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Trying to use BufferedInputStream and Base64 to Encode a large file in Java

I am new to the Java I/O so please help.
I am trying to process a large file(e.g. a pdf file of 50mb) using the apache commons library.
At first I try:
byte[] bytes = FileUtils.readFileToByteArray(file);
String encodeBase64String = Base64.encodeBase64String(bytes);
byte[] decoded = Base64.decodeBase64(encodeBase64String);
But knowing that the
FileUtils.readFileToByteArray in org.apache.commons.io will load the whole file into memory, I try to use BufferedInputStream to read the file piece by piece:
BufferedInputStream bis = new BufferedInputStream(inputStream);
StringBuilder pdfStringBuilder = new StringBuilder();
int byteArraySize = 10;
byte[] tempByteArray = new byte[byteArraySize];
while (bis.available() > 0) {
if (bis.available() < byteArraySize) { // reaching the end of file
tempByteArray = new byte[bis.available()];
}
int len = Math.min(bis.available(), byteArraySize);
read = bis.read(tempByteArray, 0, len);
if (read != -1) {
pdfStringBuilder.append(Base64.encodeBase64String(tempByteArray));
} else {
System.err.println("End of file reached.");
}
}
byte[] bytes = Base64.decodeBase64(pdfStringBuilder.toString());
However, the 2 decoded bytes array don't look quite the same... ... In fact, the only give 10 bytes, which is my temp array size... ...
Can anyone please help:
what am I doing it wrong to read the file piece by piece?
why is the decoded byte array only returns 10 bytes in the 2nd solution?
Thanks in advance:)

After some digging, it turns out that the byte array's size has to be multiple of 3 in order to avoid padding. After using a temp array size with multiple of 3, the program is able to go through.
I simply change
int byteArraySize = 10;
to be
int byteArraySize = 1024 * 3;

Java Reading large files into byte array chunk by chunk

So I've been trying to make a small program that inputs a file into a byte array, then it will turn that byte array into hex, then binary. It will then play with the binary values (I haven't thought of what to do when I get to this stage) and then save it as a custom file.
I studied a lot of internet code and I can turn a file into a byte array and into hex, but the problem is I can't turn huge files into byte arrays (out of memory).
This is the code that is not a complete failure
public void rundis(Path pp) {
byte bb[] = null;
try {
bb = Files.readAllBytes(pp); //Files.toByteArray(pathhold);
System.out.println("byte array made");
} catch (Exception e) {
e.printStackTrace();
}
if (bb.length != 0 || bb != null) {
System.out.println("byte array filled");
//send to method to turn into hex
} else {
System.out.println("byte array NOT filled");
}
}
I know how the process should go, but I don't know how to code that properly.
The process if you are interested:
Input file using File
Read the chunk by chunk of the file into a byte array. Ex. each byte array record hold 600 bytes
Send that chunk to be turned into a Hex value --> Integer.tohexstring
Send that hex value chunk to be made into a binary value --> Integer.toBinarystring
Mess around with the Binary value
Save to custom file line by line
Problem:: I don't know how to turn a huge file into a byte array chunk by chunk to be processed.
Any and all help will be appreciated, thank you for reading :)

To chunk your input use a FileInputStream:
Path pp = FileSystems.getDefault().getPath("logs", "access.log");
final int BUFFER_SIZE = 1024*1024; //this is actually bytes
FileInputStream fis = new FileInputStream(pp.toFile());
byte[] buffer = new byte[BUFFER_SIZE];
int read = 0;
while( ( read = fis.read( buffer ) ) > 0 ){
// call your other methodes here...
}
fis.close();

To stream a file, you need to step away from Files.readAllBytes(). It's a nice utility for small files, but as you noticed not so much for large files.
In pseudocode it would look something like this:
while there are more bytes available
read some bytes
process those bytes
(write the result back to a file, if needed)
In Java, you can use a FileInputStream to read a file byte by byte or chunk by chunk. Lets say we want to write back our processed bytes. First we open the files:
FileInputStream is = new FileInputStream(new File("input.txt"));
FileOutputStream os = new FileOutputStream(new File("output.txt"));
We need the FileOutputStream to write back our results - we don't want to just drop our precious processed data, right? Next we need a buffer which holds a chunk of bytes:
byte[] buf = new byte[4096];
How many bytes is up to you, I kinda like chunks of 4096 bytes. Then we need to actually read some bytes
int read = is.read(buf);
this will read up to buf.length bytes and store them in buf. It will return the total bytes read. Then we process the bytes:
//Assuming the processing function looks like this:
//byte[] process(byte[] data, int bytes);
byte[] ret = process(buf, read);
process() in above example is your processing method. It takes in a byte-array, the number of bytes it should process and returns the result as byte-array.
Last, we write the result back to a file:
os.write(ret);
We have to execute this in a loop until there are no bytes left in the file, so lets write a loop for it:
int read = 0;
while((read = is.read(buf)) > 0) {
byte[] ret = process(buf, read);
os.write(ret);
}
and finally close the streams
is.close();
os.close();
And thats it. We processed the file in 4096-byte chunks and wrote the result back to a file. It's up to you what to do with the result, you could also send it over TCP or even drop it if it's not needed, or even read from TCP instead of a file, the basic logic is the same.
This still needs some proper error-handling to work around missing files or wrong permissions but that's up to you to implement that.
A example implementation for the process method:
//returns the hex-representation of the bytes
public static byte[] process(byte[] bytes, int length) {
final char[] hexchars = "0123456789ABCDEF".toCharArray();
char[] ret = new char[length * 2];
for ( int i = 0; i < length; ++i) {
int b = bytes[i] & 0xFF;
ret[i * 2] = hexchars[b >>> 4];
ret[i * 2 + 1] = hexchars[b & 0x0F];
}
return ret;
}

