1 | Duchamp version 1.1.5 (2008/03/20) |
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2 | ---------------------------------- |
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3 | |
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4 | Bug fixes: |
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5 | * A major bug was discovered in the calculation of integrated |
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6 | fluxes. The flux was incorrectly being weighted by the spatial size |
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7 | of the detection, resulting in a (often considerable) overestimation |
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8 | of the integrated flux. This has been corrected. |
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9 | |
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10 | * The beam size calculation was also incorrect, being out by a factor |
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11 | of 1/ln(2). |
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12 | |
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13 | * The "make install" command previously failed to work properly if the |
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14 | library had not been created. This has been fixed so that the |
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15 | installation works even if there is no library file. |
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16 | |
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17 | New Features: |
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18 | * You can now provide a new flux unit string, so that the pixel fluxes |
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19 | will be converted to these new fluxes before any calculations are |
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20 | done. This is done with the newFluxUnits input parameter. The new |
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21 | units should be directly convertible from the old ones (given by the |
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22 | BUNIT header -- e.g. if BUNIT = Jy/beam, you can give newFluxUnits |
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23 | as mJy/beam, but not mJy). |
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24 | |
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25 | * You can now specify the precision used in the output files for flux, |
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26 | velocity and S/N ratio columns, via new input parameters precFlux, |
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27 | precVel and precSNR. These will apply to the VOTable output as well |
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28 | as the text table and information on the spectral plots. |
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29 | |
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30 | * The Karma annotation files previously provided just a circle at the |
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31 | spatial location of the detected object. You now have the option to |
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32 | draw a border around the detected pixels (in a similar manner to the |
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33 | PGPLOT moment maps). Karma does not do this perfectly, so the lines |
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34 | may not line up exactly with the pixel borders, so the option |
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35 | remains to keep using the circles. This is controlled by the |
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36 | parameter "annotationType", with possible options being "borders" |
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37 | (the default) or "circles". |
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38 | |
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39 | * There is a new function getMetadata() that loads the header and WCS |
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40 | data, but no pixel information. This is only of interest if you are |
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41 | doing code development with the Duchamp library -- it does not |
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42 | affect the running of Duchamp itself. |
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43 | |
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44 | Duchamp version 1.1.4 (2008/02/15) |
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45 | ---------------------------------- |
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46 | |
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47 | Most of the changes incorporated in this update result from ASKAP code |
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48 | development (that makes use of some of the Duchamp functionality), |
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49 | but do not actually affect the way Duchamp runs (other than, in a |
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50 | couple of cases, making it a bit faster). Changes that are |
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51 | relevant for regular users of Duchamp are as follows: |
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52 | |
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53 | * A new option has been made available (thanks to Mary Putman et al |
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54 | for the suggestion!) to save the spectra of all detected objects in |
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55 | a text file. This has the form of one column for the spectral |
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56 | coordinates and one column of fluxes for each object. This is |
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57 | enabled by the input parameters flagTextSpectra and spectraTextFile. |
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58 | |
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59 | * Slight changes to the output include he formatting of the way the |
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60 | detected objects are written to the log file. This meant the |
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61 | verification files were also updated. Also the cube statistics are |
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62 | not printed to the results file if a user threshold is specified (as |
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63 | they are not calculated!). |
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64 | |
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65 | * The determination of beam size has been made more reliable, as has |
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66 | the BUNIT determination. |
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67 | |
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68 | * Fixed a bug that meant source merging was not done for 2D images |
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69 | (not usually a problem, as the source-finding takes care of this, |
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70 | but came up in parallelisation development). |
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71 | |
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72 | Duchamp version 1.1.3 (2008/01/08) |
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73 | ---------------------------------- |
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74 | |
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75 | A minor update that just improves the build process. The location of |
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76 | the wcslib include files was not specified correctly, so that some |
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77 | machines were unable to find them. The configure script has been fixed |
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78 | so that the compilation should work in all cases. |
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79 | |
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80 | Some minor changes have also been made to the code in the PixelMap |
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81 | directory, and to param.cc, to fix warnings or errors that may appear |
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82 | in compilation. |
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83 | |
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84 | However, there are no changes to the actual workings of the code in |
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85 | this minor version, so if you have a working version of Duchamp 1.1.2 |
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86 | there is probably no reason to update. |
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87 | |
