Develop Reference

How do I get a NetcdfFile out of a byte array?

I am relatively new to using the netcdf-java library, and I've immediately run into a problem when trying to load a file. The problem is that there doesn't seem to be a way to load a NetcdfFile from a byte array stored in memory, and that is the base form of my data. To elaborate a little, it is actually a .cdf file uploaded through a client, which the client then converts into a byte array for the server code to read. So the server, where my code is running, cannot see the uploaded file at all. I also cannot assume the server itself is writable, so essentially there is no "location" to pass into the typical NetcdfFile loading methods.
The FAQ on ucar.edu does mention the possibility of reading from a non-file source, here. It says I should write my own IOSP, which I am happy to do. However, there is very little guidance on how to do this.
I don't know how to implement isValidFile when the only thing passed into the function is a RandomAccessFile, which the FAQ says can be ignored.
I don't know how my IOSP will obtain the byte array in question for use in readData.
I don't know why the minimal example in the FAQ advises me to make a new NetcdfFile class, when it seems I could just use the default one but pass in my custom IOSP.
This question is a little vague, but I am truly lost without many clues on where to even begin. Any guidance would be appreciated.
EDIT: I'm using 5.4.2 of the netcdf-java library.

I found this answer in the support archives. The solution is to use InMemoryRandomAccessFile. The constructor takes a String location and a byte array containing the file's contents. From my testing, I think the location can be any arbitrary string. Here is the code that worked for me.
byte[] filebytes = retrieveFileBytes(clientFilepath);
InMemoryRandomAccessFile raf = new InMemoryRandomAccessFile(clientFilepath, filebytes);
NetcdfFile file = NetcdfFiles.open(raf, clientFilepath, null, null);
Variable peakRetentionTime = file.findVariable("peak_retention_time");
if (peakRetentionTime == null) {
displayWarning("peak_retention_time null!");
} else {
Array data = peakRetentionTime.read();
displayInfo(Ncdump.printArray(data));
}

Byte array to File object without saving to disk

I have a method that takes in a byte[] that came from Files.readAllBytes() in a different part of the code for either .txt or .docx files. I want to create a new File object from the bytes to later read contents from, without saving that file to disk. Is this possible? Or is there a better way to get the contents from the File bytes?

That's not how it works. a java.io.File object is a light wrapper: Check out the source code - it's got a String field that contains the path and that is all it has aside from some bookkeeping stuff.
It is not possible to represent arbitrary data with a java.io.File object. j.i.File objects represent literal files on disk and are not capable of representing anything else.
Files.readAllBytes gets you the contents from the bytes, that's.. why the method has that name.
The usual solution is that a method in some library that takes a File is overloaded; there will also be a method that takes a byte[], or, if that isn't around, a method that takes an InputStream (you can make an IS from a byte[] easily: new ByteArrayInputStream(byteArr) will do the job).
If the API you are using doesn't contain any such methods, it's a bad API and you should either find something else, or grit your teeth and accept that you're using a bad API, with all the workarounds that this implies, including having to save bytes to disk just to satisfy the asinine API.
But look first; I bet there is a byte[] and/or InputStream variant (or possibly URL or ByteBuffer or ByteStream or a few other more exotic variants).

Writing BitSet to output file without overhead?

I get a line of overhead ("java.util.BitSet") when writing a BitSet to an output file using ObjectOutputStream.writeObject().
Anyway around it?

That is not an "overhead", that't the marker that lets Java figure out what type it needs to create when deserializing the object from that file.
Since ObjectInputStream has no idea what you have serialized into a file, and has no way for you to provide a "hint", ObjectOutputStream must "embed" something for the input stream to be able to decide what class needs to be instantiated. That is why it places the "java.util.BitSet" string in front of the data of your BitSet.
You cannot get around writing this marker when you use serialization capabilities built into BitSet class. If you are serializing the object into a file by itself, with no other objects going in with it, you could write the result of toByteArray() call into a file, and call BitSet.valueOf(byteArray) after reading byteArray from the file.

