| 1 | #pragma rtGlobals=3 // Use modern global access method and strict wave access. |
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| 2 | |
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| 3 | |
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| 4 | |
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| 5 | // |
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| 6 | // Start to build up and test the r/w accessors for VSANS |
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| 7 | // (SANS has a template, VSANS does not, so just start from scratch here, since the |
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| 8 | // file structure will be different) |
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| 9 | // |
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| 10 | // |
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| 11 | |
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| 12 | |
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| 13 | // thought this would be useful, but the file name (folder) is stuck in the middle... |
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| 14 | Strconstant ksPathPrefix = "root:(folder):entry:entry1:" |
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| 15 | |
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| 16 | |
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| 17 | |
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| 18 | // passing null file string presents a dialog |
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| 19 | Macro Read_HDF5_Raw_No_Attributes() |
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| 20 | V_LoadHDF5Data("") |
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| 21 | End |
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| 22 | |
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| 23 | Proc V_LoadHDF5Data(file) |
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| 24 | String file |
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| 25 | |
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| 26 | SetDataFolder root: |
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| 27 | Variable err= V_LoadHDF5_NoAtt(file) // reads into current folder |
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| 28 | SetDataFolder root: |
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| 29 | End |
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| 30 | |
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| 31 | |
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| 32 | // This loads for speed, since loading the attributes takes a LOT of time. |
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| 33 | // |
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| 34 | // this will load in the whole HDF file all at once. |
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| 35 | // Attributes are NOT loaded at all. |
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| 36 | // |
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| 37 | // TODO: remove the P=home restriction top make this more generic |
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| 38 | // -- get rid of bits leftover here that I don't need |
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| 39 | // -- be sure I'm using all of the correct flags in the HDF5LoadGroup operation |
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| 40 | // |
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| 41 | Function V_LoadHDF5_NoAtt(fileName, [hdf5Path]) |
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| 42 | String fileName, hdf5Path |
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| 43 | if ( ParamIsDefault(hdf5Path) ) |
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| 44 | hdf5Path = "/" |
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| 45 | endif |
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| 46 | |
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| 47 | String status = "" |
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| 48 | |
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| 49 | Variable fileID = 0 |
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| 50 | HDF5OpenFile/R/P=home/Z fileID as fileName //read file from home directory? |
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| 51 | // HDF5OpenFile/R/P=catPathName/Z fileID as fileName |
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| 52 | if (V_Flag != 0) |
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| 53 | return 0 |
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| 54 | endif |
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| 55 | |
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| 56 | String/G root:file_path = S_path |
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| 57 | String/G root:file_name = S_FileName |
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| 58 | |
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| 59 | if ( fileID == 0 ) |
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| 60 | Print fileName + ": could not open as HDF5 file" |
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| 61 | return (0) |
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| 62 | endif |
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| 63 | |
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| 64 | //s_tic() //fast |
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| 65 | |
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| 66 | SVAR tmpStr=root:file_name |
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| 67 | fileName=tmpStr //SRK - in case the file was chosen from a dialog |
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| 68 | |
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| 69 | // read the data (too bad that HDF5LoadGroup does not read the attributes) |
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| 70 | String base_name = StringFromList(0,FileName,".") |
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| 71 | HDF5LoadGroup/Z/L=7/O/R/T=$base_name :, fileID, hdf5Path // recursive |
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| 72 | if ( V_Flag != 0 ) |
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| 73 | Print fileName + ": could not open as HDF5 file" |
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| 74 | setdatafolder root: |
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| 75 | return (0) |
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| 76 | endif |
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| 77 | |
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| 78 | HDF5CloseFile fileID |
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| 79 | |
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| 80 | //s_toc() |
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| 81 | return(0) |
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| 82 | end |
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| 83 | |
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| 84 | |
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| 85 | // read a single real value |
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| 86 | // - fname passed in is the full path to the file on disk |
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| 87 | // - path is the path to the value in the HDF tree |
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| 88 | // |
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| 89 | // check to see if the value exists (It will be a wave) |
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| 90 | // -- if it does, return the value from the local folder |
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| 91 | // -- if not, read the file in, then return the value |
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| 92 | // |
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| 93 | Function V_getRealValueFromHDF5(fname,path) |
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| 94 | String fname,path |
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| 95 | |
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| 96 | String folderStr="" |
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| 97 | Variable valExists=0 |
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| 98 | |
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| 99 | folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname)) |
