X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/myo-class.git/blobdiff_plain/c67ab60de95008178e26817946990382751d91d8..refs/heads/master:/totraindir.py

diff --git a/totraindir.py b/totraindir.py
index 4917b56..374eb84 100644
--- a/totraindir.py
+++ b/totraindir.py
@@ -1,20 +1,46 @@
 from os import listdir as ls
 import png
 import pydicom
-from os.path import join
+from os.path import join, dirname
 
 # locals
-from topng import topng
-from regularjson import search, RT_PATH, JSON_GTS, INFA_STR
+from topng import topng, getimgname, mask, CROP_SIZE, EPI_MIN_PIXELS
+from regularjson import search, RT_PATH, INFA_STR, EPI_STR, ENDO_STR
 
 # constants
 GLOB_DIR = '../../Data/Images_anonymous/'
-OUT_DIR = './train/'
+OUT_DIR = './generated/updated/'
 INDICE_CASE = 'Case'
+PREFIX = '0_' # => 0_Case0002
+
+BLACK_LIST_CASES = [
+	'Case_0258', 'Case_0259',
+	'Case_0265', 'Case_0266', 'Case_0300', 'Case_0305',
+	'Case_0311', 'Case_0316',
+	'Case_0320', 'Case_0322', 'Case_0325', 'Case_0326', 'Case_0327',
+	'Case_0328', 'Case_0329', 'Case_0337', 'Case_0338', 'Case_0345',
+	'Case_0346', 'Case_0348', 'Case_0359', 'Case_0360', 'Case_0361',
+	'Case_0362', 'Case_0363', 'Case_0364', 'Case_0365', 'Case_0366',
+	'Case_0367', 'Case_0381', 'Case_0385', 'Case_0400', 'Case_0401', 'Case_0415', 'Case_0416',
+	'Case_0421','Case_0423', 'Case_0429', 'Case_0442', 'Case_0444', 'Case_0474',
+]
+
+BLACK_LIST_IMAGES = ['Case_0229-Image00002', 'Case_0229-Image00004', 'Case_0229-Image00006', 'Case_0229-Image00007',
+	'Case_0243-Image00003.png', 'Case_0243-Image00004', 'Case_0243-Image00005', 'Case_0265-Image00001', 'Case_0262-Image00007',
+	'Case_0262-Image00008', 'Case_0264-Image00006', 'Case_0275-Image00006',
+	'Case_0307-Image00006', 'Case_0314-Image00001', 'Case_0314-Image00002',
+	'Case_0314-Image00008', 'Case_0315-Image00005', 'Case_0321-Image00007',
+	'Case_0321-Image00008', 'Case_0328-Image00002',
+	'Case_0331-I7000000',
+	'Case_0356-Image00007', 'Case_0356-Image00008', 'Case_0356-Image00009', 'Case_0356-Image00009',
+	'Case_0358-Image00008', 'Case_0358-Image00009',
+	'Case_0377-Image00009', 
+]
 
 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
-END = None
-
+END = None # like Case_420, to generate just a part of the dataset
+END_INF_CASES = 309 # to manage correct case with infarctus
+END_NOINF_CASES = None # to manage correct case with noinfarctus
 
 def get(l, i, r):
 	if len(l) <= 1:
@@ -22,56 +48,195 @@ def get(l, i, r):
 
 if __name__ == '__main__':
 	l = sorted(ls(GLOB_DIR))
-	for cas in l[START:END]:# cas like 'Case0002'
+
+	# print("log", l)
+	# exit()
+
+	# Initiliaze 
+	wmin = hmin = None # None is important here, confert the 'minimum' algo
+	wmax = hmax = w = h = 0
+
+	for j, cas in enumerate(l[START:END]):# cas like 'Case0002'
 		caspath = join(GLOB_DIR, cas)
 
-		if not INDICE_CASE in cas:# if the directory name doesn't sound familiar
+		if not INDICE_CASE in cas: # if the directory name doesn't sound familiar
+			continue
+
+		if cas in BLACK_LIST_CASES: # if the directory was black listed
 			continue
 
 		l1 = sorted( ls( caspath ) )# just ls one CaseXXXX and sort the result
 		# $$NOTRUSTREF here we need to sort because there is no trusted ref or id
 
