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4634
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1 /* |
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2 |
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3 Copyright (C) 1996, 1997 John W. Eaton |
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4 |
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5 This file is part of Octave. |
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6 |
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7 Octave is free software; you can redistribute it and/or modify it |
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8 under the terms of the GNU General Public License as published by the |
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9 Free Software Foundation; either version 2, or (at your option) any |
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10 later version. |
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11 |
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12 Octave is distributed in the hope that it will be useful, but WITHOUT |
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13 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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14 FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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15 for more details. |
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16 |
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17 You should have received a copy of the GNU General Public License |
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18 along with Octave; see the file COPYING. If not, write to the Free |
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5307
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19 Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA |
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20 02110-1301, USA. |
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4634
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21 |
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22 */ |
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23 |
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24 // Author: Steven G. Johnson <stevenj@alum.mit.edu> |
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25 |
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26 #ifdef HAVE_CONFIG_H |
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27 #include <config.h> |
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28 #endif |
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29 |
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30 #if defined (HAVE_HDF5) |
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31 |
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32 #include <cfloat> |
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33 #include <cstring> |
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34 #include <cctype> |
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35 |
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36 #include <fstream> |
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37 #include <iomanip> |
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38 #include <iostream> |
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39 #include <string> |
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4726
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40 #include <vector> |
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4634
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41 |
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42 #include <hdf5.h> |
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43 |
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44 #include "byte-swap.h" |
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45 #include "data-conv.h" |
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46 #include "file-ops.h" |
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47 #include "glob-match.h" |
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48 #include "lo-mappers.h" |
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49 #include "lo-sstream.h" |
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50 #include "mach-info.h" |
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51 #include "oct-env.h" |
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52 #include "oct-time.h" |
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53 #include "quit.h" |
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54 #include "str-vec.h" |
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55 |
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56 #include "Cell.h" |
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57 #include "defun.h" |
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58 #include "error.h" |
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59 #include "gripes.h" |
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60 #include "load-save.h" |
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61 #include "oct-obj.h" |
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62 #include "oct-map.h" |
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63 #include "ov-cell.h" |
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64 #include "pager.h" |
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65 #include "pt-exp.h" |
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66 #include "symtab.h" |
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67 #include "sysdep.h" |
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68 #include "unwind-prot.h" |
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69 #include "utils.h" |
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70 #include "variables.h" |
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71 #include "version.h" |
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72 #include "dMatrix.h" |
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73 |
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74 #include "ls-utils.h" |
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75 #include "ls-hdf5.h" |
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76 |
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77 static std::string |
