#pragma rtGlobals=3 // Use modern global access method and strict wave access.

Function OS_hdf5Export()

// WARNING- currently not exporting the StimArtifactwave -needs to update at somepoint

Variable fileID

WAVE/z OS_Parameters,ROIs,Traces0_raw,Traces0_znorm,Averages0,Tracetimes0,Triggertimes,Triggertimes_Frame,Triggervalues,wDataCh0, wDataCh0_detrended, wDataCh1,wDataCh2

WAVE/z stack_ave, stack_ave_report, GeoC, Snippets0,SnippetsTimes0,wParamsNum//,wParamsStr

NewPath targetPath

variable nROIs = abs(Wavemin(ROIs)), i

//variable experiment_date = wParamsStr[4]

string exp_date

wave /T wParamsStr

exp_date = wParamsStr[4]

//print($exp_date)

string pathName = "targetPath"

HDF5CreateFile/P=$pathName /O fileID as exp_date + "_" + GetDataFolder(0) + ".h5"

WAVE wDataCh0, wDataCh1

HDF5SaveData /O /Z wDataCh0, fileID

HDF5SaveData /O /Z wDataCh0_detrended, fileID

//HDF5SaveData /O /Z wDataCh2, fileID

HDF5SaveData /O /Z /IGOR=8 wParamsNum, fileID

HDF5SaveData /O /Z /IGOR=8 wParamsStr, fileID

if (waveexists(stack_ave))

HDF5SaveData /O /Z stack_ave, fileID // Mean image across the stack in the data channel 0

endif

if (waveexists($"Triggervalues")==1)

print "Triggervalues detected, exporting preprocessed data."

HDF5SaveData /O /Z /IGOR=8 OS_parameters, fileID

HDF5SaveData /O /Z ROIs, fileID

HDF5SaveData /O /Z Traces0_raw, fileID

HDF5SaveData /O /Z Traces0_raw, fileID

HDF5SaveData /O /Z Averages0, fileID

HDF5SaveData /O /Z Triggertimes, fileID

HDF5SaveData /O /Z Triggertimes_Frame, fileID

HDF5SaveData /O /Z Triggervalues, fileID

if (waveexists(GeoC))

HDF5SaveData /O /Z GeoC, fileID // Cell positions in the field

endif

if (waveexists($"SnippetsTimes"+num2str(OS_Parameters[%Data_channel])))

HDF5SaveData /O /Z Snippets0, fileID

HDF5SaveData /O /Z SnippetsTimes0, fileID

endif

endif

// Check if 'STRF' waves exist

string check_strf = wavelist("STRF*", ";", "")

if (strlen(check_strf) > 1)

// Get list of STRFs present

string raw_strfs = wavelist("STRF0*", ";", "")

//save them to HDF5 file....

for (i=0; i< itemsinlist(raw_strfs) ; i+=1) // Using WaveList to get all STRF waves

string curr_STRF = stringfromlist(i, raw_strfs)

HDF5SaveData /O $curr_STRF, fileID

endfor

// Also grab the other related files

WAVE /z STRF_Corr0, nislands_per_ROI, islandsX, islandsY, islandTimeKernels, islandTimeKernels_Polarities, islandTimeKernels_Pol_rel, islandAmpls, islandAmpls, island_sum

HDF5SaveData /O /Z STRF_Corr0, fileID

HDF5SaveData /O /Z nislands_per_ROI, fileID

HDF5SaveData /O /Z islandsX, fileID

HDF5SaveData /O /Z islandsY, fileID

HDF5SaveData /O /Z islandTimeKernels, fileID

HDF5SaveData /O /Z islandTimeKernels_Polarities, fileID

HDF5SaveData /O /Z islandTimeKernels_Pol_rel, fileID

HDF5SaveData /O /Z islandAmpls, fileID

HDF5SaveData /O /Z island_sum, fileID

WAVE STRF_Corr_Montage_RGB, STRF_Corr_Montage_RGB2

HDF5SaveData /O /Z STRF_Corr_Montage_RGB, fileID

HDF5SaveData /O /Z STRF_Corr_Montage_RGB2, fileID

endif

if (waveexists($"Positions")==1)

WAVE Positions

HDF5SaveData /O /Z Positions, fileID

endif

HDF5CloseFile fileID