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88 | Duchamp version 1.1.2 (2007/12/07) |
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89 | ---------------------------------- |
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90 | |
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91 | Compilation: |
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92 | |
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93 | * The compilation had problems working correctly when the cfitsio and |
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94 | wcs libraries were not in standard locations. The configure script |
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95 | has been tweaked to make sure the libraries are found. |
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96 | |
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97 | * Problems with compiling in the absence of pgplot have been fixed, |
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98 | and it should now compile fine. |
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99 | |
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100 | * Improved the configure script for use with Mac OS X and gfortran. |
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101 | |
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102 | |
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103 | Bugfixing: |
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104 | |
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105 | * A major problem with the text-based output was fixed. The widths of |
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106 | the columns were not being calculated correctly, and were running |
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107 | together. This should no longer be the case. |
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108 | |
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109 | * There was a bug in the way Duchamp interpreted spectral axes, |
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110 | particularly AIPS types such as FELO-HEL, leading to incorrect |
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111 | scaling of the velocity axis. This has been fixed, so that |
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112 | non-standard types are now dealt with appropriately and the velocity |
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113 | scaling should be accurate. |
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114 | |
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115 | * Another bug meant the beam correction was always applied to the |
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116 | integrated spectra, regardless of whether the flux units involved |
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117 | the beam (e.g. Jy/beam). This has been fixed. Note that the values |
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118 | of the integrated flux presented in the results table were always |
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119 | calculated correctly. |
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120 | |
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121 | * Other minor changes to improve the speed and efficiency, especially |
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122 | of the merging code. |
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123 | |
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124 | New user parameters: |
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125 | |
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126 | * There is now the possibility to save a FITS file that contains a |
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127 | mask array, indicating where the detected objects are. This is |
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128 | governed by the flagOutputMask parameter. |
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129 | |
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130 | * The header information that is printed at the start of the results |
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131 | file -- that is, the list of parameters, the statistics of the cube, |
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132 | and the number of detections -- can now be written to a separate |
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133 | file. Set the flagSeparateHeader parameter to true or 1 and it will |
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134 | go to the file indicated by the headerFile parameter (the default is |
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135 | duchamp-Results.hdr). |
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136 | |
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137 | * A "scaleMax" parameter has been added, so that the wavelet |
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138 | reconstruction can include only a specified range of scales (for |
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139 | instance, if one wants to search just for narrow features such as |
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140 | absorption lines). |
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141 | |
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142 | * A "flagRobustStats" parameter has been added. This allows the user |
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143 | to elect to use robust statistics (median and median absolute |
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144 | deviation from the median) to estimate the noise parameters. If set |
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145 | to false, the mean and standard deviation will be used. The default |
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146 | value is true. |
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147 | |
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148 | New Feature: |
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149 | |
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150 | * When Duchamp is run on a 2D image (i.e. with no spectral output), it |
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151 | now produces a postscript file that shows information each |
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152 | individual source plus the image cutout of the source. This is |
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153 | similar to the spectral output file, but without the spectra. The |
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154 | filename is given by the spectraFile parameter. |
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155 | |
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156 | * Ability to save a FITS file containing a mask array, with pixel |
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157 | values of 1 for pixels in a detected object, and 0 elsewhere. |
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158 | |
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159 | |
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160 | Duchamp version 1.1.1 (2007/07/20) |
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161 | ------------------------------------ |
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162 | |
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163 | Minor update to the release, with just a few changes: |
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164 | |
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165 | * The verification script was generating diffs due to differences in |
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166 | the precision of some calculations when done on different machines. |
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167 | One of these was the integrated flux, and this has been corrected so |
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168 | that the same value should appear on all machines. |
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169 | The verification script has also changed so that just the number of |
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170 | sources and their positions are tested, as well as the |
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171 | logfiles. This should avoid the reporting of spurious differences. |
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172 | |
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173 | * The grey-scale used in the image cutouts (in the spectral plots) has |
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174 | been inverted. This makes it consistent with the scale used in the |
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175 | maps, and hopefully easier to see when printing. |
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176 | |
