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"Every solution will only lead to new problems."

Sunday, 1. March 2009


Testing Quicksort with NaturalSpec

Filed under: F#,NaturalSpec — Steffen Forkmann at 11:42 Uhr

In my last article I showed two ways to use parameterized scenarios in NaturalSpec. This time I will show how we can combine both to test a small Quicksort function.

First of all we define a scenario for sorting:

/// predefined sorting scenario
let sortingScenario f list =
  Given list
    |> When sorting_with f
    |> It should be sorted
    |> It should contain_all_elements_from list
    |> It should contain_no_other_elements_than list
/// predefined Quicksort scenario
let quicksortScenario list = sortingScenario QuickSort list

Now we define some concrete test cases:

[<Scenario>]
let When_sorting_empty_list() =
  quicksortScenario []
    |> Verify
    
[<Scenario>]
let When_sorting_small_list() =
  quicksortScenario [2;1;8;15;5;22]
    |> Verify      
    
[<ScenarioTemplate(100)>]
[<ScenarioTemplate(1000)>]
[<ScenarioTemplate(2500)>]
let When_sorting_ordered_list n =
  quicksortScenario [1..n]
    |> Verify  
    
[<ScenarioTemplate(100)>]
[<ScenarioTemplate(1000)>]
[<ScenarioTemplate(2500)>]
let When_sorting_random_list n =
  quicksortScenario (list_of_random_ints n)
    |> Verify  

After we defined our spec the task is now to implement the sorting function. I am using a very short (and very naïve) Quicksort implementation in F#:

/// naive implementation of QuickSort - don't use it
let rec quicksort = function
  | [] -> []
  | pivot :: rest ->
     let small,big = List.partition ((>) pivot) rest
     quicksort small @ [pivot] @ quicksort big
     
let QuickSort x =
  printMethod ""
  quicksort x   

If we run the scenario, we get the following output (I shortened a bit):

Scenario: When sorting empty list

– Given []
– When sorting with QuickSort
=> It should be sorted
=> It should contain all elements from []
=> It should contain no other elements than []
==> Result is: []
==> OK
==> Time: 0.0355s

Scenario: When sorting small list

– Given [2; 1; 8; 15; 5; 22]
– When sorting with QuickSort
=> It should be sorted
=> It should contain all elements from [2; 1; 8; 15; 5; 22]
=> It should contain no other elements than [2; 1; 8; 15; 5; 22]
==> Result is: [1; 2; 5; 8; 15; 22]
==> OK
==> Time: 0.0065s

Scenario: When sorting ordered list

[…]  100 elements
==> OK
==> Time: 0.0939s

Scenario: When sorting ordered list

[…]  1000 elements
==> OK
==> Time: 0.7130s

Scenario: When sorting ordered list

[…]  2500 elements
==> OK
==> Time: 3.0631s

Scenario: When sorting random list

[…]  100 elements
==> OK
==> Time: 0.0485s

Scenario: When sorting random list

[…]  1000 elements
==> OK
==> Time: 0.1878s

Scenario: When sorting random list

[…]  1000 elements
==> OK
==> Time: 0.8713s

As you can see the function is much faster if we sort a random list. This is because of the naïve choice of the pivot element.

I don’t want to give better implementations here (use LINQ or PLINQ). I just wanted to show how we can easily verify a test function with NaturalSpec.

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Saturday, 28. February 2009


Parameterized Scenarios with NaturalSpec

Filed under: F#,NaturalSpec — Steffen Forkmann at 16:46 Uhr

I wrote a lot about NaturalSpec in my last articles. This time I will show how we can use parameterized scenarios.

1. Using predefined scenarios

By writing predefined parameterized scenarios we can easily create a scenario suite with lots of different test cases:

// predefined scenario
let factorialScenario x result =
  Given x
    |> When calculating factorial
    |> It should equal result

[<Scenario>]
let When_calculation_factorial_of_1() =
  factorialScenario 1 1
    |> Verify   

[<Scenario>]
let When_calculation_factorial_of_10() =
  factorialScenario 10 3628800
    |> Verify

If we run these scenarios with NUnit we will get the following output:

Scenario: When calculation factorial of 1

  – Given 1

    – When calculating factorial

       => It should equal 1

==> OK

==> Time: 0.0093s

Scenario: When calculation factorial of 10

  – Given 10

    – When calculating factorial

       => It should equal 3628800

==> OK

==> Time: 0.0018s

2. Using the ScenarioTemplate attribute

The second and shorter option is to use the ScenarioTemplate attribute, which is inherited from NUnit’s new TestCase attribute:

// with ScenarioTemplate Attribute
[<ScenarioTemplate(1, 1)>]
[<ScenarioTemplate(2, 2)>]
[<ScenarioTemplate(5, 120)>]
[<ScenarioTemplate(10, 3628800)>]
let When_calculating_fac_(x,result) =
  Given x
    |> When calculating factorial
    |> It should equal result
    |> Verify

This code will create 4 different scenarios, which NUnit will display and report separately:

NUnit runner reports test cases

3. Using ScenarioSource

The third option is to use the ScenarioSource attribute. Here we define a function which generates TestData:

/// with a scenario source      
let MyTestCases =
  TestWith 12 3 4
    |> And 12 4 3
    |> And 12 6 2
    |> And 1200 40 30
    |> And 0 0 0 |> ShouldFailWith (typeof<System.DivideByZeroException>)

And then we have to tell NaturalSpec which TestData a scenario should use:

[<Scenario>]
[<ScenarioSource "MyTestCases">]
let When_dividing a b result =
 Given a 
   |> When dividing_by b
   |> It should equal result
   |> Verify
 NaturalSpec with ScenarioSource  
Summary

Sometime it makes sense to test a scenario with a bunch of different parameters. We can use the ScenarioTemplate attribute to easily parameterize our scenarios. If we want more flexibility we can use predefined scenarios with custom parameters or the ScenarioSource attribute.

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Wednesday, 25. February 2009


Mocking objects with NaturalSpec

Filed under: F#,NaturalSpec — Steffen Forkmann at 16:56 Uhr

In my last articles I gave an introduction in NaturalSpec, showed how to get started and demonstrated how we can use NaturalSpec to write automatically testable scenarios for C# projects. This time I will use the same “Car-Dealer”-sample to show how we can mock objects in NaturalSpec.

Mocking objects is an important technique in Test-driven development (TDD) and allows us to simulate complex behavior.

“If an object has any of the following characteristics, it may be useful to use a mock object in its place:

  • supplies non-deterministic results (e.g. the current time or the current temperature);
  • has states that are difficult to create or reproduce (e.g. a network error);
  • is slow (e.g. a complete database, which would have to be initialized before the test);
  • does not yet exist or may change behavior;
  • would have to include information and methods exclusively for testing purposes (and not for its actual task).”

Wikipedia

In our sample we want to mock the Dealer.SellCar() functionality. The first step is to create an C#-Interface for the Dealer:

namespace CarSellingLib
{
    public interface IDealer
    {
        Car SellCar(int amount);
    }
}

NaturalSpec is using Rhino.Mocks as the underlying mocking framework, so we have to create a reference to Rhino.Mocks.dll in our spec library.

Now we can modify our spec to:

// 1. open module
module CarSpec
// 2. open NaturalSpec-Namespace
open NaturalSpec

// 3. open project namespace
open CarSellingLib

// define reusable values
let DreamCar = new Car(CarType.BMW, 200)
let LameCar = new Car(CarType.Fiat, 45)

// 4. define a mock object and give it a name
let Bert = mock<IDealer> "Bert"

// 5. create a method in BDD-style
let selling_a_car_for amount (dealer:IDealer) =
  printMethod amount
  dealer.SellCar amount

// 6. create a scenario
[<Scenario>]
let When_selling_a_car_for_30000_it_should_equal_the_DreamCar_mocked() =
  As Bert
    |> Mock Bert.SellCar 30000 DreamCar  // 7. register mocked call
    |> When selling_a_car_for 30000
    |> It should equal DreamCar
    |> It shouldn't equal LameCar
    |> Verify

As you can see we changed part 4 (in order to get a mocked IDealer instead of the concrete Dealer). In part 7 we register our mocked behavior. We want that whenever Bert.SellCar is called with parameter 30000 the DreamCar should be returned.

The Verify-function checks if the mocked function has been called. If not the scenario will fail.

