srgorelik

#!/usr/bin/env Rscript

# sgorelik 2019

suppressPackageStartupMessages(library(optparse))
suppressPackageStartupMessages(library(rasterVis))

opt.list <- list(
    make_option(c('-b','--band'), type = 'integer', default = 1, metavar = 'INTEGER',
                help = 'The raster band to plot (default is %default).')

srgorelik

This is a quick walthrough on how to use the reticulate package to work with Python interactively in an R session.

First, to specify the Python version to call (e.g., 3 instead of 2), set a RETICULATE_PYTHON path variable:

$ which python3
/usr/bin/python3
$ echo "RETICULATE_PYTHON='/usr/bin/python3'" >> ~/.Renviron

srgorelik

#!/usr/bin/env Rscript

suppressPackageStartupMessages(library(optparse))

opt.list <- list(
     make_option(c('-r','--round'), type = 'integer', default = 2, metavar = 'INTEGER',
     help = 'Number of decimal places (default is %default)')
)

opt.parser <- OptionParser(option_list = opt.list,

srgorelik

#!/usr/bin/env Rscript

# csv - a linux CLI for nicely displaying and summarizing CSV files

suppressPackageStartupMessages(library(optparse))
suppressPackageStartupMessages(library(data.table))

file_ext <- function(x) {
	pos <- regexpr("\\.([[:alnum:]]+)$", x)
	tolower(ifelse(pos > -1L, substring(x, pos + 1L), ""))

srgorelik

colorbar <- function(pal, min, max = -min, nticks = 11, at = seq(min, max, len = nticks), title = '', border = NA, dir = 'v') {
	scale = (length(pal)-1)/(max-min)
	graphics.off()
	if (dir == 'v') {
		w <- 1; h <- 5
		xx <- c(0, 10)
		yy <- c(min, max)
		asp <- 2
		side <- 4
	} else if(dir == 'h') {

srgorelik

extractCellsFromLayers <- function(stack, index) {
  # --------------------------------------------------------------------------------
  # Purpose:
  #   Extract grid cells from different layers in a raster stack.
  #
  # Arguments:
  #   stack       A RasterStack object; the stack from which to extract cell values.
  #   index       A RasterLayer object; the index used to extract cells from the
  #               stack. Cell values in the index raster indicate from which layer 
  #               in the raster stack to extract the corresponding cell values.

srgorelik

#!/usr/bin/env python3

from osgeo import gdal
import numpy as np
import pandas as pd

def stats(raster, band = 1, nodata = None):
	"""Print descriptive statistics of a raster or numpy array"""
	if (type(raster) != str) and (type(raster) != np.ndarray):
		print("Error: input must be a raster filepath or numpy array.")

srgorelik

img <- function(x, pal = 'j', cut = F, brks = 10, units = '', rev.pal = F, vals = F, axes = T,
                na.col = 'black', fg = 'black', bg = 'white', draw.cells = F, legend = T, ...) {
  # --------------------------------------------------------------------------------
  # Purpose:
  #   Quickly plot an image (using matrix or raster objects).
  #
  # Arguments:
  #   x           Either a matrix or raster object.
  #   pal         Color palette code (either letter or number selection).
  #   cut         A logical flag to use a discrete color ramp instead of a continuous one.