[799] | 1 | Duchamp version 1.1.11 (2011/02/18) |
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| 2 | ------------------------------------- |
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| 3 | |
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| 4 | Improvements: |
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| 5 | |
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| 6 | * The largest changes in this release involved improving the |
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| 7 | efficiency of the code, resulting in further speed-ups. The code |
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| 8 | affected was the low-level object-handling code, with the merging |
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| 9 | stages in particular showing good speed-ups. |
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| 10 | |
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| 11 | * The default value for the beam size, when the beam parameters are |
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| 12 | not in the FITS header, has been dropped. Now the default behaviour |
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| 13 | is to simply not make any beam corrections if the beam is not |
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| 14 | specified by either the FITS file or the input parameters. Thanks to |
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| 15 | Tobias Westemeier for the suggestion. |
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| 16 | |
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| 17 | * The reporting of the beam size has changed slightly to provide a bit |
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| 18 | more information. |
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| 19 | |
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| 20 | Bug Fixes: |
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| 21 | |
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| 22 | * There was a problem with using a MW range and subsectioning when |
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| 23 | growing objects, as a result of changes in 1.1.10. This has been |
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| 24 | fixed. |
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| 25 | |
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| 26 | * Inversion was failing when no array was allocated (not a problem for |
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| 27 | standard Duchamp, but affected its use as a library by other code). |
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| 28 | |
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[760] | 29 | Duchamp version 1.1.10 (2010/11/15) |
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[574] | 30 | ------------------------------------- |
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[542] | 31 | |
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[760] | 32 | Improvements: |
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| 33 | |
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| 34 | * The major change for this release is a greatly improved growing |
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| 35 | algorithm. The previous incarnation was very inefficient (testing |
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| 36 | all pixels in an object, most of which only have neighbours that are |
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| 37 | already in the object), and could take an unnecessarily large amount |
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| 38 | of time in the case of extended sources. The improved algorithm |
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| 39 | makes use of voxel flags to quickly identify those voxels not yet in |
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| 40 | an object and only examines them. For a certain test case |
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| 41 | (observations of extended Galactic HI), the time required reduced |
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[761] | 42 | from about a day to about a minute! (Note that compact sources, such |
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| 43 | as HI galaxies, will not show this degree of speedup...) Many thanks |
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| 44 | to Tara Murphy for pointing out this bug and her help in |
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| 45 | diagnosing/fixing the problem. |
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[760] | 46 | |
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| 47 | * There have been a number of further improvements to the code to |
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| 48 | speed it up, based on some profiling. The most important was the |
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| 49 | function to add pixels to a 2D object, but there were several other |
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| 50 | minor changes as well. |
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| 51 | |
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| 52 | * The minimum size of the detections can now also be specified in |
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| 53 | terms of the total number of voxels (in addition or instead of |
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| 54 | specifying the minimum spatial pixels or channels). |
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| 55 | |
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| 56 | * The way memory is allocated when reading the image has been |
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| 57 | streamlined. The amount of memory being allocated is also now |
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| 58 | reported - this is in an effort to allow users to identify problems |
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| 59 | with running out of memory. |
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| 60 | |
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| 61 | * The version number is now reported in the results and log files. |
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| 62 | |
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| 63 | * Only the filename of the input image (ie. not the leading |
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| 64 | directories) is now shown on the detection and moment-0 maps. This |
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| 65 | is to avoid problems with large directory paths being too wide for |
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| 66 | the plot. |
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| 67 | |
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| 68 | * The verification script was improved for readability (although no |
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| 69 | functional change was made). |
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| 70 | |
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| 71 | Bug fixes: |
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| 72 | |
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| 73 | * Growing was not being done when a single source was found. Now |
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| 74 | fixed. |
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| 75 | |
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| 76 | * For particular WCS setups, the RA can be interpreted as being |
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| 77 | negative, which corrupted the Source ID (ie. the IAU-format |
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| 78 | string). This has been fixed. |
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| 79 | |
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| 80 | * When the flux units were changed, problems had been seen when |
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| 81 | writing a reconstructed cube to a FITS file. Any unit change is now |
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| 82 | undone prior to writing and there should now be no problem. |
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| 83 | |
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| 84 | * Filenames with spaces in them were not handled well. New functions |
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| 85 | were included and moved to a more obvious location. These filenames |
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| 86 | now work as expected. |
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| 87 | |
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| 88 | * Spectral axes of type FREQ that had a rest frequency were not being |
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| 89 | put into velocity units. Now fixed. |
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| 90 | |
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| 91 | * Improvements to the output to screen, making sure everything is |
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| 92 | covered by the verbose flag. |
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| 93 | |
