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

# # idr0001: Sysgro
# 
# <a href="http://idr.openmicroscopy.org/webclient/?show=screen-3"></a>
# <table><tr>
# <td>A quick look at one of the studies in the IDR, Sysgro.</td>
# <td><img src="http://idr.openmicroscopy.org/webclient/render_image/1230601/6/0/?c=1|50:300$00FF00,2|100:800$0000FF&m=c&p=normal&ia=0&q=0.9" width="200px"/></td>
# <td><img src="http://idr.openmicroscopy.org/webclient/render_image/1232528/6/0/?c=1|50:300$00FF00,2|100:800$0000FF&m=c&p=normal&ia=0&q=0.9" width="200px"/></td>
# <td><img src="http://idr.openmicroscopy.org/webclient/render_image/1275942/6/0/?c=1|50:300$00FF00,2|100:800$0000FF&m=c&p=normal&ia=0&q=0.9" width="200px"/></td>
# </tr></table>

# ### Dependencies
# 
#  * [Matplotlib](http://matplotlib.org/)
#  * [NumPy](http://www.numpy.org/)

# In[1]:


import matplotlib
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import matplotlib.patches as mpatches

matplotlib.rcParams['figure.figsize'] = (12.0, 8.0)

from idr import connection


# In[2]:


screen = "idr0001-graml-sysgro/screenA"


# ### Connect to the IDR server

# In[12]:


conn = connection()


# ### Load information about Sysgro

# In[3]:


idr0001 = [x for x in conn.listScreens(2) if x.name == screen][0]


# In[4]:


idr0001.name


# In[5]:


print idr0001.description


# In[11]:


annotations = idr0001.getAnnotation().getMapValueAsMap()
print """
  PubMed ID: %(PubMed ID)s
  Authors: %(Publication Authors)s
  Imaging Method: %(Imaging Method)s
""" % annotations


# In[7]:


plates = 0
images = 0
for plate in idr0001.listChildren():
    plates += 1
    for well in plate.listChildren():
        images += len(list(well.listChildren()))
print "Plates:", plates
print "Images:", images


# In[8]:


total = None
for plate in idr0001.listChildren():
    grid = plate.getWellGrid()
    single = np.zeros((len(grid), len(grid[0])))
    if total is None:
        total = np.zeros((len(grid), len(grid[0])))
    for x, row in enumerate(grid):
        for y, col in enumerate(row):
            single[x][y] = grid[x][y].getImage().getROICount()
    total += single
    break  # Continue to tally all ROIs


# ### Disconnect when done loading data

# In[13]:


conn.close()


# ### Display results

# In[14]:


plt.title('ROIs per well of %s' % plate.id)
plt.pcolor(total)
plt.colorbar()
plt.show()


# ### License
# 
# Copyright (C) 2017 University of Dundee. All Rights Reserved.
# 
# 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 2 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; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.