[1035] | 1 | Duchamp version 1.2 (2012/08/08) |
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[962] | 2 | -------------------------------- |
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[928] | 3 | |
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[951] | 4 | Key changes: |
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| 5 | |
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| 6 | * The way the wavelet reconstruction is done in the presence of BLANK |
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| 7 | voxels is slightly different, specifically when there were BLANK |
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| 8 | voxels on the edge. While BLANK voxels are always ignored by the |
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| 9 | reconstruction (and left in place), the previous approach dealt with |
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| 10 | BLANKS on the edge by moving the effective edge of the image inwards |
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| 11 | until the first non-blank voxel. This meant that the size of the |
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| 12 | dimensions used to determine the number of scales, and the location |
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| 13 | where boundary reflections took place where different to the input |
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| 14 | image size. |
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| 15 | |
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| 16 | However, this meant that BLANK voxels on the edge were treated |
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| 17 | differently to those not on the edge, so this inconsistency was |
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| 18 | removed. The full image dimensions are always used to calculate the |
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| 19 | number of scales, and reflections (which is how the reconstruction |
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| 20 | deals with the boundaries) will occur at the actual image edges. |
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| 21 | |
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| 22 | If your data has this property (BLANK pixels at the image |
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| 23 | boundaries), then any reconstruction will be affected (most likely |
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| 24 | only in a small way) and potentially any subsequent searching. You |
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[1035] | 25 | are advised to check this (for instance by saving the results of the |
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| 26 | resonstruction from 1.1.13 and 1.2 and comparing). |
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[951] | 27 | |
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[1035] | 28 | * The way the spectral world coordinate system is dealt with has been |
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| 29 | improved. Previously Duchamp tried to convert to a velocity axis, |
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| 30 | and got a bit grumpy if that didn't work well. Now it will express |
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| 31 | the spectral units in the axis type indicated by the FITS |
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| 32 | header. Duchamp will also allow you to change this type by providing |
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| 33 | an appropriate WCS type as an input parameter. You may also provide |
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| 34 | a rest frequency in the parameter file and this will be used to |
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| 35 | calculate velocities. And, as before, you can provide specific units |
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| 36 | for the spectral quantities to be converted into. |
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| 37 | |
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[951] | 38 | * Since v1.1.13 was released, the journal paper describing Duchamp has |
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| 39 | been published. It can be found at MNRAS 421, 3242 (2012), or |
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| 40 | http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2012.20548.x/full. It |
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| 41 | includes descriptions of the various algorithms used for Duchamp, as |
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| 42 | well as some indicative comparisons of the relative completeness & |
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| 43 | reliability. Please cite this paper when describing Duchamp. |
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| 44 | |
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| 45 | Other new features: |
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| 46 | |
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[1035] | 47 | * The default value of snrCut has changed from 3 to 5. This is |
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| 48 | espeically important if you use the -f option, but also if you don't |
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| 49 | provide snrCut in your parameter file. |
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| 50 | |
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[951] | 51 | * The XML VOTable output now includes a more complete list of |
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| 52 | parameters, matching the output given in text form in the results & |
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| 53 | log output files. Only those parameters affecting the results are |
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| 54 | included - things like the output file names and so on are left out. |
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| 55 | |
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| 56 | * The minVoxels parameter is now adjusted to be at least (minPix + |
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| 57 | minChannels - 1). If it is changed, a warning message is triggered. |
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| 58 | |
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| 59 | * The warning/error reporting has been overhauled, with an improved |
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| 60 | interface for developers. Also, some ERROR instances that previously |
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| 61 | resulted in the program terminating now allow it to continue |
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| 62 | (provided that is possible given the error). |
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| 63 | |
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[1026] | 64 | * It is now possible to give the convergence criterion for the wavelet |
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| 65 | reconstruction via the parameter reconConvergence. When the relative |
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| 66 | change in standard deviation of the residuals from the |
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| 67 | reconstruction falls below this value, the a trous algorithm stops |
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| 68 | iterating. |
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| 69 | |
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[991] | 70 | * The way one-dimensional arrays were dealt with was unsatisfactory, |
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| 71 | both with the way positions were registered and the format of the |
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| 72 | graphical output. Improvements have been made such that a 1D data |
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| 73 | structure is assumed to be a spectrum, and so positions in the |
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| 74 | spectrum are reported as z-pixels (or the equivalent world |
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| 75 | coordinate). Instead of a 2D moment map, the X-windows display will |
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| 76 | show the spectrum with all detected pixels plus the final list of |
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| 77 | detections highlighted, along with the detection and growth |
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[1035] | 78 | thresholds. This plot will also be written to the "detectionMap" |
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| 79 | image. |
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[991] | 80 | |
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| 81 | * All spectral plots will now show the detection (and growth, if |
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| 82 | applicable) thresholds when plotting the peak flux spectrum. |
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| 83 | |
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| 84 | * Accessing FITS files when a subsection string is provided has been |
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| 85 | streamlined. The cfitsio package, which handles the FITS access, |
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| 86 | creates a temporary file containing this image section, and this |
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| 87 | meant the previous approach was slow, particularly for large |
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| 88 | files/sections. Now the file is only opened once and the overhead of |
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| 89 | creating the temporary file is only encountered once. |
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| 90 | |
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| 91 | * Several aspects of the processing & output did not handle a |
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| 92 | non-existent WCS well. This has been improved, so that all stages of |
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| 93 | execution will proceed without errors. |
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| 94 | |
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[928] | 95 | Bug fixes: |
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| 96 | |
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[941] | 97 | * The absence of a BLANK keyword when trimming will now not trigger a |
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| 98 | failure, only a warning message. |
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[928] | 99 | |
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[941] | 100 | * The flux unit conversion (eg. from Jy/beam to mJy/beam) was not |
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| 101 | being applied correctly when an existing reconstructed or smoothed |