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| 94 | * Better management of the allocation of arrays. |
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| 95 | |
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| 96 | * The minSize parameter in Image was never initialised, leading to |
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| 97 | unpredictable behaviour. Now fixed. |
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| 98 | |
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| 99 | Code development notes: |
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| 100 | |
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| 101 | * New functionality includes: a function to return a vector list of |
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| 102 | voxels in an Object3D or Detection; a new generic Search function |
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| 103 | (basically a front-end to each of the individual functions); more |
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[766] | 104 | complete copy constructors for the DataArray classes; new methods |
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| 105 | for finding the velocity widths. |
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[760] | 106 | |
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| 107 | Duchamp version 1.1.9 (2010/03/26) |
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| 108 | ------------------------------------- |
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| 109 | |
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[654] | 110 | Improvements: |
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[616] | 111 | |
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[680] | 112 | * There is now the ability to save the moment-0 map as a FITS |
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| 113 | file. This is controlled by the parameters flagOutputMomentMap and |
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| 114 | fileOutputMomentMap, which work in the same way for the mask file. |
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| 115 | |
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[697] | 116 | * There is a new parameter flagRejectBeforeMerge that, when true, |
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[680] | 117 | rejects sources according to the minPix/minChannels requirements |
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| 118 | before the merging and growing is done. This defaults to false (so |
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| 119 | default behaviour is as before). Thanks to Tobias Westmeier for |
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| 120 | suggesting this and the above improvement. |
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| 121 | |
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[697] | 122 | * There is also a new parameter flagTwoStageMerging. When true (the |
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| 123 | default), newly-detected objects are merged with the first close |
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| 124 | object in the list. When false, they are simply added to the end of |
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| 125 | the list. In both cases, a second round of merging is done to pick |
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| 126 | up all close matches. |
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| 127 | |
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[680] | 128 | * The way the beam is specified in the absence of the BMAJ/BMIN/BPA |
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| 129 | parameters has been slightly changed. The use of "beamSize" was |
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| 130 | somewhat ambiguous (it meant the number of pixels covered by the |
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| 131 | beam, not the FWHM), so new parameters have been introduced. The |
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| 132 | beam can be specified by beamArea (which replaces beamSize), or |
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| 133 | beamFWHM (the FWHM of the beam in pixels). If beamFWHM is provided, |
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| 134 | it will be used, else the beamArea will be. |
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| 135 | |
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[687] | 136 | * There is a new parameter searchType that allows the user to choose |
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| 137 | how the searching is done. The behaviour up till now has been to |
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| 138 | search the 2D channel maps one at a time to build up the 3D |
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| 139 | detections. This is the default, and can be obtained by setting |
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| 140 | searchType=spatial. Alternatively, you can set searchType=spectral |
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| 141 | to do the searching in the 1D spectra. |
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| 142 | |
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[654] | 143 | * Profiling of the code has led to a few changes that have sped up |
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| 144 | some calculations, particularly those involving the median. Rather |
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| 145 | than using std::sort, the code now simply uses std::nth_element, |
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| 146 | which shows a substantial speedup factor. |
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| 147 | |
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| 148 | * When using the objectList parameter, the maps will now only show the |
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| 149 | selected objects, rather than all detected objects. |
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| 150 | |
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| 151 | * There is a new verification test that looks at the "growing" |
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| 152 | functionality. |
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| 153 | |
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| 154 | Bug fixes: |
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| 155 | |
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[670] | 156 | * When saving a mask FITS file, there was an occasional memory leak |
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| 157 | that caused Duchamp to crash (only when the cube was suitably |
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| 158 | large). This has been fixed. |
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| 159 | |
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[680] | 160 | * The median calculation had a bug that led to an incorrect value |
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| 161 | being reported. The difference will not be great (the element of an |
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| 162 | array being reported as the median was out by one), but could be |
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| 163 | noticeable depending on the dataset. |
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| 164 | |
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| 165 | * The MW range parameters did not respond to the use of a |
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| 166 | subsection. They should refer to channel ranges in the original |
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| 167 | cube, and changes have been made to the code to reflect this. |
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| 168 | |
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[654] | 169 | * There was an occasional error in writing out FITS keywords, due to |
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| 170 | the way comment strings were intialised. This has been improved and |
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| 171 | made more robust. |
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| 172 | |
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| 173 | * Testing with gcc-4.3.2 showed a number of compilation warnings & |
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| 174 | errors, which have been fixed. |
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| 175 | |
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| 176 | * The Gaussian smoothing kernel was too small - it is now made big |
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| 177 | enough to encompass all possible values. It was also being |
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| 178 | incorrectly scaled. This had no functional effect on the detection |
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| 179 | of objects, but for other uses was incorrect. This has been |
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| 180 | rectified. |
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| 181 | |
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| 182 | * Some outputs that weren't caught by the verbose flag now are. |
