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changed order of imports and fixed case_name #2

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changed order of imports and fixed case_name #2

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23 changes: 13 additions & 10 deletions extractTiles-ws.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,11 @@

# Requires: Openslide (https://openslide.org/download/)

from multiprocessing.dummy import Pool as ThreadPool
from os.path import join, isfile, exists
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from multiprocessing.dummy import Pool as ThreadPool
from os.path import join, isfile, exists

import os
import progressbar
Expand Down Expand Up @@ -118,8 +118,8 @@ def __init__(self, path, filetype, export_folder = None, pb = None):
return None

thumbs_path = join(export_folder, "thumbs")
if not os.path.exists(thumbs_path):
os.makedirs(thumbs_path)
#if not os.path.exists(thumbs_path):
# os.makedirs(thumbs_path)

# Load ROIs if available
roi_path_csv = self.basename + ".csv"
Expand Down Expand Up @@ -221,7 +221,7 @@ def generator():
else:
exportFlag = export

if exportFlag:
if exportFlag:
imageio.imwrite(join(tiles_path, case_name +'_('+str(c[0])+','+str(c[1])+').jpg'), region)
if augment:
imageio.imwrite(join(tiles_path, case_name +'_('+str(c[0])+','+str(c[1])+')._aug1.jpg'), np.rot90(region))
Expand Down Expand Up @@ -321,10 +321,10 @@ def export_tiles(self, slide, pb, ignoredFile_list):
case_name = slide['name']
category = slide['category']
path = slide['path']

filetype = slide['type']
self.iterator = self.iterator + 1
whole_slide = SlideReader(path, filetype, self.SAVE_FOLDER, pb=pb)

if not whole_slide.has_anno and self.skipws:
return

Expand All @@ -338,9 +338,11 @@ def export_tiles(self, slide, pb, ignoredFile_list):
if not os.path.exists(tiles_path):
os.makedirs(tiles_path)

tiles_path = tiles_path + '/' + case_name



tiles_path = tiles_path + '/' + case_name

case_name = "/".join(case_name.strip("/").split('/')[1:]) #This removes the first sub-path in the case_name. There may be a better way to do this.

if not os.path.exists(tiles_path):
os.makedirs(tiles_path)

Expand Down Expand Up @@ -383,7 +385,8 @@ def get_args():
return parser.parse_args()

###############################################################################



if __name__ == ('__main__'):

args = get_args()
Expand Down