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View Code? Open in Web Editor NEWCOVID-CT-Dataset: A CT Scan Dataset about COVID-19
COVID-CT-Dataset: A CT Scan Dataset about COVID-19
Hello,
Thank you for contributing to research revolving around COVID-19. Your data set is very valuable.
I am not a physician, but upon consulting with collaborators it appears that the following issues should be addressed.
Thank you again.
Thank you very much for providing the dataset and baseline model! I am participating in the COVID-19 CT competition (https://covid-ct.grand-challenge.org/), but I cannot find the format of the submission file on the competition page. Could you provide a sample submission file or describe the format of the submission file in detail?
FileNotFoundError: [Errno 2] No such file or directory: 'new_data/newtxt/train.txt'.
In Folder new_data and old_data/oldtxt/trainCT_NonCOVID.txt.
Is miss Train, val.txt and Test files.
Hi! Do you have any plan to upload NonCOVID-CT-Images.zip? Currently, only COVID-CT-Images.zip is available! Kindly advise. Thanks
In your setting in 'DenseNet_predict.py', it seems you miss schedule.step() to change the learning rate. Could you please check this out?
Thanks for your work to help the people in need! Your site has been added to the Open-Source-COVID-19 page, which collects open source projects related to COVID-19, including maps, data, news, api, analysis, medical and supply information, etc. Please share to anyone who might need the information in the list, or will possibly contribute to some of those projects. You are also welcome to recommend more projects.
http://open-source-covid-19.weileizeng.com/
Cheers!
The resolution of photos is not the same, but also contains a large number of annotations
Guys we are trying to run your code. The problem is this error below. I think your github is missing files. Can you please give us a workaround?:
FileNotFoundError Traceback (most recent call last) <ipython-input-18-b71253aaae34> in <module>() 156 txt_COVID='new_data/newtxt/train.txt', 157 txt_NonCOVID='/content/drive/My Drive/Covid_CT/Content2/CovidCTNew/Data-split/COVID/trainCT_NonCOVID.txt', --> 158 transform= train_transformer) 159 valset = CovidCTDataset(root_dir='new_data/4.4_image', 160 txt_COVID='new_data/newtxt/val.txt',
There's a new dataset that HM Hospitales in Spain is sharing with qualified researchers, consisting of anonymized medical records from COVID-19 patients:
https://www.hmhospitales.com/prensa/notas-de-prensa/comunicado-covid-data-save-lives
From April, 25th onwards, the 'COVID DATA SAVE LIVES' contents will be distributed online, free of cost and other access barriers to worldwide health care institutions, universities, and scientific organizations...
To access this initiative, it is mandatory to submit an application via e-mail to [email protected] which will be assessed by the HM Hospitales Data Science Commission and, where appropriate, reviewed by the HM Hospitales Clinical Research Ethics Committee.
Hello, when i run the code 'CT_predict', a error occurred: alpha doesn't exist and i found this txt also doesn't exist.
f = open('COVID-CT/model_result/DenseNet_{}.txt'.format(alpha), 'a+')
Thanks for providing images again!
Hi,
I have been spending some hours every other day to check for papers containing CT or Xray images of COVID-19 patients. Are you accepting contributions in any way? In the case of the covid-19 x-ray collection project, they keep a list of already collected papers, and one can inform of not-yet-collected papers in the issues section. Please advice us on how to contribute with papers containing CT images that you might have not yet included in your dataset.
Thank you for your effort. Please I have two questions.
Would Dicom files be part of future updates?
It seems that the data split is with image-level, which means slices from the same patient could come to tran/test/val. This will bring some data-leakage problem. It is more reasonable to split in the patient level so that images from same patient cannot be assigned to different set(train/test/val)
When I run DenseNet_predict.py, the error comes "No such file or directory: 'new_data/newtxt/train.txt'."
It seem that this code is too old to run. Can anybody update recently?
Hi,
Thanks for the effort!
In the report, you only mentioned that the images of training set are collected from papers.
Can you guarantee that none of those are originally from SIRM?
Can you provide masks (ground glass opacity, consolidation) to evaluate a segmentation algorithm?
How to download dataset?
according to your readme file, your result was F1: 0.85,Accuracy: 0.86,AUC: 0.94,but mine was F1:0.74, Accuracy:0.77, AUC:0.88. Should I use the Self-Trans.pt as a pretrained model and fine tune on it?
Hello,
Thank you for your data set .It is very valuable.
I am a graduate student, I clone your zip .But there is bug in code.
So I want a new updated code. My email [email protected]
Thank you again.
i cloned, then i install everything, but when i try to run "python CT_predict.py" i am getting following error: No such file or directory: 'COVID-CT/train_set'" can you please rell, what chnges i need to made after clone.
yes thanks for providing ct images.
Thanks
Excuse me~ when I run the baseline methods, I met the following question:
RuntimeError: Given groups=1, weight of size 32 3 3 3, expected input[10, 1, 225, 225] to have 3 channels, but got 1 channels instead.
I have no idea, can you help me?
How the non-covid images are collected. ? I did not find any information in Data creation step of the paper
NonCOVID-CT-MetaInfo.xlsx is not an excel ".xlsx" file but a csv.
$ unzip NonCOVID-CT-Images.zip
Archive: NonCOVID-CT-Images.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
unzip: cannot find zipfile directory in one of NonCOVID-CT-Images.zip or
NonCOVID-CT-Images.zip.zip, and cannot find NonCOVID-CT-Images.zip.ZIP, period.
Hi,
I am not sure how do you select the model to use for the test data. It seems to me in your code you did not use the information from the validation dataset to choose the model to use on the test data. I also did not observe any early stopping criteria being used. Is that true? If it is, how do you select the model and what is the purpose of the validation dataset?
Thanks,
Yangze
please delete this, I am sorry
Hi,
Thank you for the for the effort of putting this dataset together.
Probably you have checked the metadata that is being collected for the covid x-ray dataset project. I would suggest on collecting a more specific and detailed metadata on each scan, as in the mentioned project, so that better insights can be obtained from the dataset.
Thanks!
Dears
Based on your implementation is it possible to show any visual results? Something like a heatmap...
pls list all the requirement(packages)..
It is a bit vague: does it include all non-COVID, i.e. Normal + Common Pneumonia, or only Common Pneumonia/only Normal?
For example, in the file Data-Splits/COVID/valCT_COVID.txt
, there is a file called 2020.03.16.20036145-p19-128-4.png
.
However, in the image processed folder, Image-Processed/COVID
, the file is saved using a JPEG extension as 2020.03.16.20036145-p19-128-4.jpeg
.
There are some other files like this too such as Images-processed/CT_COVID/2020.03.18.20038125-p15-54-2.png
. I got over this by making sure all files had the same extension but please fix this.
according to your code
self.classes = ['CT_COVID', 'CT_NonCOVID']
self.num_cls = len(self.classes)
self.img_list = []
for c in range(self.num_cls):
cls_list = [[os.path.join(self.root_dir,self.classes[c],item), c] for item in read_txt(self.txt_path[c])]
self.img_list += cls_list
self.transform = transform
the label of 'CT_COVID' is 0 and 'CT_NonCOVID' is 1, but when you calculate the metrics,like TP, your code is
TP = ((predlist == 1) & (targetlist == 1)).sum()
I think this is wrong since 'CT_COVID' is positive and its label is 0, we hope the model detect CT_COVID more accurate than CT_NonCOVID, so in this circumstance TP should be?
TP = ((predlist == 0) & (targetlist == 0)).sum()
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