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| 183 | |
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| 184 | |
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| 185 | Code development notes: |
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| 186 | |
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| 187 | The following notes only apply if you want to use the code as a |
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| 188 | library, rather than the stand-alone package. These have generally |
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| 189 | come out of the ASKAP software development. If you just use the |
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| 190 | stand-alone package, they won't be a concern. |
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| 191 | |
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[616] | 192 | * The API for storing detected objects has changed, making it more |
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[654] | 193 | robust from a programming point of view. |
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[616] | 194 | |
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[654] | 195 | * Additional versions of some functions (and the Gaussian smoothing |
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| 196 | class) have been added - this has come out of the ASKAP development |
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| 197 | work. |
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| 198 | |
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| 199 | * A number of instances of "unsigned int" being used for loops have |
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| 200 | been changed to iterators or "size_t". There shouldn't be any |
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| 201 | functional change from this -- the code should just build more |
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| 202 | cleanly. |
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| 203 | |
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[687] | 204 | * The Detection class now records whether the parameters have been |
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| 205 | set, and unsets that flag when objects are merged. This allows |
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| 206 | external programs to track which objects have been merged and deal |
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| 207 | with them appropriately. |
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[654] | 208 | |
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[687] | 209 | |
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[616] | 210 | Duchamp version 1.1.8 (2009/07/20) |
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| 211 | ---------------------------------- |
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| 212 | |
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[542] | 213 | Improvements: |
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| 214 | |
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[572] | 215 | * The final source list can now be sorted on one of a range of object |
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| 216 | parameters: x-value, y-value, z-value, ra, dec, vel, w50, iflux, |
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| 217 | pflux (integrated and peak flux respectively), or snr. Simply use |
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| 218 | the new input parameter sortingParam. Its default value is vel, so |
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| 219 | the default behaviour stays the same. |
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| 220 | |
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[543] | 221 | * The FDR method involves calculating how many pixels are |
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| 222 | correlated. This previously involved multiplying the beam area by 2, |
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| 223 | implying that 2 neighbouring channels were correlated. This factor |
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| 224 | is now a user-selectable parameter, so that if you know how many |
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| 225 | spectral channels should be correlated, you can set the parameter |
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| 226 | FDRnumCorChan and the FDR calculation will be done correctly. |
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| 227 | |
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[542] | 228 | * Screen output now has more information on the growing threshold when |
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| 229 | the cube statistics are printed. |
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| 230 | |
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| 231 | |
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| 232 | Bug fixes: |
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| 233 | |
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[584] | 234 | * When reading in previous detections, there was a bug causing a |
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| 235 | segmentation fault. This has been fixed and made more robust. |
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| 236 | |
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[579] | 237 | * There was an apparent bug when writing out the reconstructed cubes |
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| 238 | to a FITS file that caused the new file to be very large. Changing |
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| 239 | the cfitsio function used has fixed this. |
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| 240 | |
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[574] | 241 | * Using NCP projections near the equator could result in a large |
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| 242 | stream of error messages, due to coordinate transformations being |
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| 243 | done in blank regions outside of the acceptable range of world |
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| 244 | coordinates. This has been fixed. |
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| 245 | |
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[542] | 246 | * The function that grows objects had a major bug, that stopped it |
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| 247 | working when flagAdjacent=false. This has been fixed and should work |
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| 248 | fine. |
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| 249 | |
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[616] | 250 | * The input parameter spectraTextFile was not being read |
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| 251 | properly. This has been remedied. |
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| 252 | |
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| 253 | * The units for the integrated flux were wrong for some types of pixel |
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| 254 | flux units. This has been fixed. |
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| 255 | |
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| 256 | * A minor bug caused incorrect calculation of the 20% widths. |
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| 257 | |
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[542] | 258 | * All calls to uint were changed to unsigned int, as some compilers |
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| 259 | had problems recognising that they were the same thing. |
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| 260 | |
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| 261 | * src/fitsHeader.cc was missing an include statement for stdlib.h, |
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| 262 | again causing some compilers to fail. |
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| 263 | |
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| 264 | |
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[529] | 265 | Duchamp version 1.1.7 (2009/01/16) |
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[520] | 266 | ---------------------------------- |
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| 267 | |
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| 268 | Improvements: |
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| 269 | |
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[522] | 270 | * The mask file that can be created with flagMask can now specify |
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| 271 | which object a given detected pixel belongs to, by taking the object |
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| 272 | ID as its value. This applies if you set flagMaskWithObjectNum=true |
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| 273 | (it defaults to false, which means each detected pixel has the value |
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| 274 | 1). Non-detected pixels still have the value 0. |
