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import gradio as gr
import numpy as np
from huggingface_hub import from_pretrained_fastai
learn_imp = from_pretrained_fastai('MikeTrizna/Prunus_lineage_classifier')
def predict(image_np, description=None):
classes = ['Neotropical racemose', 'Paleotropical racemose',
'Solitary/Corymbose', 'Temperate racemose']
pred,pred_idx,probs = learn_imp.predict(image_np)
confidences = {classes[idx]: f'{prob:.04f}' for idx, prob in enumerate(probs)}
return confidences
example_metadata = [{'idigbio_specimen': '36b28730-fd06-44b4-86a4-77d3be052ef1',
'idigbio_media': '1c086296-6d1f-4218-a18a-ca2f86c295d0',
'gbif_occurrence': '2425450644',
'gbif_media': '60d5b76a58cf28eff526d5c1d7906321',
'organism': 'Prunus myrtifolia',
'intrageneric_group': 'Neotropical racemose'},
{'idigbio_specimen': '0252042a-e14f-4437-99f8-f9c690f1d2a8',
'idigbio_media': '104f44c9-63f1-4579-93c2-54c6ddeddeda',
'gbif_occurrence': '1056985949',
'gbif_media': '65d035ce17427cba5a698850e903cbc8',
'organism': 'Prunus oleifolia',
'intrageneric_group': 'Neotropical racemose'},
{'idigbio_specimen': 'e025ff74-333b-461f-a86e-63d8f4a6bd90',
'idigbio_media': 'e3276fdd-ce58-40dc-bf20-8742f7634428',
'gbif_occurrence': '2515155769',
'gbif_media': 'd952c78c4b50825dc267d3ab915ea71e',
'organism': 'Prunus oocarpa',
'intrageneric_group': 'Paleotropical racemose'},
{'idigbio_specimen': '4a991d4d-d6a5-4a4a-9c99-9af948f9e0e0',
'idigbio_media': 'e5ac59df-5b18-4c8d-a19b-02131d358855',
'gbif_occurrence': '2515160308',
'gbif_media': 'fc94119768b9ea1c453cb0ab9887b54a',
'organism': 'Prunus pullei',
'intrageneric_group': 'Paleotropical racemose'},
{'idigbio_specimen': 'e32b4d05-5389-4466-83cb-25e319c2fa9f',
'idigbio_media': '0060a57d-e779-4984-913c-95b576daf0d3',
'gbif_occurrence': '3865356188',
'gbif_media': 'c40a3ebe7ea67f67d33b7405134f3133',
'organism': 'Prunus serotina',
'intrageneric_group': 'Temperate racemose'},
{'idigbio_specimen': '31697ac1-223d-477b-bc8d-0d10ced90ad0',
'idigbio_media': 'b9fa9ff9-2e8b-42f5-8728-5b0b5be98490',
'gbif_occurrence': '2515504033',
'gbif_media': 'be7e108416c0a052311f879642997dee',
'organism': 'Prunus grayana',
'intrageneric_group': 'Temperate racemose'},
{'idigbio_specimen': '80a8afd7-ca01-4df1-a566-305912e25166',
'idigbio_media': '52e06de9-c035-4afc-9fac-c8bee7628d38',
'organism': 'Prunus glandulosa',
'intrageneric_group': 'Solitary/Corymbose'},
{'idigbio_specimen': '7835f8bd-d78c-4884-a669-853634296371',
'idigbio_media': '0b13e5eb-73da-4e0e-9b1a-794b737f7716',
'gbif_occurrence': '2265382670',
'gbif_media': '1373276d8fdd232579e7d04c4e64edb1',
'organism': 'Prunus pensylvanica',
'intrageneric_group': 'Solitary/Corymbose'}]
table_header = """**Example Guide**
| Image | Species | Link to iDigBio Specimen Record | Intrageneric group |
| --- | --- | --- | --- |
"""
table_body = ''
gbif_scale = 150
for example in example_metadata:
if 'gbif_media' in example:
image_src = f"<image src = 'https://api.gbif.org/v1/image/cache/fit-in/{gbif_scale}x/occurrence/{example['gbif_occurrence']}/media/{example['gbif_media']}'></image>"
elif 'idigbio_media' in example:
image_src = f"<image src = 'https://api.idigbio.org/v2/media/{example['idigbio_media']}?size=thumbnail'></image>"
else:
image_src = '[No image source]'
species = f"*{example['organism']}*"
idigbio_link = f"https://www.idigbio.org/portal/records/{example['idigbio_specimen']}"
intrageneric_group = example['intrageneric_group']
table_row = ' | '.join([image_src, species,
idigbio_link, intrageneric_group])
table_body += table_row + '\n'
example_table = table_header + table_body
example_list = ["examples/myrtifolia_1c086296-6d1f-4218-a18a-ca2f86c295d0.jpg",
"examples/oleifolia_104f44c9-63f1-4579-93c2-54c6ddeddeda.jpg",
"examples/oocarpa_e3276fdd-ce58-40dc-bf20-8742f7634428.jpg",
"examples/pullei_e5ac59df-5b18-4c8d-a19b-02131d358855.jpg",
"examples/serotina_0060a57d-e779-4984-913c-95b576daf0d3.jpg",
"examples/grayana_b9fa9ff9-2e8b-42f5-8728-5b0b5be98490.jpg",
"examples/glandulosa_52e06de9-c035-4afc-9fac-c8bee7628d38.jpg",
"examples/pensylvanica_0b13e5eb-73da-4e0e-9b1a-794b737f7716.jpg"]
description = """This model can place herbarium sheet images from the genus Prunus into one of four
categories that represent key clades within the genus: Solitary/Corymbose, Temperate Racemose, Neotropical
Racemose, Paleotropical Racemose."""
demo = gr.Interface(predict,
gr.Image(type="numpy"),
outputs="label",
examples=example_list,
description=description,
title="Image classification of four major lineages in the plum genus",
article=example_table)
demo.launch() |