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

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filename = r'data\022rde11_T_minus15_acc__NT_plus10_don_1.sm'


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


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import phconvert as phc
phc.__version__


# # Author

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author = 'Eitan Lerner'
author_affiliation = 'UCLA'
creator = 'Antonino Ingargiola'
creator_affiliation = 'UCLA'


# # Sample

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comment = 'A demostrative smFRET-usALEX measurement.'
sample_name = '022rde11_T_minus15_acc__NT_plus10_don_1'
dye_names = ['ATTO550', 'ATTO647N']
buffer_name = 'Transcription buffer.'


# # Prepare data
# 
# ## Read the data

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d = phc.loader.usalex_sm(filename,
                         donor = 0,
                         acceptor = 1,
                         alex_period = 4000,
                         alex_offset = 700,
                         alex_period_donor = (2180, 3900),
                         alex_period_acceptor = (200, 1800),
                         excitation_wavelengths = (532e-9, 635e-9),
                         detection_wavelengths = (580e-9, 680e-9))


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phc.plotter.alternation_hist(d)


# ## Add author and sample info

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d['comment'] = comment

d['sample'] = dict(
    sample_name=sample_name,
    dye_names=[n.encode() for n in dye_names],
    buffer_name=buffer_name,
    num_dyes = len(dye_names))

d['identity'] = dict(
    author=author,
    author_affiliation=author_affiliation,
    creator=creator,
    creator_affiliation=creator_affiliation)


# # Validate the Photon-HDF5 structure
# 
# Before writing to disk, we assure the file structure follows the Photon-HDF5 format:

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phc.hdf5.assert_valid_photon_hdf5(d)


# # Save to Photon-HDF5

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phc.hdf5.save_photon_hdf5(d)


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d['_data_file'].close()


# # Load Photon-HDF5

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from pprint import pprint


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filename = d['_data_file'].filename


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h5data = phc.hdf5.load_photon_hdf5(filename)


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phc.hdf5.dict_from_group(h5data.identity)


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phc.hdf5.dict_from_group(h5data.setup)


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pprint(phc.hdf5.dict_from_group(h5data.photon_data))


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