Monthly Archives: December 2011

JAVA: How to programmatically scale down all images in a directory using ImageMagick?

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You can download Image Magick for free at http://www.imagemagick.org

Images are in C:\images
ImageMagick executable is in C:\ImageMagick\convert.exe

Loop through all files in folder and scale them down 25% of their original size.

Use this command to resize the image and append “s_” to the begining of the file name.

Example:
C:\ImageMagick\convert.exe C:\images\1.jpg -resize 25% C:\images\s_1.jpg

import java.io.File;
import java.io.IOException;
 
public class ImgManipulator
{
	public static void main(String[] args)
	{
		  String path = "c:\\images\\";
		  String files;
		  File folder = new File(path);
		  File[] listOfFiles = folder.listFiles();
		  for (int i = 0; i < listOfFiles.length; i++)
		  {
if (listOfFiles[i].isFile())
{
	files = listOfFiles[i].getName();
	System.out.println("Scaling"+files);
        try
	{
Process p = Runtime.getRuntime().exec(
"C:\\ImageMagick\\convert.exe C:\\images\\"+files+" -resize 25% C:\\images\\s_"+files);
        }
	catch (IOException e)
	{
		e.printStackTrace();
	}
}
		  }
	}
 
}

C#: How to programmatically resize images or create thumbnails from a variety of differently sized images using ffmpeg

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ImageMagick should be used to do this,  ffmpeg is for AV.

But to do this using ffmpeg and c#, follow these steps….

You can download ffmpeg for free at http://ffmpeg.org/download.html

My images exists in C:\image_directory and my ffmpeg exists in C:\ffmpeg.

 

I will be using the following ffmpeg command to resize each image (create a thumbnail):

C:\ffmpeg\bin>ffmpeg -i c:\image_directory\1.png -s 80×80 c:\image_directory\t\t_1.png


The above command will take an input image 1.png, resize it to 80px by 80px, save it in a sub-folder named \t\,
and append “t_” to the begining of the file name.

Here is how you would loop through every image in the folder:

using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.IO;
using System.Diagnostics;
using System.Text.RegularExpressions;
 
namespace ImgResize
{
    class Program
    {
        static void Main(string[] args)
        {
            //get an array of all the image files//
            string[] imgPaths = Directory.GetFiles(@"c:\image_directory\");
 
            //loop through each image//
            for (int i = 0; i < imgPaths.Length; i++)
            {
                string file_path = imgPaths[i];
                //get the file name out of full path//
                string filename = Regex.Match(imgPaths[i], @".*\\([^\\]+$)").Groups[1].Value;
                //output the filename about to be converted
                Console.WriteLine("converting : "+filename);
                //make arguements string
                string write2string = " -i " + file_path + " -s 80x80 "+@"c:\\image_directory\\t\\t_" + filename;
                //create a process
                Process myProcess = new Process();
                myProcess.StartInfo.UseShellExecute = false;
                myProcess.StartInfo.RedirectStandardOutput = true;
                //point ffmpeg location
                myProcess.StartInfo.FileName = @"c:\\ffmpeg\\bin\\ffmpeg";
                //set arguements
                myProcess.StartInfo.Arguments = write2string;
                myProcess.Start();
                myProcess.WaitForExit();
            }
        }
    }
}

JAVA: How to programmatically manipulate a Protégé-Frames lexicon / ontology / dictionary using Protege API and Java.

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This tutorial will give a brief overview of how to modify a Protégé-Frames dictionary using Java.

Download Protege:

protege.stanford.edu/

Reference the API:

protege.stanford.edu/protege/3.4/docs/api/core/

The Following examples will require these imports:

import edu.stanford.smi.protege.model.Cls;
import edu.stanford.smi.protege.model.Instance;
import edu.stanford.smi.protege.model.KnowledgeBase;
import edu.stanford.smi.protege.model.Project;
import edu.stanford.smi.protege.model.Slot;

Assuming you’ve successfully associated the appropriate Protege libraries with your Eclipse, lets get started with some simple HOW-TOs in programmatical Protege ontology manipulation;

For this tutorial I will be using the RadLex Lexicon/Dictionary.

The first thing you will need is the actual project files.
Mine are called : RadLex.pins, RadLex.pont, and RadLex.pprj
These files are created when you save a Lexicon/Dictionary in Frames format using Protege.

Create a pointer to them in your java code. I have mine in in C:\smelo\RadLex.pprj
You only have to point to the *.pprj file.

//Get the project file of the lexicon you want to manipulate
private static final String PROJECT_FILE_Pointer = "C:\\smelo\\RadLex.pprj";

Next, you will need to get the KnowledgeBase object.

//errors object is required in getting the project
Collection errors = new ArrayList();
//Get Project project
Project project = new Project(PROJECT_FILE_Pointer, errors);
//Get Knowledgebase kb
KnowledgeBase kb = project.getKnowledgeBase();

In Protege Frames, each Term/Concept/Lexicon Entity/Thingy is considered a “class”(Cls). The entire RadLex dictionary is nothing more then a bunch of terms(classes) with attributes(slots), and the relationships amongst them.

So lets iterate through all the classes in the KnowledgeBase.

To do this we need to get a class iterator:

//RadLex Class iterator
Iterator radClsIter = kb.getClses().iterator();

Loop through every class

In RadLex, the “name” of every class is its Radlex Id number, or “RID###..”
such as “RID1099” “RID35707” “RID3874” ….