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| 102 | array was being read in. This is now applied properly. |
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| 103 | |
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| 104 | * When saving reconstructed or smoothed arrays, the data type is now |
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| 105 | set to FLOAT, so that the correct values are written (and |
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| 106 | subsequently read in). The previous version was potentially saving |
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| 107 | to a FITS file with integer data type (this depended on the type of |
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[951] | 108 | the input array). In this case, the full precision of data values |
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| 109 | would not be preserved, so reading back in and doing an identical |
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| 110 | search could yield different sources. |
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[941] | 111 | |
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| 112 | * For certain cases, the reconstruction attempted to use a very large |
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| 113 | number of scales. This has been fixed. |
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| 114 | |
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[1026] | 115 | * The maximum scale for the reconstruction was not always being |
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| 116 | applied. The scale ranges are now enforced for all types of |
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| 117 | reconstructions. |
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| 118 | |
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[941] | 119 | * When saving a mask image while using a subsection of a cube, the |
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| 120 | offsets for the subsection were not being accounted for |
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| 121 | correctly. This is now fixed. |
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| 122 | |
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[991] | 123 | * The detection map plots were not recording pixels added from the |
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| 124 | growing stage. This has been fixed. |
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| 125 | |
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[941] | 126 | * The RA & Dec now have appropriate precision, rather than an |
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| 127 | arbitrary 2 decimal places on the seconds value. The RA will be one |
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| 128 | decimal place more than the Dec, and they will reflect the degree of |
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| 129 | precision in the image pixels. |
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| 130 | |
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| 131 | * A number of data type conversions (typically ints to floats) led to |
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| 132 | errors in some calculations, such as WCS conversions. Care has been |
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| 133 | taken to make sure all indexing is done appropriately with no |
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| 134 | overflow, and that all conversions (where necessary) are done |
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| 135 | appropriately. |
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| 136 | |
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| 137 | * It was possible to get world positions looking like 11:59:60.0! Not |
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| 138 | any more. |
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| 139 | |
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[1020] | 140 | * Reading previous detections from the log file (via the use of the |
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| 141 | usePrevious parameter) did result in error messages due to slightly |
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| 142 | incompatible formats. These have been fixed, and all graphical |
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| 143 | output should work properly. |
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[928] | 144 | |
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[1020] | 145 | * When using a spectral search, having a blank pixel in the first |
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| 146 | channel could lead to that entire spectrum being ignored, leading to |
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| 147 | inconsistent results between spectral and spatial searches. This |
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| 148 | issue has been fixed, with both types of searches returning the same |
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| 149 | catalogue. |
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| 150 | |
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| 151 | |
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[928] | 152 | Code base development notes: |
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| 153 | |
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[951] | 154 | * Most instances of integer overflow due to insufficient precision |
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| 155 | have been tracked down - many of these were indexing variables of |
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| 156 | type int, which have been changed to size_t. |
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[928] | 157 | |
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[1020] | 158 | * Importantly, for code interfacing with the duchamp::Cube and related |
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| 159 | classes, axisDim is now an array of size_t elements, rather than |
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| 160 | long. |
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| 161 | |
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[951] | 162 | * Object3D now carries its spatial map with it, rather than |
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| 163 | calculating it on the fly when requested. This saves a lot of |
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| 164 | unnecessary computational effort. |
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[928] | 165 | |
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[951] | 166 | * The warning/error interface has improved, making use of C++ |
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| 167 | exception handling. This should be compatible with external logging |
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| 168 | infrastructure (such as log4cxx). |
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| 169 | |
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[1035] | 170 | * The interface to the FitsHeader & WCS structures for external code |
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| 171 | has been improved, so that the WCS can be set up via function calls. |
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[951] | 172 | |
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| 173 | |
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| 174 | |
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[852] | 175 | Duchamp version 1.1.13 (2011/04/10) |
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| 176 | ------------------------------------- |
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| 177 | |
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| 178 | Bug fixes: |
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| 179 | |
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| 180 | * The median statistics calculations had a bug in the test for whether |
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| 181 | the array under consideration was of even size. The correction for |
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| 182 | this can mean small differences in the resulting values. This can |
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| 183 | flow through to calculated detection thresholds - please check this |
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| 184 | with your data if you use this mode! |
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| 185 | |
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| 186 | * The reconstruction code had a bug where the incorrect number of |
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| 187 | scales was being used. This occurred when the blank pixel flag was |
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| 188 | set, and when the spectral dimension was smaller than both the |
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| 189 | spatial dimensions. |
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| 190 | |
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| 191 | Other: |
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| 192 | |
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| 193 | * The default value of the blank pixel flag has been set to false, |
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| 194 | rather than true. For Duchamp, this should not matter, as it is set |
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| 195 | when the FITS file is read in. For external code using, for |
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| 196 | instance, the reconstruction algorithms, this default may be |
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| 197 | important. Having it true was contributing to the second bug listed |
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| 198 | above. It also makes more sense for it to be false unless explicitly |
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| 199 | set in some way. |
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| 200 | |
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| 201 | * The reconstruction code has been streamlined a little, reducing its |
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| 202 | memory impact and using more appropriate variable types |
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| 203 | (eg. unsigned ints instead of ints and so forth). |
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| 204 | |
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| 205 | * For those who care about the actual code base, the statistics |
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| 206 | functions have been expanded, and separated from getStats.cc into |
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| 207 | "normal" and "robust" versions. |
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| 208 | |
