integrate distinction_word, for deployment

[myo-class.git] / totraindir.py

diff --git a/totraindir.py b/totraindir.py
index 1fbaf08481a790594b088fe442c69e71ae9651c8..b901b85bb7ea34c22bf7730eb83f58f8327e717d 100644 (file)
--- a/totraindir.py
+++ b/totraindir.py
@@ -4,12 +4,12 @@ import pydicom
 from os.path import join
 
 # locals
 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/'
 
 # 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
 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])
 
                        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)
 
                                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)
                                # 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!')