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import gradio as gr
import torch
import numpy as np
import h5py
import faiss
from PIL import Image
import io
import pickle
import random
def get_image(image1, image2, dataset_image_mask, processid_to_index, idx):
if (idx < 162834):
image_enc_padded = image1[idx].astype(np.uint8)
elif(idx >= 162834):
image_enc_padded = image2[idx-162834].astype(np.uint8)
enc_length = dataset_image_mask[idx]
image_enc = image_enc_padded[:enc_length]
image = Image.open(io.BytesIO(image_enc))
return image
def searchEmbeddings(id, mod1, mod2):
# variable and index initialization
original_indx = processid_to_index[id]
dim = 768
num_neighbors = 10
# get index
index = faiss.IndexFlatIP(dim)
if (mod2 == "Image"):
index = faiss.read_index("image_index.index")
elif (mod2 == "DNA"):
index = faiss.read_index("dna_index.index")
# search index
if (mod1 == "Image"):
query = id_to_image_emb_dict[id]
elif(mod1 == "DNA"):
query = id_to_dna_emb_dict[id]
query = query.astype(np.float32)
D, I = index.search(query, num_neighbors)
id_list = []
for indx in I[0]:
id = indx_to_id_dict[indx]
id_list.append(id)
# get images
image0 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, original_indx)
image1 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][0])
image2 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][1])
image3 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][2])
image4 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][3])
image5 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][4])
image6 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][5])
image7 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][6])
image8 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][7])
image9 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][8])
image10 = get_image(dataset_image1, dataset_image2, dataset_image_mask, processid_to_index, I[0][9])
# get taxonomic information
s0 = getTax(original_indx)
s1 = getTax(I[0][0])
s2 = getTax(I[0][1])
s3 = getTax(I[0][2])
s4 = getTax(I[0][3])
s5 = getTax(I[0][4])
s6 = getTax(I[0][5])
s7 = getTax(I[0][6])
s8 = getTax(I[0][7])
s9 = getTax(I[0][8])
s10 = getTax(I[0][9])
return id_list, image0, image1, image2, image3, image4, image5, image6, image7, image8, image9, image10, s0, s1, s2, s3, s4, s5, s6, s7, s8, s9, s10
def getRandID():
indx = random.randrange(0, 325667)
return indx_to_id_dict[indx], indx
def getTax(indx):
s = species[indx]
g = genus[indx]
f = family[indx]
str = "Species: " + s + "\nGenus: " + g + "\nFamily: " + f
return str
with gr.Blocks(title="Bioscan-Clip") as demo:
# open general files
with open("dataset_image1.pickle", "rb") as f:
dataset_image1 = pickle.load(f)
with open("dataset_image2.pickle", "rb") as f:
dataset_image2 = pickle.load(f)
with open("dataset_processid_list.pickle", "rb") as f:
dataset_processid_list = pickle.load(f)
with open("dataset_image_mask.pickle", "rb") as f:
dataset_image_mask = pickle.load(f)
with open("processid_to_index.pickle", "rb") as f:
processid_to_index = pickle.load(f)
with open("indx_to_id_dict.pickle", "rb") as f:
indx_to_id_dict = pickle.load(f)
# open image files
with open("id_to_image_emb_dict.pickle", "rb") as f:
id_to_image_emb_dict = pickle.load(f)
# open dna files
with open("id_to_dna_emb_dict.pickle", "rb") as f:
id_to_dna_emb_dict = pickle.load(f)
# open taxonomy files
with open("family.pickle", "rb") as f:
family = [item.decode("utf-8") for item in pickle.load(f)]
with open("genus.pickle", "rb") as f:
genus= [item.decode("utf-8") for item in pickle.load(f)]
with open("species.pickle", "rb") as f:
species = [item.decode("utf-8") for item in pickle.load(f)]
with gr.Column():
process_id = gr.Textbox(label="ID:", info="Enter a sample ID to search for")
process_id_list = gr.Textbox(label="Closest 10 matches:" )
mod1 = gr.Radio(choices=["DNA", "Image"], label="Search From:")
mod2 = gr.Radio(choices=["DNA", "Image"], label="Search To:")
search_btn = gr.Button("Search")
with gr.Row():
with gr.Column():
image0 = gr.Image(label="Original", height=550)
tax0 = gr.Textbox(label="Taxonomy")
with gr.Column():
rand_id = gr.Textbox(label="Random ID:")
rand_id_indx = gr.Textbox(label="Index:")
id_btn = gr.Button("Get Random ID")
with gr.Row():
with gr.Column():
image1 = gr.Image(label=1)
tax1 = gr.Textbox(label="Taxonomy")
with gr.Column():
image2 = gr.Image(label=2)
tax2 = gr.Textbox(label="Taxonomy")
with gr.Column():
image3 = gr.Image(label=3)
tax3 = gr.Textbox(label="Taxonomy")
with gr.Row():
with gr.Column():
image4 = gr.Image(label=4)
tax4 = gr.Textbox(label="Taxonomy")
with gr.Column():
image5 = gr.Image(label=5)
tax5 = gr.Textbox(label="Taxonomy")
with gr.Column():
image6 = gr.Image(label=6)
tax6 = gr.Textbox(label="Taxonomy")
with gr.Row():
with gr.Column():
image7 = gr.Image(label=7)
tax7 = gr.Textbox(label="Taxonomy")
with gr.Column():
image8 = gr.Image(label=8)
tax8 = gr.Textbox(label="Taxonomy")
with gr.Column():
image9 = gr.Image(label=9)
tax9 = gr.Textbox(label="Taxonomy")
with gr.Column():
image10 = gr.Image(label=10)
tax10 = gr.Textbox(label="Taxonomy")
id_btn.click(fn=getRandID, inputs=[], outputs=[rand_id, rand_id_indx])
search_btn.click(fn=searchEmbeddings, inputs=[process_id, mod1, mod2],
outputs=[process_id_list, image0, image1, image2, image3, image4, image5, image6, image7, image8, image9, image10,
tax0, tax1, tax2, tax3, tax4, tax5, tax6, tax7, tax8, tax9, tax10])
examples = gr.Examples(
examples=[["ABOTH966-22", "DNA", "DNA"],
["CRTOB8472-22", "DNA", "Image"],
["PLOAD050-20", "Image", "DNA"],
["HELAC26711-21", "Image", "Image"]],
inputs=[process_id, mod1, mod2],)
demo.launch() |