Tagged with pyqgis

Thoughts on “FOSS4G/SOTM Oceania 2018”, and the PyQGIS API improvements which it caused

Last week the first official “FOSS4G/SOTM Oceania” conference was held at Melbourne University. This was a fantastic event, and there’s simply no way I can extend sufficient thanks to all the organisers and volunteers who put this event together. They did a brilliant job, and their efforts are even more impressive considering it was the inaugural event!

Upfront — this is not a recap of the conference (I’m sure someone else is working on a much more detailed write up of the event!), just some musings I’ve had following my experiences assisting Nathan Woodrow deliver an introductory Python for QGIS workshop he put together for the conference. In short, we both found that delivering this workshop to a group of PyQGIS newcomers was a great way for us to identify “pain points” in the PyQGIS API and areas where we need to improve. The good news is that as a direct result of the experiences during this workshop the API has been improved and streamlined! Let’s explore how:

Part of Nathan’s workshop (notes are available here) focused on a hands-on example of creating a custom QGIS “Processing” script. I’ve found that preparing workshops is guaranteed to expose a bunch of rare and tricky software bugs, and this was no exception! Unfortunately the workshop was scheduled just before the QGIS 3.4.2 patch release which fixed these bugs, but at least they’re fixed now and we can move on…

The bulk of Nathan’s example algorithm is contained within the following block (where “distance” is the length of line segments we want to chop our features up into):

for input_feature in enumerate(features):
    geom = feature.geometry().constGet()
    if isinstance(geom, QgsLineString):
        continue
    first_part = geom.geometryN(0)
    start = 0
    end = distance
    length = first_part.length()

    while start < length:
        new_geom = first_part.curveSubstring(start,end)

        output_feature = input_feature
        output_feature.setGeometry(QgsGeometry(new_geom))
        sink.addFeature(output_feature)

        start += distance
        end += distance

There’s a lot here, but really the guts of this algorithm breaks down to one line:

new_geom = first_part.curveSubstring(start,end)

Basically, a new geometry is created for each trimmed section in the output layer by calling the “curveSubstring” method on the input geometry and passing it a start and end distance along the input line. This returns the portion of that input LineString (or CircularString, or CompoundCurve) between those distances. The PyQGIS API nicely hides the details here – you can safely call this one method and be confident that regardless of the input geometry type the result will be correct.

Unfortunately, while calling the “curveSubstring” method is elegant, all the code surrounding this call is not so elegant. As a (mostly) full-time QGIS developer myself, I tend to look over oddities in the API. It’s easy to justify ugly API as just “how it’s always been”, and over time it’s natural to develop a type of blind spot to these issues.

Let’s start with the first ugly part of this code:

geom = input_feature.geometry().constGet()
if isinstance(geom, QgsLineString):
    continue
first_part = geom.geometryN(0)
# chop first_part into sections of desired length
...

This is rather… confusing… logic to follow. Here the script is fetching the geometry of the input feature, checking if it’s a LineString, and if it IS, then it skips that feature and continues to the next. Wait… what? It’s skipping features with LineString geometries?

Well, yes. The algorithm was written specifically for one workshop, which was using a MultiLineString layer as the demo layer. The script takes a huge shortcut here and says “if the input feature isn’t a MultiLineString, ignore it — we only know how to deal with multi-part geometries”. Immediately following this logic there’s a call to geometryN( 0 ), which returns just the first part of the MultiLineString geometry.

There’s two issues here — one is that the script just plain won’t work for LineString inputs, and the second is that it ignores everything BUT the first part in the geometry. While it would be possible to fix the script and add a check for the input geometry type, put in logic to loop over all the parts of a multi-part input, etc, that’s instantly going to add a LOT of complexity or duplicate code here.

Fortunately, this was the perfect excuse to improve the PyQGIS API itself so that this kind of operation is simpler in future! Nathan and I had a debrief/brainstorm after the workshop, and as a result a new “parts iterator” has been implemented and merged to QGIS master. It’ll be available from version 3.6 on. Using the new iterator, we can simplify the script:

geom = input_feature.geometry()
for part in geom.parts():
    # chop part into sections of desired length
    ...

