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We’ve done it again!

This time, Daniel O’Donohue and I talked about spatiotemporal data in GIS, including – of course – Time Manager, the new QGIS temporal support, and MovingPandas.

 

Since we need both data and tools to do spatiotemporal analysis, we also talked about file formats and data models. If you want to know more about data models for spatiotemporal (especially movement) data, have a look at the latest discussion paper I wrote together with Esteban Zimányi (MobilityDB) and Krishna Chaitanya Bommakanti (mobilitydb-sqlalchemy):

Data model of the Moving Features standard illustrated with two moving points A and B. Stars mark changes in attribute values. (Source: Graser et al. (2020))

For more details and all options for listening to this podcast, visit mapscaping.com.

 

Exploring large movement datasets is hard because visualizations of movement data quickly get cluttered and hard to interpret. Therefore, we need to aggregate the data. Density maps are commonly used since they are readily available and quick to compute but they provide only very limited insight. In contrast, meaningful aggregations that can help discover patterns are computationally expensive and therefore slow to generate.

This post serves as a starting point for a series of new approaches to exploring massive movement data. This series will summarize parts of my PhD research and – for those of you who are interested in more details – there will be links to the relevant papers.

Starting with the raw location records, we use different forms of aggregation to learn more about what information a movement dataset contains:

  1. Summarizing movement using prototypes by aggregating raw location records using our flexible M³ Massive Movement Model [1]
  2. Generating trajectories by connecting consecutive records into continuous tracks and splitting them into meaningful trajectories [2]
  3. Extracting flows by summarizing trajectory-based transitions between prototypes [3]

 

 

Besides clever aggregation approaches, massive movement datasets also require appropriate computing resources. To ensure that we can efficiently explore large datasets, we have implemented the above mentioned aggregation steps in Spark. This enables us to run the computations on general purpose computing clusters that can be scaled according to the dataset size.

In the next post, we’ll look at how to summarize movement using M³ prototypes. So stay tuned!

But if you don’t want to wait, these are the original papers:

[1] Graser. A., Widhalm, P., & Dragaschnig, M. (2020). The M³ massive movement model: a distributed incrementally updatable solution for big movement data exploration. International Journal of Geographical Information Science. doi:10.1080/13658816.2020.1776293.
[2] Graser, A., Dragaschnig, M., Widhalm, P., Koller, H., & Brändle, N. (2020). Exploratory Trajectory Analysis for Massive Historical AIS Datasets. In: 21st IEEE International Conference on Mobile Data Management (MDM) 2020. doi:10.1109/MDM48529.2020.00059
[3] Graser, A., Widhalm, P., & Dragaschnig, M. (2020). Extracting Patterns from Large Movement Datasets. GI_Forum – Journal of Geographic Information Science, 1-2020, 153-163. doi:10.1553/giscience2020_01_s153.


This post is part of a series. Read more about movement data in GIS.

QGIS Temporal Controller is a powerful successor of TimeManager. Temporal Controller is a new core feature of the current development version and will be shipped with the 3.14 release. This post demonstrates two key advantages of this new temporal support:

  1. Expression support for defining start and end timestamps
  2. Integration into the PyQGIS API

These features come in very handy in many use cases. For example, they make it much easier to create animations from folders full of GPS tracks since the files can now be loaded and configured automatically:

Script & Temporal Controller in action (click for full resolution)

All tracks start at the same location but at different times. (Kudos for Andrew Fletcher for recordings these tracks and sharing them with me!) To create an animation that shows all tracks start simultaneously, we need to synchronize them. This synchronization can be achieved on-the-fly by subtracting the start time from all track timestamps using an expression:

directory = "E:/Google Drive/QGIS_Course/05_TimeManager/Example_Dayrides/"

def load_and_configure(path):
    path = os.path.join(directory, filename)
    uri = 'file:///' + path + "?type=csv&escape=&useHeader=No&detectTypes=yes"
    uri = uri + "&crs=EPSG:4326&xField=field_3&yField=field_2"
    vlayer = QgsVectorLayer(uri, filename, "delimitedtext")
    QgsProject.instance().addMapLayer(vlayer)

    mode = QgsVectorLayerTemporalProperties.ModeFeatureDateTimeStartAndEndFromExpressions
    expression = """to_datetime(field_1) -
    make_interval(seconds:=minimum(epoch(to_datetime("field_1")))/1000)
    """

    tprops = vlayer.temporalProperties()
    tprops.setStartExpression(expression)
    tprops.setEndExpression(expression) # optional
    tprops.setMode(mode)
    tprops.setIsActive(True)

for filename in os.listdir(directory):
    if filename.endswith(".csv"):
        load_and_configure(filename)

The above script loads all CSV files from the given directory (field_1 is the timestamp, field_2 is y, and field_3 is x), enables sets the start and end expression as well as the corresponding temporal control mode and finally activates temporal rendering. The resulting config can be verified in the layer properties dialog:

To adapt this script to other datasets, it’s sufficient to change the file directory and revisit the layer uri definition as well as the field names referenced in the expression.


