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arpanmangal / CovidAID

COVID-19 Detection Using Chest X-Ray
http://arxiv.org/abs/2004.09803
61 stars 38 forks source link

System exit error #5

Closed Rukhmini closed 4 years ago

Rukhmini commented 4 years ago

I am using google colab to run the code. Whenever I am running the code using "!python trainer.py", it is showing this error. usage: trainer.py [-h] [--local_rank LOCAL_RANK] --mode {train,test,f1} --checkpoint CHECKPOINT [--combine_pneumonia] [--save SAVE] [--start START] [--lr LR] [--freeze] [--bs BS] [--cm_path CM_PATH] [--roc_path ROC_PATH] trainer.py: error: the following arguments are required: --checkpoint An exception has occurred, use %tb to see the full traceback. SystemExit: 2 Can you please help me with this?

arpanmangal commented 4 years ago

trainer.py is a python script which has to be run with the correct arguments as indicated by the error you got. Please see https://github.com/arpanmangal/CovidAID/blob/master/GETTING_STARTED.md for usage examples. Also if you want to run it on some examples rather than train/test the model, I would recommend moving directly to inference.py: https://github.com/arpanmangal/CovidAID/blob/master/GETTING_STARTED.md#inference-with-trained-models

Rukhmini commented 4 years ago

python tools/trainer.py --mode train --freeze --checkpoint models/CovidAID_transfered.pth.tar --bs 16 --save [--combine_pneumonia] does this line combine two types of pneumonia? If we don't want to combine pneumonia what would be the statement?

arpanmangal commented 4 years ago

--combine_pneumonia flag is optional (as indicated by []). Make sure you select the correct checkpoint with 4 classes.

Rukhmini commented 4 years ago

!python tools/trainer.py --mode train --freeze --checkpoint models/CovidAID_transfered.pth.tar --bs 16 --save './models' I am using this line of code and getting this error : Loading model from models/CovidAID_transfered.pth.tar Traceback (most recent call last): File "tools/trainer.py", line 434, in start_epoch=args.start, save_path=args.save, freeze_feature_layers=args.freeze) File "tools/trainer.py", line 73, in train combine_pneumonia=self.combine_pneumonia) File "/content/gdrive/My Drive/CovidAID-master/tools/read_data.py", line 88, in init label = int(items[1]) ValueError: invalid literal for int() with base 10: '(1).jpeg'

when using this !python tools/trainer.py --mode train --freeze --checkpoint models/CovidAID_transfered.pth.tar --bs 16 --save './models' [--combine_pneumonia] it is showing import pandas.util.testing as tm usage: trainer.py [-h] [--local_rank LOCAL_RANK] --mode {train,test,f1} --checkpoint CHECKPOINT [--combine_pneumonia] [--save SAVE] [--start START] [--lr LR] [--freeze] [--bs BS] [--cm_path CM_PATH] [--roc_path ROC_PATH] trainer.py: error: unrecognized arguments: [--combine_pneumonia]

arpanmangal commented 4 years ago

Please read the running instructions carefully and follow in a step by step manner. Also please get familiar with running scripts taking command line arguments.

arpanmangal commented 4 years ago

Did you download and setup the datasets using data_tools/prepare_data.py?

Rukhmini commented 4 years ago

Yes I have done that. I have followed all the instructions given in the getting started.md file. prepare_data.py run successfully and it created the text files required to train the network.

arpanmangal commented 4 years ago

Could you do a print (items) statement before tools/read_data.py:88 and report the output?

