def align_img(image_name, loss_fn=sum_of_squared_diff, max_disp = 15, big=False, name=None, hist_eq = False):
    b,g,r = get_bgr(image_name)

    if hist_eq == True:
        b, g, r = exposure.equalize_hist(b), exposure.equalize_hist(g), exposure.equalize_hist(r)

    print("Aligning green and blue: ")
    ag = align(g, b, loss_fn=loss_fn, max_disp = max_disp, big=big, name=name)
    print("Aligning blue and red: ")
    ar = align(r, b, loss_fn=loss_fn, max_disp = max_disp, big=big, name=name)
    # create a color image
    im_out = np.dstack([ar, ag, b])
    plt.show()

    # save the image
    iname = image_name.split('.')
    iname[-1] = 'jpg'
    image_name = '.'.join(iname)
    fname = 'out_' + image_name
    skio.imsave(fname, im_out)

    # display the image
    skio.imshow(im_out)
    plt.show()
    skio.show()

def PreprocessImage(path, show_img=False):
    # load image
    img = io.imread(path)
    print("Original Image Shape: ", img.shape)
    # we crop image from center
    short_egde = min(img.shape[:2])
    yy = int((img.shape[0] - short_egde) / 2)
    xx = int((img.shape[1] - short_egde) / 2)
    crop_img = img[yy : yy + short_egde, xx : xx + short_egde]
    # resize to 224, 224
    resized_img = transform.resize(crop_img, (224, 224))
    if show_img:
        io.imshow(resized_img)
    # convert to numpy.ndarray
    sample = np.asarray(resized_img) * 256
    # swap channel from RGB to BGR
    sample = sample[:, :, [2,1,0]]
    # swap axes to make image from (224, 224, 4) to (3, 224, 224)
    sample = np.swapaxes(sample, 0, 2)
    sample = np.swapaxes(sample, 1, 2)

    # sub mean
    normed_img = sample - mean_img
    normed_img.resize(1, 3, 224, 224)
    return normed_img

    def save_segmented_image(self, filepath_image, modality='t1c', show=False):
        '''
        Creates an image of original brain with segmentation overlay and save it in ./predictions
        INPUT   (1) str 'filepath_image': filepath to test image for segmentation, including file extension
                (2) str 'modality': imaging modality to use as background. defaults to t1c. options: (flair, t1, t1c, t2)
                (3) bool 'show': If true, shows output image. defaults to False.
        OUTPUT  (1) if show is True, shows image of segmentation results
                (2) if show is false, returns segmented image.
        '''
        modes = {'flair': 0, 't1': 1, 't1c': 2, 't2': 3}

        segmentation = self.predict_image(filepath_image, show=False)
        print 'segmentation = ' + str(segmentation)
        img_mask = np.pad(segmentation, (16, 16), mode='edge')
        ones = np.argwhere(img_mask == 1)
        twos = np.argwhere(img_mask == 2)
        threes = np.argwhere(img_mask == 3)
        fours = np.argwhere(img_mask == 4)

        test_im = io.imread(filepath_image)
        test_back = test_im.reshape(5, 216, 160)[modes[modality]]
        # overlay = mark_boundaries(test_back, img_mask)
        gray_img = img_as_float(test_back)

        # adjust gamma of image
        image = adjust_gamma(color.gray2rgb(gray_img), 0.65)
        sliced_image = image.copy()
        red_multiplier = [1, 0.2, 0.2]
        yellow_multiplier = [1, 1, 0.25]
        green_multiplier = [0.35, 0.75, 0.25]
        blue_multiplier = [0, 0.25, 0.9]

        print str(len(ones))
        print str(len(twos))
        print str(len(threes))
        print str(len(fours))

        # change colors of segmented classes
        for i in xrange(len(ones)):
            sliced_image[ones[i][0]][ones[i][1]] = red_multiplier
        for i in xrange(len(twos)):
            sliced_image[twos[i][0]][twos[i][1]] = green_multiplier
        for i in xrange(len(threes)):
            sliced_image[threes[i][0]][threes[i][1]] = blue_multiplier
        for i in xrange(len(fours)):
            sliced_image[fours[i][0]][fours[i][1]] = yellow_multiplier
        #if show=True show the prediction
        if show:
            print 'Showing...'
            io.imshow(sliced_image)
            plt.show()
        #save the prediction
        print 'Saving...'
        try:
            mkdir_p('./predictions/')
            io.imsave('./predictions/' + os.path.basename(filepath_image) + '.png', sliced_image)
            print 'prediction saved.'
        except:
            io.imsave('./predictions/' + os.path.basename(filepath_image) + '.png', sliced_image)
            print 'prediction saved.'

