diff --git "a/notebooks/lilabc_CT.ipynb" "b/notebooks/lilabc_CT.ipynb" --- "a/notebooks/lilabc_CT.ipynb" +++ "b/notebooks/lilabc_CT.ipynb" @@ -17,14 +17,6 @@ "execution_count": 2, "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/var/folders/nv/f0fq1p1n1_3b11x579py_0q80000gq/T/ipykernel_1497/1962403499.py:1: DtypeWarning: Columns (7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29) have mixed types. Specify dtype option on import or set low_memory=False.\n", - " df = pd.read_csv(\"lila_image_urls_and_labels.csv\")\n" - ] - }, { "data": { "text/html": [ @@ -47,15 +39,15 @@ "
5 rows × 30 columns
\n", + "5 rows × 32 columns
\n", "" ], "text/plain": [ - " dataset_name url \n", - "0 Caltech Camera Traps https://lilablobssc.blob.core.windows.net/calt... \\\n", - "1 Caltech Camera Traps https://lilablobssc.blob.core.windows.net/calt... \n", - "2 Caltech Camera Traps https://lilablobssc.blob.core.windows.net/calt... \n", - "3 Caltech Camera Traps https://lilablobssc.blob.core.windows.net/calt... \n", - "4 Caltech Camera Traps https://lilablobssc.blob.core.windows.net/calt... \n", - "\n", - " image_id \n", - "0 Caltech Camera Traps : 5968c0f9-23d2-11e8-a6a3... \\\n", + " dataset_name url_gcp \\\n", + "0 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "1 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "2 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "3 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "4 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "\n", + " url_aws \\\n", + "0 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "1 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "2 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "3 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "4 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "\n", + " url_azure \\\n", + "0 https://lilawildlife.blob.core.windows.net/lil... \n", + "1 https://lilawildlife.blob.core.windows.net/lil... \n", + "2 https://lilawildlife.blob.core.windows.net/lil... \n", + "3 https://lilawildlife.blob.core.windows.net/lil... \n", + "4 https://lilawildlife.blob.core.windows.net/lil... \n", + "\n", + " image_id \\\n", + "0 Caltech Camera Traps : 5968c0f9-23d2-11e8-a6a3... \n", "1 Caltech Camera Traps : 5a0b016f-23d2-11e8-a6a3... \n", "2 Caltech Camera Traps : 59b93afb-23d2-11e8-a6a3... \n", "3 Caltech Camera Traps : 59641f56-23d2-11e8-a6a3... \n", "4 Caltech Camera Traps : 5a1e5306-23d2-11e8-a6a3... \n", "\n", - " sequence_id \n", - "0 Caltech Camera Traps : 6f2160eb-5567-11e8-990e... \\\n", + " sequence_id \\\n", + "0 Caltech Camera Traps : 6f2160eb-5567-11e8-990e... \n", "1 Caltech Camera Traps : 6f27ed66-5567-11e8-9e92... \n", "2 Caltech Camera Traps : 6f04895c-5567-11e8-a3d6... \n", "3 Caltech Camera Traps : 6f0385b5-5567-11e8-a80b... \n", "4 Caltech Camera Traps : 6f0a3ccf-5567-11e8-92fb... \n", "\n", - " location_id frame_num original_label scientific_name \n", - "0 Caltech Camera Traps : 26 1 empty NaN \\\n", + " location_id frame_num original_label scientific_name \\\n", + "0 Caltech Camera Traps : 26 1 empty NaN \n", "1 Caltech Camera Traps : 26 1 deer odocoileus \n", "2 Caltech Camera Traps : 38 2 cat felis catus \n", "3 Caltech Camera Traps : 38 2 opossum didelphis virginiana \n", "4 Caltech Camera Traps : 33 2 empty NaN \n", "\n", - " common_name datetime ... suborder infraorder \n", - "0 NaN 10-04-2013 13:31:53 ... NaN NaN \\\n", - "1 deer 11-04-2013 18:37:07 ... ruminantia NaN \n", - "2 cat 05-09-2012 07:33:45 ... NaN NaN \n", - "3 virginia opossum 03-29-2012 02:34:13 ... NaN NaN \n", - "4 NaN 05-08-2012 19:23:36 ... NaN NaN \n", - "\n", - " superfamily family subfamily tribe genus \n", - "0 NaN NaN NaN NaN NaN \\\n", - "1 NaN cervidae capreolinae odocoileini odocoileus \n", - "2 NaN felidae felinae NaN felis \n", - "3 NaN didelphidae didelphinae didelphini didelphis \n", - "4 NaN NaN NaN NaN NaN \n", + " ... suborder infraorder superfamily family subfamily \\\n", + "0 ... NaN NaN NaN NaN NaN \n", + "1 ... ruminantia NaN NaN cervidae capreolinae \n", + "2 ... NaN NaN NaN felidae felinae \n", + "3 ... NaN NaN NaN didelphidae didelphinae \n", + "4 ... NaN NaN NaN NaN NaN \n", "\n", - " species subspecies variety \n", - "0 NaN NaN NaN \n", - "1 NaN NaN NaN \n", - "2 felis catus NaN NaN \n", - "3 didelphis virginiana NaN NaN \n", - "4 NaN NaN NaN \n", + " tribe genus species subspecies variety \n", + "0 NaN NaN NaN NaN NaN \n", + "1 odocoileini odocoileus NaN NaN NaN \n", + "2 NaN felis felis catus NaN NaN \n", + "3 didelphini didelphis didelphis virginiana NaN NaN \n", + "4 NaN NaN NaN NaN NaN \n", "\n", - "[5 rows x 30 columns]" + "[5 rows x 32 columns]" ] }, "execution_count": 2, @@ -254,28 +253,29 @@ } ], "source": [ - "df = pd.read_csv(\"../data/lila_image_urls_and_labels.csv\")\n", + "df = pd.read_csv(\"../data/lila_image_urls_and_labels.csv\", low_memory = False)\n", "df.head()" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "Index(['dataset_name', 'url', 'image_id', 'sequence_id', 'location_id',\n", - " 'frame_num', 'original_label', 'scientific_name', 'common_name',\n", - " 'datetime', 'annotation_level', 'kingdom', 'phylum', 'subphylum',\n", - " 'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order',\n", - " 'suborder', 'infraorder', 'superfamily', 'family', 'subfamily', 'tribe',\n", - " 'genus', 'species', 'subspecies', 'variety'],\n", + "Index(['dataset_name', 'url_gcp', 'url_aws', 'url_azure', 'image_id',\n", + " 'sequence_id', 'location_id', 'frame_num', 'original_label',\n", + " 'scientific_name', 'common_name', 'datetime', 'annotation_level',\n", + " 'kingdom', 'phylum', 'subphylum', 'superclass', 'class', 'subclass',\n", + " 'infraclass', 'superorder', 'order', 'suborder', 'infraorder',\n", + " 'superfamily', 'family', 'subfamily', 'tribe', 'genus', 'species',\n", + " 'subspecies', 