Duchamp version 1.6.2 (2017/09/26) ---------------------------------- A patch release after a long hiatus! This addresses a bunch of bugs and other issues that have been identified: * The plotting of spectra was failing when spectralMethod=peak was used. This has been fixed, with the consequent fixing of the verification scripts. * Numerous patches that were identified during the course of ASKAPsoft development have been incorporated back into the Duchamp code-base. These largely either provided additional flexibility for particular functions & classes, or fix bugs. The latter include: - Applying offsets for Object3D spatial maps - Correctly setting offsets in 2D images - Fixes to some compilation errors when using more recent (gcc 6+) compilers * The sizes of ellipses plotted in Karma annotation files where 60x too big (being given in arcmin rather than degrees). * A few fixes to the user guide have also been made, correcting some minor errors in equations. Duchamp version 1.6.1 (2014/05/01) ---------------------------------- Principal reason for the release is to fix a memory leak. This was occuring when making blank pixel masks, particularly in the parameterisation step. It was apparent with large files and large numbers of sources. Thanks to Quang Nguyen for raising the bug and helping with the identification of the problem. For those interested in the code base itself, all boolean masks have been moved to vector types, with the consequent change of interface for some functions (including the statistics functions, Gaussian smoothing, and some spectral utility functions). A few other potential memory leaks were identified and fixed. To aid the debugging, the progress bar now also reports the percentage complete as well as the set of hashes. Duchamp version 1.6 (2014/04/22) -------------------------------- Improvements and bug fixes: * When searching for negative features while using baseline subtraction, the parameterisation of the resulting detections was not being done correctly. Duchamp now correctly identifies the peak absorption location and measures the peak as being the peak absorption from the fitted continuum level. A future release will add more absorption-line-oriented parameters. * The way the borders of detections are displayed in annotation files has been improved. Duchamp now writes them in a polygon or join-the-dots fashion. This reduces the size of the annotation files, and is now compatible with the CASA viewer. * The VOTables now refer to version 1.3 of the VOTable schema. Note that they still use the old COOSYS method of specifying the coordinates. Moving to the preferred STC method will happen in a future release. * There were some problems with the storage and recovery of parameters in the binary catalogue - these have been fixed. * The BITPIX keyword in the mask FITS files that Duchamp writes are now SHORT_IMG, although they can be bigger if warranted by the number of objects. * Duchamp can now read .fits.gz files, and have the output FITS files appropriately named in the automatic way (the .gz suffix was not being recognised & removed properly). * Some UCDs in the VOTable were missing semicolons between elements. * When calculating the cube statistics, Duchamp makes a mask showing the locations of blank pixels, flagged channels, and the statistics subsection are, so that only the required pixels are used in the calculations. If none of these apply, however (that is, if there are no blank pixels or flagged channels, and the user is not requesting a particular stats subsection via the statsec parameter), then the mask is not created. This saves additional memory allocation, which can be important for large cubes. Thanks to Andrew Walsh for identifying this problem. * Duchamp exits better (ie. without throwing a segmentation fault) when the requested FITS file does not exist. * The reference cube used for the verification script has been changed - the sources therein are now smaller spatially (more appropriately so for the pixel size), which gives a better idea as to the performance. Documentation improvmements * The InputComplete file is more up-to-date, and has information on the type and default values of each possible input parameter (this information is also reflected in the User Guide). This is in preparation for a parameter-editing GUI that will be released in a forthcoming version. * The User's Guide now has a section on common installation issues, based on feedback and experience with new users. Build changes: * Duchamp is now linked with the C++ compiler. Accordingly, the configure script searches for libgfortran when the gfortran compiler is specified as the F77 compiler (ie. it has been used to build pgplot). * To allow Duchamp to build on Mac OS X 10.9 (Mavericks), configure searches for the libc++ library as well as stdc++. Duchamp has been successfully built on 10.9, with fresh installs of pgplot (5.2), wcslib (4.20) and cfitsio (3.36), but, as always, your mileage may vary. Please contact me via the Trac tickets if you encounter problems. * A number of warnings that came to light with recent XCode upgrades on the Mac have been fixed, as well as those from an upgrade to gcc-4.4.5 on debian. Code base changes: * There are new wcs-pix conversion functions in fitsHeader that allow the specification of a single set of pixel and world coordinates (rather than arrays). * There is cleaner separation of the writing functions in the VOTableCatalogueWriter class. * The