def doit(filename):
    dat = io.imread(filename)
    dat = rgb2gray(dat)

    blobs = blob_dog(dat, max_sigma=12, threshold=.25)
    blobs[:, 2] = blobs[:, 2] * (2 ** 0.5)

    io.imshow(dat)
    for blob in blobs:
        y, x, r = blob
        c = plt.Circle((x, y), r, color='r', linewidth=2, fill=False)
        plt.gca().add_patch(c)
    plt.show()

    print (blobs[:,2].size)

    r = (blobs[:,2])
    print (r)
    print (area_of_circle(r))
    avg_area = np.mean(area_of_circle(r))
    print (avg_area)
    
    #Distance from average x 
    avg_x = np.mean(blobs[:,0])
    x = (blobs[:,0])
    x_dist = (x-avg_x)
    print (x_dist)
    
    #Distance from average y
    avg_y = np.mean(blobs[:,1])
    y = (blobs[:,1])
    y_dist = (y-avg_y)
    print (y_dist)
    
    return blobs # for potential further processing

    def transform(self, func, params, sub_dir=None, img_ind=None):
        """
        Takes a function and apply to every img_arr in self.img_arr.
        Have to option to transform one as  a test case

        :param sub_dir: The index for the image
        :param img_ind: The index of the category of images
        """
        # Apply to one test case
        if sub_dir is not None and img_ind is not None:
            sub_dir_ind = self.label_map[sub_dir]
            img_arr = self.img_lst2[sub_dir_ind][img_ind]
            img_arr = func(img_arr, **params).astype(float)
            io.imshow(img_arr)
            plt.show()
        # Apply the function and parameters to all the images
        elif isinstance(sub_dir, list):
            if len(sub_dir) == 1:
                sub_dir_ind = self.label_map[sub_dir[0]]
                new_img_lst2 = []
                for img_arr in self.img_lst2[sub_dir_ind]:
                    new_img_lst2.append(func(img_arr, **params).astype(float))
                self.img_lst2[sub_dir_ind] = new_img_lst2
            else:
                for dir in sub_dir:
                    sub_dir_ind = self.label_map[dir]
                    new_img_lst2 = []
                    for img_arr in self.img_lst2[sub_dir_ind]:
                        new_img_lst2.append(func(img_arr, **params).astype(float))
                    self.img_lst2[sub_dir_ind] = new_img_lst2
        else:
            new_img_lst2 = []
            for img_lst in self.img_lst2:
                new_img_lst2.append([func(img_arr, **params).astype(float) for img_arr in img_lst])
            self.img_lst2 = new_img_lst2

def main():
	args = vars(parser.parse_args())
	filename = os.path.join(os.getcwd(), args["image"][0])

	image = skimage.img_as_uint(color.rgb2gray(io.imread(filename)))

	subsample = 1

	if (not args["subsample"] == 1):
		subsample = args["subsample"][0]

		image = transform.downscale_local_mean(image, (subsample, subsample))
		image = transform.pyramid_expand(image, subsample, 0, 0)

	image = exposure.rescale_intensity(image, out_range=(0,args["depth"][0]))

	if (args["visualize"]):
		io.imshow(image)
		io.show()

	source = generate_face(image, subsample, args["depth"][0], FLICKER_SPEED)

	if source:
		with open(args["output"][0], 'w') as file_:
			file_.write(source)
	else:
		print "Attempted to generate source code, failed."

def detectOpticDisc(image):
    kernel = octagon(10, 10)
    thresh = threshold_otsu(image[:,:,1])
    binary = image > thresh
    print binary.dtype
    luminance = convertToHLS(image)[:,:,2]
    t = threshold_otsu(luminance)
    t = erosion(luminance, kernel)
    
    
    labels = segmentation.slic(image[:,:,1], n_segments = 3)
    out = color.label2rgb(labels, image[:,:,1], kind='avg')
    skio.imshow(out)
    
    x, y = computeCentroid(t)
    print x, y
    rows, cols, _ = image.shape
    p1 = closing(image[:,:,1],kernel)
    p2 = opening(p1, kernel)
    p3 = reconstruction(p2, p1, 'dilation')
    p3 = p3.astype(np.uint8)
    #g = dilation(p3, kernel)-erosion(p3, kernel)
    #g = rank.gradient(p3, disk(5))
    g = cv2.morphologyEx(p3, cv2.MORPH_GRADIENT, kernel)
    #markers = rank.gradient(p3, disk(5)) < 10
    markers = drawCircle(rows, cols, x, y, 85)
    #markers = ndimage.label(markers)[0]
    #skio.imshow(markers)
    g = g.astype(np.uint8)
    #g = cv2.cvtColor(g, cv2.COLOR_GRAY2RGB)
    w = watershed(g, markers)
    print np.max(w), np.min(w)
    w = w.astype(np.uint8)
    #skio.imshow(w)
    return w

def show_user_imgs(imgs):
	'''
	Display images to new_user and prompt for response (Like / NoLike)
	Keep track of preferences in a list.
	
