X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/myo-class.git/blobdiff_plain/1d3fb87f139a53b55ceb52f3dc2db49ac2b0a0ac..d983932e5a974928a10bbab7e86fdf3e162ae2ae:/topng.py?ds=inline

diff --git a/topng.py b/topng.py
index 0000a58..8722d98 100644
--- a/topng.py
+++ b/topng.py
@@ -6,16 +6,20 @@ import pydicom
 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
@@ -24,13 +28,13 @@ def ftrim(Mat):
 	# 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
@@ -44,6 +48,80 @@ def trim(Mat):
 	# 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
 
@@ -67,9 +145,10 @@ def affine(Mat, ab, cd):
 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
@@ -91,12 +170,15 @@ def topng(inputfile, outfile=None, overwrite=True):
 
 	# 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 ):
@@ -115,7 +197,10 @@ def topng(inputfile, outfile=None, overwrite=True):
 	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):
 	"""
@@ -127,5 +212,5 @@ 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')