--- /dev/null
+import os
+import png
+import dicom
+import argparse
+
+
+def mri_to_png(mri_file, png_file):
+ """ Function to convert from a DICOM image to png
+
+ @param mri_file: An opened file like object to read te dicom data
+ @param png_file: An opened file like object to write the png data
+ """
+
+ # Extracting data from the mri file
+ plan = dicom.read_file(mri_file)
+ shape = plan.pixel_array.shape
+
+ image_2d = []
+ max_val = 0
+ for row in plan.pixel_array:
+ pixels = []
+ for col in row:
+ pixels.append(col)
+ if col > max_val: max_val = col
+ image_2d.append(pixels)
+
+ # Rescaling grey scale between 0-255
+ image_2d_scaled = []
+ for row in image_2d:
+ row_scaled = []
+ for col in row:
+ col_scaled = int((float(col) / float(max_val)) * 255.0)
+ row_scaled.append(col_scaled)
+ image_2d_scaled.append(row_scaled)
+
+ # Writing the PNG file
+ w = png.Writer(shape[0], shape[1], greyscale=True)
+ w.write(png_file, image_2d_scaled)
+
+
+def convert_file(mri_file_path, png_file_path):
+ """ Function to convert an MRI binary file to a
+ PNG image file.
+
+ @param mri_file_path: Full path to the mri file
+ @param png_file_path: Fill path to the png file
+ """
+
+ # Making sure that the mri file exists
+ if not os.path.exists(mri_file_path):
+ raise Exception('File "%s" does not exists' % mri_file_path)
+
+ # Making sure the png file does not exist
+ if os.path.exists(png_file_path):
+ raise Exception('File "%s" already exists' % png_file_path)
+
+ mri_file = open(mri_file_path, 'rb')
+ png_file = open(png_file_path, 'wb')
+
+ mri_to_png(mri_file, png_file)
+
+ png_file.close()
+
+
+def convert_folder(mri_folder, png_folder):
+ """ Convert all MRI files in a folder to png files
+ in a destination folder
+ """
+
+ # Create the folder for the pnd directory structure
+ os.makedirs(png_folder)
+
+ # Recursively traverse all sub-folders in the path
+ for mri_sub_folder, subdirs, files in os.walk(mri_folder):
+ for mri_file in os.listdir(mri_sub_folder):
+ mri_file_path = os.path.join(mri_sub_folder, mri_file)
+
+ # Make sure path is an actual file
+ if os.path.isfile(mri_file_path):
+
+ # Replicate the original file structure
+ rel_path = os.path.relpath(mri_sub_folder, mri_folder)
+ png_folder_path = os.path.join(png_folder, rel_path)
+ if not os.path.exists(png_folder_path):
+ os.makedirs(png_folder_path)
+ png_file_path = os.path.join(png_folder_path, '%s.png' % mri_file)
+
+ try:
+ # Convert the actual file
+ convert_file(mri_file_path, png_file_path)
+ print('SUCCESS>', mri_file_path, '-->', png_file_path)
+ except Exception as e:
+ print('FAIL>', mri_file_path, '-->', png_file_path, ':', e)
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description="Convert a dicom MRI file to png")
+ parser.add_argument('-f', action='store_true')
+ parser.add_argument('dicom_path', help='Full path to the mri file')
+ parser.add_argument('png_path', help='Full path to the generated png file')
+
+ args = parser.parse_args()
+ print(args)
+ if args.f:
+ convert_folder(args.dicom_path, args.png_path)
+ else:
+ convert_file(args.dicom_path, args.png_path)
\ No newline at end of file
--- /dev/null
+def getdir(filepath):
+ return '/'.join(filepath.split('/')[:-1]) + '/'
--- /dev/null
+# ---------- README
+
+# Edit constants in regularjson.py file, and execute it
+python3 regularjson.py
+
+# Edit constants in totraindir.py file, and execute it
+python3 totraindir.py
+
+# Edit paths in tosample.py file, and execute it
+python3 tosample.py
\ No newline at end of file
--- /dev/null
+"""
+by @res
+
+1) Read -R json_GT* and recup "Feature Refs" & labels (0: Infarctus, 1: No
+2) store "Feature Refs" & labels
+ Format:
+ {
+ nb_infarct: 2,
+ infarcts: [],
+ no_infarcts: [],
+ }
+"""
+from os import listdir as ls