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[520] | 275 | |
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[535] | 276 | * The names of the output FITS files are now able to be specified |
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| 277 | directly by input parameters. These will override the default names |
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| 278 | that Duchamp provides. |
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| 279 | |
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[520] | 280 | * The Karma annotation file now specifies a font - previously it did |
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| 281 | not and so was at the mercy of whatever was specified in other |
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| 282 | annotation files being viewed at the same time. Please let me know |
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| 283 | if the font I've chosen (lucidasans-12) is not suitable. |
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| 284 | |
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| 285 | * The default flag, used in the absence of 'E', 'S' or 'N', is now '-' |
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| 286 | rather than blank. This will ensure that each column in the results |
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| 287 | file has something in it. |
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| 288 | |
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[522] | 289 | * The configure script is somewhat more robust to non-standard |
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| 290 | systems, particularly when the X11 libraries are in unusual |
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| 291 | places. It can also deal with the slightly different way that |
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| 292 | wcslib-4.3 installs itself. |
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| 293 | |
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[520] | 294 | * The installation part of the Makefile was altered so that the |
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| 295 | symbolic link Duchamp that points to Duchamp-1.1.7 does not have the |
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| 296 | absolute path encoded in it. This will enable the files to be moved |
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| 297 | around at a later date. |
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| 298 | |
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| 299 | Bug Fixes: |
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| 300 | |
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| 301 | * Fixed a bug that caused problems when the flux units were less than |
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| 302 | 5 characters long (e.g. 'K') |
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| 303 | |
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| 304 | * The new velocity width values were not getting proper headers in the |
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| 305 | VOTable output. This has been remedied. |
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| 306 | |
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| 307 | * Minor improvements to help non-pgplot use |
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| 308 | |
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| 309 | * Minor fix in WCS functionality. |
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| 310 | |
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| 311 | * Minor fixes to the FitsHeader class. |
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| 312 | |
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| 313 | * Improved FITS data reading, that doesn't require a nullarray |
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| 314 | array. This will reduce memory usage. |
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| 315 | |
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| 316 | * Improved subsection parsing, particularly for non-standard WCS |
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| 317 | systems. |
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| 318 | |
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| 319 | * Improving the memory allocation of the Cube class. |
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| 320 | |
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| 321 | * Fixed a bug that meant the growthThreshold values were sometimes |
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| 322 | being lost. |
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| 323 | |
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| 324 | * Improving the way the growing and merging is done, particularly in |
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| 325 | the case of non-adjacent merging. |
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| 326 | |
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[529] | 327 | * Fixed a scaling bug in the GaussSmooth function. |
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| 328 | |
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[520] | 329 | Other: |
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| 330 | |
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| 331 | * Numerous changes to the code that do not affect how Duchamp itself |
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| 332 | runs, but were necessary for code development with the Duchamp |
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| 333 | libraries (primarily as a part of the ASKAP code development). |
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| 334 | |
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[522] | 335 | |
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[482] | 336 | Duchamp version 1.1.6 (2008/09/08) |
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[480] | 337 | ---------------------------------- |
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| 338 | |
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| 339 | New features: |
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| 340 | |
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| 341 | * The velocity widths can now be quoted in two additional ways: the |
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| 342 | full width at 50% of the peak flux (ie. the FWHM) and the full width |
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| 343 | at 20% of the peak flux (w_50 and w_20 respectively). The w_50 |
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| 344 | parameter is now quoted in the results printed to the screen |
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| 345 | (instead of w_VEL), but all three are written to the results file. |
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| 346 | |
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| 347 | * The facility now exists to bypass the searching step and go straight |
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| 348 | to the output stage using a list of previously detected objects. The |
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| 349 | list is extracted from a previously-created log file. The user can |
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| 350 | change the way the spectra are plotted (e.g. choose to plot |
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| 351 | integrated rather than peak spectra), and select a subset of the |
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| 352 | detected objects to be printed to individual postscript files. Use |
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| 353 | the input parameter usePrevious (set to true) to use this facility, |
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| 354 | and provide a list of objects using the objectList parameter |
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| 355 | (eg. 1,2,4,7-10,15) |
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| 356 | |
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[482] | 357 | * A new parameter "growthThreshold" has been created, that goes with |
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| 358 | "threshold". If you manually specify a threshold, and you wish to |
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| 359 | grow detections, you need to manually specify a growthThreshold (in |
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| 360 | flux units). |
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| 361 | |
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[480] | 362 | Bug fixes: |
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| 363 | |
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[482] | 364 | * Cubes that do not have a spectral axis (such as Stokes cubes) were |
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| 365 | causing memory leaks and crashing, due to some assumptions of the |
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| 366 | existence of the spectral axis. These bugs have been fixed, so that |
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| 367 | Duchamp will run on such cubes, although the WCS transforms may not |
