File Formats
============

breastCompress requires several input files that characterize the uncompressed breast phantom.  Several types of intermediate temporary files are generated during
the compression process in addition to the final compressed breast phantom output files.  In the following filename descriptions *nnnnnnnn* represents the seed
number specified as a command line option to breastCompress.

Input Files
-----------

The breastCompress input files are created using breastPhantom.  breastCompress expects the following files to be present in the input directory specified on the command line:

p\_\ *nnnnnnnn*\ .raw.gz
   The raw phantom volume stored as 8-bit unsigned integers in a gzip archive.  There is no file header.

p\_\ *nnnnnnnn*\ .mhd
   A metaImage header file containing information about the phantom data stored in the file p\_\ *nnnnnnnn*\ .raw.gz

p\_\ *nnnnnnnn*\ .loc
   This file lists candidate locations for insertion of masses and calcifications.  Each location is where a TDLU has been randomly generated.

Intermediate Files
------------------

These are temporary files generated during the compression process.  They are not automatically deleted once the breast compression is complete.  Compression is an iterative
process and depending on the desired compressed thickness and breast shape, several remeshing steps may be required.  Each remeshing step will create new intermediate files.

febio\_\ *nnnnnnnn*\_\ *m*\ .feb
   This is an XML file generated by breastCompress that is passed as input to FeBiO.  A new file will be generated for each remeshing step.  Minimally m=0 will be present.

febio\_\ *nnnnnnnn*\_\ *m*\ .log
   This is a log file generated by FeBiO.  It contains information regarding the convergence of the finite element compression procedure.

febio\_\ *nnnnnnnn*\_\ *m*\ .xplt
   This file contains the results of the FeBiO compression process.  The compression process and produced stress/strain and displacement maps can be visualized
   by opening this file with PostView, which is available for download from the FeBiO website.

p\_\ *nnnnnnnn*\_\ *m*\ .raw.gz
   Intermediate voxelization of the breast phantom during compression at remeshing step *m*

p\_\ *nnnnnnnn*\_\ *m*\ .mhd
   A metaImage header file for the intermediate voxelization contained in the associated .raw.gz file

p\_ *nnnnnnnn*\_\ *m*\ .loc
   Intermediate TDLU locations

Output Files
------------

Final output file have formats indentical to the input files with prefix *pc_* to designate they represent a compressed phantom

pc\_\ *nnnnnnnn*\ .raw.gz
   The raw compressed phantom volume stored as 8-bit unsigned integers in a gzip archive.

pc\_\ *nnnnnnnn*\ .mhd
   A metaImage header file containing information about the phantom data stored in the file pc\_\ *nnnnnnnn*\ .raw.gz

pc\_\ *nnnnnnnn*\ .loc
   Final post-compression TDLU locations.