management of the wavelet filters has been improved, with new classes to handle the different filter types, and a factory class to generate them. The interface via the Param class is largely the same, however. * The annotation file changes noted above involve a new PixelInfo class called Line, with associated files. The method for drawing the borders has been moved into its own file (drawBorders.cc) to allow dependence on the pgplot library. * The function Cube::reInvert() has been removed - use Cube::invert() instead. Note that the interface for the latter now has two optional bool parameters. * There are improved front-end functions for the writing of arrays to the various FITS files. Duchamp version 1.5 (2013/08/29) -------------------------------- New features & algorithms: * There is now a more flexible way to specify channels that should be ignored by the source-finding. Use flaggedChannels to provide a list of single channels or channel ranges that should be ignored. This replaces the flagMW/minMW/maxMW parameters, extending their functionality and allowing more than one set of channels to be specified. * There is now an alternative way to find (and remove) spectral baselines, using a median baselining algorithm. This calculates the baseline value for a given pixel to be the median value within a box of a specified size centred on that pixel. There are two input parameters now available, baselineType (atrous or median), and baselineBoxWidth (the width of the median box). Consult the User's Guide for further information. * There is now more flexibility in running the spatial smoothing. The cutoff value in determining the size of the smoothing kernel can now be set via the input parameters, as can the way the edge pixels get treated. Conult the User's Guide for details. * You can now also specify the maximum number of voxels, spatial pixels and/or channels, in a way analogous to the minimum values. Detections with more than the maximum are rejected. Negative values (such as the defaults) mean this comparison is not done. Output changes: * The results files now include the Nchan and Nspatpix columns, showing the number of distinct channels and the number of spatial pixels in each detection. For clarity, the Npix column has been renamed Nvoxel. * The VOTable now includes the pixel location X, Y, Z columns, and the pixel ranges - this makes it much closer to the ASCII results file (it is just missing the string versions of RA/DEC, and F_tot when F_int is calculated). Bug fixes: * Negative velocity (and other) values were resulting in the column widths not adjusting correctly, leading to columns running into each other. This has been fixed, so that the spacing in the results files should be correct. * Fixed a problem applicable to cubes with blank/masked pixels in the same spectra as detections. The velocity width calculations could sometimes fail due to the mask not being applied. Code changes: * The plotting code has been refactored, improving its class structure and inheritance. No functional change from this should be evident, but it improves the maintainability of the code. Duchamp version 1.4 (2013/06/20) -------------------------------- Installation: * The "make lib" command will now create a shared library libduchamp.1.4.so as well as the static library libduchamp.1.4.a (formerly just called libduchamp.a). Bug Fixes: * The orientation of ellipses in the DS9 region files are now correct (they were wrong by 90 degrees). * Corrected the output FITS filenames so that they work when the input filename does *not* end in ".fits". Code changes: * The code that manages the output columns for the ASCII and VOTable output has been overhauled and streamlined. Little functional change should be evident, but it should be much more robust. And easier to use in derived software. Duchamp version 1.3.2 (2013/05/02) ---------------------------------- Bug fixes: * The units for the integrated flux (for F_int) were not being calculated for cases of a FITS file without a spectral axis. Additionally, a vestigial default value meant this column had units of "counts". This has been fixed so that a FITS file with Jy/beam units will have F_int values in Jy. * The ellipse fitting to find the MAJ/MIN/PA was not working correctly in the case of negative searches. This has been fixed. * The scaling of MAJ/MIN values was not being done correctly in all cases, so that the values were out by a factor of 60 or 3600. This was particularly the case when the ellipse fitting failed (due to small numbers of pixels, for instance). * The principle axes calculations have been simplified slightly, and now are done only on pixels above half the peak in the moment-0 map (to estimate the FWHM). Duchamp version 1.3.1 (2013/04/18) ---------------------------------- Bug fixes: * The kernel used in the 2D smoothing was not normalised properly, which meant the fluxes in the smoothed array were scaled incorrectly. The kernel is now normalised, so that the fluxes in the smoothed array decrease (and to an increasing degree with larger kernels, as expected). * The way the position angle of the smoothing kernel was interpreted was wrong. It now conforms to the typical astronomical position angle definition of degrees east of north. * The Z_PEAK column was being left out of the results file for Duchamp-1.3. It has been put back in. * The calculation of S/Nmax has changed so that when smoothing or reconstruction is done, the peak flux used is measured in