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| 100 | |
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| 101 | if(Exists("root:"+folderStr+":"+path)) |
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| 102 | valExists=1 |
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| 103 | endif |
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| 104 | |
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| 105 | if(!valExists) |
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| 106 | //then read in the file |
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| 107 | V_LoadHDF5_NoAtt(fname) |
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| 108 | endif |
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| 109 | |
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| 110 | // this should exist now - if not, I need to see the error |
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| 111 | Wave/Z w = $("root:"+folderStr+":"+path) |
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| 112 | |
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| 113 | if(WaveExists(w)) |
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| 114 | return(w[0]) |
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| 115 | else |
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| 116 | return(-999999) |
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| 117 | endif |
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| 118 | End |
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| 119 | |
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| 120 | // Returns a wave reference, not just a single value |
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| 121 | // ---then you pick what you need from the wave |
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| 122 | // |
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| 123 | // - fname passed in is the full path to the file on disk |
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| 124 | // - path is the path to the value in the HDF tree |
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| 125 | // |
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| 126 | // check to see if the value exists (It will be a wave) |
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| 127 | // -- if it does, return the value from the local folder |
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| 128 | // -- if not, read the file in, then return the value |
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| 129 | // |
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| 130 | Function/WAVE V_getRealWaveFromHDF5(fname,path) |
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| 131 | String fname,path |
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| 132 | |
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| 133 | String folderStr="" |
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| 134 | Variable valExists=0 |
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| 135 | |
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| 136 | folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname)) |
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| 137 | |
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| 138 | if(Exists("root:"+folderStr+":"+path)) |
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| 139 | valExists=1 |
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| 140 | endif |
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| 141 | |
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| 142 | if(!valExists) |
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| 143 | //then read in the file |
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| 144 | V_LoadHDF5_NoAtt(fname) |
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| 145 | endif |
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| 146 | |
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| 147 | // this should exist now - if not, I need to see the error |
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| 148 | Wave wOut = $("root:"+folderStr+":"+path) |
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| 149 | |
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| 150 | return wOut |
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| 151 | |
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| 152 | End |
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| 153 | |
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| 154 | // |
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| 155 | // TODO |
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| 156 | // depricated? in HDF5 - store all of the values as real? |
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| 157 | // Igor sees no difference in real and integer variables (waves are different) |
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| 158 | // BUT-- Igor 7 will have integer variables |
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| 159 | // |
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| 160 | // truncate to integer before returning?? |
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| 161 | // |
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| 162 | ////// integer values |
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| 163 | // reads 32 bit integer |
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| 164 | Function V_getIntegerFromHDF5(fname,path) |
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| 165 | String fname //full path+name |
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| 166 | String path //path to the hdf5 location |
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| 167 | |
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| 168 | Variable val = V_getRealValueFromHDF5(fname,path) |
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| 169 | |
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| 170 | val = round(val) |
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| 171 | return(val) |
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| 172 | End |
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| 173 | |
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| 174 | |
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| 175 | // read a single string |
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| 176 | // - fname passed in is the full path to the file on disk |
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| 177 | // - path is the path to the value in the HDF tree |
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| 178 | // - num is the number of characters in the VAX string |
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| 179 | // check to see if the value exists (It will be a wave) |
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| 180 | // -- if it does, return the value from the local folder |
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| 181 | // -- if not, read the file in, then return the value |
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| 182 | // |
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| 183 | // TODO -- string could be checked for length, but returned right or wrong |
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| 184 | // |
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| 185 | Function/S V_getStringFromHDF5(fname,path,num) |
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| 186 | String fname,path |
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| 187 | Variable num |
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| 188 | |
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| 189 | String folderStr="" |
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| 190 | Variable valExists=0 |
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| 191 | |
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| 192 | folderStr = V_RemoveDotExtension(V_GetFileNameFromPathNoSemi(fname)) |
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| 193 | |
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| 194 | if(Exists("root:"+folderStr+":"+path)) |
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| 195 | valExists=1 |
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| 196 | endif |
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| 197 | |
