| import os | |
| import re | |
| from microscopium import io | |
| from microscopium.preprocess import correct_multiimage_illumination | |
| from microscopium.preprocess import find_background_illumination | |
| def main(): | |
| IMAGE_FILE_PATH = "/data/" |
| import time | |
| import logging | |
| # See the docs: https://docs.python.org/3/library/logging.html | |
| timestamp = time.strftime('%d-%b-%Y_%H-%M%p', time.localtime()) | |
| log_filename = "path/to/log.txt" | |
| logging.basicConfig( | |
| format="%(asctime)s %(message)s", | |
| level=logging.DEBUG, |
| name: envname | |
| channels: | |
| - defaults | |
| - conda-forge | |
| dependencies: | |
| - python=3 | |
| - pytest | |
| - pytest-cov | |
| - pytest-flake8 | |
| - coveralls |
| language: python | |
| python: | |
| - "2.7" | |
| - "3.4" | |
| - "3.5" | |
| - "3.6" | |
| - "3.7" | |
| before_install: | |
| - pip install -r requirements.txt | |
| install: |
| pytest | |
| pytest-cov | |
| pytest-flake8 | |
| coveralls |
| # https://gist.github.com/althonos/6914b896789d3f2078d1e6237642c35c | |
| [metadata] | |
| name = {name} | |
| version = {version} | |
| author = Martin Larralde | |
| author-email = [email protected] | |
| home-page = https://github.com/althonos/{name} | |
| description = {description} | |
| long-description = file: README.rst, CHANGELOG.rst |
| def drift_correct(image, shifts, shift_axes=[], kwargs*): | |
| """Align image array to correct for motion over time. | |
| Parameters | |
| ---------- | |
| image : ndarray | |
| Image to drift correct. | |
| shifts : ndarray | |
| Amount to shift each image at each timepoint. | |
| Returned from skimage.feature.register_translation() |
Locate the section for your github remote in the .git/config file. It looks like this:
[remote "origin"]
fetch = +refs/heads/*:refs/remotes/origin/*
url = [email protected]:joyent/node.git
Now add the line fetch = +refs/pull/*/head:refs/remotes/origin/pr/* to this section. Obviously, change the github url to match your project's URL. It ends up looking like this:
| In [1]: from skimage.io import imread as skimage_imread | |
| In [2]: from matplotlib.pyplot import imread as plt_imread | |
| In [3]: from scipy.ndimage import imread as scipy_imread | |
| In [4]: skimage_imread('bulk_water_000.png') | |
| Out[4]: | |
| array([[[146, 125, 54, 255], | |
| [146, 125, 54, 255], |
autopy - simple, cross-platform GUI automation toolkit. MIT - https://github.com/autopilot-rs/autopy