	INPUT: list of pairs, (username, img_id)

	OUTPUT: np.array of new_user's preferences (zero or one)
	'''
	# initialize the list of preferences
	likes = []
	for img in imgs:
		# generate the path to the image
		fname = '../imgs/{}'.format(img)
		# update status to terminal
		print fname
		# show image to user
		imshow(fname)
		plt.show()
		# initialize string of preferences
		pref = ''
		# logical xor in python is != ... i know, right??
		while not pref in ['0', '1']:
			# survey whether user liked photo
			print 'you entered: {}'.format(pref)
			pref = raw_input('Did you like that photo? Yes:1, No:0...')
			# keep track of the result in list 'likes'
			likes.append(int(pref))
	# convert list 'likes' to np.array for better handling downstream
	likes = np.array(likes).astype('bool')
	return likes

def threshold_image(image, threshold=0):
	"""
	This function takes out any values in an image's RGB matrix that are
	below the threshold value.

	Inputs:
	- image: a matrix describing an image with only one channel represented.
	- threshold: a value, between 0 and 1, for which if an image matrix's
				 value is below, will be set to 0, and if above, will be 
				 set to 1.

				 If the threshold is set to 0, then an Otsu thresholding will
				 be returned.

	Outputs:
	- thresholded_image: a matrix representation of the thresholded image.
						 this is essentially a black and white image.
	- thresh: the threshold value

	To screen: the black-and-white image representation.
	- 
	"""
	if threshold == 0:
		thresh = threshold_otsu(image)

	if threshold != 0:
		thresh = threshold

	thresholded_image = closing(image > thresh, square(3), out=None)
	imshow(thresholded_image)

	return thresholded_image, thresh

    def predict_image(self, test_img, show=False):
        '''
        predicts classes of input image
        INPUT   (1) str 'test_image': filepath to image to predict on
                (2) bool 'show': True to show the results of prediction, False to return prediction
        OUTPUT  (1) if show == False: array of predicted pixel classes for the center 208 x 208 pixels
                (2) if show == True: displays segmentation results
        '''
        imgs = io.imread(test_img).astype('float').reshape(5,240,240)
        plist = []

        # create patches from an entire slice
        for img in imgs[:-1]:
            if np.max(img) != 0:
                img /= np.max(img)
            p = extract_patches_2d(img, (33,33))
            plist.append(p)
        patches = np.array(zip(np.array(plist[0]), np.array(plist[1]), np.array(plist[2]), np.array(plist[3])))

        # predict classes of each pixel based on model
        full_pred = self.model_comp.predict_classes(patches)
        fp1 = full_pred.reshape(208,208)
        if show:
            io.imshow(fp1)
            plt.show
        else:
            return fp1

def draw_window(frame):
    # setup initial location of window
    r,h,c,w = 250,90,400,125  # simply hardcoded the values
    track_window = (c,r,w,h)    

    # set up the ROI for tracking
    roi = frame[r:r+h, c:c+w]
    hsv_roi =  cv2.cvtColor(roi, cv2.COLOR_BGR2HSV)
    mask = cv2.inRange(hsv_roi, np.array((0., 60.,32.)), np.array((180.,255.,255.)))
    roi_hist = cv2.calcHist([hsv_roi],[0],mask,[180],[0,180])
    cv2.normalize(roi_hist,roi_hist,0,255,cv2.NORM_MINMAX)    

    # Setup the termination criteria, either 10 iteration or move by atleast 1 pt
    term_crit = ( cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT, 10, 1 )

    hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV)
    dst = cv2.calcBackProject([hsv],[0],roi_hist,[0,180],1)

    # apply meanshift to get the new location
    ret, track_window = cv2.CamShift(dst, track_window, term_crit)
    # Draw it on image
    pts = cv2.boxPoints(ret)
    pts = np.int0(pts)
    img2 = cv2.polylines(frame,[pts],True, 255,2)
    io.imshow(img2)

def just_do_it(limit_cont):
	fig = plt.figure(facecolor='black')
	plt.gray()
	print("Rozpoczynam przetwarzanie obrazow...")
    
