jfnavarro
commented
1 year ago This is a known issue related to the image size limit in matplotlib. There are multiple work-arounds for this.
Open lili03080317 opened 1 year ago
jfnavarro
commented
1 year ago This is a known issue related to the image size limit in matplotlib. There are multiple work-arounds for this.
Hi, When I run python st_data_plotter.py --counts-table-files stdata.tsv --image-files ST_rep1.jpg --outdir /root/home/ --show-genes CASP7 ,I got a error like this.
Total number of spots 1933 Total number of genes 17138 Number of expressed genes a spot must have to be kept (0.01% of total expressed genes) 193 Dropped 19 spots Removing genes that are expressed in less than 19 spots with a count of at least 1 Dropped 4804 genes Computing per spot normalization... Plotting data... Traceback (most recent call last): File "st_data_plotter.py", line 214, in
args.use_log_scale)
File "st_data_plotter.py", line 156, in main
vmax=vmax)
File "/opt/miniconda3/envs/scgpt/lib/python3.7/site-packages/stanalysis-0.5.1-py3.7.egg/stanalysis/visualization.py", line 187, in scatter_plot
img = plt.imread(image)
File "/opt/miniconda3/envs/scgpt/lib/python3.7/site-packages/matplotlib/pyplot.py", line 2158, in imread
return matplotlib.image.imread(fname, format)
File "/opt/miniconda3/envs/scgpt/lib/python3.7/site-packages/matplotlib/image.py", line 1560, in imread
with img_open(fname) as image:
File "/opt/miniconda3/envs/scgpt/lib/python3.7/site-packages/PIL/Image.py", line 3277, in open
im = _open_core(fp, filename, prefix, formats)
File "/opt/miniconda3/envs/scgpt/lib/python3.7/site-packages/PIL/Image.py", line 3264, in _open_core
_decompression_bomb_check(im.size)
File "/opt/miniconda3/envs/scgpt/lib/python3.7/site-packages/PIL/Image.py", line 3173, in _decompression_bomb_check
raise DecompressionBombError(msg)
PIL.Image.DecompressionBombError: Image size (251920384 pixels) exceeds limit of 178956970 pixels, could be decompression bomb DOS attack.
How to fix it?Thank you.