Duchamp version 1.1.4 (2008/02/15) ---------------------------------- Most of the changes incorporated in this update result from ASKAP code development (that makes use of some of the Duchamp functionality), but do not actually affect the way Duchamp runs (other than, in a couple of cases, making it a bit faster). Changes that are relevant for regular users of Duchamp are as follows: * A new option has been made available (thanks to Mary Putman et al for the suggestion!) to save the spectra of all detected objects in a text file. This has the form of one column for the spectral coordinates and one column of fluxes for each object. This is enabled by the input parameters flagTextSpectra and spectraTextFile. * Slight changes to the output include he formatting of the way the detected objects are written to the log file. This meant the verification files were also updated. Also the cube statistics are not printed to the results file if a user threshold is specified (as they are not calculated!). * The determination of beam size has been made more reliable, as has the BUNIT determination. * Fixed a bug that meant source merging was not done for 2D images (not usually a problem, as the source-finding takes care of this, but came up in parallelisation development). Duchamp version 1.1.3 (2008/01/08) ---------------------------------- A minor update that just improves the build process. The location of the wcslib include files was not specified correctly, so that some machines were unable to find them. The configure script has been fixed so that the compilation should work in all cases. Some minor changes have also been made to the code in the PixelMap directory, and to param.cc, to fix warnings or errors that may appear in compilation. However, there are no changes to the actual workings of the code in this minor version, so if you have a working version of Duchamp 1.1.2 there is probably no reason to update. Duchamp version 1.1.2 (2007/12/07) ---------------------------------- Compilation: * The compilation had problems working correctly when the cfitsio and wcs libraries were not in standard locations. The configure script has been tweaked to make sure the libraries are found. * Problems with compiling in the absence of pgplot have been fixed, and it should now compile fine. * Improved the configure script for use with Mac OS X and gfortran. Bugfixing: * A major problem with the text-based output was fixed. The widths of the columns were not being calculated correctly, and were running together. This should no longer be the case. * There was a bug in the way Duchamp interpreted spectral axes, particularly AIPS types such as FELO-HEL, leading to incorrect scaling of the velocity axis. This has been fixed, so that non-standard types are now dealt with appropriately and the velocity scaling should be accurate. * Another bug meant the beam correction was always applied to the integrated spectra, regardless of whether the flux units involved the beam (e.g. Jy/beam). This has been fixed. Note that the values of the integrated flux presented in the results table were always calculated correctly. * Other minor changes to improve the speed and efficiency, especially of the merging code. New user parameters: * There is now the possibility to save a FITS file that contains a mask array, indicating where the detected objects are. This is governed by the flagOutputMask parameter. * The header information that is printed at the start of the results file -- that is, the list of parameters, the statistics of the cube, and the number of detections -- can now be written to a separate file. Set the flagSeparateHeader parameter to true or 1 and it will go to the file indicated by the headerFile parameter (the default is duchamp-Results.hdr). * A "scaleMax" parameter has been added, so that the wavelet reconstruction can include only a specified range of scales (for instance, if one wants to search just for narrow features such as absorption lines). * A "flagRobustStats" parameter has been added. This allows the user to elect to use robust statistics (median and median absolute deviation from the median) to estimate the noise parameters. If set to false, the mean and standard deviation will be used. The default value is true. New Feature: * When Duchamp is run on a 2D image (i.e. with no spectral output), it now produces a postscript file that shows information each individual source plus the image cutout of the source. This is similar to the spectral output file, but without the spectra. The filename is given by the spectraFile parameter. * Ability to save a FITS file containing a mask array, with pixel values of 1 for pixels in a detected object, and 0 elsewhere. Duchamp version 1.1.1 (2007/07/20) ------------------------------------ Minor update to the release, with just a few changes: * The verification script was generating diffs due to differences in the precision of some calculations when done on different machines. One of these was the integrated flux, and this has been corrected so that the same value should appear on all machines. The verification script has also changed so that just the number of sources and their positions are tested, as well as the logfiles. This should avoid the reporting of spurious differences. * The grey-scale used in the image cutouts (in the spectral plots) has been inverted. This makes it consistent with the scale used in the maps, and hopefully easier to see when printing. * The configure/make system has been altered to make it easier to install, and to specify different external libraries. In particular, it is now not necessary to have PGPLOT installed on your system to run Duchamp. In the absence of PGPLOT, Duchamp will run as normal, just without any graphical output. Some source code needed to be restructured to make this work. Please read the README file, or the Installation appendix in the User's Guide, for complete details. * The time of completion is now written to the log file, so that the user can have some idea of how long the program took. Duchamp version 1.1 (2007/05/17) ------------------------------------ Changes made since the last numbered release: EFFICIENCY OF EXECUTION: * Major change to the way detections are stored. They are now recorded via run-length encoding in the x-y plane, and stored as collections of channel-maps. This improves the memory usage and the speed of execution (particularly for routines such as the merging routines). The memory usage has also been improved by changing the way the list of detected objects is