initial commit

.gitattributes

@@ -31,3 +31,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.json filter=lfs diff=lfs merge=lfs -text

Dockerfile

@@ -0,0 +1,10 @@
+FROM python:3.7
+
+RUN apt-get update \
+    && apt-get install ffmpeg libsm6 libxext6 -y
+
+RUN pip install yolov5 tator gradio
+
+COPY . ./
+
+CMD [ "python", "-u", "./tator_inference.py" ]

app.py

@@ -0,0 +1,43 @@
+import glob
+import gradio as gr
+from inference import *
+from PIL import Image
+
+
+def gradio_app(image_path):
+    """A function that send the file to the inference pipeline, and filters
+    some predictions before outputting to gradio interface."""
+
+    predictions = run_inference(image_path)
+
+    out_img = Image.fromarray(predictions.render()[0])
+
+    return out_img
+
+
+title = "MBARI Monterey Bay Benthic"
+description = "Gradio demo for MBARI Monterey Bay Benthic: This model was " \
+              "trained on 691 classes using 33,667 localized images from " \
+              "MBARI’s Video Annotation and Reference System (VARS). Note: " \
+              "only a subset of the VARS database is uploaded to FathomNet " \
+              "because of institutional concept embargos. For training, " \
+              "images were split 80/20 train/test. Classes were selected " \
+              "because they are commonly observed concepts (primarily " \
+              "benthic organisms, along with equipment and marine litter or " \
+              "trash) within the Monterey Bay and Submarine Canyon system " \
+              "from 500 to 4000 m deep. Many of these organisms will be seen " \
+              "throughout the entire NE Pacific within the continental " \
+              "slope, shelf, and abyssal regions. We used the PyTorch " \
+              "framework and the yolov5 ‘YOLOv5x’ pretrained checkpoint to " \
+              "train for 28 epochs with a batch size of 18 and image size of " \
+              "640 pixels. DOI: 10.5281/zenodo.5539915 "
+
+examples = glob.glob("images/*.png")
+
+gr.Interface(gradio_app,
+             inputs=[gr.inputs.Image(type="filepath")],
+             outputs=gr.outputs.Image(type="pil"),
+             enable_queue=True,
+             title=title,
+             description=description,
+             examples=examples).launch()

inference.py

@@ -0,0 +1,69 @@
+import cv2
+import glob
+import numpy as np
+import torch
+import yolov5
+from typing import Dict, Tuple, Union, List, Optional
+
+
+# -----------------------------------------------------------------------------
+# Configs
+# -----------------------------------------------------------------------------
+
+model_path = "models/mbari-mb-benthic-33k.pt"
+
+
+# -----------------------------------------------------------------------------
+# YOLOv5 class
+# -----------------------------------------------------------------------------
+
+class YOLO:
+    """Wrapper class for loading and running YOLO model"""
+
+    def __init__(self, model_path: str, device: Optional[str] = None):
+
+        # load model
+        self.model = yolov5.load(model_path, device=device)
+
+    def __call__(
+            self,
+            img: Union[str, np.ndarray],
+            conf_threshold: float = 0.25,
+            iou_threshold: float = 0.45,
+            image_size: int = 720,
+            classes: Optional[List[int]] = None) -> torch.Tensor:
+        self.model.conf = conf_threshold
+        self.model.iou = iou_threshold
+
+        if classes is not None:
+            self.model.classes = classes
+
+        # pylint: disable=not-callable
+        detections = self.model(img, size=image_size)
+
+        return detections
+
+
+def run_inference(image_path):
+    """Helper function to execute the inference."""
+
+    predictions = model(image_path)
+
+    return predictions
+
+
+# -----------------------------------------------------------------------------
+# Model Creation
+# -----------------------------------------------------------------------------
+model = YOLO(model_path, device='cpu')
+
+if __name__ == "__main__":
+
+    # For demo purposes: run through a couple of test
+    # images and then output the predictions in a folder.
+    test_images = glob.glob("images/*.png")
+
+    for test_image in test_images:
+        predictions = run_inference(test_image)
+
+    print("Done.")