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177 | * The configure/make system has been altered to make it easier to |
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178 | install, and to specify different external libraries. In particular, |
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179 | it is now not necessary to have PGPLOT installed on your system to |
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180 | run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, |
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181 | just without any graphical output. Some source code needed to be |
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182 | restructured to make this work. Please read the README file, or the |
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183 | Installation appendix in the User's Guide, for complete details. |
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184 | |
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185 | * The time of completion is now written to the log file, so that the |
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186 | user can have some idea of how long the program took. |
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187 | |
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188 | |
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189 | Duchamp version 1.1 (2007/05/17) |
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190 | ------------------------------------ |
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191 | |
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192 | Changes made since the last numbered release: |
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193 | |
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194 | EFFICIENCY OF EXECUTION: |
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195 | |
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196 | * Major change to the way detections are stored. They are now recorded |
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197 | via run-length encoding in the x-y plane, and stored as collections |
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198 | of channel-maps. This improves the memory usage and the speed of |
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199 | execution (particularly for routines such as the merging |
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200 | routines). The memory usage has also been improved by changing the |
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201 | way the list of detected objects is stored. |
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202 | |
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203 | SMOOTHING: |
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204 | |
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205 | * Addition of ability to spatially smooth the cube before |
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206 | searching. This is done with a Gaussian kernel, the size and shape |
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207 | of which can be specified by the user, using the parameters kernMaj |
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208 | & kernMin (which are the FWHM for the major & minor axes -- if |
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209 | kernMin is not given it is assumed to match kernMaj) and kernPA (the |
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210 | position angle of the major axis). There is a new parameter |
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211 | smoothType that distinguishes this method from the spectral (Hanning) |
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212 | smoothing already in use. |
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213 | |
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214 | DETECTIONS: |
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215 | |
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216 | * Changed the way detection is done -- now only search in 2D images, |
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217 | keeping all detections (ie. no minimum-pixel requirement). This |
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218 | should be the same as doing both the 1D and 2D searches with the |
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219 | minimum pixel requirement in, but simpler. The rejection is done at |
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220 | the end after all the merging and growing has been done. This leads |
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221 | to a larger number of intermediate detections (ie. the number |
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222 | before merging), which may increase the run-time slightly, although |
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223 | this is offset by the changes to the efficiency (see above). |
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224 | |
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225 | * Increased the range over which objects can be grown to match the |
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226 | threshSpatial & threshVelocity parameters, as well as rejecting new |
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227 | pixels based on the BLANK and MW tests. |
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228 | |
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229 | INPUTS: |
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230 | |
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231 | * There has been a subtle change in the way BLANK pixels are dealt |
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232 | with. To enable trimming of BLANK pixels, users should use the new |
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233 | parameter flagTrim. The parameters flagBlankPix and blankPixVal are |
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234 | no longer accessible via the parameter file -- warning messages are |
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235 | given if they are provided in the parameter file. |
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236 | |
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237 | * Added ability to specify a statsec, so that the statistics are only |
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238 | calculated from a given subsection of the cube, rather than the full |
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239 | cube. |
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240 | |
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241 | * The subsections can also specify the ability to remove a border of n |
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242 | pixels from the edges of an axis (ie. n from the start and from the |
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243 | end) -- as requested in Trac ticket #5. |
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244 | |
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245 | * Changed the default value of the reconDim parameter from 3 to 1, and |
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246 | the default value of the flagATrous parameter to false. |
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247 | |
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248 | OUTPUTS: |
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249 | |
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250 | * The output now includes three different estimates of the "centre" of |
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251 | the detection: peak location, centroid (flux-weighted), or average. |
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252 | |
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253 | * Some slight improvements to the user feedback during execution. |
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254 | |
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255 | * Spectral output now includes the baseline, if one was fitted. The |
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256 | format of the plot headers is slightly changed, to stop information |
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257 | falling off the edge of the page. |
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258 | |
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259 | * Added command-line option -x to directly disable the PGPLOT X-window |
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260 | map plotting. This overrides the setting of flagXOutput in the |
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261 | parameter file. |
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262 | |
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263 | * Fallback spectral units (in case the FITS header fails to record |
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264 | them) changed to SPC, but code has been fixed so that any problem |
