Introduction to Scientific Computing at DC Python

This Saturday the DC Python group ran a coding meetup. As part of the event I ran an introduction to scientific computing for about 7 people.

After a quick introduction to numpy, matplotlib, pandas and scikit-learn we decided to pick a dataset and apply some machine learning. The dataset we decided to use was from a Kaggle competition looking at the Titanic disaster. This competition had been posted to help the community get started with machine learning so it seemed perfect.

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Strategies for data collection

19 Aug.
2012
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I am currently working on a fairly complex data collection task. This is the third in the past year and by now I'm reasonably comfortable handling the mechanics, especially when I can utilise tools like Scrapy, lxml and a reasonable ORM for database access. Deciding exactly what to store seems like an easy question and yet it is this question which seems to be causing me the most trouble.

The difficulty exists because in deciding what to store multiple competing interests need to be balanced.

Store everything

Storing everything is the easiest to implement and enables the decision of which data points you are interested in to be delayed. The disadvantages with storing everything is that it can place significant demands on storage capacity and risks silent failure.

Store just what you need

Storing just the data you are interested in minimises storage requirements and makes it easier to detect failures. If the information you want is moved, more common for html scraping than APIs, or you realise you have not been collecting everything you want there is no way to go back and alter what you extract or how you extract it.

Failure detection

Failure detection is easier with storing just what you need because your expectations are more detailed. If you expect to find an integer at a certain node in the DOM and either fail to find the node or the content is not an integer you can be relatively certain that there is an error. If you are storing the entire document a request to complete a CAPTCHA or a notice that you have exceeded a rate limit may be indistinguishable from the data you are hoping to collect.

So far I've taken an approach somewhere between these two extremes although I doubt I am close to the optimal solution. For the current project I need to parse much of the data I am interested in so that I can collect the remainder. It feels natural in this situation to favour storing only what I intend to use even though this decision has slowed down development.

Have you been in a similar situation and faced these same choices? Which approach did you take?

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Disk space used by databases and tables in MySQL PostgreSQL

07 July
2012
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I don't use raw SQL very often so when I do I usually end up checking the manual for the correct syntax. One query I've wanted to run a couple of times recently and always struggled to find the correct statement for is checking the amount of disk space used by a table or database.

For the ease of future reference here they are.

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Django and Scrapy

08 Feb.
2012
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I'm currently working on a project which centres around pulling in data from an external website, "mashing" it up with some additional content, and then displaying it on a website.

The website is going to be interactive and reasonably complex so I decided to use django. To acquire the external data there isn't a webservice so I'm stuck parsing html (and excel spreadsheets but that's a separate story). Scrapy seemed ideal for this and although I wish I had used some other approach than xpath it largely has been.

Having set up my database models in django and built my spider in scrapy the next step was putting the data from the spider in the database. There are plenty of posts detailing how to use the django ORM from outside a django project, even some specific to scrapy but they didn't seem to be working for me.

The issue was the way I handled development and production environment settings.

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Numpy talk at Python Northwest

05 Jan.
2012
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Back in December I gave a talk introducing Numpy to the PyNorthwest group. The slides are available as a pdf.

Although I frequently use Numpy I'm far from an expert and the content of my talk reflected this. I started with a general introduction to the array object and then expanded the scope of the talk to highlight some of the projects that use Numpy. I gave an example of using MDP and matplotlib.

The talk was followed by some excellent discussion. We went through some of the code on slide 6 in a lot of detail.

The PyNorthwest group meets at Madlab in Manchester city centre on the third Thursday of each month. If you're in the area check it out. The January event is on the 19th, starting at 7pm.

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Full text visualisation

At BarcampNortheast4 last weekend and at the Python Northwest meetup on Thursday I gave a presentation on the work I've been doing generating full text visualisations of PDF document libraries.

This was the third BarcampNortheast event I have attended. Each has been slightly different but they have all been a weekend well spent. This year felt a little smaller than previous years but that may have partly been because we were in a bigger space.