This post is part of a series. Read more about movement data in GIS.

TimeManager turns 10 this year. The code base has made the transition from QGIS 1.x to 2.x and now 3.x and it would be wrong to say that it doesn’t show ;-)

Now, it looks like the days of TimeManager are numbered. Four days ago, Nyall Dawson has added native temporal support for vector layers to QGIS. This is part of a larger effort of adding time support for rasters, meshes, and now also vectors.

The new Temporal Controller panel looks similar to TimeManager. Layers are configured through the new Temporal tab in Layer Properties. The temporal dimension can be used in expressions to create fancy time-dependent styles:

temporal1

TimeManager Geolife demo converted to Temporal Controller (click for full resolution)

Obviously, this feature is brand new and will require polishing. Known issues listed by Nyall include limitations of supported time fields (only fields with datetime type are supported right now, strings cannot be used) and worse performance than TimeManager since features are filtered in QGIS rather than in the backend.

If you want to give the new Temporal Controller a try, you need to install the current development version, e.g. qgis-dev in OSGeo4W.


Update from May 16:

Many of the limitations above have already been addressed.

Last night, Nyall has recorded a one hour tutorial on this new feature, enjoy:

In previous posts, I already wrote about Trajectools and some of the functionality it provides to QGIS Processing including:

There are also tools to compute heading and speed which I only talked about on Twitter.

Trajectools is now available from the QGIS plugin repository.

The plugin includes sample data from MarineCadastre downloads and the Geolife project.

Under the hood, Trajectools depends on GeoPandas!

If you are on Windows, here’s how to install GeoPandas for OSGeo4W:

  1. OSGeo4W installer: install python3-pip
  2. Environment variables: add GDAL_VERSION = 2.3.2 (or whichever version your OSGeo4W installation currently includes)
  3. OSGeo4W shell: call C:\OSGeo4W64\bin\py3_env.bat
  4. OSGeo4W shell: pip3 install geopandas (this will error at fiona)
  5. From https://www.lfd.uci.edu/~gohlke/pythonlibs/#fiona: download Fiona-1.7.13-cp37-cp37m-win_amd64.whl
  6. OSGeo4W shell: pip3 install path-to-download\Fiona-1.7.13-cp37-cp37m-win_amd64.whl
  7. OSGeo4W shell: pip3 install geopandas
  8. (optionally) From https://www.lfd.uci.edu/~gohlke/pythonlibs/#rtree: download Rtree-0.8.3-cp37-cp37m-win_amd64.whl and pip3 install it

If you want to use this functionality outside of QGIS, head over to my movingpandas project!

In Movement data in GIS #16, I presented a new way to deal with trajectory data using GeoPandas and how to load the trajectory GeoDataframes as a QGIS layer. Following up on this initial experiment, I’ve now implemented a first version of an algorithm that performs a spatial analysis on my GeoPandas trajectories.

The first spatial analysis algorithm I’ve implemented is Clip trajectories by extent. Implementing this algorithm revealed a couple of pitfalls:

  • To achieve correct results, we need to compute spatial intersections between linear trajectory segments and the extent. Therefore, we need to convert our point GeoDataframe to a line GeoDataframe.
  • Based on the spatial intersection, we need to take care of computing the corresponding timestamps of the events when trajectories enter or leave the extent.
  • A trajectory can intersect the extent multiple times. Therefore, we cannot simply use the global minimum and maximum timestamp of intersecting segments.
  • GeoPandas provides spatial intersection functionality but if the trajectory contains consecutive rows without location change, these will result in zero length lines and those cause an empty intersection result.

So far, the clip result only contains the trajectory id plus a suffix indicating the sequence of the intersection segments for a specific trajectory (because one trajectory can intersect the extent multiple times). The following screenshot shows one highlighted trajectory that intersects the extent three times and the resulting clipped trajectories:

This algorithm together with the basic trajectory from points algorithm is now available in a Processing algorithm provider plugin called Processing Trajectory.

Note: This plugin depends on GeoPandas.

