How to get array of region drawn with lasso selector?

Question

I'm completely new to Python, but what I would like to do is to draw a region in an image and then analyze it. This shall be done inside a GUI. My program can now draw a region with Lasso Selector (thanks to http://matplotlib.org/examples/event_handling/lasso_demo.html) and the vertices are saved in a numpy array. I would like the whole region to be saved as an array (or matrix). Is there an built-in function do to this? Do I need to make a foor-loop and if-statements and loop through all elements in the image and check which element is inside and which one is not. If that's the case, I don't know how to, since the elements from the vertice-array are not integers and unpaired (that is for row 45 there isn't exactly one vertice in column 3 and one in column 17). I use a mix of tkinter, matplotlib, numpy and what not.. (There are ofcourse tutorials on how to do this for a rectangle or so, I cannot apply that to this region.)

In short: What I would like is a numpy array with all the elements and their pixel values inside the region that I've drawn. The program shall be able to change that region and then replace it in the old image.

from tkinter import *

from matplotlib.widgets import LassoSelector
import matplotlib.image as mpimg
from pylab import *
from matplotlib import path
from tkinter.filedialog import askopenfilename
import tkinter as tk
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg

global fig, v
fname = "bild3.png" #Starting with file

def onselect(verts):
    global v, length_y
    print(verts)
    p = path.Path(verts) #path array of verts
    print(v)
    ind = p.contains_points(v)

root = tk.Tk()

# Creating two frames
topFrame = tk.Frame()
bottomFrame = tk.Frame()
topFrame.pack(side="top")
bottomFrame.pack(side="bottom")

# Create buttons
button_open = tk.Button(topFrame, text="Open image", command=lambda: selectIm())
button_draw = tk.Button(topFrame, text="Draw ROI")
button_quit = tk.Button(topFrame, text="Quit", command=root.quit)
button_clear= tk.Button(topFrame, text="Clear")
button_save = tk.Button(topFrame, text="Save")

#  Place buttons
button_open.pack(side="left")
button_draw.pack(side="left")
button_quit.pack(side="right") #fill makes it fill the frame
button_save.pack(side="left")
button_clear.pack(side = "left")


# Set figure on canvas
fig = plt.figure() #displays image and creates figure object??
img = mpimg.imread(fname) #ndarray  [rows [cols [rgb 3 val]]]

plt.imshow(img) #also needed to display image
ax = plt.gca() #Axlarna hänger med ..

canvas = FigureCanvasTkAgg(fig, bottomFrame)
canvas.show()
canvas.get_tk_widget().pack(side='top', fill='both', expand=1)
lasso = LassoSelector(ax, onselect) #Should be in draw-function


def selectIm():
    # global fig,
    global v, length_y
    print("Hej")

    fname=askopenfilename()
    img = mpimg.imread(fname)
    plt.imshow(img) #does this overwrite or plot another one?
    canvas.show() #updates canvas, or overwrites?

    length_y=img.shape[0] #Number of rows
    length_x=img.shape[1] #Number of cols
    v = np.zeros((length_x*length_y, 2), dtype=np.int) #Creates zero array

    #For y
    a = np.array(range(0,length_x))
    y = np.tile(a, length_y)

    #For x
    b = np.array(range(0,length_y))
    x = np.repeat(b, length_x)

    v[:,0] = x
    v[:,1] = y


root.title("Ett nytt test")
root.mainloop()

In the example in the link given (http://matplotlib.org/examples/event_handling/lasso_demo.html) I suspect that the following lines does the trick, but I don't understand that with include = False. Also in my program I don't have such a good structure since I don't understand all with classes, objects, etc at the moment. This is more of a image-analysis project.

class Datum(object):
    colorin = colorConverter.to_rgba('red')
    colorout = colorConverter.to_rgba('blue')
    def __init__(self, x, y, include=False):
        self.x = x
        self.y = y
        if include: self.color = self.colorin
        else: self.color = self.colorout

Thank you for any input in this problem!

Forgot to add, p.contains_points(v) just gives me a vector with True/False if the image element is on the line, I would like one that gives me all points if inside the enclosed region. If you run the program you need to click Open Image and select one, to draw in it properly. — Mianen, Apr 17 '15 at 13:59

score 5 · Answer 1 · answered Apr 28 '16 at 17:18

I came up with the following solution using some parts of your script:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.widgets import LassoSelector
from matplotlib import path

fig = plt.figure()
ax1 = fig.add_subplot(121)
ax1.set_title('lasso selection:')
ax1.plot()
ax1.set_xlim([0, 10])
ax1.set_ylim([0, 10])
ax1.set_aspect('equal')

# Empty array to be filled with lasso selector
array = np.zeros((10,10))
ax2 = fig.add_subplot(122)
ax2.set_title('numpy array:')
msk = ax2.imshow(array, origin='lower',vmax=1, interpolation='nearest')
ax2.set_xlim([-1, 10])
ax2.set_ylim([-1, 10])

# Pixel coordinates
pix = np.arange(10)
xv, yv = np.meshgrid(pix,pix)
pix = np.vstack( (xv.flatten(), yv.flatten()) ).T

def updateArray(array, indices):
    lin = np.arange(array.size)
    newArray = array.flatten()
    newArray[lin[indices]] = 1
    return newArray.reshape(array.shape)

def onselect(verts):
    global array, pix
    p = path.Path(verts)
    ind = p.contains_points(pix, radius=1)
    array = updateArray(array, ind)
    msk.set_data(array)
    fig.canvas.draw_idle()

lasso = LassoSelector(ax1, onselect)

plt.show()

Output figure

How to get array of region drawn with lasso selector?

1 Answers1