X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/myo-class.git/blobdiff_plain/bdfe02afe03428e59b3c85b6cae19d579d82f55c..refs/heads/master:/totraindir.py diff --git a/totraindir.py b/totraindir.py index b901b85..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, mask, CROP_SIZE -from regularjson import search, RT_PATH, JSON_GTS, INFA_STR, EPI_STR, ENDO_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 = './generated/90/' +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: @@ -23,134 +49,191 @@ def get(l, i, r): if __name__ == '__main__': l = sorted(ls(GLOB_DIR)) + # print("log", l) + # exit() + # Initiliaze wmin = hmin = None # None is important here, confert the 'minimum' algo wmax = hmax = w = h = 0 - for cas in l[START:END]:# cas like 'Case0002' + 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 - - for i, dic in enumerate(l1): - # print('join', r, l2[i]) - ref = join(r, l2[i]) # logically, should be the json ref's "parent directory" of i dicom image - - infarctus = search(ref, INFA_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('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( + # 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') + + + # 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('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-hollow/{}-{}'.format(join(OUT_DIR, + outfile='{}/crop-mask/{}-{}'.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 + 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))