Note for Windows users: GeoPandas is not a standard package that is available in OSGeo4W, so you’ll have to install it manually. (For the necessary steps, see this answer on gis.stackexchange.com)

The implemented tests show how to use the Trajectory class independently of QGIS. So far, I’m only testing the spatial properties though:

def test_two_intersections_with_same_polygon(self):
    polygon = Polygon([(5,-5),(7,-5),(7,12),(5,12),(5,-5)])
    data = [{'id':1, 'geometry':Point(0,0), 't':datetime(2018,1,1,12,0,0)},
        {'id':1, 'geometry':Point(6,0), 't':datetime(2018,1,1,12,10,0)},
        {'id':1, 'geometry':Point(10,0), 't':datetime(2018,1,1,12,15,0)},
        {'id':1, 'geometry':Point(10,10), 't':datetime(2018,1,1,12,30,0)},
        {'id':1, 'geometry':Point(0,10), 't':datetime(2018,1,1,13,0,0)}]
    df = pd.DataFrame(data).set_index('t')
    geo_df = GeoDataFrame(df, crs={'init': '31256'})
    traj = Trajectory(1, geo_df)
    intersections = traj.intersection(polygon)
    result = []
    for x in intersections:
        result.append(x.to_linestring())
    expected_result = [LineString([(5,0),(6,0),(7,0)]), LineString([(7,10),(5,10)])]
    self.assertEqual(result, expected_result) 

One issue with implementing the algorithms as QGIS Processing tools in this way is that the tools are independent of one another. That means that each tool has to repeat the expensive step of creating the trajectory objects in memory. I’m not sure this can be solved.

Working with movement data analysis, I’ve banged my head against performance issues every once in a while. For example, PostgreSQL – and therefore PostGIS – run queries in a single thread of execution. This is now changing, with more and more functionality being parallelized. PostgreSQL version 9.6 (released on 2016-09-29) included important steps towards parallelization, including parallel execution of sequential scans, joins and aggregates. Still, there is no parallel processing in PostGIS so far (but it is under development as described by Paul Ramsey in his posts “Parallel PostGIS II” and “PostGIS Scaling” from late 2017).

At the FOSS4G2016 in Bonn, I had the pleasure to chat with Shoaib Burq who ran the “An intro to Apache PySpark for Big Data GeoAnalysis” workshop. Back home, I downloaded the workshop material and gave it a try but since I wanted a scalable system for storing, analyzing, and visualizing spatial data, it didn’t really seem to fit the bill.

Around one year ago, my search grew more serious since we needed a solution that would support our research group’s new projects where we expected to work with billions of location records (timestamped points and associated attributes). I was happy to find that the fine folks at LocationTech have some very promising open source projects focusing on big spatial data, most notably GeoMesa and GeoWave. Both tools take care of storing and querying big spatio-temporal datasets and integrate into GeoServer for publication and visualization. (A good – if already slightly outdated – comparison of the two has been published by Azavea.)

My understanding at the time was that GeoMesa had a stronger vector data focus while GeoWave was more focused on raster data. This lead me to try out GeoMesa. I published my first steps in “Getting started with GeoMesa using Geodocker” but things only really started to take off once I joined the developer chats and was pointed towards CCRI’s cloud-local “a collection of bash scripts to set up a single-node cloud on your desktop, laptop, or NUC”. This enabled me to skip most of the setup pains and go straight to testing GeoMesa’s functionality.

The learning curve is rather significant: numerous big data stack components (including HDFS, Accumulo, and GeoMesa), a most likely new language (Scala), as well as the Spark computing system require some getting used to. One thing that softened the blow is the fact that writing queries in SparkSQL + GeoMesa is pretty close to writing PostGIS queries. It’s also rather impressive to browse hundreds of millions of points by connecting QGIS TimeManager to a GeoServer WMS-T with GeoMesa backend.

Spatial big data stack with GeoMesa

One of the first big datasets I’ve tested are taxi floating car data (FCD). At one million records per day, the three years in the following example amount to a total of around one billion timestamped points. A query for travel times between arbitrary start and destination locations took a couple of seconds:

Travel time statistics with GeoMesa (left) compared to Google Maps predictions (right)

Besides travel time predictions, I’m also looking into the potential for predicting future movement. After all, it seems not unreasonable to assume that an object would move in a similar fashion as other similar objects did in the past.

Early results of a proof of concept for GeoMesa based movement prediction

Big spatial data – both vector and raster – are an exciting challenge bringing new tools and approaches to our ever expanding spatial toolset. Development of components in open source big data stacks is rapid – not unlike the development speed of QGIS. This can make it challenging to keep up but it also holds promises for continuous improvements and quick turn-around times.

If you are using GeoMesa to work with spatio-temporal data, I’d love to hear about your experiences.