mbari-mb-benthic-33k.names

@@ -0,0 +1,691 @@
+Anoplopoma fimbria
+Crossaster
+Myxoderma sacculatum
+Sebastolobus
+Neptunea-Buccinum Complex
+Ceriantharia
+Merluccius productus
+Pannychia moseleyi
+Octopus rubescens
+Actiniaria
+Solasteridae
+Antimora microlepis
+Macrouridae
+Heteropolypus ritteri
+Liponema brevicorne
+Ophiuroidea
+Octocorallia
+Porifera
+Brisingida
+Chorilia longipes
+Asteroidea
+equipment
+Metridium farcimen
+Embassichthys bathybius
+Funiculina
+Strongylocentrotus fragilis
+Chionoecetes tanneri
+Actinostoloidea
+Myxoderma platyacanthum
+Gastropoda
+Umbellula
+Psolus squamatus
+Hexactinellida
+Swiftia simplex
+Galatheidae
+Coryphaenoides
+Dosidicus gigas
+Microstomus pacificus
+Sebastolobus alascanus
+Farrea
+Poralia rufescens
+Acanthoptilum
+Isosicyonis
+Paragorgia arborea
+Pannychia sp. 2
+Bothrocara brunneum
+Hormathiidae
+Lycenchelys
+Pteraster
+Paragorgia
+Sebastes
+Bathyraja abyssicola
+Eptatretus
+Lycenchelys crotalinus
+Pennatulacea
+Pandalidae
+Tunicata
+Actinernus
+Asbestopluma rickettsi
+Apostichopus leukothele
+Stylasterias forreri
+Sebastes elongatus
+Sebastomus complex
+Parastenella
+Bathyraja trachura
+Laqueus californicus
+Eutonina indicans
+Keratoisis
+Apristurus
+Mysida
+Tritonia tetraquetra
+Mediaster aequalis
+Anthoptilum grandiflorum
+Virgulariidae
+Vesicomyidae
+Sebastolobus altivelis
+Neptunea
+Rathbunaster californicus
+Bathyraja kincaidii
+Scyliorhinidae
+Lycodapus
+Paralomis
+Isididae
+Crinoidea
+Acanthogorgia
+Swiftia
+Enteroctopus dofleini
+Pagurus tanneri
+Mediaster
+Pyrosoma atlanticum
+Nanomia bijuga
+Lycodes diapterus
+Pectinidae
+Asbestopluma
+Isidella
+Hippasteria
+Osedax
+Corallimorphus
+Florometra serratissima
+Scotoplanes
+Asteronyx
+Swiftia kofoidi
+Pandalus
+Pennatula phosphorea
+Ascidiacea
+Laminariales
+Doryteuthis opalescens
+Sebastidae
+Bathyraja
+Paelopatides confundens
+Suction Sampler
+Lycodes cortezianus
+Pandalus platyceros
+Lumpenus sagitta
+Pandalopsis ampla
+Hydrolagus colliei
+Bathyraja spinosissima
+Solaster hypothrissus
+Hyalonema (Corynonema) populiferum
+Holothuroidea
+Apostichopus
+Synallactidae
+Caridea
+Lithodidae
+Tonrometra
+Stomphia didemon
+Solmissus
+Euphausia
+Lycodapus fierasfer
+Munidopsis depressa
+Cataetyx
+Sebastes diploproa
+Pleurobranchaea californica
+Paguroidea
+Lycodes
+Heterochone calyx
+Isidella tentaculum
+Psathyrometra fragilis
+Sebastes melanostomus
+trash
+Xeneretmus latifrons
+Bathyraja microtrachys
+Bathybembix
+Pyrosoma detritus
+Luidia foliolata
+Lycodes pacificus
+Munida
+Beringraja rhina
+Lophaster
+Gersemia juliepackardae
+Paralomis multispina
+Stomphia
+Primnoidae
+Funiculina-Halipteris complex
+Pleuronectiformes
+Sibogagorgia cauliflora
+Sebastes chlorostictus
+Sebastes zacentrus
+Sebastes babcocki
+Solaster
+Akoya platinum
+Opisthoteuthis sp. A
+Lepidisis
+Branchiocerianthus
+Antedonidae
+Gorgonocephalus eucnemis
+Staurocalyptus
+Glyptocephalus zachirus
+Phyllospadix-Zostera detritus
+Careproctus melanurus
+Amphipoda
+LRJ complex
+Careproctus
+Benthopecten
+Squalus suckleyi
+Eopsetta jordani