I have been attending the python Edinburgh meetups for a while. They have always been interesting and the Northwest meetup this Thursday was the first since I moved back to the Northwest. The format, alternating talks and coding sessions, is different to Edinburgh, regular pub meetups with irregular talks, coding sessions and miniconferences. It was an interesting crowd and the other talks, on Apache Thrift and teaching programming to GCSE students (15-16 year olds), gave a really good variety of subjects to discuss later.

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Images and Vision in Python: Slides from talk at Python Edinburgh Mini-Conf 2011

28 May
2011
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Last weekend the Python Edinburgh users group hosted a mini-conference. Saturday morning was kicked off with a series of talks followed by sessions introducing and then focusing on contributing to django prior to sprints which really got going on the Sunday.

The slides for my talk on, "Images and Vision in Python" are now available in pdf format here.

The slide deck I used is relatively lightweight with my focus being on demonstrating using the different packages available. The code I went through is below.

from PIL import Image

#Open an image and show it
pil1 = Image.open('filename')
pil1.show()

#Get its size
pil1.size
#Resize
pil1s = pil1.resize((100,100))
#or - thumbnail
pil1.thumbnail((100,100), Image.ANTIALIAS)

#New image
bg = Image.new('RGB', (500,500), '#ffffff')

#Two ways of accessing the pixels
#getpixel/putpixel and load
#load is faster
pix = bg.load()

for a in range(100, 200):
	for b in range(100,110):
		pix[a,b] = (0,0,255)
bg.show()

#Drawing shapes is slightly more involved
from PIL import ImageDraw
draw = ImageDraw.Draw(bg)
draw.ellipse((300,300,320,320), fill='#ff0000')
bg.show()

from PIL import ImageFont
font = ImageFont.truetype("/usr/share/fonts/truetype/freefont/FreeSerif.ttf", 72)
draw.text((10,10), "Hello", font=font, fill='#00ff00')
bg.show()


#Demo's for vision
from scipy import ndimage
import mahotas

#Create a sample image
v1 = np.zeros((10,10), bool)
v1[1:4,1:4] = True
v1[4:7,2:6] = True
imshow(v1, interpolation="Nearest")
imshow(mahotas.dilate(v1), interpolation="Nearest")
imshow(mahotas.erode(v1), interpolation="Nearest")
imshow(mahotas.thin(v1), interpolation="Nearest")

#Opening, closing and top-hat as combinations of dilate and erode

#Labeling
#Latest version of mahotas has a label func
v1[8:,8:] = True
imshow(v1)
labeled, nr_obj = ndimage.label(v1)
nr_obj
imshow(labeled, interpolation="Nearest")
pylab.jet()

#Thresholding
#Convert a grayscale image to a binary image
v2 = mahotas.imread("/home/jonathan/openplaques/blueness_images/1.jpg")
T = mahotas.otsu(v2)
imshow(v2)
imshow(v2 > T)

#Distance Transforms
dist = mahotas.distance(v2 > T)
imshow(dist)

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Newcastle Maker Faire 2011

I'm writing this on the train back from Newcastle after attending this years Maker Faire. I've attended each Newcastle Maker Faire and it's been fantastic witnessing it grow each year. Many of the groups displaying their projects are veterans of previous Faires and it's inspiring seeing their projects develop from one year to the next. A growing faire means new groups and although some themes are repeated many groups have truly unique projects.

As last year I've put together a short video capturing some of the activity at this maker faire. It's difficult capturing more than a sliver of what makes this event great so I encourage you to click through to the project websites. I'll link to as many as I can below the video over the next few days but for the moment would encourage you to visit the official website.

Links

I can't find a link for the roving wheelie bins but more information on the fire breathing dragon is available here.

I can't find a link for the first robot. The second robot was from mbed. The third robot was part of a very large exhibit but again I'm struggling to find a link. The fourth scene of robots were from robochallenge. The final ground based bot was from robosavvy.

The underwater bot was from underwater rov. The aerial photography using a model plane was done by Simon Clark. The rocketry was from Black Streak.

It was difficult keeping track of all the 3D printers so I'll just highlight two focusing specifically on 3D printers - bodgeitquick and emakershop.

The first automata was from Richard Broderick, the second from Philip Lowndes and I'm unsure about the third though I suspect Richard again.