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| 209 | |
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[836] | 210 | Duchamp version 1.1.12 (2011/03/18) |
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| 211 | ------------------------------------- |
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| 212 | |
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| 213 | Bug fixes: |
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| 214 | |
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| 215 | * The velocity width calculations had a bug that occasionally led to |
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| 216 | very large values. The widths are calculated using the integrated |
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| 217 | spectrum, using a threshold relative to its peak. In v.1.1.10 and |
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| 218 | 1.1.11, however, the peak was searched for over the entire spectral |
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| 219 | range, rather than just the range for the current object. This led |
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| 220 | to spurious values. This has been fixed, so that the peak is only |
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| 221 | searched for within the detected ranage of the object. |
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| 222 | |
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| 223 | * Both the pixel and statistics subsections are now more carefully |
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| 224 | examined, with errors reported if there are no valid pixels in the |
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| 225 | pixel subsection, or if the statistics subsection does not intersect |
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| 226 | with the pixel subsection. |
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| 227 | |
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| 228 | Other: |
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| 229 | |
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| 230 | * The configure script has been slightly improved so that the pgsbox |
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| 231 | library is only added if PGPlot has been enabled - this is |
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| 232 | particularly necessary with the slightly changed build procedure for |
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| 233 | recent wcslib versions. |
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| 234 | |
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| 235 | * In a related note, one file - momentMap.cc - had some #include |
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| 236 | statements that failed when PGPlot (and hence pgsbox in WCSLIB) was |
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| 237 | not enabled. These were actually unnecesssary and have been removed. |
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| 238 | |
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| 239 | * There is a new input parameter - flagPlotSpectra - that allows the |
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| 240 | user to turn off the production of the spectral plots. It defaults |
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| 241 | to true (meaning the plots are produced). |
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| 242 | |
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| 243 | |
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[819] | 244 | Duchamp version 1.1.11 (2011/03/01) |
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[799] | 245 | ------------------------------------- |
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| 246 | |
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| 247 | Improvements: |
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| 248 | |
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| 249 | * The largest changes in this release involved improving the |
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| 250 | efficiency of the code, resulting in further speed-ups. The code |
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| 251 | affected was the low-level object-handling code, with the merging |
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| 252 | stages in particular showing good speed-ups. |
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| 253 | |
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| 254 | * The default value for the beam size, when the beam parameters are |
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| 255 | not in the FITS header, has been dropped. Now the default behaviour |
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| 256 | is to simply not make any beam corrections if the beam is not |
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| 257 | specified by either the FITS file or the input parameters. Thanks to |
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| 258 | Tobias Westemeier for the suggestion. |
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| 259 | |
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| 260 | * The reporting of the beam size has changed slightly to provide a bit |
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| 261 | more information. |
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| 262 | |
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| 263 | Bug Fixes: |
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| 264 | |
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[819] | 265 | * The statistics section (statSec) could be larger than the image |
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| 266 | subsection (if provided), yet the pixels required would never be |
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| 267 | read in from the FITS file. The behaviour has been changed so that |
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| 268 | the statSec, if requested, is trimmed to be wholly within the image |
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| 269 | section. |
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| 270 | |
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| 271 | * It was possible to request, for instance, spectral smoothing on a 2D |
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| 272 | image. This resulted in a blank smoothed array, which led to |
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| 273 | problems in the calculations of statistics (and hence the |
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| 274 | threshold), as well as subsequent calculations. This has been fixed, |
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| 275 | so that in cases like this the smoothing is turned off (and a |
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| 276 | warning message is displayed). |
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| 277 | |
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[799] | 278 | * There was a problem with using a MW range and subsectioning when |
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| 279 | growing objects, as a result of changes in 1.1.10. This has been |
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| 280 | fixed. |
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| 281 | |
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| 282 | * Inversion was failing when no array was allocated (not a problem for |
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| 283 | standard Duchamp, but affected its use as a library by other code). |
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| 284 | |
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[812] | 285 | * Writing text spectra would only occur when PGPlot output was enabled |
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| 286 | in the build (it was combined with the plotting of the spectral |
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[810] | 287 | graphs). This has been changed so that this output can be requested |
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[812] | 288 | without requiring PGPlot. |
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[810] | 289 | |
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[804] | 290 | * The equation for the beam size in Sec.4.2 of the User Guide was |
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| 291 | incorrect and has been fixed. |
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| 292 | |
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[819] | 293 | * Minor change to the configure script to improve the detection of the |
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| 294 | PGPlot library. |
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| 295 | |
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| 296 | Code development notes: |
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| 297 | |
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| 298 | * The main work has been additions and improvements to the interfaces |
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| 299 | for the Param and the Section classes, as well as new classes to |
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| 300 | manage the beam information. The efficiency changes mentioned above |
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| 301 | also affected the internals of some of the PixelInfo classes, and |
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| 302 | provided additional functions for judging the closeness of |
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| 303 | neighbouring objects. |
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| 304 | |
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[760] | 305 | Duchamp version 1.1.10 (2010/11/15) |
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[574] | 306 | ------------------------------------- |
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[542] | 307 | |
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[760] | 308 | Improvements: |
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| 309 | |
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| 310 | * The major change for this release is a greatly improved growing |
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| 311 | algorithm. The previous incarnation was very inefficient (testing |
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| 312 | all pixels in an object, most of which only have neighbours that are |
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| 313 | already in the object), and could take an unnecessarily large amount |
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| 314 | of time in the case of extended sources. The improved algorithm |
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| 315 | makes use of voxel flags to quickly identify those voxels not yet in |
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| 316 | an object and only examines them. For a certain test case |