Rukhmini commented 4 years ago

import pandas.util.testing as tm Distributed training OFF Loading model from models/CovidAID_transfered.pth.tar ['./chest_xray/train/NORMAL/IM-0509-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0506-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0511-0001-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0519-0001-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0523-0001-0003.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0511-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0544-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0530-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0545-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0549-0001-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0533-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0551-0001-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0548-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0529-0001.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0549-0001-0002.jpeg', '0'] ['./chest_xray/train/NORMAL/IM-0545-0001-0002.jpeg', '0'] 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['./chest_xray/train/PNEUMONIA/person502_bacteria_2119.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person508_virus_1021.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person518_bacteria_2198.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person515_bacteria_2186.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person517_virus_1035.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person471_bacteria_2005.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person49_bacteria_236.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person51_bacteria_246.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person461_virus_949.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person520_bacteria_2203.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person51_bacteria_244.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person502_virus_1011.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person490_virus_996.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person497_virus_1005.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person478_bacteria_2032.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person475_bacteria_2020.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person566_bacteria_2351.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person531_virus_1053.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person532_virus_1054.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person550_virus_1090.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person593_bacteria_2435.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person560_bacteria_2330.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person539_bacteria_2270.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person535_bacteria_2256.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person556_virus_1096.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person549_virus_1089.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person588_bacteria_2423.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person58_bacteria_276.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person580_bacteria_2387.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person582_bacteria_2404.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person596_bacteria_2444.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person598_bacteria_2453.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person581_virus_1125.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person541_bacteria_2275.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person535_bacteria_2255.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person574_bacteria_2370.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person549_bacteria_2304.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person55_bacteria_263.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person533_bacteria_2245.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person581_bacteria_2400.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person550_bacteria_2308.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person529_bacteria_2229.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person564_bacteria_2347.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person583_virus_1127.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person536_bacteria_2258.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person591_virus_1139.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person585_bacteria_2414.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person543_bacteria_2281.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person52_bacteria_251.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person538_virus_1068.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person590_virus_1138.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person529_bacteria_2228.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person58_bacteria_273.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person58_bacteria_274.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person553_virus_1093.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person563_bacteria_2335.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person567_virus_1107.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person585_bacteria_2411.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person579_bacteria_2381.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person554_bacteria_2323.jpeg', '1'] 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['./chest_xray/train/PNEUMONIA/person1430_bacteria_3697.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1393_virus_2396.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1363_bacteria_3484.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1413_bacteria_3615.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person140_virus_284.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1388_bacteria_3529.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1397_virus_2400.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1366_virus_2349.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1414_bacteria_3627.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1403_bacteria_3559.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1411_virus_2415.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1439_virus_2453.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1432_bacteria_3699.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person140_virus_285.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1377_bacteria_3512.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1391_bacteria_3536.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1367_virus_2351.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1418_bacteria_3637.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1395_virus_2398.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1411_bacteria_3593.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1385_virus_2380.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1374_virus_2365.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1365_virus_2348.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1359_virus_2340.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1396_bacteria_3545.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1426_bacteria_3667.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1402_virus_2405.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1436_bacteria_3712.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1358_bacteria_3463.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1381_bacteria_3517.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1406_virus_2409.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1405_bacteria_3571.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1411_bacteria_3607.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1377_virus_2369.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1369_virus_2356.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1378_bacteria_3513.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1400_bacteria_3554.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1412_bacteria_3612.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1438_bacteria_3721.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1424_virus_2437.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1384_bacteria_3522.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1418_virus_2429.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1441_virus_2457.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person143_virus_289.jpeg', '2'] ['./chest_xray/train/PNEUMONIA/person1424_bacteria_3651.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1430_bacteria_3693.jpeg', '1'] ['./chest_xray/train/PNEUMONIA/person1455_virus_2496', '(1).jpeg', '2'] Traceback (most recent call last): File "tools/trainer.py", line 434, in start_epoch=args.start, save_path=args.save, freeze_feature_layers=args.freeze) File "tools/trainer.py", line 73, in train combine_pneumonia=self.combine_pneumonia) File "/content/gdrive/My Drive/CovidAID-master/tools/read_data.py", line 89, in init label = int(items[1]) ValueError: invalid literal for int() with base 10: '(1).jpeg'

arpanmangal commented 4 years ago

Clearly you have an image with a space(`) within the name:./chest_xray/train/PNEUMONIA/person1455_virus_2496 (1).jpeg`. Just go to the directory, rename the image, and issue resolved..