+Eusergestes similis
+Sabellida
+Brachyura
+Serpulidae
+Lyopsetta exilis
+Mycale
+Poraniopsis inflata
+Eualus macrophthalmus
+Chonelasma
+Acanthascinae
+Rajiformes
+Corallimorphus pilatus
+Zoarcidae
+Aegina
+medusa carcass
+Neogastropoda
+Pleuronectidae
+Calyptogena
+Pleuronectinae
+Hymenaster
+Munidopsis
+Swiftia sim
+Munnopsidae
+Lobata
+Pannychia
+Lithodes couesi
+Myctophidae
+Thrissacanthias penicillatus
+geology
+Dofleinia
+Asthenactis fisheri
+Cydippida
+Harriotta raleighana
+Metacarcinus magister
+Gobiidae
+Albatrossia pectoralis
+Lampocteis cruentiventer
+Buccinidae
+Alcyonacea
+Ophiacanthidae
+Careproctus kamikawai
+Stylatula
+Paragorgiidae
+Majidae
+Megalodicopia hians
+Moridae
+Ptilosarcus gurneyi
+Isopoda
+Asbestopluma monticola
+Octopoda
+Bivalvia
+Desmophyllum dianthus
+Fungiacyathus (Bathyactis) marenzelleri
+Peniagone
+Elpidia
+Scotoplanes globosa
+Teuthoidea
+Peniagone gracilis
+Oneirophanta mutabilis complex
+Nanomia bijuga nectosome
+fishing-debris
+Peniagone papillata
+Synallactidae gen. et sp. indet.
+Sebastes rufus
+Hydrolagus cf. trolli
+Psychropotes sp. 2
+Tjalfiella
+Poeobius meseres
+Bathochordaeus stygius inner filter
+Bathochordaeus stygius outer filter
+Hydrozoa
+Cnemidocarpa
+Hyalonema
+Malacostraca
+Iosactis vagabunda
+Abyssocucumis abyssorum
+Peniagone vitrea
+Ophiodon elongatus
+Parastichopus leukothele
+Cystechinus loveni
+Ceramaster
+Hexacorallia
+Octopus californicus
+Neolithodes diomedeae
+Benthocodon pedunculata
+Styelidae
+Physiculus rastrelliger
+Laetmogone
+Sebastes saxicola
+Bathochordaeus
+Cladorhizidae
+Peribolaster biserialis
+Muusoctopus robustus
+Hydrolagus melanophasma
+Beroe forskalii
+Sebastes flavidus
+Nemichthyidae
+Poraniopsis
+Sebastes brevispinis
+Sebastes rubrivinctus
+Octopodidae
+Paraliparis sp. 2
+Pythonaster
+Synallactes
+Sebastes ensifer
+Sebastes miniatus
+Hyalonema (Oonema) bianchoratum
+Anomura
+Echinocrepis rostrata
+Prayidae
+Physonectae nectosome
+Physonectae
+Sebastes paucispinis
+Sebastes head
+Hirudinea
+Urticina
+Astropecten
+Leptogorgia
+Galatheoidea
+Beroe cucumis
+Bolocera
+Fariometra parvula
+Neptunea-Buccinum Complex eggcase
+Graneledone boreopacifica
+Polynoidae
+Psamminidae
+Psychrolutes phrictus
+Sergestes similis
+Calycophorae nectosome
+Beroe
+Thenea muricata
+Gonatus
+Henricia
+Nudibranchia
+Sebastes aurora
+Zoantharia
+Clavularia
+Terebratulina complex
+Macrourinae
+Ptychogastria
+Delectopecten
+Phacellophora camtschatica
+Siboglinidae
+Gorgoniidae
+eggcase
+Sibogagorgia
+Comatulida
+Diogenidae
+eggs
+Apolemia
+Midwater Respirometry System
+Pycnogonida
+Calliostoma
+Sebastes aleutianus-melanostictus complex
+Brachiopoda
+Medusae
+Lamellibrachia
+Bathyphellia australis
+Ophiuridae
+Lycodes brevipes
+Atolla
+Plectobranchus evides
+Asteriidae
+Farrea occa
+Agonidae
+Bathymetrinae
+Decapoda
+Corallium
+Halipteris californica
+Dipsacaster
+Chonelasmatinae sp. 2
+shell
+Phyllospadix detritus
+Spectrunculus grandis
+shell fragment
+Paralomis verrilli
+Hydrolagus
+Actinopterygii
+Parmaturus xaniurus
+whale carcass
+Pterasteridae arm
