A FAT32 fragmenter, because I am a horrible person.

frag32.py

#!/usr/bin/env python
  
import random
import struct
import sys

# Most of the Fat32 class was cribbed from https://gist.github.com/jonte/4577833
  
def ppNum(num):
  return "%s (%s)" % (hex(num), num)
  
class Fat32:
    def __init__(self, filename):
        self.fs = open(filename, 'r+b')
  
    def getRawBytes(self, pos, numBytes):
        self.fs.seek(pos)
        return self.fs.read(numBytes)
  
    def putRawBytes(self, pos, data):
        self.fs.seek(pos)
        self.fs.write(data)
  
    def putUInt32(self, pos, n):
        print 'write %10s@%08x' % (n, pos) 
        self.fs.seek(pos)
        self.putRawBytes(pos, struct.pack('<i', n))
  
    def putUInt16(self, pos, n):
        self.fs.seek(pos)
        self.putRawBytes(pos, struct.pack('<H', n))
  
    def putUInt8(self, pos, n):
        self.fs.seek(pos)
        self.putRawBytes(pos, struct.pack('<B', n))
  
    def getBytes(self, pos, numBytes):
        byte = self.getRawBytes(pos, numBytes)
        if (numBytes == 2):
            formatString = "H"
        elif (numBytes == 1):
            formatString = "B"
        elif (numBytes == 4):
            formatString = "i"
        else:
            raise Exception("Not implemented")
        return struct.unpack("<"+formatString, byte)[0]
  
    def getString(self, pos, numBytes):
        raw = self.getRawBytes(pos, numBytes)
        return struct.unpack(str(numBytes)+"s", raw)[0]
  
    @property
    def bytesPerSector(self):
        return self.getBytes(11,2)
  
    @property
    def sectorsPerCluster(self):
        return self.getBytes(13,1)
  
    @property
    def bytesPerCluster(self):
        return self.bytesPerSector * self.sectorsPerCluster
  
    @property
    def reservedSectorCount(self):
        return self.getBytes(14,2)
  
    @property
    def numberOfFATs(self):
        return self.getBytes(16,1)
  
    def FATStart(self, numFat):
        return self.reservedSectorCount * self.bytesPerSector + (self.FATSize * self.bytesPerSector * (numFat - 1))
  
    def FATEnd(self, numFat):
        return self.FATStart(numFat+1)
  
    @property
    def FATSize(self):
        return self.getBytes(36,4)
  
    @property
    def rootStart(self):
        return self.FATStart(1) + (self.FATSize * self.numberOfFATs * self.bytesPerSector)
  
    @property
    def fsIdentityString(self):
        return self.getString(82,8)
  
class ClEntry:
    def __init__(self, offset, length, nextclidx, prevclidx=None):
        self.offset = offset
        self.length = length
        self.next = nextclidx
        self.prev = prevclidx
  
    def __repr__(self):
        return 'ClEnt(%s, %s, %s, %s)' % (self.offset, self.length, self.next, self.prev)
  
class Clusters:
    def __init__(self, fs):
        self.fs = fs
        self.fat = []
        self.free = set()
        self.fs.fs.seek(0, 2)
        eof = self.fs.fs.tell()
        for pos in range(self.fs.FATStart(1), self.fs.FATEnd(1), 4):
            clidx = (pos - self.fs.FATStart(1)) / 4
            # not entirely sure why -2 is required here
            offset = self.fs.rootStart + (clidx-2) * self.fs.bytesPerCluster
            if offset + self.fs.bytesPerCluster >= eof:
                break
            nextcluster = self.fs.getBytes(pos, 4)
            self.fat.append(ClEntry(offset, self.fs.bytesPerCluster, nextcluster))
            if nextcluster == 0:
                self.free.add(clidx)
  
        for clidx in xrange(0, len(self.fat)):
            cluster = self.fat[clidx]
            if cluster.next > 2 and cluster.next < 0xffffff8:
                self.fat[cluster.next].prev = clidx
  
    def setNextCluster(self, target, value):
        if value is None:
            value = 0
        if target is not None:
            writeOffset = self.fs.FATStart(1) + target * 4
            self.fs.putUInt32(writeOffset, value)
            self.fat[target].next = value
            if value == 0:
                # clear the previous cluster reference
                self.fat[target].prev = None
                # add cluster to the free list
                self.free.add(target)
            else:
                if value < 0xffffff8:
                    # set the previous cluster reference 
                    self.fat[value].prev = target
                # remove cluster from the free list
                self.free.discard(target)
  
    def swap(self, clidx1, clidx2):
        c1 = self.fat[clidx1]
        c2 = self.fat[clidx2]
  
        n1 = c1.next
        n2 = c2.next
  
        p1 = c1.prev
        p2 = c2.prev
  
        o1 = c1.offset
        o2 = c2.offset
  
        d1 = self.fs.getRawBytes(o1, c1.length)
        d2 = self.fs.getRawBytes(o2, c2.length)
  
        self.setNextCluster(p1, clidx2)
        self.setNextCluster(clidx2, n1)
        self.setNextCluster(p2, clidx1)
        self.setNextCluster(clidx1, n2)
  
        print o1
        print o2
        self.fs.putRawBytes(o1, d2)
        self.fs.putRawBytes(o2, d1)
  
fs = Fat32(sys.argv[1])
print "Bytes per sector:",        ppNum(fs.bytesPerSector)
print "Sectors per cluster:",     ppNum(fs.sectorsPerCluster)
print "Reserved sector count:",   ppNum(fs.reservedSectorCount)
print "Size of FAT (sectors):",   ppNum(fs.FATSize)
print "Number of FATs:",          ppNum(fs.numberOfFATs)
print "Start of FAT1:",           ppNum(fs.FATStart(1))
print "Start of root directory:", ppNum(fs.rootStart)
print "Identity string:",         fs.fsIdentityString
clusters = Clusters(fs)
if 0:
    clusters.swap(4, 6)
    clusters.fs.fs.flush()
    sys.exit(0)
for arg in sys.argv[2:]:
    clidx = clusters.fat[int(arg)].next
    while clidx > 2 and clidx < 0xffffff8:
        free = random.sample(clusters.free, 1)[0]
        nextidx = clusters.fat[clidx].next
        print 'swap %10s <=> %10s next %10s' % (clidx, free, nextidx)
        clusters.swap(clidx, free)
        clidx = nextidx
#print clusters.fat
#clusters.swap(5, 9)
#clusters.swap(6, 10)
clusters.fs.fs.flush()

Regarding the fragmentation method: what theme was it written with in mind? Maximal fragmentation? Parity with natural fragmentation? Performance?

I could see this used in security research to emulate data that hides itself in dark drive space. Developing a model for what natural fragmentation looks like would help malware evade heuristics.

Themes, that is an interesting idea .. making one that could display ascii art into the older windows or dos defragmenter would be an interesting theme ...

That is a thing of beauty!

@FesterCluck Maximal fragmentation of a single file (It currently can't move the first cluster, though).

No jQuery :c.