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| 317 | (observations of extended Galactic HI), the time required reduced |
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[761] | 318 | from about a day to about a minute! (Note that compact sources, such |
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| 319 | as HI galaxies, will not show this degree of speedup...) Many thanks |
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| 320 | to Tara Murphy for pointing out this bug and her help in |
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| 321 | diagnosing/fixing the problem. |
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[760] | 322 | |
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| 323 | * There have been a number of further improvements to the code to |
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| 324 | speed it up, based on some profiling. The most important was the |
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| 325 | function to add pixels to a 2D object, but there were several other |
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| 326 | minor changes as well. |
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| 327 | |
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| 328 | * The minimum size of the detections can now also be specified in |
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| 329 | terms of the total number of voxels (in addition or instead of |
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| 330 | specifying the minimum spatial pixels or channels). |
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| 331 | |
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| 332 | * The way memory is allocated when reading the image has been |
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| 333 | streamlined. The amount of memory being allocated is also now |
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| 334 | reported - this is in an effort to allow users to identify problems |
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| 335 | with running out of memory. |
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| 336 | |
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| 337 | * The version number is now reported in the results and log files. |
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| 338 | |
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| 339 | * Only the filename of the input image (ie. not the leading |
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| 340 | directories) is now shown on the detection and moment-0 maps. This |
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| 341 | is to avoid problems with large directory paths being too wide for |
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| 342 | the plot. |
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| 343 | |
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| 344 | * The verification script was improved for readability (although no |
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| 345 | functional change was made). |
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| 346 | |
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| 347 | Bug fixes: |
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| 348 | |
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| 349 | * Growing was not being done when a single source was found. Now |
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| 350 | fixed. |
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| 351 | |
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| 352 | * For particular WCS setups, the RA can be interpreted as being |
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| 353 | negative, which corrupted the Source ID (ie. the IAU-format |
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| 354 | string). This has been fixed. |
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| 355 | |
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| 356 | * When the flux units were changed, problems had been seen when |
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| 357 | writing a reconstructed cube to a FITS file. Any unit change is now |
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| 358 | undone prior to writing and there should now be no problem. |
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| 359 | |
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| 360 | * Filenames with spaces in them were not handled well. New functions |
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| 361 | were included and moved to a more obvious location. These filenames |
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| 362 | now work as expected. |
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| 363 | |
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| 364 | * Spectral axes of type FREQ that had a rest frequency were not being |
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| 365 | put into velocity units. Now fixed. |
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| 366 | |
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| 367 | * Improvements to the output to screen, making sure everything is |
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| 368 | covered by the verbose flag. |
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| 369 | |
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| 370 | * Better management of the allocation of arrays. |
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| 371 | |
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| 372 | * The minSize parameter in Image was never initialised, leading to |
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| 373 | unpredictable behaviour. Now fixed. |
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| 374 | |
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| 375 | Code development notes: |
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| 376 | |
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| 377 | * New functionality includes: a function to return a vector list of |
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| 378 | voxels in an Object3D or Detection; a new generic Search function |
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| 379 | (basically a front-end to each of the individual functions); more |
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[766] | 380 | complete copy constructors for the DataArray classes; new methods |
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| 381 | for finding the velocity widths. |
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[760] | 382 | |
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| 383 | Duchamp version 1.1.9 (2010/03/26) |
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| 384 | ------------------------------------- |
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| 385 | |
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[654] | 386 | Improvements: |
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[616] | 387 | |
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[680] | 388 | * There is now the ability to save the moment-0 map as a FITS |
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| 389 | file. This is controlled by the parameters flagOutputMomentMap and |
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| 390 | fileOutputMomentMap, which work in the same way for the mask file. |
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| 391 | |
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[697] | 392 | * There is a new parameter flagRejectBeforeMerge that, when true, |
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[680] | 393 | rejects sources according to the minPix/minChannels requirements |
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| 394 | before the merging and growing is done. This defaults to false (so |
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| 395 | default behaviour is as before). Thanks to Tobias Westmeier for |
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| 396 | suggesting this and the above improvement. |
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| 397 | |
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[697] | 398 | * There is also a new parameter flagTwoStageMerging. When true (the |
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| 399 | default), newly-detected objects are merged with the first close |
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| 400 | object in the list. When false, they are simply added to the end of |
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| 401 | the list. In both cases, a second round of merging is done to pick |
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| 402 | up all close matches. |
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| 403 | |
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[680] | 404 | * The way the beam is specified in the absence of the BMAJ/BMIN/BPA |
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| 405 | parameters has been slightly changed. The use of "beamSize" was |
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| 406 | somewhat ambiguous (it meant the number of pixels covered by the |
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| 407 | beam, not the FWHM), so new parameters have been introduced. The |
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| 408 | beam can be specified by beamArea (which replaces beamSize), or |
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| 409 | beamFWHM (the FWHM of the beam in pixels). If beamFWHM is provided, |
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| 410 | it will be used, else the beamArea will be. |
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| 411 | |
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[687] | 412 | * There is a new parameter searchType that allows the user to choose |
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| 413 | how the searching is done. The behaviour up till now has been to |
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| 414 | search the 2D channel maps one at a time to build up the 3D |
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| 415 | detections. This is the default, and can be obtained by setting |
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| 416 | searchType=spatial. Alternatively, you can set searchType=spectral |
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| 417 | to do the searching in the 1D spectra. |
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| 418 | |
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[654] | 419 | * Profiling of the code has led to a few changes that have sped up |
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| 420 | some calculations, particularly those involving the median. Rather |
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| 421 | than using std::sort, the code now simply uses std::nth_element, |
