots(nrows=4, ncols=3, figsize=(10, 10))
for i, specie in enumerate(species):
@@ -12,10 +21,10 @@ plt.tight_layout()
plt.savefig('annot_distrib.pdf')
-a = "Specie & \# Classes & \# Annotated samples & \# Samples & Proportion of annotations\\\\ \hline \n"
+a = "Specie & \# Classes & \# Samples & Annotations \% \\\\ \hline \n"
for specie in species:
df = pd.read_csv(f'{specie}/{specie}.csv')
- a += f"{specie.replace('_',' ')} & {df.label.nunique()} & {(~df.label.isna()).sum()} & {len(df)} & {int(100*(~df.label.isna()).sum()/len(df))} \\\\ \hline \n"
+ a += f"{info[specie][0]} \cite{{{info[specie][1]}}} & {df.label.nunique()} & {len(df)} & {int(100*(~df.label.isna()).sum()/len(df))} \\\\ \hline \n"
f = open('annot_distrib.tex', 'w')
f.write(a)
f.close()
diff --git a/plot_results_hdbcsan.py b/plot_results_hdbcsan.py
index 67c0cd0be6ffb1d5d8912c66646b89ee83a80b88..4cee2973e7b9735c0684a986a621d6ae4bfbdd10 100755
--- a/plot_results_hdbcsan.py
+++ b/plot_results_hdbcsan.py
@@ -5,7 +5,7 @@ import numpy as np
from sklearn import metrics
species = np.loadtxt('good_species.txt', dtype=str)
-frontends = ['16_pcenMel128', '16_logMel128', '16_logSTFT', '16_Mel128', '8_pcenMel64', '32_pcenMel128']
+frontends = ['16_logMel128', '16_logSTFT', '16_Mel128', '16_pcenMel128', '8_pcenMel64', '32_pcenMel128', '64_pcenMel128']
plt.figure()
for specie in species:
df = pd.read_csv(f'{specie}/{specie}.csv')
@@ -30,3 +30,4 @@ plt.grid()
plt.tight_layout()
plt.legend()
plt.savefig('NMIs_hdbscan.pdf')
+plt.close()
diff --git a/print_annot.py b/print_annot.py
index 7d6bae53f460893d1c45d0ee7772e04c8f56f82e..7861c00d69d03d2d57caff7178a106f18e52c59f 100755
--- a/print_annot.py
+++ b/print_annot.py
@@ -8,7 +8,7 @@ import torch
parser = argparse.ArgumentParser()
parser.add_argument("specie", type=str)
parser.add_argument("-frontend", type=str, default='logMel')
-parser.add_argument("-nMel", type=int, default=64)
+parser.add_argument("-nMel", type=int, default=128)
args = parser.parse_args()
meta = models.meta[args.specie]
diff --git a/run_baseline.py b/run_baseline.py
index 1d55f221c7f74699894eb973c53356d81d49d196..39c20daf61b5ae61a4c5b1caee9d9e2aee1c0342 100755
--- a/run_baseline.py
+++ b/run_baseline.py
@@ -12,8 +12,8 @@ args = parser.parse_args()
df = pd.read_csv(f'{args.specie}/{args.specie}.csv')
-def norm(arr):
- return (arr - np.mean(arr) ) / np.std(arr)
+norm = lambda arr: (arr - np.mean(arr) ) / np.std(arr)
+
meta = models.meta[args.specie]
feats = ['fund', 'cvfund', 'maxfund', 'minfund', 'meansal', 'meanspect', 'stdspect', 'skewspect',\
@@ -32,7 +32,7 @@ def process(idx):
if fs != meta['sr']:
sig = resample(sig, int(len(sig)/fs*meta['sr']))
sound = BioSound(soundWave=norm(sig), fs=fs)
- sound.spectroCalc(max_freq=meta['sr']//2)
+ sound.spectroCalc(max_freq=meta['sr']//2, spec_sample_rate=128//meta['sampleDur'])
sound.rms = sound.sound.std()
sound.ampenv(cutoff_freq = 20, amp_sample_rate = 1000)
sound.spectrum(f_high=meta['sr']//2 - 1)
@@ -43,10 +43,10 @@ def process(idx):
return [sound.__dict__[f] for f in feats]
-res = p_tqdm.p_map(process, df.index[:10])
+res = p_tqdm.p_map(process, df.index[:100], num_cpus=16)
-for i, mr in zip(df.index[:10], res):
+for i, mr in zip(df.index[:100], res):
for f, r in zip(feats, mr):
df.loc[i, f] = r
-df.to_csv(f'{args.specie}/{args.specie}_biosound.csv', index=False)
\ No newline at end of file
+df.to_csv(f'{args.specie}/{args.specie}_biosound.csv', index=False)
diff --git a/run_vggish.py b/run_vggish.py
new file mode 100755
index 0000000000000000000000000000000000000000..cc42a8101d895f262a1ed4c75404bd6e68d70457
--- /dev/null
