X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/myo-class.git/blobdiff_plain/d983932e5a974928a10bbab7e86fdf3e162ae2ae..bdfe02afe03428e59b3c85b6cae19d579d82f55c:/totraindir.py

diff --git a/totraindir.py b/totraindir.py
index 1fbaf08..b901b85 100644
--- a/totraindir.py
+++ b/totraindir.py
@@ -4,12 +4,12 @@ import pydicom
 from os.path import join
 
 # locals
-from topng import topng, mask
-from regularjson import search, RT_PATH, JSON_GTS, INFA_STR, EPI_STR
+from topng import topng, mask, CROP_SIZE
+from regularjson import search, RT_PATH, JSON_GTS, INFA_STR, EPI_STR, ENDO_STR
 
 # constants
 GLOB_DIR = '../../Data/Images_anonymous/'
-OUT_DIR = './generated/train/'
+OUT_DIR = './generated/90/'
 INDICE_CASE = 'Case'
 
 START = None # to manage the number of Patient Case to use in training + validation, if START == None => 0, if END == None => last index, it will use all in GLOB_DIR
@@ -65,27 +65,95 @@ if __name__ == '__main__':
 
 			for i, dic in enumerate(l1):
 				# print('join', r, l2[i])
-				ref = join(r, l2[i]) # logically, should be the json ref of i dicom image
+				ref = join(r, l2[i]) # logically, should be the json ref's "parent directory" of i dicom image
 
 				infarctus = search(ref, INFA_STR)
-				# epimask = mask(ref, EPI_STR)
+				epimask = search(ref, EPI_STR)
+				endomask = search(ref, ENDO_STR)
+				# print("ref left:", l1[i]) # Testing..
+				# print("ref right:", ref) # Testing..
 				# print("infarctus:", infarctus) # Testing..
 				# topng(join(caspath, dic), '%/%-%' % (join(OUT_DIR, 'infarctus'), cas, dic)
-				w, h = topng(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'infarctus' if infarctus else 'noinfarctus'), cas, dic))
-
-				# search maximums
-				if wmax < w: wmax = w 
-				if hmax < h: hmax = h
-
-				# search width minimum
-				if wmin is None: wmin = w
-				elif wmin > w: wmin = w
-				
-				# search height minimum
-				if hmin is None: hmin = h
-				elif hmin > h: hmin = h
-
-	print('min-width, max-width:', (wmin, wmax))
-	print('min-height, max-height:', (hmin, hmax))
-
-	print('Ended!')
+				# print('epimask', epimask)
+
+				if epimask:# this condition could be if necessary
+					# w, h = topng(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'infarctus' if infarctus else 'noinfarctus'), cas, dic), epimask=epimask['path'] if epimask else None)
+					# img_, dicimg_, minmax_ = topng(join(caspath, dic),
+					# 	'{}/{}-{}'.format(join(OUT_DIR, 'infarctus' if infarctus else 'noinfarctus'), cas, dic),
+					# 	epimask=epimask['path'] if epimask else None,
+					# 	verbose=True,
+					# )
+
+					# Possibly data augmentation purpose here
+					w, h = topng(
+						join(caspath, dic),
+						outfile='{}/crop-mask/{}-{}'.format(join(OUT_DIR,
+							'infarctus' if infarctus else 'noinfarctus'),
+							cas,
+							dic,
+						),
+						epimask=epimask['path'] if epimask else None,
+						centercrop=CROP_SIZE,
+						blackmask=True,
+					) # crop and mask with black
+
+					if endomask:
+						w, h = topng(
+							join(caspath, dic),
+							outfile='{}/crop-mask-hollow/{}-{}'.format(join(OUT_DIR,
+								'infarctus' if infarctus else 'noinfarctus'),
+								cas,
+								dic,
+							),
+							epimask=epimask['path'] if epimask else None,
+							endomask=endomask['path'] if endomask else None,
+							centercrop=CROP_SIZE,
+							blackmask=True,
+						) # crop and (mask and fill hollow) with black
+
+					w, h = topng(
+						join(caspath, dic),
+						outfile='{}/crop-nomask/{}-{}'.format(join(OUT_DIR,
+							'infarctus' if infarctus else 'noinfarctus'),
+							cas,
+							dic,
+						),
+						epimask=epimask['path'] if epimask else None,
+						centercrop=CROP_SIZE,
+					) # just crop, don't apply black mask
+
+					# w, h = topng(
+					# 	join(caspath, dic),
+					# 	outfile='{}/contour/{}-{}'.format(join(OUT_DIR,
+					# 		'infarctus' if infarctus else 'noinfarctus'),
+					# 		cas,
+					# 		dic,
+					# 	),
+					# 	epimask=epimask['path'] if epimask else None,
+					# 	redcontour=True,
+					# ) # draw a red contour for visibily purpose
+
+					# segmentation width & height <<
+					# xmin, ymin, xmax, ymax = minmax_
+					# w = xmax - xmin + 1 # +1 : even the position takes a bit
+					# h = ymax - ymin + 1
+					# segmentation width & height >>
+
+
+					# # search maximums
+					# if wmax < w: wmax = w 
+					# if hmax < h: hmax = h
+
+					# # search width minimum
+					# if wmin is None: wmin = w
+					# elif wmin > w: wmin = w
+					
+					# # search height minimum
+					# if hmin is None: hmin = h
+					# elif hmin > h: hmin = h
+
+
+	# print('min-width, max-width:', (wmin, wmax))
+	# print('min-height, max-height:', (hmin, hmax))
+
+	# print('Ended!')