Difference between revisions of "Analytical data visualizations at ICC 2017"

From GRASS-Wiki
Jump to navigation Jump to search
Line 299: Line 299:
  g.region raster=dsm
  g.region raster=dsm


The second command is handy When we want to run the script again. In that case, we first need to remove the created raster maps, for example:
The second command is handy when we want to run the script again and again. In that case, we first need to remove the created raster maps, for example:


  g.remove type=raster pattern="viewshed_*"
  g.remove type=raster pattern="viewshed*"
 
The above command actually won't remove the maps, but it will inform you which it will remove if you provide the <tt>-f</tt> flag.


== Batch processing using Python ==
== Batch processing using Python ==

Revision as of 17:58, 22 June 2017

Icc2017 logo.png
Grassgis logo colorlogo text whitebg.png

This is material for two sessions at the ICC 2017 workshop called Analytical data visualizations with GRASS GIS and Blender and Mapping open data with open source geospatial tools held in Washington, DC, July 1-2, 2017. These two sessions introduce GRASS GIS, example of its processing capabilities, and visualization techniques relevant to spatio-temporal data and high performance computing (HPC). Participants interactively visualize open data and design maps with several open source geospatial tools including Tangible Landscape system.

We start the workshop with a presentation about the overview of geospatial tools used in this workshop.

Data

Prepared data

  • digital surface model derived from North Carolina Flood Plain Mapping lidar
  • orthophoto

Download OpenStreetMap data

We will use overpass turbo (web-based data filtering tool) to create and run Overpass API queries to obtain OpenStreetMap data.

You can use Wizard to create simple queries on the currently zoomed extent. Zoom to a small area and paste for example this into the Wizard and run the query:

highway=* and type:way

The query was built in the editor and ran and you can see the results in a map now.

Now, paste this query in the editor window:

[out:json][timeout:25];
// gather results
(
  // query part for: “highway=*”
  way["highway"](35.76599,-78.66249,35.77230,-78.65261);
);
// print results
out body;
>;
out skel qt;

It finds roads in our study area. When you run the query, the roads appear on the map and we can export them as GeoJSON (Export - Data - as GeoJSON). Name the vector file roads.geojson.

Now let's also download all building footprints and again export them as GeoJSON. Name the vector file buildings.geojson.

[out:json][timeout:25];
// gather results
(
  // query part for: “building=*”
  way["building"](35.76599,-78.66249,35.77260,-78.65261);

);
// print results
out body;
>;
out skel qt;

In the next steps we will import this data into GRASS GIS.

Introduction to GRASS GIS

Here we provide an overview of GRASS GIS. For this exercise it's not necessary to have a full understanding of how to use GRASS GIS. However, you will need to know how to place your data in the correct GRASS GIS database directory, as well as some basic GRASS functionality.

Structure of the GRASS GIS Spatial Database

GRASS uses unique database terminology and structure (GRASS GIS Spatial Database) that are important to understand for working in GRASS GIS efficiently. You will create a new location and import the required data into that location. In the following we review important terminology and give step by step directions on how to download and place you data in the correct place.

  • A GRASS GIS Spatial Database (GRASS database) consists of directory with specific Locations (projects) where data (data layers/maps) are stored.
  • Location is a directory with data related to one geographic location or a project. All data within one Location has the same coordinate reference system.
  • Mapset is a collection of maps within Location, containing data related to a specific task, user or a smaller project.

Creating a GRASS database for the tutorial

Start GRASS GIS, a start-up screen should appear. Unless you already have a directory called grassdata in your Documents directory (on MS Windows) or in your home directory (on Linux), create one. You can use the Browse button and the dialog in the GRASS GIS start up screen to do that.

We will create a new location for our project with CRS (coordinate reference system) NC State Plane Meters with EPSG code 3358. Open Location Wizard with button New in the left part of the welcome screen. Select a name for the new location, select EPSG method and code 3358. When the wizard is finished, the new location will be listed on the start-up screen. Select the new location and mapset PERMANENT and press Start GRASS session.


Importing data

Import raster data

In this step we import into GRASS GIS the provided data. In menu File - Import raster data select Common formats import and in the dialog browse to find dem.tif and click button Import. Repeat for raster files dsm.tif and ortho.

Similarly, go to File - Import vector data - Common formats import and import files roads.geojson and buildings.geojson. Note that in this case we need to change the output name from default OGRGeoJSON to roads and buildings, respectively. This vector data has different CRS, so a dialog informing you about the need to reproject the data appears and we confirm it.

All the imported layers should be added to GUI, if not, add them manually.