If we verify our spec with a NUnit runner we get the following output:

Scenario: When selling a car for 30000 it should equal the DreamCar mocked

– As Bert

– With Mocking

– When selling a car for 30000

=> It should equal BMW (200 HP)

=> It should not equal Fiat (45 HP)

==> OK

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https://pillenonline247.nl
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Monday, 23. February 2009


Using NaturalSpec to create a spec for C# projects (Updated 08.11.2009)

Filed under: F#,NaturalSpec — Steffen Forkmann at 18:07 Uhr

In my last two articles I gave an introduction in NaturalSpec and showed how to get started. This time I will show how we can use NaturalSpec to write automatically testable scenarios for C# projects.

Like the TDD principle “Write the tests first” we should write our spec first and use the “Red-Green-Refactor” method.

"Red" – Create a spec scenario that fails

At first I created a F# class library project called “Spec.CarSelling” and added project references to NaturalSpec.dll and nunit.framework.dll (see “Getting started” for further explanations).

Now I can write my first scenario:

// 1. define the module
module CarSpec
// 2. open the NaturalSpec namespace
open NaturalSpec // 3. open project namespace open CarSellingLib // 4. define a test context let Bert = new Dealer("Bert") // 5. create a method in BDD-style let selling_a_car_for amount (dealer:Dealer) = printMethod amount dealer.SellCar amount // 6. create a scenario [<Scenario>] let When_selling_a_car_for_30000_it_should_equal_my_DreamCar() = As Bert |> When selling_a_car_for 30000 |> It should equal (new Car(CarType.BMW, 200)) |> Verify

At this stage the scenario is ready but doesn’t compile. This means we are ready with the "Red"-stage.

"Green" – Make the test the pass

In order to get the test green we have to create a C# class library called CarSellingLib and define the enum CarType and the classes Dealer and Car. Sticking to the YAGNI-principle we implement only the minimum to get the spec green (and ToString()-members for the output functionality).

namespace CarSellingLib
{
    public enum CarType
    {
        BMW
    }
}

namespace CarSellingLib
{
    public class Car
    {
        public Car(CarType type, int horsePower)
        {
            Type = type;
            HorsePower = horsePower;
        }

        public CarType Type { get; set; }
        public int HorsePower { get; set; }

        public override string ToString()
        {
            return string.Format("{0} ({1} HP)", Type, HorsePower);
        }

        public override bool Equals(object obj)
        {
            var y = obj as Car;
            if(y == null) return false;
            return Type == y.Type && HorsePower == y.HorsePower;
        }
    }
}
using System;

namespace CarSellingLib
{
    public class Dealer
    {
        public Dealer(string name)
        {
            Name = name;
        }

        public string Name { get; set; }

        public Car SellCar(int amount)
        {
            return new Car(CarType.BMW, 200);
        }

        public override string ToString()
        {
            return Name;
        }
    }
}


When we add a project reference to our spec-project the UnitTests should pass and we have completed the "Green" step. (See "Getting started" if you don’t know how to run the spec.) Now we can add some more scenarios to our spec:

// 1. define the module 
module CarSpec
// 2. open NaturalSpec-Namespace
open NaturalSpec

// 3. open project namespace
open CarSellingLib

// 4. define a test context
let Bert = new Dealer("Bert")

// define reusable values
let DreamCar = new Car(CarType.BMW, 200)
let LameCar = new Car(CarType.Fiat, 45)

// 5. create a method in BDD-style
let selling_a_car_for amount (dealer:Dealer) =
  printMethod amount
  dealer.SellCar amount

// 6. create a scenario
[<Scenario>]
let When_selling_a_car_for_30000_it_should_equal_the_DreamCar() =
  As Bert
    |> When selling_a_car_for 30000
    |> It should equal DreamCar
    |> It shouldn't equal LameCar
    |> Verify      

[<Scenario>]
let When_selling_a_car_for_19000_it_should_equal_the_LameCar() =
  As Bert
    |> When selling_a_car_for 19000
    |> It should equal LameCar
    |> It shouldn't equal DreamCar
    |> Verify

// create a scenario that expects an error
[<Scenario>]
[<Fails_with "Need more money">]
let When_selling_a_car_for_1000_it_should_fail_with_Need_More_Money() =
  As Bert
    |> When selling_a_car_for 1000
    |> Verify

Now we are in the “Red”-Phase again.