+Annelida
+Lyrocteis
+Echiura
+Vanhoeffenura pulchra
+Bolinopsis infundibulum
+Colossendeidae
+Bathochordaeus stygius
+Sebastes jordani
+Platyctenida
+Saxipendium implicatum
+TorquaratoridaeB sp. 2
+Pachycara bulbiceps
+Hydractiniidae
+Psamminidae sp. 2
+Tjalfiellidae
+Myxoderma
+Hyocrinidae
+Chondrocladia
+Cystocrepis setigera
+Munidopsis kensmithi
+Radiozoa
+Chaetognatha
+Siphonophorae
+Chrysogorgia
+Pseudostichopus mollis
+Benthothuria
+Bolocera kensmithi
+Sebastes semicinctus
+Galiteuthis phyllura
+Octopodinae
+Serrivomer
+Demospongiae
+Latrunculia (Latrunculia) austini
+Dromalia alexandri
+Scleractinia
+Plesionika
+bacterial mat
+Chondrocladia (Symmetrocladia) lyra
+Neoloricata
+asteroid feeding depression
+Bathyalcyon robustum
+Bathypterois
+Distichoptilum
+Paraliparis cephalus
+Sebastes serranoides
+Goniasteridae
+ledge
+Tromikosoma panamense
+Ctenophora
+Docosaccus maculatus
+sinker
+Lophaster furcilliger
+Sebastes cortezi
+Culeolus
+Mysidacea
+Bathydorus laevis pseudospinosus
+Alepocephalus tenebrosus
+Echinoidea
+Heterozonias alternatus
+Smithsonius dorothea
+Heterocarpus sp. 2
+Eucryphycus californicus
+Polychaeta tube
+Cirroteuthis
+Tergivelum baldwinae
+Tiburonia granrojo
+Liparidae
+Riftia pachyptila
+Hydroidolina
+Plexauridae
+Bathylagidae
+Lepidion
+Sclerothamnopsis
+Careproctus ovigerus
+Psychropotes depressa
+Icelinus filamentosus
+Chrysogorgia monticola
+wood
+Bathochordaeus inner filter
+Sebastes entomelas
+Anthozoa
+Bathypterois pectinatus
+Cladorhiza kensmithi
+Aporocidaris milleri
+Ischnomesidae
+Staurocalyptus solidus
+Anthoptilum lithophilum
+Atolla wyvillei
+Erenna richardi
+Hyalonematidae
+Pleurobranchaea
+Sergestidae
+Thermarces cerberus
+Pennatula
+Moloha faxoni
+Munida quadrispina
+Lophiiformes
+Benthoctopus
+Strongylocentrotus
+kelp
+Nanomia nectosome
+Sicyonis
+Chrysogorgia pinnata
+Forskalia formosa
+Sebastes ruberrimus
+Sebastes levis
+Praya dubia nectosome
+Praya dubia
+Pleuronectiformes 3
+Chuniphyes multidentata
+Dictyocalyx
+Zaniolepis frenata
+Octopus
+Forcipulatacea
+Eretmichthys pinnatus
+Dibranchus hystrix
+Coelorinchus spilonotus
+Pseudobathylagus
+Benthodytes
+Alternatipathes
+Lillipathes
+Protoptilum sp. 2
+Hastigerinella digitata
+Bargmannia elongata
+Bargmannia elongata nectosome
+Psychronaetes
+Bathysaurus mollis
+Lycodinae
+Euplectellidae
+Pasiphaea
+Bathysiphon
+Beroe abyssicola
+Tomopteris
+Polychaeta
+Articulata
+Apostichopus californicus
+Kophobelemnon
+Bolinopsis
+Euryalida
+Pennatulidae
+Gastroptychus
+molt
+Corallimorphus denhartogi
+Neptunea eggcase
+Octacnemidae sp. 2
+Xeneretmus
+Dibranchus spinosus
+Epizoanthus stellaris
+Pennatulacea sp. 2
+Sebastes borealis
+Aeolidiidae
+Mitrocoma cellularia
+Tromikosoma
+Icichthys lockingtoni
+Solmissus incisa
+Sebastes pinniger
+Enteropneusta
+Sebastes auriculatus
+Megalodicopia
+Asthenactis papyraceus
+Sebastes miniatus-pinniger complex
+Asthenactis
+test
+Icelinus
+Parantipathes
+Sebastes macdonaldi
+Sebastes mystinus
+Physiculus nematopus-rastrelliger complex
+Sebastes rosenblatti
+Bathochordaeus sinker
