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

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

sbalci

First Method

Deleting the .git folder may cause problems in our git repository. If we want to delete all of our commits history, but keep the code in its current state, try this:

# Check out to a temporary branch:
git checkout --orphan TEMP_BRANCH

# Add all the files:
git add -A

sbalci

Collections of scripts harvested mainly from Pete, but also picked up from the forums

TOC

Accessing dynamic measurements.groovy - Most annotation measurements are dynamically created when you click on the annotation, and 
are not accessible through the standard getMeasurement function. This is a way around that.

Affine transformation.groovy - access more accurate measurements for the affine transformation used in the image alignment (m5/m6+)

Alignment of local cells.groovy - check neighborhood for similarly aligned cells