./ # the working directory for Piscal processing
./piscal.cfg # Piscal configuration - first line has Photosynthetic Pathway type
             # followed by a list of all files in ./input
             # C3_photosynthesis_leafweb, C4_photosynthesis_leafweb
             # CAM_photosynthesis_leafweb
./piscal.err # Contains any stderr output from launching Piscal, should be empty
             # unless there is a problem with the system or executable
./piscal.pid # file containing one line - the process ID which Piscal
             # is running under. this is used to check if Piscal is currently
             # executing or if it has completed

./input/     # directory containing all unprocessed LeafInput files
./input/Wild_Capsicum1.csv # example input copied from LeafWeb
./input/Wild_Capsicum2.csv # ""

./output/    # directory piscal creates to store all output

./output/clninput/ # directory containing cleaned leaf input, for the purpose
                   # of making that data available for search in LeafWeb
./output/clninput/20160311152630Wild_Capsicum1.csv # example cleaned input
./output/clninput/20160311152630Wild_Capsicum2.csv # ""

./output/fitresult/ # directory containing fitresult generated by Piscal
./output/fitresult/touser/    # output results sent to user and to storage
./output/fitresult/touser/cntrlbestparameters.csv # example output
./output/fitresult/touser/errormessage   # file containing any error 
                                         # messages processed by Piscal
./output/fitresult/touser/warningmessage # file containing any warning
                                         # messages processed by Piscal

./output/fitresult/nottouser/ # Output results sent to storage only