''' ---------------------------------------- * Creation Time : Sun Aug 28 21:38:58 2022 * Last Modified : Sun Aug 28 21:41:36 2022 * Author : Charles N. Christensen * Github : github.com/charlesnchr ----------------------------------------''' from turtle import title import gradio as gr import numpy as np from PIL import Image import io import base64 import skimage from NNfunctions import * opt = GetOptions_Swin_2702() net = LoadModel(opt) gr.close_all() def predict(imagefile): # img = np.array(skimage.io.imread(imagefile.name)) # img = np.concatenate((img,img,img),axis=2) # img = np.transpose(img, (2,0,1)) img = skimage.io.imread(imagefile.name) # sr,wf,out = EvaluateModel(net,opt,img,outfile) sr, wf, sr_download = EvaluateModel(net,opt,img) return wf, sr, sr_download def process_example(filename): basename = os.path.basename(filename) basename = basename.replace('.png','.tif') img = skimage.io.imread('TestImages/%s' % basename) sr, wf, sr_download = EvaluateModel(net,opt,img) return wf, sr title = '

VSR-SIM: Spatio-temporal reconstruction method for SIM using vision transformer

' description = """ This space demonstrates the VSR-SIM method for reconstruction of structured illumination microscopy images. _Charles N. Christensen1,2 - GitHub: [charlesnchr](http://github.com/charlesnchr) - Email: charles.n.chr@gmail.com - Publication: Preprint --- ## 🔬 To run VSR-SIM Upload a TIFF image and hit submit or select one from the examples below. """ article = """ ![Example test images](https://i.imgur.com/Lidkbib.jpeg "Example test image for VSR-SIM") --- ### Read more - VSR-SIM.github.io - Website - Github - Twitter """ # inputs = gr.inputs.Image(label="Upload a TIFF image", type = 'pil', optional=False) inputs = gr.inputs.File(label="Upload a TIFF image", type = 'file', optional=False) outputs = [ gr.outputs.Image(label="INPUT (Wide-field projection)"), gr.outputs.Image(label="OUTPUT (VSR-SIM)"), gr.outputs.File(label="Download SR image" ) # , gr.outputs.Textbox(type="auto",label="Pet Prediction") ] examples = glob.glob('*.tif') interface = gr.Interface(fn=predict, inputs=inputs, outputs=outputs, title = title, description=description, article=article, examples=examples, allow_flagging='never', cache_examples=False ) interface.launch() # with gr.Blocks() as interface: # gr.Markdown(title) # gr.Markdown(description) # with gr.Row(): # input1 = gr.inputs.File(label="Upload a TIFF image", type = 'file', optional=False) # submit_btn = gr.Button("Reconstruct") # with gr.Row(): # output1 = gr.outputs.Image(label="Wide-field projection") # output2 = gr.outputs.Image(label="SIM Reconstruction") # output3 = gr.File(label="Download SR image", visible=False) # submit_btn.click( # predict, # input1, # [output1, output2, output3] # ) # gr.Examples(examples, input1, [output1, output2, output3]) # interface.launch()