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| 422 | which shows a substantial speedup factor. |
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| 423 | |
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| 424 | * When using the objectList parameter, the maps will now only show the |
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| 425 | selected objects, rather than all detected objects. |
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| 426 | |
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| 427 | * There is a new verification test that looks at the "growing" |
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| 428 | functionality. |
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| 429 | |
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| 430 | Bug fixes: |
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| 431 | |
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[670] | 432 | * When saving a mask FITS file, there was an occasional memory leak |
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| 433 | that caused Duchamp to crash (only when the cube was suitably |
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| 434 | large). This has been fixed. |
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| 435 | |
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[680] | 436 | * The median calculation had a bug that led to an incorrect value |
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| 437 | being reported. The difference will not be great (the element of an |
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| 438 | array being reported as the median was out by one), but could be |
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| 439 | noticeable depending on the dataset. |
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| 440 | |
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| 441 | * The MW range parameters did not respond to the use of a |
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| 442 | subsection. They should refer to channel ranges in the original |
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| 443 | cube, and changes have been made to the code to reflect this. |
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| 444 | |
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[654] | 445 | * There was an occasional error in writing out FITS keywords, due to |
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| 446 | the way comment strings were intialised. This has been improved and |
---|
| 447 | made more robust. |
---|
| 448 | |
---|
| 449 | * Testing with gcc-4.3.2 showed a number of compilation warnings & |
---|
| 450 | errors, which have been fixed. |
---|
| 451 | |
---|
| 452 | * The Gaussian smoothing kernel was too small - it is now made big |
---|
| 453 | enough to encompass all possible values. It was also being |
---|
| 454 | incorrectly scaled. This had no functional effect on the detection |
---|
| 455 | of objects, but for other uses was incorrect. This has been |
---|
| 456 | rectified. |
---|
| 457 | |
---|
| 458 | * Some outputs that weren't caught by the verbose flag now are. |
---|
| 459 | |
---|
| 460 | |
---|
| 461 | Code development notes: |
---|
| 462 | |
---|
| 463 | The following notes only apply if you want to use the code as a |
---|
| 464 | library, rather than the stand-alone package. These have generally |
---|
| 465 | come out of the ASKAP software development. If you just use the |
---|
| 466 | stand-alone package, they won't be a concern. |
---|
| 467 | |
---|
[616] | 468 | * The API for storing detected objects has changed, making it more |
---|
[654] | 469 | robust from a programming point of view. |
---|
[616] | 470 | |
---|
[654] | 471 | * Additional versions of some functions (and the Gaussian smoothing |
---|
| 472 | class) have been added - this has come out of the ASKAP development |
---|
| 473 | work. |
---|
| 474 | |
---|
| 475 | * A number of instances of "unsigned int" being used for loops have |
---|
| 476 | been changed to iterators or "size_t". There shouldn't be any |
---|
| 477 | functional change from this -- the code should just build more |
---|
| 478 | cleanly. |
---|
| 479 | |
---|
[687] | 480 | * The Detection class now records whether the parameters have been |
---|
| 481 | set, and unsets that flag when objects are merged. This allows |
---|
| 482 | external programs to track which objects have been merged and deal |
---|
| 483 | with them appropriately. |
---|
[654] | 484 | |
---|
[687] | 485 | |
---|
[616] | 486 | Duchamp version 1.1.8 (2009/07/20) |
---|
| 487 | ---------------------------------- |
---|
| 488 | |
---|
[542] | 489 | Improvements: |
---|
| 490 | |
---|
[572] | 491 | * The final source list can now be sorted on one of a range of object |
---|
| 492 | parameters: x-value, y-value, z-value, ra, dec, vel, w50, iflux, |
---|
| 493 | pflux (integrated and peak flux respectively), or snr. Simply use |
---|
| 494 | the new input parameter sortingParam. Its default value is vel, so |
---|
| 495 | the default behaviour stays the same. |
---|
| 496 | |
---|
[543] | 497 | * The FDR method involves calculating how many pixels are |
---|
| 498 | correlated. This previously involved multiplying the beam area by 2, |
---|
| 499 | implying that 2 neighbouring channels were correlated. This factor |
---|
| 500 | is now a user-selectable parameter, so that if you know how many |
---|
| 501 | spectral channels should be correlated, you can set the parameter |
---|
| 502 | FDRnumCorChan and the FDR calculation will be done correctly. |
---|
| 503 | |
---|
[542] | 504 | * Screen output now has more information on the growing threshold when |
---|
| 505 | the cube statistics are printed. |
---|
| 506 | |
---|
| 507 | |
---|
| 508 | Bug fixes: |
---|
| 509 | |
---|
[584] | 510 | * When reading in previous detections, there was a bug causing a |
---|
| 511 | segmentation fault. This has been fixed and made more robust. |
---|
| 512 | |
---|
[579] | 513 | * There was an apparent bug when writing out the reconstructed cubes |
---|
| 514 | to a FITS file that caused the new file to be very large. Changing |
---|
| 515 | the cfitsio function used has fixed this. |
---|
| 516 | |
---|
[574] | 517 | * Using NCP projections near the equator could result in a large |
---|
| 518 | stream of error messages, due to coordinate transformations being |
---|
| 519 | done in blank regions outside of the acceptable range of world |
---|
| 520 | coordinates. This has been fixed. |
---|
| 521 | |
---|
[542] | 522 | * The function that grows objects had a major bug, that stopped it |
---|
| 523 | working when flagAdjacent=false. This has been fixed and should work |
---|
| 524 | fine. |
---|
| 525 | |
---|
[616] | 526 | * The input parameter spectraTextFile was not being read |
---|
| 527 | properly. This has been remedied. |
---|
| 528 | |
---|
| 529 | * The units for the integrated flux were wrong for some types of pixel |
---|
| 530 | flux units. This has been fixed. |
---|
| 531 | |
---|
| 532 | * A minor bug caused incorrect calculation of the 20% widths. |
---|
| 533 | |
---|
[542] | 534 | * All calls to uint were changed to unsigned int, as some compilers |
---|
| 535 | had problems recognising that they were the same thing. |
---|
| 536 | |
---|
| 537 | * src/fitsHeader.cc was missing an include statement for stdlib.h, |
---|
| 538 | again causing some compilers to fail. |
---|
| 539 | |
---|
| 540 | |
---|
[529] | 541 | Duchamp version 1.1.7 (2009/01/16) |
---|
[520] | 542 | ---------------------------------- |
---|
| 543 | |
---|
| 544 | Improvements: |
---|
| 545 | |
---|
[522] | 546 | * The mask file that can be created with flagMask can now specify |
---|
| 547 | which object a given detected pixel belongs to, by taking the object |
---|
| 548 | ID as its value. This applies if you set flagMaskWithObjectNum=true |
---|
| 549 | (it defaults to false, which means each detected pixel has the value |
---|
| 550 | 1). Non-detected pixels still have the value 0. |
---|
[520] | 551 | |
---|
[535] | 552 | * The names of the output FITS files are now able to be specified |
---|
| 553 | directly by input parameters. These will override the default names |
---|
| 554 | that Duchamp provides. |
---|
| 555 | |
---|
[520] | 556 | * The Karma annotation file now specifies a font - previously it did |
---|
| 557 | not and so was at the mercy of whatever was specified in other |
---|
| 558 | annotation files being viewed at the same time. Please let me know |
---|
| 559 | if the font I've chosen (lucidasans-12) is not suitable. |
---|
| 560 | |
---|
| 561 | * The default flag, used in the absence of 'E', 'S' or 'N', is now '-' |
---|
| 562 | rather than blank. This will ensure that each column in the results |
---|
| 563 | file has something in it. |
---|
| 564 | |
---|
[522] | 565 | * The configure script is somewhat more robust to non-standard |
---|
| 566 | systems, particularly when the X11 libraries are in unusual |
---|
| 567 | places. It can also deal with the slightly different way that |
---|
| 568 | wcslib-4.3 installs itself. |
---|
| 569 | |
---|
[520] | 570 | * The installation part of the Makefile was altered so that the |
---|
| 571 | symbolic link Duchamp that points to Duchamp-1.1.7 does not have the |
---|
| 572 | absolute path encoded in it. This will enable the files to be moved |
---|
| 573 | around at a later date. |
---|
| 574 | |
---|
| 575 | Bug Fixes: |
---|
| 576 | |
---|
| 577 | * Fixed a bug that caused problems when the flux units were less than |
---|
| 578 | 5 characters long (e.g. 'K') |
---|
| 579 | |
---|
| 580 | * The new velocity width values were not getting proper headers in the |
---|
| 581 | VOTable output. This has been remedied. |
---|
| 582 | |
---|
| 583 | * Minor improvements to help non-pgplot use |
---|
| 584 | |
---|
| 585 | * Minor fix in WCS functionality. |
---|
| 586 | |
---|
| 587 | * Minor fixes to the FitsHeader class. |
---|
| 588 | |
---|
| 589 | * Improved FITS data reading, that doesn't require a nullarray |
---|
| 590 | array. This will reduce memory usage. |
---|
| 591 | |
---|
| 592 | * Improved subsection parsing, particularly for non-standard WCS |
---|
| 593 | systems. |
---|
| 594 | |
---|
| 595 | * Improving the memory allocation of the Cube class. |
---|
| 596 | |
---|
| 597 | * Fixed a bug that meant the growthThreshold values were sometimes |
---|
| 598 | being lost. |
---|
| 599 | |
---|
| 600 | * Improving the way the growing and merging is done, particularly in |
---|
| 601 | the case of non-adjacent merging. |
---|
| 602 | |
---|
[529] | 603 | * Fixed a scaling bug in the GaussSmooth function. |
---|
| 604 | |
---|
[520] | 605 | Other: |
---|
| 606 | |
---|
| 607 | * Numerous changes to the code that do not affect how Duchamp itself |
---|
| 608 | runs, but were necessary for code development with the Duchamp |
---|
| 609 | libraries (primarily as a part of the ASKAP code development). |
---|
| 610 | |
---|
[522] | 611 | |
---|
[482] | 612 | Duchamp version 1.1.6 (2008/09/08) |
---|
[480] | 613 | ---------------------------------- |