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| 368 | always work appropriately. Please let me know via bug reports of |
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| 369 | difficulties you encounter! |
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[480] | 370 | |
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[482] | 371 | * The growing function has had a few bugs fixed and is now more |
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| 372 | efficient. |
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| 373 | |
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| 374 | * The FDR method was previously overriding any manually-specified |
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| 375 | threshold. This has been fixed so that if the user specifies |
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| 376 | threshold=X, then the FDR method is not called. |
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| 377 | |
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| 378 | * Some undefined things were happening with textual output when no |
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| 379 | objects were detected. This has been fixed. |
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| 380 | |
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| 381 | * Memory leaks caused by FITS WCS irregularities have been fixed |
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| 382 | (specifically, if a FITS header had NAXIS=2 but more than two WCS |
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| 383 | axes were defined). |
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| 384 | |
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| 385 | |
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| 386 | |
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[438] | 387 | Duchamp version 1.1.5 (2008/03/20) |
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| 388 | ---------------------------------- |
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| 389 | |
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| 390 | Bug fixes: |
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| 391 | * A major bug was discovered in the calculation of integrated |
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| 392 | fluxes. The flux was incorrectly being weighted by the spatial size |
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| 393 | of the detection, resulting in a (often considerable) overestimation |
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[447] | 394 | of the integrated flux. This has been corrected. |
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[438] | 395 | |
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[447] | 396 | * The beam size calculation was also incorrect, being out by a factor |
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| 397 | of 1/ln(2). |
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[438] | 398 | |
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[447] | 399 | * The "make install" command previously failed to work properly if the |
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| 400 | library had not been created. This has been fixed so that the |
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| 401 | installation works even if there is no library file. |
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| 402 | |
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| 403 | New Features: |
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| 404 | * You can now provide a new flux unit string, so that the pixel fluxes |
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| 405 | will be converted to these new fluxes before any calculations are |
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| 406 | done. This is done with the newFluxUnits input parameter. The new |
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| 407 | units should be directly convertible from the old ones (given by the |
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| 408 | BUNIT header -- e.g. if BUNIT = Jy/beam, you can give newFluxUnits |
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| 409 | as mJy/beam, but not mJy). |
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| 410 | |
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| 411 | * You can now specify the precision used in the output files for flux, |
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| 412 | velocity and S/N ratio columns, via new input parameters precFlux, |
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| 413 | precVel and precSNR. These will apply to the VOTable output as well |
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| 414 | as the text table and information on the spectral plots. |
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| 415 | |
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| 416 | * The Karma annotation files previously provided just a circle at the |
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| 417 | spatial location of the detected object. You now have the option to |
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| 418 | draw a border around the detected pixels (in a similar manner to the |
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| 419 | PGPLOT moment maps). Karma does not do this perfectly, so the lines |
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| 420 | may not line up exactly with the pixel borders, so the option |
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| 421 | remains to keep using the circles. This is controlled by the |
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| 422 | parameter "annotationType", with possible options being "borders" |
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| 423 | (the default) or "circles". |
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| 424 | |
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| 425 | * There is a new function getMetadata() that loads the header and WCS |
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| 426 | data, but no pixel information. This is only of interest if you are |
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| 427 | doing code development with the Duchamp library -- it does not |
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| 428 | affect the running of Duchamp itself. |
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| 429 | |
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[425] | 430 | Duchamp version 1.1.4 (2008/02/15) |
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| 431 | ---------------------------------- |
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| 432 | |
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| 433 | Most of the changes incorporated in this update result from ASKAP code |
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| 434 | development (that makes use of some of the Duchamp functionality), |
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| 435 | but do not actually affect the way Duchamp runs (other than, in a |
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| 436 | couple of cases, making it a bit faster). Changes that are |
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| 437 | relevant for regular users of Duchamp are as follows: |
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| 438 | |
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| 439 | * A new option has been made available (thanks to Mary Putman et al |
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| 440 | for the suggestion!) to save the spectra of all detected objects in |
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| 441 | a text file. This has the form of one column for the spectral |
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| 442 | coordinates and one column of fluxes for each object. This is |
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| 443 | enabled by the input parameters flagTextSpectra and spectraTextFile. |
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| 444 | |
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| 445 | * Slight changes to the output include he formatting of the way the |
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| 446 | detected objects are written to the log file. This meant the |
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| 447 | verification files were also updated. Also the cube statistics are |
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| 448 | not printed to the results file if a user threshold is specified (as |
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| 449 | they are not calculated!). |
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| 450 | |
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| 451 | * The determination of beam size has been made more reliable, as has |
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| 452 | the BUNIT determination. |
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| 453 | |
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| 454 | * Fixed a bug that meant source merging was not done for 2D images |
---|
| 455 | (not usually a problem, as the source-finding takes care of this, |
---|
| 456 | but came up in parallelisation development). |