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78 make_valid_identifier (const std::string& nm) |
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79 { |
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80 std::string retval; |
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81 |
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82 size_t nm_len = nm.length (); |
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83 |
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84 if (nm_len > 0) |
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85 { |
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86 if (! isalpha (nm[0])) |
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87 retval += '_'; |
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88 |
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89 for (size_t i = 0; i < nm_len; i++) |
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90 { |
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91 char c = nm[i]; |
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92 retval += (isalnum (c) || c == '_') ? c : '_'; |
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93 } |
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94 } |
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95 |
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96 return retval; |
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97 } |
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98 |
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99 // Define this to 1 if/when HDF5 supports automatic conversion between |
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100 // integer and floating-point binary data: |
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101 #define HAVE_HDF5_INT2FLOAT_CONVERSIONS 0 |
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102 |
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103 // Given two compound types t1 and t2, determine whether they |
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104 // are compatible for reading/writing. This function only |
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105 // works for non-nested types composed of simple elements (ints, floats...), |
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106 // which is all we need it for |
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107 |
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108 bool |
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109 hdf5_types_compatible (hid_t t1, hid_t t2) |
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110 { |
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111 int n; |
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112 if ((n = H5Tget_nmembers (t1)) != H5Tget_nmembers (t2)) |
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113 return false; |
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114 |
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115 for (int i = 0; i < n; ++i) |
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116 { |
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117 hid_t mt1 = H5Tget_member_type (t1, i); |
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118 hid_t mt2 = H5Tget_member_type (t2, i); |
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119 |
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120 if (H5Tget_class (mt1) != H5Tget_class (mt2)) |
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121 return false; |
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122 |
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123 H5Tclose (mt2); |
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124 H5Tclose (mt1); |
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125 } |
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126 |
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127 return true; |
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128 } |
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129 |
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130 // Return true if loc_id has the attribute named attr_name, and false |
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131 // otherwise. |
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132 |
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133 bool |
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134 hdf5_check_attr (hid_t loc_id, const char *attr_name) |
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135 { |
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136 bool retval = false; |
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137 |
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138 // we have to pull some shenanigans here to make sure |
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139 // HDF5 doesn't print out all sorts of error messages if we |
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140 // call H5Aopen for a non-existing attribute |
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141 |
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142 H5E_auto_t err_func; |
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143 void *err_func_data; |
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144 |
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145 // turn off error reporting temporarily, but save the error |
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146 // reporting function: |
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147 |
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148 H5Eget_auto (&err_func, &err_func_data); |
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149 H5Eset_auto (0, 0); |
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150 |
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151 hid_t attr_id = H5Aopen_name (loc_id, attr_name); |
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152 |
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153 if (attr_id >= 0) |
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154 { |
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155 // successful |
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156 retval = 1; |
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157 H5Aclose (attr_id); |
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158 } |
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159 |
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160 // restore error reporting: |
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161 H5Eset_auto (err_func, err_func_data); |
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162 |
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163 return retval; |
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164 } |
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165 |
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4687
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166 // The following subroutines creates an HDF5 representations of the way |
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167 // we will store Octave complex types (pairs of floating-point numbers). |
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168 // NUM_TYPE is the HDF5 numeric type to use for storage (e.g. |
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169 // H5T_NATIVE_DOUBLE to save as 'double'). Note that any necessary |
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170 // conversions are handled automatically by HDF5. |
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4634
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171 |
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4687
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172 hid_t |
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4634
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173 hdf5_make_complex_type (hid_t num_type) |
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174 { |
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175 hid_t type_id = H5Tcreate (H5T_COMPOUND, sizeof (double) * 2); |
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176 |
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177 H5Tinsert (type_id, "real", 0 * sizeof (double), num_type); |
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178 H5Tinsert (type_id, "imag", 1 * sizeof (double), num_type); |
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179 |
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180 return type_id; |
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181 } |
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182 |
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183 // This variable, set in read_hdf5_data(), tells whether we are using |
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184 // a version of HDF5 with a buggy H5Giterate (i.e. which neglects to |
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185 // increment the index parameter to the next unread item). |
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186 static bool have_h5giterate_bug = false; |
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187 |
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188 // This function is designed to be passed to H5Giterate, which calls it |
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189 // on each data item in an HDF5 file. For the item whose name is NAME in |
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190 // the group GROUP_ID, this function sets dv->tc to an Octave representation |
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191 // of that item. (dv must be a pointer to hdf5_callback_data.) (It also |
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192 // sets the other fields of dv). |
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193 // |
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194 // It returns 1 on success (in which case H5Giterate stops and returns), |
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195 // -1 on error, and 0 to tell H5Giterate to continue on to the next item |
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196 // (e.g. if NAME was a data type we don't recognize). |
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197 |
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4687
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198 herr_t |
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4634
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199 hdf5_read_next_data (hid_t group_id, const char *name, void *dv) |
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200 { |
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201 hdf5_callback_data *d = static_cast <hdf5_callback_data *> (dv); |
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4687
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202 hid_t type_id = -1, type_class_id = -1, data_id = -1, subgroup_id = -1, |
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203 space_id = -1; |
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4634
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204 |
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205 H5G_stat_t info; |
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206 herr_t retval = 0; |
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207 bool ident_valid = valid_identifier (name); |
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208 |
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209 std::string vname = name; |
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210 |
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211 // Allow identifiers as all digits so we can load lists saved by |
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212 // earlier versions of Octave. |
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213 |
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4687
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214 if (! ident_valid ) |
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4634
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215 { |
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216 // fix the identifier, replacing invalid chars with underscores |
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217 vname = make_valid_identifier (vname); |
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218 |
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219 // check again (in case vname was null, empty, or some such thing): |
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220 ident_valid = valid_identifier (vname); |
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221 } |
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222 |