---|
| 614 | |
---|
| 615 | New features: |
---|
| 616 | |
---|
| 617 | * The velocity widths can now be quoted in two additional ways: the |
---|
| 618 | full width at 50% of the peak flux (ie. the FWHM) and the full width |
---|
| 619 | at 20% of the peak flux (w_50 and w_20 respectively). The w_50 |
---|
| 620 | parameter is now quoted in the results printed to the screen |
---|
| 621 | (instead of w_VEL), but all three are written to the results file. |
---|
| 622 | |
---|
| 623 | * The facility now exists to bypass the searching step and go straight |
---|
| 624 | to the output stage using a list of previously detected objects. The |
---|
| 625 | list is extracted from a previously-created log file. The user can |
---|
| 626 | change the way the spectra are plotted (e.g. choose to plot |
---|
| 627 | integrated rather than peak spectra), and select a subset of the |
---|
| 628 | detected objects to be printed to individual postscript files. Use |
---|
| 629 | the input parameter usePrevious (set to true) to use this facility, |
---|
| 630 | and provide a list of objects using the objectList parameter |
---|
| 631 | (eg. 1,2,4,7-10,15) |
---|
| 632 | |
---|
[482] | 633 | * A new parameter "growthThreshold" has been created, that goes with |
---|
| 634 | "threshold". If you manually specify a threshold, and you wish to |
---|
| 635 | grow detections, you need to manually specify a growthThreshold (in |
---|
| 636 | flux units). |
---|
| 637 | |
---|
[480] | 638 | Bug fixes: |
---|
| 639 | |
---|
[482] | 640 | * Cubes that do not have a spectral axis (such as Stokes cubes) were |
---|
| 641 | causing memory leaks and crashing, due to some assumptions of the |
---|
| 642 | existence of the spectral axis. These bugs have been fixed, so that |
---|
| 643 | Duchamp will run on such cubes, although the WCS transforms may not |
---|
| 644 | always work appropriately. Please let me know via bug reports of |
---|
| 645 | difficulties you encounter! |
---|
[480] | 646 | |
---|
[482] | 647 | * The growing function has had a few bugs fixed and is now more |
---|
| 648 | efficient. |
---|
| 649 | |
---|
| 650 | * The FDR method was previously overriding any manually-specified |
---|
| 651 | threshold. This has been fixed so that if the user specifies |
---|
| 652 | threshold=X, then the FDR method is not called. |
---|
| 653 | |
---|
| 654 | * Some undefined things were happening with textual output when no |
---|
| 655 | objects were detected. This has been fixed. |
---|
| 656 | |
---|
| 657 | * Memory leaks caused by FITS WCS irregularities have been fixed |
---|
| 658 | (specifically, if a FITS header had NAXIS=2 but more than two WCS |
---|
| 659 | axes were defined). |
---|
| 660 | |
---|
| 661 | |
---|
| 662 | |
---|
[438] | 663 | Duchamp version 1.1.5 (2008/03/20) |
---|
| 664 | ---------------------------------- |
---|
| 665 | |
---|
| 666 | Bug fixes: |
---|
| 667 | * A major bug was discovered in the calculation of integrated |
---|
| 668 | fluxes. The flux was incorrectly being weighted by the spatial size |
---|
| 669 | of the detection, resulting in a (often considerable) overestimation |
---|
[447] | 670 | of the integrated flux. This has been corrected. |
---|
[438] | 671 | |
---|
[447] | 672 | * The beam size calculation was also incorrect, being out by a factor |
---|
| 673 | of 1/ln(2). |
---|
[438] | 674 | |
---|
[447] | 675 | * The "make install" command previously failed to work properly if the |
---|
| 676 | library had not been created. This has been fixed so that the |
---|
| 677 | installation works even if there is no library file. |
---|
| 678 | |
---|
| 679 | New Features: |
---|
| 680 | * You can now provide a new flux unit string, so that the pixel fluxes |
---|
| 681 | will be converted to these new fluxes before any calculations are |
---|
| 682 | done. This is done with the newFluxUnits input parameter. The new |
---|
| 683 | units should be directly convertible from the old ones (given by the |
---|
| 684 | BUNIT header -- e.g. if BUNIT = Jy/beam, you can give newFluxUnits |
---|
| 685 | as mJy/beam, but not mJy). |
---|
| 686 | |
---|
| 687 | * You can now specify the precision used in the output files for flux, |
---|
| 688 | velocity and S/N ratio columns, via new input parameters precFlux, |
---|
| 689 | precVel and precSNR. These will apply to the VOTable output as well |
---|
| 690 | as the text table and information on the spectral plots. |
---|
| 691 | |
---|
| 692 | * The Karma annotation files previously provided just a circle at the |
---|
| 693 | spatial location of the detected object. You now have the option to |
---|
| 694 | draw a border around the detected pixels (in a similar manner to the |
---|
| 695 | PGPLOT moment maps). Karma does not do this perfectly, so the lines |
---|
| 696 | may not line up exactly with the pixel borders, so the option |
---|
| 697 | remains to keep using the circles. This is controlled by the |
---|
| 698 | parameter "annotationType", with possible options being "borders" |
---|
| 699 | (the default) or "circles". |
---|
| 700 | |
---|
| 701 | * There is a new function getMetadata() that loads the header and WCS |
---|
| 702 | data, but no pixel information. This is only of interest if you are |
---|
| 703 | doing code development with the Duchamp library -- it does not |
---|
| 704 | affect the running of Duchamp itself. |
---|
| 705 | |
---|
[425] | 706 | Duchamp version 1.1.4 (2008/02/15) |
---|
| 707 | ---------------------------------- |
---|
| 708 | |
---|
| 709 | Most of the changes incorporated in this update result from ASKAP code |
---|
| 710 | development (that makes use of some of the Duchamp functionality), |
---|
| 711 | but do not actually affect the way Duchamp runs (other than, in a |
---|
| 712 | couple of cases, making it a bit faster). Changes that are |
---|
| 713 | relevant for regular users of Duchamp are as follows: |
---|
| 714 | |
---|
| 715 | * A new option has been made available (thanks to Mary Putman et al |
---|
| 716 | for the suggestion!) to save the spectra of all detected objects in |
---|
| 717 | a text file. This has the form of one column for the spectral |
---|
| 718 | coordinates and one column of fluxes for each object. This is |
---|
| 719 | enabled by the input parameters flagTextSpectra and spectraTextFile. |
---|
| 720 | |
---|
| 721 | * Slight changes to the output include he formatting of the way the |
---|
| 722 | detected objects are written to the log file. This meant the |
---|
| 723 | verification files were also updated. Also the cube statistics are |
---|
| 724 | not printed to the results file if a user threshold is specified (as |
---|
| 725 | they are not calculated!). |
---|
| 726 | |
---|
| 727 | * The determination of beam size has been made more reliable, as has |
---|
| 728 | the BUNIT determination. |
---|
| 729 | |
---|
| 730 | * Fixed a bug that meant source merging was not done for 2D images |
---|
| 731 | (not usually a problem, as the source-finding takes care of this, |
---|
| 732 | but came up in parallelisation development). |
---|
| 733 | |
---|
[406] | 734 | Duchamp version 1.1.3 (2008/01/08) |
---|
| 735 | ---------------------------------- |
---|
[404] | 736 | |
---|
| 737 | A minor update that just improves the build process. The location of |
---|
| 738 | the wcslib include files was not specified correctly, so that some |
---|
| 739 | machines were unable to find them. The configure script has been fixed |
---|
| 740 | so that the compilation should work in all cases. |
---|
| 741 | |
---|
[405] | 742 | Some minor changes have also been made to the code in the PixelMap |
---|
[412] | 743 | directory, and to param.cc, to fix warnings or errors that may appear |
---|
| 744 | in compilation. |
---|
[404] | 745 | |
---|
[405] | 746 | However, there are no changes to the actual workings of the code in |
---|
| 747 | this minor version, so if you have a working version of Duchamp 1.1.2 |
---|
| 748 | there is probably no reason to update. |
---|
| 749 | |
---|
[389] | 750 | Duchamp version 1.1.2 (2007/12/07) |
---|
| 751 | ---------------------------------- |
---|
[349] | 752 | |
---|
[363] | 753 | Compilation: |
---|
| 754 | |
---|
[349] | 755 | * The compilation had problems working correctly when the cfitsio and |
---|
[373] | 756 | wcs libraries were not in standard locations. The configure script |
---|
[349] | 757 | has been tweaked to make sure the libraries are found. |
---|
| 758 | |
---|
| 759 | * Problems with compiling in the absence of pgplot have been fixed, |
---|
| 760 | and it should now compile fine. |
---|
| 761 | |
---|
[362] | 762 | * Improved the configure script for use with Mac OS X and gfortran. |
---|
[349] | 763 | |
---|
[363] | 764 | |
---|
| 765 | Bugfixing: |
---|
| 766 | |
---|
[362] | 767 | * A major problem with the text-based output was fixed. The widths of |
---|
| 768 | the columns were not being calculated correctly, and were running |
---|
[373] | 769 | together. This should no longer be the case. |
---|
[349] | 770 | |
---|
[374] | 771 | * There was a bug in the way Duchamp interpreted spectral axes, |
---|
| 772 | particularly AIPS types such as FELO-HEL, leading to incorrect |
---|
| 773 | scaling of the velocity axis. This has been fixed, so that |
---|
| 774 | non-standard types are now dealt with appropriately and the velocity |
---|
| 775 | scaling should be accurate. |
---|
[362] | 776 | |
---|
[376] | 777 | * Another bug meant the beam correction was always applied to the |
---|
| 778 | integrated spectra, regardless of whether the flux units involved |
---|
| 779 | the beam (e.g. Jy/beam). This has been fixed. Note that the values |
---|
| 780 | of the integrated flux presented in the results table were always |
---|
| 781 | calculated correctly. |
---|
| 782 | |
---|
[389] | 783 | * Other minor changes to improve the speed and efficiency, especially |
---|
| 784 | of the merging code. |
---|
| 785 | |
---|
[363] | 786 | New user parameters: |
---|
| 787 | |
---|
[381] | 788 | * There is now the possibility to save a FITS file that contains a |
---|
| 789 | mask array, indicating where the detected objects are. This is |
---|
| 790 | governed by the flagOutputMask parameter. |
---|
| 791 | |
---|
[363] | 792 | * The header information that is printed at the start of the results |
---|
| 793 | file -- that is, the list of parameters, the statistics of the cube, |
---|
| 794 | and the number of detections -- can now be written to a separate |
---|
| 795 | file. Set the flagSeparateHeader parameter to true or 1 and it will |
---|
| 796 | go to the file indicated by the headerFile parameter (the default is |
---|
| 797 | duchamp-Results.hdr). |
---|
| 798 | |
---|
[362] | 799 | * A "scaleMax" parameter has been added, so that the wavelet |
---|
| 800 | reconstruction can include only a specified range of scales (for |
---|
[373] | 801 | instance, if one wants to search just for narrow features such as |
---|
[362] | 802 | absorption lines). |
---|
| 803 | |
---|
[389] | 804 | * A "flagRobustStats" parameter has been added. This allows the user |
---|