---|
| 457 | |
---|
[406] | 458 | Duchamp version 1.1.3 (2008/01/08) |
---|
| 459 | ---------------------------------- |
---|
[404] | 460 | |
---|
| 461 | A minor update that just improves the build process. The location of |
---|
| 462 | the wcslib include files was not specified correctly, so that some |
---|
| 463 | machines were unable to find them. The configure script has been fixed |
---|
| 464 | so that the compilation should work in all cases. |
---|
| 465 | |
---|
[405] | 466 | Some minor changes have also been made to the code in the PixelMap |
---|
[412] | 467 | directory, and to param.cc, to fix warnings or errors that may appear |
---|
| 468 | in compilation. |
---|
[404] | 469 | |
---|
[405] | 470 | However, there are no changes to the actual workings of the code in |
---|
| 471 | this minor version, so if you have a working version of Duchamp 1.1.2 |
---|
| 472 | there is probably no reason to update. |
---|
| 473 | |
---|
[389] | 474 | Duchamp version 1.1.2 (2007/12/07) |
---|
| 475 | ---------------------------------- |
---|
[349] | 476 | |
---|
[363] | 477 | Compilation: |
---|
| 478 | |
---|
[349] | 479 | * The compilation had problems working correctly when the cfitsio and |
---|
[373] | 480 | wcs libraries were not in standard locations. The configure script |
---|
[349] | 481 | has been tweaked to make sure the libraries are found. |
---|
| 482 | |
---|
| 483 | * Problems with compiling in the absence of pgplot have been fixed, |
---|
| 484 | and it should now compile fine. |
---|
| 485 | |
---|
[362] | 486 | * Improved the configure script for use with Mac OS X and gfortran. |
---|
[349] | 487 | |
---|
[363] | 488 | |
---|
| 489 | Bugfixing: |
---|
| 490 | |
---|
[362] | 491 | * A major problem with the text-based output was fixed. The widths of |
---|
| 492 | the columns were not being calculated correctly, and were running |
---|
[373] | 493 | together. This should no longer be the case. |
---|
[349] | 494 | |
---|
[374] | 495 | * There was a bug in the way Duchamp interpreted spectral axes, |
---|
| 496 | particularly AIPS types such as FELO-HEL, leading to incorrect |
---|
| 497 | scaling of the velocity axis. This has been fixed, so that |
---|
| 498 | non-standard types are now dealt with appropriately and the velocity |
---|
| 499 | scaling should be accurate. |
---|
[362] | 500 | |
---|
[376] | 501 | * Another bug meant the beam correction was always applied to the |
---|
| 502 | integrated spectra, regardless of whether the flux units involved |
---|
| 503 | the beam (e.g. Jy/beam). This has been fixed. Note that the values |
---|
| 504 | of the integrated flux presented in the results table were always |
---|
| 505 | calculated correctly. |
---|
| 506 | |
---|
[389] | 507 | * Other minor changes to improve the speed and efficiency, especially |
---|
| 508 | of the merging code. |
---|
| 509 | |
---|
[363] | 510 | New user parameters: |
---|
| 511 | |
---|
[381] | 512 | * There is now the possibility to save a FITS file that contains a |
---|
| 513 | mask array, indicating where the detected objects are. This is |
---|
| 514 | governed by the flagOutputMask parameter. |
---|
| 515 | |
---|
[363] | 516 | * The header information that is printed at the start of the results |
---|
| 517 | file -- that is, the list of parameters, the statistics of the cube, |
---|
| 518 | and the number of detections -- can now be written to a separate |
---|
| 519 | file. Set the flagSeparateHeader parameter to true or 1 and it will |
---|
| 520 | go to the file indicated by the headerFile parameter (the default is |
---|
| 521 | duchamp-Results.hdr). |
---|
| 522 | |
---|
[362] | 523 | * A "scaleMax" parameter has been added, so that the wavelet |
---|
| 524 | reconstruction can include only a specified range of scales (for |
---|
[373] | 525 | instance, if one wants to search just for narrow features such as |
---|
[362] | 526 | absorption lines). |
---|
| 527 | |
---|
[389] | 528 | * A "flagRobustStats" parameter has been added. This allows the user |
---|
| 529 | to elect to use robust statistics (median and median absolute |
---|
| 530 | deviation from the median) to estimate the noise parameters. If set |
---|
| 531 | to false, the mean and standard deviation will be used. The default |
---|
| 532 | value is true. |
---|
[362] | 533 | |
---|
[369] | 534 | New Feature: |
---|
[362] | 535 | |
---|
[369] | 536 | * When Duchamp is run on a 2D image (i.e. with no spectral output), it |
---|
| 537 | now produces a postscript file that shows information each |
---|
| 538 | individual source plus the image cutout of the source. This is |
---|
| 539 | similar to the spectral output file, but without the spectra. The |
---|
| 540 | filename is given by the spectraFile parameter. |
---|
| 541 | |
---|
[381] | 542 | * Ability to save a FITS file containing a mask array, with pixel |
---|
| 543 | values of 1 for pixels in a detected object, and 0 elsewhere. |
---|
[369] | 544 | |
---|
[381] | 545 | |
---|
[328] | 546 | Duchamp version 1.1.1 (2007/07/20) |
---|
| 547 | ------------------------------------ |
---|
| 548 | |
---|
[329] | 549 | Minor update to the release, with just a few changes: |
---|
[328] | 550 | |
---|
| 551 | * The verification script was generating diffs due to differences in |
---|
| 552 | the precision of some calculations when done on different machines. |
---|
| 553 | One of these was the integrated flux, and this has been corrected so |
---|
| 554 | that the same value should appear on all machines. |
---|
| 555 | The verification script has also changed so that just the number of |
---|
| 556 | sources and their positions are tested, as well as the |
---|
| 557 | logfiles. This should avoid the reporting of spurious differences. |
---|
| 558 | |
---|
| 559 | * The grey-scale used in the image cutouts (in the spectral plots) has |
---|
| 560 | been inverted. This makes it consistent with the scale used in the |
---|
| 561 | maps, and hopefully easier to see when printing. |
---|
| 562 | |
---|
[338] | 563 | * The configure/make system has been altered to make it easier to |
---|
| 564 | install, and to specify different external libraries. In particular, |
---|
| 565 | it is now not necessary to have PGPLOT installed on your system to |
---|
| 566 | run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, |
---|
| 567 | just without any graphical output. Some source code needed to be |
---|
[344] | 568 | restructured to make this work. Please read the README file, or the |
---|
| 569 | Installation appendix in the User's Guide, for complete details. |
---|
[328] | 570 | |
---|
[329] | 571 | * The time of completion is now written to the log file, so that the |
---|
| 572 | user can have some idea of how long the program took. |
---|
[328] | 573 | |
---|
| 574 | |
---|
[310] | 575 | Duchamp version 1.1 (2007/05/17) |
---|
[259] | 576 | ------------------------------------ |
---|
| 577 | |
---|
| 578 | Changes made since the last numbered release: |
---|
| 579 | |
---|
[295] | 580 | EFFICIENCY OF EXECUTION: |
---|
| 581 | |
---|
[259] | 582 | * Major change to the way detections are stored. They are now recorded |
---|
| 583 | via run-length encoding in the x-y plane, and stored as collections |
---|
| 584 | of channel-maps. This improves the memory usage and the speed of |
---|
[298] | 585 | execution (particularly for routines such as the merging |
---|
| 586 | routines). The memory usage has also been improved by changing the |
---|
| 587 | way the list of detected objects is stored. |
---|
[259] | 588 | |
---|
[295] | 589 | SMOOTHING: |
---|
| 590 | |
---|
[279] | 591 | * Addition of ability to spatially smooth the cube before |
---|
| 592 | searching. This is done with a Gaussian kernel, the size and shape |
---|
[287] | 593 | of which can be specified by the user, using the parameters kernMaj |
---|
| 594 | & kernMin (which are the FWHM for the major & minor axes -- if |
---|
| 595 | kernMin is not given it is assumed to match kernMaj) and kernPA (the |
---|
| 596 | position angle of the major axis). There is a new parameter |
---|
[279] | 597 | smoothType that distinguishes this method from the spectral (Hanning) |
---|
| 598 | smoothing already in use. |
---|
| 599 | |
---|
[295] | 600 | DETECTIONS: |
---|
| 601 | |
---|
[264] | 602 | * Changed the way detection is done -- now only search in 2D images, |
---|
| 603 | keeping all detections (ie. no minimum-pixel requirement). This |
---|
| 604 | should be the same as doing both the 1D and 2D searches with the |
---|
| 605 | minimum pixel requirement in, but simpler. The rejection is done at |
---|
[295] | 606 | the end after all the merging and growing has been done. This leads |
---|
| 607 | to a larger number of intermediate detections (ie. the number |
---|
| 608 | before merging), which may increase the run-time slightly, although |
---|
| 609 | this is offset by the changes to the efficiency (see above). |
---|
[264] | 610 | |
---|
| 611 | * Increased the range over which objects can be grown to match the |
---|
| 612 | threshSpatial & threshVelocity parameters, as well as rejecting new |
---|
| 613 | pixels based on the BLANK and MW tests. |
---|
| 614 | |
---|
[295] | 615 | INPUTS: |
---|
[259] | 616 | |
---|
[287] | 617 | * There has been a subtle change in the way BLANK pixels are dealt |
---|
