totraindir.py

   1 from os import listdir as ls
   2 import png
   3 import pydicom
   4 from os.path import join
   5
   6 # locals
   7 from topng import topng, mask, CROP_SIZE
   8 from regularjson import search, RT_PATH, JSON_GTS, INFA_STR, EPI_STR, ENDO_STR
   9
  10 # constants
  11 GLOB_DIR = '../../Data/Images_anonymous/'
  12 OUT_DIR = './generated/90/'
  13 INDICE_CASE = 'Case'
  14
  15 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
  16 END = None
  17
  18
  19 def get(l, i, r):
  20         if len(l) <= 1:
  21                 return sorted( ls(r) )
  22
  23 if __name__ == '__main__':
  24         l = sorted(ls(GLOB_DIR))
  25
  26         # Initiliaze
  27         wmin = hmin = None # None is important here, confert the 'minimum' algo
  28         wmax = hmax = w = h = 0
  29
  30         for cas in l[START:END]:# cas like 'Case0002'
  31                 caspath = join(GLOB_DIR, cas)
  32
  33                 if not INDICE_CASE in cas:# if the directory name doesn't sound familiar
  34                         continue
  35
  36                 l1 = sorted( ls( caspath ) )# just ls one CaseXXXX and sort the result
  37                 # $$NOTRUSTREF here we need to sort because there is no trusted ref or id
  38
  39                 r = search(RT_PATH, cas)
  40
  41                 print(cas, end=' ', flush=True) # log CaseXXXX
  42
  43                 if not r: # if the feature doesn't yet labeled by an expert go to next
  44                         continue
  45                 r = search(r['path'], '.') # to be more dynamic, here can just be '.' instead of '1.2.3.4.5.6'
  46
  47                 if r:
  48                         r = r['path']
  49                         try:
  50                                 l2 = sorted( ls(r) ) # $$NOTRUSTREF
  51                         except NotADirectoryError as e:
  52                                 print("WARN", "a file in unexcepted place")
  53                                 continue
  54
  55                         if 0 < len(l2) < len(l1):
  56                                 r = join(r, l2[0])
  57                                 l2 = sorted( ls(r) ) # $$NOTRUSTREF
  58                                 # Try once : check subdirectory if i'am not the right
  59
  60                         if 0 < len(l2) < len(l1):
  61                                 # TODO: log, json doesn't match with images (labels != features)
  62                                 print("WARN", "json doesn't match with images (labels != features), Case", cas)
  63                                 continue
  64                                 pass
  65
  66                         for i, dic in enumerate(l1):
  67                                 # print('join', r, l2[i])
  68                                 ref = join(r, l2[i]) # logically, should be the json ref's "parent directory" of i dicom image
  69
  70                                 infarctus = search(ref, INFA_STR)
  71                                 epimask = search(ref, EPI_STR)
  72                                 endomask = search(ref, ENDO_STR)
  73                                 # print("ref left:", l1[i]) # Testing..
  74                                 # print("ref right:", ref) # Testing..
  75                                 # print("infarctus:", infarctus) # Testing..
  76                                 # topng(join(caspath, dic), '%/%-%' % (join(OUT_DIR, 'infarctus'), cas, dic)
  77                                 # print('epimask', epimask)
  78
  79                                 if epimask:# this condition could be if necessary
  80                                         # w, h = topng(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'infarctus' if infarctus else 'noinfarctus'), cas, dic), epimask=epimask['path'] if epimask else None)
  81                                         # img_, dicimg_, minmax_ = topng(join(caspath, dic),
  82                                         #       '{}/{}-{}'.format(join(OUT_DIR, 'infarctus' if infarctus else 'noinfarctus'), cas, dic),
  83                                         #       epimask=epimask['path'] if epimask else None,
  84                                         #       verbose=True,
  85                                         # )
  86
  87                                         # Possibly data augmentation purpose here
  88                                         w, h = topng(
  89                                                 join(caspath, dic),
  90                                                 outfile='{}/crop-mask/{}-{}'.format(join(OUT_DIR,
  91                                                         'infarctus' if infarctus else 'noinfarctus'),
  92                                                         cas,
  93                                                         dic,
  94                                                 ),
  95                                                 epimask=epimask['path'] if epimask else None,
  96                                                 centercrop=CROP_SIZE,
  97                                                 blackmask=True,
  98                                         ) # crop and mask with black
  99
 100                                         if endomask:
 101                                                 w, h = topng(
 102                                                         join(caspath, dic),
 103                                                         outfile='{}/crop-mask-hollow/{}-{}'.format(join(OUT_DIR,
 104                                                                 'infarctus' if infarctus else 'noinfarctus'),
 105                                                                 cas,
 106                                                                 dic,
 107                                                         ),
 108                                                         epimask=epimask['path'] if epimask else None,
 109                                                         endomask=endomask['path'] if endomask else None,
 110                                                         centercrop=CROP_SIZE,
 111                                                         blackmask=True,
 112                                                 ) # crop and (mask and fill hollow) with black
 113
 114                                         w, h = topng(
 115                                                 join(caspath, dic),
 116                                                 outfile='{}/crop-nomask/{}-{}'.format(join(OUT_DIR,
 117                                                         'infarctus' if infarctus else 'noinfarctus'),
 118                                                         cas,
 119                                                         dic,
 120                                                 ),
 121                                                 epimask=epimask['path'] if epimask else None,
 122                                                 centercrop=CROP_SIZE,
 123                                         ) # just crop, don't apply black mask
 124
 125                                         # w, h = topng(
 126                                         #       join(caspath, dic),
 127                                         #       outfile='{}/contour/{}-{}'.format(join(OUT_DIR,
 128                                         #               'infarctus' if infarctus else 'noinfarctus'),
 129                                         #               cas,
 130                                         #               dic,
 131                                         #       ),
 132                                         #       epimask=epimask['path'] if epimask else None,
 133                                         #       redcontour=True,
 134                                         # ) # draw a red contour for visibily purpose
 135
 136                                         # segmentation width & height <<
 137                                         # xmin, ymin, xmax, ymax = minmax_
 138                                         # w = xmax - xmin + 1 # +1 : even the position takes a bit
 139                                         # h = ymax - ymin + 1
 140                                         # segmentation width & height >>
 141
 142
 143                                         # # search maximums
 144                                         # if wmax < w: wmax = w
 145                                         # if hmax < h: hmax = h
 146
 147                                         # # search width minimum
 148                                         # if wmin is None: wmin = w
 149                                         # elif wmin > w: wmin = w
 150
 151                                         # # search height minimum
 152                                         # if hmin is None: hmin = h
 153                                         # elif hmin > h: hmin = h
 154
 155
 156         # print('min-width, max-width:', (wmin, wmax))
 157         # print('min-height, max-height:', (hmin, hmax))
 158
 159         # print('Ended!')