The DIYBio presence was organised by Cathal Garvey and Brian Degger.

The standing wave flame tube was from Steve Mould. The wind up music disc was from the North of England Arduino Group organised by Mike Cook. I'm not sure who was responsible for the heart beat light sculpture. The interactive light table was built by Oli and the digital grafetti wall was built by the Jam Jar Collective and the musical tesla coils were from Brightarcs.

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Quick tips for data analysis in python MDP and matplotlib

19 Dec.
2010
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I've been using MDP and matplotlib a lot recently and although overall I've been very pleased with the documentation for both projects I have run into a few problems for which the solutions were not immediately obvious. This post gives the solution for each in the expectation it will certainly be useful to me in the future and the hope that it may also be useful to others.

Principal Component Analysis with MDP

Data Layout

The tutorial for the Modular Toolkit for Data Processing (MDP) starts with a quick example of using the toolkit for a pca analysis and yet I still ran into a couple of problems. The first issue I had was how the pca function expects to receive data. I suspect this is simply due to unfamiliarity with the field and the language used within the field. For future reference the data is expected to be in the following format.

Gene 1 Gene 2 Gene 3 Gene 4
Experimental Condition 1 . . . .
Experimental Condition 2 . . . .
Variance Accounted For in PC1, 2, etc

The previously mentioned quick start tutorial was very useful in getting something useful out quickly but I couldn't find a way to get a value for how much of the variance present in the data was accounted for in the principal components. To get that, as far as I've been able to determine, you need to interact with the PCANode directly rather than using the convenience function. The code is still relative straightforward.

import mdp
import numpy as np
import matplotlib.pyplot as plt

#Create sample data
var1 = np.random.normal(loc=0., scale=0.5, size=(10,5))
var2 = np.random.normal(loc=4., scale=1., size=(10,5))
var = np.concatenate((var1,var2), axis=0)

#Create the PCA node and train it
pcan = mdp.nodes.PCANode(output_dim=3)
pcar = pcan.execute(var)

#Graph the results
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(pcar[:10,0], pcar[:10,1], 'bo')
ax.plot(pcar[10:,0], pcar[10:,1], 'ro')

#Show variance accounted for
ax.set_xlabel('PC1 (%.3f%%)' % (pcan.d[0]))
ax.set_ylabel('PC2 (%.3f%%)' % (pcan.d[1]))

plt.show()

Running this code produces an image similar to the one below.

PCA graph

Growing neural gas with MDP

The growing neural gas implementation was another sample application highlighted in the tutorial for MDP. It held my interest for a while as a technique which could potentially be applied to the transcription of plaques for the openplaques project. It wasn't immediately obvious how to get the position of a node from a connected nodes object. As the tutorial left the details of visualisation up to the user I'll present the solution to getting the node location in the form of the necessary code to visualise the node training. The end result will look something like the following.

Matplotlib

I've been using Matplotlib to plot data exclusively for a while now. The defaults produce reasonable quality graphs and any differences in opinion can be quickly fixed either by altering options in matplotlib or, as the graphs can be saved in svg format, in a vector image manipulation program such as Inkscape. Although most options can be changed in matplotlib it can sometimes be difficult to find the correct option. Most of the time the naming of variables are, to my mind, logical but sometimes I just can't find the right way to describe what I want to do.

Hiding axes

I wanted to have a grid of 6 graphs but didn't want to display the axes on all the graphs as I felt this looked cluttered.

Fixing the axis range

If I was going to display the axes on only some of the graphs then the values for the axes needed to be the same on all of them.

import numpy as np
import matplotlib.pyplot as plt

#Generate sample data
var = np.random.random_sample((40,2))

fig = plt.figure()
for i in range(4):
    ax = fig.add_subplot(220 + i + 1)
    start = i * 10
    ax.plot(var[start:start+10,0], var[start:start+10,1], 'bo')
    
    #Hide the x axis on the top row of charts
    if i in [0,1]:
        ax.set_xticklabels(ax.get_xticklabels(), visible=False)
        
    #Hide the y axis on the right column of charts
    if i in [1,3]:
        ax.set_yticklabels(ax.get_yticklabels(), visible=False)
    
    #Set the axis range
    ax.axis([0,1,0,1])
plt.show()

Running this code should produce an image similar to the one below.

