Install SimpleITK on Linux/Ubuntu for Java Application

In this tutorial, we are going to learn how to install SimpleITK which is very handy for medical image analysis.

SimpleITK is a simplified programming interface to the algorithms and data structures of the Insight Toolkit (ITK). It supports bindings for multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby, and TCL. These bindings enable scientists to develop image analysis workflows in the programming language they are most familiar with. The toolkit supports more than 15 different image file formats, provides over 280 image analysis filters, and implements a unified interface to the ITK intensity-based registration framework. you can check out official documentation from here.

For the windows system, we can find the prebuilt library where we can simply download and install it. But for Linux os, we need to build by ourselves.

Installation:

Download SimpleItk: 

Clone the SimpleITK from the github.  We can select the desired version from release and download or clone it.

git clone https://github.com/SimpleITK/SimpleITK.git

Now change to the SimpleITK directory:

cd SimpleITK

Install Cmake:

sudo apt-get  install cmake

Install Java:

sudo apt install openjdk-8-jdk

Build SimpleITK

mkdir SimpleITK-build
cd SimpleITK-build
sudo cmake ../SuperBuild

The SuperBuild generates make files that take care of downloading and building ITK. Now start the build

make -j4

Note: Be careful not to run out of memory during the build. We need 4GB of memory per core. For example, if we compile with 4 cores (e.g. make -j4) we need a machine with at least 16GB of RAM.

It will take some time. After the installation, you can find the .so library file which we are going to use. Also, you can find the .jar file for java under the created build folder.

First, we need to load the ITK .jar file in our project and .so file by providing the JVM argument as

Djava.library.path=/path/to/SimpleITKRuntime

Where, /path/to/SimpleITKRuntime is the directory that contains the .so file. Otherwise, you will get the following error

Exception in thread "main" java.lang.UnsatisfiedLinkError: no SimpleITKJava in java.library.path
	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1860)
	at java.lang.Runtime.loadLibrary0(Runtime.java:871)
	at java.lang.System.loadLibrary(System.java:1124)
	at org.itk.simple.SimpleITKJNI.<clinit>(SimpleITKJNI.java:226)
	at org.itk.simple.SimpleITK.readImage(SimpleITK.java:475)
	at simpleitk.SimpleItkTest.main(SimpleItkTest.java:8)

Run the sample Java example

package simpleitk;

import org.itk.simple.Image;
import org.itk.simple.SimpleITK;

public class SimpleItkTest {
    public static void main(String[] args) {
		String inputImagePath = "/path/to/image";
		String outputImagePath = "/path/to/output/image";
        Image image = SimpleITK.readImage(inputImagePath);
        SimpleITK.writeImage(image, outputImagePath);
    }
}

This is a sample example for reading and writing images using simpleITK library.

Note if we are using the Gradle project, then we can add the .so library path as below

bootRun {
    jvmArgs('-Djava.library.path=/opt/SimpleItk/')
}

Where, /opt/SimpleItk/ is the directory which contains the .so file.

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How to enable dark theme in google chrome dev tools

This is a quick tutorial on how to enable dark themes in google chrome dev tools.

1. Set up the dark theme from Settings:

First, inspect element to open the chrome dev tools by Ctrl + Shift + I

Click the Settings gear icon as below.

Go to Preferences  >>  Appearance  >> Theme  >>  select Dark from dropdown

Now, close the setting windows, we can see the Reload DevTools button as below. Click on it to refresh.

We can see the dark theme applied to the dev tools

2. Using Command line:

Navigate to dev tools using inspect element (Ctr + Shift + I)

Type the following command:

Ctr + Shift + P

We can see the popup dialog. Simply type and search dark in the search bar where we can click the option called Appearance Switch to dark theme 

After that, we can see the Reload DevTools button. Click on it to refresh.

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How to record GIF on Ubuntu Linux

This is a quick tutorial on how we can record the animated GIF on a Linux Ubuntu machine.

 For this, there is a software called Peek, a simple screen recorder with an easy to use interface

Peek is very easy to create short screencasts of specific screen areas. We can simply place the Peek window over the area where we want to record and start recording.

Although it is optimized for recording and generating animated GIFs, we can also record WebM and MP4 videos too.