| 618 | with. To enable trimming of BLANK pixels, users should use the new |
---|
| 619 | parameter flagTrim. The parameters flagBlankPix and blankPixVal are |
---|
[295] | 620 | no longer accessible via the parameter file -- warning messages are |
---|
| 621 | given if they are provided in the parameter file. |
---|
[287] | 622 | |
---|
[295] | 623 | * Added ability to specify a statsec, so that the statistics are only |
---|
| 624 | calculated from a given subsection of the cube, rather than the full |
---|
| 625 | cube. |
---|
| 626 | |
---|
| 627 | * The subsections can also specify the ability to remove a border of n |
---|
| 628 | pixels from the edges of an axis (ie. n from the start and from the |
---|
| 629 | end) -- as requested in Trac ticket #5. |
---|
| 630 | |
---|
| 631 | * Changed the default value of the reconDim parameter from 3 to 1, and |
---|
| 632 | the default value of the flagATrous parameter to false. |
---|
| 633 | |
---|
| 634 | OUTPUTS: |
---|
| 635 | |
---|
[279] | 636 | * The output now includes three different estimates of the "centre" of |
---|
| 637 | the detection: peak location, centroid (flux-weighted), or average. |
---|
| 638 | |
---|
[295] | 639 | * Some slight improvements to the user feedback during execution. |
---|
| 640 | |
---|
[282] | 641 | * Spectral output now includes the baseline, if one was fitted. The |
---|
| 642 | format of the plot headers is slightly changed, to stop information |
---|
| 643 | falling off the edge of the page. |
---|
[279] | 644 | |
---|
[295] | 645 | * Added command-line option -x to directly disable the PGPLOT X-window |
---|
| 646 | map plotting. This overrides the setting of flagXOutput in the |
---|
| 647 | parameter file. |
---|
[259] | 648 | |
---|
[295] | 649 | * Fallback spectral units (in case the FITS header fails to record |
---|
| 650 | them) changed to SPC, but code has been fixed so that any problem |
---|
| 651 | should be caught before this becomes an issue. |
---|
| 652 | |
---|
| 653 | BUGFIXES: |
---|
| 654 | |
---|
[259] | 655 | * Fixed bug (Trac ticket #4) that meant the velocity units were not |
---|
| 656 | correctly dealt with. Duchamp should be more robust for different |
---|
| 657 | velocity axis setups now. |
---|
| 658 | |
---|
| 659 | * Fixed bug (ticket #9) with the VOTable output, where the tags were |
---|
| 660 | not closing. |
---|
| 661 | |
---|
[305] | 662 | * Fixed a bug that meant the integrated fluxes were not calculated |
---|
| 663 | properly -- no allowance was made for the number of spatial |
---|
| 664 | pixels. This should also work properly for 2D images now as well. |
---|
| 665 | |
---|
[264] | 666 | * Fixed minor bug in calculating the flux threshold from the p-value |
---|
| 667 | threshold when the FDR method is used. This did not affect the |
---|
| 668 | actual thresholding, merely the quoted flux threshold in the results |
---|
| 669 | file. Also, the MW channels are kept out of the p-value threshold |
---|
| 670 | determination if they are being flagged. |
---|
| 671 | |
---|
[259] | 672 | |
---|
| 673 | |
---|
[211] | 674 | Duchamp version 1.0.7 (2006/11/22) |
---|
| 675 | ---------------------------------- |
---|
| 676 | |
---|
| 677 | One new feature, and some improvements and bug-fixes. |
---|
| 678 | |
---|
[264] | 679 | * The user can now elect to Hanning-smooth the spectral direction of |
---|
| 680 | the cube before the searching is done. This can be done instead of the |
---|
| 681 | wavelet reconstruction (although if both are selected, the |
---|
| 682 | reconstruction takes precendence). This functionality is switched on |
---|
| 683 | and off by the flagSmooth parameter, and the width of the Hanning |
---|
| 684 | kernel is governed by the hanningWidth parameter. |
---|
[211] | 685 | |
---|
[264] | 686 | * The smoothed array can also be written to a FITS file and read in at |
---|
| 687 | the start in the same manner as the reconstructed array. |
---|
[211] | 688 | |
---|
[264] | 689 | * Several improvements have been made to the memory |
---|
| 690 | management. Several memory leaks were fixed, and the memory usage of |
---|
| 691 | Duchamp is considerably less, which will be a help for running it on |
---|
| 692 | large cubes. The speed of some routines has also been improved, by |
---|
| 693 | removing unnecessarily repetitive loops. |
---|
[211] | 694 | |
---|
[287] | 695 | * The sorting routines have been changed, and should now be slightly quicker |
---|
[215] | 696 | (and a bit more robust). |
---|
| 697 | |
---|
[287] | 698 | * Enabled the scale bar (plotted on the 0th moment map in the spectral |
---|
| 699 | output file) to be able to deal with much finer spatial scales (as |
---|
| 700 | may be expected from VLBI data). |
---|
[211] | 701 | |
---|
[215] | 702 | * Other minor changes to code and presentation. |
---|
[211] | 703 | |
---|
| 704 | |
---|
[194] | 705 | Duchamp version 1.0.6 (2006/11/01) |
---|
| 706 | ---------------------------------- |
---|
| 707 | |
---|
| 708 | Some incremental improvements and changes to the code: |
---|
| 709 | |
---|
| 710 | * The statistics used for the detection are now calculated once for |
---|
| 711 | the entire cube, rather than being calculated separately for each |
---|
| 712 | channel map and spectrum. This results in a uniform threshold value |
---|
| 713 | across the entire cube. The way the statistics calculations are |
---|
| 714 | implemented in the code was changed, using a new statistics class. |
---|
| 715 | |
---|
| 716 | * This means we can report a peak signal-to-noise value for each |
---|
| 717 | detection. This is given in the text-based output, as well as in the |
---|
| 718 | summary information above the spectral output for each source. |
---|
| 719 | |
---|
[195] | 720 | * The user can now elect not to have the moment map displayed in a |
---|
| 721 | PGPlot window, through the use of the new flagXOutput |
---|
| 722 | parameter. This should help in cases of running Duchamp on a dumb |
---|
| 723 | terminal (with no X-display capabilities), or as part of a batch |
---|
| 724 | script where the continual popping-up of the PGPlot window might |
---|
| 725 | become annoying. |
---|
| 726 | |
---|
[265] | 727 | * There are different Flags reported for the case of an object lying on |
---|
[194] | 728 | the spatial edge and spectral edge of the cube (E and S respectively). |
---|
| 729 | |
---|
| 730 | * A few minor bug fixes: |
---|
| 731 | - When providing a subsection, any axes with the range given by * |
---|
| 732 | had the pixel values offset incorrectly. This has been fixed. |
---|
| 733 | - Negative searches now correctly invert the reconstructed array |
---|
| 734 | when it is read in from a file. |
---|
| 735 | |
---|
| 736 | * Other minor changes to the code, to improve memory handling and |
---|
| 737 | remove redundant arrays and variables. |
---|
| 738 | |
---|
| 739 | |
---|
[146] | 740 | Duchamp version 1.0.5 (2006/09/06) |
---|
[142] | 741 | ---------------------------------- |
---|
| 742 | |
---|
[146] | 743 | Since version 1.0, there have been a range of mostly minor |
---|
| 744 | changes. These are generally bug-fixes, thanks to feedback from a |
---|
[157] | 745 | number of users, as well as a few extra features. |
---|
[146] | 746 | |
---|
[157] | 747 | Here is a summary of the changes since version 1.0: |
---|
[142] | 748 | |
---|
[157] | 749 | USER INTERFACE: |
---|
[146] | 750 | |
---|
[142] | 751 | * The user is now able to enter the value of flag parameters in the |
---|
| 752 | parameter file as strings, as well as integers (so one can enter |
---|
| 753 | true or 1 to give the same result). |
---|
| 754 | |
---|
[157] | 755 | GRAPHICAL OUTPUT: |
---|
| 756 | |
---|
[142] | 757 | * Added a new function that draws the edge of the blank region on the |
---|
[146] | 758 | maps and image cutouts. There is a new flag parameter -- |
---|
| 759 | drawBlankEdges -- that controls the use of this function (the |
---|
| 760 | default is true). |
---|
| 761 | Also, the edge of the field is plotted on the image cutouts as a |
---|
| 762 | yellow line. This distinguishes it from the purple blank pixel |
---|
| 763 | dividing line. |
---|
[142] | 764 | |
---|
[146] | 765 | * The size of the tick mark in the image cutout (indicating the |
---|
| 766 | spatial scale of the image) is now adaptable, so that it shows the |
---|
| 767 | scale that best fits the image (ranging from 1 arcsec to 15 |
---|
| 768 | degrees). (This is a change from the previous standard length of 15 |
---|
| 769 | arcmin.) |
---|
[142] | 770 | |
---|
[113] | 771 | * The zoomed spectrum had its flux scale determined by all points in |
---|
[146] | 772 | the zoom box,including those flagged by the Milky Way (MW) |
---|
| 773 | range. This has been fixed so that any MW channels will not affect |
---|
| 774 | the flux scaling, potentially improving the appearance of objects |
---|
| 775 | detected close in velocity to strong MW emission or absorption. |
---|
[112] | 776 | |
---|
[157] | 777 | * Improved Karma Annotation file output, so that files without good |
---|
| 778 | WCS are dealt with appropriately. |
---|
| 779 | |
---|
| 780 | TEXT-BASED OUTPUT: |
---|
| 781 | |
---|
[113] | 782 | * The position resolution in the IAU-format names has been increased, |
---|
| 783 | so that distinct objects close to one another are more readily |
