Update data files, including pre-webdataset catalog, this is v3.3.

data/catalog.csv

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:315576dd390920972ad48accbef002b5f19ca6838a6035cd1f32f09e3ee6d411
-size 2018327986
+oid sha256:ef5edf6a6e6048c98e74787cc143981095efaa27ba0aa4cebbac8116b24c9735
+size 2024176607

data/missing_taxa_output.txt

@@ -70,3 +70,27 @@ Output of taxa check for catalog.csv v3.2 (taxa check now also removes duplicate
 [2023-10-26 13:44:14,425] [WARNING] [root] There are 149057 samples for which the species column may have genus and species.
 
 ------------------------------------------------------------------------------------------------------
+
+Output of taxa check for catalog.csv v3.3 (from pr3):
+
+[2023-10-30 17:31:38,357] [WARNING] [root] There are 12 kingdoms instead of 3.
+[2023-10-30 17:31:39,420] [WARNING] [root] 39574 entries are missing rank kingdom, but have genus label.
+[2023-10-30 17:31:39,681] [WARNING] [root] 38324 entries are missing rank phylum, but have genus label.
+[2023-10-30 17:31:39,942] [WARNING] [root] 44828 entries are missing rank class, but have genus label.
+[2023-10-30 17:31:40,199] [WARNING] [root] 42771 entries are missing rank order, but have genus label.
+[2023-10-30 17:31:40,456] [WARNING] [root] 40131 entries are missing rank family, but have genus label.
+[2023-10-30 17:31:40,733] [WARNING] [root] 232 entries are missing rank kingdom, but have family label.
+[2023-10-30 17:31:40,759] [WARNING] [root] 223 entries are missing rank phylum, but have family label.
+[2023-10-30 17:31:40,785] [WARNING] [root] 493 entries are missing rank class, but have family label.
+[2023-10-30 17:31:40,812] [WARNING] [root] 345 entries are missing rank order, but have family label.
+[2023-10-30 17:31:40,853] [WARNING] [root] 170 entries are missing rank kingdom, but have order label.
+[2023-10-30 17:31:40,854] [WARNING] [root] 105 entries are missing rank phylum, but have order label.
+[2023-10-30 17:31:40,855] [WARNING] [root] 1263 entries are missing rank class, but have order label.
+[2023-10-30 17:31:40,893] [WARNING] [root] 41 entries have kingdom and species labels but no genus.
+[2023-10-30 17:31:40,897] [WARNING] [root] 41 entries have phylum and species labels but no genus.
+[2023-10-30 17:31:40,901] [WARNING] [root] 41 entries have class and species labels but no genus.
+[2023-10-30 17:31:40,905] [WARNING] [root] 41 entries have order and species labels but no genus.
+[2023-10-30 17:31:40,908] [WARNING] [root] 41 entries have family and species labels but no genus.
+[2023-10-30 17:31:42,311] [WARNING] [root] There are 137661 samples with species label longer than one word.
+
+------------------------------------------------------------------------------------------------------

data/predicted-catalog.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e17a9325927e2dff21bc30bb8b3151a300fd456e4f725a626692e76fca6a0f2b
+size 1847398611

data/stats_avg_std_byClass.csv

@@ -1,9 +1,9 @@
 class,average_all_imgs,standard_deviation,avg_labeled,std_dev_labeled
-kingdom,1490931.5714285714,1221.0370884737988,1383385.142857143,1176.1739424324717
-phylum,115961.34444444445,340.53097428052627,107705.3111111111,328.1848733733947
-class,36748.31338028169,191.69849603030715,34047.58450704225,184.5198756422794
-order,7841.1126972201355,88.55005757886403,7262.970698722765,85.22306435890911
-family,1339.3892453798767,36.59766721226746,1236.6025410677619,35.165359959308844
-genus,141.30713405635214,11.887267728807664,120.2536794075037,10.966023864988792
-species,63.3115005702361,7.9568524285823035,52.917740409114074,7.274458083535438
-common,23.458496762142808,4.8433972335688935,22.625316649171822,4.756607682915612
+kingdom,869710.0833333334,932.582480713279,817063.9166666666,903.9158791982065
+phylum,96634.45370370371,310.86082690442635,90799.6574074074,301.32981499912586
+class,30076.42939481268,173.4255730704462,28203.440922190202,167.93880112168898
+order,6980.9505016722405,83.55208256933061,6542.110367892977,80.88331328458904
+family,1309.8043423694778,36.19121913350637,1223.4554467871485,34.977927994481725
+genus,141.30713405635214,11.887267728807664,120.25013201186076,10.96586211895174
+species,63.770697250957795,7.9856557182837395,53.29990773385801,7.300678580368952
+common,23.511079121780227,4.848822446922575,22.675425435573036,4.761872051575203