trim image, remove bad black border

diff --git a/topng.py b/topng.py
index c9b72d963fb31594be3d1a350daf771c956c4873..0000a58988c2daea60b800241cbc17080cd69436 100644 (file)
--- 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
 
 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)
 
 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
 
 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
        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 
 
        # 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
        # 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
        # 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, 
        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)
        )
        
                (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__':
                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 0fead801d5287346787cd7bb35ed8bf44b9a27f3..8d90c144aade6b664502cac42ace7c611de5a8da 100644 (file)
--- 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/'
 
 # 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
 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