In Movement data in GIS #2: visualization I mentioned that it should be possible to label trajectory segments without having to break the original trajectory feature. While it’s not a straightforward process, it is indeed possible to create timestamp labels at desired intervals:

The main point here is that we cannot use regular labels because there would be only one label for the whole trajectory feature. Instead, we are using a marker line with a font marker:

By default, font markers only display one character from a given font but by using expressions we can make it display longer text, including datetime strings:

If you want to have a label at every node of the trajectory, the expression looks like this:

format_date( 
   to_datetime('1970-01-01T00:00:00Z')+to_interval(
      m(start_point(geometry_n(
         segments_to_lines( $geometry ),
         @geometry_part_num)
      ))||' seconds'
   ),
   'HH:mm:ss'
)

You probably remember those parts of the expression that extract the m value from previous posts. Note that – compared to 2016 – it is now necessary to add the segments_to_lines() function.

The m value (which stores time as seconds since Unix epoch) is then converted to datetime and finally formatted to only show time. Of course you can edit the datetime format string to also include the date.

If we only want a label every 30 seconds, we can add a case statement around that:

CASE WHEN 
m(start_point(geometry_n(
   segments_to_lines( $geometry ),
   @geometry_part_num)
)) % 30 = 0
THEN
format_date( 
   to_datetime('1970-01-01T00:00:00Z')+to_interval(
      m(start_point(geometry_n(
         segments_to_lines( $geometry ),
         @geometry_part_num)
      ))||' seconds'
   ),
   'HH:mm:ss'
)
END

This works well if the trajectory sampling interval is fairly regular. This is not always the case and that means that the above case statement wouldn’t find many nodes with a timestamp that ends in :30 or :00. In such a case, we could resort to labeling nodes based on their order in the linestring:

CASE WHEN 
 @geometry_part_num  % 30 = 0
THEN
...

Thanks a lot to @JuergenEFischer for providing a solution for converting seconds since Unix epoch to datetime without a custom function!

Note that expressions using @geometry_part_num currently suffer from the following issue: Combination of segments_to_lines($geometry) and @geometry_part_num gives wrong segment numbers


This post is part of a series. Read more about movement data in GIS.

TimeManager 2.5 is quite likely going to be the final TimeManager release for the QGIS 2 series. It comes with a couple of bug fixes and enhancements:

  • Fixed #245: updated help.htm
  • Fixed #240: now hiding unmanageable WFS layers
  • Fixed #220: fixed issues with label size
  • Fixed #194: now exposing additional functions: animation_time_frame_size, animation_time_frame_type, animation_start_datetime, animation_end_datetime

Besides updating the help, I also decided to display it more prominently in the settings dialog (similarly to how the help is displayed in the field calculator or in Processing):

So far, I haven’t started porting to QGIS 3 yet. If you are interested in TimeManager and want to help, please get in touch.

On this note, let me leave you with a couple of animation inspirations from the Twitterverse:

In this post, we use TimeManager to visualize the position of a moving object over time along a trajectory. This is another example of what is possible thanks to QGIS’ geometry generator feature. The result can look like this:

What makes this approach interesting is that the trajectory is stored in PostGIS as a LinestringM instead of storing individual trajectory points. So there is only one line feature loaded in QGIS:

(In part 2 of this series, we already saw how a geometry generator can be used to visualize speed along a trajectory.)

The layer is added to TimeManager using t_start and t_end attributes to define the trajectory’s temporal extent.

TimeManager exposes an animation_datetime() function which returns the current animation timestamp, that is, the timestamp that is also displayed in the TimeManager dock, as well as on the map (if we don’t explicitly disable this option).

Once TimeManager is set up, we can edit the line style to add a point marker to visualize the position of the moving object at the current animation timestamp. To do that, we interpolate the position along the trajectory segments. The first geometry generator expression splits the trajectory in its segments:

The second geometry generator expression interpolates the position on the segment that contains the current TimeManager animation time:

The WHEN statement compares the trajectory segment’s start and end times to the current TimeManager animation time. Afterwards, the line_interpolate_point function is used to draw the point marker at the correct position along the segment:

CASE 
WHEN (
m(end_point(geometry_n($geometry,@geometry_part_num)))
> second(age(animation_datetime(),to_datetime('1970-01-01 00:00')))
AND
m(start_point(geometry_n($geometry,@geometry_part_num)))
<= second(age(animation_datetime(),to_datetime('1970-01-01 00:00')))
)
THEN
line_interpolate_point( 
  geometry_n($geometry,@geometry_part_num),
  1.0 * (
    second(age(animation_datetime(),to_datetime('1970-01-01 00:00')))
	- m(start_point(geometry_n($geometry,@geometry_part_num)))
  ) / (
    m(end_point(geometry_n($geometry,@geometry_part_num)))
	- m(start_point(geometry_n($geometry,@geometry_part_num)))
  ) 
  * length(geometry_n($geometry,@geometry_part_num))
)
END

Here is the animation result for a part of the trajectory between 08:00 and 09:00:


This post is part of a series. Read more about movement data in GIS.

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