Every RadLex class contains a number of “slots” or attributes that you can populate:

Using the method .getOwnSlots() on a Cls Object will show you a list of all the slots and their names

These are all different attributes(slots) of a single concept(Cls) in RadLex:

Slot(Related_Condition), Slot(Anatomical_Site), Slot(Related_modality), Slot(ACR_ID), Slot(UMLS_Term), Slot(Is_A), Slot(UMLS_ID), Slot(Misspelling of term), Slot(Has_Subtype), Slot(Non-English_name), Slot(Member_Of), Slot(Preferred_name), Slot(Source), Slot(Non-Sanctioned Synonym), Slot(Synonym), Slot(Version_Number), Slot(Term_Status), Slot(SNOMED_ID), Slot(Acronym), Slot(SNOMED_Term), Slot(ACR_Term), Slot(Comment), Slot(Image_URL), Slot(Definition), Slot(:ROLE), Slot(:DOCUMENTATION), Slot(:SLOT-CONSTRAINTS), Slot(:DIRECT-INSTANCES), Slot(:DIRECT-SUPERCLASSES), Slot(:DIRECT-SUBCLASSES), Slot(:DIRECT-TEMPLATE-SLOTS), Slot(:NAME), Slot(:DIRECT-TYPE)

Some slot types are simple strings, while others are more complex Instances.

while( radClsIter.hasNext() )
{
	Cls currentClass = radClsIter.next();
}

So now that we have a brief scattered overview of the RadLex Lexicon/Dictionary,
and we know how to iterate through each Concept/Term/Class within it. Lets do some practical HOW-TOs.

HOW TO get the value of “Preferred_name” slot from a class object(currentClass)?

One way of retrieving of the content of a slot of a class would be by the slot’s name.
So all you have to do is, get another slot iterator this time for the class(term/concept), and compare its name with the one you want.
Then, iterate through the content of the slot and display its value.(You might not have to do this last step; it depends of the type of slot)

In RadLex the Preferred_name slot of a class is populated with an Instance type.
So we have to get the instance of a slot then get the name of the Instance.

String slotName = "Preferred_name"; 
 
Iterator slotIter = currentClass.getOwnSlots().iterator();
 
//Iterate through the slots
while( slotIter.hasNext() )
{
	Slot currentSlot = slotIter.next();
 
	//Compare the slot name with your slotName String
	if( slotName.equals( currentSlot.getName() ) )
    	{
		Object slotContentObject = null;
 
		//Create another iterator for the content of the slot
    		Iterator iterSlotContent = currentClass.getOwnSlotValues(currentSlot).iterator();
 
    		if( iterSlotContent.hasNext() )
    		{
    			slotContentObject = iterSlotContent.next(); 
 
			//if the content of a slot is of type Instance
    			if(slotContentObject instanceof Instance)
  			{
				//cast to Instance
    				Instance instSlotValue = (Instance) slotContentObject;
 
				//use the method getBrowserText() on the Instance to get its String content
    				System.out.println(instSlotValue.getBrowserText());
    			}
    		}
    	}
}

HOW TO change the Definition slot of a Class/Concept/Term by specific “name” (RID) and save to project file?

Say we want to change the content of the “Definition” slot in Cls “RID35712”:

String slotName = "Definition"; 
 
//get the Cls object of the Term/Concept/Class
Cls myConcept = kb.getCls( "RID35712" );
 
Iterator myConceptClsIter = myConcept.getOwnSlots().iterator();
while( myConceptClsIter.hasNext() )
{
	Slot currentSlot = myConceptClsIter.next();
	if(slotName.equals(currentSlot.getName()) )
	{
		//set new Definition
		myConcept.setOwnSlotValue(currentSlot, "This is my new Definition for Term RID35712");
	}
}
 
//save changes
project.save(errors);

HOW TO display ALL synonyms of the entire project?

What if we want to list the names of ALL synonyms throughout the entire dictionary

Iterator radClsIter = kb.getClses().iterator();
 
while( radClsIter.hasNext() ){
        Cls currentClass = radClsIter.next();
        String prefName = findPreferredName(currentClass);
 
        String slotName = "Synonym";
        Iterator slotIter = currentClass.getOwnSlots().iterator();
 
        while( slotIter.hasNext() )
        {
    		Slot currentSlot = slotIter.next();
    		if(slotName.equals(currentSlot.getName()) )
    		{
    			Object slotContentObject = null;
    			Iterator iterSlotContent = currentClass.getOwnSlotValues(currentSlot).iterator();
    			if( iterSlotContent.hasNext() )
    			{
    				slotContentObject = iterSlotContent.next();
    				if(slotContentObject instanceof Instance)
    				{
    					Instance instSlotValue = (Instance) slotContentObject;
    					System.out.println(instSlotValue.getBrowserText());
    				}
    			}
    		}
    	}
}

HOW TO create a new Class/Concept/Term and Add it as a child of RID35712?

We will be assigning the “name” as new unique “RID12345” and adding it as child of the term “RID35712”

Collection myCol =   kb.getClsNameMatches("RID35712",1);
kb.createCls("RID12345", myCol);

That covers a few basics, if you would like an example of something I havent covered, feel free to leave a comment.

GL & HF :D