Displaying and exploring data

The GUI interface allows you to display raster, vector data as well as navigate through zooming in and out. More advanced exploration and visualization is also possible using, e.g., queries and adding legend. The screenshots below depicts how you can add different map layers (left) and display the metadata of your data layers.

GRASS GIS modules

One of the advantages of GRASS is the diversity and number of modules that let you analyze all manner of spatial and temporal. GRASS GIS has over 500 different modules in the core distribution and over 230 addon modules that can be used to prepare and analyze data layers.

GRASS functionality is available through modules (tools, functions). Modules respect the following naming conventions:

Prefix Function Example
r.* raster processing r.mapcalc: map algebra
v.* vector processing v.clean: topological cleaning
i.* imagery processing i.segment: object recognition
db.* database management db.select: select values from table
r3.* 3D raster processing r3.stats: 3D raster statistics
t.* temporal data processing t.rast.aggregate: temporal aggregation
g.* general data management g.rename: renames map
d.* display d.rast: display raster map

These are the main groups of modules. There is few more for specific purposes. Note also that some modules have multiple dots in their names. This often suggests further grouping. For example, modules staring with v.net. deal with vector network analysis.

The name of the module helps to understand its function, for example v.in.lidar starts with v so it deals with vector maps, the name follows with in which indicates that the module is for importing the data into GRASS GIS Spatial Database and finally lidar indicates that it deals with lidar point clouds.

Finding and running a module

To find a module for your analysis, type the term into the search box into the Modules tab in the Layer Manager, then keep pressing Enter until you find your module.

Alternatively, you can just browse through the module tree in the Modules tab. You can also browse through the main menu. For example, to find information about a raster map, use: Raster → Reports and statistics → Basic raster metadata.

Running a module as a command

If you already know the name of the module, you can just use it in the command line. The GUI offers a Command console tab with command line specifically build for running GRASS GIS modules. If you type module name there, you will get suggestions for automatic completion of the name. After pressing Enter, you will get GUI dialog for the module.

You can use the command line to run also whole commands for example when you get a command, i.e. module and list of parameters, in the instructions.

Command line vs. GUI interface

GRASS modules can be executed either through a GUI or command line interface. The GUI offers a user-friendly approach to executing modules where the user can navigate to data layers that they would like to analyze and modify processing options with simple check boxes. The GUI also offers an easily accessible manual on how to execute a model. The command line interface allows users to execute a module using command prompts specific to that module. This is handy when you are running similar analyses with minor modification or are familiar with the module commands for quick efficient processing. In this workshop we provide module prompts that can be copy and pasted into the command line for our workflow, but you can use both GUI and command line depending on personal preference. Look how GUI and command line interface represent the same tool.
Task: compute aspect (orientation) from provided digital elevation model using module r.slope.aspect using both module dialog and command line.

  • How to find modules? Modules are organized by their functionality in wxGUI menu, or we can search for them in Search modules tab. If we already know which module to use, we can just type it in the wxGUI command console.

Module parameters

The same analysis can be done using the following command:

r.neighbors -c input=elevation output=elev_smooth size=5

Conversely, you can fill the GUI dialog parameter by parameter when you have the command.

Computational region

Before we use a module to compute a new raster map, we must set properly computational region. All raster computations will be performed in the specified extent and with the given resolution.

Computational region is an important raster concept in GRASS GIS. In GRASS a computational region can be set, subsetting larger extent data for quicker testing of analysis or analysis of specific regions based on administrative units. We provide a few points to keep in mind when using the computational region function:

  • defined by region extent and raster resolution
  • applies to all raster operations
  • persists between GRASS sessions, can be different for different mapsets
  • advantages: keeps your results consistent, avoid clipping, for computationally demanding tasks set region to smaller extent, check your result is good and then set the computational region to the entire study area and rerun analysis
  • run g.region -p or in menu Settings - Region - Display region to see current region settings

The numeric values of computational region can be checked using:

g.region -p

After executing the command you will get something like this:

north:      220750
south:      220000
west:       638300
east:       639000
nsres:      1
ewres:      1
rows:       750
cols:       700
cells:      525000

Computational region can be set using a raster map:

g.region raster=dsm -p

Running modules

Find the module for computing viewshed in the menu or the module tree under Raster → Terrain analysis → Visibility and aspect or simply run r.viewshed from the Console.

r.viewshed input=dsm output=viewshed coordinates=638587.6,220649.5

3D view

We can explore our study area in 3D view.