	for i in range(20):
		img = data.imread(images[i])

		gray_img = to_gray(images[i])				# samoloty1.pdf
		#gray_img = to_gray2(images[i],  1001, 0.2, 5, 9, 12) 	# samoloty2.pdf
		#gray_img = to_gray2(images[i],  641, 0.2, 5, 20, 5)	# samoloty3.pdf
		conts = find_contours(gray_img, limit_cont)
		centrs = [find_centroid(cont) for cont in conts]

		ax = fig.add_subplot(4,5,i)
		ax.set_yticks([])
		ax.set_xticks([])
		io.imshow(img)
		print("Przetworzono: " + images[i])
        
		for n, cont in enumerate(conts):
			ax.plot(cont[:, 1], cont[:, 0], linewidth=2)
            
		for centr in centrs:
			ax.add_artist(plt.Circle(centr, 5, color='white'))
            
	fig.tight_layout()
	#plt.show()
	plt.savefig('samoloty3.pdf')

def test(frame):
    hsv = cv2.cvtColor(frame, cv2.COLOR_BGR2HSV)
    lower_white = np.array([0,0,200])
    upper_white = np.array([300,100,300])
    # Threshold the HSV image to get only white colors
    mask = cv2.inRange(hsv, lower_white, upper_white)
    gray = cv2.cvtColor(mask, cv2.COLOR_BAYER_GB2GRAY)
    gradX = cv2.Sobel(gray, ddepth = cv2.CV_32F, dx = 1, dy = 0, ksize = -1)
    gradY = cv2.Sobel(gray, ddepth = cv2.CV_32F, dx = 0, dy = 1, ksize = -1)
    # subtract the y-gradient from the x-gradient
    gradient = cv2.subtract(gradX, gradY)
    gradient = cv2.convertScaleAbs(gradient)
    # blur and threshold the image
    blurred=cv2.blur(gray,(9,9))
    blurred = cv2.blur(gradient, (9, 9))
    (_, thresh) = cv2.threshold(blurred, 225, 255, cv2.THRESH_BINARY)
    kernel = cv2.getStructuringElement(cv2.MORPH_RECT, (21, 7))
    closed = cv2.morphologyEx(thresh, cv2.MORPH_CLOSE, kernel)
    # perform a series of erosions and dilations
    closed = cv2.erode(closed, None, iterations = 4)
    closed = cv2.dilate(closed, None, iterations = 4)

    image, contours,hierarchy= cv2.findContours(closed,
                               cv2.RETR_TREE,cv2.CHAIN_APPROX_SIMPLE)
    img= cv2.drawContours(frame, contours, -1,(0,0,0),3)
    io.imshow(img)

def background_sub(frame): 
    '''
    out 
    '''
    return gray

    io.imshow(img)

def main():
  imgs = MultiImage(data_dir + '/multipage.tif')

  for a, i in zip(range(0, 4), [1, 9, 7, 8]):
    fig = plt.figure()
    ax = fig.add_axes([-0.1, -0.1, 1.2, 1.2])
    # ax.set_axis_off()
    im = data.imread('samolot0' + str(i) + '.jpg', as_grey = True)
    im = invert(im)
    im = process(im)
    out = np.ones_like(im)
    io.imshow(out)
    contours = measure.find_contours(im, 0.9)
    for n, contour in enumerate(contours):
      plt.plot(contour[:, 1], contour[:, 0], linewidth=2, color = 'white')
    plt.savefig(str(a) + '.jpg', bbox_inches = 0, frameon = False)

  fig = plt.figure()
  grid = AxesGrid(fig, rect = (1, 1, 1), nrows_ncols = (2, 2), axes_pad = 0.1)

  for i in range(0, 4):
    frame = data.imread(str(i) + '.jpg')
    grid[i].imshow(frame)
    grid[i].set_xticks([])
    grid[i].set_yticks([])

  plt.savefig('na3.jpg')

def hsi_equalize_hist():
    image=data.astronaut()
    h=color.rgb2hsv(image)
    h[:,:,2]=exposure.equalize_hist(h[:,:,2])
    image_equal=color.hsv2rgb(h)
    io.imshow(image_equal)
    io.imsave('astronautequal.png',image_equal)

def recognize(breaker, show, sample, LEVEL, THRESHOLD):
    img = io.imread(sample)
    if show:
        io.imshow(img, 'pil')
    res = ''
    for cat in breaker.match(img, LEVEL, THRESHOLD):
        res += cat.name
    print res

def main():
    from skimage import data, io, filters
    testfolder='/Users/davidgreenfield/Downloads/pics_boots/'
    testimage='B00A0GVP8A.jpg'
    image = io.imread(testfolder+testimage,flatten=True) # or any NumPy array!
    edges = filters.sobel(image)
    io.imshow(edges)
    io.show()

def get_rect(path):
    e, img = detect(path)
    img = img[40:, :]
    imshow(img)
    # import Image
    # im = Image.fromarray(img)
    # im.save("your_file.jpg")
    return img

 def doEigengesichter(self,pos):
     dim = int(math.sqrt(self.VT.shape[1]))
     mdata = np.zeros((dim,dim))
     imageVector = self.VT[pos,:]
     for i in range(0,len(imageVector),int(dim)):
         row = np.array(imageVector)[i:i+dim]
         mdata[int(i/dim),:] = row
     io.imshow(mdata)