+Distichoptilum gracile
+kelp holdfast
+Rhinochimaeridae
+Echinocrepis setigera
+Sebastes caurinus
+Egregia menziesii
+Myriothelidae
+coiled fecal cast
+Cystechinus giganteus
+Bathochordaeus mcnutti inner filter
+Bathochordaeus mcnutti
+Cladorhiza
+Cirripedia
+Swiftia kol
+Phyllochaetopterus gigas
+Hymenaster koehleri
+sinker outer filter
+Allocentrotus fragilis
+Luciobrotula sp. A
+Opisthoteuthis
+Haliscera bigelowi
+Scotoplanes clarki
+Lyssacinosida sp. 2
+larvacean outer filter
+Ophichthus frontalis
+Calyptrophora
+Provannidae
+Marine organism
+Farrea truncata complex
+Actinoscyphia
+Exocoelactis
+Kophobelemnidae
+Lychnagalma nectosome
+Lychnagalma
+Caenogastropoda
+Zoroasteridae
+Bathochordaeus outer filter
+Vanhoeffenura
+Stylasterias
+Calycophorae
+Vitreosalpa gemini
+Anguilliformes
+Calocarides quinqueseriatus
+Fungiacyathus
+Candelabridae sp. 2
+Tergivelum sp. A
+Mesochordaeus erythrocephalus
+Monothalamea
+Paradiopatra
+Munida bapensis
+Sebastes crameri-melanostomus complex
+Asterozoa
+Patiria miniata
+Ophidiiformes
+Salpida
+Coelorinchus scaphopsis
+Tomopteris nisseni
+Camptoplites sp. A
+Psychropotidae
+Paxillosida
+Dendronotus patricki
+Oneirophanta
+Lensia conoidea nectosome
+Lensia conoidea
+Glyphocrangon vicaria
+Dipsacaster eximius
+Bathydorus
+Bathycrinidae
+Sebastolobus head
+Doryteuthis (Amerigo) opalescens eggs
+Sebastes crameri
+Thetys vagina
+Sebastes ovalis
+Lycodapus mandibularis
+Sebastolobus tail
+Sebastes goodei
+Pseudobathylagus milleri
+Narcomedusa
+Chiroteuthis calyx
+Heterobranchia
+Octacnemidae
+inner filter
+Pentametrocrinus paucispinulus
+Beroe gracilis
+Schizopathidae
+Dytaster gilberti
+Physiculus sp. 2
+Octopodidae tentacle
+Mysidae
+Antipatharia
+Lychnagalma utricularia nectosome
+Lychnagalma utricularia
+Ridgeia
+Actinauge verrillii
+Oikopleuridae outer filter
+Fecampiid eggcase
+Chilara taylori
+Acesta
+Caulophacus
+Parophrys vetulus
+Dibranchus sp. A
+Holothuria (Vaneyothuria) zacae
+Prayidae nectosome
+Acanthephyra
+Bathycrinus complanatus
+Munnopsis
+Alcyoniidae
+Microstomus bathybius
+Theudoidea
+Hydromedusae
+Protoptilum
+Bathyphellia
+Euplokamidae
+Microstomus pacificus sole
+Hormiphora californensis
+Leptocephalus-3
+Verum proximum
+Lepidopsetta bilineata
+Corolla spectabilis
+Haliscera conica
+Brisaster
+Oikopleura outer filter
+Paulasterias mcclaini
+Sicyonis careyi
+Iosactis
+Oikopleuridae inner filter
+Chromista
+Mola mola
+Melanostigma pammelas
+Scrippsia pacifica
+larvacean house
+Sebastes phillipsi
+Peinaleopolynoe orphanae
+Cnidaria
+salp detritus
+Atolla vanhoeffeni
+Appendicularia outer filter
+Appendicularia inner filter
+Sebastes simulator
+Acharax
+Plesionika sp. A
+Mediaster tenellus
+Eutonina
+Octopoteuthis deletron
+Crustacea
+Psathyrometra
+Patellogastropoda
+Sebastes cortezi tail
+Yoda sp. A
+Lophiodes caulinaris
+Ptilosarcus
+Gnathophis cinctus
+Munidopsis sp. 2
+salp chain
+Oikopleuridae
+Vogtia
+Rossellidae
+detrital aggregate
+Sebastes maliger
+Tuscaretta
+Chaunacops coloratus
+Pleurobrachiidae
+Tenebrincola cukri
+Amblyraja hyperborea