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| 198 | if(!valExists) |
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| 199 | //then read in the file |
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| 200 | V_LoadHDF5_NoAtt(fname) |
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| 201 | endif |
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| 202 | |
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| 203 | // this should exist now - if not, I need to see the error |
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| 204 | Wave/T/Z tw = $("root:"+folderStr+":"+path) |
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| 205 | |
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| 206 | if(WaveExists(tw)) |
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| 207 | |
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| 208 | // if(strlen(tw[0]) != num) |
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| 209 | // Print "string is not the specified length" |
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| 210 | // endif |
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| 211 | |
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| 212 | return(tw[0]) |
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| 213 | else |
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| 214 | return("The specified wave does not exist: " + path) |
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| 215 | endif |
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| 216 | End |
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| 217 | |
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| 218 | |
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| 219 | |
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| 220 | /////////////////////////////// |
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| 221 | |
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| 222 | // |
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| 223 | //Write Wave 'wav' to hdf5 file 'fname' |
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| 224 | //Based on code from ANSTO (N. Hauser. nha 8/1/09) |
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| 225 | // |
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| 226 | // TODO: |
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| 227 | // -- figure out if this will write in the native format of the |
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| 228 | // wave as passed in, or if it will only write as DP. |
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| 229 | // -- do I need to write separate functions for real, integer, etc.? |
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| 230 | // |
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| 231 | // -- change the /P=home to the user-defined data path (which may be home) |
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| 232 | // |
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| 233 | Function V_WriteWaveToHDF(fname, groupName, varName, wav) |
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| 234 | String fname, groupName, varName |
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| 235 | Wave wav |
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| 236 | |
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| 237 | variable err=0, fileID,groupID |
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| 238 | String cDF = getDataFolder(1), temp |
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| 239 | String NXentry_name |
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| 240 | |
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| 241 | try |
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| 242 | HDF5OpenFile/P=home /Z fileID as fname //open file read-write |
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| 243 | if(!fileID) |
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| 244 | err = 1 |
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| 245 | abort "HDF5 file does not exist" |
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| 246 | endif |
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| 247 | |
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| 248 | //get the NXentry node name |
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| 249 | HDF5ListGroup /TYPE=1 fileID, "/" |
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| 250 | //remove trailing ; from S_HDF5ListGroup |
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| 251 | |
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| 252 | Print "S_HDF5ListGroup = ",S_HDF5ListGroup |
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| 253 | |
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| 254 | NXentry_name = S_HDF5ListGroup |
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| 255 | NXentry_name = ReplaceString(";",NXentry_name,"") |
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| 256 | if(strsearch(NXentry_name,":",0)!=-1) //more than one entry under the root node |
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| 257 | err = 1 |
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| 258 | abort "More than one entry under the root node. Ambiguous" |
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| 259 | endif |
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| 260 | //concatenate NXentry node name and groupName |
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| 261 | // SRK - NOV2015 - dropped this and require the full group name passed in |
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| 262 | // groupName = "/" + NXentry_name + groupName |
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| 263 | Print "groupName = ",groupName |
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| 264 | HDF5OpenGroup /Z fileID , groupName, groupID |
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| 265 | |
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| 266 | if(!groupID) |
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| 267 | HDF5CreateGroup /Z fileID, groupName, groupID |
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| 268 | //err = 1 |
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| 269 | //abort "HDF5 group does not exist" |
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| 270 | else |
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| 271 | // get attributes and save them |
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| 272 | //HDF5ListAttributes /Z fileID, groupName this is returning null. expect it to return semicolon delimited list of attributes |
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| 273 | //Wave attributes = S_HDF5ListAttributes |
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| 274 | endif |
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| 275 | |
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| 276 | HDF5SaveData /O /Z /IGOR=0 wav, groupID, varName |
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| 277 | if (V_flag != 0) |
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| 278 | err = 1 |
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| 279 | abort "Cannot save wave to HDF5 dataset " + varName |
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| 280 | endif |
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| 281 | |
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| 282 | |
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| 283 | //attributes - something could be added here as optional parameters and flagged |
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| 284 | // String attributes = "units" |
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| 285 | // Make/O/T/N=1 tmp |
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| 286 | // tmp[0] = "dimensionless" |
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| 287 | // HDF5SaveData /O /Z /IGOR=0 /A=attributes tmp, groupID, varName |
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| 288 | // if (V_flag != 0) |
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| 289 | // err = 1 |
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| 290 | // abort "Cannot save attributes to HDF5 dataset" |
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| 291 | // endif |
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| 292 | catch |
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| 293 | |
