+++ /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
from pprint import pprint
import numpy as np
import pathlib
+import json
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_0350/'
+INPUT_DIR = '../../Data/Images_anonymous/Case_0002/'
OUT_DIR = './generated/'
#os.mkdir(outdir)
+def roundall(*l):
+ return (round(e) for e in l)
+
def ftrim(Mat):
# private func to trim the Matrix, but in one direction, vertically | horizontally
# return the slice, don't affect the Matrix
# not my fault, numpy architecture
y1 = y2 = i = 0
while i < len(Mat):# search by top
- if max(Mat[i]) > 0:
+ if Mat[i].max() > 0:
y1 = i
break
i += 1
i = len(Mat) - 1
while i >= 0:# search by bottom
- if max(Mat[i]) > 0:
+ if Mat[i].max() > 0:
y2 = i
break
i -= 1
# print('horizontal:vertical', horizontal, vertical)
return Mat[horizontal, vertical]
+def mask(Mat, maskfile):
+ # return
+ xmin, ymin, xmax, ymax = minmax(Mat, maskfile)
+
+ y1 = y2 = i = 0
+ while i < len(Mat):# search by top
+ if i < ymin:
+ Mat[i].fill(0)# paint the row in black
+ else: break
+ i += 1
+
+ i = len(Mat) - 1
+ while i >= 0:# search by bottom
+ if i > ymax:
+ Mat[i].fill(0)# paint the row in black
+ else: break
+ i -= 1
+ # print('y1, y2', y1, y2)
+ # return slice(y1, y2+1)# +1 to stop at y2
+
+
+
+def minmax(Mat, file):
+ """
+ {
+ 'Image00001': [{
+ 'color': '#ff0000',
+ 'points': [
+ {'x': 94.377, 'y': 137.39},
+ {'x': 100.38, 'y': 139.55},
+ {'x': 103.26, 'y': 142.67},
+ {'x': 105.91, 'y': 147.95},
+ {'x': 105.42, 'y': 152.76},
+ {'x': 100.62, 'y': 156.84},
+ {'x': 95.338, 'y': 159.96},
+ {'x': 89.573, 'y': 158.52},
+ {'x': 84.53, 'y': 153},
+ {'x': 82.848, 'y': 149.15},
+ {'x': 82.368, 'y': 142.91},
+ {'x': 85.01, 'y': 138.11},
+ {'x': 89.813, 'y': 137.39},
+ {'x': 94.377, 'y': 137.39}
+ ]
+ }]
+ }
+ return xmin, ymin, xmax, ymax
+ """
+ with open(file) as jsonfile:
+ data = json.load(jsonfile)
+ pprint(data)
+
+ for imgXXX in data:pass # get the value of key ~= "Image00001", cause it's dynamic
+
+ for obj in data[imgXXX]:pass # get the object that contains the points, cause it's a list
+ points = obj['points']
+
+
+ # print("print, ", data)
+ # print("imgXXX, ", imgXXX)
+ # print("points, ", points)
+ # print("imgXXX, ", obj['points'])
+ tmp = [(pt['x'], pt['y']) for pt in points ] # extract x,y. {'x': 94.377, 'y': 137.39} => (94.377, 137.39)
+ r = np.array(tmp)
+
+ print(r) # log
+
+ xmin, ymin = np.min(r, axis=0)
+ xmax, ymax = np.max(r, axis=0)
+
+ print('xmax, ymax', xmax, ymax)
+ print('xmin, ymin', xmin, ymin)
+
+ return roundall(xmin, ymin, xmax, ymax)
+
def map16(array):# can be useful in future
return array * 16
def getdir(filepath):
return '/'.join(filepath.split('/')[:-1]) + '/'
-def topng(inputfile, outfile=None, overwrite=True):
+def topng(inputfile, outfile=None, overwrite=True, verbose=False):
"""
- return (64, 64) : the width and height
+ (verbose) return (64, 64) : the width and height
+ (not verbose) return (img, dicimg) : the image and the dicimg objects
"""
try:
dicimg = pydicom.read_file(inputfile) # read dicom image
# affine transfo to png 16 bits, func affects img variable
maxdepth = pow(2, dicimg.BitsStored) - 1
- print('dicimg.BitsStored, PNG8_MAX', dicimg.BitsStored, PNG8_MAX) # testing..
+ print('dicimg.BitsStored, (img.min(), img.max())', dicimg.BitsStored, (img.min(), img.max())) # testing..
affine(img,
(0, maxdepth), # img.min() replace 0 may be, but not sure it would be good choice
(0, PNG16_MAX if maxdepth > PNG8_MAX else PNG8_MAX)
)
+ mask(img, '/Users/user/Desktop/Master/Stage/Data/json/json_GT/0_Case_0002/contours/1.2.3.4.5.6/31/-85.9968/Epicardic.json')
+
+
savepath = (outfile or inputfile) + '.png'
savedir = getdir(savepath)
if overwrite and not isdir( savedir ):
cv2.imwrite(savepath, img, [cv2.IMWRITE_PNG_COMPRESSION, 0]) # write png image
# test
- return img.shape
+ if verbose:
+ return img, dicimg
+ else:
+ return img.shape
def topngs(inputdir, outdir):
"""
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')
+ # topngs( INPUT_DIR, join(OUT_DIR, INPUT_DIR.split('/')[-2]) )
+ topng(INPUT_DIR+'Image00003', OUT_DIR + INPUT_DIR.split('/')[-2] +'-Image00003')
from os.path import join
# locals
-from topng import topng
-from regularjson import search, RT_PATH, JSON_GTS, INFA_STR
+from topng import topng, mask
+from regularjson import search, RT_PATH, JSON_GTS, INFA_STR, EPI_STR
# constants
GLOB_DIR = '../../Data/Images_anonymous/'
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..
- w, h = 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..
- w, h = topng(join(caspath, dic), '{}/{}-{}'.format(join(OUT_DIR, 'noinfarctus'), cas, dic))
+ # epimask = mask(ref, EPI_STR)
+ # 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