Win! This is simultaneously more readable, more Pythonic, and automatically works for both LineString and MultiLineString inputs (and in the case of MultiLineStrings, we now correctly handle all parts).

Here’s another pain-point. Looking at the block:

new_geom = part.curveSubstring(start,end)
output_feature = input_feature
output_feature.setGeometry(QgsGeometry(new_geom))

At first glance this looks reasonable – we use curveSubstring to get the portion of the curve, then make a copy of the input_feature as output_feature (this ensures that the features output by the algorithm maintain all the attributes from the input features), and finally set the geometry of the output_feature to be the newly calculated curve portion. The ugliness here comes in this line:

output_feature.setGeometry(QgsGeometry(new_geom))

What’s that extra QgsGeometry(…) call doing here? Without getting too sidetracked into the QGIS geometry API internals, QgsFeature.setGeometry requires a QgsGeometry argument, not the QgsAbstractGeometry subclass which is returned by curveSubstring.

This is a prime example of a “paper-cut” style issue in the PyQGIS API. Experienced developers know and understand the reasons behind this, but for newcomers to PyQGIS, it’s an obscure complexity. Fortunately the solution here was simple — and after the workshop Nathan and I added a new overload to QgsFeature.setGeometry which accepts a QgsAbstractGeometry argument. So in QGIS 3.6 this line can be simplified to:

output_feature.setGeometry(new_geom)

Or, if you wanted to make things more concise, you could put the curveSubstring call directly in here:

output_feature = input_feature
output_feature.setGeometry(part.curveSubstring(start,end))

Let’s have a look at the simplified script for QGIS 3.6:

for input_feature in enumerate(features):
    geom = feature.geometry()
    for part in geom.parts():
        start = 0
        end = distance
        length = part.length()

        while start < length:
            output_feature = input_feature
            output_feature.setGeometry(part.curveSubstring(start,end))
            sink.addFeature(output_feature)

            start += distance
            end += distance

This is MUCH nicer, and will be much easier to explain in the next workshop! The good news is that Nathan has more niceness on the way which will further improve the process of writing QGIS Processing script algorithms. You can see some early prototypes of this work here:

So there we go. The process of writing and delivering a workshop helps to look past “API blind spots” and identify the ugly points and traps for those new to the API. As a direct result of this FOSS4G/SOTM Oceania 2018 Workshop, the QGIS 3.6 PyQGIS API will be easier to use, more readable, and less buggy! That’s a win all round!

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Speeding up your PyQGIS scripts

I’ve recently spent some time optimising the performance of various QGIS plugins and algorithms, and I’ve noticed that there’s a few common performance traps which developers fall into when fetching features from a vector layer. In this post I’m going to explore these traps, what makes them slow, and how to avoid them.

As a bit of background, features are fetched from a vector layer in QGIS using a QgsFeatureRequest object. Common use is something like this:

request = QgsFeatureRequest()
for feature in vector_layer.getFeatures(request):
    # do something

This code would iterate over all the features in layer. Filtering the features is done by tweaking the QgsFeatureRequest, such as:

request = QgsFeatureRequest().setFilterFid(1001)
feature_1001 = next(vector_layer.getFeatures(request))

In this case calling getFeatures(request) just returns the single feature with an ID of 1001 (which is why we shortcut and use next(…) here instead of iterating over the results).

Now, here’s the trap: calling getFeatures is expensive. If you call it on a vector layer, QGIS will be required to setup an new connection to the data store (the layer provider), create some query to return data, and parse each result as it is returned from the provider. This can be slow, especially if you’re working with some type of remote layer, such as a PostGIS table over a VPN connection. This brings us to our first trap:

Trap #1: Minimise the calls to getFeatures()

A common task in PyQGIS code is to take a list of feature IDs and then request those features from the layer. A see a lot of older code which does this using something like:

for id in some_list_of_feature_ids:
    request = QgsFeatureRequest().setFilterFid(id)
    feature = next(vector_layer.getFeatures(request))
    # do something with the feature

Why is this a bad idea? Well, remember that every time you call getFeatures() QGIS needs to do a whole bunch of things before it can start giving you the matching features. In this case, the code is calling getFeatures() once for every feature ID in the list. So if the list had 100 features, that means QGIS is having to create a connection to the data source, set up and prepare a query to match a single feature, wait for the provider to process that, and then finally parse the single feature result. That’s a lot of¬†wasted processing!

