1 | Duchamp version 1.1.2 (2007/09/19) |
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2 | ------------------------------------ |
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3 | |
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4 | * The compilation had problems working correctly when the cfitsio and |
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5 | wcs libraries were not in standard locations. The configure script |
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6 | has been tweaked to make sure the libraries are found. |
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7 | |
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8 | * Problems with compiling in the absence of pgplot have been fixed, |
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9 | and it should now compile fine. |
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10 | |
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11 | |
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12 | |
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13 | Duchamp version 1.1.1 (2007/07/20) |
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14 | ------------------------------------ |
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15 | |
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16 | Minor update to the release, with just a few changes: |
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17 | |
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18 | * The verification script was generating diffs due to differences in |
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19 | the precision of some calculations when done on different machines. |
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20 | One of these was the integrated flux, and this has been corrected so |
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21 | that the same value should appear on all machines. |
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22 | The verification script has also changed so that just the number of |
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23 | sources and their positions are tested, as well as the |
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24 | logfiles. This should avoid the reporting of spurious differences. |
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25 | |
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26 | * The grey-scale used in the image cutouts (in the spectral plots) has |
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27 | been inverted. This makes it consistent with the scale used in the |
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28 | maps, and hopefully easier to see when printing. |
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29 | |
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30 | * The configure/make system has been altered to make it easier to |
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31 | install, and to specify different external libraries. In particular, |
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32 | it is now not necessary to have PGPLOT installed on your system to |
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33 | run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, |
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34 | just without any graphical output. Some source code needed to be |
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35 | restructured to make this work. Please read the README file, or the |
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36 | Installation appendix in the User's Guide, for complete details. |
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37 | |
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38 | * The time of completion is now written to the log file, so that the |
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39 | user can have some idea of how long the program took. |
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40 | |
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41 | |
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42 | Duchamp version 1.1 (2007/05/17) |
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43 | ------------------------------------ |
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44 | |
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45 | Changes made since the last numbered release: |
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46 | |
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47 | EFFICIENCY OF EXECUTION: |
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48 | |
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49 | * Major change to the way detections are stored. They are now recorded |
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50 | via run-length encoding in the x-y plane, and stored as collections |
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51 | of channel-maps. This improves the memory usage and the speed of |
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52 | execution (particularly for routines such as the merging |
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53 | routines). The memory usage has also been improved by changing the |
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54 | way the list of detected objects is stored. |
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55 | |
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56 | SMOOTHING: |
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57 | |
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58 | * Addition of ability to spatially smooth the cube before |
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59 | searching. This is done with a Gaussian kernel, the size and shape |
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60 | of which can be specified by the user, using the parameters kernMaj |
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61 | & kernMin (which are the FWHM for the major & minor axes -- if |
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62 | kernMin is not given it is assumed to match kernMaj) and kernPA (the |
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63 | position angle of the major axis). There is a new parameter |
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64 | smoothType that distinguishes this method from the spectral (Hanning) |
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65 | smoothing already in use. |
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66 | |
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67 | DETECTIONS: |
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68 | |
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69 | * Changed the way detection is done -- now only search in 2D images, |
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70 | keeping all detections (ie. no minimum-pixel requirement). This |
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71 | should be the same as doing both the 1D and 2D searches with the |
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72 | minimum pixel requirement in, but simpler. The rejection is done at |
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73 | the end after all the merging and growing has been done. This leads |
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74 | to a larger number of intermediate detections (ie. the number |
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75 | before merging), which may increase the run-time slightly, although |
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76 | this is offset by the changes to the efficiency (see above). |
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77 | |
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78 | * Increased the range over which objects can be grown to match the |
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79 | threshSpatial & threshVelocity parameters, as well as rejecting new |
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80 | pixels based on the BLANK and MW tests. |
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81 | |
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82 | INPUTS: |
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83 | |
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84 | * There has been a subtle change in the way BLANK pixels are dealt |
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85 | with. To enable trimming of BLANK pixels, users should use the new |
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86 | parameter flagTrim. The parameters flagBlankPix and blankPixVal are |
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87 | no longer accessible via the parameter file -- warning messages are |
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88 | given if they are provided in the parameter file. |
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89 | |
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90 | * Added ability to specify a statsec, so that the statistics are only |
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91 | calculated from a given subsection of the cube, rather than the full |
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92 | cube. |
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93 | |
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94 | * The subsections can also specify the ability to remove a border of n |
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95 | pixels from the edges of an axis (ie. n from the start and from the |
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96 | end) -- as requested in Trac ticket #5. |
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97 | |
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98 | * Changed the default value of the reconDim parameter from 3 to 1, and |
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99 | the default value of the flagATrous parameter to false. |
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100 | |
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101 | OUTPUTS: |
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102 | |
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103 | * The output now includes three different estimates of the "centre" of |
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104 | the detection: peak location, centroid (flux-weighted), or average. |
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105 | |
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106 | * Some slight improvements to the user feedback during execution. |
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107 | |
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108 | * Spectral output now includes the baseline, if one was fitted. The |
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109 | format of the plot headers is slightly changed, to stop information |
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110 | falling off the edge of the page. |
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111 | |
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112 | * Added command-line option -x to directly disable the PGPLOT X-window |
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113 | map plotting. This overrides the setting of flagXOutput in the |
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114 | parameter file. |
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115 | |
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116 | * Fallback spectral units (in case the FITS header fails to record |
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117 | them) changed to SPC, but code has been fixed so that any problem |
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118 | should be caught before this becomes an issue. |
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119 | |
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120 | BUGFIXES: |
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121 | |
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122 | * Fixed bug (Trac ticket #4) that meant the velocity units were not |
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123 | correctly dealt with. Duchamp should be more robust for different |
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124 | velocity axis setups now. |
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125 | |
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126 | * Fixed bug (ticket #9) with the VOTable output, where the tags were |
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127 | not closing. |
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128 | |
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129 | * Fixed a bug that meant the integrated fluxes were not calculated |
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130 | properly -- no allowance was made for the number of spatial |
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131 | pixels. This should also work properly for 2D images now as well. |
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132 | |
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133 | * Fixed minor bug in calculating the flux threshold from the p-value |
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134 | threshold when the FDR method is used. This did not affect the |
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135 | actual thresholding, merely the quoted flux threshold in the results |
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136 | file. Also, the MW channels are kept out of the p-value threshold |
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137 | determination if they are being flagged. |
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138 | |
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139 | |
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140 | |
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141 | Duchamp version 1.0.7 (2006/11/22) |
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142 | ---------------------------------- |
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143 | |
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144 | One new feature, and some improvements and bug-fixes. |
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145 | |
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146 | * The user can now elect to Hanning-smooth the spectral direction of |
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147 | the cube before the searching is done. This can be done instead of the |
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148 | wavelet reconstruction (although if both are selected, the |
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149 | reconstruction takes precendence). This functionality is switched on |
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150 | and off by the flagSmooth parameter, and the width of the Hanning |
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151 | kernel is governed by the hanningWidth parameter. |
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152 | |
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153 | * The smoothed array can also be written to a FITS file and read in at |
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154 | the start in the same manner as the reconstructed array. |
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155 | |
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156 | * Several improvements have been made to the memory |
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157 | management. Several memory leaks were fixed, and the memory usage of |
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158 | Duchamp is considerably less, which will be a help for running it on |
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159 | large cubes. The speed of some routines has also been improved, by |
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160 | removing unnecessarily repetitive loops. |
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161 | |
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162 | * The sorting routines have been changed, and should now be slightly quicker |
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163 | (and a bit more robust). |
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164 | |
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165 | * Enabled the scale bar (plotted on the 0th moment map in the spectral |
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166 | output file) to be able to deal with much finer spatial scales (as |
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167 | may be expected from VLBI data). |
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168 | |
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169 | * Other minor changes to code and presentation. |
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170 | |
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171 | |
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172 | Duchamp version 1.0.6 (2006/11/01) |
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173 | ---------------------------------- |
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174 | |
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175 | Some incremental improvements and changes to the code: |
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176 | |
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177 | * The statistics used for the detection are now calculated once for |
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178 | the entire cube, rather than being calculated separately for each |
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179 | channel map and spectrum. This results in a uniform threshold value |
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180 | across the entire cube. The way the statistics calculations are |
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181 | implemented in the code was changed, using a new statistics class. |
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182 | |
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183 | * This means we can report a peak signal-to-noise value for each |
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184 | detection. This is given in the text-based output, as well as in the |
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185 | summary information above the spectral output for each source. |
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186 | |
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187 | * The user can now elect not to have the moment map displayed in a |
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188 | PGPlot window, through the use of the new flagXOutput |
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189 | parameter. This should help in cases of running Duchamp on a dumb |
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190 | terminal (with no X-display capabilities), or as part of a batch |
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191 | script where the continual popping-up of the PGPlot window might |
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192 | become annoying. |
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193 | |
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194 | * There are different Flags reported for the case of an object lying on |
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195 | the spatial edge and spectral edge of the cube (E and S respectively). |
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196 | |
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197 | * A few minor bug fixes: |
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198 | - When providing a subsection, any axes with the range given by * |
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199 | had the pixel values offset incorrectly. This has been fixed. |
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200 | - Negative searches now correctly invert the reconstructed array |
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201 | when it is read in from a file. |
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202 | |
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203 | * Other minor changes to the code, to improve memory handling and |
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204 | remove redundant arrays and variables. |
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205 | |
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206 | |
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207 | Duchamp version 1.0.5 (2006/09/06) |
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208 | ---------------------------------- |
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209 | |
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210 | Since version 1.0, there have been a range of mostly minor |
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211 | changes. These are generally bug-fixes, thanks to feedback from a |
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212 | number of users, as well as a few extra features. |
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213 | |
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214 | Here is a summary of the changes since version 1.0: |
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215 | |
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216 | USER INTERFACE: |
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217 | |
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218 | * The user is now able to enter the value of flag parameters in the |
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219 | parameter file as strings, as well as integers (so one can enter |
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220 | true or 1 to give the same result). |
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221 | |
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222 | GRAPHICAL OUTPUT: |
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223 | |
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224 | * Added a new function that draws the edge of the blank region on the |
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225 | maps and image cutouts. There is a new flag parameter -- |
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226 | drawBlankEdges -- that controls the use of this function (the |
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227 | default is true). |
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228 | Also, the edge of the field is plotted on the image cutouts as a |
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229 | yellow line. This distinguishes it from the purple blank pixel |
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230 | dividing line. |
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231 | |
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232 | * The size of the tick mark in the image cutout (indicating the |
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233 | spatial scale of the image) is now adaptable, so that it shows the |
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234 | scale that best fits the image (ranging from 1 arcsec to 15 |
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235 | degrees). (This is a change from the previous standard length of 15 |
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236 | arcmin.) |
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237 | |
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238 | * The zoomed spectrum had its flux scale determined by all points in |
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239 | the zoom box,including those flagged by the Milky Way (MW) |
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240 | range. This has been fixed so that any MW channels will not affect |
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241 | the flux scaling, potentially improving the appearance of objects |
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242 | detected close in velocity to strong MW emission or absorption. |
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243 | |
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244 | * Improved Karma Annotation file output, so that files without good |
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245 | WCS are dealt with appropriately. |
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246 | |
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247 | TEXT-BASED OUTPUT: |
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248 | |
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249 | * The position resolution in the IAU-format names has been increased, |
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250 | so that distinct objects close to one another are more readily |
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251 | distinguished. Overlapping sources at different velocities may |
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252 | still have the same name, but this is a more general problem. |
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253 | |
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254 | * The presentation of the results in tabular format has been improved, |
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255 | so that the precision of faint sources is sufficient to show their |
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256 | flux, for instance, is not 0. This also applies to the information |
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257 | presented above the spectral plots. |
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258 | |
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259 | * Improved error and warning reporting, so that the formatting and |
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260 | presentation of information is clearer. |
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261 | |
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262 | FITS I/O RELATED: |
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263 | |
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264 | * The previous version was did not deal well with 4 (or greater) |
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265 | dimensions in the FITS file -- the memory allocation was badly done, |
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266 | and the axes needed to be in a particular order. This has been |
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267 | fixed, so that the FITS I/O routines can now handle any sized FITS |
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268 | file, with axes in any order (as long as there are two spatial and one |
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269 | spectral axes). |
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270 | |
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271 | * When the FITS file does not have a rest frequency defined, there is |
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272 | no way to transform the frequency axis into velocity. In this case, |
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273 | the spectral axis is left as frequency, and put into units of MHz. |
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274 | |
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275 | * If the beam size is not indicated by the FITS header (through the |
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276 | BMAJ and BMIN keywords), the user can manually specify the size |
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277 | through the parameter file (using parameter beamSize). |
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278 | |
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279 | * The FITS I/O routines make use of the command fits_file_exists. This |
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280 | was introduced into the CFITSIO package from version 2.5, so Duchamp |
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281 | will only work with this version or higher. Version 3+ is preferred. |
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282 | |
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283 | OTHER BUG-FIXING: |
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284 | |
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285 | * Several bugs related to the blank-pixels were dealt with. |
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286 | The correct values were not propagating through correctly, meaning |
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287 | that the default values were being used. Also, there was the |
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288 | potential for blank pixels to be detected when the FDR method was |
