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

# # Reading µs-ALEX data from Photon-HDF5 with h5py
# 
# *In this notebook we show how to read a µs-ALEX smFRET measurement stored in*
# *[Photon-HDF5 format](http://photon-hdf5.readthedocs.org/)*
# *using python and a few common scientific libraries (numpy, **h5py**, matplotlib).*
# *Specifically, we show how to load timestamps, build an alternation histogram*
# *and select photons in the donor and acceptor excitation periods.*
# 
# *See also a [similar notebook](Reading µs-ALEX data from Photon-HDF5.ipynb) using* 
# *[pytables](http://www.pytables.org/) instead of [h5py](http://www.h5py.org/).*

# In[1]:


from __future__ import division, print_function  # only needed on py2
get_ipython().run_line_magic('matplotlib', 'inline')
import numpy as np
import h5py
import matplotlib.pyplot as plt


# # 1. Utility functions
# 
# Here we define an utility function to print HDF5 file contents:

# In[2]:


def print_children(group):
    """Print all the sub-groups in `group` and leaf-nodes children of `group`.

    Parameters:
        data_file (h5py HDF5 file object): the data file to print
    """
    for name, value in group.items():
        if isinstance(value, h5py.Group):
            content = '(Group)'
        else:
            content = value[()]
        print(name)
        print('    Content:     %s' % content)
        print('    Description: %s\n' % value.attrs['TITLE'].decode())


# # 2. Open the data file
# 
# Let assume we have a Photon-HDF5 file at the following location:

# In[3]:


filename = '../data/0023uLRpitc_NTP_20dT_0.5GndCl.hdf5'


# We can open the file, as a normal HDF5 file

# In[4]:


h5file = h5py.File(filename)


# The object `h5file` is a pytables file reference. The root group is accessed with `h5file.root`.

# # 3. Print the content
# 
# Let's start by taking a look at the file content:

# In[5]:


print_children(h5file)


# We see the typical Photon-HDF5 structure. In particular the field `description` provides a short description of the measurement and `acquisition_duration` tells that the acquisition lasted 600 seconds.
# 
# As an example let's take a look at the content of the `sample` group:

# In[6]:


print_children(h5file['sample'])


# Finally, we define a shortcut to the `photon_data` group to save some typing later:

# In[7]:


photon_data = h5file['photon_data']


# # 4. Reading the data

# First, we make sure the file contains the right type of measurement:

# In[8]:


photon_data['measurement_specs']['measurement_type'][()].decode()


# Ok, tha's what we espect. 
# 
# Now we can load all the timestamps (including timestamps unit) and detectors arrays:

# In[9]:


timestamps = photon_data['timestamps'][:]
timestamps_unit = photon_data['timestamps_specs']['timestamps_unit'][()]
detectors = photon_data['detectors'][:]


# In[10]:


print('Number of photons: %d' % timestamps.size)
print('Timestamps unit:   %.2e seconds' % timestamps_unit)
print('Detectors:         %s' % np.unique(detectors))


# We may want to check the excitation wavelengths used in the measurement. This information is found in the setup group:

# In[11]:


h5file['setup']['excitation_wavelengths'][:]


# Now, let's load the definitions of donor/acceptor channel and excitation periods:

# In[12]:


donor_ch = photon_data['measurement_specs']['detectors_specs']['spectral_ch1'][()]
acceptor_ch = photon_data['measurement_specs']['detectors_specs']['spectral_ch2'][()]
print('Donor CH: %d     Acceptor CH: %d' % (donor_ch, acceptor_ch))


# In[13]:


alex_period = photon_data['measurement_specs']['alex_period'][()]
donor_period = photon_data['measurement_specs']['alex_excitation_period1'][()]
offset = photon_data['measurement_specs']['alex_offset'][()]
acceptor_period = photon_data['measurement_specs']['alex_excitation_period2'][()]
print('ALEX period:     %d  \nOffset:         %4d      \nDonor period:    %s      \nAcceptor period: %s' % \
      (alex_period, offset, donor_period, acceptor_period))


# These numbers define the donor and acceptor alternation periods as shown below:
# 
# $$2180 < \widetilde{t} < 3900 \qquad \textrm{donor period}$$
# 
# $$200 < \widetilde{t} < 1800 \qquad \textrm{acceptor period}$$
# 
# where $\widetilde{t}$ represent the (`timestamps` - `offset`) **MODULO** `alex_period`.
# 
# For more information
# please refer to the [measurements_specs section](http://photon-hdf5.readthedocs.org/en/latest/phdata.html#measurement-specs)
# of the *Reference Documentation*.

# # 5. Plotting the alternation histogram
# 
# Let start by separating timestamps from donor and acceptor channels:

# In[14]:


timestamps_donor = timestamps[detectors == donor_ch]
timestamps_acceptor = timestamps[detectors == acceptor_ch]


# Now that the data has been loaded we can plot an alternation histogram using *matplotlib*:

# In[15]:


fig, ax = plt.subplots()
ax.hist((timestamps_acceptor - offset) % alex_period, bins=100, alpha=0.8, color='red', label='donor')
ax.hist((timestamps_donor - offset) % alex_period, bins=100, alpha=0.8, color='green', label='acceptor')
ax.axvspan(donor_period[0], donor_period[1], alpha=0.3, color='green')
ax.axvspan(acceptor_period[0], acceptor_period[1], alpha=0.3, color='red')
ax.set_xlabel('(timestamps - offset) MOD alex_period')
ax.set_title('ALEX histogram')
ax.legend(loc='center left', bbox_to_anchor=(1, 0.5), frameon=False);


# # 6. Timestamps in different excitation periods
# 
# We conclude by showing, as an example, how to create arrays of timestamps containing only donor or acceptor exitation photons.
# 

# In[16]:


timestamps_mod = (timestamps - offset) % alex_period
donor_excitation = (timestamps_mod < donor_period[1])*(timestamps_mod > donor_period[0])
acceptor_excitation = (timestamps_mod < acceptor_period[1])*(timestamps_mod > acceptor_period[0])
timestamps_Dex = timestamps[donor_excitation]
timestamps_Aex = timestamps[acceptor_excitation]


# In[17]:


fig, ax = plt.subplots()
ax.hist((timestamps_Dex - offset) % alex_period, bins=np.arange(0, alex_period, 40), alpha=0.8, color='green', label='D_ex')
ax.hist((timestamps_Aex - offset) % alex_period, bins=np.arange(0, alex_period, 40), alpha=0.8, color='red', label='A_ex')
ax.set_xlabel('(timestamps - offset) MOD alex_period')
ax.set_title('ALEX histogram (selected periods only)')
ax.legend(loc='center left', bbox_to_anchor=(1, 0.5), frameon=False);


# In[18]:


#plt.close('all')


# In[ ]: