Comments (8)
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)
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BUT, I still lack "*_croods.tsv", if anybody has a solution? @OnkarMulay
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I am trying running it manually not using any functions
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run sudo apt install python-openslide
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Thanks @chenyang1999, I am also missing the "_Coords.tsv". @bryanhe any chance you could provide it? Thank you!
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@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
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I got the same error message "
OSError: libopenslide.so.0: cannot open shared object file: No such file or directory
" after run "python3 -m stnet prepare spatial" command at virtual env python3. I also preprocess the images in ./data/hist2tscript" as suggested here by chanyang1999, the same error. Any one has suggestions?
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Related Issues (10)
- Question about breast cancer dataset HOT 1
- create_tifs.sh requires "histonet" HOT 1
- No ensembl.tsv in the utils folder HOT 13
- Cannot access the data HOT 4
- Cannot find "_Coords.tsv" file HOT 7
- The dataset is not available HOT 1
- ensembl.tsv HOT 5
- Computer beeps while running cross validation with GPU
- Decompression Bomb Warning & KeyError: 'pixel_x' HOT 5
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