validation-sets.json

[wyq2018]

Hi @bdecost, there occurres the following errors when i run your project. Firstly, the labels of both uhcs and spheroidite dataset are damaged when I downloa ded them from your website. Secondly thevalidation-sets.json does not exist in your project, can you provide it?

[pabaldonedo]

Any news on this topic? I am also having same issue.

Thanks!

[bdecost]

sorry about this -- could you give a bit more detail on what you mean regarding the labels being damaged? I downloaded a fresh copy of the dataset from materialsdata.nist.gov, I can't find any issues with the label images.

The uhcs labels are int64 TIFs, and they contain some negative pixel values that correspond to the micron bar. I wasn't able to display them in my primary image viewer (Preview on MacOS), but loading them with scikit-image or similar should work.

The particles labels are stored in uint8 TIFs, and the values are in [0,1], so they might appear completely dark in some image viewers (they do in Preview).

from skimage import io
i = io.imread('uhcs/labels/uhcs0006.tif')
plt.imshow(i)

[bdecost]

For the validation sets -- thanks, I had overlooked that before. I just pushed all of the images, labels, and validation splits to https://github.com/bdecost/uhcs-segment/tree/master/data

[pabaldonedo]

Thanks @bdecost for the json files.
Regarding the images, you are right that opening with skimage works. However, just for the record for anyone else, with either:

• some image viewers
• PIL/matplotlib.pyplot:

from PIL import Image
Image.open('uhcs/labels/uhcs0006.tif')

The following error arises: OSError: cannot identify image file 'data/uhcs/labels/uhcs0006.tif'

[pabaldonedo]

Maybe not the correct place to comment this, but apart from the .jsons file that you uploaded (thanks again!) in transfer_pixelnet.py line 55 you are loading ".h5" files for loading the dataset but those files are missing in the data folder. Could you make available those?

Apologize for keep posting questions, but I would like to replicate the paper results and while doing that, any changes/fixes that I find that I can make I will try to put them together and make a Pull-request so anyone else can do the same :)

[pabaldonedo]

Ok I have noted that you create h5 files in mitk_tohdf5.py. However, for that you load .mitk files from data/mitk/*.mitk and those are also missing in the repo. With those .mitk I understand we can generate h5 and then run transfer_pix.

Could you upload those mitk files? Thanks!

[JobNicolas17]

Hi, any news about ".h5 files"? I am having same issue.

Thanks,