Java writing to File or System.out

I need to write characters to a file or to standard output. And I am curious if it could be done with one method.
Now I have something like this:
OutputStream out;
if(toConsole)
out = System.out;
else
out = new FileOutputStream(file);
write(out);
}
void write (OutputStream str){
....
str.write(string);
But it is a problem that I am using (in case when "str" is System.out) write instead print?
(print java doc: "string's characters are converted into bytes according to the platform's default character encoding")
In case if I would use PrintWriter(or PrintStream) as a parameter then i cannot use BufferedWriter and writing to the file would be slower.
It is possible to use a same code (and same methods) for writing to a file and to System.out?
(This is for my school project so I want it to be a "pure" and fully correct)

What you're trying to accomplish, is to treat the fileoutput and the consoleoutput the same. This is possible, because System.out is a PrintStream, and you can create a PrintStream for a file like this
new PrintStream(yourFile)
or insert a BufferedOutputStream in between
new PrintStream(new BufferedOutputStream(new FileOutputStream(yourFile))).
Note that this is not needed, because PrintStream does buffer its output itself.
I would create a variable (global or not), representing the current output.
This might be a PrintStream, either System.out, or a PrintStream around a FileOutputStream, whatever you desire. You would then pass this stream to the write method or call the print methods on it directly.
The advantage is that you can easily switch this without much code modification, you can redirect it wherever you wan't. It's no problem to redirect it to a file and System.out! You wouldn't get that pure flexibility with the way you're writing the method currently.
You could (not saying you should), also redirect System.out directly, using System.setOut. This however is bad style, because it is quite uncommon and might confuse everyone else, if they have not seen the call to System.setOut.

System.out is an object of type PrintStream. So yes, you can write to
System.out and/or to another file using exactly the same methods. Just
construct a PrintStream object and direct it to your file. So declare
your out variable as PrintStream to start with.
See also:
http://docs.oracle.com/javase/7/docs/api/java/lang/System.html
http://docs.oracle.com/javase/7/docs/api/java/io/PrintStream.html

Reading and writing objects via GZIP streams?

I am new to Java. I want to learn to use GZIPstreams. I already have tried this:
ArrayList<SubImage>myObject = new ArrayList<SubImage>(); // SubImage is a Serializable class
ObjectOutputStream compressedOutput = new ObjectOutputStream(
new BufferedOutputStream(new GZIPOutputStream(new FileOutputStream(
new File("....")))));
compressedOutput.writeObject(myObject);
and
ObjectInputStream compressedInput = new ObjectInputStream(
new BufferedInputStream(new GZIPInputStream(new FileInputStream(
new File("....")))));
myObject=(ArrayList<SubImage>)compressedInput.readObject();
When the program writes myObject to a file without throwing any exception, but when it reaches the line
myObject=(ArrayList<SubImage>)compressedInput.readObject();
it throws this exception:
Exception in thread "main" java.io.EOFException: Unexpected end of ZLIB input stream
How can I solve this problem?

You have to flush and close your outputstream. Otherwhise, at least, the BufferedOutputStream will not write everything to the file (it does in big chucks to avoid penalizing performance).
If you call compressedOutput.flush() and compressedOutput.close() it will suffice.
You can try writing a simple string object and checking if the file is well written.
How? If you write a xxx.txt.gz file you can open it with your preferred zip app and look at the xxx.txt. If the app complains, then the content is not full written.
Extended answer to a comment: compressing even more the data
Changing serialization
You could change the standard serialization of SubImage object if it's an object of your own. Check java.io.Serializable javadoc to know how to do it. It's pretty straightforward.
Writing just what you need
Serialization has the drawback that needs to write "it's a SubImage" just before every instance you write. It's not necessary if you know what's going to be there beforehand. So you could try to serialize it more manually.
To write your list, instead of writing an object write directly the values that conform your list. You will need just a DataOutputStream (but ObjectOutputStream is a DOS so you can use it anyway).
dos.writeInt(yourList.size()); // tell how many items
for (SubImage si: yourList) {
// write every field, in order (this should be a method called writeSubImage :)
dos.writeInt(...);
dos.writeInt(...);
...
}
// to read the thing just:
int size = dis.readInt();
for (int i=0; i<size; i++) {
// read every field, in the same order (this should be a method called readSubImage :)
dis.readInt(...);
dis.readInt(...);
...
// create the subimage
// add it to the list you are recreating
}
This method is more manual but if:
you know what's going to be written
you will not need this kind of serialization for many types
it's pretty affordable and definitively more compressed than the Serializable counterpart.
Have in mind that there are alternative frameworks to serialize objects or create string messages (XStream for xml, Google Protocol Buffers for binary messages, and so on). That frameworks could work directly to binary or writing a string that could be then written.
If your app will need more on this, or just curious, maybe you should look at them.
Alternative serialization frameworks
Just looked in SO and found several questions (and answers) addressing this issue:
https://stackoverflow.com/search?q=alternative+serialization+frameworks+java
I've found that XStream is pretty easy and straightforward to use. And JSON is a format pretty readable and succint (and Javascript compatible which could be a plus :).
I should go for:
Object -> JSON -> OutputStreamWriter(UTF-8) -> GZippedOutputStream -> FileOutputStream