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289 | used. Finally, the image cutout displays occasionally did not |
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290 | obscure the blank pixels. All these problems should be fixed now. |
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291 | |
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292 | * The FDR setup routine was occasionally failing with a segmentation |
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293 | fault, due to it accessing unallocated memory. This has been fixed. |
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294 | |
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295 | * Fixed bugs that affected the way 2D images (rather than 3D cubes) |
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296 | were dealt with. The minChannels test failed when minChannels=0. |
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297 | |
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298 | * If there is no beam information in the FITS header, the user can now |
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299 | enter a beam size as a parameter. |
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300 | |
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301 | * Other minor fixes to the code, to improve its structure and |
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302 | robustness. |
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303 | |
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304 | |
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305 | Duchamp version 1.0 (2006/06/30) |
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306 | -------------------------------- |
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307 | |
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308 | The first full release version. |
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309 | |
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310 | Several major changes compared to previous version: |
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311 | |
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312 | * Incorporated a FitsHeader class, to keep track of header information |
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313 | (including WCS) from the FITS file. All units-related calculations |
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314 | are done with this class, such as conversion to velocity, and |
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315 | pixel-to-WCS conversion. The main advantage of this is improved |
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316 | speed of execution, more adaptable to different units, and improved |
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317 | code (easier for me!). |
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318 | |
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319 | * Able to select the dimensionality of the reconstruction, rather than |
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320 | just doing it in 3-D. |
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321 | |
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322 | * Robust text output, so that the columns are sized correctly given |
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323 | the data being written, and the relevant units (derived from the |
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324 | FITS header) are included in the output table. |
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325 | |
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326 | * Improved the way the reconstructed image is saved and read back in, |
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327 | with a better naming scheme and a better set of new FITS header |
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328 | keywords. The MW headers are now not written. |
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329 | |
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330 | Other, more minor changes include: |
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331 | |
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332 | * MW channels now not set to 0, but just ignored for searching |
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333 | purposes (and for the scaling of the spectral output -- they are |
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334 | plotted though and highlighted with a hashed box). |
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335 | |
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336 | * The scale bar in the moment map in the spectral output file has its |
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337 | length indicated. |
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338 | |
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339 | * Improved VOTable output, with more information about the way Duchamp |
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340 | was run. |
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341 | |
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342 | * Made sure all statistics calculations in the reconstruction are |
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343 | based on robust (ie. median) methods. |
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344 | |
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345 | Also moved to an autoconf based configure/make compilation, for ease of use. |
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346 | |
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347 | |
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348 | Duchamp version 0.9.2 (2006/06/27) |
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349 | -------------------------------- |
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350 | |
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351 | * Added the use of warning flags for detections: for either edge |
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352 | location or negative enclosed flux. |
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353 | |
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354 | * A new command line option added so that the user can specify a FITS |
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355 | file to be searched with the default parameters, rather than giving |
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356 | a full parameter file. |
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357 | |
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358 | * The scale bar on the moment cutout now works in general case, using |
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359 | an iterative process to get to the correct length. |
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360 | |
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361 | * RA axes are now done correctly on the full-scale maps. |
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362 | |
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363 | * Various coding fixes, improving the readability of the code, |
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364 | particularly regarding the declaration of temporary variables. |
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365 | |
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366 | * Changed the way the time of execution is called : now using time.h |
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367 | functions, rather than a system call. |
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368 | |
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369 | * Changed output in Detection/outputDetection.cc for the pixel |
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370 | information of detected objects (the info printed above the spectral |
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371 | plots) -- now print out number of voxels in object, and have |
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372 | improved the formatting a little. |
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373 | |
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374 | * Improved the functionality of saving the FITS file containing the |
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375 | reconstructed array. Added ability to save and read back in the MW |
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376 | parameters when saving a reconstructed cube (if a reconstructed cube |
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377 | has different MW range to that being considered, it would cause |
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378 | problems). ReadRecon now just returns a FAILURE and will reconstruct |
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379 | the cube anew. |
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380 | |
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381 | * Changed default value of flagGrowth to 0. |
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382 | |
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383 | |
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384 | |
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385 | Duchamp version 0.9 (2006/05/05) |
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386 | -------------------------------- |
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387 | |
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388 | First public release version. |
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