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265 | should be caught before this becomes an issue. |
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266 | |
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267 | BUGFIXES: |
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268 | |
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269 | * Fixed bug (Trac ticket #4) that meant the velocity units were not |
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270 | correctly dealt with. Duchamp should be more robust for different |
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271 | velocity axis setups now. |
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272 | |
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273 | * Fixed bug (ticket #9) with the VOTable output, where the tags were |
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274 | not closing. |
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275 | |
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276 | * Fixed a bug that meant the integrated fluxes were not calculated |
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277 | properly -- no allowance was made for the number of spatial |
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278 | pixels. This should also work properly for 2D images now as well. |
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279 | |
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280 | * Fixed minor bug in calculating the flux threshold from the p-value |
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281 | threshold when the FDR method is used. This did not affect the |
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282 | actual thresholding, merely the quoted flux threshold in the results |
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283 | file. Also, the MW channels are kept out of the p-value threshold |
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284 | determination if they are being flagged. |
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285 | |
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286 | |
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287 | |
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288 | Duchamp version 1.0.7 (2006/11/22) |
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289 | ---------------------------------- |
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290 | |
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291 | One new feature, and some improvements and bug-fixes. |
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292 | |
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293 | * The user can now elect to Hanning-smooth the spectral direction of |
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294 | the cube before the searching is done. This can be done instead of the |
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295 | wavelet reconstruction (although if both are selected, the |
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296 | reconstruction takes precendence). This functionality is switched on |
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297 | and off by the flagSmooth parameter, and the width of the Hanning |
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298 | kernel is governed by the hanningWidth parameter. |
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299 | |
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300 | * The smoothed array can also be written to a FITS file and read in at |
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301 | the start in the same manner as the reconstructed array. |
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302 | |
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303 | * Several improvements have been made to the memory |
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304 | management. Several memory leaks were fixed, and the memory usage of |
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305 | Duchamp is considerably less, which will be a help for running it on |
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306 | large cubes. The speed of some routines has also been improved, by |
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307 | removing unnecessarily repetitive loops. |
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308 | |
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309 | * The sorting routines have been changed, and should now be slightly quicker |
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310 | (and a bit more robust). |
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311 | |
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312 | * Enabled the scale bar (plotted on the 0th moment map in the spectral |
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313 | output file) to be able to deal with much finer spatial scales (as |
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314 | may be expected from VLBI data). |
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315 | |
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316 | * Other minor changes to code and presentation. |
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317 | |
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318 | |
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319 | Duchamp version 1.0.6 (2006/11/01) |
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320 | ---------------------------------- |
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321 | |
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322 | Some incremental improvements and changes to the code: |
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323 | |
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324 | * The statistics used for the detection are now calculated once for |
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325 | the entire cube, rather than being calculated separately for each |
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326 | channel map and spectrum. This results in a uniform threshold value |
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327 | across the entire cube. The way the statistics calculations are |
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328 | implemented in the code was changed, using a new statistics class. |
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329 | |
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330 | * This means we can report a peak signal-to-noise value for each |
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331 | detection. This is given in the text-based output, as well as in the |
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332 | summary information above the spectral output for each source. |
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333 | |
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334 | * The user can now elect not to have the moment map displayed in a |
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335 | PGPlot window, through the use of the new flagXOutput |
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336 | parameter. This should help in cases of running Duchamp on a dumb |
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337 | terminal (with no X-display capabilities), or as part of a batch |
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338 | script where the continual popping-up of the PGPlot window might |
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339 | become annoying. |
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340 | |
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341 | * There are different Flags reported for the case of an object lying on |
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342 | the spatial edge and spectral edge of the cube (E and S respectively). |
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343 | |
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344 | * A few minor bug fixes: |
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345 | - When providing a subsection, any axes with the range given by * |
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346 | had the pixel values offset incorrectly. This has been fixed. |
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347 | - Negative searches now correctly invert the reconstructed array |
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348 | when it is read in from a file. |
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349 | |
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350 | * Other minor changes to the code, to improve memory handling and |
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351 | remove redundant arrays and variables. |
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352 | |
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353 | |
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354 | Duchamp version 1.0.5 (2006/09/06) |
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355 | ---------------------------------- |
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356 | |
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357 | Since version 1.0, there have been a range of mostly minor |
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358 | changes. These are generally bug-fixes, thanks to feedback from a |
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359 | number of users, as well as a few extra features. |
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360 | |
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361 | Here is a summary of the changes since version 1.0: |
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362 | |
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363 | USER INTERFACE: |
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364 | |
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365 | * The user is now able to enter the value of flag parameters in the |
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366 | parameter file as strings, as well as integers (so one can enter |
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367 | true or 1 to give the same result). |
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368 | |
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369 | GRAPHICAL OUTPUT: |
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370 | |
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371 | * Added a new function that draws the edge of the blank region on the |
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372 | maps and image cutouts. There is a new flag parameter -- |
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373 | drawBlankEdges -- that controls the use of this function (the |
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374 | default is true). |
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375 | Also, the edge of the field is plotted on the image cutouts as a |
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376 | yellow line. This distinguishes it from the purple blank pixel |
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377 | dividing line. |
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378 | |
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379 | * The size of the tick mark in the image cutout (indicating the |
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380 | spatial scale of the image) is now adaptable, so that it shows the |
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381 | scale that best fits the image (ranging from 1 arcsec to 15 |
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382 | degrees). (This is a change from the previous standard length of 15 |
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383 | arcmin.) |
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384 | |
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385 | * The zoomed spectrum had its flux scale determined by all points in |
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386 | the zoom box,including those flagged by the Milky Way (MW) |
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387 | range. This has been fixed so that any MW channels will not affect |
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388 | the flux scaling, potentially improving the appearance of objects |
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389 | detected close in velocity to strong MW emission or absorption. |
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390 | |
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391 | * Improved Karma Annotation file output, so that files without good |
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392 | WCS are dealt with appropriately. |
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393 | |
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394 | TEXT-BASED OUTPUT: |
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395 | |
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396 | * The position resolution in the IAU-format names has been increased, |
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397 | so that distinct objects close to one another are more readily |
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398 | distinguished. Overlapping sources at different velocities may |
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399 | still have the same name, but this is a more general problem. |
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400 | |
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401 | * The presentation of the results in tabular format has been improved, |
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402 | so that the precision of faint sources is sufficient to show their |
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403 | flux, for instance, is not 0. This also applies to the information |
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404 | presented above the spectral plots. |
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405 | |
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406 | * Improved error and warning reporting, so that the formatting and |
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407 | presentation of information is clearer. |
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408 | |
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409 | FITS I/O RELATED: |
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410 | |
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411 | * The previous version was did not deal well with 4 (or greater) |
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412 | dimensions in the FITS file -- the memory allocation was badly done, |
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413 | and the axes needed to be in a particular order. This has been |
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414 | fixed, so that the FITS I/O routines can now handle any sized FITS |
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415 | file, with axes in any order (as long as there are two spatial and one |
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416 | spectral axes). |
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417 | |
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418 | * When the FITS file does not have a rest frequency defined, there is |
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419 | no way to transform the frequency axis into velocity. In this case, |
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420 | the spectral axis is left as frequency, and put into units of MHz. |
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421 | |
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422 | * If the beam size is not indicated by the FITS header (through the |
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423 | BMAJ and BMIN keywords), the user can manually specify the size |
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424 | through the parameter file (using parameter beamSize). |
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425 | |
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426 | * The FITS I/O routines make use of the command fits_file_exists. This |
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427 | was introduced into the CFITSIO package from version 2.5, so Duchamp |
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428 | will only work with this version or higher. Version 3+ is preferred. |
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429 | |
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430 | OTHER BUG-FIXING: |
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431 | |
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432 | * Several bugs related to the blank-pixels were dealt with. |
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433 | The correct values were not propagating through correctly, meaning |
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434 | that the default values were being used. Also, there was the |
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435 | potential for blank pixels to be detected when the FDR method was |
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436 | used. Finally, the image cutout displays occasionally did not |
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437 | obscure the blank pixels. All these problems should be fixed now. |
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438 | |
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439 | * The FDR setup routine was occasionally failing with a segmentation |
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440 | fault, due to it accessing unallocated memory. This has been fixed. |
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441 | |
