ftirAperture.py 5.09 KB
Newer Older
Josef Brandt's avatar
Josef Brandt committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
# -*- coding: utf-8 -*-
"""
GEPARD - Gepard-Enabled PARticle Detection
Copyright (C) 2018  Lars Bittrich and Josef Brandt, Leibniz-Institut für 
Polymerforschung Dresden e. V. <bittrich-lars@ipfdd.de>    

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program, see COPYING.  
If not, see <https://www.gnu.org/licenses/>.
"""

import numpy as np
from scipy import optimize
import cv2
25
from ..cythonModules.getMaxRect import findMaxRect  # TODO: UNCOMMENT!!!
Josef Brandt's avatar
Josef Brandt committed
26 27 28 29 30 31


####################################################
'''Code taken from https://github.com/pogam/ExtractRect/blob/master/extractRect.py and modified for our use'''
####################################################

Josef Brandt's avatar
Josef Brandt committed
32

Josef Brandt's avatar
Josef Brandt committed
33 34 35 36
def residual(angle, img):
    img_rot, rotationMatrix = rotateImageAroundAngle(img, angle)
    point1, point2, width, height, max_area = findMaxRect(img_rot)
    return 1/max_area
Josef Brandt's avatar
Josef Brandt committed
37 38


Josef Brandt's avatar
Josef Brandt committed
39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
def getFinalRectangle(angle, img, shiftScaleParam):
    ny = img.shape[1]
    img_rot, rotationMatrix = rotateImageAroundAngle(img, angle)
    point1, point2, width, height, max_area = findMaxRect(img_rot)
    width *= shiftScaleParam.scale_factor
    height *= shiftScaleParam.scale_factor
    
    #invert rectangle 
    M_invert = cv2.invertAffineTransform(rotationMatrix)
    rect_coord = [point1, [point1[0],point2[1]] , 
                  point2, [point2[0],point1[1]] ]
   
    rect_coord_ori = []
    for coord in rect_coord:
        rect_coord_ori.append(np.dot(M_invert,[coord[0],(ny-1)-coord[1],1]))
        
    #transform to numpy coord of input image
    coord_out = []
    for coord in rect_coord_ori:
        coord_out.append([shiftScaleParam.scale_factor*round(       coord[0],0)-shiftScaleParam.shift_x,\
                          shiftScaleParam.scale_factor*round((ny-1)-coord[1],0)-shiftScaleParam.shift_y])
        
   #transpose back the original coords:
    coord_out = transposeRectCoords(coord_out)
     
    return coord_out, round(width), round(height)

Josef Brandt's avatar
Josef Brandt committed
66

Josef Brandt's avatar
Josef Brandt committed
67 68 69 70 71 72
def transposeRectCoords(rectCoords):
    #mirror x and y:
    newCoords = []
    for i in range(len(rectCoords)):
        newCoords.append([rectCoords[i][1], rectCoords[i][0]])
    return newCoords
Josef Brandt's avatar
Josef Brandt committed
73 74


Josef Brandt's avatar
Josef Brandt committed
75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92
def addBorderToMakeImageSquare(img):
    nx, ny = img.shape
    if nx != ny:
        n = max([nx,ny])
        img_square = np.ones([n,n])
        xshift = (n-nx)/2
        yshift = (n-ny)/2
        if yshift == 0:
            img_square[int(xshift):int(xshift+nx),:] = img
        else: 
            img_square[:,int(yshift):int(yshift+ny)] = img
    else:
        xshift = 0
        yshift = 0
        img_square = img

    return img_square, xshift, yshift

Josef Brandt's avatar
Josef Brandt committed
93

Josef Brandt's avatar
Josef Brandt committed
94 95 96 97 98 99 100 101 102 103
def limitImageSize(img, limitSize):
    if img.shape[0] > limitSize:
        img_small = cv2.resize(img,(limitSize, limitSize),interpolation=0)
        scale_factor = 1.*img.shape[0]/img_small.shape[0]
    else:
        img_small = img
        scale_factor = 1
    
    return img_small, scale_factor

Josef Brandt's avatar
Josef Brandt committed
104

Josef Brandt's avatar
Josef Brandt committed
105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
def makeImageOddSized(img):
    # set the input data with an odd number of point in each dimension to make rotation easier
    nx,ny = img.shape
    nx_extra = -nx
    ny_extra = -ny   
    if nx%2==0:
        nx+=1
        nx_extra = 1
    if ny%2==0:
        ny+=1
        ny_extra = 1
    img_odd = np.ones([img.shape[0]+max([0,nx_extra]),img.shape[1]+max([0,ny_extra])], dtype=np.uint8)
    img_odd[:-nx_extra, :-ny_extra] = img
    return img_odd

Josef Brandt's avatar
Josef Brandt committed
120

Josef Brandt's avatar
Josef Brandt committed
121
def rotateImageAroundAngle(img, angle):
Josef Brandt's avatar
Josef Brandt committed
122 123
    nx, ny = img.shape
    rotationMatrix = cv2.getRotationMatrix2D(((nx-1)/2, (ny-1)/2), float(angle), 1)
Josef Brandt's avatar
Josef Brandt committed
124 125 126 127
    img_rot = np.array(cv2.warpAffine(img, rotationMatrix, img.shape, flags=cv2.INTER_NEAREST, borderValue=1))
    img_rot = img_rot.astype(np.uint8)
    return img_rot, rotationMatrix

Josef Brandt's avatar
Josef Brandt committed
128

Josef Brandt's avatar
Josef Brandt committed
129 130 131 132 133 134 135 136 137
def findRotatedMaximalRectangle(img, nbre_angle=4, limit_image_size=300):
    img_square, shift_x, shift_y = addBorderToMakeImageSquare(img)
    img_small, scale_factor = limitImageSize(img_square, limit_image_size)
    img_odd = makeImageOddSized(img_small)
    nx,ny = nx_odd, ny_odd = img_odd.shape
    shiftScaleParam = ShiftAndScaleParam(shift_x, shift_y, scale_factor)

    # angle_range = ([(90.,180.),])
    angle_range = ([(0., 90.), ])
Josef Brandt's avatar
Josef Brandt committed
138
    coeff1 = optimize.brute(residual, angle_range, args=(img_odd,), Ns=nbre_angle, finish=None)
Josef Brandt's avatar
Josef Brandt committed
139 140 141 142 143 144 145
    popt = optimize.fmin(residual, coeff1, args=(img_odd,), xtol=5, ftol=1.e-5, disp=False)
    opt_angle = popt[0]

    rectangleCoords, width, height = getFinalRectangle(opt_angle, img_odd, shiftScaleParam)

    return rectangleCoords, opt_angle, width, height

Josef Brandt's avatar
Josef Brandt committed
146

Josef Brandt's avatar
Josef Brandt committed
147 148 149 150
class ShiftAndScaleParam(object):
    def __init__(self, shift_x=0, shift_y=0, scale_factor=1):
        self.shift_x = shift_x
        self.shift_y = shift_y
Josef Brandt's avatar
Josef Brandt committed
151
        self.scale_factor = scale_factor