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| 294 | endtry |
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| 295 | |
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| 296 | // it is not necessary to close the group here. HDF5CloseFile will close the group as well |
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| 297 | if(groupID) |
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| 298 | HDF5CloseGroup /Z groupID |
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| 299 | endif |
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| 300 | |
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| 301 | if(fileID) |
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| 302 | HDF5CloseFile /Z fileID |
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| 303 | endif |
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| 304 | |
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| 305 | setDataFolder $cDF |
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| 306 | return err |
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| 307 | end |
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| 308 | |
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| 309 | //Write Wave 'wav' to hdf5 file 'fname' |
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| 310 | //Based on code from ANSTO (N. Hauser. nha 8/1/09) |
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| 311 | // |
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| 312 | // TODO |
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| 313 | // |
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| 314 | // -- change the /P=home to the user-defined data path (which may be home) |
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| 315 | // |
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| 316 | Function V_WriteTextWaveToHDF(fname, groupName, varName, wav) |
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| 317 | String fname, groupName, varName |
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| 318 | Wave/T wav |
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| 319 | |
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| 320 | variable err=0, fileID,groupID |
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| 321 | String cDF = getDataFolder(1), temp |
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| 322 | String NXentry_name |
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| 323 | |
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| 324 | try |
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| 325 | HDF5OpenFile/P=home /Z fileID as fname //open file read-write |
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| 326 | if(!fileID) |
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| 327 | err = 1 |
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| 328 | abort "HDF5 file does not exist" |
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| 329 | endif |
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| 330 | |
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| 331 | //get the NXentry node name |
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| 332 | HDF5ListGroup /TYPE=1 fileID, "/" |
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| 333 | //remove trailing ; from S_HDF5ListGroup |
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| 334 | |
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| 335 | Print "S_HDF5ListGroup = ",S_HDF5ListGroup |
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| 336 | |
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| 337 | NXentry_name = S_HDF5ListGroup |
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| 338 | NXentry_name = ReplaceString(";",NXentry_name,"") |
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| 339 | if(strsearch(NXentry_name,":",0)!=-1) //more than one entry under the root node |
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| 340 | err = 1 |
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| 341 | abort "More than one entry under the root node. Ambiguous" |
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| 342 | endif |
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| 343 | |
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| 344 | //concatenate NXentry node name and groupName |
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| 345 | // SRK - NOV2015 - dropped this and require the full group name passed in |
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| 346 | // groupName = "/" + NXentry_name + groupName |
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| 347 | Print "groupName = ",groupName |
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| 348 | |
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| 349 | HDF5OpenGroup /Z fileID , groupName, groupID |
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| 350 | |
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| 351 | if(!groupID) |
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| 352 | HDF5CreateGroup /Z fileID, groupName, groupID |
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| 353 | //err = 1 |
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| 354 | //abort "HDF5 group does not exist" |
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| 355 | else |
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| 356 | // get attributes and save them |
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| 357 | //HDF5ListAttributes /Z fileID, groupName this is returning null. expect it to return semicolon delimited list of attributes |
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| 358 | //Wave attributes = S_HDF5ListAttributes |
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| 359 | endif |
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| 360 | |
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| 361 | HDF5SaveData /O /Z /IGOR=0 wav, groupID, varName |
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| 362 | if (V_flag != 0) |
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| 363 | err = 1 |
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| 364 | abort "Cannot save wave to HDF5 dataset " + varName |
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| 365 | endif |
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| 366 | |
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| 367 | |
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| 368 | //attributes - something could be added here as optional parameters and flagged |
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| 369 | // String attributes = "units" |
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| 370 | // Make/O/T/N=1 tmp |
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| 371 | // tmp[0] = "dimensionless" |
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| 372 | // HDF5SaveData /O /Z /IGOR=0 /A=attributes tmp, groupID, varName |
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| 373 | // if (V_flag != 0) |
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| 374 | // err = 1 |
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| 375 | // abort "Cannot save attributes to HDF5 dataset" |
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| 376 | // endif |
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| 377 | catch |
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| 378 | |
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| 379 | endtry |
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| 380 | |
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| 381 | if(groupID) |
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| 382 | HDF5CloseGroup /Z groupID |
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| 383 | endif |
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| 384 | |
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| 385 | if(fileID) |
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| 386 | HDF5CloseFile /Z fileID |
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| 387 | endif |
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| 388 | |
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| 389 | setDataFolder $cDF |
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| 390 | return err |
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| 391 | end |
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