the reconstructed/smoothed array (where the noise is measured). * The flux errors are now not reported in the case of smoothing, since we don't measure the noise in the original input image array. Other fixes: * The vertical range of the spectral plots now properly takes into account all spectra (not just the input array), and quirks with a MW range lying outside the plotted range have been fixed. * The flux scaling for the moment-0 map plot now ignores negative values, meaning the scale should be sensible. * The spelling of the Object2D::getPrincipalAxes() has been corrected. * Minor code optimisations have been made to the smoothing code. * The subsection class is now initialised with a blank string. Duchamp version 1.3 (2013/03/08) -------------------------------- New features: * New source parameters: # Each source now has a measurement of the major & minor axis sizes, along with the position angle of the major axis. The sizes are the full-width at half maximum, measured from the moment-0 map. These now appear in the catalogue and in the spectral plots, with the ellipse drawn on the moment map cutout in the spectral plots. The old measurements of w_RA & w_DEC are still made and included in the full catalogue, but are no longer reported in the smaller catalogue printed to screen (nor in the XML/VOTable output). # Each source also now has a measurement of the error on the integrated and total fluxes. This is calculated from summing in quadrature the statistical noise on each detected voxel. This is from a request by Sara Shakouri. * Output files - new types and changes to the way they are written: # Ability to create CASA region format files showing the location of the detected sources. This is analogous to the Karma annotation files or DS9 region files, for use with the casa viewer, but can also be imported into casapy. # Ability to save baseline values to a FITS file (in the same way as for the reconstructed or smoothed array). # Ability to save the moment-0 mask to a FITS file (that is, a mask indicating which spatial pixels form part of the moment-0 map). # There is an improved way to store the detected pixels for later re-use. While previously the detected pixels were written as scans to the logfile, and then read in when the usePrevious flag was set, we now write the scans and other metadata to a binary catalogue that can be read in again. Writing as a binary file leads to much better compression of the data, particularly when combined with the run-length encoding. It is anticipated future tools will be provided to allow additional interaction with these binary catalogues. # There are slight changes to the format of the ASCII catalogues, where lines not containing sources are prefixed with a comment character '#'. This will facilitate their use in other software. * There is a new command-line parameter, -t THRESH, which specifies the flux threshold for searching. It is designed to be used with the -f option, as a quick way of searching a FITS image to a specified flux level. Bug fixes: * A bug in the spatial smoothing has been fixed. The mask was being interpreted incorrectly, so that no valid pixels were getting smoothed. * The WCS for the moment-0 FITS cube has been fixed (specifically, the axis names). * When usePrevious was used, the behaviour in previous versions was to always write individual spectra. This is now controlled by a new parameter flagPlotIndividualSpectra. * Minor improvements to the output when verbose=false. * Improvements to the Makefile, so that header files from a previously-installed version of Duchamp do not get used instead of those from the current version. * The vertical range for the spectral plots now take into account the baseline and reconstructed/smoothed arrays as well (outside of any MW range, of course). Other * The code-base for reading from and writing to FITS files has been overhauled and streamlined. It can now be found in the FitsIO directory. The interface for the writing of FITS files via the Cube class has not changed. * The User Guide has been slightly re-ordered to provide more explicit information about the source parameters. Duchamp version 1.2.2 (2012/10/29) ---------------------------------- Bug fixes: * The reading of reconstructed & smoothed arrays in the case of large (>2GB) cubes has been improved. While the most recent versions of cfitsio were able to handle these, earlier versions would result in a segementation fault using the previous interface. An alternative interface has been implemented that avoids these faults, even for the older cfitsio libraries. * A bug affecting the writing of FITS mask files (apparently for the case of flagging by the object number) has been fixed. * The moment map occasionally failed if sources lay spatially within the blank pixel region of the first channel. This check has been removed and the moment map should be produced successfully in all situations. Other: * The UCDs used in the VOTable catalogue output have been updated. Several of these were shared between different columns, and so they have been changed so that each UCD is unique to one column. The column ID strings have been updated for clarity. * The determination of default output image filenames has been improved -- it previously assumed the input filename ended in '.fits', but this is no longer the case. Duchamp version 1.2.1 (2012/10/09) ---------------------------------- New feature: * Duchamp can now produce region files to annotate images