OTB RAM memory limit

calculate_and_run.py

# This example shows how to limit the memory usage of OTB 
# with the OTB_MAX_RAM_HINT variable in MB we configurate OTB to use
# that value as limit, if it needs more memory for a image then it
# will chunk the image to fit the memory limit. 
# 
# Also, a function which calculates the limit memory base on the system
# is provided. It requires psutil to be installed in the environment:
#   pip install psutil
#
# For more information refer to OTB Docs:
# https://www.orfeo-toolbox.org/CookBook-6.6.1/AdvancedUse.html

import psutil
import subprocess

def calculate_otb_ram(rate=0.6):
    """Based on the available memory in the system, 
    it calculates a percentage of that memory to be used
    by OTB
    https://www.orfeo-toolbox.org/CookBook-6.6.1/AdvancedUse.html
    """
    avail = (psutil.virtual_memory().available / (1024*1024))
    ram=round(avail * rate)
    return ram

NIR="NIR_utm.tif"
RGB="RGB_utm.tif"
NIR_SI="NIR_si.tif"
superimpose=f"""/bin/bash -c 'source /opt/OTB/otbenv.profile; OTB_MAX_RAM_HINT={RAM} otbcli_Superimpose -inr {RGB} -inm {NIR} -out "{NIR_SI}?&gdal:co:COMPRESS=LZW&gdal:co:TILED=YES&gdal:co:BIGTIFF=YES" uint8'"""

subprocess.run(superimpose, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE)

Dockerfile

# from https://github.com/labfunctions/containers/
ARG ROOT_CONTAINER=jupyter/minimal-notebook:python-3.8.8
FROM $ROOT_CONTAINER

LABEL maintainer="Damián Silvani <[email protected]>"

SHELL ["/bin/bash", "-o", "pipefail", "-c"]

USER root

# ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update \
	&& apt-get install -y --no-install-recommends \
	apt-transport-https \
	build-essential \
	ca-certificates \
	curl \
	file \
	gdal-bin \
	gnupg \
	libgdal-dev \
	libgl1 \
	libproj-dev \
	libspatialindex-dev \
	proj-bin \
	python3-dev \
	python3-venv \
	wget \
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*

## Install gcloud SDK
RUN echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] http://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list \
	&& curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key --keyring /usr/share/keyrings/cloud.google.gpg  add - \
	&& apt-get update -y && apt-get install google-cloud-cli -y \
	&& apt-get clean \
	&& rm -rf /var/lib/apt/lists/*

## Install Orfeo Toolbox
ARG otb_version=8.1.0
ENV OTB_PACKAGE_NAME=OTB-${otb_version}-Linux64
# Install numpy (needed for OTB)
USER ${NB_UID}
RUN pip install --upgrade pip \
	&& pip install numpy
# Download and run OTB setup
USER root
WORKDIR /opt
RUN wget -q https://www.orfeo-toolbox.org/packages/$OTB_PACKAGE_NAME.run \
	&& chmod +x ./$OTB_PACKAGE_NAME.run \
	&& ./$OTB_PACKAGE_NAME.run \
	&& rm -f $OTB_PACKAGE_NAME.run \
	&& ln -s /opt/$OTB_PACKAGE_NAME /opt/OTB

USER ${NB_UID}

## Install python requirements
ADD requirements.txt /tmp/requirements.txt
RUN pip install --upgrade pip \
	&& pip install -r /tmp/requirements.txt

WORKDIR "${HOME}"

requirements.txt

GDAL==3.0.4
markupsafe==2.0.1
pysatproc==0.1.9
unetseg==0.2.2