  1. Add elev_lid792_1m and uncheck or remove any other layers.
  2. Set computational region to this raster. Switch to 3D view (in the right corner on Map Display).
  3. Adjust the view (perspective, height, vertical exaggeration)
  4. In Data tab, set Fine mode resolution to 1 and set slope (computed in the previous step) as the color of the surface.
  5. When finished, switch back to 2D view.
3D visualization of elev_lid792_1m DEM with slope draped over

Introduction to scripting in GRASS GIS with Python

The simplest way to execute the Python code which uses GRASS GIS packages is to use Simple Python editor integrated in GRASS GIS accessible from the toolbar or the Python tab in the Layer Manager. Another option is to write the Python code in your favorite plain text editor like Notepad++ (note that Python editors are plain text editors). Then run the script in GRASS GIS using the main menu File -> Launch script.



The GRASS GIS 7 Python Scripting Library provides functions to call GRASS modules within scripts as subprocesses. The most often used functions include:

Besides, this library provides several wrapper functions for often called modules.

Calling GRASS GIS modules

We will use GRASS GUI Simple Python Editor to run the commands. You can open it from Python tab. For longer scripts, you can create a text file, save it into your current working directory and run it with python myscript.py from the GUI command console or terminal.

When you open Simple Python Editor, you find a short code snippet. It starts with importing GRASS GIS Python Scripting Library:

import grass.script as gscript

In the main function we call g.region to see the current computational region settings:

gscript.run_command('g.region', flags='p')

Note that the syntax is similar to bash syntax (g.region -p), just the flag is specified in a parameter. Now we can run the script by pressing the Run button in the toolbar. In Layer Manager we get the output of g.region.

Before running any GRASS raster modules, you need to set the computational region. In this example, we set the computational extent and resolution to the raster layer elevation. Replace the previous g.region command with the following line:

gscript.run_command('g.region', raster='dsm')

The run_command() function is the most commonly used one. We will use it to compute viewshed using r.viewshed. Add the following line after g.region command:

gscript.run_command('r.viewshed', input='dsm', output='viewshed_python', coordinates=TODO, overwrite=True)

Parameter overwrite is needed if we rerun the script and rewrite the raster. Now let's look at how big the viewshed is by using r.univar. Here we use parse_command to obtain the statistics as a Python dictionary

univar = gscript.parse_command('r.univar', map='viewshed_python', flags='g')
print univar['n']

The printed result is the number of cells of the viewshed.

List of convenient wrapper functions with examples:

Here are two commands (to be executed in the Console) often used when working with scripts. First is setting the computational region. We can do that in a script, but it better and more general to do it before executing the script (so that the script can be used with different computational region settings):

g.region raster=dsm

The second command is handy when we want to run the script again and again. In that case, we first need to remove the created raster maps, for example:

g.remove type=raster pattern="viewshed*"

The above command actually won't remove the maps, but it will inform you which it will remove if you provide the -f flag.

Batch processing using Python

In this example, we will calculate the viewsheds along a road to simulate in a simple way what a driver would see.

First we extract only segments of road with name 'Umstead Drive':

v.extract input=roads where="name = 'Umstead Drive'" output=umstead_drive_segments

We will join the segments into one polyline using v.build.polylines

v.build.polylines input=umstead_drive_segments output=umstead_drive cats=first

Now we generate viewpoints in regular intervals along the line:

v.to.points input=umstead_drive type=line output=viewpoints dmax=50

We compute viewshed from each point using a Python script. From these viewsheds we can then easily compute Cumulative viewshed (how much a place is visible). For that we will use module r.series, which overlays the viewshed rasters and computes how many times each cell is visible in all the rasters.

Copy the following code into Python Simple Editor and press Run button.

#!/usr/bin/env python

import grass.script as gscript

def main():
    # obtain the coordinates of viewpoints
    viewpoints = gscript.read_command('v.out.ascii', input='viewpoints',
                                      separator='comma', layer=2).strip()
    # loop through the viewpoints and compute viewshed from each of them
    for point in viewpoints.splitlines():
        x, y, cat = point.split(',')
        gscript.run_command('r.viewshed', input='dsm', output='viewshed' + cat,
                            coordinates=(x, y), max_distance=300, overwrite=True)
    # obtain all viewshed results and set their color to yellow
    # export the list of viewshed map names to a file
    maps_file = gscript.run_command('g.list', type='raster', pattern='viewshed*', output='viewsheds.txt')
    gscript.write_command('r.colors', file=maps_file, rules='-',
                          stdin='0% yellow \n 100% yellow')
    # cumulative viewshed
    gscript.run_command('r.series', file='viewsheds.txt', output='cumulative_viewshed', method='count')
    # set color of cumulative viewshed from grey to yellow
    gscript.write_command('r.colors', map='cumulative_viewshed, rules='-',
                          stdin='0% 70:70:70 \n 100% yellow')

if __name__ == '__main__':
    main()

We can visualize the cumulative viewshed draped over the DSM using 3D view.