'variety'],\n", " dtype='object')" ] }, - "execution_count": 4, + "execution_count": 3, "metadata": {}, "output_type": "execute_result" } @@ -286,20 +286,20 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "annotation_level\n", - "sequence 12710844\n", + "sequence 12710778\n", "unknown 3382215\n", - "image 740789\n", + "image 3258163\n", "Name: count, dtype: int64" ] }, - "execution_count": 5, + "execution_count": 4, "metadata": {}, "output_type": "execute_result" } @@ -312,12 +312,115 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Annotation level indicates iimage vs sequence (or unknown), not analogous to `taxonomy_level` from lila-taxonomy-mapping_release.csv. It seems `original_label` may be the analogous column." + "Annotation level indicates iimage vs sequence (or unknown), not analogous to `taxonomy_level` from lila-taxonomy-mapping_release.csv. It seems `original_label` may be the analogous column.\n", + "\n", + "We'll likely want to pull out the image-level before doing any sequence checks and such since those should be \"clean\" images. Though we will want to label them with how many distinct species are in the image first.\n", + "\n", + "We now have 66 less sequence-level annotations and 2,517,374 more image-level! That's quite the update! The unknown count has not changed.\n", + "\n", + "### Check Dataset Counts\n", + "\n", + "1. Make sure we have all datasets expected.\n", + "2. Check which/how many datasets are labeled to the image level (and check for match to [Andrey's spreadsheet](https://docs.google.com/spreadsheets/d/1sC90DolAvswDUJ1lNSf0sk_norR24LwzX2O4g9OxMZE/edit?usp=drive_link))." ] }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "dataset_name\n", + "Snapshot Serengeti 7261545\n", + "NACTI 3382215\n", + "Trail Camera Images of New Zealand Animals 2453840\n", + "SWG Camera Traps 2039657\n", + "Idaho Camera Traps 1551552\n", + "WCS Camera Traps 1369953\n", + "Wellington Camera Traps 270450\n", + "Channel Islands Camera Traps 245644\n", + "Caltech Camera Traps 243177\n", + "Island Conservation Camera Traps 128207\n", + "Orinoquia Camera Traps 112267\n", + "Snapshot Mountain Zebra 73606\n", + "Desert Lion Conservation Camera Traps 63468\n", + "Snapshot Karoo 38320\n", + "Snapshot Camdeboo 30717\n", + "Snapshot Enonkishu 30542\n", + "Missouri Camera Traps 24673\n", + "Snapshot Kruger 10637\n", + "Snapshot Kgalagadi 10402\n", + "ENA24 10284\n", + "Name: count, dtype: int64" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.dataset_name.value_counts()" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "dataset_name annotation_level\n", + "Caltech Camera Traps image 243177\n", + "Channel Islands Camera Traps image 245644\n", + "Desert Lion Conservation Camera Traps image 63468\n", + "ENA24 image 10284\n", + "Idaho Camera Traps sequence 1551552\n", + "Island Conservation Camera Traps image 128207\n", + "Missouri Camera Traps sequence 23397\n", + " image 1276\n", + "NACTI unknown 3382215\n", + "Orinoquia Camera Traps image 112267\n", + "SWG Camera Traps sequence 2039657\n", + "Snapshot Camdeboo sequence 30717\n", + "Snapshot Enonkishu sequence 30542\n", + "Snapshot Karoo sequence 38320\n", + "Snapshot Kgalagadi sequence 10402\n", + "Snapshot Kruger sequence 10637\n", + "Snapshot Mountain Zebra sequence 73606\n", + "Snapshot Serengeti sequence 7261545\n", + "Trail Camera Images of New Zealand Animals image 2453840\n", + "WCS Camera Traps sequence 1369953\n", + "Wellington Camera Traps sequence 270450\n", + "Name: count, dtype: int64" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.groupby([\"dataset_name\"]).annotation_level.value_counts()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "It seems all the unknown annotation level images are in NACTI (North American Camera Trap Images). At first glance I don't see annotation level information on HF or on [their LILA page](https://lila.science/datasets/nacti)--will require more looking.\n", + "\n", + "Desert Lion Conservation Camera Traps & Trail Camera Images of New Zealand Animals are _not_ included in the [Hugging Face dataset](https://huggingface.co/datasets/society-ethics/lila_camera_traps).\n", + "\n", + "There are definitely more in [Andrey's spreadsheet](https://docs.google.com/spreadsheets/d/1sC90DolAvswDUJ1lNSf0sk_norR24LwzX2O4g9OxMZE/edit?usp=drive_link) that aren't included here. We'll have him go through those too." + ] + }, + { + "cell_type": "code", + "execution_count": 7, "metadata": {}, "outputs": [ { @@ -342,15 +445,15 @@ "10 rows × 30 columns
\n", + "10 rows × 32 columns
\n", "" ], "text/plain": [ - " dataset_name \n", - "14570597 Snapshot Camdeboo \\\n", - "13334717 Snapshot Serengeti \n", - "11278580 Snapshot Serengeti \n", - "9459516 Snapshot Serengeti \n", - "2969662 NACTI \n", - "1361914 NACTI \n", - "560812 NACTI \n", - "6040643 Idaho Camera Traps \n", - "1855600 NACTI \n", - "9890853 Snapshot Serengeti \n", - "\n", - " url \n", - "14570597 https://lilablobssc.blob.core.windows.net/snap... \\\n", - "13334717 https://lilablobssc.blob.core.windows.net/snap... \n", - "11278580 https://lilablobssc.blob.core.windows.net/snap... \n", - "9459516 https://lilablobssc.blob.core.windows.net/snap... \n", - "2969662 https://lilablobssc.blob.core.windows.net/nact... \n", - "1361914 https://lilablobssc.blob.core.windows.net/nact... \n", - "560812 https://lilablobssc.blob.core.windows.net/nact... \n", - "6040643 https://lilablobssc.blob.core.windows.net/idah... \n", - "1855600 https://lilablobssc.blob.core.windows.net/nact... \n", - "9890853 https://lilablobssc.blob.core.windows.net/snap... \n", - "\n", - " image_id \n", - "14570597 Snapshot Camdeboo : CDB_S1/B04/B04_R1/CDB_S1_B... \\\n", - "13334717 Snapshot Serengeti : S10/C05/C05_R1/S10_C05_R1... \n", - "11278580 Snapshot Serengeti : S7/T10/T10_R3/S7_T10_R3_I... \n", - "9459516 Snapshot