Is it possible to read images without ImageIO?

I am trying to read an image and deliver it through a Java socket. But there are some bits that does not fit. When viewing in a diff tool I realized that all numbers bigger than 127 were truncated.
So I wanted to just convert it to a char[] array and return it instead. Now I'm getting a complette different image, perhaps due to char's size.
try (PrintWriter out = new PrintWriter(this.socket.getOutputStream(), true);
BufferedInputStream in = new BufferedInputStream(new FileInputStream(filename), BUFSIZ)) {
byte[] buffer = new byte[BUFSIZ];
while (in.read(buffer) != -1) {
response.append(new String(buffer));
out.print(response.toString());
response.setLength(0);
}
} catch (IOException e) {
System.err.println(e.getMessage());
}
This is my reading and delivering code.
I've read many times to use ImageIO but I want to do it without, since I don't know whether it's an image or not. (And what about other file types like executables?)
So, is there any way to convert it to something like an unsigned byte that'll be delivered correctly on the client? Do I have to use something different than read() to achieve that?

Writers are for character data. Use the OutputStream. And you're making the usual mistake of assuming that read() filled the buffer.
The following loop will copy anything correctly. Memorize it.
int count;
byte[] buffer = new byte[8192];
while ((count = in.read(buffer)) > 0)
{
out.write(buffer, 0, count);
}

Repeat after me: a char is not a byte and it's not a code point.
Repeat after me: a Writer is not an OutputStream.
try (OutputStream out = this.socket.getOutputStream();
BufferedInputStream in = new BufferedInputStream(new FileInputStream(filename), BUFSIZ)) {
byte[] buffer = new byte[BUFSIZ];
int len;
while ((len = in.read(buffer))) != -1) {
out.write(buffer, 0, len);
}
} catch (IOException e) {
System.err.println(e.getMessage());
}
(this is from memory, check the args for write()).

difference between input.read and input.read(array, offset, length)

I'm trying to understand how inputstreams work. The following block of code is one of the many ways to read data from a text file:-
File file = new File("./src/test.txt");
InputStream input = new BufferedInputStream (new FileInputStream(file));
int data = 0;
while (data != -1) (-1 means we reached the end of the file)
{
data = input.read(); //if a character was read, it'll be turned to a bite and we get the integer representation of it so a is 97 b is 98
System.out.println(data + (char)data); //this will print the numbers followed by space then the character
}
input.close();
Now to use input.read(byte, offset, length) i have this code. I got it from here
File file = new File("./src/test.txt");
InputStream input = new BufferedInputStream (new FileInputStream(file));
int totalBytesRead = 0, bytesRemaining, bytesRead;
byte[] result = new byte[ ( int ) file.length()];
while ( totalBytesRead < result.length )
{
bytesRemaining = result.length - totalBytesRead;
bytesRead = input.read ( result, totalBytesRead, bytesRemaining );
if ( bytesRead > 0 )
totalBytesRead = totalBytesRead + bytesRead;
//printing integer version of bytes read
for (int i = 0; i < bytesRead; i++)
System.out.print(result[i] + " ");
System.out.println();
//printing character version of bytes read
for (int i = 0; i < bytesRead; i++)
System.out.print((char)result[i]);
}
input.close();
I'm assuming that based on the name BYTESREAD, this read method is returning the number of bytes read. In the documentation, it says that the function will try to read as many as possible. So there might be a reason why it wouldn't.
My first question is: What are these reasons?
I could replace that entire while loop with one line of code: input.read(result, 0, result.length)
I'm sure the creator of the article thought about this. It's not about the output because I get the same output in both cases. So there has to be a reason. At least one. What is it?

The documentation of read(byte[],int,int says that it:
Reads up to len bytes of data.
An attempt is made to read as many as len bytes
A smaller number may be read.
Since we are working with files that are right there in our hard disk, it seems reasonable to expect that the attempt will read the whole file, but input.read(result, 0, result.length) is not guaranteed to read the whole file (it's not said anywhere in the documentation). Relying in undocumented behaviors is a source for bugs when the undocumented behavior change.
For instance, the file stream may be implemented differently in other JVMs, some OS may impose a limit on the number of bytes that you may read at once, the file may be located in the network, or you may later use that piece of code with another implementation of stream, which doesn't behave in that way.
Alternatively, if you are reading the whole file in an array, perhaps you could use DataInputStream.readFully
About the loop with read(), it reads a single byte each time. That reduces performance if you are reading a big chunk of data, since each call to read() will perform several tests (has the stream ended? etc) and may ask the OS for one byte. Since you already know that you want file.length() bytes, there is no reason for not using the other more efficient forms.