Let's look at how we can install it. For this open your terminal and type the following command

For Ubuntu:

sudo add-apt-repository ppa:peek-developers/stable
sudo apt update
sudo apt install peek

Here, we are adding PPA repositories required, while doing so use enter key to allow. Now, after running the above command you can simply open the peek recorder and start recording the GIFs animation.

The sample recording screen looks as below:

For Debian:

sudo apt install peek

For ElementaryOS:

sudo apt install software-properties-common
sudo add-apt-repository ppa:peek-developers/stable
sudo apt update
sudo apt install peek

For Arch Linux:

sudo pacman -S peek

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How to create copy to clipboard in Vuetify VujeJs application

This is a quick tutorial on how we can add copy to clipboard functionality in the VueJs application.

In this example, we are going to create the invitation code where users can copy that code in the clipboard so that they can share it simply by copy-paste.

Let's create a simple component called CopyToClipBoard.vue and add a template

<template>
    <div>
        <v-card height="460" class="mt-8">
            <v-card-title class="justify-center mb-2 pb-0">
                <span class="text-center red--text">Your invite code</span>
            </v-card-title>
            <v-card-text class="text-center mb-0 pb-0">
                <v-chip color="grey" text-color="white" class="font-weight-bold">
                    <span class="inv-text">A0xU76E</span>
                    <v-divider
                            class="mx-4"
                            vertical
                            light
                    ></v-divider>
                    <v-tooltip top>
                        <template v-slot:activator="{ on, attrs }">
                  <span @click="copyCode" @mouseout="reset" style="cursor: pointer;" v-bind="attrs"
                        v-on="on">Copy</span>
                        </template>
                        <span>{{copyText}}</span>
                    </v-tooltip>
                </v-chip>
            </v-card-text>
        </v-card>
    </div>
</template>

Here, we are using vuetify UI framework, you can use your own HTML CSS. We are adding two events called @click for copy text to clipboard and @mouseout event for resetting the default value. 

Let's add the data:

created() {
    this.copyText = this.text
  },
data () {
    return {
      invitationCode:"A0xU76EJK",
      text: "Copy to invite",
      copyText: ''
    }
  },

Create the methods used in template:

methods : {
    async copyCode() {
      await navigator.clipboard.writeText(this.invitationCode);
      this.copyText = "Copied"
    },
    reset() {
      this.copyText = this.text
    }
  }
}

We are using vuetify tooltip to give the copy information. 

When the user clicks on the button it will call copyCode function and will copy in clipboard. In order to do so, we are using navigator.clipboard API which allows user to grant the website or app permission to access the clipboard. 

After that, we have to copy the invitationCode value so we pass this value as a parameter.

The sample demo looks like below:

The overall implementation looks as:

<template>
    <div>
        <v-card height="460" class="mt-8">
            <v-card-title class="justify-center mb-2 pb-0">
                <span class="text-center red--text">Your invite code</span>
            </v-card-title>
            <v-card-text class="text-center mb-0 pb-0">
                <v-chip color="grey" text-color="white" class="font-weight-bold">
                    <span class="inv-text">A0xU76E</span>
                    <v-divider
                            class="mx-4"
                            vertical
                            light
                    ></v-divider>
                    <v-tooltip top>
                        <template v-slot:activator="{ on, attrs }">
                  <span @click="copyCode" @mouseout="reset" style="cursor: pointer;" v-bind="attrs"
                        v-on="on">Copy</span>
                        </template>
                        <span>{{copyText}}</span>
                    </v-tooltip>
                </v-chip>
            </v-card-text>
        </v-card>
    </div>
</template>

<script>
    export default {
        name: "CopyToClipBoard",
        data () {
            return {
                invitationCode:"A0xU76EJK",
                text: "Copy to invite",
                copyText: ''
            }
        },
        created() {
            this.copyText = this.text
        },
        methods : {
            async copyCode() {
                await navigator.clipboard.writeText(this.invitationCode);
                this.copyText = "Copied"
            },
            reset() {
                this.copyText = this.text
            }
        }
    }
</script>

<style scoped>
    .inv-text {
        min-width: 150px;
        font-size: 20px;
    }
</style>

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How to install icon fonts in vuetify vue application

This is a quick tutorial on how we can install icon fonts for material icons and font awesome. 

Although vuetify uses material design icons, that might not be sufficient all the time so we need to use some other library for it.

We can simply install a font by including the specified icon library CDN. For this, go to the project directory and inside it, you can see the index.html file under the public folder.  

Here, add the material icons and font awesome icon CDN link as below.

<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:100,300,400,500,700,900">
<link href="https://cdn.jsdelivr.net/npm/font-awesome@4.x/css/font-awesome.min.css" rel="stylesheet">
<link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/@mdi/font@4.x/css/materialdesignicons.min.css">

After adding this, we can simply use icons for e.g: 

From font awesome, simply use the fa- prefixed on icon name:

<v-icon left color="blue" size="50">fa-twitter</v-icon>

For google fonts, go to the google font and click the icon, we can see the icon font name similar as below, simply use the name.

<v-icon left color="blue" size="50">logout</v-icon>

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How to implement social media share buttons in Vue.js

In this tutorial, we are going to implement the social media share button using Vue.js.

Here, we are using the dependency called vue-socials which is very handy while implementing social media share buttons. It contains almost all the social share button functionality that we need and is lightweight and highly customizable.

In this tutorial, we are going to implement the Facebook and Twitter share button as an example. 

Install Dependency:

Go to your project directory and install the dependency.

If you are using the npm package manager

For Vue 2: 

npm install vue-socials

For Vue 3:

npm install vue-socials@next

If you are using the yarn package manager

# Vue 2
yarn add vue-socials

# Vue 3
yarn add vue-socials@next

Now, it's time to import the required share button components. Here we are creating the SocialMediaShare.vue component for demo. 

Inside this component, we are going to import the Facebook and Twitter share button component as below:

import { SFacebook, STwitter } from 'vue-socials'

Now, we need to register the components

  components: { SFacebook, STwitter }

After component registration, let us use it into the template

<div >
    <s-facebook
            :window-features="windowFeatures"
            :share-options="facebookShareOptions"
            :use-native-behavior="useNativeBehavior"
            @popup-close="onClose"
            @popup-open="onOpen"
            @popup-block="onBlock"
            @popup-focus="onFocus"
            style="text-decoration:none"
    >
        <svg
                xmlns="http://www.w3.org/2000/svg"
                width="24"
                height="24"
                viewBox="0 0 24 24"
                aria-hidden="true"
                focusable="false"
        >
            <path d="M9 8h-3v4h3v12h5v-12h3.642l.358-4h-4v-1.667c0-.955.192-1.333 1.115-1.333h2.885v-5h-3.808c-3.596 0-5.192 1.583-5.192 4.615v3.385z"/>
        </svg>
    </s-facebook>
    <s-twitter
            :window-features="windowFeatures"
            :share-options="twitterShareOptions"
            :use-native-behavior="useNativeBehavior"
            @popup-close="onClose"
            @popup-open="onOpen"
            @popup-block="onBlock"
            @popup-focus="onFocus"
            style="text-decoration:none"
    >
        <svg
                xmlns="http://www.w3.org/2000/svg"
                width="24"
                height="24"
                viewBox="0 0 24 24"
                aria-hidden="true"
                focusable="false"
        >
            <path
                    d="M24 4.557c-.883.392-1.832.656-2.828.775 1.017-.609 1.798-1.574 2.165-2.724-.951.564-2.005.974-3.127 1.195-.897-.957-2.178-1.555-3.594-1.555-3.179 0-5.515 2.966-4.797 6.045-4.091-.205-7.719-2.165-10.148-5.144-1.29 2.213-.669 5.108 1.523 6.574-.806-.026-1.566-.247-2.229-.616-.054 2.281 1.581 4.415 3.949 4.89-.693.188-1.452.232-2.224.084.626 1.956 2.444 3.379 4.6 3.419-2.07 1.623-4.678 2.348-7.29 2.04 2.179 1.397 4.768 2.212 7.548 2.212 9.142 0 14.307-7.721 13.995-14.646.962-.695 1.797-1.562 2.457-2.549z"
            />
        </svg>
    </s-twitter>
</div>

We are using some random SVG for icons, we can use the images or custom icons. 

Let's create the data and methods:

data () {
    return {
      windowFeatures: {},
      facebookShareOptions: {
        url: 'https://github.com/',
        quote: 'Quote',
        hashtag: '#Github',
      },
      twitterShareOptions: {
        url: 'https://github.com/',
        text: 'Hello world',
        hashtags: ['hash', 'tag'],
        via: 'twitterdev',
      },
      useNativeBehavior: false,
    }
  },
  methods:{
    onClose() {},
    onOpen() {},
    onBlock() {},
    onFocus() {},
  }

If we run the application we can see something like this:

Click on icons, we can share the content on those social media. We can change the content from data in component. 

