This package creates useful helper functions for python API
Project description
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
0.1.9 Rename, performance for visulize in 1D case 0.1.8 Add documentation
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