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

# # Reading ns-ALEX data from Photon-HDF5
# 
# *In this notebook we show how to read a ns-ALEX  smFRET measurement stored in *
# *[Photon-HDF5 format](http://photon-hdf5.readthedocs.org/)*
# *using python and a few common scientific libraries (numpy, pytables, matplotlib).*
# *Specifically, we show how to load timestamps, detectors and nanotimes arrays*
# *and how to plot a TCSPC histogram.* 
# 
# *For a µs-ALEX example see [Reading µs-ALEX data from Photon-HDF5](Reading µs-ALEX data from Photon-HDF5.ipynb).*

# In[1]:


from __future__ import division, print_function  # only needed on py2
get_ipython().run_line_magic('matplotlib', 'inline')
import numpy as np
import tables
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:
        group (pytables group): the group to be printed.
    """
    for name, value in group._v_children.items():
        if isinstance(value, tables.Group):
            content = '(Group)'
        else:
            content = value.read()
        print(name)
        print('    Content:     %s' % content)
        print('    Description: %s\n' % value._v_title.decode())


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

# In[3]:


filename = '../data/Pre.hdf5'


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

# In[4]:


h5file = tables.open_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.root)


# 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 900 seconds.
# 
# As an example, let's take a look at the content of the `sample` group:

# In[6]:


print_children(h5file.root.sample)


# Let's define a shortcut to the photon_data group to save some typing later:

# In[7]:


photon_data = h5file.root.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.read().decode()


# Ok, tha's what we espect. 
# 
# Now we can load all the `photon_data` arrays an their specs:

# In[9]:


timestamps = photon_data.timestamps.read()
timestamps_unit = photon_data.timestamps_specs.timestamps_unit.read()
detectors = photon_data.detectors.read()
nanotimes = photon_data.nanotimes.read()
tcspc_num_bins = photon_data.nanotimes_specs.tcspc_num_bins.read()
tcspc_unit = photon_data.nanotimes_specs.tcspc_unit.read()


# In[10]:


print('Number of photons: %d' % timestamps.size)
print('Timestamps unit:   %.2e seconds' % timestamps_unit)
print('TCSPC unit:        %.2e seconds' % tcspc_unit)
print('TCSPC number of bins:    %d' % tcspc_num_bins)
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.root.setup.excitation_wavelengths.read()


# 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.read()
acceptor_ch = photon_data.measurement_specs.detectors_specs.spectral_ch2.read()
print('Donor CH: %d     Acceptor CH: %d' % (donor_ch, acceptor_ch))


# In[13]:


laser_rep_rate = photon_data.measurement_specs.laser_repetition_rate.read()
donor_period = photon_data.measurement_specs.alex_excitation_period1.read()
acceptor_period = photon_data.measurement_specs.alex_excitation_period2.read()
print('Laser repetion rate: %5.1f MHz \nDonor period:    %s      \nAcceptor period: %s' % \
      (laser_rep_rate*1e-6, donor_period, acceptor_period))


# These numbers define the donor and acceptor excitation periods as shown below:
# 
# $$150 < \widetilde{t} < 1500 \qquad \textrm{donor period}$$
# 
# $$1540 < \widetilde{t} < 3050 \qquad \textrm{acceptor period}$$
# 
# where $\widetilde{t}$ represent the `nanotimes` array. 
# 
# 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 TCSPC histogram
# 
# Let start by separating nanotimes from donor and acceptor channels:

# In[14]:


nanotimes_donor = nanotimes[detectors == donor_ch]
nanotimes_acceptor = nanotimes[detectors == acceptor_ch]


# Next, we compute the histograms:

# In[15]:


bins = np.arange(0, tcspc_num_bins + 1)
hist_d, _ = np.histogram(nanotimes_donor, bins=bins)
hist_a, _ = np.histogram(nanotimes_acceptor, bins=bins)


# And finally we plot the TCSPC histogram using *matplotlib*:

# In[16]:


fig, ax = plt.subplots(figsize=(10, 4.5))
scale = tcspc_unit*1e9
ax.plot(bins[:-1]*scale, hist_d, color='green', label='donor')
ax.plot(bins[:-1]*scale, hist_a, color='red', label='acceptor')
ax.axvspan(donor_period[0]*scale, donor_period[1]*scale, alpha=0.3, color='green')
ax.axvspan(acceptor_period[0]*scale, acceptor_period[1]*scale, alpha=0.3, color='red')
ax.set_xlabel('TCSPC Nanotime (ns) ')
ax.set_title('TCSPC Histogram')
ax.set_yscale('log')
ax.set_ylim(10)
ax.legend(loc='center left', bbox_to_anchor=(1, 0.5));


# In[17]:


#plt.close('all')


# In[ ]: