GenevieveBuckley

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()

GenevieveBuckley

# https://gist.github.com/althonos/6914b896789d3f2078d1e6237642c35c

[metadata]
name = {name}
version = {version}
author = Martin Larralde
author-email = martin.larralde@ens-paris-saclay.fr
home-page = https://github.com/althonos/{name}
description = {description}
long-description = file: README.rst, CHANGELOG.rst

GenevieveBuckley

language: python
python:
    - "2.7"
    - "3.4"
    - "3.5"
    - "3.6"
    - "3.7"
before_install:
    - pip install -r requirements.txt
install:

GenevieveBuckley

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,

GenevieveBuckley

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/"

GenevieveBuckley

Check out a pull request locally

ID = the pull request ID number (eg: 3544) BRANCHNAME = the name of the pull request branch (eg: 'image-registration')

git fetch upstream pull/ID/head:BRANCHNAME
git checkout BRANCHNAME

See: https://help.github.com/articles/checking-out-pull-requests-locally/

GenevieveBuckley

Python testing

pytest

https://docs.pytest.org/en/latest/usage.html

pytest
pytest path/to/tests/
pytest path/to/tests/test_file.py
pytest path/to/tests/test_file.py::test_func
pytest path/to/tests/test_file.py::TestClass

GenevieveBuckley

from bokeh.io import push_notebook, output_notebook, show, save
from bokeh.layouts import row, column, layout
from bokeh.plotting import figure
output_notebook()

GenevieveBuckley

Install

Either copy the aliases from the .gitconfig or run the commands in add-pr-alias.sh

Usage

Easily checkout local copies of pull requests from remotes:

• git pr 4 - creates local branch pr/4 from the github upstream(if it exists) or origin remote and checks it out
• git pr 4 someremote - creates local branch pr/4 from someremote remote and checks it out

GenevieveBuckley

import pickle

from autoscript_sdb_microscope_client import SdbMicroscopeClient
from autoscript_sdb_microscope_client.enumerations import *
from autoscript_sdb_microscope_client.structures import *

microscope = SdbMicroscopeClient()
microscope.connect()
object_to_pickle = microscope.imaging.get_image()