If the code is rewritten to take the call to getFeatures() outside of the loop, then the result is:

request = QgsFeatureRequest().setFilterFids(some_list_of_feature_ids)
for feature in vector_layer.getFeatures(request):
    # do something with the feature

Now there’s just a single call to getFeatures() here. QGIS optimises this request by using a single connection to the data source, preparing the query just once, and fetching the results in appropriately sized batches. The difference is huge, especially if you’re dealing with a large number of features.

Trap #2: Use QgsFeatureRequest filters appropriately

Here’s another common mistake I see in PyQGIS code. I often see this one when an author is trying to do something with all the selected features in a layer:

for feature in vector_layer.getFeatures():
    if not feature.id() in vector_layer.selectedFeaturesIds():
        continue

    # do something with the feature

What’s happening here is that the code is iterating over all the features in the layer, and then skipping over any which aren’t in the list of selected features. See the problem here? This code iterates over EVERY feature in the layer. If you’re layer has 10 million features, we are fetching every one of these from the data source, going through all the work of parsing it into a QGIS feature, and then promptly discarding it if it’s not in our list of selected features. It’s very inefficient, especially if fetching features is slow (such as when connecting to a remote database source).

Instead, this code should use the setFilterFids() method for QgsFeatureRequest:

request = QgsFeatureRequest().setFilterFids(vector_layer.selectedFeaturesIds())
for feature in vector_layer.getFeatures(request):
    # do something with the feature

Now, QGIS will only fetch¬†features from the provider with matching feature IDs from the list. Instead of fetching and processing every feature in the layer, only the actual selected features will be fetched. It’s not uncommon to see operations which previously took many minutes (or hours!) drop down to a few seconds after applying this fix.

Another variant of this trap uses expressions to test the returned features:

filter_expression = QgsExpression('my_field &gt; 20')
for feature in vector_layer.getFeatures():
    if not filter_expression.evaluate(feature):
        continue

    # do something with the feature

Again, this code is fetching every single feature from the layer and then discarding it if it doesn’t match the “my_field > 20” filter expression. By rewriting this to:

request = QgsFeatureRequest().setFilterExpression('my_field &gt; 20')
for feature in vector_layer.getFeatures(request):
    # do something with the feature

we hand over the bulk of the filtering to the data source itself. Recent QGIS versions intelligently translate the filter into a format which can be applied directly at the provider, meaning that any relevant indexes and other optimisations can be applied by the provider itself. In this case the rewritten code means that ONLY the features matching the ‘my_field > 20’ criteria are fetched from the provider – there’s no time wasted messing around with features we don’t need.

 

Trap #3: Only request values you need

The last trap I often see is that more values are requested from the layer then are actually required. Let’s take the code:

my_sum = 0
for feature in vector_layer.getFeatures(request):
    my_sum += feature['value']

In this case there’s no way we can optimise the filters applied, since we need to process every feature in the layer. But – this code is still inefficient. By default QGIS will fetch all the details for a feature from the provider. This includes all attribute values and the feature’s geometry. That’s a lot of processing – QGIS needs to transform the values from their original format into a format usable by QGIS, and the feature’s geometry needs to be parsed from it’s original type and rebuilt as a QgsGeometry object. In our sample code above we aren’t doing anything with the geometry, and we are only using a single attribute from the layer. By calling setFlags( QgsFeatureRequest.NoGeometry ) and setSubsetOfAttributes() we can tell QGIS that we don’t need the geometry, and we only require a single attribute’s value:

my_sum = 0
request = QgsFeatureRequest().setFlags(QgsFeatureRequest.NoGeometry).setSubsetOfAttributes(['value'], vector_layer.fields() )
for feature in vector_layer.getFeatures(request):
    my_sum += feature['value']

None of the unnecessary geometry parsing will occur, and only the ‘value’ attribute will be fetched and populated in the features. This cuts down both on the processing required AND the amount of data transfer between the layer’s provider and QGIS. It’s a significant¬†improvement¬†if you’re dealing with larger layers.