Imagine you are reading from a network socket, not from a file. In this case you don't have any information about the total amount of bytes in the stream. You would allocate a buffer of fixed size and read from the stream in a loop. During one iteration of the loop you can't expect there are BUFFERSIZE bytes available in the stream. So you would fill the buffer as much as possible and iterate again, until the buffer is full. This can be useful, if you have data blocks of fixed size, for example serialized object.
ArrayList<MyObject> list = new ArrayList<MyObject>();
try {
InputStream input = socket.getInputStream();
byte[] buffer = new byte[1024];
int bytesRead;
int off = 0;
int len = 1024;
while(true) {
bytesRead = input.read(buffer, off, len);
if(bytesRead == len) {
list.add(createMyObject(buffer));
// reset variables
off = 0;
len = 1024;
continue;
}
if(bytesRead == -1) break;
// buffer is not full, adjust size
off += bytesRead;
len -= bytesRead;
}
} catch(IOException io) {
// stream was closed
}
ps. Code is not tested and should only point out, how this function can be useful.

You specify the amount of bytes to read because you might not want to read the entire file at once or maybe you couldn't or might not want to create a buffer as large as the file.

Reading a binary input stream into a single byte array in Java

The documentation says that one should not use available() method to determine the size of an InputStream. How can I read the whole content of an InputStream into a byte array?
InputStream in; //assuming already present
byte[] data = new byte[in.available()];
in.read(data);//now data is filled with the whole content of the InputStream
I could read multiple times into a buffer of a fixed size, but then, I will have to combine the data I read into a single byte array, which is a problem for me.

The simplest approach IMO is to use Guava and its ByteStreams class:
byte[] bytes = ByteStreams.toByteArray(in);
Or for a file:
byte[] bytes = Files.toByteArray(file);
Alternatively (if you didn't want to use Guava), you could create a ByteArrayOutputStream, and repeatedly read into a byte array and write into the ByteArrayOutputStream (letting that handle resizing), then call ByteArrayOutputStream.toByteArray().
Note that this approach works whether you can tell the length of your input or not - assuming you have enough memory, of course.

Please keep in mind that the answers here assume that the length of the file is less than or equal to Integer.MAX_VALUE(2147483647).
If you are reading in from a file, you can do something like this:
File file = new File("myFile");
byte[] fileData = new byte[(int) file.length()];
DataInputStream dis = new DataInputStream(new FileInputStream(file));
dis.readFully(fileData);
dis.close();
UPDATE (May 31, 2014):
Java 7 adds some new features in the java.nio.file package that can be used to make this example a few lines shorter. See the readAllBytes() method in the java.nio.file.Files class. Here is a short example:
import java.nio.file.FileSystems;
import java.nio.file.Files;
import java.nio.file.Path;
// ...
Path p = FileSystems.getDefault().getPath("", "myFile");
byte [] fileData = Files.readAllBytes(p);
Android has support for this starting in Api level 26 (8.0.0, Oreo).

You can use Apache commons-io for this task:
Refer to this method:
public static byte[] readFileToByteArray(File file) throws IOException
Update:
Java 7 way:
byte[] bytes = Files.readAllBytes(Paths.get(filename));
and if it is a text file and you want to convert it to String (change encoding as needed):
StandardCharsets.UTF_8.decode(ByteBuffer.wrap(bytes)).toString()

You can read it by chunks (byte buffer[] = new byte[2048]) and write the chunks to a ByteArrayOutputStream. From the ByteArrayOutputStream you can retrieve the contents as a byte[], without needing to determine its size beforehand.

I believe buffer length needs to be specified, as memory is finite and you may run out of it
Example:
InputStream in = new FileInputStream(strFileName);
long length = fileFileName.length();
if (length > Integer.MAX_VALUE) {
throw new IOException("File is too large!");
}
byte[] bytes = new byte[(int) length];
int offset = 0;
int numRead = 0;
while (offset < bytes.length && (numRead = in.read(bytes, offset, bytes.length - offset)) >= 0) {
offset += numRead;
}
if (offset < bytes.length) {
throw new IOException("Could not completely read file " + fileFileName.getName());
}
in.close();

Max value for array index is Integer.MAX_INT - it's around 2Gb (2^31 / 2 147 483 647).
Your input stream can be bigger than 2Gb, so you have to process data in chunks, sorry.
InputStream is;
final byte[] buffer = new byte[512 * 1024 * 1024]; // 512Mb
while(true) {
final int read = is.read(buffer);
if ( read < 0 ) {
break;
}
// do processing
}