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223 H5Gget_objinfo (group_id, name, 1, &info); |
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224 |
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4687
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225 if (info.type == H5G_GROUP && ident_valid) |
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4634
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226 { |
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4687
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227 subgroup_id = H5Gopen (group_id, name); |
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4634
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228 |
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229 if (subgroup_id < 0) |
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230 { |
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231 retval = subgroup_id; |
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232 goto done; |
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233 } |
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234 |
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4687
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235 if (hdf5_check_attr (subgroup_id, "OCTAVE_NEW_FORMAT")) |
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236 { |
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237 data_id = H5Dopen (subgroup_id, "type"); |
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4634
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238 |
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4687
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239 if (data_id < 0) |
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4634
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240 { |
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4687
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241 retval = data_id; |
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242 goto done; |
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4634
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243 } |
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244 |
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4687
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245 type_id = H5Dget_type (data_id); |
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246 |
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247 type_class_id = H5Tget_class (type_id); |
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248 |
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249 if (type_class_id != H5T_STRING) |
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250 goto done; |
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251 |
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252 space_id = H5Dget_space (data_id); |
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253 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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254 |
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255 if (rank != 0) |
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256 goto done; |
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257 |
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258 int slen = H5Tget_size (type_id); |
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259 if (slen < 0) |
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260 goto done; |
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261 |
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262 OCTAVE_LOCAL_BUFFER (char, typ, slen); |
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263 |
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264 // create datatype for (null-terminated) string to read into: |
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265 hid_t st_id = H5Tcopy (H5T_C_S1); |
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266 H5Tset_size (st_id, slen); |
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267 |
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268 if (H5Dread (data_id, st_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, |
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269 (void *) typ) < 0) |
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270 goto done; |
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271 |
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272 H5Tclose (st_id); |
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273 H5Dclose (data_id); |
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274 |
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275 d->tc = octave_value_typeinfo::lookup_type (typ); |
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276 |
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277 retval = (d->tc.load_hdf5 (subgroup_id, "value", |
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278 have_h5giterate_bug) ? 1 : -1); |
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279 |
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280 // check for OCTAVE_GLOBAL attribute: |
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281 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); |
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282 |
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283 H5Gclose (subgroup_id); |
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4634
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284 } |
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285 else |
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286 { |
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4687
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287 // an HDF5 group is treated as an octave structure by |
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288 // default (since that preserves name information), and an |
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289 // octave list otherwise. |
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290 |
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291 if (hdf5_check_attr (subgroup_id, "OCTAVE_LIST")) |
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292 d->tc = octave_value_typeinfo::lookup_type ("list"); |
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293 else |
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4948