-		r = search(RT_PATH, cas)
+		# print('RT_PATH', RT_PATH)
+		# print('PREFIX + cas', PREFIX + cas)
+		r = search(RT_PATH, PREFIX + cas)
+		# print('r', r)
 
 		print(cas, end=' ', flush=True) # log CaseXXXX
 
 		if not r: # if the feature doesn't yet labeled by an expert go to next
 			continue
-		r = search(r['path'], '.') # to be more dynamic, here can just be '.' instead of '1.2.3.4.5.6'
+
+		# ------<< Searching for .json files
+		r = search(r['path'], 'contours') # contours/1.2.3.4.5.6
+		if not r:
+			continue
+		r = search(r['path'], '1.2.3.4.5.6') # to be more dynamic, here can just be '.' instead of '1.2.3.4.5.6'
+		# ------>>
 
 		if r:
 			r = r['path']
+			# print('ls(r)', ls(r))
 			try:
 				l2 = sorted( ls(r) ) # $$NOTRUSTREF
 			except NotADirectoryError as e:
 				print("WARN", "a file in unexcepted place")
 				continue
 
-			if 0 < len(l2) < len(l1):
+			# IF THIS KIND OF ERROR OCCURS, CHANGE ON DISK TO GET IT CONFORMED
+			if 1 == len(l2) < len(l1): # l2 == ["37"] and l1 == ["image001", "image002"..], may be "37" contains searched dirs, so enter..
 				r = join(r, l2[0])
 				l2 = sorted( ls(r) ) # $$NOTRUSTREF
 				# Try once : check subdirectory if i'am not the right
 
-			if 0 < len(l2) < len(l1):
-				# TODO: log, json doesn't match with images (labels != features)
-				print("WARN", "json doesn't match with images (labels != features), Case", cas)
-				continue
-				pass
+			# if 0 < len(l2) < len(l1):
+			# 	# TODO: log, json doesn't match with images (labels != features)
+			# 	print("WARN", "json doesn't match with images (labels != features), Case", cas)
+			# 	continue
+			# 	pass
+
+			for i, dic in enumerate(l1): # l1 => ["image001", "image002"], l2 => ["37", "42"]
+				if True:
+					if "{}-{}".format(cas, dic) in BLACK_LIST_IMAGES: # if image was black listed
+						continue
+
+					epimask = ''
+					infarctus = ''
+					endomask = ''
+					# debug <<
+					# infarctus = True
+					# debug >>
+					# search the right json, for that, we open the json
+					for elt in l2:
+						# print('join', r, l2[i])
+						ref = join(r, elt) # logically, should be the json ref's "parent directory" of i dicom image
+
+						t_epimask = search(ref, EPI_STR)
+
+						parent = dirname(ref) # get the parent dir
+
+						infarctus = search(parent, INFA_STR)
+						endomask = search(parent, ENDO_STR)
+
+						if t_epimask and t_epimask.get("path"):
+							timgname = getimgname(t_epimask["path"])
 
+							if timgname == dic:
+								epimask = t_epimask
+								break
+						else:
+							print('no epicardic')
 
-			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
 
-				infarctus = search(ref, INFA_STR)
-				if infarctus:
+					# 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)
-					# print(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'infarctus'), cas, dic)) # Testing..
-					topng(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'infarctus'), cas, dic))
-				else:
-					# print("no infarctus:", infarctus) # Testing..
-					# print(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'noinfarctus'), cas, dic)) # Testing..
-					topng(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'noinfarctus'), cas, dic))
-
-	print('Ended!')
\ No newline at end of file
+					# print('epimask', epimask)
+
+					# debug <<
+					# epimask = False
+					# debug >>
+
+					if epimask:# this condition could be if necessary
+						if infarctus and (END_INF_CASES is not None) and j > END_INF_CASES:
+							continue
+						if not infarctus and (END_NOINF_CASES is not None) and j > END_NOINF_CASES:
+							continue
+						# 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
+						print("EPI_MIN_PIXELS", EPI_MIN_PIXELS)
+						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,
+							epiminpixels=EPI_MIN_PIXELS
+						) # crop and mask with black
+
+						# if endomask:
+						# 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
+
+						# 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 = BE CAREFULL, be sure w, h is needed, and that topng returns something
+						# 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
+				# except Exception as e:
+				# 	print("WARN", "something went wrong with this image", dic, str(e))
+				# 	continue
+
+
+	# print('min-width, max-width:', (wmin, wmax))
+	# print('min-height, max-height:', (hmin, hmax))
+
+	# print('Ended!')