"Refactor" – rearrange your code to eliminate duplication and follow patterns

After making the spec "Green" and doing some refactoring the project code could look like this:

namespace CarSellingLib
{
    public enum CarType
    {
        Fiat,
        BMW
    }
}

namespace CarSellingLib
{
    public class Car
    {
        public Car(CarType type, int horsePower)
        {
            Type = type;
            HorsePower = horsePower;
        }

        public CarType Type { get; set; }
        public int HorsePower { get; set; }

        # region ToString, Equals 

        public override string ToString()
        {
            return string.Format("{0} ({1} HP)", Type, HorsePower);
        }

        public override bool Equals(object obj)
        {
            var y = obj as Car;
            if(y == null) return false;
            return Type == y.Type && HorsePower == y.HorsePower;
        }

        #endregion
    }
}

using System;

namespace CarSellingLib
{
    public class Dealer
    {
        public Dealer(string name)
        {
            Name = name;
        }

        public string Name { get; set; }

        public Car SellCar(int amount)
        {
            if (amount > 20000)
                return new Car(CarType.BMW, 200);

            if (amount > 3000)
                return new Car(CarType.Fiat, 45);

            throw new Exception("Need more money");
        }

        public override string ToString()
        {
            return Name;
        }
    }
}

The spec output should look like the following:

Scenario: When selling a car for 1000 it should fail with Need More Money

– Should fail…
– As Bert
– When selling a car for 1000

Scenario: When selling a car for 19000 it should equal the LameCar

– As Bert
– When selling a car for 19000
=> It should equal Fiat (45 HP)
=> It should not equal BMW (200 HP)
==> OK

Scenario: When selling a car for 30000 it should equal my DreamCar

– As Bert
– When selling a car for 30000
=> It should equal BMW (200 HP)
==> OK

Scenario: When selling a car for 30000 it should equal the DreamCar

– As Bert
– When selling a car for 30000
=> It should equal BMW (200 HP)
=> It should not equal Fiat (45 HP)
>==> OK

4 passed, 0 failed, 0 skipped, took 1,81 seconds (NUnit 2.5).

Summary

I showed how we can use NaturalSpec for the Red-Green-Refactor process of C# projects and how easy it is to get a spec in natural language.

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Introducing NaturalSpec – A Domain-specific language (DSL) for testing – Part I

Filed under: C#,F#,NaturalSpec,Tools — Steffen Forkmann at 11:31 Uhr

Test-Driven development (TDD) is a well known software development technique and follows the mantra “Red-Green-Refactor”. Behavior-Driven Development (BDD) is a response to TDD and introduces the idea of using natural language to express the Unit Test scenarios.

There are a lot of popular testing frameworks around which can be used for BDD including xUnit.net ,NUnit, StoryQ, MSpec, NSpec and NBehave. Most of them can be used with fluent interfaces and therefore provides a good readability of the sources. Some of them even provide the possibility to generate a spec in natural language out of passed Unit tests.

What is a spec?

“A specification is an explicit set of requirements to be satisfied by a material, product, or service.”

American Society for Testing and Materials (ASTM) definition

A spec is an important document for the communication process – it enables domain experts to communicate with developers. But how can you verify the compliance with the spec? The answer is: you have to write unit tests. Even with the mentioned frameworks there is a lot of work to do in order to translate a spec scenario into a Unit Test.

Question 7 in the famous Joel Test is “Do you have a spec?”.

The idea of NaturalSpec is to give domain experts the possibility to express their scenarios directly in compilable Unit Test scenarios by using a Domain-specific language (DSL) for Unit Tests. NaturalSpec is completely written in F# – but you don’t have to learn F# to use it. You don’t even have to learn programming at all.

Example 1 – Specifying a list

Let’s consider a small example. If we want to test a new List implementation a spec could look like this:

[<Scenario>]
let When_removing_an_3_from_a_small_list_it_should_not_contain_3() =
  Given [1;2;3;4;5]              // “Arrange” test context
    |> When removing 3           // “Act|> It shouldn't contain 3    // “Assert|> It should contain 4       // another assertion
    |> Verify                    // Verify scenario

I used BDD style here and expressed my scenario in a quite natural language. As the comments are indicating the scenario is following the Arrange Act Assert (“AAA”) pattern.