Serengeti : S5/G07/G07_R1/S5_G07_R1_I... \n", - "2969662 NACTI : FL-33_07_06_2016_FL-33_0018047.JPG \n", - "1361914 NACTI : CA-45_08_03_2015_CA-45_0007619.jpg \n", - "560812 NACTI : 2016_Unit074_Ivan093_img0754.jpg \n", - "6040643 Idaho Camera Traps : loc_0026_im_007478 \n", - "1855600 NACTI : FL-07_08_16_2016_FL-07_0242508.JPG \n", - "9890853 Snapshot Serengeti : S5/Q12/Q12_R4/S5_Q12_R4_I... \n", - "\n", - " sequence_id \n", - "14570597 Snapshot Camdeboo : CDB_S1#B04#1#126 \\\n", - "13334717 Snapshot Serengeti : SER_S10#C05#1#719 \n", - "11278580 Snapshot Serengeti : SER_S7#T10#3#325 \n", - "9459516 Snapshot Serengeti : SER_S5#G07#1#859 \n", - "2969662 NACTI : unknown \n", - "1361914 NACTI : unknown \n", - "560812 NACTI : unknown \n", - "6040643 Idaho Camera Traps : loc_0026_seq_006588 \n", - "1855600 NACTI : unknown \n", - "9890853 Snapshot Serengeti : SER_S5#Q12#4#343 \n", - "\n", - " location_id frame_num original_label \n", - "14570597 Snapshot Camdeboo : B04 1 monkeyvervet \\\n", - "13334717 Snapshot Serengeti : C05 3 empty \n", - "11278580 Snapshot Serengeti : T10 2 hartebeest \n", - "9459516 Snapshot Serengeti : G07 3 empty \n", - "2969662 NACTI : Archbold, FL -1 bos taurus \n", - "1361914 NACTI : Lebec, California -1 bos taurus \n", - "560812 NACTI : San Juan Mntns, Colorado -1 cervus elaphus \n", - "6040643 Idaho Camera Traps : 26 0 empty \n", - "1855600 NACTI : Archbold, FL -1 equus africanus \n", - "9890853 Snapshot Serengeti : Q12 1 empty \n", - "\n", - " scientific_name common_name datetime ... \n", - "14570597 chlorocebus pygerythrus vervet monkey NaN ... \\\n", - "13334717 NaN NaN 01-18-2015 09:23:50 ... \n", - "11278580 alcelaphus buselaphus hartebeest 11-17-2013 11:54:56 ... \n", - "9459516 NaN NaN 06-05-2012 13:24:53 ... \n", - "2969662 bos taurus domestic cow NaN ... \n", - "1361914 bos taurus domestic cow NaN ... \n", - "560812 cervus elaphus red deer NaN ... \n", - "6040643 NaN NaN 02-18-2016 06:10:00 ... \n", - "1855600 equus africanus african wild ass NaN ... \n", - "9890853 NaN NaN 11-09-2012 18:46:47 ... \n", - "\n", - " suborder infraorder superfamily family \n", - "14570597 haplorhini simiiformes NaN cercopithecidae \\\n", - "13334717 NaN NaN NaN NaN \n", - "11278580 ruminantia NaN NaN bovidae \n", - "9459516 NaN NaN NaN NaN \n", - "2969662 ruminantia NaN NaN bovidae \n", - "1361914 ruminantia NaN NaN bovidae \n", - "560812 ruminantia NaN NaN cervidae \n", - "6040643 NaN NaN NaN NaN \n", - "1855600 NaN NaN NaN equidae \n", - "9890853 NaN NaN NaN NaN \n", - "\n", - " subfamily tribe genus \n", - "14570597 cercopithecinae cercopithecini chlorocebus \\\n", - "13334717 NaN NaN NaN \n", - "11278580 antilopinae alcelaphini alcelaphus \n", - "9459516 NaN NaN NaN \n", - "2969662 bovinae bovini bos \n", - "1361914 bovinae bovini bos \n", - "560812 cervinae cervini cervus \n", - "6040643 NaN NaN NaN \n", - "1855600 NaN NaN equus \n", - "9890853 NaN NaN NaN \n", - "\n", - " species subspecies variety \n", - "14570597 chlorocebus pygerythrus NaN NaN \n", - "13334717 NaN NaN NaN \n", - "11278580 alcelaphus buselaphus NaN NaN \n", - "9459516 NaN NaN NaN \n", - "2969662 bos taurus NaN NaN \n", - "1361914 bos taurus NaN NaN \n", - "560812 cervus elaphus NaN NaN \n", - "6040643 NaN NaN NaN \n", - "1855600 equus africanus NaN NaN \n", - "9890853 NaN NaN NaN \n", - "\n", - "[10 rows x 30 columns]" + " dataset_name \\\n", + "12061234 Snapshot Serengeti \n", + "6586492 Idaho Camera Traps \n", + "2786883 NACTI \n", + "13855386 Snapshot Serengeti \n", + "9992570 Snapshot Serengeti \n", + "2900006 NACTI \n", + "16472694 SWG Camera Traps \n", + "18408513 Trail Camera Images of New Zealand Animals \n", + "17944687 Trail Camera Images of New Zealand Animals \n", + "674082 NACTI \n", + "\n", + " url_gcp \\\n", + "12061234 https://storage.googleapis.com/public-datasets... \n", + "6586492 https://storage.googleapis.com/public-datasets... \n", + "2786883 https://storage.googleapis.com/public-datasets... \n", + "13855386 https://storage.googleapis.com/public-datasets... \n", + "9992570 https://storage.googleapis.com/public-datasets... \n", + "2900006 https://storage.googleapis.com/public-datasets... \n", + "16472694 https://storage.googleapis.com/public-datasets... \n", + "18408513 https://storage.googleapis.com/public-datasets... \n", + "17944687 https://storage.googleapis.com/public-datasets... \n", + "674082 https://storage.googleapis.com/public-datasets... \n", + "\n", + " url_aws \\\n", + "12061234 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "6586492 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "2786883 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "13855386 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "9992570 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "2900006 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "16472694 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "18408513 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "17944687 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "674082 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "\n", + " url_azure \\\n", + "12061234 https://lilawildlife.blob.core.windows.net/lil... \n", + "6586492 https://lilawildlife.blob.core.windows.net/lil... \n", + "2786883 https://lilawildlife.blob.core.windows.net/lil... \n", + "13855386 https://lilawildlife.blob.core.windows.net/lil... \n", + "9992570 https://lilawildlife.blob.core.windows.net/lil... \n", + "2900006 https://lilawildlife.blob.core.windows.net/lil... \n", + "16472694 https://lilawildlife.blob.core.windows.net/lil... \n", + "18408513 https://lilawildlife.blob.core.windows.net/lil... \n", + "17944687 https://lilawildlife.blob.core.windows.net/lil... \n", + "674082 https://lilawildlife.blob.core.windows.net/lil... \n", + "\n", + " image_id \\\n", + "12061234 Snapshot Serengeti : S8/N06/N06_R2/S8_N06_R2_I... \n", + "6586492 Idaho Camera Traps : loc_0067_im_006951 \n", + "2786883 NACTI : FL-28_09_01_2016_FL-28_0059198.JPG \n", + "13855386 Snapshot Serengeti : S10/O12/O12_R1/S10_O12_R1... \n", + "9992570 Snapshot Serengeti : S5/U12/U12_R1/S5_U12_R1_I... \n", + "2900006 NACTI : FL-31_01_21_2016_FL-31_0036063.jpg \n", + "16472694 SWG Camera Traps : d98b4691-8c29-11eb-85d7-000... \n", + "18408513 Trail Camera Images of New Zealand Animals : E... \n", + "17944687 Trail Camera Images of New Zealand Animals : E... \n", + "674082 NACTI : CA-06_08_10_2016_CA-06_0015357.JPG \n", + "\n", + " sequence_id \\\n", + "12061234 Snapshot Serengeti : SER_S8#N06#2#628 \n", + "6586492 Idaho Camera Traps : loc_0067_seq_006947 \n", + "2786883 NACTI : unknown \n", + "13855386 Snapshot Serengeti : SER_S10#O12#1#104 \n", + "9992570 Snapshot Serengeti : SER_S5#U12#1#63 \n", + "2900006 NACTI : unknown \n", + "16472694 SWG Camera Traps : fad4a034-8c29-11eb-8cda-000... \n", + "18408513 Trail Camera Images of New Zealand Animals : u... \n", + "17944687 Trail Camera Images of New Zealand Animals : u... \n", + "674082 NACTI : unknown \n", + "\n", + " location_id frame_num \\\n", + "12061234 Snapshot Serengeti : N06 3 \n", + "6586492 Idaho Camera Traps : 67 0 \n", + "2786883 NACTI : archbold_FL-28 -1 \n", + "13855386 Snapshot Serengeti : O12 1 \n", + "9992570 Snapshot Serengeti : U12 1 \n", + "2900006 NACTI : archbold_FL-31 -1 \n", + "16472694 SWG Camera Traps : loc_0890 0 \n", + "18408513 Trail Camera Images of New Zealand Animals : E... -1 \n", + "17944687 Trail Camera Images of New Zealand Animals : E... -1 \n", + "674082 NACTI : lebec_CA-06 -1 \n", + "\n", + " original_label scientific_name ... suborder \\\n", + "12061234 hartebeest alcelaphus buselaphus ... ruminantia \n", + "6586492 empty NaN ... NaN \n", + "2786883 unidentified bird aves ... NaN \n", + "13855386 empty NaN ... NaN \n", + "9992570 zebra equus quagga ... NaN \n", + "2900006 bos taurus bos taurus ... ruminantia \n", + "16472694 unidentified_murid muridae ... myomorpha \n", + "18408513 robin petroica australis ... NaN \n", + "17944687 mouse mus ... myomorpha \n", + "674082 bos taurus bos taurus ... ruminantia \n", + "\n", + " infraorder superfamily family subfamily tribe \\\n", + "12061234 NaN NaN bovidae antilopinae alcelaphini \n", + "6586492 NaN NaN NaN NaN NaN \n", + "2786883 NaN NaN NaN NaN NaN \n", + "13855386 NaN NaN NaN NaN NaN \n", + "9992570 NaN NaN equidae NaN NaN \n", + "2900006 NaN NaN bovidae bovinae bovini \n", + "16472694 NaN muroidea muridae NaN NaN \n", + "18408513 NaN NaN petroicidae NaN NaN \n", + "17944687 NaN muroidea muridae murinae murini \n", + "674082 NaN NaN bovidae bovinae bovini \n", + "\n", + " genus species subspecies variety \n", + "12061234 alcelaphus alcelaphus buselaphus NaN NaN \n", + "6586492 NaN NaN NaN NaN \n", + "2786883 NaN NaN NaN NaN \n", + "13855386 NaN NaN NaN NaN \n", + "9992570 equus equus quagga NaN NaN \n", + "2900006 bos bos taurus NaN NaN \n", + "16472694 NaN NaN NaN NaN \n", + "18408513 petroica petroica australis NaN NaN \n", + "17944687 mus NaN NaN NaN \n", + "674082 bos bos taurus NaN NaN \n", + "\n", + "[10 rows x 32 columns]" ] }, - "execution_count": 9, + "execution_count": 7, "metadata": {}, "output_type": "execute_result" } @@ -731,9 +846,16 @@ "df.sample(10)" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Observe that we also now get multiple URL options; `url_aws` will likely be best/fastest for use with [`distributed-downloader`](https://github.com/Imageomics/distributed-downloader) to get the images." + ] + }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 8, "metadata": {}, "outputs": [ { @@ -741,42 +863,44 @@ "output_type": "stream", "text": [ "0 rows × 30 columns
\n", + "0 rows × 32 columns
\n", "" ], "text/plain": [ "Empty DataFrame\n", - "Columns: [dataset_name, url, image_id, sequence_id, location_id, frame_num, original_label, scientific_name, common_name, datetime, annotation_level, kingdom, phylum, subphylum, superclass, class, subclass, infraclass, superorder, order, suborder, infraorder, superfamily, family, subfamily, tribe, genus, species, subspecies, variety]\n", + "Columns: [dataset_name, url_gcp, url_aws, url_azure, image_id, sequence_id, location_id, frame_num, original_label, scientific_name, common_name, datetime, annotation_level, kingdom, phylum, subphylum, superclass, class, subclass, infraclass, superorder, order, suborder, infraorder, superfamily, family, subfamily, tribe, genus, species, subspecies, variety]\n", "Index: []\n", "\n", - "[0 rows x 30 columns]" + "[0 rows x 32 columns]" ] }, "execution_count": 10, @@ -923,108 +1062,90 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ - "df_cleaned = df.loc[df.original_label != \"empty\"]" + "df_cleaned = df.loc[df.original_label != \"empty\"].copy()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "We started with 16,833,848 entries, and are left with 8,448,597 after removing all labeled as `empty`, so about half the images. \n", - "\n", - "Note that there are still about 2 million that don't have the species label, 1.5 million that are missing genus designation." + "## Save the Reduced Data (no more \"empty\" labels)" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "10 rows × 31 columns
\n", + "5 rows × 34 columns
