sbalci

Update a git repo

With this script, you can easily update a git repo.

Install

curl -# https://gist.githubusercontent.com/Menencia/6435756/raw/update.sh > update.sh
curl -# https://gist.githubusercontent.com/Menencia/6435756/raw/version.sh > version.sh

sbalci

#### 1. Sign up at GitHub.com ################################################

## If you do not have a GitHub account, sign up here:
## https://github.com/join

# ----------------------------------------------------------------------------

#### 2. Install git ##########################################################

## If you do not have git installed, please do so: 

sbalci

https://github.com/brentthorne/posterdown

https://github.com/rstudio/pagedown

https://github.com/GerkeLab/betterposter

https://github.com/pzhaonet/postr

https://github.com/odeleongt/postr

sbalci

import qupath.lib.scripting.QP
import qupath.lib.geom.Point2
import qupath.lib.roi.PolygonROI
import qupath.lib.objects.PathAnnotationObject
import qupath.lib.images.servers.ImageServer


//Aperio Image Scope displays images in a different orientation
def rotated = true

sbalci

`<-` <- function(lhs, rhs, envir = parent.frame()) {
  assign(as.character(substitute(lhs)), rhs, envir)
  lockBinding(substitute(lhs), envir)
  invisible(rhs)
}

sbalci

When you use knit_expand it appears that the inclusion of the Rmd is done on the first pass, and then the complete document evaluated. This means that a Rmd block referenced in loop with knit_expand will only evaluate changing variables at their last value.

This can be worked around by passing the literal value of the variable at the time of the knit_expand with {{var}} syntax.

This is documented in the knitr_expand docs, but less clear (to an R noob like me) for embedded documents rather than strings.

sbalci

How to use Gephi to visualize from Wikidata

I'm a long-time fan of the graph visualization tool Gephi and since Wikimania 2019 I got involved with Wikidata. I was aware of the Gephi plugin "Semantic Web Importer", but when I check it out, I only find old tutorials connecting to DBpedia, not Wikidata:

• "Visualising Related Entries in Wikipedia Using Gephi" by Tony Hirst, 2012-07-03
• "Let’s Play Gephi: Dbpedia, RDF, Sparql and your favorite Actors" by Matthieu Totet, 2015-10-06
• ["Gephi tutorials: Semantic Web Importer" by Matthieu

sbalci

Collection of scripts mostly from Pete, but also taken from the forums. Note you can always run a saved classifier using the
runClassifier() command, with the file path included as a string.

TOC

A simple cell classifier.groovy - One way to classify cells.

A simple classifier 2.groovy - Another way.

Annotation Classifications to Name field.groovy - Sets the Name of the annotation to its classification. Useful for applying a second

sbalci

<?php
/*
Add bcc for checkout emails
*/
function my_pmpro_email_headers_admin_emails($headers, $email)
{		
	//bcc checkout emails
	if($email->template == "membership_expiring" || $email->template == "membership_expired")
	{
		//add bcc

sbalci

/**
 * QuPath script to calculate areas (e.g. of tumor) based upon classified cells only.
 *
 * It works by using a distance transform applied to binary images generated from the
 * objects of each class, and then assigns each pixel to the closest object.
 *
 * Having done this, new annotations are generated for these regions.
 *
 * WARNINGS!
 * - This will remove *all* previous annotations & replace them with new annotations