With the Keyword “Given” I can create a test context (the objects I want to test). In this sample I created a list with 5 elements. With the keyword “When” I call a function which does something with my test context. In this case I want to remove the value 3. In the Assert section (keywords “It should” or “It shouldn’t”) I can give some observations, which should hold for my manipulated test context.

When I run this scenario via a NUnit runner (i am using TestDriven.Net) I get the following output:

Scenario: When removing an 3 from a small list it should not contain 3

– Given [1; 2; 3; 4; 5]
– When removing 3
=> It should not contain 3
=> It should contain 4
==> OK

Example 2 – Specifying a factorial function

If you implement factorial function the spec could look like this:

[<Scenario>]
let When_calculating_fac_5_it_should_equal_120() =
  Given 5
    |> When calculating factorial
    |> It should equal 120
    |> Verify    

[<Scenario>]
let When_calculating_fac_1_it_should_equal_1() =
  Given 1
    |> When calculating factorial
    |> It should equal 1
    |> Verify          

[<Scenario>]
let When_calculating_fac_0_it_should_equal_0() =
  Given 0
    |> When calculating factorial
    |> It should equal 1
    |> Verify

And the output of NaturalSpec would look like this:

Scenario: When calculating fac 0 it should equal 0

– Given 0
– When calculating factorial
=> It should equal 1
==> OK

Scenario: When calculating fac 1 it should equal 1

– Given 1
– When calculating factorial
=> It should equal 1
==> OK

Scenario: When calculating fac 5 it should equal 120

– Given 5
– When calculating factorial
=> It should equal 120
==> OK

Getting started

Of course you can use NaturalSpec to specify C# objects. I see my post "Using NaturalSpec to create a spec for C# projects" for a small sample.

You can download NaturalSpec at GoogleCode and follow the “Getting started” tutorial in order to write your first automatically testable spec.

I am very interested in your feedback. Do you like the syntax? What should I change? Do you consider using a spec tool like NaturalSpec?

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Monday, 9. February 2009


Finding the m smallest elements in a collection in F#

Filed under: English posts,F#,Informatik — Steffen Forkmann at 11:56 Uhr

Sometimes we need a function which finds the m smallest elements in a list or array.

We can use the idea of bubble sort to maintain an sorted array of the m smallest elements so far. This idea gives us a O(m*n) algorithm which solves our problem:

let bubble array element =
  let rec bubbleStep i =
    if i < (array |> Array.length) then
      match array.[i] with
        | None -> 
           if i = array.Length - 1 || array.[i+1] <> None then
             array.[i] <- Some element
                          
           bubbleStep (i+1)
        | Some x -> 
           if element < x then
             if i = 0 then 
               array.[i] <- Some element 
             else
               array.[i-1] <- Some x
               array.[i] <- Some element
             bubbleStep (i+1)
  
  bubbleStep 0
  array    
  
let mMin seq m =
  Seq.fold bubble (Array.create m None) seq

We can easily generalize this function to compute maximum and minimum:

let bubble f array element =
  let rec bubbleStep i =
    if i < (array |> Array.length) then
      match array.[i] with
        | None -> 
           if i = array.Length - 1 || array.[i+1] <> None then
             array.[i] <- Some element
                          
           bubbleStep (i+1)
        | Some x -> 
           if f element x then
             if i = 0 then 
               array.[i] <- Some element 
             else
               array.[i-1] <- Some x
               array.[i] <- Some element
             bubbleStep (i+1)
  
  bubbleStep 0
  array    
    
let mBubble f seq m =
  Seq.fold (bubble f) (Array.create m None) seq
  
let mMin seq m = mBubble (<) seq m
let mMax seq m = mBubble (>) seq m

If we don’t want to store Option-Values we can use this simplification:

let bubble f m array element =
  let rec bubbleStep i =
    if i < (array |> Array.length) then
      let x = array.[i]
      if f element x then
         if i = 0 then 
           array.[i] <- element 
         else
           array.[i-1] <- x
           array.[i] <- element
         bubbleStep (i+1)
  
  if Array.length array < m then
    let newArray = Array.append [|element|] array 
    newArray 
      |> Array.sort 
          (fun a b -> 
            if a = b then 0 
            elif f a b then 1 else -1)
    newArray
  else
    bubbleStep 0
    array    
    
let mBubble f seq m =    
  Seq.fold (bubble f m) Array.empty seq
  
let mMin seq m = mBubble (<) seq m
let mMax seq m = mBubble (>) seq m
Tags:

Monday, 2. February 2009


F# Vortrag bei der .NET Developer Group Braunschweig

Filed under: F#,Veranstaltungen — Steffen Forkmann at 12:02 Uhr

Am Dienstag dem 16.6.2009 werde ich bei der .NET Developer Group Braunschweig einen Vortrag zum Thema “Funktionale Programmierung in F#” halten. Veranstaltungsort ist das Restaurant Kilian’s Raffinerie.

