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spreka / biomagdsb

This repository contains the codes to run the nuclei segmentation pipeline of the BIOMAG group inspired by Kaggle's Data Science Bowl 2018 competition
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Error for single channel grayscale images #3

Closed PetterRanefall closed 5 years ago

PetterRanefall commented 5 years ago

If I run start_prediction_full.bat on a single channel grayscale image I get an error: File "C:\Code\Python3\biomagdsb\UNet\utils.py", line 264, in getitem image = io.imread(image_path)[:, :, :3] IndexError: too many indices for Array

and later: Error using imread>get_full_filename (line 481) File "C:\Code\Python3\biomagdsb\kaggle_workflow\outputs\ensemble\output\BE_300_01_rescaled.png" does not exist.

Error in imread (line 344) filename = get_full_filename(fid, errmsg, filename);

Error in postProcCodeFINAL (line 104) probMap = (imread([probFolder filesep imageList(i).name(1:end-5) '.png']));

Error in postProcCodeRunnerFINAL (line 94) postProcCodeFINAL(inMainFolder,outMainFolder,...

(It works if I convert the image to RGB before starting)

spreka commented 5 years ago

@PetterRanefall Please take a look at start_image_preprocessing.bat, it converts your images to 8-bit RGB.

PetterRanefall commented 5 years ago

OK, thanks!

spreka commented 5 years ago

@PetterRanefall I am closing this now as the suggested script solves the error. Please feel free to reopen it if the issue still occurs.