This Jupyter notebook will guide you through the conversion of a µs-ALEX data file from SM (WeissLab) to Photon-HDF5 format. For more info on how to edit a jupyter notebook refer to this example.
Please send feedback and report any problems to the [Photon-HDF5 google group](https://groups.google.com/forum/#!forum/photon-hdf5).
The notebook is composed by "text cells", such as this paragraph, and "code cells"
containing the code to be executed (and identified by an In [ ] prompt).
To execute a code cell, select it and press SHIFT+ENTER.
To modify an cell, click on it to enter "edit mode" (indicated by a green frame),
then type.
You can run this notebook directly online (for demo purposes), or you can run it on your on desktop. For a local installation please refer to:
Note: Skip to section 2.2 if you are running the notebook locally.
Before starting, you have to upload a data file to be converted to Photon-HDF5. You can use one of our example data files available on figshare.
To upload a file (up to 35 MB) switch to the "Home" tab in your browser, click the upload button and select the data file. Wait until the upload completes. For larger files (like some of our example files) please use the Upload notebook instead.
Once the file is uploaded, come back here and follow the instructions below.
Specify the input data file in the following cell:
In [ ]:
filename = '0023uLRpitc_NTP_20dT_0.5GndCl.sm'
The next cell will check if the filename location is correct:
In [ ]:
import os
try:
with open(filename): pass
print('Data file found, you can proceed.')
except IOError:
print('ATTENTION: Data file not found, please check the filename.\n'
' (current value "%s")' % filename)
In case of file not found, please double check the file name and that the file has been uploaded.
In [ ]:
%matplotlib inline
import numpy as np
import phconvert as phc
print('phconvert version: ' + phc.__version__)
Then we load the input file:
In [ ]:
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))
And we plot the alternation histogram:
In [ ]:
phc.plotter.alternation_hist(d)
The previous plot is the alternation histogram for the donor and acceptor channel separately. The shaded areas marks the donor (green) and acceptor (red) excitation periods.
If the histogram looks wrong in some aspects (no photons, wrong detectors assignment, wrong period selection) please go back to the previous cell which loads the file and change the parameters until the histogram looks correct.
You may also find useful to see how many different detectors are present and their number of photons. This information is shown in the next cell:
In [ ]:
detectors = d['photon_data']['detectors']
print("Detector Counts")
print("-------- --------")
for det, count in zip(*np.unique(detectors, return_counts=True)):
print("%8d %8d" % (det, count))
In [ ]:
author = 'John Doe'
author_affiliation = 'Research Institution'
description = 'us-ALEX measurement of a doubly-labeled ssDNA sample.'
sample_name = '20dt ssDNA oligo doubly labeled with Cy3B and Atto647N'
dye_names = 'Cy3B, ATTO647N'
buffer_name = 'TE50 + 0.5M GndCl'
Once you finished editing the the previous sections you can proceed with the actual conversion. To do that, click on the menu Cells -> Run All Below.
After the execution go to Section 6 to download the Photon-HDF5 file.
The cells below contain the code to convert the input file to Photon-HDF5.
In [ ]:
d['description'] = description
d['sample'] = dict(
sample_name=sample_name,
dye_names=dye_names,
buffer_name=buffer_name,
num_dyes = len(dye_names.split(',')))
d['identity'] = dict(
author=author,
author_affiliation=author_affiliation)
In [ ]:
phc.hdf5.save_photon_hdf5(d, overwrite=True)
You can check it's content by using an HDF5 viewer such as HDFView.
We can load the newly created Photon-HDF5 file to check its content:
In [ ]:
from pprint import pprint
In [ ]:
filename = d['_data_file'].filename
In [ ]:
h5data = phc.hdf5.load_photon_hdf5(filename)
In [ ]:
phc.hdf5.dict_from_group(h5data.identity)
In [ ]:
phc.hdf5.dict_from_group(h5data.setup)
In [ ]:
pprint(phc.hdf5.dict_from_group(h5data.photon_data))
In [ ]:
h5data._v_file.close()