+++ b/run_vggish.py
@@ -0,0 +1,75 @@
+from sklearn import metrics
+import matplotlib.pyplot as plt
+import umap, hdbscan
+from tqdm import tqdm
+import argparse, os
+import models, utils as u
+import pandas as pd, numpy as np, torch
+torch.multiprocessing.set_sharing_strategy('file_system')
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument("specie", type=str)
+args = parser.parse_args()
+
+df = pd.read_csv(f'{args.specie}/{args.specie}.csv')
+
+meta = models.meta[args.specie]
+
+if not os.path.isfile(f'{args.specie}/encodings_vggish.npy'):
+ gpu = torch.device('cuda')
+ frontend = models.frontend['logMel_vggish'](meta['sr'], meta['nfft'], meta['sampleDur'], 64)
+ vggish = torch.hub.load('harritaylor/torchvggish', 'vggish')
+ # vggish.preprocess = False
+ vggish.postprocess = False
+ model = torch.nn.Sequential(frontend, vggish).to(gpu)
+ model.eval()
+ loader = torch.utils.data.DataLoader(u.Dataset(df, f'{args.specie}/audio/', 16000, 1), batch_size=1, shuffle=True, num_workers=8, collate_fn=u.collate_fn)
+ with torch.no_grad():
+ encodings, idxs = [], []
+ for x, idx in tqdm(loader, desc='test '+args.specie, leave=False):
+ # encoding = model(x.to(gpu))
+ encoding = vggish(x.numpy().squeeze(0), fs=16000)
+ idxs.extend(idx)
+ encodings.extend(encoding.cpu().detach())
+
+ idxs, encodings = np.array(idxs), np.stack(encodings)
+ X = umap.UMAP(n_jobs=-1).fit_transform(encodings)
+ np.save(f'{args.specie}/encodings_vggish.npy', {'idxs':idxs, 'encodings':encodings, 'umap':X})
+else:
+ dic = np.load(f'{args.specie}/encodings_vggish.npy', allow_pickle=True).item()
+ idxs, encodings, X = dic['idxs'], dic['encodings'], dic['umap']
+
+clusters = hdbscan.HDBSCAN(min_cluster_size=50, min_samples=5, cluster_selection_epsilon=0.05, core_dist_n_jobs=-1, cluster_selection_method='leaf').fit_predict(X)
+df.loc[idxs, 'cluster'] = clusters.astype(int)
+mask = ~df.loc[idxs].label.isna()
+
+#print('Found clusters : \n', pd.Series(clusters).value_counts())
+
+plt.figure(figsize=(20, 10))
+plt.scatter(X[clusters==-1,0], X[clusters==-1,1], s=2, alpha=.2, color='Grey')
+plt.scatter(X[clusters!=-1,0], X[clusters!=-1,1], s=2, c=clusters[clusters!=-1], cmap='tab20')
+plt.tight_layout()
+plt.savefig(f'{args.specie}/vggish_projection_clusters.png')
+
+plt.figure(figsize=(20, 10))
+plt.scatter(X[~mask,0], X[~mask,1], s=2, alpha=.2, color='Grey')
+for l, grp in df.groupby('label'):
+ plt.scatter(X[df.loc[idxs].label==l, 0], X[df.loc[idxs].label==l, 1], s=4, label=l)
+plt.legend()
+plt.tight_layout()
+plt.savefig(f'{args.specie}/vggish_projection_labels.png')
+
+
+clusters, labels = clusters[mask], df.loc[idxs[mask]].label
+print('Silhouette', metrics.silhouette_score(encodings[mask], clusters))
+print('NMI', metrics.normalized_mutual_info_score(labels, clusters))
+print('Homogeneity', metrics.homogeneity_score(labels, clusters))
+print('Completeness', metrics.completeness_score(labels, clusters))
+print('V-Measure', metrics.v_measure_score(labels, clusters))
+
+labelled = df[~df.label.isna()]
+for l, grp in labelled.groupby('label'):
+ best = (grp.groupby('cluster').fn.count() / labelled.groupby('cluster').fn.count()).idxmax()
+ print(f'Best precision for {l} is for cluster {best} with {(df.cluster==best).sum()} points, \
+with precision {((labelled.cluster==best)&(labelled.label==l)).sum()/(labelled.cluster==best).sum():.2f} and recall {((labelled.cluster==best)&(labelled.label==l)).sum()/(labelled.label==l).sum():.2f}')
diff --git a/test_AE.py b/test_AE.py
index 17e8716fde6e5995b80fe0a6be8c74101c91a3d6..b3d80e64110b86c3fd2c3370837d9e4539523467 100755
--- a/test_AE.py
+++ b/test_AE.py
@@ -7,6 +7,7 @@ from sklearn import metrics
import umap, hdbscan
torch.multiprocessing.set_sharing_strategy('file_system')
+
parser = argparse.ArgumentParser()
parser.add_argument("specie", type=str)
parser.add_argument("-bottleneck", type=int, default=16)
@@ -21,8 +22,6 @@ df = pd.read_csv(f'{args.specie}/{args.specie}.csv')
print(f'Tests for model {modelname}')
print(f'{len(df)} available vocs')
-loader = torch.utils.data.DataLoader(u.Dataset(df, f'{args.specie}/audio/', meta['sr'], meta['sampleDur']), batch_size=64, shuffle=True, num_workers=8, collate_fn=u.collate_fn)
-
if os.path.isfile(f'{args.specie}/encodings_{modelname[:-4]}npy'):
dic = np.load(f'{args.specie}/encodings_{modelname[:-4]}npy', allow_pickle=True).item()
idxs, encodings, X = dic['idxs'], dic['encodings'], dic['umap']
@@ -34,6 +33,7 @@ else:
model = torch.nn.Sequential(frontend, encoder, decoder).to(gpu)
model.load_state_dict(torch.load(f'{args.specie}/{modelname}'))
model.eval()
+ loader = torch.utils.data.DataLoader(u.Dataset(df, f'{args.specie}/audio/', meta['sr'], meta['sampleDur']), batch_size=64, shuffle=True, num_workers=8, collate_fn=u.collate_fn)
with torch.no_grad():
encodings, idxs = [], []
for x, idx in tqdm(loader, desc='test '+args.specie, leave=False):
@@ -45,7 +45,7 @@ else:
X = umap.UMAP(n_jobs=-1).fit_transform(encodings)
np.save(f'{args.specie}/encodings_{modelname[:-4]}npy', {'idxs':idxs, 'encodings':encodings, 'umap':X})
-clusters = hdbscan.HDBSCAN(min_cluster_size=10, min_samples=5, cluster_selection_epsilon=0.0, core_dist_n_jobs=-1, cluster_selection_method='eom').fit_predict(X)
+clusters = hdbscan.HDBSCAN(min_cluster_size=50, min_samples=5, cluster_selection_epsilon=0.05, core_dist_n_jobs=-1, cluster_selection_method='leaf').fit_predict(X)
df.loc[idxs, 'cluster'] = clusters.astype(int)
mask = ~df.loc[idxs].label.isna()
@@ -74,7 +74,15 @@ print('Completeness', metrics.completeness_score(labels, clusters))
print('V-Measure', metrics.v_measure_score(labels, clusters))
labelled = df[~df.label.isna()]
+goodClusters = []
for l, grp in labelled.groupby('label'):
- best = (grp.groupby('cluster').fn.count() / labelled.groupby('cluster').fn.count()).idxmax()
+ precisions = grp.groupby('cluster').fn.count() / labelled.groupby('cluster').fn.count()
+ best = precisions.idxmax()
+ goodClusters.extend(precisions[precisions > 0.9].index)
print(f'Best precision for {l} is for cluster {best} with {(df.cluster==best).sum()} points, \
-with precision {((labelled.cluster==best)&(labelled.label==l)).sum()/(labelled.cluster==best).sum():.2f} and recall {((labelled.cluster==best)&(labelled.label==l)).sum()/(labelled.label==l).sum():.2f}')
+ with precision {((labelled.cluster==best)&(labelled.label==l)).sum()/(labelled.cluster==best).sum():.2f}\
+ and recall {((labelled.cluster==best)&(labelled.label==l)).sum()/(labelled.label==l).sum():.2f}')
+
+
+print(f'{len(goodClusters)} clusters would sort {df.cluster.isin(goodClusters).sum()/len(df)*100:.0f}% of samples')
+print(f'{len(goodClusters)/df.label.nunique():.1f} cluster per label in avg)')
\ No newline at end of file
diff --git a/train_AE.py b/train_AE.py
index e24c26cc7c9bbcb151838298eab5c023aa0e96b9..0b351fd62e9711ec01819820dea76f2a5fbab5b0 100755
--- a/train_AE.py
+++ b/train_AE.py
@@ -67,8 +67,10 @@ for epoch in range(100_000//len(loader)):
if len(loss) > 2000 and np.median(loss[-2000:-1000]) < np.median(loss[-1000:]):
print('Early stop')
+ torch.save(model.state_dict(), f'{args.specie}/{modelname}')
exit()
-
+ step += 1
+ continue
# TEST ROUTINE
if step % 500 == 0:
# Plot reconstructions