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Today’s post continues where “Why you should be using PostGIS trajectories” leaves off. It’s the result of a collaboration with Eva Westermeier. I had the pleasure to supervise her internship at AIT last year and also co-supervised her Master’s thesis [0] on the topic of enriching trajectories with information about their geographic context.

Context-aware analysis of movement data is crucial for different domains and applications, from transport to ecology. While there is a wealth of data, efficient and user-friendly contextual trajectory analysis is still hampered by a lack of appropriate conceptual approaches and practical methods. (Westermeier, 2018)

Part of the work was focused on evaluating different approaches to adding context information from vector datasets to trajectories in PostGIS. For example, adding land cover context to animal movement data or adding information on anchoring and harbor areas to vessel movement data.

Classic point-based model vs. line-based model

The obvious approach is to intersect the trajectory points with context data. This is the classic point data model of contextual trajectories. It’s straightforward to add context information in the point-based model but it also generates large numbers of repeating annotations. In contrast, the line data model using, for example, PostGIS trajectories (LinestringM) is more compact since trajectories can be split into segments at context borders. This creates one annotation per segment and the individual segments are convenient to analyze (as described in part #12).

Spatio-temporal interpolation as provided by the line data model offers additional advantages for the analysis of annotated segments. Contextual segments start and end at the intersection of the trajectory linestring with context polygon borders. This means that there are no gaps like in the point-based model. Consequently, while the point-based model systematically underestimates segment length and duration, the line-based approach offers more meaningful segment length and duration measurements.

Schematic illustration of a subset of an annotated trajectory in two context classes, a) systematic underestimation of length or duration in the point data model, b) full length or duration between context polygon borders in the line data model (source: Westermeier (2018))

Another issue of the point data model is that brief context changes may be missed or represented by just one point location. This makes it impossible to compute the length or duration of the respective context segment. (Of course, depending on the application, it can be desirable to ignore brief context changes and make the annotation process robust towards irrelevant changes.)

Schematic illustration of context annotation for brief context changes, a) and b)
two variants for the point data model, c) gapless annotation in the line data model (source: Westermeier (2018) based on Buchin et al. (2014))

Beyond annotations, context can also be considered directly in an analysis, for example, when computing distances between trajectories and contextual point objects. In this case, the point-based approach systematically overestimates the distances.

Schematic illustration of distance measurement from a trajectory to an external
object, a) point data model, b) line data model (source: Westermeier (2018))

The above examples show that there are some good reasons to dump the classic point-based model. However, the line-based model is not without its own issues.

Issues

Computing the context annotations for trajectory segments is tricky. The main issue is that ST_Intersection drops the M values. This effectively destroys our trajectories! There are ways to deal with this issue – and the corresponding SQL queries are published in the thesis (p. 38-40) – but it’s a real bummer. Basically, ST_Intersection only provides geometric output. Therefore, we need to reconstruct the temporal information in order to create usable trajectory segments.

Finally, while the line-based model is well suited to add context from other vector data, it is less useful for context data from continuous rasters but that was beyond the scope of this work.

Conclusion

After the promising results of my initial investigations into PostGIS trajectories, I was optimistic that context annotations would be a straightforward add-on. The line-based approach has multiple advantages when it comes to analyzing contextual segments. Unfortunately, generating these contextual segments is much less convenient and also slower than I had hoped. Originally, I had planned to turn this work into a plugin for the Processing toolbox but the results of this work motivated me to look into other solutions. You’ve already seen some of the outcomes in part #20 “Trajectools v1 released!”.

References

[0] Westermeier, E.M. (2018). Contextual Trajectory Modeling and Analysis. Master Thesis, Interfaculty Department of Geoinformatics, University of Salzburg.


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

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MovingPandas is my attempt to provide a pure Python solution for trajectory data handling in GIS. MovingPandas provides trajectory classes and functions built on top of GeoPandas. 

To lower the entry barrier to getting started with MovingPandas, there’s now an interactive iPython notebook hosted on MyBinder. This notebook provides all the necessary imports and demonstrates how to create a Trajectory object.

Launch MyBinder for MovingPandas to get started!

When QGIS 3.0 was release, I published a Processing script template for QGIS3. While the script template is nicely pythonic, it’s also pretty long and daunting for non-programmers. This fact didn’t go unnoticed and Nathan Woodrow in particular started to work on a QGIS enhancement proposal to improve the situation and make writing Processing scripts easier, while – at the same time – keeping in line with common Python styles.

While the previous template had 57 lines of code, the new template only has 26 lines – 50% less code, same functionality! (Actually, this template provides more functionality since it also tracks progress and ensures that the algorithm can be cancelled.)

from qgis.processing import alg
from qgis.core import QgsFeature, QgsFeatureSink

@alg(name="split_lines_new_style", label=alg.tr("Alg name"), group="examplescripts", group_label=alg.tr("Example Scripts"))
@alg.input(type=alg.SOURCE, name="INPUT", label="Input layer")
@alg.input(type=alg.SINK, name="OUTPUT", label="Output layer")
def testalg(instance, parameters, context, feedback, inputs):
    """
    Description goes here. (Don't delete this! Removing this comment will cause errors.)
    """
    source = instance.parameterAsSource(parameters, "INPUT", context)

    (sink, dest_id) = instance.parameterAsSink(
        parameters, "OUTPUT", context,
        source.fields(), source.wkbType(), source.sourceCrs())

    total = 100.0 / source.featureCount() if source.featureCount() else 0
    features = source.getFeatures()
    for current, feature in enumerate(features):
        if feedback.isCanceled():
            break
        out_feature = QgsFeature(feature)
        sink.addFeature(out_feature, QgsFeatureSink.FastInsert)
        feedback.setProgress(int(current * total))

    return {"OUTPUT": dest_id}

The key improvement are the new decorators that turn an ordinary function (such as testalg in the template) into a Processing algorithm. Decorators start with @ and are written above a function definition. The @alg decorator declares that the following function is a Processing algorithm, defines its name and assigns it to an algorithm group. The @alg.input decorator creates an input parameter for the algorithm. Similarly, there is a @alg.output decorator for output parameters.

For a longer example script, check out the original QGIS enhancement proposal thread!

For now, this new way of writing Processing scripts is only supported by QGIS 3.6 but there are plans to back-port this improvement to 3.4 once it is more mature. So give it a try and report back!

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!

Yesterday, I learned about a cool use case in data-driven agriculture that requires dealing with delayed measurements. As Bert mentions, for example, potatoes end up in the machines and are counted a few seconds after they’re actually taken out of the ground:

Therefore, in order to accurately map yield, we need to take this temporal offset into account.

We need to make sure that time and location stay untouched, but need to shift the potato count value. To support this use case, I’ve implemented apply_offset_seconds() for trajectories in movingpandas:

    def apply_offset_seconds(self, column, offset):
        self.df[column] = self.df[column].shift(offset, freq='1s')

The following test illustrates its use: you can see how the value column is shifted by 120 second. Geometry and time remain unchanged but the value column is shifted accordingly. In this test, we look at the row with index 2 which we access using iloc[2]:

    def test_offset_seconds(self):
        df = pd.DataFrame([
            {'geometry': Point(0, 0), 't': datetime(2018, 1, 1, 12, 0, 0), 'value': 1},
            {'geometry': Point(-6, 10), 't': datetime(2018, 1, 1, 12, 1, 0), 'value': 2},
            {'geometry': Point(6, 6), 't': datetime(2018, 1, 1, 12, 2, 0), 'value': 3},
            {'geometry': Point(6, 12), 't': datetime(2018, 1, 1, 12, 3, 0), 'value':4},
            {'geometry': Point(6, 18), 't': datetime(2018, 1, 1, 12, 4, 0), 'value':5}
        ]).set_index('t')
        geo_df = GeoDataFrame(df, crs={'init': '31256'})
        traj = Trajectory(1, geo_df)
        traj.apply_offset_seconds('value', -120)
        self.assertEqual(traj.df.iloc[2].value, 5)
        self.assertEqual(traj.df.iloc[2].geometry, Point(6, 6))

Pandas is great for data munging and with the help of GeoPandas, these capabilities expand into the spatial realm.

With just two lines, it’s quick and easy to transform a plain headerless CSV file into a GeoDataFrame. (If your CSV is nice and already contains a header, you can skip the header=None and names=FILE_HEADER parameters.)

usecols=USE_COLS is also optional and allows us to specify that we only want to use a subset of the columns available in the CSV.

After the obligatory imports and setting of variables, all we need to do is read the CSV into a regular DataFrame and then construct a GeoDataFrame.

import pandas as pd
from geopandas import GeoDataFrame
from shapely.geometry import Point

FILE_NAME = "/temp/your.csv"
FILE_HEADER = ['a', 'b', 'c', 'd', 'e', 'x', 'y']
USE_COLS = ['a', 'x', 'y']

df = pd.read_csv(
    FILE_NAME, delimiter=";", header=None,
    names=FILE_HEADER, usecols=USE_COLS)
gdf = GeoDataFrame(
    df.drop(['x', 'y'], axis=1),
    crs={'init': 'epsg:4326'},
    geometry=[Point(xy) for xy in zip(df.x, df.y)])

It’s also possible to create the point objects using a lambda function as shown by weiji14 on GIS.SE.

PyQGIS 101: Introduction to QGIS Python programming for non-programmers has now reached the part 10 milestone!

Beyond the obligatory Hello world! example, the contents so far include:

If you’ve been thinking about learning Python programming, but never got around to actually start doing it, give PyQGIS101 a try.

I’d like to thank everyone who has already provided feedback to the exercises. Every comment is important to help me understand the pain points of learning Python for QGIS.

I recently read an article – unfortunately I forgot to bookmark it and cannot locate it anymore – that described the problems with learning to program very well: in the beginning, it’s rather slow going, you don’t know the right terminology and therefore don’t know what to google for when you run into issues. But there comes this point, when you finally get it, when the terminology becomes clearer, when you start thinking “that might work” and it actually does! I hope that PyQGIS101 will be a help along the way.

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