| 805 | to elect to use robust statistics (median and median absolute |
---|
| 806 | deviation from the median) to estimate the noise parameters. If set |
---|
| 807 | to false, the mean and standard deviation will be used. The default |
---|
| 808 | value is true. |
---|
[362] | 809 | |
---|
[369] | 810 | New Feature: |
---|
[362] | 811 | |
---|
[369] | 812 | * When Duchamp is run on a 2D image (i.e. with no spectral output), it |
---|
| 813 | now produces a postscript file that shows information each |
---|
| 814 | individual source plus the image cutout of the source. This is |
---|
| 815 | similar to the spectral output file, but without the spectra. The |
---|
| 816 | filename is given by the spectraFile parameter. |
---|
| 817 | |
---|
[381] | 818 | * Ability to save a FITS file containing a mask array, with pixel |
---|
| 819 | values of 1 for pixels in a detected object, and 0 elsewhere. |
---|
[369] | 820 | |
---|
[381] | 821 | |
---|
[328] | 822 | Duchamp version 1.1.1 (2007/07/20) |
---|
| 823 | ------------------------------------ |
---|
| 824 | |
---|
[329] | 825 | Minor update to the release, with just a few changes: |
---|
[328] | 826 | |
---|
| 827 | * The verification script was generating diffs due to differences in |
---|
| 828 | the precision of some calculations when done on different machines. |
---|
| 829 | One of these was the integrated flux, and this has been corrected so |
---|
| 830 | that the same value should appear on all machines. |
---|
| 831 | The verification script has also changed so that just the number of |
---|
| 832 | sources and their positions are tested, as well as the |
---|
| 833 | logfiles. This should avoid the reporting of spurious differences. |
---|
| 834 | |
---|
| 835 | * The grey-scale used in the image cutouts (in the spectral plots) has |
---|
| 836 | been inverted. This makes it consistent with the scale used in the |
---|
| 837 | maps, and hopefully easier to see when printing. |
---|
| 838 | |
---|
[338] | 839 | * The configure/make system has been altered to make it easier to |
---|
| 840 | install, and to specify different external libraries. In particular, |
---|
| 841 | it is now not necessary to have PGPLOT installed on your system to |
---|
| 842 | run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, |
---|
| 843 | just without any graphical output. Some source code needed to be |
---|
[344] | 844 | restructured to make this work. Please read the README file, or the |
---|
| 845 | Installation appendix in the User's Guide, for complete details. |
---|
[328] | 846 | |
---|
[329] | 847 | * The time of completion is now written to the log file, so that the |
---|
| 848 | user can have some idea of how long the program took. |
---|
[328] | 849 | |
---|
| 850 | |
---|
[310] | 851 | Duchamp version 1.1 (2007/05/17) |
---|
[259] | 852 | ------------------------------------ |
---|
| 853 | |
---|
| 854 | Changes made since the last numbered release: |
---|
| 855 | |
---|
[295] | 856 | EFFICIENCY OF EXECUTION: |
---|
| 857 | |
---|
[259] | 858 | * Major change to the way detections are stored. They are now recorded |
---|
| 859 | via run-length encoding in the x-y plane, and stored as collections |
---|
| 860 | of channel-maps. This improves the memory usage and the speed of |
---|
[298] | 861 | execution (particularly for routines such as the merging |
---|
| 862 | routines). The memory usage has also been improved by changing the |
---|
| 863 | way the list of detected objects is stored. |
---|
[259] | 864 | |
---|
[295] | 865 | SMOOTHING: |
---|
| 866 | |
---|
[279] | 867 | * Addition of ability to spatially smooth the cube before |
---|
| 868 | searching. This is done with a Gaussian kernel, the size and shape |
---|
[287] | 869 | of which can be specified by the user, using the parameters kernMaj |
---|
| 870 | & kernMin (which are the FWHM for the major & minor axes -- if |
---|
| 871 | kernMin is not given it is assumed to match kernMaj) and kernPA (the |
---|
| 872 | position angle of the major axis). There is a new parameter |
---|
[279] | 873 | smoothType that distinguishes this method from the spectral (Hanning) |
---|
| 874 | smoothing already in use. |
---|
| 875 | |
---|
[295] | 876 | DETECTIONS: |
---|
| 877 | |
---|
[264] | 878 | * Changed the way detection is done -- now only search in 2D images, |
---|
| 879 | keeping all detections (ie. no minimum-pixel requirement). This |
---|
| 880 | should be the same as doing both the 1D and 2D searches with the |
---|
| 881 | minimum pixel requirement in, but simpler. The rejection is done at |
---|
[295] | 882 | the end after all the merging and growing has been done. This leads |
---|
| 883 | to a larger number of intermediate detections (ie. the number |
---|
| 884 | before merging), which may increase the run-time slightly, although |
---|
| 885 | this is offset by the changes to the efficiency (see above). |
---|
[264] | 886 | |
---|
| 887 | * Increased the range over which objects can be grown to match the |
---|
| 888 | threshSpatial & threshVelocity parameters, as well as rejecting new |
---|
| 889 | pixels based on the BLANK and MW tests. |
---|
| 890 | |
---|
[295] | 891 | INPUTS: |
---|
[259] | 892 | |
---|
[287] | 893 | * There has been a subtle change in the way BLANK pixels are dealt |
---|
| 894 | with. To enable trimming of BLANK pixels, users should use the new |
---|
| 895 | parameter flagTrim. The parameters flagBlankPix and blankPixVal are |
---|
[295] | 896 | no longer accessible via the parameter file -- warning messages are |
---|
| 897 | given if they are provided in the parameter file. |
---|
[287] | 898 | |
---|
[295] | 899 | * Added ability to specify a statsec, so that the statistics are only |
---|
| 900 | calculated from a given subsection of the cube, rather than the full |
---|
| 901 | cube. |
---|
| 902 | |
---|
| 903 | * The subsections can also specify the ability to remove a border of n |
---|
| 904 | pixels from the edges of an axis (ie. n from the start and from the |
---|
| 905 | end) -- as requested in Trac ticket #5. |
---|
| 906 | |
---|
| 907 | * Changed the default value of the reconDim parameter from 3 to 1, and |
---|
| 908 | the default value of the flagATrous parameter to false. |
---|
| 909 | |
---|
| 910 | OUTPUTS: |
---|
| 911 | |
---|
[279] | 912 | * The output now includes three different estimates of the "centre" of |
---|
| 913 | the detection: peak location, centroid (flux-weighted), or average. |
---|
| 914 | |
---|
[295] | 915 | * Some slight improvements to the user feedback during execution. |
---|
| 916 | |
---|
[282] | 917 | * Spectral output now includes the baseline, if one was fitted. The |
---|
| 918 | format of the plot headers is slightly changed, to stop information |
---|
| 919 | falling off the edge of the page. |
---|
[279] | 920 | |
---|
[295] | 921 | * Added command-line option -x to directly disable the PGPLOT X-window |
---|
| 922 | map plotting. This overrides the setting of flagXOutput in the |
---|
| 923 | parameter file. |
---|
[259] | 924 | |
---|
[295] | 925 | * Fallback spectral units (in case the FITS header fails to record |
---|
| 926 | them) changed to SPC, but code has been fixed so that any problem |
---|
| 927 | should be caught before this becomes an issue. |
---|
| 928 | |
---|
| 929 | BUGFIXES: |
---|
| 930 | |
---|
[259] | 931 | * Fixed bug (Trac ticket #4) that meant the velocity units were not |
---|
| 932 | correctly dealt with. Duchamp should be more robust for different |
---|
| 933 | velocity axis setups now. |
---|
| 934 | |
---|
| 935 | * Fixed bug (ticket #9) with the VOTable output, where the tags were |
---|
| 936 | not closing. |
---|
| 937 | |
---|
[305] | 938 | * Fixed a bug that meant the integrated fluxes were not calculated |
---|
| 939 | properly -- no allowance was made for the number of spatial |
---|
| 940 | pixels. This should also work properly for 2D images now as well. |
---|
| 941 | |
---|
[264] | 942 | * Fixed minor bug in calculating the flux threshold from the p-value |
---|
| 943 | threshold when the FDR method is used. This did not affect the |
---|
| 944 | actual thresholding, merely the quoted flux threshold in the results |
---|
| 945 | file. Also, the MW channels are kept out of the p-value threshold |
---|
| 946 | determination if they are being flagged. |
---|
| 947 | |
---|
[259] | 948 | |
---|
| 949 | |
---|
[211] | 950 | Duchamp version 1.0.7 (2006/11/22) |
---|
| 951 | ---------------------------------- |
---|
| 952 | |
---|
| 953 | One new feature, and some improvements and bug-fixes. |
---|
| 954 | |
---|
[264] | 955 | * The user can now elect to Hanning-smooth the spectral direction of |
---|
| 956 | the cube before the searching is done. This can be done instead of the |
---|
| 957 | wavelet reconstruction (although if both are selected, the |
---|
| 958 | reconstruction takes precendence). This functionality is switched on |
---|
| 959 | and off by the flagSmooth parameter, and the width of the Hanning |
---|
| 960 | kernel is governed by the hanningWidth parameter. |
---|
[211] | 961 | |
---|
[264] | 962 | * The smoothed array can also be written to a FITS file and read in at |
---|
| 963 | the start in the same manner as the reconstructed array. |
---|
[211] | 964 | |
---|
[264] | 965 | * Several improvements have been made to the memory |
---|
| 966 | management. Several memory leaks were fixed, and the memory usage of |
---|
| 967 | Duchamp is considerably less, which will be a help for running it on |
---|
| 968 | large cubes. The speed of some routines has also been improved, by |
---|
| 969 | removing unnecessarily repetitive loops. |
---|
[211] | 970 | |
---|
[287] | 971 | * The sorting routines have been changed, and should now be slightly quicker |
---|
[215] | 972 | (and a bit more robust). |
---|
| 973 | |
---|
[287] | 974 | * Enabled the scale bar (plotted on the 0th moment map in the spectral |
---|
| 975 | output file) to be able to deal with much finer spatial scales (as |
---|
| 976 | may be expected from VLBI data). |
---|
[211] | 977 | |
---|
[215] | 978 | * Other minor changes to code and presentation. |
---|
[211] | 979 | |
---|
| 980 | |
---|
[194] | 981 | Duchamp version 1.0.6 (2006/11/01) |
---|
| 982 | ---------------------------------- |
---|
| 983 | |
---|
| 984 | Some incremental improvements and changes to the code: |
---|
| 985 | |
---|
| 986 | * The statistics used for the detection are now calculated once for |
---|
| 987 | the entire cube, rather than being calculated separately for each |
---|
| 988 | channel map and spectrum. This results in a uniform threshold value |
---|
| 989 | across the entire cube. The way the statistics calculations are |
---|
| 990 | implemented in the code was changed, using a new statistics class. |
---|
| 991 | |
---|
| 992 | * This means we can report a peak signal-to-noise value for each |
---|
| 993 | detection. This is given in the text-based output, as well as in the |
---|
| 994 | summary information above the spectral output for each source. |
---|
| 995 | |
---|
[195] | 996 | * The user can now elect not to have the moment map displayed in a |