stored. SMOOTHING: * Addition of ability to spatially smooth the cube before searching. This is done with a Gaussian kernel, the size and shape of which can be specified by the user, using the parameters kernMaj & kernMin (which are the FWHM for the major & minor axes -- if kernMin is not given it is assumed to match kernMaj) and kernPA (the position angle of the major axis). There is a new parameter smoothType that distinguishes this method from the spectral (Hanning) smoothing already in use. DETECTIONS: * Changed the way detection is done -- now only search in 2D images, keeping all detections (ie. no minimum-pixel requirement). This should be the same as doing both the 1D and 2D searches with the minimum pixel requirement in, but simpler. The rejection is done at the end after all the merging and growing has been done. This leads to a larger number of intermediate detections (ie. the number before merging), which may increase the run-time slightly, although this is offset by the changes to the efficiency (see above). * Increased the range over which objects can be grown to match the threshSpatial & threshVelocity parameters, as well as rejecting new pixels based on the BLANK and MW tests. INPUTS: * There has been a subtle change in the way BLANK pixels are dealt with. To enable trimming of BLANK pixels, users should use the new parameter flagTrim. The parameters flagBlankPix and blankPixVal are no longer accessible via the parameter file -- warning messages are given if they are provided in the parameter file. * Added ability to specify a statsec, so that the statistics are only calculated from a given subsection of the cube, rather than the full cube. * The subsections can also specify the ability to remove a border of n pixels from the edges of an axis (ie. n from the start and from the end) -- as requested in Trac ticket #5. * Changed the default value of the reconDim parameter from 3 to 1, and the default value of the flagATrous parameter to false. OUTPUTS: * The output now includes three different estimates of the "centre" of the detection: peak location, centroid (flux-weighted), or average. * Some slight improvements to the user feedback during execution. * Spectral output now includes the baseline, if one was fitted. The format of the plot headers is slightly changed, to stop information falling off the edge of the page. * Added command-line option -x to directly disable the PGPLOT X-window map plotting. This overrides the setting of flagXOutput in the parameter file. * Fallback spectral units (in case the FITS header fails to record them) changed to SPC, but code has been fixed so that any problem should be caught before this becomes an issue. BUGFIXES: * Fixed bug (Trac ticket #4) that meant the velocity units were not correctly dealt with. Duchamp should be more robust for different velocity axis setups now. * Fixed bug (ticket #9) with the VOTable output, where the tags were not closing. * Fixed a bug that meant the integrated fluxes were not calculated properly -- no allowance was made for the number of spatial pixels. This should also work properly for 2D images now as well. * Fixed minor bug in calculating the flux threshold from the p-value threshold when the FDR method is used. This did not affect the actual thresholding, merely the quoted flux threshold in the results file. Also, the MW channels are kept out of the p-value threshold determination if they are being flagged. Duchamp version 1.0.7 (2006/11/22) ---------------------------------- One new feature, and some improvements and bug-fixes. * The user can now elect to Hanning-smooth the spectral direction of the cube before the searching is done. This can be done instead of the wavelet reconstruction (although if both are selected, the reconstruction takes precendence). This functionality is switched on and off by the flagSmooth parameter, and the width of the Hanning kernel is governed by the hanningWidth parameter. * The smoothed array can also be written to a FITS file and read in at the start in the same manner as the reconstructed array. * Several improvements have been made to the memory management. Several memory leaks were fixed, and the memory usage of Duchamp is considerably less, which will be a help for running it on large cubes. The speed of some routines has also been improved, by removing unnecessarily repetitive loops. * The sorting routines have been changed, and should now be slightly quicker (and a bit more robust). * Enabled the scale bar (plotted on the 0th moment map in the spectral output file) to be able to deal with much finer spatial scales (as may be expected from VLBI data). * Other minor changes to code and presentation. Duchamp version 1.0.6 (2006/11/01) ---------------------------------- Some incremental improvements and changes to the code: * The statistics used for the detection are now calculated once for the entire cube, rather than being calculated separately for each channel map and spectrum. This results in a uniform threshold value across the entire cube. The way the statistics calculations are implemented in the code was changed, using a new statistics class. * This means we can report a peak signal-to-noise value for each detection. This is given in the text-based output, as well as in the summary information above the spectral output for each source. * The user can now elect not to have the moment map displayed in a PGPlot window, through the use of the new flagXOutput parameter. This should help in cases of running Duchamp on a dumb terminal (with no X-display capabilities), or as part of a batch script where the continual popping-up of the PGPlot window might become annoying. * There are different Flags reported for the case of an object lying on the spatial edge and spectral edge of the cube (E and S respectively). * A few minor bug fixes: - When providing a subsection, any axes with the range given by * had the pixel values offset incorrectly. This has been fixed. - Negative searches now correctly invert the reconstructed array when it is read in from a file. * Other minor changes to the code, to improve memory handling and remove redundant arrays and variables. Duchamp version 1.0.5 (2006/09/06) ---------------------------------- Since version 1.0, there have been a range of mostly minor changes. These are generally bug-fixes, thanks to feedback from a number of users, as well as a few extra features. Here is a summary of the changes since version 1.0: USER INTERFACE: * The user is now able to enter the value of flag parameters in the