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OSError: libopenslide.so.0: cannot open shared object file: No such file or directory #4
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Maybe you need to preprocess the dataset, I wrote a code to preprocess it and put it under ./data import os
import glob
file_path="./hist2tscript"
for img in glob.glob(file_path+"/*"):
if "HE_" in img:
fn=img.replace("HE_","")
command=f"mv {img} {fn}"
print(command)
os.system(command)
if "_stdata" in img:
fn=img.replace("_stdata","")
command=f"mv {img} {fn}"
print(command)
os.system(command)
if "spots" in img:
fn=img.replace("spots_","").replace(".csv",".spots.txt")
command=f"mv {img} {fn}"
print(command)
os.system(command)
file_list=glob.glob(file_path+"/*.jpg")
# print(file_list)
sample_id=[]
for f in file_list:
sample_id.append(f.split("/")[-1].split(".")[0].split("_")[0])
# print(sample_id)
# sample_id=[x[2:] for x in sample_id]
print(sample_id)
# print(glob.glob(file_path+"/*"))
for sid in sample_id:
print(sid)
temp_path=file_path+"/BRCA/"+sid
print(temp_path)
os.makedirs(file_path+"/BRCA/"+sid,exist_ok=True)
for f in glob.glob(file_path+"/*"):
if sid[2:] in f:
print(f)
command=f"mv {f} {temp_path}"
print(command)
os.system(command)
for img in glob.glob(file_path+"/*/*/*"):
patient_id=img.split("/")[-2]
# print(patient_id)
stdata = img.split("/")[-1]
# print(stdata)
if patient_id not in stdata:
fn=img.replace("BC","BT")
command = f"mv {img} {fn}"
print(command)
os.system(command)
|
BUT, I still lack "*_croods.tsv", if anybody has a solution? @OnkarMulay |
I am trying running it manually not using any functions |
run |
Thanks @chenyang1999, I am also missing the "_Coords.tsv". @bryanhe any chance you could provide it? Thank you! |
@andrewbrown1022 我没有这个肿瘤标记数据,我现在是直接拿全部 spots 的基因表达训练 |
I got the same error message " |
I have solved it by running "sudo apt-get install libopenslide-dev". |
python3 -m stnet prepare spatial
On running this command I have got this error, any idea how should I tackle this...??
File not found, where can I download it from?
Thanking for the help in advance
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