applied mask horizontally

diff --git a/formatdicom.py b/formatdicom.py
deleted file mode 100644 (file)
index 54aa277..0000000
--- a/formatdicom.py
+++ /dev/null
@@ -1,107 +0,0 @@
-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

diff --git a/regularjson.py b/regularjson.py
index fa89890474bc8079a510dc77b6b43746f061c917..ba7f97e9d1bfe9ce86204d7907e968972fc6707a 100644 (file)
--- a/regularjson.py
+++ b/regularjson.py
@@ -22,6 +22,8 @@ from pprint import pprint
 RT_PATH = '../../Data/json/'
 JSON_GTS = ['json_GT', 'json_GT_part2']
 INFA_STR = 'Infa'
 RT_PATH = '../../Data/json/'
 JSON_GTS = ['json_GT', 'json_GT_part2']
 INFA_STR = 'Infa'

+EPI_STR = 'Epi'
+ENDO_STR = 'Endo'

 
 # Globals
 featurerefs = []
 
 # Globals
 featurerefs = []

diff --git a/topng.py b/topng.py
index 0000a58988c2daea60b800241cbc17080cd69436..8722d98c785f756ab87452b1574fb0d97966fa3c 100644 (file)
--- a/topng.py
+++ b/topng.py
@@ -6,16 +6,20 @@ import pydicom
 from pprint import pprint
 import numpy as np
 import pathlib
 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
 
 
 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)
 
 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
 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
        # 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
                        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
                        y2 = i
                        break
                i -= 1


@@ -44,6 +48,80 @@ def trim(Mat):
        # print('horizontal:vertical', horizontal, vertical)
        return Mat[horizontal, vertical]
 
        # 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 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 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
        """
        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
 
        # 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)
        )
        
        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 ):
        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
        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):
        """
 
 def topngs(inputdir, outdir):
        """


@@ -127,5 +212,5 @@ 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+'Image00003', OUT_DIR + INPUT_DIR.split('/')[-2] +'-Image00003')

diff --git a/totraindir.py b/totraindir.py
index 8d90c144aade6b664502cac42ace7c611de5a8da..1fbaf08481a790594b088fe442c69e71ae9651c8 100644 (file)
--- a/totraindir.py
+++ b/totraindir.py
@@ -4,8 +4,8 @@ import pydicom
 from os.path import join
 
 # locals
 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/'
 
 # constants
 GLOB_DIR = '../../Data/Images_anonymous/'


@@ -68,15 +68,10 @@ if __name__ == '__main__':
                                ref = join(r, l2[i]) # logically, should be the json ref of i dicom image
 
                                infarctus = search(ref, INFA_STR)
                                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 
 
                                # search maximums
                                if wmax < w: wmax = w