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

# ### Getting started ###
# 
# This notebook provides a few examples of working with the IDR data.
# Functions can be found in [idr-py](https://github.com/IDR/idr-py/). Feel free
# to copy notebooks into the scratch space and edit as necessary.
# 
# **All** changes should be considered temporary. Download a copy of
# notebooks and results when your session is complete.

# In[1]:


get_ipython().run_line_magic('matplotlib', 'inline')
import matplotlib.pyplot as plt


# In[2]:


from IPython.display import display, Image


# In[3]:


from idr import connection
from idr import images_by_phenotype, attributes_by_attributes
from idr import simple_colocalisation


# In[4]:


conn = connection()


# In[5]:


images = images_by_phenotype(conn, "CMPO_0000077")
display(*tuple([Image(img.getThumbnail()) for img in images[100:2500:500]]))


# In[6]:


simple_colocalisation(images[999])


# In[7]:


args = {
    "name": "Gene Symbol",
    "value": "cdc14",
    "ns": "openmicroscopy.org/mapr/gene",
    "ns2": "openmicroscopy.org/mapr/phenotype",
    # "name2": "Phenotype Term Accession", # optional
}
attributes_by_attributes(conn, **args)


# ### Disconnect

# In[ ]:


conn.close()