+from os.path import getsize as size, join
+from pprint import pprint
+
+
+# constants
+# json
+# |--> json_GT
+# |--> json_GT_part2
+RT_PATH = '../../Data/json/'
+JSON_GTS = ['json_GT', 'json_GT_part2']
+INFA_STR = 'Infa'
+
+# Globals
+featurerefs = []
+labellist = []
+details = []
+
+from os.path import isfile, join
+
+def search(path, name, recursive=True, fsize=True):
+ """
+ :param path:
+ :param name:
+ :param recursive: Recursive or not
+ :param fsize: show the size of not
+ :return: {path: p, size: None}
+ """
+ for d in ls(path):
+ p = join(path, d)
+ if name in d:
+ return {'path': p, 'size': size(p) if fsize else None}
+ elif recursive and not isfile(p):# only enter if it's a directory
+ res = search(p, name)# stop if found
+ if res:
+ return res
+
+def merge(dirlist, root='', indice='Case'):
+ l = []
+ for d in dirlist:
+ l += [e for e in ls(join(root, d)) if indice in e]
+
+ return sorted(l)
+
+def mergejsons():
+ return merge(JSON_GTS, RT_PATH)
+
+def featurerefs():
+ """
+ fill l with features references
+ use JSON_GTS, a little bit static in this sens
+ :return:
+ """
+ global featurerefs
+ # for d in JSON_GTS:
+ # #frefs += ls(RT_PATH + d)
+ # featurerefs += [e for e in ls(join(RT_PATH, d)) if "Case" in e]
+
+ featurerefs = sorted(mergejsons())
+
+def label(fref):
+ res = search(RT_PATH, fref)
+ b = search(res['path'], INFA_STR)
+ return (0, b['size']) if b else (1, None)
+
+def labels():
+ global labellist, details
+ for name in featurerefs:
+ lab, detail = label(name)
+ labellist.append(lab)
+ details.append(detail)
+
+
+
+if __name__ == '__main__':
+ featurerefs()
+ labels()
+
+ print('featurerefs:', len(featurerefs), featurerefs)
+ print('labels:', len(labellist), labellist)
+ print('details:', len(details), details)
+
+ # print( label('Case_02') )
+ # print( search(RT_PATH, INFA_STR) )
+
+
+
--- /dev/null
+import cv2
+import os
+from os.path import isdir, join
+from os import mkdir
+import pydicom
+from pprint import pprint
+import numpy as np
+import pathlib
+
+from decimal import Decimal as d, ROUND_HALF_UP as rhu
+
+PNG16_MAX = pow(2, 16) - 1 # here if thinks the heaviest weight bit is for transparency or something not in use with dicom imgs
+PNG8_MAX = pow(2, 8+1) - 1 # heaviest weight bit is 8 => 2**8, but dont forget the others: the reason of +1
+
+INPUT_DIR = '../../Data/Images_anonymous/Case_0449/'
+OUT_DIR = './generated/'
+#os.mkdir(outdir)
+
+def map16(array):# can be useful in future
+ return array * 16
+
+# def dround(n):
+# return d(str(n)).quantize(d('1'), rounding=rhu)# safe round without
+
+def affine(Mat, ab, cd):
+ """
+ Affine transformation
+ ab: the 'from' interval (2, 384) or {begin:2, end:384} begin is 0, and end is 1
+ cd: the 'to' interval (0, 1024) {begin:0, end:1024}
+ """
+ a, b = ab[0], ab[1]
+ c, d = cd[0], cd[1]
+
+ with np.nditer(Mat, op_flags=['readwrite']) as M:
+ for x in M:
+ x[...] = max( 0, round( (x-a) * (d-c) / (b-a) + c ) ) # could not be negative
+
+
+def getdir(filepath):
+ return '/'.join(filepath.split('/')[:-1]) + '/'
+
+def topng(inputfile, outfile=None, overwrite=True):
+ try:
+ dicimg = pydicom.read_file(inputfile) # read dicom image
+ except pydicom.errors.InvalidDicomError as e:
+ # @TODO: log, i can't read this file
+ return
+ img = dicimg.pixel_array# get image array (12bits)
+
+ # test <<
+ print('img', img)
+ # print('img', type(img))
+ # print('min', img.min(), 'max', img.max())
+ # dicimg.convert_pixel_data() # same as using dicimg.pixel_array
+ # pixa = dicimg._pixel_array
+ # print('dicimg._pixel_array', pixa)
+ # print('dicimg.pixel_array==pixa', dicimg.pixel_array==pixa)
+ # test >>
+
+ # affine transfo to png 16 bits, func affects img variable
+ maxdepth = img.max()
+ # print('maxdepth, PNG8_MAX', maxdepth, PNG8_MAX) # testing..