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294 d->tc = octave_value_typeinfo::lookup_type ("struct"); |
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4687
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295 |
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296 // check for OCTAVE_GLOBAL attribute: |
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297 d->global = hdf5_check_attr (subgroup_id, "OCTAVE_GLOBAL"); |
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298 |
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299 H5Gclose (subgroup_id); |
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4634
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300 |
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4687
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301 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) |
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302 ? 1 : -1); |
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303 } |
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304 |
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305 } |
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306 else if (info.type == H5G_DATASET && ident_valid) |
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307 { |
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308 // For backwards compatiability. |
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309 data_id = H5Dopen (group_id, name); |
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310 |
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311 if (data_id < 0) |
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312 { |
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313 retval = data_id; |
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314 goto done; |
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4634
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315 } |
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316 |
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4687
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317 type_id = H5Dget_type (data_id); |
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318 |
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319 type_class_id = H5Tget_class (type_id); |
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320 |
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321 if (type_class_id == H5T_FLOAT) |
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322 { |
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323 space_id = H5Dget_space (data_id); |
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324 |
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325 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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326 |
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327 if (rank == 0) |
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328 d->tc = octave_value_typeinfo::lookup_type ("scalar"); |
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329 else |
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330 d->tc = octave_value_typeinfo::lookup_type ("matrix"); |
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331 |
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332 H5Sclose (space_id); |
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333 } |
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4948
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334 else if (type_class_id == H5T_INTEGER) |
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335 { |
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336 // What integer type do we really have.. |
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337 std::string int_typ; |
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338 #ifdef HAVE_H5T_GET_NATIVE_TYPE |
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5351
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339 // XXX FIXME XX test this code and activated with an autoconf |
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340 // test!! It is also incorrect for 64-bit indexing!! |
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341 |
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4948
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342 switch (H5Tget_native_type (type_id, H5T_DIR_ASCEND)) |
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343 { |
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344 case H5T_NATIVE_CHAR: |
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345 int_typ = "int8 "; |
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346 break; |
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347 |
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348 case H5T_NATIVE_SHORT: |
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349 int_typ = "int16 "; |
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350 break; |
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351 |
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352 case H5T_NATIVE_INT: |
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353 case H5T_NATIVE_LONG: |
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354 int_typ = "int32 "; |
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355 break; |
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356 |
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357 case H5T_NATIVE_LLONG: |
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358 int_typ = "int64 "; |
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359 break; |
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360 |
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361 case H5T_NATIVE_UCHAR: |
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362 int_typ = "uint8 "; |
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363 break; |
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364 |
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365 case H5T_NATIVE_USHORT: |
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366 int_typ = "uint16 "; |
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367 break; |
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368 |
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369 case H5T_NATIVE_UINT: |
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370 case H5T_NATIVE_ULONG: |
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371 int_typ = "uint32 "; |
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372 break; |
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373 |
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374 case H5T_NATIVE_ULLONG: |
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375 int_typ = "uint64 "; |
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376 break; |
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377 } |
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378 #else |
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379 hid_t int_sign = H5Tget_sign (type_id); |
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380 |
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381 if (int_sign == H5T_SGN_ERROR) |
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382 warning ("load: can't read `%s' (unknown datatype)", name); |
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383 else |
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384 { |
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385 if (int_sign == H5T_SGN_NONE) |
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386 int_typ.append ("u"); |
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387 int_typ.append ("int"); |
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388 |
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389 int slen = H5Tget_size (type_id); |
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390 if (slen < 0) |
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391 warning ("load: can't read `%s' (unknown datatype)", name); |
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392 else |
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393 { |
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394 switch (slen) |
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395 { |
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396 case 1: |
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397 int_typ.append ("8 "); |
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398 break; |
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399 |
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400 case 2: |
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401 int_typ.append ("16 "); |
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402 break; |
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403 |
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404 case 4: |
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405 int_typ.append ("32 "); |
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406 break; |
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407 |
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408 case 8: |
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409 int_typ.append ("64 "); |
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410 break; |
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411 |
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412 default: |
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413 warning ("load: can't read `%s' (unknown datatype)", |
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414 name); |
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415 int_typ = ""; |
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416 break; |
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417 } |
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418 } |
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419 } |
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420 #endif |
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421 if (int_typ == "") |
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422 warning ("load: can't read `%s' (unknown datatype)", name); |
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423 else |
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424 { |
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425 // Matrix or scalar? |
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426 space_id = H5Dget_space (data_id); |
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427 |
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428 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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429 |
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430 if (rank == 0) |
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431 int_typ.append ("scalar"); |
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432 else |
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433 int_typ.append ("matrix"); |
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434 |
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435 d->tc = octave_value_typeinfo::lookup_type (int_typ); |
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436 H5Sclose (space_id); |
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437 } |
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438 } |
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4687
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439 else if (type_class_id == H5T_STRING) |
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440 d->tc = octave_value_typeinfo::lookup_type ("string"); |
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441 else if (type_class_id == H5T_COMPOUND) |
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442 { |
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443 hid_t complex_type = hdf5_make_complex_type (H5T_NATIVE_DOUBLE); |
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444 |
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445 if (hdf5_types_compatible (type_id, complex_type)) |
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446 { |
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|
447 // read complex matrix or scalar variable |
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|
448 space_id = H5Dget_space (data_id); |
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|
449 hsize_t rank = H5Sget_simple_extent_ndims (space_id); |
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450 |
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451 if (rank == 0) |
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452 d->tc = octave_value_typeinfo::lookup_type ("complex scalar"); |