\n", "" ], "text/plain": [ - " dataset_name \n", - "15355844 SWG Camera Traps \\\n", - "15098255 SWG Camera Traps \n", - "15750309 SWG Camera Traps \n", - "812622 NACTI \n", - "2050788 NACTI \n", - "12610859 Snapshot Serengeti \n", - "2463379 NACTI \n", - "1296206 NACTI \n", - "4026992 WCS Camera Traps \n", - "4754539 WCS Camera Traps \n", - "\n", - " url \n", - "15355844 https://lilablobssc.blob.core.windows.net/swg-... \\\n", - "15098255 https://lilablobssc.blob.core.windows.net/swg-... \n", - "15750309 https://lilablobssc.blob.core.windows.net/swg-... \n", - "812622 https://lilablobssc.blob.core.windows.net/nact... \n", - "2050788 https://lilablobssc.blob.core.windows.net/nact... \n", - "12610859 https://lilablobssc.blob.core.windows.net/snap... \n", - "2463379 https://lilablobssc.blob.core.windows.net/nact... \n", - "1296206 https://lilablobssc.blob.core.windows.net/nact... \n", - "4026992 https://lilablobssc.blob.core.windows.net/wcs-... \n", - "4754539 https://lilablobssc.blob.core.windows.net/wcs-... \n", - "\n", - " image_id \n", - "15355844 SWG Camera Traps : cebffb73-8c29-11eb-92ab-000... \\\n", - "15098255 SWG Camera Traps : cc2b9e0b-8c29-11eb-bd63-000... \n", - "15750309 SWG Camera Traps : d29fd7c0-8c29-11eb-9d65-000... \n", - "812622 NACTI : CA-17_07_01_2016_CA-17_0038090.JPG \n", - "2050788 NACTI : FL-12_08_04_2016_FL-12_0071339.JPG \n", - "12610859 Snapshot Serengeti : S9/F07/F07_R2/S9_F07_R2_I... \n", - "2463379 NACTI : FL-21_07_29_2015_FL-21_0010466.jpg \n", - "1296206 NACTI : CA-42_10_06_2016_CA-42_0022200.JPG \n", - "4026992 WCS Camera Traps : 098d7290-92d5-11e9-bb41-000... \n", - "4754539 WCS Camera Traps : 8f8a4dee-92d5-11e9-a3af-000... \n", - "\n", - " sequence_id \n", - "15355844 SWG Camera Traps : e42a22f0-8c29-11eb-9c41-000... \\\n", - "15098255 SWG Camera Traps : 2801caa6-8c2a-11eb-9118-000... \n", - "15750309 SWG Camera Traps : 39b3e643-8c2a-11eb-b05f-000... \n", - "812622 NACTI : unknown \n", - "2050788 NACTI : unknown \n", - "12610859 Snapshot Serengeti : SER_S9#F07#2#50 \n", - "2463379 NACTI : unknown \n", - "1296206 NACTI : unknown \n", - "4026992 WCS Camera Traps : bol-017-d0050-90 \n", - "4754539 WCS Camera Traps : unknown \n", - "\n", - " location_id frame_num original_label \n", - "15355844 SWG Camera Traps : loc_0263 2 large_antlered_muntjac \\\n", - "15098255 SWG Camera Traps : loc_0512 2 ferret_badger \n", - "15750309 SWG Camera Traps : loc_0588 7 stump_tailed_macaque \n", - "812622 NACTI : Lebec, California -1 bos taurus \n", - "2050788 NACTI : Archbold, FL -1 bos taurus \n", - "12610859 Snapshot Serengeti : F07 1 elephant \n", - "2463379 NACTI : Archbold, FL -1 bos taurus \n", - "1296206 NACTI : Lebec, California -1 lynx rufus \n", - "4026992 WCS Camera Traps : 650 12 tayassu pecari \n", - "4754539 WCS Camera Traps : 4326 -1 tinamus major \n", - "\n", - " scientific_name common_name datetime \n", - "15355844 muntiacus vuquangensis large-antlered muntjac 06-24-2019 19:36:35 \\\n", - "15098255 melogale ferret badger 07-08-2020 21:03:55 \n", - "15750309 macaca arctoides stump-tailed macaque 08-26-2019 10:52:49 \n", - "812622 bos taurus domestic cow NaN \n", - "2050788 bos taurus domestic cow NaN \n", - "12610859 loxodonta africana african bush elephant 10-16-2014 09:44:07 \n", - "2463379 bos taurus domestic cow NaN \n", - "1296206 lynx rufus bobcat NaN \n", - "4026992 tayassu pecari white-lipped peccary 08-28-2012 11:19:47 \n", - "4754539 tinamus major great tinamou 07-31-2013 05:43:18 \n", - "\n", - " ... infraorder superfamily family subfamily \n", - "15355844 ... NaN NaN cervidae cervinae \\\n", - "15098255 ... NaN NaN mustelidae helictidinae \n", - "15750309 ... simiiformes NaN cercopithecidae cercopithecinae \n", - "812622 ... NaN NaN bovidae bovinae \n", - "2050788 ... NaN NaN bovidae bovinae \n", - "12610859 ... NaN NaN elephantidae NaN \n", - "2463379 ... NaN NaN bovidae bovinae \n", - "1296206 ... NaN NaN felidae felinae \n", - "4026992 ... NaN NaN tayassuidae NaN \n", - "4754539 ... NaN NaN tinamidae NaN \n", - "\n", - " tribe genus species subspecies variety \n", - "15355844 muntiacini muntiacus muntiacus vuquangensis NaN NaN \\\n", - "15098255 NaN melogale NaN NaN NaN \n", - "15750309 papionini macaca macaca arctoides NaN NaN \n", - "812622 bovini bos bos taurus NaN NaN \n", - "2050788 bovini bos bos taurus NaN NaN \n", - "12610859 NaN loxodonta loxodonta africana NaN NaN \n", - "2463379 bovini bos bos taurus NaN NaN \n", - "1296206 NaN lynx lynx rufus NaN NaN \n", - "4026992 NaN tayassu tayassu pecari NaN NaN \n", - "4754539 NaN tinamus tinamus major NaN NaN \n", + " dataset_name url_gcp \\\n", + "1 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "2 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "3 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "5 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "6 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "\n", + " url_aws \\\n", + "1 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "2 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "3 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "5 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "6 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "\n", + " url_azure \\\n", + "1 https://lilawildlife.blob.core.windows.net/lil... \n", + "2 https://lilawildlife.blob.core.windows.net/lil... \n", + "3 https://lilawildlife.blob.core.windows.net/lil... \n", + "5 https://lilawildlife.blob.core.windows.net/lil... \n", + "6 https://lilawildlife.blob.core.windows.net/lil... \n", + "\n", + " image_id \\\n", + "1 Caltech Camera Traps : 5a0b016f-23d2-11e8-a6a3... \n", + "2 Caltech Camera Traps : 59b93afb-23d2-11e8-a6a3... \n", + "3 Caltech Camera Traps : 59641f56-23d2-11e8-a6a3... \n", + "5 Caltech Camera Traps : 5a096955-23d2-11e8-a6a3... \n", + "6 Caltech Camera Traps : 59b93a3b-23d2-11e8-a6a3... \n", "\n", - " url_dupe \n", - "15355844 False \n", - "15098255 False \n", - "15750309 False \n", - "812622 False \n", - "2050788 False \n", - "12610859 True \n", - "2463379 False \n", - "1296206 False \n", - "4026992 False \n", - "4754539 False \n", + " sequence_id \\\n", + "1 Caltech Camera Traps : 6f27ed66-5567-11e8-9e92... \n", + "2 Caltech Camera Traps : 6f04895c-5567-11e8-a3d6... \n", + "3 Caltech Camera Traps : 6f0385b5-5567-11e8-a80b... \n", + "5 Caltech Camera Traps : 