Genevieve Buckley GenevieveBuckley

PyConlineAU 2020 https://pretalx.com/pycon-au-2020/talk/review/RP9LMHZUMYZZWUB73ESTKG9SGT9QCBMJ

dask-image: distributed image processing for large data

Abstract

This talk introduces dask-image, a python library for distributed image processing. Targeted towards applications involving large array data too big to fit in memory, dask-image is built on top of numpy, scipy, and dask allowing easy scalability and portability from your laptop to the supercomputing cluster. It is of broad interest for a diverse range of data analysis applications such as video/streaming data, computer vision, and scientific fields including astronomy, microscopy and geosciences. We will provide a general overview of the dask-image library, then discuss mixing and matching with your own custom functions, and present a practical case study of a python image processing pipeline.

Detailed abstract

Image datasets are large, and becoming larger. The widely used benchmark dataset COCO (Common Objects in Context) contains 330,000

	briefcase android project

	phone MUST be in file transfer mode
	Must wait for the computer to recognise that the phone has been plugged in
	Must allow USB debugging

	https://pastebin.com/0xpejQPB

	Traceback (most recent call last):
	File "/home/xero/.virtualenvs/beeware-venv/bin/briefcase", line 8, in <module>

	# -- coding: utf-8 --

	__author__ = """John Kirkham"""
	__email__ = "[email protected]"


	import scipy.ndimage

	from . import _utils
	from . import _ops

	Compare means
	* Two groups (control vs drug)
	* Same subjects measured twice (before/after)
	* Pairwise differences normal -> Paired t-test (parametric test)
	* Pairwise differences non-normal -> Wilcoxon matched pairs signed rank test (nonparametric test)
	* Each subject measured once
	* Each group normal and variances equal -> Unpaired t-test (parametric test)
	* Each group normal -> Unpaired t-test with Welch's correction (parametric test)
	* One or both groups non-normal -> Mann-Whitney test (nonparametric test)

	"""
	This script is adapted from https://github.com/napari/napari/blob/master/examples/interactive_scripting.py

	Instead of replacing the entire layer data, we want to append to the data stack.
	However it produces "WARNING: Cannot make QOpenGLContext current in a different thread"
	"""
	import numpy as np
	import napari
	from napari.qt import thread_worker
	import time

	# From https://coderwall.com/p/-wbo5q/pip-install-a-specific-github-repo-tag-or-branch
	pip install -e git://github.com/{ username }/{ reponame }.git@{ tag name }#egg={ desired egg name }