From: Bernardo TOD <bernardo.tod52@gmail.com>
Date: Thu, 23 May 2019 22:57:29 +0000 (+0200)
Subject: trim image, remove bad black border
X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/myo-class.git/commitdiff_plain/1d3fb87f139a53b55ceb52f3dc2db49ac2b0a0ac

trim image, remove bad black border
---

diff --git a/topng.py b/topng.py
index c9b72d9..0000a58 100644
--- a/topng.py
+++ b/topng.py
@@ -12,10 +12,38 @@ 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/'
+INPUT_DIR = '../../Data/Images_anonymous/Case_0350/'
 OUT_DIR = './generated/'
 #os.mkdir(outdir)
 
+def ftrim(Mat):
+	# private func to trim the Matrix, but in one direction, vertically | horizontally
+	# return the slice, don't affect the Matrix
+	# y | : for column, x -> : for rows
+	#   v
+	# not my fault, numpy architecture
+	y1 = y2 = i = 0
+	while i < len(Mat):# search by top
+		if max(Mat[i]) > 0:
+			y1 = i
+			break
+		i += 1
+	i = len(Mat) - 1
+	while i >= 0:# search by bottom
+		if max(Mat[i]) > 0:
+			y2 = i
+			break
+		i -= 1
+	# print('y1, y2', y1, y2)
+	return slice(y1, y2+1)# +1 to stop at y2
+
+def trim(Mat):
+	# most use who make implicit call of ftrim twice
+	horizontal = ftrim(Mat)
+	vertical = ftrim(Mat.T)
+	# print('horizontal:vertical', horizontal, vertical)
+	return Mat[horizontal, vertical]
+
 def map16(array):# can be useful in future
 	return array * 16
 
@@ -48,11 +76,11 @@ def topng(inputfile, outfile=None, overwrite=True):
 	except pydicom.errors.InvalidDicomError as e:
 		# @TODO: log, i can't read this file
 		return
-	img = dicimg.pixel_array# get image array (12bits)
+	img = trim(dicimg.pixel_array)# get image array (12bits)
 
 	# test <<
 	# return img.shape # $$ COMMENT OR REMOVE THIS LINE 
-	print('img', img)
+	# print('img', img)
 	# print('img', type(img))
 	# print('min', img.min(), 'max', img.max())
 	# dicimg.convert_pixel_data() # same as using dicimg.pixel_array
@@ -62,10 +90,10 @@ def topng(inputfile, outfile=None, overwrite=True):
 	# test >>
 
 	# affine transfo to png 16 bits, func affects img variable
-	maxdepth = img.max()
-	# print('maxdepth, PNG8_MAX', maxdepth, PNG8_MAX) # testing..
+	maxdepth = pow(2, dicimg.BitsStored) - 1
+	print('dicimg.BitsStored, PNG8_MAX', dicimg.BitsStored, PNG8_MAX) # testing..
 	affine(img, 
-		(img.min(), maxdepth),
+		(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)
 	)
 	
@@ -99,5 +127,5 @@ 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+'Image00001', OUT_DIR + INPUT_DIR.split('/')[-2] +'-Image00001')
diff --git a/totraindir.py b/totraindir.py
index 0fead80..8d90c14 100644
--- a/totraindir.py
+++ b/totraindir.py
@@ -9,7 +9,7 @@ from regularjson import search, RT_PATH, JSON_GTS, INFA_STR
 
 # constants
 GLOB_DIR = '../../Data/Images_anonymous/'
-OUT_DIR = './train/'
+OUT_DIR = './generated/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