hdcms 0.1.10

This package creates useful helper functions for python API

hdcms-helper

This library is available on pypi here. Install using pip install hdcms.

How to use

import hdcms as hdc

hdc.generate_examples(visualize=True)
gaussian_sum_stat = hdc.regex2stats1d(r"gaus_\d+.txt")
laplacian_sum_stat = hdc.regex2stats1d(r"laplace_\d+\.txt")

# data in another directory for example:
# regex2stats2d(r"CM1_11_\d+.txt", dir="~/src/hdcms/data/")

print(hdc.compare(gaussian_sum_stat, laplacian_sum_stat))
hdc.write_image(gaussian_sum_stat, "tmp.png")

This library is built on top of the hdcms-bindings package, which exposes python bindings to a C library. That bindings package contains only a few functions and lacks a nice user experience. But, if you are only interested in that, check it out.

Summary of provided functions

regex2stats1d, regex2stats2d - takes regex and converts to summary statistic array2stats1d, array2stats2d - takes a varargs list of numpy arrays and converts them into 1d summary statistic file2stats1d, file2stats2d - takes filename and converts it to a summary stat. it is expected that the file contents are a list of filenames on separate lines filenames2stats1d, filenames2stats2d - takes list of filenames and converts it to a summary stat compare - compares two summary statistics write_image - visualizes a summary statistic clean - takes list of filenames and shows you what changes need to be made generate_examples - generate synthetic data as an example

Dependencies

Numpy is a necessary dependency for every function. Matplotlib and scipy are needed for \verb|generate_example()|, which will generate a raondom synthetic data set. opencv is required for \verb|write_image()|, which will visualize summary statistics. You can see a complete list of functions (and where they are located) by running the following code. Look at the output of \verb|help(hdc)| to get the right filename.

TODO

filter function for 2d spectra to filter out peaks with large x variation

Change Log

0.1.10 Really rename 0.1.9 Rename, performance for visulize in 1D case 0.1.8 Add documentation