For now, we are using the Github link and dummy text as examples.

If we want to import all the share buttons available then import all components as below inside main.js file.

 // Vue 2
import Vue from 'vue'
import VueSocials from 'vue-socials';

Vue.use(VueSocials)

// Vue 3

import { createApp } from 'vue'
import VueSocials from 'vue-socials';
import App from './App.vue'

const app = createApp(App)
app.use(VueSocials)

The overall implementation of the above example looks as below:

<template>
    <div >
        <s-facebook
                :window-features="windowFeatures"
                :share-options="facebookShareOptions"
                :use-native-behavior="useNativeBehavior"
                @popup-close="onClose"
                @popup-open="onOpen"
                @popup-block="onBlock"
                @popup-focus="onFocus"
                style="text-decoration:none"
        >
            <svg
                    xmlns="http://www.w3.org/2000/svg"
                    width="24"
                    height="24"
                    viewBox="0 0 24 24"
                    aria-hidden="true"
                    focusable="false"
            >
                <path d="M9 8h-3v4h3v12h5v-12h3.642l.358-4h-4v-1.667c0-.955.192-1.333 1.115-1.333h2.885v-5h-3.808c-3.596 0-5.192 1.583-5.192 4.615v3.385z"/>
            </svg>
        </s-facebook>
        <s-twitter
                :window-features="windowFeatures"
                :share-options="twitterShareOptions"
                :use-native-behavior="useNativeBehavior"
                @popup-close="onClose"
                @popup-open="onOpen"
                @popup-block="onBlock"
                @popup-focus="onFocus"
                style="text-decoration:none"
        >
            <svg
                    xmlns="http://www.w3.org/2000/svg"
                    width="24"
                    height="24"
                    viewBox="0 0 24 24"
                    aria-hidden="true"
                    focusable="false"
            >
                <path
                        d="M24 4.557c-.883.392-1.832.656-2.828.775 1.017-.609 1.798-1.574 2.165-2.724-.951.564-2.005.974-3.127 1.195-.897-.957-2.178-1.555-3.594-1.555-3.179 0-5.515 2.966-4.797 6.045-4.091-.205-7.719-2.165-10.148-5.144-1.29 2.213-.669 5.108 1.523 6.574-.806-.026-1.566-.247-2.229-.616-.054 2.281 1.581 4.415 3.949 4.89-.693.188-1.452.232-2.224.084.626 1.956 2.444 3.379 4.6 3.419-2.07 1.623-4.678 2.348-7.29 2.04 2.179 1.397 4.768 2.212 7.548 2.212 9.142 0 14.307-7.721 13.995-14.646.962-.695 1.797-1.562 2.457-2.549z"
                />
            </svg>
        </s-twitter>
    </div>
</template>

<script>
    import { SFacebook, STwitter } from 'vue-socials'

    export default {
        name: "SocialMediaShare",
        components: { SFacebook, STwitter },
        data () {
            return {
                windowFeatures: {},
                facebookShareOptions: {
                    url: 'https://github.com/',
                    quote: 'Quote',
                    hashtag: '#Github',
                },
                twitterShareOptions: {
                    url: 'https://github.com/',
                    text: 'Hello world',
                    hashtags: ['hash', 'tag'],
                    via: 'twitterdev',
                },
                useNativeBehavior: false,
            }
        },
        methods:{
            onClose() {},
            onOpen() {},
            onBlock() {},
            onFocus() {},
        }
    }
</script>

Check out for other share button lists, usage, and demo from these links.

vue social website

github page

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How to resolve the encoding issue while building Java Application

In this tutorial, we are going to understand the different scenarios where we might get encoding issues while building the Java application as a war or jar file and deploy it to the server. 

The main encoding issue here is, for some languages like Hebrew, Chinese, Arabic, etc there might get the chance of appearing as question marks instead of actual specific text. This issue might be due to different cases.

1. Sometimes the serverside rendering language like jsp, gsp pages might cause the issue we can use the following tag in those pages.

<%@ page language="java" contentType="text/html; charset=UTF-8" pageEncoding="UTF-8"%>

2. We might get the issue due to database data where we don't set the configugre the utf-8 encoding. To resolve the issue we can set the jdbc connection url as follows:

jdbc:mysql://hostname/database_naeme?useUnicode=yes&&characterEncoding=UTF-8

3. If our application contains some other language that requires saving operation in the database. Better to create the database using encoding using the following command for the MySQL database.