parameter file as strings, as well as integers (so one can enter true or 1 to give the same result). GRAPHICAL OUTPUT: * Added a new function that draws the edge of the blank region on the maps and image cutouts. There is a new flag parameter -- drawBlankEdges -- that controls the use of this function (the default is true). Also, the edge of the field is plotted on the image cutouts as a yellow line. This distinguishes it from the purple blank pixel dividing line. * The size of the tick mark in the image cutout (indicating the spatial scale of the image) is now adaptable, so that it shows the scale that best fits the image (ranging from 1 arcsec to 15 degrees). (This is a change from the previous standard length of 15 arcmin.) * The zoomed spectrum had its flux scale determined by all points in the zoom box,including those flagged by the Milky Way (MW) range. This has been fixed so that any MW channels will not affect the flux scaling, potentially improving the appearance of objects detected close in velocity to strong MW emission or absorption. * Improved Karma Annotation file output, so that files without good WCS are dealt with appropriately. TEXT-BASED OUTPUT: * The position resolution in the IAU-format names has been increased, so that distinct objects close to one another are more readily distinguished. Overlapping sources at different velocities may still have the same name, but this is a more general problem. * The presentation of the results in tabular format has been improved, so that the precision of faint sources is sufficient to show their flux, for instance, is not 0. This also applies to the information presented above the spectral plots. * Improved error and warning reporting, so that the formatting and presentation of information is clearer. FITS I/O RELATED: * The previous version was did not deal well with 4 (or greater) dimensions in the FITS file -- the memory allocation was badly done, and the axes needed to be in a particular order. This has been fixed, so that the FITS I/O routines can now handle any sized FITS file, with axes in any order (as long as there are two spatial and one spectral axes). * When the FITS file does not have a rest frequency defined, there is no way to transform the frequency axis into velocity. In this case, the spectral axis is left as frequency, and put into units of MHz. * If the beam size is not indicated by the FITS header (through the BMAJ and BMIN keywords), the user can manually specify the size through the parameter file (using parameter beamSize). * The FITS I/O routines make use of the command fits_file_exists. This was introduced into the CFITSIO package from version 2.5, so Duchamp will only work with this version or higher. Version 3+ is preferred. OTHER BUG-FIXING: * Several bugs related to the blank-pixels were dealt with. The correct values were not propagating through correctly, meaning that the default values were being used. Also, there was the potential for blank pixels to be detected when the FDR method was used. Finally, the image cutout displays occasionally did not obscure the blank pixels. All these problems should be fixed now. * The FDR setup routine was occasionally failing with a segmentation fault, due to it accessing unallocated memory. This has been fixed. * Fixed bugs that affected the way 2D images (rather than 3D cubes) were dealt with. The minChannels test failed when minChannels=0. * If there is no beam information in the FITS header, the user can now enter a beam size as a parameter. * Other minor fixes to the code, to improve its structure and robustness. Duchamp version 1.0 (2006/06/30) -------------------------------- The first full release version. Several major changes compared to previous version: * Incorporated a FitsHeader class, to keep track of header information (including WCS) from the FITS file. All units-related calculations are done with this class, such as conversion to velocity, and pixel-to-WCS conversion. The main advantage of this is improved speed of execution, more adaptable to different units, and improved code (easier for me!). * Able to select the dimensionality of the reconstruction, rather than just doing it in 3-D. * Robust text output, so that the columns are sized correctly given the data being written, and the relevant units (derived from the FITS header) are included in the output table. * Improved the way the reconstructed image is saved and read back in, with a better naming scheme and a better set of new FITS header keywords. The MW headers are now not written. Other, more minor changes include: * MW channels now not set to 0, but just ignored for searching purposes (and for the scaling of the spectral output -- they are plotted though and highlighted with a hashed box). * The scale bar in the moment map in the spectral output file has its length indicated. * Improved VOTable output, with more information about the way Duchamp was run. * Made sure all statistics calculations in the reconstruction are based on robust (ie. median) methods. Also moved to an autoconf based configure/make compilation, for ease of use. Duchamp version 0.9.2 (2006/06/27) -------------------------------- * Added the use of warning flags for detections: for either edge location or negative enclosed flux. * A new command line option added so that the user can specify a FITS file to be searched with the default parameters, rather than giving a full parameter file. * The scale bar on the moment cutout now works in general case, using an iterative process to get to the correct length. * RA axes are now done correctly on the full-scale maps. * Various coding fixes, improving the readability of the code, particularly regarding the declaration of temporary variables. * Changed the way the time of execution is called : now using time.h functions, rather than a system call. * Changed output in Detection/outputDetection.cc for the pixel information of detected objects (the info printed above the spectral plots) -- now print out number of voxels in object, and have improved the formatting a little. * Improved the functionality of saving the FITS file containing the reconstructed array. Added ability to save and read back in the MW parameters when saving a reconstructed cube (if a reconstructed cube has different MW range to that being considered, it would cause problems). ReadRecon now just returns a FAILURE and will reconstruct the cube anew. * Changed default value of flagGrowth to 0. Duchamp version 0.9 (2006/05/05) -------------------------------- First public release version.