---|
| 997 | PGPlot window, through the use of the new flagXOutput |
---|
| 998 | parameter. This should help in cases of running Duchamp on a dumb |
---|
| 999 | terminal (with no X-display capabilities), or as part of a batch |
---|
| 1000 | script where the continual popping-up of the PGPlot window might |
---|
| 1001 | become annoying. |
---|
| 1002 | |
---|
[265] | 1003 | * There are different Flags reported for the case of an object lying on |
---|
[194] | 1004 | the spatial edge and spectral edge of the cube (E and S respectively). |
---|
| 1005 | |
---|
| 1006 | * A few minor bug fixes: |
---|
| 1007 | - When providing a subsection, any axes with the range given by * |
---|
| 1008 | had the pixel values offset incorrectly. This has been fixed. |
---|
| 1009 | - Negative searches now correctly invert the reconstructed array |
---|
| 1010 | when it is read in from a file. |
---|
| 1011 | |
---|
| 1012 | * Other minor changes to the code, to improve memory handling and |
---|
| 1013 | remove redundant arrays and variables. |
---|
| 1014 | |
---|
| 1015 | |
---|
[146] | 1016 | Duchamp version 1.0.5 (2006/09/06) |
---|
[142] | 1017 | ---------------------------------- |
---|
| 1018 | |
---|
[146] | 1019 | Since version 1.0, there have been a range of mostly minor |
---|
| 1020 | changes. These are generally bug-fixes, thanks to feedback from a |
---|
[157] | 1021 | number of users, as well as a few extra features. |
---|
[146] | 1022 | |
---|
[157] | 1023 | Here is a summary of the changes since version 1.0: |
---|
[142] | 1024 | |
---|
[157] | 1025 | USER INTERFACE: |
---|
[146] | 1026 | |
---|
[142] | 1027 | * The user is now able to enter the value of flag parameters in the |
---|
| 1028 | parameter file as strings, as well as integers (so one can enter |
---|
| 1029 | true or 1 to give the same result). |
---|
| 1030 | |
---|
[157] | 1031 | GRAPHICAL OUTPUT: |
---|
| 1032 | |
---|
[142] | 1033 | * Added a new function that draws the edge of the blank region on the |
---|
[146] | 1034 | maps and image cutouts. There is a new flag parameter -- |
---|
| 1035 | drawBlankEdges -- that controls the use of this function (the |
---|
| 1036 | default is true). |
---|
| 1037 | Also, the edge of the field is plotted on the image cutouts as a |
---|
| 1038 | yellow line. This distinguishes it from the purple blank pixel |
---|
| 1039 | dividing line. |
---|
[142] | 1040 | |
---|
[146] | 1041 | * The size of the tick mark in the image cutout (indicating the |
---|
| 1042 | spatial scale of the image) is now adaptable, so that it shows the |
---|
| 1043 | scale that best fits the image (ranging from 1 arcsec to 15 |
---|
| 1044 | degrees). (This is a change from the previous standard length of 15 |
---|
| 1045 | arcmin.) |
---|
[142] | 1046 | |
---|
[113] | 1047 | * The zoomed spectrum had its flux scale determined by all points in |
---|
[146] | 1048 | the zoom box,including those flagged by the Milky Way (MW) |
---|
| 1049 | range. This has been fixed so that any MW channels will not affect |
---|
| 1050 | the flux scaling, potentially improving the appearance of objects |
---|
| 1051 | detected close in velocity to strong MW emission or absorption. |
---|
[112] | 1052 | |
---|
[157] | 1053 | * Improved Karma Annotation file output, so that files without good |
---|
| 1054 | WCS are dealt with appropriately. |
---|
| 1055 | |
---|
| 1056 | TEXT-BASED OUTPUT: |
---|
| 1057 | |
---|
[113] | 1058 | * The position resolution in the IAU-format names has been increased, |
---|
| 1059 | so that distinct objects close to one another are more readily |
---|
| 1060 | distinguished. Overlapping sources at different velocities may |
---|
| 1061 | still have the same name, but this is a more general problem. |
---|
[112] | 1062 | |
---|
[146] | 1063 | * The presentation of the results in tabular format has been improved, |
---|
| 1064 | so that the precision of faint sources is sufficient to show their |
---|
| 1065 | flux, for instance, is not 0. This also applies to the information |
---|
| 1066 | presented above the spectral plots. |
---|
[112] | 1067 | |
---|
[146] | 1068 | * Improved error and warning reporting, so that the formatting and |
---|
| 1069 | presentation of information is clearer. |
---|
| 1070 | |
---|
[157] | 1071 | FITS I/O RELATED: |
---|
| 1072 | |
---|
[172] | 1073 | * The previous version was did not deal well with 4 (or greater) |
---|
| 1074 | dimensions in the FITS file -- the memory allocation was badly done, |
---|
| 1075 | and the axes needed to be in a particular order. This has been |
---|
| 1076 | fixed, so that the FITS I/O routines can now handle any sized FITS |
---|
| 1077 | file, with axes in any order (as long as there are two spatial and one |
---|
| 1078 | spectral axes). |
---|
[157] | 1079 | |
---|
| 1080 | * When the FITS file does not have a rest frequency defined, there is |
---|
| 1081 | no way to transform the frequency axis into velocity. In this case, |
---|
| 1082 | the spectral axis is left as frequency, and put into units of MHz. |
---|
| 1083 | |
---|
[172] | 1084 | * If the beam size is not indicated by the FITS header (through the |
---|
| 1085 | BMAJ and BMIN keywords), the user can manually specify the size |
---|
| 1086 | through the parameter file (using parameter beamSize). |
---|
| 1087 | |
---|
| 1088 | * The FITS I/O routines make use of the command fits_file_exists. This |
---|
| 1089 | was introduced into the CFITSIO package from version 2.5, so Duchamp |
---|
| 1090 | will only work with this version or higher. Version 3+ is preferred. |
---|
| 1091 | |
---|
[157] | 1092 | OTHER BUG-FIXING: |
---|
| 1093 | |
---|
| 1094 | * Several bugs related to the blank-pixels were dealt with. |
---|
| 1095 | The correct values were not propagating through correctly, meaning |
---|
| 1096 | that the default values were being used. Also, there was the |
---|
| 1097 | potential for blank pixels to be detected when the FDR method was |
---|
| 1098 | used. Finally, the image cutout displays occasionally did not |
---|
| 1099 | obscure the blank pixels. All these problems should be fixed now. |
---|
| 1100 | |
---|
| 1101 | * The FDR setup routine was occasionally failing with a segmentation |
---|
| 1102 | fault, due to it accessing unallocated memory. This has been fixed. |
---|
| 1103 | |
---|
| 1104 | * Fixed bugs that affected the way 2D images (rather than 3D cubes) |
---|
| 1105 | were dealt with. The minChannels test failed when minChannels=0. |
---|
| 1106 | |
---|
[165] | 1107 | * If there is no beam information in the FITS header, the user can now |
---|
| 1108 | enter a beam size as a parameter. |
---|
| 1109 | |
---|
[146] | 1110 | * Other minor fixes to the code, to improve its structure and |
---|
| 1111 | robustness. |
---|
| 1112 | |
---|
| 1113 | |
---|
[112] | 1114 | Duchamp version 1.0 (2006/06/30) |
---|
| 1115 | -------------------------------- |
---|
| 1116 | |
---|
[113] | 1117 | The first full release version. |
---|
| 1118 | |
---|
| 1119 | Several major changes compared to previous version: |
---|
| 1120 | |
---|
| 1121 | * Incorporated a FitsHeader class, to keep track of header information |
---|
| 1122 | (including WCS) from the FITS file. All units-related calculations |
---|
| 1123 | are done with this class, such as conversion to velocity, and |
---|
| 1124 | pixel-to-WCS conversion. The main advantage of this is improved |
---|
| 1125 | speed of execution, more adaptable to different units, and improved |
---|
| 1126 | code (easier for me!). |
---|
| 1127 | |
---|
| 1128 | * Able to select the dimensionality of the reconstruction, rather than |
---|
| 1129 | just doing it in 3-D. |
---|
| 1130 | |
---|
| 1131 | * Robust text output, so that the columns are sized correctly given |
---|
| 1132 | the data being written, and the relevant units (derived from the |
---|
| 1133 | FITS header) are included in the output table. |
---|
| 1134 | |
---|
| 1135 | * Improved the way the reconstructed image is saved and read back in, |
---|
| 1136 | with a better naming scheme and a better set of new FITS header |
---|
| 1137 | keywords. The MW headers are now not written. |
---|
| 1138 | |
---|
| 1139 | Other, more minor changes include: |
---|
| 1140 | |
---|
| 1141 | * MW channels now not set to 0, but just ignored for searching |
---|
| 1142 | purposes (and for the scaling of the spectral output -- they are |
---|
| 1143 | plotted though and highlighted with a hashed box). |
---|
| 1144 | |
---|
| 1145 | * The scale bar in the moment map in the spectral output file has its |
---|
| 1146 | length indicated. |
---|
| 1147 | |
---|
| 1148 | * Improved VOTable output, with more information about the way Duchamp |
---|
| 1149 | was run. |
---|
| 1150 | |
---|
| 1151 | * Made sure all statistics calculations in the reconstruction are |
---|
| 1152 | based on robust (ie. median) methods. |
---|
| 1153 | |
---|
| 1154 | Also moved to an autoconf based configure/make compilation, for ease of use. |
---|
| 1155 | |
---|
| 1156 | |
---|
| 1157 | Duchamp version 0.9.2 (2006/06/27) |
---|
| 1158 | -------------------------------- |
---|
| 1159 | |
---|
| 1160 | * Added the use of warning flags for detections: for either edge |
---|
| 1161 | location or negative enclosed flux. |
---|
| 1162 | |
---|
| 1163 | * A new command line option added so that the user can specify a FITS |
---|
| 1164 | file to be searched with the default parameters, rather than giving |
---|
| 1165 | a full parameter file. |
---|
| 1166 | |
---|
| 1167 | * The scale bar on the moment cutout now works in general case, using |
---|
| 1168 | an iterative process to get to the correct length. |
---|
| 1169 | |
---|
| 1170 | * RA axes are now done correctly on the full-scale maps. |
---|
| 1171 | |
---|
| 1172 | * Various coding fixes, improving the readability of the code, |
---|
| 1173 | particularly regarding the declaration of temporary variables. |
---|
| 1174 | |
---|
| 1175 | * Changed the way the time of execution is called : now using time.h |
---|
| 1176 | functions, rather than a system call. |
---|
| 1177 | |
---|
| 1178 | * Changed output in Detection/outputDetection.cc for the pixel |
---|
| 1179 | information of detected objects (the info printed above the spectral |
---|
| 1180 | plots) -- now print out number of voxels in object, and have |
---|
| 1181 | improved the formatting a little. |
---|
| 1182 | |
---|
| 1183 | * Improved the functionality of saving the FITS file containing the |
---|
| 1184 | reconstructed array. Added ability to save and read back in the MW |
---|
| 1185 | parameters when saving a reconstructed cube (if a reconstructed cube |
---|
| 1186 | has different MW range to that being considered, it would cause |
---|
| 1187 | problems). ReadRecon now just returns a FAILURE and will reconstruct |
---|
| 1188 | the cube anew. |
---|
| 1189 | |
---|
| 1190 | * Changed default value of flagGrowth to 0. |
---|
| 1191 | |
---|
| 1192 | |
---|
| 1193 | |
---|
| 1194 | Duchamp version 0.9 (2006/05/05) |
---|
| 1195 | -------------------------------- |
---|
| 1196 | |
---|
| 1197 | First public release version. |
---|