+ affine(img,
+ (img.min(), maxdepth),
+ (0, PNG16_MAX if maxdepth > PNG8_MAX else PNG8_MAX)
+ )
+
+ savepath = (outfile or inputfile) + '.png'
+ savedir = getdir(savepath)
+ if overwrite and not isdir( savedir ):
+ pathlib.Path(savedir).mkdir(parents=True, exist_ok=True)
+
+
+ # test <<
+ # tmp = np.array(img) # to get eye on the numpy format of img
+ # tmp = np.array(img) # to get eye on the numpy format of img
+ # print("img[0,0]", img[0,0])
+ # img[0,0] = 0
+ # tmp.dtype = 'uint32'
+ # np.savetxt(savepath + '.npy', img)
+ # test >>
+
+ cv2.imwrite(savepath, img, [cv2.IMWRITE_PNG_COMPRESSION, 0]) # write png image
+
+
+def topngs(inputdir, outdir):
+ """
+ inputdir : directory which contains directly dicom files
+ """
+ files = [f for f in os.listdir(inputdir)]
+
+ for f in files:
+ topng( inputdir + f, join(outdir, f) )
+
+if __name__ == '__main__':
+ # topngs( INPUT_DIR, join(OUT_DIR, INPUT_DIR.split('/')[-2]) )
+ topng(INPUT_DIR+'Image00001', OUT_DIR + INPUT_DIR.split('/')[-2] +'-Image00001')
--- /dev/null
+from os import listdir as ls
+from os.path import join
+from shutil import move as mv
+import pathlib
+
+def move(indir, outdir, n):# move n ordered files from indir to outdir
+ l = sorted(ls(indir))
+ for filename in l[:n]:
+ # print(join(indir, filename), join(outdir, filename))
+ pathlib.Path(outdir).mkdir(parents=True, exist_ok=True)
+ mv(join(indir, filename), join(outdir, filename))
+
+if __name__ == '__main__':
+
+ move('./train/infarctus', './sample/train/infarctus', 1000) # move 1000 ordered files from param 1 to param 2
+ move('./train/noinfarctus', './sample/train/noinfarctus', 1000)
+ move('./train/infarctus', './sample/valid/infarctus', 300)
+ move('./train/noinfarctus', './sample/valid/noinfarctus', 300)
\ No newline at end of file
--- /dev/null
+from os import listdir as ls
+import png
+import pydicom
+from os.path import join
+
+# locals
+from topng import topng
+from regularjson import search, RT_PATH, JSON_GTS, INFA_STR
+
+# constants
+GLOB_DIR = '../../Data/Images_anonymous/'
+OUT_DIR = './train/'
+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
+END = None
+
+
+def get(l, i, r):
+ if len(l) <= 1:
+ return sorted( ls(r) )
+
+if __name__ == '__main__':
+ l = sorted(ls(GLOB_DIR))
+ for cas in 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
+ continue
+
+ l1 = sorted( ls( caspath ) )# just ls one CaseXXXX and sort the result
+ # $$NOTRUSTREF here we need to sort because there is no trusted ref or id
+
+ r = search(RT_PATH, cas)
+
+ print(cas, end=' ', flush=True) # log CaseXXXX
+
+ if not r: # if the feature doesn't yet labeled by an expert go to next
+ continue
+ r = search(r['path'], '.') # to be more dynamic, here can just be '.' instead of '1.2.3.4.5.6'
+
+ if r:
+ r = r['path']
+ try:
+ l2 = sorted( ls(r) ) # $$NOTRUSTREF
+ except NotADirectoryError as e:
+ print("WARN", "a file in unexcepted place")
+ continue
+
+ if 0 < len(l2) < len(l1):
+ 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 of i dicom image
+
+ infarctus = search(ref, INFA_STR)
+ if infarctus:
+ # 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
