Prerequisite for a new PC/Mac before they can do scientific analyses

Google Earth Engine (GEE)

• Command line tool installation (for PC)

  1. Make sure you have a valid VPN
     

  2. Conda install
     Follow this page.
     Maybe add other channels, e.g.,
     conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/main/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/free/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/msys2/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/
conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/menpo/
     Change conda to default channel: conda config --remove-key channels
     Set environment variables following this page.
     

  3. Install the Google Cloud CLI
     Follow this page.
     

  4. Authentication Earth Engine
     First set environment variables as
     name: http_proxy
     value: socks5://server:port (e.g., socks5://127.0.0.1:7890)
     name: https_proxy
     value: socks5://server:port (e.g., socks5://127.0.0.1:7890)
     and then authenticate Earth Engine

     set http_proxy=socks5://127.0.0.1:7890
     set https_proxy=socks5://127.0.0.1:7890
     earthengine authenticate
     set http_proxy=
     set https_proxy=
     
     

  5. Make python3 available
     Follow this page.
     

  6. Install geeup
     First re-open Terminal, and enter the ee environment you just created by conda activate ee. Install geeup by the command pip install geeup. After installation, test it by geeup -h.
     

  7. Disable python aliases (optional)
     Follow this page.
     

  8. Set up geeup (cookies)
     Follow this page.
     

  9. Examples
     

     • help

     geeup -h
     

     • get metadata

     geeup getmeta --input "C:/Users/zhao_/Nutstore/1/Nutstore/wc_10m_prec" --metadata "C:/Users/zhao_/Nutstore/1/Nutstore/wc_10m_prec/metadata.csv"
     

     • image batch upload

     geeup upload --source "C:/Users/jzhao/Downloads/tif" --dest "projects/ee-jzhao-external-dataset/assets/raster/urban-climate-in-europe/paris" -m "C:/Users/jzhao/Downloads/tif/metadata.csv" -u "[email protected]"
     

     • delete image/image collection

     geeup delete --id projects/ee-jzhao-crop-response-to-o3/assets/viirs-sr-red-500-filling
     

     • upgrade geeup

     pip install --upgrade geeup
     

• Command line tool installation (for Mac)

  1. Use /bin/sh
     Open Terminal on Mac then command + , to Preferences. Change Default login shell to /bin/sh.
     
     
     
  2. Conda install
     Follow this page.
     
  3. Install the Google Cloud CLI
     Follow this page.
     
  4. Install pip on Mac
     Follow this page. You may need to install the command line developer tools.
     
  5. Set up environmental variables
     
     • Create a profile file if you don't have one by opening Terminal and issuing the command touch .profile, then close Terminal.
       
     • Add the two lines below to the profile file either manually (the file should be hidden in /Users/<your username>/.profile) or by vim ~/.profile.
       

     export PATH=/Users/<your username>/miniconda3/bin:$PATH
     export PATH=/Users/<your username>/google-cloud-sdk/bin:$PATH
     

  6. Install geeup
     First re-open Terminal, and enter the ee environment you just created by source $HOME/miniconda3/bin/activate and then conda activate ee. Install geeup by the command pip install geeup. After installation, test it by geeup -h.
     
  7. Set up geeup (cookies)
     Follow this page.
     

  geeup getmeta --input "C:/Users/jzhao/Downloads/nc" --metadata "C:/Users/jzhao/Downloads/nc/metadata.csv"

Python was not found; run without arguments to install from the Microsoft Store, or disable this shortcut from Settings https://stackoverflow.com/questions/65348890/python-was-not-found-run-without-arguments-to-install-from-the-microsoft-store

• Image batch upload

geeup upload --source "D:/Data/MSWX/Monthly/Processed" --dest "projects/ee-jzhao-external-dataset/assets/raster/mswx/past/monthly" -m "D:/Data/MSWX/Monthly/Processed/metadata.csv" -u "[email protected]"

• Reproject image1 to image2

image1.resample('bilinear').reproject({
    crs: image2.projection().crs(),
    scale: image2.projection().nominalScale()
});

R

• Import Windows fonts to R

install.packages('remotes')
remotes::install_version('Rttf2pt1', version = '1.3.8')
install.packages('extrafont')
extrafont::font_import()
extrafont::loadfonts(device = 'win')

• Rstudio header

snippet header
	## ----------------------------------
	# Title: 
	# Objective: 
	# Created by: Jiacheng Zhao
	# Created on: `r Sys.Date()`
	# Copyright (c) Jiacheng Zhao, `r format(Sys.Date(), "%Y")`
	# Nanjing University of Information Science & Technology (NUIST)
	# Email: [email protected]
	## ----------------------------------

snippet par
	# cex --------------------------------
	cex.axis = 1.1
	cex.point = 1.7
	cex.legend = 1
	cex.label = 0.7
	cex.axis.label = 0.8
	cex.title = 1.5
	
	# font -------------------------------
	font = 'Calibri'
	
	# lwd --------------------------------
	lwd = 0.5
	medlwd = 1.3
	boxwex = 0.18
	lwd.axis = 0.5
	
	# axis -------------------------------
	x.axis.line = 2.2; y.axis.line = 1.8
	mgp1 = c(3, 0.1, 0)
	mgp2 = c(3, 0.2, 0)
	mgp3 = c(3, 0.1, 0)
	mgp4 = c(3, 0.2, 0)
	tck = 0.03
	
	# legend -----------------------------
	inset = c(0, 2)
	x.intersp = 0.9; y.intersp = x.intersp
	
	# color ------------------------------
	col = 'red'
	cols = c('seagreen', 'gold')
	
	# par --------------------------------
	par(
	cex.axis = cex.axis,
	family = font,
	las = 1,
	lwd = lwd,
	mai = c(0, 0.5, 0, 0.2),
	mfrow = c(6, 1),
	oma = c(6.5, 1.5, 2, 1),
	tck = tck
	)

• Create an r package

require(devtools)
setwd('C:/Users/jzhao/Documents/Nutstore/Projects')
create('smot')

• Pattern matching and replacement

DT[grep('(?=.*A)(?!.*W)', group, perl = T)]

era5cli

• Requests of ERA5-Land hourly data

  era5cli hourly --land --variables 2m_temperature  --startyear 1950 --endyear 1950 --splitmonths True
  

7zip

• Batch unzip

  "C:\Program Files\7-zip\7z.exe" e *.zip