Getting started with eartrack¶

In [1]:

%matplotlib notebook

import os
import numpy as np
import matplotlib.pyplot as plt

import openalea.eartrack
import openalea.eartrack.eartrack as et_lib
import openalea.eartrack.binarisation_folder as st_lib
from openalea.deploy.shared_data import shared_data

def img_show(imgs, titles):
    fig, axes = plt.subplots(nrows=int((len(imgs)-1)/3) + 1, ncols=min(3, len(imgs)))
    axlist = fig.get_axes()
    for i in range(len(imgs)):
        axlist[i].axis('off')
        axlist[i].set_title(titles[i])
        axlist[i].imshow(imgs[i])

NOT using graph editor observer No module named grapheditor

Get example images and parameters needed for segmentation and ear tracking¶

In [2]:

# Read images' information and create output folders
share_data_directory = shared_data(openalea.eartrack)
param_folder = os.path.join(share_data_directory, "parameters")
images_folder = os.path.join(share_data_directory, "images")

img_desc, parameters = st_lib.init(param_folder, images_folder, "", log=False)

Selection of one plant and one imaging task¶

In [3]:

plant = img_desc.keys()[0]
task = img_desc[plant].keys()[0]

cabin = img_desc[plant][task]['cabin']

Read images and show them¶

In [4]:

images = st_lib.read_images(img_desc, plant, task)

img_show([images["top"][0][:,:,::-1], images["side"][0][:,:,::-1], images["side"][90][:,:,::-1]], 
         ["Top view", "Side view\nangle 0", "Side view\nangle 90"])