“Funktionale Programmiersprachen nehmen seit geraumer Zeit einen hohen Stellenwert in der Wissenschaft ein. Demnächst könnte es eine dieser Sprachen sogar aus dem Forschungsbereich direkt in den Mainstream schaffen. Visual Studio 2010 wird neben C# und VB.NET die funktionale Programmiersprache F# als dritte Hauptsprache anbieten. Der Vortrag soll einen Einblick in funktionale Konzepte und deren Umsetzung in F# geben. Insbesondere soll auf “Funktionen höherer Ordnung”, Typinferenz, Currying, Pattern Matching, “Unveränderlichkeit” und parallele Programmierung eingegangen werden.”

[Abstract]


Warning: Creating default object from empty value in /www/htdocs/w007928a/blog/wp-content/plugins/wp-referencesmap/GoogleMapsWrapper.php on line 55

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Sunday, 1. February 2009


Von Barcelona nach Marseille – Google Maps hat’s einfach drauf

Filed under: Google — Steffen Forkmann at 19:03 Uhr

Irgendwie bringt Google Maps doch immer wieder neue Kuriositäten. Wenn man sich den Fußweg von Barcelona nach Marseille anzeigen lässt, dann schlägt das Programm eine Fährtour über Genua und Korsika vor und weist auch ausdrücklich darauf hin, dass es dort möglicherweise keine Bürgersteige gibt. 😉

Von Barcelona nach Marseille

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Saturday, 31. January 2009


n-dimensional k-means clustering with F# – part II

Filed under: BioInformatik,English posts,F#,Informatik — Steffen Forkmann at 11:28 Uhr

In the last post I show how we can calculate clusters of n-dimensional Objects with the K-means-Algorithm in F#. This time I will simplify the code by using the built-in type vector.

First of all we redefine the interface for “clusterable” objects:

type IClusterable =
  abstract DimValues: vector with get

This time we do not need any dimension information – the vector type will care about this. Now we can reduce our distance function to:

let calcDist (p1:vector) (p2:vector) = (p1 - p2).Norm

The function Norm calculates the 2-Norm of a vector.

2-Norm ==> Eulidean distance 

So calcDist will still compute the n-dimensional Euclidean distance.

The next step is the definition of a n-dimensional Centroid type. This time we will only use a type alias of vector:

type Centroid = vector

The calculation of the centroid and the centroid error can be written as:

let calcCentroid (items:'a list when 'a :> IClusterable)
     (oldCentroid:Centroid) =
  let count = items.Length
  if count = 0 then oldCentroid else  
  let sum =
    items
      |> List.fold_left 
        (fun vec item -> vec + item.DimValues) // vector addition
        (nullVector oldCentroid)
   
  sum * (1./(count |> float))  // multiply with scalar
     

let calcError centroid (items:'a list when 'a :> IClusterable) =
  let sq x = x * x

  items
    |> List.sum_by (fun i -> calcDist centroid i.DimValues |> sq)

The calcError function is straight forward but not perfect in terms of performance. As we use the calcDist function and hence the 2-Norm the function will first calculate a square root and then squares the result.