Selectively displaying axes

Removing second point in plot legend

The legend assumes that values are connected so two points and the connecting line are shown by default. If the points on the graph aren't connected then this looked strange. To remove the duplicate symbol is straightforward.

import numpy as np
import matplotlib.pyplot as plt

#Generate sample data
var = np.random.random_sample((10,2))

#Plot data with labels
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(var[0:5,0], var[0:5,1], 'bo', label="First half")
ax.plot(var[5:10,0], var[5:10,1], 'r^', label="Second half")
ax.legend(numpoints=1)
plt.show()

Display one point in plot legend

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AI Cookbook Competition - Month Three

A little over two months ago I wrote about the first round of the AI cookbook competition. Since then there have been two further rounds and a considerable amount of further progress. For the latest round I was able to get the error score down to 10.867 using an additional image pre-processing step and then a variety of text clean-up improvements.

Image Pre-processing

Ian, who writes the AI Cookbook, had the theory that the curved text present at the top of many of the plaques in the test set were causing tesseract, our OCR software of choice, significant problems in transcribing the main text. If we could automatically recognise the curved text and block it out the transcription should be significantly improved. In the diagram below the text we want to be transcribed is in green and the text we don't want is in red.

I couldn't think of a good method to actually recognise the curved text at the top so decided to use a 'dumb' approach. The curved text is in the same place on all the plaques so I built a system to apply the same mask to all the images. To do this I went back to what I could still remember from high school math lessons. To the probable delight of my old math teachers I quickly had some working code. The code I wrote cycles through all the pixels in the image and converts them to a distance and angle relative to the centre of the image. This process is hopefully easier to visualise in the image below. The distance is simple enough to calculate as we're dealing with a right-angle triangle; we simply square the x and y values, add them together and take the square root. The angle is a little trickier. The y-value represents the opposite length of the triangle and the x-value represents the adjacent length so from the mnemonic SOH CAH TOA we known the angle will be tan-1 (O/A). Knowing that we can then apply our rules for distance and angle.

Text Clean-up

The text clean-up was lots of little steps. Briefly I've,

  1. Made various improvements to the regexes for cleaning up the years
  2. Converted any instances of 'vv' (two v's) to 'w' (one w)
  3. Switched 0 (zero) to o (letter o) in words
  4. Removed any one/two character tokens from the end of the string
  5. Improved the selection of suggestions from the spell checker
  6. Broken up long words to see if a valid word can be found in the two halves
  7. Changed "s to 's
  8. Improved correction for endings where the ending is lived|worked|died here and the spelling checker returns bad results
  9. Removed any words containing three of lowercase, uppercase, digits and punctuation.

The regex for that last item is something of a monstrosity and as I'm far from an expert it wouldn't surprise me if it doesn't entirely do what I think it does. I've used whitespace to make it slightly easier to follow. Each line represents a sub-expression, if any sub-expression matches the string then the expression as a whole is considered to match. Each line matches a different combination of three from digits, lowercase, uppercase and punctuation. The .+ at the end means we match one or more of any character. The expressions in brackets starting with a question mark are look ahead assertions. The .+ still matches any character but the look ahead assertions state that at least one of the characters matched must be a digit for instance. It doesn't matter in what order the characters are present as long as they are present. If you suspect there is a flaw in the pattern or know some way to simplify it then I would really appreciate a quick note in the comments field below.

re.compile(r""" #matching a combination of digits, lowercase, uppercase and punctuation
            ((?=.*\d)(?=.*[a-z])(?=.*['"-,\.]).+| #d,l,p
            (?=.*[A-Z])(?=.*[a-z])(?=.*['"-,\.]).+| #u,l,p
            (?=.*\d)(?=.*[A-Z])(?=.*[a-z]).+| #d,u,l
            (?=.*\d)(?=.*[A-Z])(?=.*['"-,\.]).+ #u,p,d
            )""", re.VERBOSE)

That's all for now. I believe Ian is planning to run the competition for a further month and there are still considerable improvements to be made so it would be great to see more people taking part.

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