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442 | * Fixed bugs that affected the way 2D images (rather than 3D cubes) |
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443 | were dealt with. The minChannels test failed when minChannels=0. |
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444 | |
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445 | * If there is no beam information in the FITS header, the user can now |
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446 | enter a beam size as a parameter. |
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447 | |
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448 | * Other minor fixes to the code, to improve its structure and |
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449 | robustness. |
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450 | |
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451 | |
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452 | Duchamp version 1.0 (2006/06/30) |
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453 | -------------------------------- |
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454 | |
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455 | The first full release version. |
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456 | |
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457 | Several major changes compared to previous version: |
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458 | |
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459 | * Incorporated a FitsHeader class, to keep track of header information |
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460 | (including WCS) from the FITS file. All units-related calculations |
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461 | are done with this class, such as conversion to velocity, and |
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462 | pixel-to-WCS conversion. The main advantage of this is improved |
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463 | speed of execution, more adaptable to different units, and improved |
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464 | code (easier for me!). |
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465 | |
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466 | * Able to select the dimensionality of the reconstruction, rather than |
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467 | just doing it in 3-D. |
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468 | |
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469 | * Robust text output, so that the columns are sized correctly given |
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470 | the data being written, and the relevant units (derived from the |
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471 | FITS header) are included in the output table. |
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472 | |
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473 | * Improved the way the reconstructed image is saved and read back in, |
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474 | with a better naming scheme and a better set of new FITS header |
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475 | keywords. The MW headers are now not written. |
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476 | |
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477 | Other, more minor changes include: |
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478 | |
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479 | * MW channels now not set to 0, but just ignored for searching |
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480 | purposes (and for the scaling of the spectral output -- they are |
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481 | plotted though and highlighted with a hashed box). |
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482 | |
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483 | * The scale bar in the moment map in the spectral output file has its |
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484 | length indicated. |
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485 | |
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486 | * Improved VOTable output, with more information about the way Duchamp |
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487 | was run. |
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488 | |
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489 | * Made sure all statistics calculations in the reconstruction are |
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490 | based on robust (ie. median) methods. |
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491 | |
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492 | Also moved to an autoconf based configure/make compilation, for ease of use. |
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493 | |
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494 | |
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495 | Duchamp version 0.9.2 (2006/06/27) |
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496 | -------------------------------- |
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497 | |
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498 | * Added the use of warning flags for detections: for either edge |
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499 | location or negative enclosed flux. |
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500 | |
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501 | * A new command line option added so that the user can specify a FITS |
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502 | file to be searched with the default parameters, rather than giving |
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503 | a full parameter file. |
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504 | |
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505 | * The scale bar on the moment cutout now works in general case, using |
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506 | an iterative process to get to the correct length. |
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507 | |
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508 | * RA axes are now done correctly on the full-scale maps. |
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509 | |
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510 | * Various coding fixes, improving the readability of the code, |
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511 | particularly regarding the declaration of temporary variables. |
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512 | |
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513 | * Changed the way the time of execution is called : now using time.h |
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514 | functions, rather than a system call. |
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515 | |
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516 | * Changed output in Detection/outputDetection.cc for the pixel |
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517 | information of detected objects (the info printed above the spectral |
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518 | plots) -- now print out number of voxels in object, and have |
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519 | improved the formatting a little. |
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520 | |
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521 | * Improved the functionality of saving the FITS file containing the |
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522 | reconstructed array. Added ability to save and read back in the MW |
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523 | parameters when saving a reconstructed cube (if a reconstructed cube |
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524 | has different MW range to that being considered, it would cause |
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525 | problems). ReadRecon now just returns a FAILURE and will reconstruct |
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526 | the cube anew. |
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527 | |
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528 | * Changed default value of flagGrowth to 0. |
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529 | |
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530 | |
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531 | |
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532 | Duchamp version 0.9 (2006/05/05) |
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533 | -------------------------------- |
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534 | |
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535 | First public release version. |
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