---|
| 784 | distinguished. Overlapping sources at different velocities may |
---|
| 785 | still have the same name, but this is a more general problem. |
---|
[112] | 786 | |
---|
[146] | 787 | * The presentation of the results in tabular format has been improved, |
---|
| 788 | so that the precision of faint sources is sufficient to show their |
---|
| 789 | flux, for instance, is not 0. This also applies to the information |
---|
| 790 | presented above the spectral plots. |
---|
[112] | 791 | |
---|
[146] | 792 | * Improved error and warning reporting, so that the formatting and |
---|
| 793 | presentation of information is clearer. |
---|
| 794 | |
---|
[157] | 795 | FITS I/O RELATED: |
---|
| 796 | |
---|
[172] | 797 | * The previous version was did not deal well with 4 (or greater) |
---|
| 798 | dimensions in the FITS file -- the memory allocation was badly done, |
---|
| 799 | and the axes needed to be in a particular order. This has been |
---|
| 800 | fixed, so that the FITS I/O routines can now handle any sized FITS |
---|
| 801 | file, with axes in any order (as long as there are two spatial and one |
---|
| 802 | spectral axes). |
---|
[157] | 803 | |
---|
| 804 | * When the FITS file does not have a rest frequency defined, there is |
---|
| 805 | no way to transform the frequency axis into velocity. In this case, |
---|
| 806 | the spectral axis is left as frequency, and put into units of MHz. |
---|
| 807 | |
---|
[172] | 808 | * If the beam size is not indicated by the FITS header (through the |
---|
| 809 | BMAJ and BMIN keywords), the user can manually specify the size |
---|
| 810 | through the parameter file (using parameter beamSize). |
---|
| 811 | |
---|
| 812 | * The FITS I/O routines make use of the command fits_file_exists. This |
---|
| 813 | was introduced into the CFITSIO package from version 2.5, so Duchamp |
---|
| 814 | will only work with this version or higher. Version 3+ is preferred. |
---|
| 815 | |
---|
[157] | 816 | OTHER BUG-FIXING: |
---|
| 817 | |
---|
| 818 | * Several bugs related to the blank-pixels were dealt with. |
---|
| 819 | The correct values were not propagating through correctly, meaning |
---|
| 820 | that the default values were being used. Also, there was the |
---|
| 821 | potential for blank pixels to be detected when the FDR method was |
---|
| 822 | used. Finally, the image cutout displays occasionally did not |
---|
| 823 | obscure the blank pixels. All these problems should be fixed now. |
---|
| 824 | |
---|
| 825 | * The FDR setup routine was occasionally failing with a segmentation |
---|
| 826 | fault, due to it accessing unallocated memory. This has been fixed. |
---|
| 827 | |
---|
| 828 | * Fixed bugs that affected the way 2D images (rather than 3D cubes) |
---|
| 829 | were dealt with. The minChannels test failed when minChannels=0. |
---|
| 830 | |
---|
[165] | 831 | * If there is no beam information in the FITS header, the user can now |
---|
| 832 | enter a beam size as a parameter. |
---|
| 833 | |
---|
[146] | 834 | * Other minor fixes to the code, to improve its structure and |
---|
| 835 | robustness. |
---|
| 836 | |
---|
| 837 | |
---|
[112] | 838 | Duchamp version 1.0 (2006/06/30) |
---|
| 839 | -------------------------------- |
---|
| 840 | |
---|
[113] | 841 | The first full release version. |
---|
| 842 | |
---|
| 843 | Several major changes compared to previous version: |
---|
| 844 | |
---|
| 845 | * Incorporated a FitsHeader class, to keep track of header information |
---|
| 846 | (including WCS) from the FITS file. All units-related calculations |
---|
| 847 | are done with this class, such as conversion to velocity, and |
---|
| 848 | pixel-to-WCS conversion. The main advantage of this is improved |
---|
| 849 | speed of execution, more adaptable to different units, and improved |
---|
| 850 | code (easier for me!). |
---|
| 851 | |
---|
| 852 | * Able to select the dimensionality of the reconstruction, rather than |
---|
| 853 | just doing it in 3-D. |
---|
| 854 | |
---|
| 855 | * Robust text output, so that the columns are sized correctly given |
---|
| 856 | the data being written, and the relevant units (derived from the |
---|
| 857 | FITS header) are included in the output table. |
---|
| 858 | |
---|
| 859 | * Improved the way the reconstructed image is saved and read back in, |
---|
| 860 | with a better naming scheme and a better set of new FITS header |
---|
| 861 | keywords. The MW headers are now not written. |
---|
| 862 | |
---|
| 863 | Other, more minor changes include: |
---|
| 864 | |
---|
| 865 | * MW channels now not set to 0, but just ignored for searching |
---|
| 866 | purposes (and for the scaling of the spectral output -- they are |
---|
| 867 | plotted though and highlighted with a hashed box). |
---|
| 868 | |
---|
| 869 | * The scale bar in the moment map in the spectral output file has its |
---|
| 870 | length indicated. |
---|
| 871 | |
---|
| 872 | * Improved VOTable output, with more information about the way Duchamp |
---|
| 873 | was run. |
---|
| 874 | |
---|
| 875 | * Made sure all statistics calculations in the reconstruction are |
---|
| 876 | based on robust (ie. median) methods. |
---|
| 877 | |
---|
| 878 | Also moved to an autoconf based configure/make compilation, for ease of use. |
---|
| 879 | |
---|
| 880 | |
---|
| 881 | Duchamp version 0.9.2 (2006/06/27) |
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| 882 | -------------------------------- |
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| 883 | |
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| 884 | * Added the use of warning flags for detections: for either edge |
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| 885 | location or negative enclosed flux. |
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| 886 | |
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| 887 | * A new command line option added so that the user can specify a FITS |
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| 888 | file to be searched with the default parameters, rather than giving |
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| 889 | a full parameter file. |
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| 890 | |
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| 891 | * The scale bar on the moment cutout now works in general case, using |
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| 892 | an iterative process to get to the correct length. |
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| 893 | |
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| 894 | * RA axes are now done correctly on the full-scale maps. |
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| 895 | |
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| 896 | * Various coding fixes, improving the readability of the code, |
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| 897 | particularly regarding the declaration of temporary variables. |
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| 898 | |
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| 899 | * Changed the way the time of execution is called : now using time.h |
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| 900 | functions, rather than a system call. |
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| 901 | |
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| 902 | * Changed output in Detection/outputDetection.cc for the pixel |
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| 903 | information of detected objects (the info printed above the spectral |
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| 904 | plots) -- now print out number of voxels in object, and have |
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| 905 | improved the formatting a little. |
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| 906 | |
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| 907 | * Improved the functionality of saving the FITS file containing the |
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| 908 | reconstructed array. Added ability to save and read back in the MW |
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| 909 | parameters when saving a reconstructed cube (if a reconstructed cube |
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| 910 | has different MW range to that being considered, it would cause |
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| 911 | problems). ReadRecon now just returns a FAILURE and will reconstruct |
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| 912 | the cube anew. |
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| 913 | |
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| 914 | * Changed default value of flagGrowth to 0. |
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| 915 | |
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| 916 | |
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| 917 | |
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| 918 | Duchamp version 0.9 (2006/05/05) |
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| 919 | -------------------------------- |
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| 920 | |
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| 921 | First public release version. |
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