The rest of the code is pretty much same as in the last post:

/// creates n-dimensional 0 - vector
let nullVector (v:vector) = v * 0.
    
type Cluster<'a> when 'a :> IClusterable =
  {Items: 'a list;
   Count: int;
   Centroid: Centroid;
   Error: float}

  member x.Print =
     printfn "(Items: %d, Centroid: %A, Error: %.2f)"
       x.Count x.Centroid x.Error

  static member CreateCluster (item:'a) =
    let items = [item]
    let empty = nullVector item.DimValues

    let centroid = calcCentroid items empty
    {new Cluster<'a> with
      Items = items and
      Count = 1 and
      Centroid = centroid and
      Error = calcError centroid items}

  member x.EvolveCluster (items:'a list) =
    let l = items.Length
    let centroid = calcCentroid items x.Centroid
    {x with
      Items = items;
      Count = l;
      Centroid = centroid;
      Error = calcError centroid items} 

let rand = new Random()  

let InitClusters (k:int)
      (items:'a array when 'a :> IClusterable)  =
  let length = items.Length
  let getInitItem() = items.[rand.Next length]
  Array.init k (fun x ->
                  getInitItem()
                    |> Cluster<'a>.CreateCluster)
                    
                    
let AssignItemsToClusters k (clusters:Cluster<'a> array)
      (items:'a seq when 'a :> IClusterable) =
  if k <= 0 then failwith "KMeans needs k > 0"
  let findNearestCluster (item:'a) =
    let minDist,nearest,lastPos =
      clusters
        |> Array.fold_left
            (fun (minDist,nearest,pos) cluster ->
               let distance = calcDist item.DimValues (cluster.Centroid)
               if distance < minDist then
                 (distance,pos,pos+1)
               else
                 (minDist,nearest,pos+1))
            (Double.PositiveInfinity,0,0)
    nearest

  let assigned =
    items
      |> Seq.map (fun item -> item,findNearestCluster item)

  let newClusters = Array.create k []
  for item,nearest in assigned do
    newClusters.[nearest] <- item::(newClusters.[nearest])

  clusters
    |> Array.mapi (fun i c -> c.EvolveCluster newClusters.[i])  

    
let calcClusterError (clusters:Cluster<'a> array) =
  clusters
    |> Array.fold_left (fun acc cluster -> acc + cluster.Error) 0.  
                      
let kMeansClustering K epsilon
       (items:'a array when 'a :> IClusterable) =
  let k = if K <= 0 then 1 else K
  let rec clustering lastError (clusters:Cluster<'a> array) =
    let newClusters =
      AssignItemsToClusters k clusters items
    let newError = calcClusterError newClusters

    if abs(lastError - newError) > epsilon then
      clustering newError newClusters
    else
      newClusters,newError    

  InitClusters k items
    |> clustering Double.PositiveInfinity

This vector approach shortens the code for the kMeans algorithm, but has a little longer runtime. I am interested in any suggestions.

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Thursday, 29. January 2009


n-dimensional k-means clustering with F#

Filed under: BioInformatik,English posts,F#,Informatik — Steffen Forkmann at 11:38 Uhr

The K-means-Algorithm is one of the simplest unsupervised learning algorithms that solve the well known clustering problem. In this article I will show how we can implement this in F#.

First of all we define an interface for “clusterable” objects:

type IClusterable =

  abstract DimValues: float array with get

  abstract Dimensions: int

The next step is to define a distance function. We will use n-dimensional Euclidean distance here.

Euclidean distance

let calcDist (p1:IClusterable) (p2:IClusterable) =

  let sq x = x * x

  if p1.Dimensions <> p2.Dimensions then

    failwith "Cluster dimensions aren’t equal."

 

  p2.DimValues

    |> Array.fold2

        (fun acc x y -> x – y |> sq |> (+) acc)

        0. p1.DimValues

   |> sqrt 

Now we define a n-dimensional Centroid type. Our kMeans-Algorithm will minimize the squared distances to k centroids (or “means”).

type Centroid =

  {Values: float array;

   dimensions: int}

  member x.Print = printfn "%A" x.Values

  interface IClusterable with

    member x.DimValues = x.Values   

    member x.Dimensions = x.dimensions   

The centroid of a finite set of n-dimensional points x1, x2, …, xn is calculated as

image

let calcCentroid (items:’a list when ‘a :> IClusterable)

     (oldCentroid:Centroid) =

  let count = items.Length

  if count = 0 then oldCentroid else

  let mValues =    

    [|for d in 0..oldCentroid.dimensions-1 do

        let sum =

          items

            |> List.sumBy (fun item -> item.DimValues.[d])

 

        yield sum / (count |> float)|]

 

  { Values = mValues;

    dimensions = oldCentroid.dimensions}

We made a small modification – if we don’t have any items assigned to a cluster the centroid won’t change. This is important for the robustness of the algorithm.