mbari-mb-benthic-33k_stats.txt

@@ -0,0 +1,691 @@
+339 Anoplopoma fimbria
+320 Crossaster
+27 Myxoderma sacculatum
+5114 Sebastolobus
+252 Neptunea-Buccinum Complex
+264 Ceriantharia
+6291 Merluccius productus
+2554 Pannychia moseleyi
+1751 Octopus rubescens
+3316 Actiniaria
+186 Solasteridae
+479 Antimora microlepis
+131 Macrouridae
+1408 Heteropolypus ritteri
+621 Liponema brevicorne
+3706 Ophiuroidea
+289 Octocorallia
+2575 Porifera
+413 Brisingida
+209 Chorilia longipes
+2803 Asteroidea
+235 equipment
+594 Metridium farcimen
+744 Embassichthys bathybius
+3848 Funiculina
+8631 Strongylocentrotus fragilis
+2790 Chionoecetes tanneri
+151 Actinostoloidea
+120 Myxoderma platyacanthum
+811 Gastropoda
+1723 Umbellula
+3965 Psolus squamatus
+786 Hexactinellida
+743 Swiftia simplex
+287 Galatheidae
+411 Coryphaenoides
+50 Dosidicus gigas
+1214 Microstomus pacificus
+65 Sebastolobus alascanus
+907 Farrea
+54 Poralia rufescens
+757 Acanthoptilum
+812 Isosicyonis
+3546 Paragorgia arborea
+25 Pannychia sp. 2
+14 Bothrocara brunneum
+409 Hormathiidae
+621 Lycenchelys
+488 Pteraster
+484 Paragorgia
+1368 Sebastes
+199 Bathyraja abyssicola
+403 Eptatretus
+86 Lycenchelys crotalinus
+788 Pennatulacea
+92 Pandalidae
+584 Tunicata
+803 Actinernus
+293 Asbestopluma rickettsi
+525 Apostichopus leukothele
+214 Stylasterias forreri
+44 Sebastes elongatus
+74 Sebastomus complex
+215 Parastenella
+504 Bathyraja trachura
+300 Laqueus californicus
+2 Eutonina indicans
+3829 Keratoisis
+8 Apristurus
+66 Mysida
+68 Tritonia tetraquetra
+284 Mediaster aequalis
+41 Anthoptilum grandiflorum
+22 Virgulariidae
+766 Vesicomyidae
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+29 Hyalonema
+21 Malacostraca
+17 Iosactis vagabunda
+499 Abyssocucumis abyssorum
+811 Peniagone vitrea
+18 Ophiodon elongatus
+10 Parastichopus leukothele
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+51 Hexacorallia
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+17 Neolithodes diomedeae
+381 Benthocodon pedunculata
+4 Styelidae
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+11 Bathochordaeus
+62 Cladorhizidae
+8 Peribolaster biserialis
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+43 Hydrolagus melanophasma
+8 Beroe forskalii
+15 Sebastes flavidus
+3 Nemichthyidae
+22 Poraniopsis
+12 Sebastes brevispinis
+16 Sebastes rubrivinctus
+32 Octopodidae
+1 Paraliparis sp. 2
+33 Pythonaster
+74 Synallactes
+6 Sebastes ensifer
+19 Sebastes miniatus
+40 Hyalonema (Oonema) bianchoratum
+2 Anomura
+92 Echinocrepis rostrata
+8 Prayidae
+2 Physonectae nectosome
+2 Physonectae
+9 Sebastes paucispinis
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+45 Hirudinea
+2 Urticina
+2 Astropecten
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+7 Polynoidae
+55 Psamminidae
+29 Psychrolutes phrictus
+2 Sergestes similis
+2 Calycophorae nectosome
+40 Beroe
+37 Thenea muricata
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+18 Henricia
+1 Nudibranchia
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+681 Zoantharia
+112 Clavularia
+33 Terebratulina complex
+4 Macrourinae
+34 Ptychogastria
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+20 Phacellophora camtschatica
+10 Siboglinidae
+6 Gorgoniidae
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+106 Comatulida
+3 Diogenidae
+2 eggs
+12 Apolemia
+7 Midwater Respirometry System
+15 Pycnogonida
+25 Calliostoma
+14 Sebastes aleutianus-melanostictus complex
+57 Brachiopoda
+8 Medusae
+31 Lamellibrachia
+28 Bathyphellia australis
+6 Ophiuridae
+8 Lycodes brevipes
+13 Atolla
+4 Plectobranchus evides
+3 Asteriidae
+84 Farrea occa
+7 Agonidae
+9 Bathymetrinae
+7 Decapoda
+17 Corallium
+87 Halipteris californica
+8 Dipsacaster
+2 Chonelasmatinae sp. 2
+29 shell
+3 Phyllospadix detritus
+1 Spectrunculus grandis
+18 shell fragment
+9 Paralomis verrilli
+5 Hydrolagus
+21 Actinopterygii
+26 Parmaturus xaniurus
+3 whale carcass
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+5 Annelida
+2 Lyrocteis
+14 Echiura
+11 Vanhoeffenura pulchra
+14 Bolinopsis infundibulum
+31 Colossendeidae
+18 Bathochordaeus stygius
+44 Sebastes jordani
+3 Platyctenida
+2 Saxipendium implicatum
+2 TorquaratoridaeB sp. 2
+28 Pachycara bulbiceps
+10 Hydractiniidae
+47 Psamminidae sp. 2
+1 Tjalfiellidae
