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