70096335-5567-11e8-a99a... \n", + "6 Caltech Camera Traps : 7013c982-5567-11e8-be89... \n", "\n", - "[10 rows x 31 columns]" + " location_id frame_num original_label scientific_name \\\n", + "1 Caltech Camera Traps : 26 1 deer odocoileus \n", + "2 Caltech Camera Traps : 38 2 cat felis catus \n", + "3 Caltech Camera Traps : 38 2 opossum didelphis virginiana \n", + "5 Caltech Camera Traps : 36 1 car NaN \n", + "6 Caltech Camera Traps : 61 2 rabbit leporidae \n", + "\n", + " ... superfamily family subfamily tribe genus \\\n", + "1 ... NaN cervidae capreolinae odocoileini odocoileus \n", + "2 ... NaN felidae felinae NaN felis \n", + "3 ... NaN didelphidae didelphinae didelphini didelphis \n", + "5 ... NaN NaN NaN NaN NaN \n", + "6 ... NaN leporidae NaN NaN NaN \n", + "\n", + " species subspecies variety multi_species num_species \n", + "1 NaN NaN NaN False NaN \n", + "2 felis catus NaN NaN False NaN \n", + "3 didelphis virginiana NaN NaN False NaN \n", + "5 NaN NaN NaN False NaN \n", + "6 NaN NaN NaN False NaN \n", + "\n", + "[5 rows x 34 columns]" ] }, - "execution_count": 30, + "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "df_genusSpecies.sample(10)" + "for img in multi_sp_imgs:\n", + " df_cleaned.loc[df_cleaned[\"image_id\"] == img, \"num_species\"] = df_cleaned.loc[df_cleaned[\"image_id\"] == img].shape[0]\n", + " \n", + "df_cleaned.head()" ] }, { - "cell_type": "code", - "execution_count": 31, + "cell_type": "markdown", "metadata": {}, - "outputs": [ - { - "data": { + "source": [ + "#### Save this to CSV now we got those counts" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "metadata": {}, + "outputs": [], + "source": [ + "df_cleaned.to_csv(\"../data/lila_image_urls_and_labels.csv\", index = False)" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "metadata": {}, + "outputs": [ + { + "data": { "text/html": [ "| \n", - " | dataset_name | \n", - "url | \n", - "image_id | \n", - "sequence_id | \n", - "location_id | \n", - "frame_num | \n", - "original_label | \n", - "scientific_name | \n", - "common_name | \n", - "datetime | \n", - "... | \n", - "infraorder | \n", - "superfamily | \n", - "family | \n", - "subfamily | \n", - "tribe | \n", - "genus | \n", - "species | \n", - "subspecies | \n", - "variety | \n", - "url_dupe | \n", - "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | \n", - "Caltech Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/calt... | \n", - "Caltech Camera Traps : 5a0b016f-23d2-11e8-a6a3... | \n", - "Caltech Camera Traps : 6f27ed66-5567-11e8-9e92... | \n", - "Caltech Camera Traps : 26 | \n", - "1 | \n", - "deer | \n", - "odocoileus | \n", - "deer | \n", - "11-04-2013 18:37:07 | \n", - "... | \n", - "NaN | \n", - "NaN | \n", - "cervidae | \n", - "capreolinae | \n", - "odocoileini | \n", - "odocoileus | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "
| 2 | \n", - "Caltech Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/calt... | \n", - "Caltech Camera Traps : 59b93afb-23d2-11e8-a6a3... | \n", - "Caltech Camera Traps : 6f04895c-5567-11e8-a3d6... | \n", - "Caltech Camera Traps : 38 | \n", - "2 | \n", - "cat | \n", - "felis catus | \n", - "cat | \n", - "05-09-2012 07:33:45 | \n", - "... | \n", - "NaN | \n", - "NaN | \n", - "felidae | \n", - "felinae | \n", - "NaN | \n", - "felis | \n", - "felis catus | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "
| 3 | \n", - "Caltech Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/calt... | \n", - "Caltech Camera Traps : 59641f56-23d2-11e8-a6a3... | \n", - "Caltech Camera Traps : 6f0385b5-5567-11e8-a80b... | \n", - "Caltech Camera Traps : 38 | \n", - "2 | \n", - "opossum | \n", - "didelphis virginiana | \n", - "virginia opossum | \n", - "03-29-2012 02:34:13 | \n", - "... | \n", - "NaN | \n", - "NaN | \n", - "didelphidae | \n", - "didelphinae | \n", - "didelphini | \n", - "didelphis | \n", - "didelphis virginiana | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "
| 7 | \n", - "Caltech Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/calt... | \n", - "Caltech Camera Traps : 5a217843-23d2-11e8-a6a3... | \n", - "Caltech Camera Traps : 70115511-5567-11e8-a1fd... | \n", - "Caltech Camera Traps : 41 | \n", - "1 | \n", - "deer | \n", - "odocoileus | \n", - "deer | \n", - "09-29-2012 18:14:45 | \n", - "... | \n", - "NaN | \n", - "NaN | \n", - "cervidae | \n", - "capreolinae | \n", - "odocoileini | \n", - "odocoileus | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "
| 8 | \n", - "Caltech Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/calt... | \n", - "Caltech Camera Traps : 5a2176e7-23d2-11e8-a6a3... | \n", - "Caltech Camera Traps : 6f011019-5567-11e8-a650... | \n", - "Caltech Camera Traps : 38 | \n", - "2 | \n", - "dog | \n", - "canis familiaris | \n", - "domestic dog | \n", - "11-29-2011 17:28:26 | \n", - "... | \n", - "NaN | \n", - "NaN | \n", - "canidae | \n", - "NaN | \n", - "NaN | \n", - "canis | \n", - "canis familiaris | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "
5 rows × 31 columns
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| 3717318 | \n", - "WCS Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/wcs-... | \n", - "WCS Camera Traps : d16366f0-92d4-11e9-9412-000... | \n", - "WCS Camera Traps : ken-004-d0051-1 | \n", - "WCS Camera Traps : 338 | \n", - "1 | \n", - "litocranius walleri | \n", - "litocranius walleri | \n", - "gerenuk | \n", - "11-17-2010 01:51:16 | \n", - "... | \n", - "NaN | \n", - "bovidae | \n", - "antilopinae | \n", - "antilopini | \n", - "litocranius | \n", - "litocranius walleri | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "False | \n", - "
