I manged to solve the problem. don't read the data manualy from the stream by "textSec.stream.read" use "textSec.data()" instead. Internaly (see "sections.py") a seek operation in the file is done. Afterwards the data is read. The result will be the valid data chunk. The following code reads the code(text) section of a atxmega firmware and copies it into a bytearray which has the layout of the flash of an atxmega128a4u device. @vlas_tepesch: the hex conversation is not needed and the the 64k pitfall is avoided.

sys.path[0:0] = ['.', '..']

from elftools.common.py3compat import bytes2str
from elftools.elf.elffile import ELFFile

# 128k flash for the ATXmega128a4u
flashsize = 128 * 1024


def __printSectionInfo (s):
    print ('[{nr}] {name} {type} {addr} {offs} {size}'.format(
                nr = s.header['sh_name'],
                name = s.name,
                type = s.header['sh_type'],
                addr = s.header['sh_addr'],
                offs = s.header['sh_offset'],
                size = s.header['sh_size']
                                                              )
           )

def process_file(filename):
    print('In file: ' + filename)
    with open(filename, 'rb') as f:
        # get the data
        elffile = ELFFile(f)
        print ('sections:')
        for s in elffile.iter_sections():
            __printSectionInfo(s)
        print ('get the code from the .text section')
        textSec = elffile.get_section_by_name(b'.text')
        # prepare the memory
        flashMemory = bytearray(flashsize)
        # the text section
        startAddr = textSec.header['sh_addr']
        val = textSec.data()

        flashMemory[startAddr:startAddr+len(val)] = val

        # print memory

        print('finished')

if __name__ == '__main__':
    process_file('firmware.elf')

Tanks for the comments!

There's a sample in pyelftools that does that: https://github.com/eliben/pyelftools/blob/master/examples/dwarf_decode_address.py

Specifically, finding the line for the address goes like this:

def decode_file_line(dwarfinfo, address):
    # Go over all the line programs in the DWARF information, looking for
    # one that describes the given address.
    for CU in dwarfinfo.iter_CUs():
        # First, look at line programs to find the file/line for the address
        lineprog = dwarfinfo.line_program_for_CU(CU)
        prevstate = None
        for entry in lineprog.get_entries():
            # We're interested in those entries where a new state is assigned
            if entry.state is None:
                continue
            if entry.state.end_sequence:
                # if the line number sequence ends, clear prevstate.
                prevstate = None
                continue
            # Looking for a range of addresses in two consecutive states that
            # contain the required address.
            if prevstate and prevstate.address <= address < entry.state.address:
                filename = lineprog['file_entry'][prevstate.file - 1].name
                line = prevstate.line
                return filename, line
            prevstate = entry.state
    return None, None

According to the author @eli-bendersky, pyelftools is a module for parsing and analyzing ELF/DWARF files and it has no direct way of modifying them. I had a look at the module source files and could not find any methods to edit/save either.

On the introductory post, within comments author acknowledges that pyelftools has no API-level support to do this but some tinkering around can help achieve what you need.

If pyelftools is not a hard dependency, here's an example on how to do the same using elffile:

Copyimport elffile

eo = elffile.open(name="/bin/ls")
eo.fileHeader.shnum = 30
with open('./ls.bin', 'wb') as f: f.write(eo.pack())

Using readelf, you can verify that changes were saved correctly:

Copyreadelf -h ls.bin 
ELF Header:
  Magic:   7f 45 4c 46 01 01 01 00 00 00 00 00 00 00 00 00 
  Class:                             ELF32
  Data:                              2's complement, little endian
  Version:                           1 (current)
  OS/ABI:                            UNIX - System V
  ABI Version:                       0
  Type:                              EXEC (Executable file)
  Machine:                           Intel 80386
  Version:                           0x1
  Entry point address:               0x804be34
  Start of program headers:          105068 (bytes into file)
  Start of section headers:          103948 (bytes into file)
  Flags:                             0x0
  Size of this header:               52 (bytes)
  Size of program headers:           32 (bytes)
  Number of program headers:         9
  Size of section headers:           40 (bytes)
  Number of section headers:         30
  Section header string table index: 27
readelf: Error: Unable to read in 0x708 bytes of section headers

There's not much documentation on elffile but you can have a look at the source and figure out ways to replicate pyelftools-specific functionality. If that doesn't work, you can try using both pyelftools for reading/analyzing tasks and elffile to edit sections and write changes.