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453 else |
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454 d->tc = octave_value_typeinfo::lookup_type ("complex matrix"); |
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455 |
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456 H5Sclose (space_id); |
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457 } |
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458 else |
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|
459 // Assume that if its not complex its a range. If its not |
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|
460 // it'll be rejected later in the range code |
|
|
461 d->tc = octave_value_typeinfo::lookup_type ("range"); |
|
|
462 |
|
|
463 H5Tclose (complex_type); |
|
|
464 } |
|
|
465 else |
|
|
466 { |
|
|
467 warning ("load: can't read `%s' (unknown datatype)", name); |
|
|
468 retval = 0; // unknown datatype; skip |
|
|
469 } |
|
|
470 |
|
|
471 // check for OCTAVE_GLOBAL attribute: |
|
|
472 d->global = hdf5_check_attr (data_id, "OCTAVE_GLOBAL"); |
|
|
473 |
|
|
474 H5Tclose (type_id); |
|
|
475 H5Dclose (data_id); |
|
|
476 |
|
|
477 retval = (d->tc.load_hdf5 (group_id, name, have_h5giterate_bug) |
|
|
478 ? 1 : -1); |
|
4634
|
479 } |
|
4687
|
480 |
|
|
481 if (!ident_valid) |
|
4634
|
482 { |
|
|
483 // should we attempt to handle invalid identifiers by converting |
|
|
484 // bad characters to '_', say? |
|
|
485 warning ("load: skipping invalid identifier `%s' in hdf5 file", |
|
|
486 name); |
|
|
487 } |
|
|
488 |
|
|
489 done: |
|
|
490 if (retval < 0) |
|
|
491 error ("load: error while reading hdf5 item %s", name); |
|
4687
|
492 |
|
4634
|
493 if (retval > 0) |
|
|
494 { |
|
|
495 // get documentation string, if any: |
|
|
496 int comment_length = H5Gget_comment (group_id, name, 0, 0); |
|
|
497 |
|
|
498 if (comment_length > 1) |
|
|
499 { |
|
|
500 OCTAVE_LOCAL_BUFFER (char, tdoc, comment_length); |
|
|
501 H5Gget_comment (group_id, name, comment_length, tdoc); |
|
|
502 d->doc = tdoc; |
|
|
503 } |
|
|
504 else if (vname != name) |
|
|
505 { |
|
4687
|
506 // the name was changed; store the original name |
|
4634
|
507 // as the documentation string: |
|
|
508 d->doc = name; |
|
|
509 } |
|
|
510 |
|
|
511 // copy name (actually, vname): |
|
|
512 d->name = vname; |
|
|
513 } |
|
|
514 |
|
|
515 return retval; |
|
|
516 } |
|
|
517 |
|
|
518 // Read the next Octave variable from the stream IS, which must really be |
|
|
519 // an hdf5_ifstream. Return the variable value in tc, its doc string |
|
|
520 // in doc, and whether it is global in global. The return value is |
|
|
521 // the name of the variable, or NULL if none were found or there was |
|
4687
|
522 // and error. |
|
4634
|
523 std::string |
|
4687
|
524 read_hdf5_data (std::istream& is, const std::string& /* filename */, |
|
|
525 bool& global, octave_value& tc, std::string& doc) |
|
4634
|
526 { |
|
|
527 std::string retval; |
|
|
528 |
|
|
529 doc.resize (0); |
|
|
530 |
|
|
531 hdf5_ifstream& hs = (hdf5_ifstream&) is; |
|
|
532 hdf5_callback_data d; |
|
|
533 |
|
|
534 // Versions of HDF5 prior to 1.2.2 had a bug in H5Giterate where it |
|
|
535 // would return the index of the last item processed instead of the |
|
|
536 // next item to be processed, forcing us to increment the index manually. |
|
|
537 |
|
|
538 unsigned int vers_major, vers_minor, vers_release; |
|
|
539 |
|
|
540 H5get_libversion (&vers_major, &vers_minor, &vers_release); |
|
|
541 |
|
|
542 // XXX FIXME XXX -- this test looks wrong. |
|
|
543 have_h5giterate_bug |
|
|
544 = (vers_major < 1 |
|
|
545 || (vers_major == 1 && (vers_minor < 2 |
|
|
546 || (vers_minor == 2 && vers_release < 2)))); |
|
|
547 |
|
4696
|
548 herr_t H5Giterate_retval = -1; |
|
|
549 |
|
|
550 #ifdef HAVE_H5GGET_NUM_OBJS |
|
|
551 hsize_t num_obj = 0; |
|
5060
|
552 hid_t group_id = H5Gopen (hs.file_id, "/"); |
|
|
553 H5Gget_num_objs (group_id, &num_obj); |
|
|
554 H5Gclose (group_id); |
|
4696
|
555 if (hs.current_item < static_cast<int> (num_obj)) |
|
|
556 #endif |
|
|
557 H5Giterate_retval = H5Giterate (hs.file_id, "/", &hs.current_item, |
|
|
558 hdf5_read_next_data, &d); |
|
4634
|
559 |
|
|
560 if (have_h5giterate_bug) |
|
|
561 { |
|
|
562 // H5Giterate sets current_item to the last item processed; we want |
|
|
563 // the index of the next item (for the next call to read_hdf5_data) |
|
|
564 |
|
|
565 hs.current_item++; |
|
|
566 } |
|
|
567 |
|
|
568 if (H5Giterate_retval > 0) |
|
|
569 { |
|
|
570 global = d.global; |
|
|
571 tc = d.tc; |
|
|
572 doc = d.doc; |
|
|
573 } |
|
|
574 else |
|
|
575 { |
|
|
576 // an error occurred (H5Giterate_retval < 0) or there are no |
|
|
577 // more datasets print an error message if retval < 0? |
|
|
578 // hdf5_read_next_data already printed one, probably. |
|
|
579 } |
|
|
580 |
|
|
581 if (! d.name.empty ()) |
|
|
582 retval = d.name; |
|
|
583 |
|
|
584 return retval; |
|
|
585 } |
|
|
586 |
|
|
587 // Add an attribute named attr_name to loc_id (a simple scalar |
|
|
588 // attribute with value 1). Return value is >= 0 on success. |
|
|
589 static herr_t |
|
|
590 hdf5_add_attr (hid_t loc_id, const char *attr_name) |
|
|
591 { |
|
|
592 herr_t retval = 0; |
|
|
593 |
|
|
594 hid_t as_id = H5Screate (H5S_SCALAR); |
|
|
595 |
|
|
596 if (as_id >= 0) |
|
|
597 { |
|
|
598 hid_t a_id = H5Acreate (loc_id, attr_name, |
|
|
599 H5T_NATIVE_UCHAR, as_id, H5P_DEFAULT); |
|
|
600 |
|
|
601 if (a_id >= 0) |
|
|
602 { |
|
|
603 unsigned char attr_val = 1; |
|
|
604 |
|
|
605 retval = H5Awrite (a_id, H5T_NATIVE_UCHAR, (void*) &attr_val); |
|
|
606 |
|
|
607 H5Aclose (a_id); |
|
|
608 } |
|
|
609 else |
|
|
610 retval = a_id; |
|
|
611 |
|
|
612 H5Sclose (as_id); |
|
|
613 } |
|
|
614 else |
|
|
615 retval = as_id; |
|
|
616 |
|
|
617 return retval; |
|
|
618 } |
|
|
619 |
|
4805
|
620 // Save an empty matrix, if needed. Returns |
|
|
621 // > 0 Saved empty matrix |
|
|
622 // = 0 Not an empty matrix; did nothing |
|
|
623 // < 0 Error condition |
|
|
624 int |
|
|
625 save_hdf5_empty (hid_t loc_id, const char *name, const dim_vector d) |
|
|
626 { |
|
|
627 hsize_t sz = d.length (); |
|
5351
|
628 octave_idx_type dims[sz]; |
|
4805
|
629 bool empty = false; |
|
|
630 hid_t space_hid = -1, data_hid = -1; |
|
|
631 int retval; |
|
|
632 for (hsize_t i = 0; i < sz; i++) |
|
|
633 { |
|
|
634 dims[i] = d(i); |
|
|
635 if (dims[i] < 1) |
|
|
636 empty = true; |