| 15724471 | \n", - "SWG Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/swg-... | \n", - "SWG Camera Traps : d26dc2c7-8c29-11eb-a99a-000... | \n", - "SWG Camera Traps : 3550f0a8-8c2a-11eb-b40a-000... | \n", - "SWG Camera Traps : loc_0577 | \n", - "0 | \n", - "spotted_linsang | \n", - "prionodon pardicolor | \n", - "spotted linsang | \n", - "07-24-2019 04:51:19 | \n", - "... | \n", - "NaN | \n", - "prionodontidae | \n", - "NaN | \n", - "NaN | \n", - "prionodon | \n", - "prionodon pardicolor | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "False | \n", - "
| 4167844 | \n", - "WCS Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/wcs-... | \n", - "WCS Camera Traps : 23c2cb9f-92d5-11e9-8dda-000... | \n", - "WCS Camera Traps : ken-010-d0054-2 | \n", - "WCS Camera Traps : 1370 | \n", - "1 | \n", - "struthio camelus | \n", - "struthio camelus | \n", - "common ostrich | \n", - "06-22-2011 17:28:43 | \n", - "... | \n", - "NaN | \n", - "struthionidae | \n", - "NaN | \n", - "NaN | \n", - "struthio | \n", - "struthio camelus | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "False | \n", - "
| 8980365 | \n", - "Snapshot Serengeti | \n", - "https://lilablobssc.blob.core.windows.net/snap... | \n", - "Snapshot Serengeti : S4/L08/L08_R1/S4_L08_R1_I... | \n", - "Snapshot Serengeti : SER_S4#L08#1#544 | \n", - "Snapshot Serengeti : L08 | \n", - "1 | \n", - "wildebeest | \n", - "connochaetes taurinus | \n", - "blue wildebeest | \n", - "02-27-2012 14:25:40 | \n", - "... | \n", - "NaN | \n", - "bovidae | \n", - "antilopinae | \n", - "alcelaphini | \n", - "connochaetes | \n", - "connochaetes taurinus | \n", - "NaN | \n", - "NaN | \n", - "False | \n", - "False | \n", - "
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 158597 | \n", - "Caltech Camera Traps | \n", - "https://lilablobssc.blob.core.windows.net/calt... | \n", - "Caltech Camera Traps : 5862934b-23d2-11e8-a6a3... | \n", - "Caltech Camera Traps : 6fa348e3-5567-11e8-be87... | \n", - "Caltech Camera Traps : 96 | \n", - "1 | \n", - "empty | \n", - "NaN | \n", - "NaN | \n", - "05-08-2014 13:23:40 | \n", - "... | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "NaN | \n", - "
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1 rows × 30 columns
\n", - "1 rows × 36 columns
\n", "" ], "text/plain": [ - " file max_detection_conf \n", - "0 cct_images/586ae111-23d2-11e8-a6a3-ec086b02610... 0.893 \\\n", - "1 cct_images/586ae112-23d2-11e8-a6a3-ec086b02610... 0.958 \n", - "2 cct_images/586ae113-23d2-11e8-a6a3-ec086b02610... 0.724 \n", - "3 cct_images/586ae114-23d2-11e8-a6a3-ec086b02610... 0.918 \n", - "4 cct_images/586ae115-23d2-11e8-a6a3-ec086b02610... 0.815 \n", - "5 cct_images/586ae117-23d2-11e8-a6a3-ec086b02610... 0.000 \n", - "6 cct_images/586ae118-23d2-11e8-a6a3-ec086b02610... 0.691 \n", - "7 cct_images/586ae119-23d2-11e8-a6a3-ec086b02610... 0.798 \n", - "8 cct_images/586ae11a-23d2-11e8-a6a3-ec086b02610... 0.954 \n", - "9 cct_images/586ae11c-23d2-11e8-a6a3-ec086b02610... 0.000 \n", + " dataset_name url_gcp \\\n", + "5 Caltech Camera Traps https://storage.googleapis.com/public-datasets... \n", + "\n", + " url_aws \\\n", + "5 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "\n", + " url_azure \\\n", + "5 https://lilawildlife.blob.core.windows.net/lil... \n", + "\n", + " image_id \\\n", + "5 Caltech Camera Traps : 5a096955-23d2-11e8-a6a3... \n", + "\n", + " sequence_id \\\n", + "5 Caltech Camera Traps : 70096335-5567-11e8-a99a... \n", + "\n", + " location_id frame_num original_label scientific_name ... \\\n", + "5 Caltech Camera Traps : 36 1 car NaN ... \n", + "\n", + " subfamily tribe genus species subspecies variety multi_species num_species \\\n", + "5 NaN NaN NaN NaN NaN NaN False 1.0 \n", + "\n", + " lin_duplicate full_duplicate \n", + "5 False False \n", "\n", - " detections \n", - "0 [{'category': '1', 'conf': 0.893, 'bbox': [0.6... \n", - "1 [{'category': '1', 'conf': 0.958, 'bbox': [0.5... \n", - "2 [{'category': '1', 'conf': 0.724, 'bbox': [0.8... \n", - "3 [{'category': '1', 'conf': 0.918, 'bbox': [0.5... \n", - "4 [{'category': '1', 'conf': 0.815, 'bbox': [0.2... \n", - "5 [] \n", - "6 [{'category': '1', 'conf': 0.691, 'bbox': [0.5... \n", - "7 [{'category': '1', 'conf': 0.122, 'bbox': [0.0... \n", - "8 [{'category': '1', 'conf': 0.954, 'bbox': [0.2... \n", - "9 [] " + "[1 rows x 36 columns]" ] }, - "execution_count": 72, + "execution_count": 40, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "cct_mdv5a.head(10)" + "df_unique_all_taxa.loc[(df_unique_all_taxa[\"scientific_name\"].isna()) | (df_unique_all_taxa[\"common_name\"].isna())]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "`file` matches the end of the `url` value in our DataFame. We want to filter out any empty detections that are still in `dedupe_species`. We could also consider lower confidences, but maybe start there." + "#### Let's remove those cars" ] }, { "cell_type": "code", - "execution_count": 73, + "execution_count": 45, "metadata": {}, "outputs": [ { - "data": { - "text/plain": [ - "244584" - ] - }, - "execution_count": 73, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "| \n", - " | file | \n", - "max_detection_conf | \n", - "detections | \n", - "
|---|---|---|---|
| 5 | \n", - "cct_images/586ae117-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 9 | \n", - "cct_images/586ae11c-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 11 | \n", - "cct_images/586ae11e-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 23 | \n", - "cct_images/585a65f2-23d2-11e8-a6a3-ec086b02610... | \n", - "-1.0 | \n", - "[] | \n", - "
| 27 | \n", - "cct_images/585a65f6-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| ... | \n", - "... | \n", - "... | \n", - "... | \n", - "
| 244568 | \n", - "cct_images/5a14a56f-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 244577 | \n", - "cct_images/5a14a705-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 244579 | \n", - "cct_images/5a14a707-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 244581 | \n", - "cct_images/5a14a709-23d2-11e8-a6a3-ec086b02610... | \n", - "0.0 | \n", - "[] | \n", - "
