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mueller-lab / EmbryoNet

EmbryoNet initial commit
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How To Get The Class Activation Heatmaps #16

Closed Leondyw closed 4 months ago

Leondyw commented 8 months ago

Dear Authors, I really appreciate your work on early detection of zebrafish embryo development, and I would like to get the class activation heatmaps in the fig3 of your article 'EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways' . Is it the files in the folder "train_eval/model" . I try to creat the environment , but I got many problems , such as the version of python and others , it shows I can't get the proper version of the packpages ,how can I solve these . I would really appreciate it if you could help me get these .

best regrads, Leon

hagorms commented 8 months ago

Hello, Leon! Could you please provide more information about this issue, about the system, add logs and errors or screenshots. Project works with python 3.8 Please provide errors and screenshot for every step described here https://github.com/mueller-lab/EmbryoNet/tree/main/Train_Eval

Best regards, Matvey

Leondyw commented 8 months ago

Dear Mr.hagorms! I try to use "generate_cam.py" in 'EmbryoNet-main\Train_Eval\tools\GenerateVideos' . When I type 

python D:\EmbryoNet-main\EmbryoNet-main\Train_Eval\tools\GenerateVideos\generate_cam.py -f D:\EmbryoNet\byh_1-11_3h_0\qwe\images -mp D:\EmbryoNet-main\EmbryoNet-main\GUI\Default_Models\ZebraFish\bioImage_embryonet\EmbryoNet_GPU_batch_1.onnx -sp D:\heatmap

in the cmd , it turns out

File "D:\EmbryoNet-main\EmbryoNet-main\Train_Eval\tools\GenerateVideos\generate_cam.py", line 185, in <module>
    images = sorted(os.listdir(os.path.join(args.folder, full_path_to_image_folder)))
NotADirectoryError: [WinError 267] The directory name is invalid.: 'D:\\EmbryoNet\\byh_1-11_3h_0\\qwe\\images\\-B003--PO01--LO476--CO6--SL001--PX32500--PW0100--IN0100--TM280--X053545--Y033148--Z190000--T3328249152--WE00010.jpg'

I put all the images in the folder "D:\EmbryoNet\byh_1-11_3h_0\qwe\images" ,what should I do to solve this problem.And I also try to type "D:\EmbryoNet\byh_1-11_3h_0\qwe" and "D:\EmbryoNet\byh_1-11_3h_0" ,but they all don't work properly. I would appreciate it greatly if you can help me solve this . Best regards, Leon

hagorms commented 7 months ago

Script tells you that you are giving the wrong path to the script. Try giving -f D:\EmbryoNet\byh_1-11_3h_0\qwe instead.