|
|
637 } |
|
|
638 |
|
|
639 if (!empty) |
|
|
640 return 0; |
|
|
641 |
|
|
642 space_hid = H5Screate_simple (1, &sz, (hsize_t *) 0); |
|
|
643 if (space_hid < 0) return space_hid; |
|
|
644 |
|
5351
|
645 data_hid = H5Dcreate (loc_id, name, H5T_NATIVE_IDX, space_hid, |
|
4805
|
646 H5P_DEFAULT); |
|
|
647 if (data_hid < 0) |
|
|
648 { |
|
|
649 H5Sclose (space_hid); |
|
|
650 return data_hid; |
|
|
651 } |
|
|
652 |
|
5351
|
653 retval = H5Dwrite (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, |
|
4805
|
654 H5P_DEFAULT, (void*) dims) >= 0; |
|
|
655 |
|
|
656 H5Dclose (data_hid); |
|
|
657 H5Sclose (space_hid); |
|
|
658 |
|
|
659 if (retval >= 0) |
|
|
660 retval = hdf5_add_attr (loc_id, "OCTAVE_EMPTY_MATRIX"); |
|
|
661 |
|
|
662 return (retval == 0 ? 1 : retval); |
|
|
663 } |
|
|
664 |
|
|
665 // Load an empty matrix, if needed. Returns |
|
|
666 // > 0 loaded empty matrix, dimensions returned |
|
|
667 // = 0 Not an empty matrix; did nothing |
|
|
668 // < 0 Error condition |
|
|
669 int |
|
|
670 load_hdf5_empty (hid_t loc_id, const char *name, dim_vector &d) |
|
|
671 { |
|
|
672 if (!hdf5_check_attr(loc_id, "OCTAVE_EMPTY_MATRIX")) |
|
|
673 return 0; |
|
|
674 |
|
|
675 hsize_t hdims, maxdims; |
|
|
676 hid_t data_hid = H5Dopen (loc_id, name); |
|
|
677 hid_t space_id = H5Dget_space (data_hid); |
|
|
678 H5Sget_simple_extent_dims (space_id, &hdims, &maxdims); |
|
|
679 int retval; |
|
|
680 |
|
5351
|
681 OCTAVE_LOCAL_BUFFER (octave_idx_type, dims, hdims); |
|
|
682 |
|
|
683 retval = H5Dread (data_hid, H5T_NATIVE_IDX, H5S_ALL, H5S_ALL, |
|
4805
|
684 H5P_DEFAULT, (void *) dims); |
|
|
685 if (retval >= 0) |
|
|
686 { |
|
|
687 d.resize (hdims); |
|
|
688 for (hsize_t i = 0; i < hdims; i++) |
|
|
689 d(i) = dims[i]; |
|
|
690 } |
|
|
691 |
|
|
692 H5Sclose (space_id); |
|
|
693 H5Dclose (data_hid); |
|
|
694 |
|
|
695 return (retval == 0 ? hdims : retval); |
|
|
696 } |
|
|
697 |
|
4634
|
698 // save_type_to_hdf5 is not currently used, since hdf5 doesn't yet support |
|
|
699 // automatic float<->integer conversions: |
|
|
700 |
|
|
701 #if HAVE_HDF5_INT2FLOAT_CONVERSIONS |
|
|
702 |
|
|
703 // return the HDF5 type id corresponding to the Octave save_type |
|
|
704 |
|
4687
|
705 hid_t |
|
4634
|
706 save_type_to_hdf5 (save_type st) |
|
|
707 { |
|
|
708 switch (st) |
|
|
709 { |
|
|
710 case LS_U_CHAR: |
|
|
711 return H5T_NATIVE_UCHAR; |
|
|
712 |
|
|
713 case LS_U_SHORT: |
|
|
714 return H5T_NATIVE_USHORT; |
|
|
715 |
|
|
716 case LS_U_INT: |
|
|
717 return H5T_NATIVE_UINT; |
|
|
718 |
|
|
719 case LS_CHAR: |
|
|
720 return H5T_NATIVE_CHAR; |
|
|
721 |
|
|
722 case LS_SHORT: |
|
|
723 return H5T_NATIVE_SHORT; |
|
|
724 |
|
|
725 case LS_INT: |
|
|
726 return H5T_NATIVE_INT; |
|
|
727 |
|
|
728 case LS_FLOAT: |
|
|
729 return H5T_NATIVE_FLOAT; |
|
|
730 |
|
|
731 case LS_DOUBLE: |
|
|
732 default: |
|
|
733 return H5T_NATIVE_DOUBLE; |
|
|
734 } |
|
|
735 } |
|
|
736 #endif /* HAVE_HDF5_INT2FLOAT_CONVERSIONS */ |
|
|
737 |
|
|
738 // Add the data from TC to the HDF5 location loc_id, which could |
|
|
739 // be either a file or a group within a file. Return true if |
|
|
740 // successful. This function calls itself recursively for lists |
|
|
741 // (stored as HDF5 groups). |
|
|
742 |
|
4687
|
743 bool |
|
4634
|
744 add_hdf5_data (hid_t loc_id, const octave_value& tc, |
|
|
745 const std::string& name, const std::string& doc, |
|
|
746 bool mark_as_global, bool save_as_floats) |
|
|
747 { |
|
|
748 hsize_t dims[3]; |
|
4687
|
749 hid_t type_id = -1, space_id = -1, data_id = -1, data_type_id = -1; |
|
|
750 bool retval = false; |
|
|
751 octave_value val = tc; |
|
|
752 std::string t = tc.type_name(); |
|
4634
|
753 |
|
4687
|
754 data_id = H5Gcreate (loc_id, name.c_str (), 0); |
|
|
755 if (data_id < 0) |
|
|
756 goto error_cleanup; |
|
4634
|
757 |
|
4687
|
758 // attach the type of the variable |
|
|
759 type_id = H5Tcopy (H5T_C_S1); H5Tset_size (type_id, t.length () + 1); |
|
|
760 if (type_id < 0) |
|
|
761 goto error_cleanup; |
|
4634
|
762 |
|
4687
|
763 dims[0] = 0; |
|
|
764 space_id = H5Screate_simple (0 , dims, (hsize_t*) 0); |
|
|
765 if (space_id < 0) |
|
|
766 goto error_cleanup; |
|
4634
|
767 |
|
4687
|
768 data_type_id = H5Dcreate (data_id, "type", type_id, space_id, H5P_DEFAULT); |
|
|
769 if (data_type_id < 0 || H5Dwrite (data_type_id, type_id, H5S_ALL, H5S_ALL, |
|
|
770 H5P_DEFAULT, (void*) t.c_str ()) < 0) |
|
|
771 goto error_cleanup; |
|
4634
|
772 |
|
4687
|
773 // Now call the real function to save the variable |
|
|
774 retval = val.save_hdf5 (data_id, "value", save_as_floats); |
|
4634
|
775 |
|
|
776 // attach doc string as comment: |
|
4687
|
777 if (retval && doc.length () > 0 |
|
4634
|
778 && H5Gset_comment (loc_id, name.c_str (), doc.c_str ()) < 0) |
|
4687
|
779 retval = false; |
|
4634
|
780 |
|
|
781 // if it's global, add an attribute "OCTAVE_GLOBAL" with value 1 |
|
4687
|
782 if (retval && mark_as_global) |
|
4634
|
783 retval = hdf5_add_attr (data_id, "OCTAVE_GLOBAL") >= 0; |
|
|
784 |
|
4687
|
785 // We are saving in the new variable format, so mark it |
|
|
786 if (retval) |
|
|
787 retval = hdf5_add_attr (data_id, "OCTAVE_NEW_FORMAT") >= 0; |
|
|
788 |
|
4634
|
789 error_cleanup: |
|
|
790 |
|
4687
|
791 if (data_type_id >= 0) |
|
|
792 H5Dclose (data_type_id); |
|
4634
|
793 |
|
4687
|
794 if (type_id >= 0) |
|
|
795 H5Tclose (type_id); |
|
4634
|
796 |
|
|
797 if (space_id >= 0) |
|
|
798 H5Sclose (space_id); |
|
|
799 |
|
4687
|
800 if (data_id >= 0) |
|
|
801 H5Gclose (data_id); |
|
|
802 |
|
|
803 if (! retval) |
|
|
804 error ("save: error while writing `%s' to hdf5 file", name.c_str ()); |
|
4634
|
805 |
|
|
806 return retval; |
|
|
807 } |
|
|
808 |
|
|
809 // Write data from TC in HDF5 (binary) format to the stream OS, |
|
|
810 // which must be an hdf5_ofstream, returning true on success. |
|
|
811 |
|
|
812 bool |
|
|
813 save_hdf5_data (std::ostream& os, const octave_value& tc, |
|
|
814 const std::string& name, const std::string& doc, |
|
|
815 bool mark_as_global, bool save_as_floats) |
|
|
816 { |
|
|
817 hdf5_ofstream& hs = (hdf5_ofstream&) os; |
|
|
818 |
|
|
819 return add_hdf5_data (hs.file_id, tc, name, doc, |
|
|
820 mark_as_global, save_as_floats); |
|
|
821 } |
|
|
822 |
|
|
823 #endif |
|
|
824 |
|
|
825 /* |
|
|
826 ;;; Local Variables: *** |
|
|
827 ;;; mode: C++ *** |
|
|
828 ;;; End: *** |
|
|
829 */ |
