shareloc-utils 0.1.0

Utility tools for ShareLoc.XYZ

ShareLoc Utilities

Utility tools for ShareLoc.XYZ in Python

Features

• Batch Downloading datasets from https://shareloc.xyz website
• Parser for *.smlm files

Installation

pip install -U shareloc-utils

Usage for Batch Download

You can pass datasets url directly to the command line like this:

python -m shareloc_utils.batch_download --datasets=https://sandbox.zenodo.org/record/891810 --output_dir=./output --conversion

If you want to downlaod multiple datasets, use comma to separate multiple dataset URL.

To print all other options type:

python -m shareloc_utils.batch_download --help

Use the SMLM file parser

In Python, you use the read_smlm_file function to parse the *.smlm file downloaded from ShareLoc(https://shareloc.xyz).

In the following example, we first parse the tables in the smlm file, then generate a histogram image:

from PIL import Image
from shareloc_utils.smlm_file import read_smlm_file, plot_histogram

# parse the .smlm file
manifest = read_smlm_file("./localization_table.smlm")
# one file can contain multiple localization tables
tables = manifest["files"]

# generate an histogram image for the first table
histogram = plot_histogram(tables[0]["data"], value_range=(0, 255))

# save the histogram image as 16-bit png file
im = Image.fromarray(histogram.astype("uint16"))
im.save("output.png")

Development

• Install and set up development environment.

  pip install -r requirements_dev.txt
  

  This will install all requirements. It will also install this package in development mode, so that code changes are applied immediately without reinstall necessary.

• Here's a list of development tools we use.

  • black
  • flake8
  • mypy
  • pydocstyle
  • pylint
  • pytest
  • tox

• It's recommended to use the corresponding code formatter and linters also in your code editor to get instant feedback. A popular editor that can do this is vscode.

• Run all tests, check formatting and linting.

  tox
  

• Run a single tox environment.

  tox -e lint
  

• Reinstall all tox environments.

  tox -r
  

• Run pytest and all tests.

  pytest
  

• Run pytest and calculate coverage for the package.

  pytest --cov-report term-missing --cov=shareloc_utils
  

• Continuous integration is by default supported via GitHub actions. GitHub actions is free for public repositories and comes with 2000 free Ubuntu build minutes per month for private repositories.