Now we can calculate the squared errors to a centroid:

let calcError centroid (items:’a list when ‘a :> IClusterable) =

  let calcDiffToCentroid (item:’a) =

    centroid.Values

      |> Array.fold2

          (fun acc c i -> acc + (c-i)*(c-i))

          0. item.DimValues

 

  items

    |> List.sumBy calcDiffToCentroid 

For storing cluster information we create a cluster type:

type Cluster<‘a> when ‘a :> IClusterable =

  {Items: ‘a list;

   Count: int;

   Centroid: Centroid;

   Error: float}

 

  member x.Print =

     printfn "(Items: %d, Centroid: %A, Error: %.2f)"

       x.Count x.Centroid x.Error

 

  static member CreateCluster dimensions (item:’a) =

    let items = [item]

    let empty =

      { Values = [||];

        dimensions = dimensions}

 

    let centroid = calcCentroid items empty

    { Items = items;

      Count = 1;

      Centroid = centroid;

      Error = calcError centroid items}

 

  member x.EvolveCluster (items:’a list) =

    let l = items.Length

    let centroid = calcCentroid items x.Centroid

    {x with

      Items = items;

      Count = l;

      Centroid = centroid;

      Error = calcError centroid items} 

Now we need a function to initialize the clusters and a function to assign a items to the nearest cluster:

open System

 

let rand = new Random() 

 

let InitClusters (k:int) dimensions

      (items:’a array when ‘a :> IClusterable)  =

  let length = items.Length

  let getInitItem() = items.[rand.Next length]

  Array.init k (fun _ ->

                  getInitItem()

                    |> Cluster<‘a>.CreateCluster dimensions) 

 

let AssignItemsToClusters k dimensions (clusters:Cluster<‘a> array)

      (items:’a seq when ‘a :> IClusterable) =

  if k <= 0 then failwith "KMeans needs k > 0"  

  let findNearestCluster item =

    let minDist,nearest,lastPos =

      clusters

        |> Array.fold

            (fun (minDist,nearest,pos) cluster ->

               let distance = calcDist item (cluster.Centroid)

               if distance < minDist then

                 (distance,pos,pos+1)

               else

                 (minDist,nearest,pos+1))

            (Double.PositiveInfinity,0,0) 

    nearest

 

  let assigned =

    items

      |> Seq.map (fun item -> item,findNearestCluster item)

 

  let newClusters = Array.create k []  

  for item,nearest in assigned do        

    newClusters.[nearest] <- item::(newClusters.[nearest])

 

  clusters

    |> Array.mapi (fun i c -> c.EvolveCluster newClusters.[i])   

The last step is a function which calculates the squared error over all clusters:

let calcClusterError (clusters:Cluster<‘a> array) =

  clusters

    |> Array.sumBy (fun cluster -> cluster.Error)

Now it is an easy task to write the kMeans algorithm:

let kMeansClustering K dimensions epsilon

       (items:’a array when ‘a :> IClusterable) =

  let k = if K <= 0 then 1 else K

  let rec clustering lastError (clusters:Cluster<‘a> array) =

    let newClusters =

      AssignItemsToClusters k dimensions clusters items

    let newError = calcClusterError newClusters

 

    if abs(lastError – newError) > epsilon then       

      clustering newError newClusters

    else

      newClusters,newError   

 

  InitClusters k dimensions items

    |> clustering Double.PositiveInfinity 

We can test this algorithm with random 2-dimensional points:

type Point =

  {X:float; Y: float} 

  member x.Print = printfn "(%.2f,%.2f)" x.X x.Y

  interface IClusterable with

    member x.DimValues = [| x.X; x.Y |]

    member x.Dimensions = 2  

 

let point x y = {X = x; Y = y}

let getRandomCoordinate() = rand.NextDouble() – 0.5 |> (*) 10. 

let randPoint _ = point (getRandomCoordinate()) (getRandomCoordinate())    

let points n = Array.init n randPoint

let items = points 1000

 

printfn "Items:"

items |> Seq.iter (fun i -> i.Print)

 

let clusters,error = kMeansClustering 3 2 0.0001 items

printfn "\n"

clusters |> Seq.iter (fun c -> c.Print)   

printfn "Error: %A" error   

Next time I will show how we can simplify the code by using F#’s built-in type vector instead of array.

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