| 244582 | \n", - "cct_images/5a14a70a-23d2-11e8-a6a3-ec086b02610... | \n", - "-1.0 | \n", - "[] | \n", - "
67945 rows × 3 columns
\n", - "| \n", - " | file | \n", - "max_detection_conf | \n", - "detections | \n", - "
|---|---|---|---|
| 0 | \n", - "0000/0239.jpg | \n", - "0.970 | \n", - "[{'category': '1', 'conf': 0.97, 'bbox': [0.42... | \n", - "
| 1 | \n", - "0000/0240.jpg | \n", - "0.961 | \n", - "[{'category': '1', 'conf': 0.0102, 'bbox': [0.... | \n", - "
| 2 | \n", - "0000/0241.jpg | \n", - "0.968 | \n", - "[{'category': '1', 'conf': 0.0229, 'bbox': [0.... | \n", - "
| 3 | \n", - "0000/0242.jpg | \n", - "0.847 | \n", - "[{'category': '1', 'conf': 0.017, 'bbox': [0.5... | \n", - "
| 4 | \n", - "0000/0243.jpg | \n", - "0.779 | \n", - "[{'category': '1', 'conf': 0.0119, 'bbox': [0.... | \n", - "
5 rows × 36 columns
\n", "" ], "text/plain": [ - " file max_detection_conf \n", - "0 0000/0239.jpg 0.974 \\\n", - "1 0000/0240.jpg 0.968 \n", - "2 0000/0241.jpg 0.966 \n", - "3 0000/0242.jpg 0.745 \n", - "4 0000/0243.jpg 0.797 \n", - "\n", - " detections \n", - "0 [{'category': '1', 'conf': 0.974, 'bbox': [0.4... \n", - "1 [{'category': '1', 'conf': 0.0535, 'bbox': [0.... \n", - "2 [{'category': '1', 'conf': 0.0637, 'bbox': [0.... \n", - "3 [{'category': '1', 'conf': 0.0244, 'bbox': [0.... \n", - "4 [{'category': '1', 'conf': 0.0174, 'bbox': [0.... " + " dataset_name \\\n", + "4451993 WCS Camera Traps \n", + "4995616 WCS Camera Traps \n", + "4916766 WCS Camera Traps \n", + "5729969 Idaho Camera Traps \n", + "10798486 Snapshot Serengeti \n", + "\n", + " url_gcp \\\n", + "4451993 https://storage.googleapis.com/public-datasets... \n", + "4995616 https://storage.googleapis.com/public-datasets... \n", + "4916766 https://storage.googleapis.com/public-datasets... \n", + "5729969 https://storage.googleapis.com/public-datasets... \n", + "10798486 https://storage.googleapis.com/public-datasets... \n", + "\n", + " url_aws \\\n", + "4451993 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "4995616 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "4916766 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "5729969 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "10798486 http://us-west-2.opendata.source.coop.s3.amazo... \n", + "\n", + " url_azure \\\n", + "4451993 https://lilawildlife.blob.core.windows.net/lil... \n", + "4995616 https://lilawildlife.blob.core.windows.net/lil... \n", + "4916766 https://lilawildlife.blob.core.windows.net/lil... \n", + "5729969 https://lilawildlife.blob.core.windows.net/lil... \n", + "10798486 https://lilawildlife.blob.core.windows.net/lil... \n", + "\n", + " image_id \\\n", + "4451993 WCS Camera Traps : 5768343a-92d5-11e9-8890-000... \n", + "4995616 WCS Camera Traps : bc7c7b89-92d5-11e9-b600-000... \n", + "4916766 WCS Camera Traps : adc8775e-92d5-11e9-afee-000... \n", + "5729969 Idaho Camera Traps : loc_0004_im_000009 \n", + "10798486 Snapshot Serengeti : S7/H07/H07_R1/S7_H07_R1_I... \n", + "\n", + " sequence_id location_id \\\n", + "4451993 WCS Camera Traps : unknown WCS Camera Traps : 2812 \n", + "4995616 WCS Camera Traps : unknown WCS Camera Traps : 4607 \n", + "4916766 WCS Camera Traps : unknown WCS Camera Traps : 4446 \n", + "5729969 Idaho Camera Traps : loc_0004_seq_000000 Idaho Camera Traps : 4 \n", + "10798486 Snapshot Serengeti : SER_S7#H07#1#1523 Snapshot Serengeti : H07 \n", + "\n", + " frame_num original_label scientific_name ... subfamily tribe \\\n", + "4451993 -1 human homo sapiens ... homininae NaN \n", + "4995616 -1 human homo sapiens ... homininae NaN \n", + "4916766 -1 human homo sapiens ... homininae NaN \n", + "5729969 9 human homo sapiens ... homininae NaN \n", + "10798486 1 human homo sapiens ... homininae NaN \n", + "\n", + " genus species subspecies variety multi_species num_species \\\n", + "4451993 homo homo sapiens NaN NaN False 1.0 \n", + "4995616 homo homo sapiens NaN NaN False 1.0 \n", + "4916766 homo homo sapiens NaN NaN False 1.0 \n", + "5729969 homo homo sapiens NaN NaN False 1.0 \n", + "10798486 homo homo sapiens NaN NaN False 1.0 \n", + "\n", + " lin_duplicate full_duplicate \n", + "4451993 True True \n", + "4995616 True True \n", + "4916766 True True \n", + "5729969 True True \n", + "10798486 True True \n", + "\n", + "[5 rows x 36 columns]" ] }, - "execution_count": 104, + "execution_count": 57, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "wcs_mdv5b = pd.json_normalize(data[\"images\"], max_level = 1)\n", - "wcs_mdv5b.head()" + "df_clean.loc[df_clean[\"original_label\"] == \"human\"].sample(5)" ] }, { - "cell_type": "code", - "execution_count": 105, + "cell_type": "markdown", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[]" - ] - }, - "execution_count": 105, - "metadata": {}, - "output_type": "execute_result" - } - ], "source": [ - "dedupe_wcs_empties = []\n", - "for file in list(wcs_mdv5b.loc[wcs_mdv5b['detections'].astype(str) == '[]', 'file']):\n", - " if file in dedupe_url_wcs:\n", - " dedupe_wcs_empties.append(file)\n", - "\n", - "dedupe_wcs_empties" + "It does seem to have full taxa...interesting." ] }, { - "cell_type": "markdown", + "cell_type": "code", + "execution_count": 58, "metadata": {}, + "outputs": [], "source": [ - "#### NACTI" + "df_clean.to_csv(\"../data/lila_image_urls_and_labels_wHumans.csv\", index = False)" ] }, { "cell_type": "code", - "execution_count": 106, + "execution_count": 59, "metadata": {}, "outputs": [], "source": [ - "with open(\"../MegaDetector_results/nacti_mdv5b.0.0_results.json\") as file:\n", - " data = json.load(file)" + "df_clean.loc[df_clean[\"original_label\"] != \"human\"].to_csv(\"../data/lila_image_urls_and_labels.csv\", index = False)" ] }, { "cell_type": "code", - "execution_count": 107, + "execution_count": 62, "metadata": {}, "outputs": [ { @@ -20621,630 +3427,469 @@ " \n", "