+62 Myxoderma
+5 Hyocrinidae
+3 Chondrocladia
+78 Cystocrepis setigera
+19 Munidopsis kensmithi
+2 Radiozoa
+22 Chaetognatha
+14 Siphonophorae
+36 Chrysogorgia
+13 Pseudostichopus mollis
+10 Benthothuria
+21 Bolocera kensmithi
+11 Sebastes semicinctus
+1 Galiteuthis phyllura
+2 Octopodinae
+2 Serrivomer
+8 Demospongiae
+6 Latrunculia (Latrunculia) austini
+15 Dromalia alexandri
+82 Scleractinia
+16 Plesionika
+27 bacterial mat
+2 Chondrocladia (Symmetrocladia) lyra
+13 Neoloricata
+2 asteroid feeding depression
+8 Bathyalcyon robustum
+2 Bathypterois
+2 Distichoptilum
+2 Paraliparis cephalus
+9 Sebastes serranoides
+12 Goniasteridae
+3 ledge
+21 Tromikosoma panamense
+10 Ctenophora
+7 Docosaccus maculatus
+2 sinker
+20 Lophaster furcilliger
+46 Sebastes cortezi
+8 Culeolus
+4 Mysidacea
+64 Bathydorus laevis pseudospinosus
+2 Alepocephalus tenebrosus
+12 Echinoidea
+13 Heterozonias alternatus
+19 Smithsonius dorothea
+2 Heterocarpus sp. 2
+2 Eucryphycus californicus
+104 Polychaeta tube
+4 Cirroteuthis
+20 Tergivelum baldwinae
+2 Tiburonia granrojo
+7 Liparidae
+19 Riftia pachyptila
+2 Hydroidolina
+9 Plexauridae
+5 Bathylagidae
+4 Lepidion
+7 Sclerothamnopsis
+1 Careproctus ovigerus
+3 Psychropotes depressa
+11 Icelinus filamentosus
+24 Chrysogorgia monticola
+3 wood
+13 Bathochordaeus inner filter
+15 Sebastes entomelas
+11 Anthozoa
+6 Bathypterois pectinatus
+20 Cladorhiza kensmithi
+15 Aporocidaris milleri
+6 Ischnomesidae
+9 Staurocalyptus solidus
+18 Anthoptilum lithophilum
+5 Atolla wyvillei
+6 Erenna richardi
+4 Hyalonematidae
+1 Pleurobranchaea
+3 Sergestidae
+6 Thermarces cerberus
+43 Pennatula
+3 Moloha faxoni
+5 Munida quadrispina
+2 Lophiiformes
+11 Benthoctopus
+60 Strongylocentrotus
+2 kelp
+5 Nanomia nectosome
+10 Sicyonis
+17 Chrysogorgia pinnata
+4 Forskalia formosa
+39 Sebastes ruberrimus
+10 Sebastes levis
+14 Praya dubia nectosome
+17 Praya dubia
+2 Pleuronectiformes 3
+3 Chuniphyes multidentata
+1 Dictyocalyx
+1 Zaniolepis frenata
+4 Octopus
+6 Forcipulatacea
+2 Eretmichthys pinnatus
+2 Dibranchus hystrix
+1 Coelorinchus spilonotus
+2 Pseudobathylagus
+6 Benthodytes
+6 Alternatipathes
+10 Lillipathes
+46 Protoptilum sp. 2
+5 Hastigerinella digitata
+8 Bargmannia elongata
+7 Bargmannia elongata nectosome
+8 Psychronaetes
+6 Bathysaurus mollis
+12 Lycodinae
+3 Euplectellidae
+6 Pasiphaea
+23 Bathysiphon
+4 Beroe abyssicola
+11 Tomopteris
+8 Polychaeta
+5 Articulata
+3 Apostichopus californicus
+23 Kophobelemnon
+6 Bolinopsis
+3 Euryalida
+2 Pennatulidae
+2 Gastroptychus
+3 molt
+2 Corallimorphus denhartogi
+8 Neptunea eggcase
+11 Octacnemidae sp. 2
+5 Xeneretmus
+3 Dibranchus spinosus
+30 Epizoanthus stellaris
+4 Pennatulacea sp. 2
+2 Sebastes borealis
+2 Aeolidiidae
+43 Mitrocoma cellularia
+3 Tromikosoma
+1 Icichthys lockingtoni
+6 Solmissus incisa
+13 Sebastes pinniger
+5 Enteropneusta
+5 Sebastes auriculatus
+6 Megalodicopia
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+8 Asthenactis
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+3 Icelinus
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+3 Distichoptilum gracile
+1 kelp holdfast
+1 Rhinochimaeridae
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+2 Egregia menziesii
+1 Myriothelidae
+5 coiled fecal cast
+1 Cystechinus giganteus
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+8 Bathochordaeus mcnutti
+1 Cladorhiza
+6 Cirripedia
+2 Swiftia kol
+4 Phyllochaetopterus gigas
+10 Hymenaster koehleri
+3 sinker outer filter
+11 Allocentrotus fragilis
+2 Luciobrotula sp. A
+1 Opisthoteuthis
+1 Haliscera bigelowi
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+2 larvacean outer filter
+1 Ophichthus frontalis
+3 Calyptrophora
+6 Provannidae
+3 Marine organism
+3 Farrea truncata complex
+3 Actinoscyphia
+5 Exocoelactis
+12 Kophobelemnidae
+1 Lychnagalma nectosome
+1 Lychnagalma
+8 Caenogastropoda
+5 Zoroasteridae
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+3 Vanhoeffenura
+2 Stylasterias
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+1 Leptocephalus-3
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+2 salp chain
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+1 Tuscaretta
+1 Chaunacops coloratus
+1 Pleurobrachiidae
+1 Tenebrincola cukri
+1 Amblyraja hyperborea

