CLEtools/MKTreader.py at master · maubreville/CLEtools · GitHub

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#!/usr/bin/env python

"""MKTreader.py: Read MKT (Cellvizio) raw files."""
__author__ = "Marc Aubreville"
__license__ = "GPL"
__version__ = "0.0.1"

import numpy as np
import struct
from os import stat
from auxfiles import circularMask

class fileinfo:
    offset = 16 # 16 byte header
    gapBetweenImages = 32
    size = 0
    width = 0
    height = 0
    nImages = 0
    circMask = 0;

class MKTreader:
    fileName = ''
    fileHandle = 0
    fi = fileinfo()

    def __init__(self,filename):
       self.fileName = filename;
       self.fileHandle = open(filename, 'rb');

       self.fileHandle.seek(5) # we find the FPS at position 05
       fFPSByte = self.fileHandle.read(4)
       self.fps = struct.unpack('>f', fFPSByte)[0]
       print('FPS: '+str(self.fps))

       self.fileHandle.seek(10) # we find the image size at position 10
       fSizeByte = self.fileHandle.read(4)
       self.fi.size = int.from_bytes(fSizeByte, byteorder='big', signed=True)
       self.fi.nImages=1000
       print("Image size: "+str(self.fi.size)+ " bytes")

       self.fi.width = 576
       if ((self.fi.size/(2*self.fi.width))%2!=0):
            self.fi.width=512
            self.fi.height=int(self.fi.size/(2*self.fi.width))
       else:
            self.fi.height=int(self.fi.size/(2*self.fi.width))

       print("Resolution is " +str(self.fi.width) + " x " + str(self.fi.height))

       filestats = stat(self.fileName)

       self.fi.nImages = int(filestats.st_size / (self.fi.size))
       print("Number of images "+str(self.fi.nImages))

       # generate circular mask for this file
       self.circMask = circularMask.circularMask(self.fi.width,self.fi.height, self.fi.width-2).mask

    def readImage(self, position=0):

       self.fileHandle.seek(self.fi.offset + self.fi.size*position + self.fi.gapBetweenImages*position)

       image = np.fromfile(self.fileHandle, dtype=np.int16, count=int(self.fi.size/2))
       image = np.clip(image, 0, 1000)
       image=np.reshape(image, newshape=(self.fi.height, self.fi.width))
       return image

    def readImageUINT8(self, position=0):
       # read image and scale to uint8 [0;255] format
       image=self.readImage(position)

       maskedImage = image[self.circMask]

       cmin,cmax = np.min(maskedImage), np.max(maskedImage)
       # another option to increase contrast would be:
       #cmin,cmax = np.percentile(maskedImage,0.5), np.percentile(maskedImage,99.5)
       # print("Scaling from ["+str(cmin)+","+str(cmax)+"] to [0,255]")

       # scale [cmin,cmax] to [0,255]
       dyn=cmax-cmin

       # compress
       compr=255/dyn
       image = image-cmin
       image = image*compr

       # limit to 0
       image = np.clip(np.round(image),0,255)
       image=np.uint8(image)

       return image

# Example: x = MKTreader('Laesion031-2014.mkt')