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README.md

ISCE2

This is the Interferometric synthetic aperture radar Scientific Computing Environment (ISCE). Its initial development was funded by NASA's Earth Science Technology Office (ESTO) under the Advanced Information Systems Technology (AIST) 2008 and is currently being funded under the NASA-ISRO SAR (NISAR) project.

THIS IS RESEARCH CODE PROVIDED TO YOU "AS IS" WITH NO WARRANTIES OF CORRECTNESS. USE AT YOUR OWN RISK.

This software is open source under the terms of the the Apache License. Its export classification is 'EAR99 NLR', which entails some restrictions and responsibilities. Please read the accompanying LICENSE.txt and LICENSE-2.0 files.

ISCE is a framework designed for the purpose of processing Interferometric Synthetic Aperture Radar (InSAR) data. The framework aspects of it have been designed as a general software development framework. It may have additional utility in a general sense for building other types of software packages. In its InSAR aspect ISCE supports data from many space-borne satellites and one air-borne platform. We continue to increase the number of sensors supported. At this time the sensors that are supported are the following: ALOS, ALOS2, COSMO_SKYMED, ENVISAT, ERS, KOMPSAT5, RADARSAT1, RADARSAT2, RISAT1, Sentinel1, TERRASARX, and UAVSAR.

Contents

  1. Software Dependencies
  2. Building ISCE
  3. Running ISCE
  4. Input Files
  5. Component Configurability
  6. User community Forums

1. Software Dependencies

Basic:

  • gcc >= 4.8+ (with C++11 support)
  • fftw >= 3.2.2 (with single precision support)
  • Python >= 3.5 (3.6 preferred)
  • scons >= 2.0.1
  • curl - for automatic DEM downloads
  • GDAL and its Python bindings >= 2.2

Optional:

For a few sensor types:

  • hdf5 >= 1.8.5 and h5py >= 1.3.1 - for COSMO-SkyMed, Kompsat5, and 'Generic' sensor

For mdx (image visualization tool) options:

  • Motif libraries and include files
  • ImageMagick - for mdx production of kml file (advanced feature)
  • grace - for mdx production of color table and line plots (advanced feature)

For the "unwrap 2 stage" option:

RelaxIV and Pulp are required. Information on getting these packages if you want to try the unwrap 2 stage option:

  • RelaxIV (a minimum cost flow relaxation algorithm coded in C++ by Antonio Frangioni and Claudio Gentile at the University of Pisa, based on the Fortran code developed by by Dimitri Bertsekas while at MIT) available by request at http://www.di.unipi.it/~frangio. So that ISCE will compile it properly, the RelaxIV files should be placed in the directory: 'contrib/UnwrapComp/src/RelaxIV'.

  • PULP: Use easy_install or pip to install it or else clone it from, https://github.com/coin-or/pulp. Make sure the path to the installed pulp.py is on your PYTHONPATH environment variable (it should be the case if you use easy_install or pip).

For splitSpectrum and GPU modules:

  • cython3 - must have an executable named cython3 (use a symbolic link)
  • cuda - for GPUtopozero and GPUgeo2rdr
  • opencv - for split spectrum

With Anaconda

The conda requirements file is shown below:

cython
gdal
git
h5py
libgdal
pytest
numpy
fftw
scipy
basemap
scons
opencv

With the above contents in a textfile named "requirements.txt"

> conda install --yes --file requirements.txt

Ensure that you create a link in the anaconda bin directory for cython3.

With Macports

The following ports (assuming gcc7 and python36) are needed on OSX

gcc7
openmotif
python36
fftw-3 +gcc7 
fftw-3-single +gcc7
xorg-libXt +flat_namespace
git 
hdf5 +gcc7 
h5utils
netcdf +gcc7
netcdf-cxx
netcdf-fortran
postgresql95
postgresql95-server
proj
cairo
scons
opencv +python36
ImageMagick
gdal +expat +geos +hdf5 +netcdf +postgresql95 +sqlite3
py36-numpy +gcc7 +openblas
py36-scipy +gcc7 +openblas
py36-matplotlib +cairo +tkinter
py36-matplotlib-basemap
py36-h5py

Python3 Convention

We follow the convention of most package managers in using the executable 'python3' for Python3.x and 'python' for Python2.x. This makes it easy to turn Python code into executable commands that know which version of Python they should invoke by naming the appropriate version at the top of the executable file (as in #!/usr/bin/env python3 or #!/usr/bin/env python). Unfortunately, not all package managers (such as macports) follow this convention. Therefore, if you use one of a package manager that does not create the 'python3' executable automatically, then you should place a soft link on your path to have the command 'python3' on your path. Then you will be able to execute an ISCE application such as 'stripmapApp.py as "> stripmapApp.py" rather than as "> /path-to-Python3/python stripmapApp.py".

License required for dependencies to enable some workflows in ISCE

Some of the applications, or workflows (such as insarApp.py and isceApp.py), in ISCE that may be familiar to users will not work with this open source version of ISCE without obtaining licensed components. WinSAR users who have downloaded ISCE from the UNAVCO website (https://winsar.unavco.org/software/isce) have signed the licence agreement and will be given access to those licensed components. Others wanting to use those specific workflows and components may be able to sign the agreement through UNAVCO if they become members there. Further instructions will be available for a possible other procedure for obtaining a license directly from the supplier of those components.

ISCE provides workflows that do not require the licensed components that may be used effectively and that will be supported going forward by the ISCE team. Users that need to work with newly processed data along with older processed data may require those licensed components as a convenience unless they also reprocess the older data with the same workflows available in this open source release.


Building ISCE

Configuration control

Scons requires that configuration information be present in a directory specified by the environment variable SCONS_CONFIG_DIR. First, create a build configuration file, called SConfigISCE and place it in your chosen SCONS_CONFIG_DIR. The SConfigISCE file should contain the following information, note that the #-symbol denotes a comment and does not need to be present in the SConfigISCE file:

NOTE: Locations vary from system to system, so make sure to use the appropriate location. The one listed here are just for illustrative purpose.

# The directory in which ISCE will be built
PRJ_SCONS_BUILD = $ISCE_BUILD_ROOT/isce

# The directory into which ISCE will be installed
PRJ_SCONS_INSTALL = $ISCE_INSTALL_ROOT/isce

# The location of libraries, such as libstdc++, libfftw3 (for most system
# it's /usr/lib and/or /usr/local/lib/ and/or /opt/local/lib)
LIBPATH = $YOUR_LIB_LOCATION_HOME/lib64 $YOUR_LIB_LOCATION_HOME/lib

# The location of Python.h. If you have multiple installations of python
# make sure that it points to the right one
CPPPATH = $YOUR_PYTHON_INSTALLATION_LOCATION/include/python3.xm $YOUR_PYTHON_INSTALLATION_LOCATION/lib/python3.x/site-packages/numpy/core/include

# The location of the fftw3.h (most likely something like /usr/include or
# /usr/local/include /opt/local/include
FORTRANPATH =  $YOUR_FFTW3_INSTALLATION_LOCATION/include

# The location of your Fortran compiler. If not specified it will use the system one
FORTRAN = $YOUR_COMPILER_LOCATION/bin/gfortran

# The location of your C compiler. If not specified it will use the system one
CC = $YOUR_COMPILER_LOCATION/bin/gcc

# The location of your C++ compiler. If not specified it will use the system one
CXX = $YOUR_COMPILER_LOCATION/bin/g++

#libraries needed for mdx display utility
MOTIFLIBPATH = /opt/local/lib       # path to libXm.dylib
X11LIBPATH = /opt/local/lib         # path to libXt.dylib
MOTIFINCPATH = /opt/local/include   # path to location of the Xm
                                    # directory with various include files (.h)
X11INCPATH = /opt/local/include     # path to location of the X11 directory
                                    # with various include files

#Explicitly enable cuda if needed
ENABLE_CUDA = True
CUDA_TOOLKIT_PATH = $YOUR_CUDA_INSTALLATION  #/usr/local/cuda

In the above listing of the SConfigISCE file, ISCE_BUILD_ROOT and ISCE_INSTALL_ROOT may be actual environment variables that you create or else you can replace them with the actual paths you choose to use for the build files and the install files. Also, in the following the capitalization of 'isce' as lower case does matter. This is the case-sensitive package name that Python code uses for importing isce.

Install ISCE

cd isce scons install

For a verbose install run: scons -Q install

The scons command also allows you to explicitly specify the name of the SConfigISCE file, which could be used to specify an alternative file for (say SConfigISCE_NEW) which must still be located in the same SCONS_CONFIG_DIR, run

scons install --setupfile=SConfigISCE_NEW

This will build the necessary components and install them into the location specified in the configuration file as PRJ_SCONS_INSTALL.

Note about compiling ISCE after an unsuccessful build.

When building ISCE, scons will check the list of header files and libraries that ISCE requires. Scons will cache the results of this dependency checking. So, if you try to build ISCE and scons tells you that you are missing headers or libraries, then you should remove the cached files before trying to build ISCE again after installing the missing headers and libraries. The cached files are config.log, .sconfig.dblite, and the files in directory .sconf_temp. You should run the following command while in the top directory of the ISCE source (the directory containing the SConstruct file):

> rm -rf config.log .sconfig.dblite .sconf_temp

and then try "scons install" again.

Setup Your Environment

Once everything is installed, you will need to set the following environment variables to run the programs included in ISCE ($ISCE_INSTALL_ROOT may be an environment variable you created above or else replace it with the actual path to where you installed ISCE):

export PYTHONPATH=$ISCE\_INSTALL\_ROOT:$PYTHONPATH

and to put the executable commands in the ISCE applications directory on your PATH for convenience,

export ISCE_HOME=$ISCE_INSTALL_ROOT/isce
export PATH=$ISCE_HOME/applications:$PATH

An optional environment variable is $ISCEDB. This variable points to a directory in which you may place xml files containing global preferences. More information on this directory and the files that you might place there is given below in Section on Input Files. For now you can ignore this environment variable.

To test your installation and your environment, do the following:

> python3
>>> import isce
>>> isce.version.release_version

Running ISCE

Running ISCE from the command line

Copy the example xml files located in the example directory in the ISCE source tree to a working directory and modify them to point to your own data. Run them using the command:

> $ISCE_HOME/applications/stripmapApp.py isceInputFile.xml

or (with $ISCE_HOME/applications on your PATH) simply,

> stripmapApp.py isceInputFile.xml

The name of the input file on the command line is arbitrary. ISCE also looks for appropriately named input files in the local directory

You can also ask ISCE for help from the command line:

> stripmapApp.py --help

This will tell you the basic command and the options for the input file. Example input files are also given in the 'examples/input_files' directory.

As explained in the Component Configurability section below, it is also possible to run stripmapApp.py without giving an input file on the command line. ISCE will automatically find configuration files for applications and components if they are named appropriately.

Running ISCE in the Python interpreter

It is also possible to run ISCE from within the Python interpreter. If you have an input file named insarInputs.xml you can do the following:

%> python3
>>> import isce
>>> from stripmapApp import Insar
>>> a = Insar(name="stripmapApp", cmdline="insarInputs.xml")
>>> a.configure()
>>> a.run()

(As explained in the Component Configurability section below, if the file insarInputs.xml were named stripmapApp.xml or insar.xml, then the 'cmdline' input on the line creating 'a' would not be necessary. The file 'stripmapApp.xml' would be loaded automatically because when 'a' is created above it is given the name 'stripmapApp'. A file named 'insar.xml' would also be loaded automatically if it exists because the code defining stripmapApp.py gives all instances of it the 'family' name 'insar'. See the Component Configurability section below for details.)

Running ISCE with steps

An other way to run ISCE is the following:

stripmapApp.py insar.xml --steps

This will run stripmapApp.py from beginning to end as is done without the --steps option, but with the added feature that the workflow state is stored in files after each step in the processing using Python's pickle module. This method of running stripmapApp.py is only a little slower and it uses extra disc space to store the pickle files, but it provides some advantage for debugging and for stopping and starting a workflow at any predetermined point in the flow.

The full options for running stripmapApp.py with steps is the following:

stripmapApp.py insar.xml [--steps] [--start=<s>] [--end=<s>] [--dostep=<s>]

where "<s>" is the name of a step. To see the full ordered list of steps the user can issue the following command:

stripmapApp.py insar.xml --steps --help

The --steps option was explained above. The --start and --end option can be used together to process a range of steps. The --dostep option is used to process a single step.

For the --start and --dostep options to work, of course, requires that the steps preceding the starting step have been run previously because the state of the work flow at the beginning of the first step to be run must be stored from a previous run.

An example for using steps might be to execute the end-to-end workflow with --steps to store the state of the workflow after every step as in,

stripmapApp.py insar.xml --steps

Then use --steps to rerun some of the steps (perhaps you made a code modification for one of the steps and want to test it without starting from the beginning) as in

stripmapApp.py insar.xml --start=<step-name1> --end=<step-name2>

or to rerun a single step as in

stripmapApp.py insar.xml --dostep=<step-name>

Running stripmapApp.py with --steps also enables one to enter the Python interpreter after a run and load the state of the workflow at any stage and introspect the objects in the flow and play with them as follows, for example:

%> python3
>>> import isce
>>> f = open("PICKLE/formslc")
>>> import pickle
>>> a = pickle.load(f)
>>> o = f.getMasterOrbit()
>>> t, x, p, off = o._unpackOrbit()
>>> print(t)
>>> print(x)

Someone with familiarity of the inner workings of ISCE can exploit this mode of interacting with the pickle object to discover much about the workflow states and also to edit the state to see its effect on a subsequent run with --dostep or --start.

Notes on Digital Elevation Models

  • ISCE will automatically download SRTM Digital Elevation Models when you run an application that requires a DEM. In order for this to work follow the next 2 instructions:
  1. You will need to have a user name and password from urs.earthdata.nasa.gov and you need to include LPDAAC applications to your account.

    a. If you don't already have an earthdata username and password, you can set them at https://urs.earthdata.nasa.gov/

    b. If you already have an earthdata account, please ensure that you add LPDAAC applications to your account: - Login to earthdata here: https://urs.earthdata.nasa.gov/home - Click on my applications on the profile - Click on “Add More Applications” - Search for “LP DAAC” - Select “LP DAAC Data Pool” and “LP DAAC OpenDAP” and approve.

  2. create a file named .netrc with the following 3 lines:

machine urs.earthdata.nasa.gov
    login your_earthdata_login_name
    password your_earthdata_password
  1. set permissions to prevent others from viewing your credentials:
> chmod go-rwx .netrc
  • When you run applications that require a dem, such as stripmapApp.py, if a dem component is provided but the dem is referenced to the EGM96 geo reference (which is the case for SRTM DEMs) it will be converted to have the WGS84 ellipsoid as its reference. A new dem file with suffix wgs84 will be created.

  • If no dem component is specified as an input a EGM96 will be automatically downloaded (provided you followed the preceding instructions to register at earthdata) and then it will be converted into WGS84.

  • If you define an environment variable named DEMDB to contain the path to a directory, then ISCE applications will download the DEM (and water body mask files into the directory indicated by DEMDB. Also ISCE applications will look for the DEMs in the DEMDB directory and the local processing directory before downloading a new DEM. This will prevent ISCE from downloading multiple copies of a DEM if you work with data in different subdirectories that cover similar geographic locations.

Input Files

Input files are structured 'xml' documents. This section will briefly introduce their structure using a special case appropriate for processing ALOS data. Examples for the other sensor types can be found in the directory 'examples/input_files'.

The basic (ALOS) input file looks like this (indentation is optional):

stripmapApp.xml (Option 1)

<stripmapApp>
<component name="stripmapApp">
    <property name="sensor name">ALOS</property>
    <component name="Master">
        <property name="IMAGEFILE">
            /a/b/c/20070215/IMG-HH-ALPSRP056480670-H1.0__A
        </property>
        <property name="LEADERFILE">
            /a/b/c/20070215/LED-ALPSRP056480670-H1.0__A
        </property>
        <property name="OUTPUT">20070215</property>
    </component>
    <component name="Slave">
        <property name="IMAGEFILE">
            /a/b/c/20061231/IMG-HH-ALPSRP049770670-H1.0__A
        </property>
        <property name="LEADERFILE">
            /a/b/c/20061231/LED-ALPSRP049770670-H1.0__A
        </property>
        <property name="OUTPUT">20061231</property>
    </component>
</component>
</stripmapApp>

The data are enclosed between an opening tag and a closing tag. The <stripmapApp> tag is closed by the </stripmapApp> tag for example. This outer tag is necessary but its name has no significance. You can give it any name you like. The other tags, however, need to have the names shown above. There are 'property', and 'component' tags shown in this example.

The component tags have names that match a Component name in the ISCE code. The component tag named 'stripmapApp' refers to the configuration information for the Application (which is a Component) named "stripmapApp". Components contain properties and other components that are configurable. The property tags give the values of a single variable in the ISCE code. One of the properties defined in stripmapApp.py is the "sensor name" property. In the above example it is given the value ALOS. In order to run stripmapApp.py two images need to be specified. These are defined as components named 'Master' and 'Slave'. These components have properties named 'IMAGEFILE', 'LEADERFILE', and 'OUTPUT' with the values given in the above example.

NOTE: the capitalization of the property and component names are not of any importance. You could enter 'imagefile' instead of 'IMAGEFILE', for example, and it would work correctly. Also extra spaces in names that include spaces, such as "sensor name" do not matter.

There is a lot of flexibility provided by ISCE when constructing these input files through the use of "catalog" tags and "constant" tags.

A "catalog" tag can be used to indicate that the contents that would normally be found between an opening ad closing "component" tag are defined in another xml file. For example, the stripmapApp.xml file shown above could have been split between three files as follows:

stripmapApp.xml (Option 2)

<stripmapApp>
    <component name="insar">
        <property  name="Sensor name">ALOS</property>
        <component name="master">
            <catalog>20070215.xml</catalog>
        </component>
        <component name="slave">
            <catalog>20061231.xml</catalog>
        </component>
    </component>
</stripmapApp>

20070215.xml

<component name="Master">
    <property name="IMAGEFILE">
        /a/b/c/20070215/IMG-HH-ALPSRP056480670-H1.0__A
    </property>
    <property name="LEADERFILE">
        /a/b/c/20070215/LED-ALPSRP056480670-H1.0__A
    </property>
    <property name="OUTPUT">20070215 </property>
</component>

20061231.xml

<component name="Slave">
    <property name="IMAGEFILE">
        /a/b/c/20061231/IMG-HH-ALPSRP049770670-H1.0__A
    </property>
    <property name="LEADERFILE">
        /a/b/c/20061231/LED-ALPSRP049770670-H1.0__A
    </property>
    <property name="OUTPUT">20061231</property>
</component>

Component Configurability

In the examples for running stripmapApp.py (Here and Here above) the input data were entered by giving the name of an 'xml' file on the command line. The ISCE framework parses that 'xml' file to assign values to the configurable variables in the isce Application stripmapApp.py. The Application executes several steps in its workflow. Each of those steps are handled by a Component that is also configurable from input data. Each component may be configured independently from user input using appropriately named and placed xml files. This section will explain how to name these xml files and where to place them.

Component Names: Family and Instance

Each configurable component has two "names" associated with it. These names are used in locating possible configuration xml files for those components. The first name associated with a configurable component is its "family" name. For stripmapApp.py, the family name is "insar". Inside the stripmapApp.py file an Application is created from a base class named Insar. That base class defines the family name "insar" that is given to every instance created from it. The particular instance that is created in the file stripmapApp.py is given the 'instance name' 'stripmapApp'. If you look in the file near the bottom you will see the line,

insar = Insar(name="stripmapApp")

This line creates an instance of the class Insar (that is given the family name 'insar' elsewhere in the file) and gives it the instance name "stripmapApp".

Other applications could be created that could make several different instances of the Insar. Each instance would have the family name "insar" and would be given a unique instance name. This is possible for every component. In the above example xml files instances name "Master" and "Slave" of a family named "alos" are created.

Component Configuration Files: Locations, Names, Priorities

The ISCE framework looks for xml configuration files when configuring every Component in its flow in 3 different places with different priorities. The configuration sequence loads configuration parameters found in these xml files in the sequence lowest to highest priority overwriting any parameters defined as it moves up the priority sequence. This layered approach allows a couple of advantages. It allows the user to define common parameters for all instances in one file while defining specific instance parameters in files named for those specific instances. It also allows global preferences to be set in a special directory that will apply unless the user overrides them with a higher priority xml file.

The priority sequence has two layers. The first layer is location of the xml file and the second is the name of the file. Within each of the 3 location priorities indicated below, the filename priority goes from 'family name' to 'instance name'. That is, within a given location priority level, a file named after the 'family name' is loaded first and then a file with the 'instance name' is loaded next and overwrites any property values read from the 'family name' file.

The priority sequence for location is as follows:

(1) The highest priority location is on the command line. On the command line the filename can be anything you choose. Configuration parameters can also be entered directly on the command line as in the following example:

> stripmapApp.py insar.master.output=master_c.raw

This example indicates that the variable named 'output' of the Component named 'master' belonging to the Component (or Application) named 'insar' will be given the name "master_c.raw".

The priority sequence on the command line goes from lowest priority on the left to highest priority on the right. So, if we use the command line,

> stripmapApp.py myInputFile.xml insar.master.output=master_c.raw

where the myInputFile.xml file also gives a value for the insar master output file as master_d.raw, then the one defined on the right will win, i.e., master_c.raw.

(2) The next priority location is the local directory in which stripmapApp.py is executed. Any xml file placed in this directory named according to either the family name or the instance name for any configurable component in ISCE will be read while configuring the component.

(3) If you define an environment variable named ISCEDB, you can place xml files with family names or instance names that will be read when configuring Configurable Components. These files placed in the ISCEDB directory have the lowest priority when configuring properties of the Components. The files placed in the ISCEDB directory can be used to define global settings that will apply unless the xml files in the local directory or the command line override those preferences.

Component Configuration Structure

However, the component tag has to have the family name of the Component/ Application. In the above examples you see that the outermost component tag has the name "insar", which is the family name of the class Insar of which stripmapApp is an instance.

Component Configuration Help

At this time there is limited information about component configurability through the command

> stripmapApp.py --help

Future deliveries will improve this situation. In the meantime we describe here how to discover from the code which Components and parameters are configurable. One note of caution is that it is possible for a parameter to appear to be configurable from user input when the particular flow will not allow this degree of freedom. Experience and evolving documentation will be of use in determining these cases.

How to find out whether a component is configurable, what its configurable parameters are, what "name" to use in the xml file, and what name to give to the xml file.

Let's take as an example, Ampcor.py, which is in components/mroipac/ampcor.

Open it in an editor and search for the string "class Ampcor". It is on line 263. You will see that it inherits from Component. This is the minimum requirement for it to be a configurable component.

Now look above that line and you will see several variable names being set equal to a call to Component.Parameter. These declarations define these variables as configurable parameters. They are entered in the "parameter_list" starting on line 268. That is the method by which these Parameters are made configurable parameters of the Component Nstage.

Each of the parameters defines the "public_name", which is the "name" that you would enter in the xml file. For instance if you want to set the gross offset in range, which is defined starting on line 88 in the variable ACROSS_GROSS_OFFSET, then you would use an xml tag like the following (assuming you have determined that the gross offset in range is about 150 pixels):

<property name="ACROSS_GROSS_OFFSET">150</property>

Now, to determine what to call the xml file and what "name" to use in the component tag. A configurable component has a "family" name and an instance "name". It is registered as having these names by calling the Component.__init__ constructor, which is done on line 806. On that line you will see that the call to __init__ passes 'family=self.class.family' and 'name=name' to the Component constructor (super class of Ampcor). The family name is given as "nstage" on line 265. The instance name is passed as the value of the 'name=name' and was passed to it from whatever program created it. Nstage is created in components/isceobj/StripmapProc/runRefineSlaveTiming.py where it is given the name 'master_offset1' on line 35. If you are setting a parameter that should be the same for all uses of Ampcor, then you can use the family name 'ampcor' for the name of the xml file as 'ampcor.xml'. It is more likely that you will want to use the instance name 'master_offset1.xml' Use the family name 'ampcor' for the component tag 'name'.

Example for SLC matching use of Ampcor:

Filename: master_offset1.xml:

<dummy>
<component name="ampcor">
    <property name="ACROSS_GROSS_OFFSET">150</property>
</component>
</dummy>

User community forums

Sign up to participate in the ISCE user communities at the following website:

http://earthdef.caltech.edu/account/register

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http://earthdef.caltech.edu/projects/isce_forum/boards

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