Cumulative viewshed computed along a road

To proceed with the next part, we will export the viewpoints and cumulative viewshed in order for Blender to use it. Copy and paste the individual lines to GRASS GUI command console and execute them separately, omit the lines starting with #.

# turn 2D points into 3D using the DSM information
v.drape input=viewpoints output=viewpoints_3d elevation=dsm method=bilinear
# export them, ignore errors coming from too long attribute column names
v.out.ogr input=viewpoints_3d output=viewpoints_3d.shp format=ESRI_Shapefile
# export cumulative viewshed as PNG
r.out.gdal input=cumulative_viewshed output=cumulative_viewshed.png format=PNG

Introduction to Blender

Animation in GRASS GIS

In the following exercise we will visualize the viewsheds along the road (we computed above) as an animation. We will use GRASS GIS Animation Tool. Start it from menu File - Animation Tool:

Animation tool in the main menu


Start with Add new animation and click on Add space-time dataset or series of map layers. In the Add space-time dataset layer click on a button next to the entry field and type ^viewshed. This filters the rasters which start with "viewshed". Confirm the dialog and return to the dialog Add new animation.

Next we want to add orthophoto as base layer. Use Add raster map layer and select raster ortho.

Add series of viewsheds rasters to animation tool.
Add ortho as base raster


Do the same for the road vector umstead_drive, just instead of raster, add vector. Then rearrange the layers so that the ortho is below all other layers. Confirm the dialog and the animation should be loaded.

Change the order of layers
Resulting animation

Further exploration:

  • If you want to zoom in, go back to Map Display, and set the computational region to the extent you want using toolbar button 'Various zoom options - Set computational region extent interactively'. Then press Render map in the Animation tool toolbar and it will re-render the animation based on the current computational region extent.

Scripting of rendering in GRASS GIS

Rendering of maps can be done in GRASS GIS using Python API in way which follows what is done in the GUI. Similarly to running the processing modules, GUI dialogs have a Copy button which will put a command line equivalent of what is current set in the GUI dialog. For example, a raster properties dialog can give the code: d.rast map=viewshed. This code is written in Python syntax as run_command('d.rast', map='viewshed'). In addition to the rendering commands, we need to specify where (filename) and how (e.g. file format) to render this can be done using the d.mon command as below or environmental variables (in GUI we don't need to say anything because the context is clear). A full example follows.

import grass.script as gscript

viewsheds = gscript.list_grouped(type=['raster'], pattern='viewshed')

for viewshed in viewsheds:
    gscript.run_command('d.mon', start='cairo', output='{}.png'.format(viewshed))
    gscript.run_command('d.rast', map=viewshed)
    gscript.run_command('d.mon', stop='cairo')

In scripting, the d.mon is actually often not used because only one monitor can be active. This is very convenient simplification for interactive use, but limiting for scripting. When the rendering runs in parallel, it is necessary to use environmental variables instead of the d.mon module. Variables are set globally (using os.environ dictionary) or for each function call (using env parameter). The following three variables are the most important: GRASS_RENDER_IMMEDIATE (usually set to cairo), GRASS_RENDER_FILE_READ (set to TRUE), and GRASS_RENDER_FILE (resulting image filename). Additional variables include GRASS_FONT (name of the font to be used, e.g. sans) and GRASS_LEGEND_FILE (file for vector legend, can be path to a temporary file).

Software

Software should be pre-installed at ICC, but the following instructions can be used to install software on participants' laptops.

We use GRASS GIS 7.2 and Blender 2.78.

MS Windows

Then download standalone GRASS GIS 7.2. binaries (64-bit version, or 32-bit version) from grass.osgeo.org. During the installation you can also download North Carolina sample dataset so please select this option. You can also download the dataset later (see the following section).

Mac OS

Install GRASS GIS 7.2 using Homebrew osgeo4mac:

brew tap osgeo/osgeo4mac
brew install grass7

OSGeo-Live

All needed software is included except for Blender.

Ubuntu

Install GRASS GIS from packages:

sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install grass

Linux

Install GRASS GIS from packages:

sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
sudo apt-get update
sudo apt-get install grass

For other Linux distributions other then Ubuntu, please try to find GRASS GIS in their package managers.

See also