models/mbari-mb-benthic-33k.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:2dbb08d510681eb6fa3bc457958039067d4423dbcbc6edefe3b4f70d6e7760cf
+size 184365763

requirements.txt

@@ -0,0 +1,3 @@
+yolov5
+tator
+gradio

tator_inference.py

@@ -0,0 +1,100 @@
+import os
+import logging
+from tempfile import TemporaryFile
+
+import cv2
+import numpy as np
+from PIL import Image
+
+import tator
+import inference
+
+
+logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
+
+# Read environment variables that are provided from TATOR
+host = os.getenv('HOST')
+token = os.getenv('TOKEN')
+project_id = int(os.getenv('PROJECT_ID'))
+media_ids = [int(id_) for id_ in os.getenv('MEDIA_IDS').split(',')]
+frames_per_inference = int(os.getenv('FRAMES_PER_INFERENCE', 30))
+
+# Set up the TATOR API.
+api = tator.get_api(host, token)
+
+# Iterate through each video.
+for media_id in media_ids:
+
+    # Download video.
+    media = api.get_media(media_id)
+    logger.info(f"Downloading {media.name}...")
+    out_path = f"/tmp/{media.name}"
+    for progress in tator.util.download_media(api, media, out_path):
+        logger.info(f"Download progress: {progress}%")
+
+    # Do inference on each video.
+    logger.info(f"Doing inference on {media.name}...")
+    localizations = []
+    vid = cv2.VideoCapture(out_path)
+    frame_number = 0
+
+    # Read *every* frame from the video, break when at the end.
+    while True:
+        ret, frame = vid.read()
+        if not ret:
+            break
+
+        # Create a temporary file, access the image data, save data to file.
+        framefile = TemporaryFile(suffix='.jpg')
+        im = Image.fromarray(frame)
+        im.save(framefile)
+
+        # For every N frames, make a prediction; append prediction results
+        # to a list, increase the frame count.
+        if frame_number % frames_per_inference == 0:
+
+            spec = {}
+
+            # Predictions contains all information inside pandas dataframe
+            predictions = inference.run_inference(framefile)
+
+            for i, r in predictions.pandas().xyxy[0].iterrows:
+
+                spec['media_id'] = media_id
+                spec['type'] = None # Unsure, docs not specific
+                spec['frame'] = frame_number
+
+                x, y, x2, y2 = r['xmin'], r['ymin'], r['xmax'], r['ymax']
+                w, h = x2 - x, y2 - y
+
+                spec['x'] = x
+                spec['y'] = y
+                spec['width'] = w
+                spec['height'] = h
+                spec['class_category'] = r['name']
+                spec['confidence'] = r['confidence']
+
+                localizations.append(spec)
+
+        frame_number += 1
+
+    # End interaction with video properly.
+    vid.release()
+
+    logger.info(f"Uploading object detections on {media.name}...")
+
+    # Create the localizations in the video.
+    num_created = 0
+    for response in tator.util.chunked_create(api.create_localization_list,
+                                              project_id,
+                                              localization_spec=localizations):
+        num_created += len(response.id)
+
+    # Output pretty logging information.
+    logger.info(f"Successfully created {num_created} localizations on "
+                f"{media.name}!")
+
+    logger.info("-------------------------------------------------")
+
+logger.info(f"Completed inference on {len(media_ids)} files.")