#!/usr/bin/env python
# coding: utf-8

# # RhizoScan Pipeline

# This pipeline is a step by step pipeline

# ## Common import

# In[1]:


get_ipython().run_line_magic('pylab', 'inline')
from matplotlib import pyplot as plt
from IPython.display import Image


# ## RhizoScan Import

# In[2]:


from rhizoscan import get_data_path
from rhizoscan.root.pipeline import load_image, detect_petri_plate, compute_graph, compute_tree
from rhizoscan.root.pipeline.arabidopsis import segment_image, detect_leaves
from rhizoscan.root.graph.mtg import tree_to_mtg


# ## RSA Image

# In[3]:


image_filename = get_data_path('pipeline/arabido.png')
Image(image_filename)


# ### Load Image

# In[4]:


image = load_image(image_filename)
imshow(image)


# ### Detect features (Petri plate)

# In[5]:


pmask, px_scale, hull = detect_petri_plate(image,border_width=25, plate_size=120, fg_smooth=1)
imshow(pmask)


# ### Image Segmentation

# In[6]:


rmask, bbox = segment_image(image,pmask,root_max_radius=5)
imshow(rmask)


# ### Detect leaves and seed

# In[7]:


seed_map = detect_leaves(rmask, image, bbox, plant_number=2, leaf_bbox=[0,0,1,.4])
#imshow(seed_map)
imshow(seed_map+rmask)


# ### Compute the graph corresponding to the RSA

# In[8]:


graph = compute_graph(rmask,seed_map,bbox)
graph.plot(linewidth=4)


# ### Extract a tree from the graph

# In[9]:


tree = compute_tree(graph, px_scale=px_scale)
tree.plot(linewidth=4)


# ### Save the RSA into an MTG

# In[10]:


g = rsa = tree_to_mtg(tree)
g.display()


# In[ ]:





# In[ ]: