Filippo Arcadu arcaduf

## Find command from your terminal history
history
Ctrl+R
Type the subject of your search, e.g. screen
Type Ctrl+R repeatedly until you find your match.

## Convert \t into 4 spaces in each file inside a folder (and viceversa)
From \t to 4 spaces:
find . -type f -exec sed -i.orig 's/\t/    /g' {} +

From 4 spaces to \t:
find . -type f -exec sed -i.orig 's/    /\t/g' {} +

## Create and save annotations with ImageJ
Load image.
Duplicate it as many times as many types of ROI you want to draw.
GO --> Edit --> Selection --> Add to Manager.
Draw the ROI and add it to the manager.
Click on each ROI / each group of ROIs and then click "More" --> "Fill" inside the manager.
Save the resulting image as separate .png.

In case you want to work with the .roi format of ImageJ, use this python code to read the .zip and the .roi:
                https://gist.githubusercontent.com/luispedro/3437255/raw/d3f0be5efbe37efe27946c5fa21f5ef523cdac43/readroi.py

## Sanitize python script by converting tabs into spaces
sudo apt-get install moreutils
expand -t 4 filein | sponge fileout

## Python: read and dump dictionary to YAML preserving order
```python
import collections , yaml

_mapping_tag = yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG

def dict_representer(dumper, data):
  return dumper.represent_mapping(_mapping_tag, data.iteritems())

def dict_constructor(loader, node):
  return collections.OrderedDict(loader.construct_pairs(node))

## Start an interactive CPU session with Slurm
interactive -c 24 -t 08:00:00

## Work with screen sessions
Start a screen session:
screen -S "vgg-regression"

To detach a screen session:
Ctrl-a d

To reattach the only screen session
Ctrl-a r

To reattach a session of given PID

## Install R package directly from main repository
Example with 'mlbench':
install.packages('mlbench', dependencies=TRUE, repos='http://cran.rstudio.com/')

## Basic commands for Windows Prompt
Change disk:
cd /d C:\

Go back:
cd..

## Create symbolic links to a dataset maintaining its folder tree structure
cp -as absolute_path_to_source/ absolute_path_to_target/
	history
	Ctrl+R
	Type the subject of your search, e.g. screen
	Type Ctrl+R repeatedly until you find your match.
	From \t to 4 spaces:
	find . -type f -exec sed -i.orig 's/\t/ /g' {} +

	From 4 spaces to \t:
	find . -type f -exec sed -i.orig 's/ /\t/g' {} +
	Load image.
	Duplicate it as many times as many types of ROI you want to draw.
	GO --> Edit --> Selection --> Add to Manager.
	Draw the ROI and add it to the manager.
	Click on each ROI / each group of ROIs and then click "More" --> "Fill" inside the manager.
	Save the resulting image as separate .png.

	In case you want to work with the .roi format of ImageJ, use this python code to read the .zip and the .roi:
	https://gist.githubusercontent.com/luispedro/3437255/raw/d3f0be5efbe37efe27946c5fa21f5ef523cdac43/readroi.py
	sudo apt-get install moreutils
	expand -t 4 filein \| sponge fileout
	```python
	import collections , yaml

	_mapping_tag = yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG

	def dict_representer(dumper, data):
	return dumper.represent_mapping(_mapping_tag, data.iteritems())

	def dict_constructor(loader, node):
	return collections.OrderedDict(loader.construct_pairs(node))
	Start a screen session:
	screen -S "vgg-regression"

	To detach a screen session:
	Ctrl-a d

	To reattach the only screen session
	Ctrl-a r

	To reattach a session of given PID
	Example with 'mlbench':
	install.packages('mlbench', dependencies=TRUE, repos='http://cran.rstudio.com/')