CREATE DATABASE database_name DEFAULT CHARACTER SET "utf8" COLLATE "utf8_general_ci";

Make sure to change the actual database instead of [database_name].

4. If we are using hibernate then better to configure the settings as

hibernate.connection.charSet=UTF-8
hibernate.connection.characterEncoding=UTF-8
hibbernate.connection.useUnicode=true

5. If we are using build tools like Jenkins for deployment we need to configure the encoding In Jenkins: we can create a global variable and set encoding config as below:

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How to open the Dicom Image in Linux

This is a short tutorial on how we can open and view the Dicom images in Linux operating system.

Here, we will install weasis desktop application to view the Dicom images.

Installation: 

Download the desired weasis installer compatible with your operating system from weasis website. 

For Linux, download the .deb installer. Go to the download folder and open the terminal and execute the .deb file

sudo dpkg -i weasis_3.8.0-1_amd64.deb

Here, weasis_3.8.0-1_amd64.deb is the downloaded file, you can use your own downloaded .deb file.

Now, you are good to go to open the Dicom images. Go to the sample image and select the image and right-click, you can see open with weasis option, select and view the image. Or simply double click on the image which will open the installed weasis application to view the Dicom image.

Key Features: 

• Display all kinds of DICOM files (including multi-frame, enhanced, MPEG-2, MPEG-4, MIME Encapsulation, SR, PR, KOS, AU, RT and ECG)
• Image manipulation (pan, zoom, windowing, presets, rotation, flip, scroll, crosshair, filtering...)
• Viewer for common image formats (TIFF, BMP, GIF, JPEG, PNG, RAS, HDR, and PNM)
• Layouts for comparing series or studies
• Advanced series synchronization options
• Display Presentation States (GSPS) and Key Object Selection
• Create key images (Key Object Selection object) by selection
• Support of Modality LUTs, VOI LUTs, and Presentation LUTs (even non-linear) 
• Support of several screens with different calibration, support of HiDPI (High Dots Per Inch) monitors, full-screen mode
• Multiplanar reconstructions and Maximum Intensity Projection
• Display Structured Reports
• Display and search into all DICOM attributes
• Display cross-lines Measurement and annotation tools
• Region statistics of pixels (Min, Max, Mean, StDev, Skewness, Kurtosis, Entropy)
• Histogram of modality values 
• SUV measurement 
• Save measurements and annotations in DICOM PR or XML file
• Import CD/DVD and local DICOM files 
• Export DICOM with several options (DICOMDIR, ZIP, ISO image file with Weasis, TIFF, JPEG, PNG...)
• Magnifier glass Native and DICOM printing 
• Read DICOM image containing float or double data (Parametric Map)
• DICOM ECG Viewer

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How to change Grails App server port in application.yml

This is a quick tutorial on how to set server port while running grails application. By default, grails will use the embedded tomcat server running on port 8080.

Sometimes if another process is using port 8080 then we might get a port address already in use error.

So, what we will do is to change the default port in the config. In grails 3.x version we can set up the custom port inside application.yml file.

Inside application.yml file lets add the following config setup to override the default port 8080.

server:
    port : "8090"

Now if we run the application, it will run on port 8090. 

If we want to configure the setup within the environment then we can do as below:

environments:
    development:
        server:
            port : "8090"

This will set the server port only for the development environment. Re-run the application.

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How to resolve port already in use or kill the running process

 On Linux:

step1: if the process is running at port 3000 then, firstly we have to kill this process for this open your terminal and type

lsof -w -n -i tcp:3000

which shows all the list of open file which is running at port 3000. Here, lsof stands for ls = list and of = opened file. You can see list with pid number.

step2: type sudo kill -9 6911 where 6911 is pid number. Here 9 has its own meaning which is defined as kill command "SIGKILL" you can see this by typing in the terminal as kill -l . You can use -SIGKILL instead of -9.

On Windows:

- Open and run command prompt as administrator and type the following command:

   

   netstat -ano | findstr :8080

This command will find and list the process that uses this port 8080.

Now, we need to kill the process, for this use following command:

   taskkill /pid 5884 /f

Where 5884 is the PID number. Use the process PID number obtained previously.

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