Conclusion

Optimising your feature requests is one of the easiest ways to speed up your PyQGIS script! It’s worth spending some time looking over all your uses of getFeatures() to see whether you can cut down on what you’re requesting – the results can often be mind blowing!

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Two book recommendations

I recently finished reading two books which may be of interest to open-source GIS users – “PostGIS Cookbook” and “The PyQGIS Programmer’s Guide“, both of which I highly recommend:

PostGIS Cookbook

PostGIS CookbookI’ve been a fan of Stephen Mather’s blog¬†for a while now, and have consistently found it to be a great source of trustworthy information and creative solutions to GIS problems. So when I first saw mention of his work on the PostGIS Cookbook I knew it would be a must-read for me. PostGIS is an essential part of my daily toolkit, and I’ll quickly devour any tutorial or guide which can lead me to better ways to put it to use. And that’s exactly what this book is! It’s full of tips and guides which has inspired me in a lot of techniques I’d never tried or even thought possible in PostGIS.

It’s important to point out that this book isn’t a training manual or beginner’s guide to PostGIS. It assumes readers are already familiar with using PostGIS and have a good understanding of GIS software in general. (If you’re looking for a book to start from scratch with PostGIS, PostGIS in Action is a better fit). I think that’s really what makes this book stand out though. There’s currently not a lot of books available covering PostGIS, and as far as I’m aware the PostGIS Cookbook is the only book available which is targeted to experienced PostGIS users.

Highlights for me are:

  • A great explanation and write up on optimised KNN filtering in PostGIS (something which often trips me up)
  • The detailed guide to topologically correct simplification of features
  • The exploration of PgRouting, which is a great introduction to PostGIS’ routing abilities
  • The “PostGIS and the web” chapter – I really wasn’t expecting this, but it’s quite eye opening (I’m going to have to do some digging into GeoDjango sometime)

The only criticism I have with this book is that it jumps around a lot between operating systems. While most of the code is provided for both Linux/OSX and Windows, there’s occasional examples which only have code for one specific operating system. It’s a little jarring and assumes the user is well versed in their particular operating system to workaround these omissions.

Overall, I strongly recommend the PostGIS Cookbook, and would consider it a must have for anyone serious about expanding their PostGIS abilities. (Also, looks like the publisher, Packt, have a two-for-one sale going at the moment, so it’s a good time to grab this title).

The PyQGIS Programmer’s Guide

The PyQGIS Programmer's GuideThe second book I’ve just finished reading is Gary Sherman’s “The PyQGIS Programmer’s Guide“. For those who are unaware, Gary was the original founder of QGIS back in 2002, so you can be confident that he knows exactly what he’s writing about. In¬†The PyQGIS Programmer’s Guide¬†¬†Gary has created an in-depth guide on how to get started with programming for QGIS using python. It takes readers all the way from simple scripts right through to developing QGIS plugins and standalone applications based on the QGIS API.

This book fills an important void in the literature available for QGIS. Previously, the¬†PyQGIS Developer Cookbook¬†was the only available guide for QGIS python scripting, and unfortunately it’s a little out-of-date now. PyQGIS scripting can be a steep learning curve and that’s why this book is so appreciated.

It would be valuable to have some python knowledge and experience prior to reading this book. While the “Python Basics” chapter quickly runs through an introduction to the language, the book makes no claims to be a comprehensive python tutorial. But if you’ve dabbled in the language before and have familiarity with the python way of doing things you’ll easily be able to follow along.

Highlights are:

  • The “Tips and Techniques” chapter, which is a great mini-reference for performing a range of common tasks in PyQGIS (including loading layers, changing symbol styles, editing feature attributes, etc).
  • A complete tutorial for creating a QGIS plugin
  • A guide to debugging PyQGIS code and plugins

I’d definitely recommend that anyone who wants to get started with PyQGIS start with Gary’s work – you’ll find it the perfect place to begin.

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