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Optimised inference pipeline #104

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Optimised inference pipeline #104

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d845e57
Minor cleanup.
jjhbw Feb 22, 2021
fc375c4
Optimized alternative inference pipeline.
jjhbw Feb 22, 2021
e019105
Add new requirements.
jjhbw Feb 22, 2021
c0cfb16
Try to fix broken tissue mask polygon topologies when encountering them.
jjhbw Apr 7, 2021
65963c1
Solved `TypeError: 'Polygon' object is not iterable` when trying to b…
jjhbw Apr 26, 2021
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,6 @@ exp_output/
*.npz
*.png
*.log

# chunk feature maps
*.h5
11 changes: 1 addition & 10 deletions infer/wsi.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import multiprocessing as mp
from concurrent.futures import FIRST_EXCEPTION, ProcessPoolExecutor, as_completed, wait
from multiprocessing import Lock, Pool
from multiprocessing import Pool

mp.set_start_method("spawn", True) # ! must be at top for VScode debugging

Expand Down Expand Up @@ -38,15 +38,6 @@

from . import base

thread_lock = Lock()


####
def _init_worker_child(lock_):
global lock
lock = lock_


####
def _remove_inst(inst_map, remove_id_list):
"""Remove instances with id in remove_id_list.
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