displayed in SAOImage DS9. There are new parameters flagDS9 and ds9File that work in the same way as the Karma annotation file parameters. The region files can also be displayed in (at least some versions of) casaviewer. * There is a new script to fix occasional problems with the automatically-detected Makefile, and the verification script has been updated and improved. Bug fixes: * The main bug fix for this release corrects a problem with the velocity width measurements made when searching for negative detections. It was possible to get very small (and incorrect) widths in some cases - this was due to the integrated spectrum not being inverted correctly. * In the case of smoothing, the stats of the full cube that were being reported in the output files were actually those of the un-smoothed (input cube). This only affected the output files, not the detection process itself. * The units were not being reported in the VOTable. This has been fixed. * The UCDs for the spectral parameters in the VOTable were not being adapted to the user requests, so didn't always match the types of the parameters. All should be consistent now. Other changes: * The codebase relating to the creation of and writing to output files (results, logs, annotation, VOTables) has been overhauled, with a cleaner interface. Most of this code is in the new subdirectory src/Outputs, to where the columns code has been moved as well. This was instigated by ASKAP/Selavy development, but also allowed the expansion of output formats to include DS9 region files. No change to the user should be visible, but anyone using the software will notice differences. Please get in touch if changes are difficult to follow. Duchamp version 1.2 (2012/08/08) -------------------------------- Key changes: * The way the wavelet reconstruction is done in the presence of BLANK voxels is slightly different, specifically when there were BLANK voxels on the edge. While BLANK voxels are always ignored by the reconstruction (and left in place), the previous approach dealt with BLANKS on the edge by moving the effective edge of the image inwards until the first non-blank voxel. This meant that the size of the dimensions used to determine the number of scales, and the location where boundary reflections took place where different to the input image size. However, this meant that BLANK voxels on the edge were treated differently to those not on the edge, so this inconsistency was removed. The full image dimensions are always used to calculate the number of scales, and reflections (which is how the reconstruction deals with the boundaries) will occur at the actual image edges. If your data has this property (BLANK pixels at the image boundaries), then any reconstruction will be affected (most likely only in a small way) and potentially any subsequent searching. You are advised to check this (for instance by saving the results of the resonstruction from 1.1.13 and 1.2 and comparing). * The way the spectral world coordinate system is dealt with has been improved. Previously Duchamp tried to convert to a velocity axis, and got a bit grumpy if that didn't work well. Now it will express the spectral units in the axis type indicated by the FITS header. Duchamp will also allow you to change this type by providing an appropriate WCS type as an input parameter. You may also provide a rest frequency in the parameter file and this will be used to calculate velocities. And, as before, you can provide specific units for the spectral quantities to be converted into. * Since v1.1.13 was released, the journal paper describing Duchamp has been published. It can be found at MNRAS 421, 3242 (2012), or http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2966.2012.20548.x/full. It includes descriptions of the various algorithms used for Duchamp, as well as some indicative comparisons of the relative completeness & reliability. Please cite this paper when describing Duchamp. Other new features: * The default value of snrCut has changed from 3 to 5. This is espeically important if you use the -f option, but also if you don't provide snrCut in your parameter file. * The XML VOTable output now includes a more complete list of parameters, matching the output given in text form in the results & log output files. Only those parameters affecting the results are included - things like the output file names and so on are left out. * The minVoxels parameter is now adjusted to be at least (minPix + minChannels - 1). If it is changed, a warning message is triggered. * The warning/error reporting has been overhauled, with an improved interface for developers. Also, some ERROR instances that previously resulted in the program terminating now allow it to continue (provided that is possible given the error). * It is now possible to give the convergence criterion for the wavelet reconstruction via the parameter reconConvergence. When the relative change in standard deviation of the residuals from the reconstruction falls below this value, the a trous algorithm stops iterating. * The way one-dimensional arrays were dealt with was unsatisfactory, both with the way positions were registered and the format of the graphical output. Improvements have been made such that a 1D data structure is assumed to be a spectrum, and so positions in the spectrum are reported as z-pixels (or the equivalent world coordinate). Instead of a 2D moment map, the X-windows display will show the spectrum with all detected pixels plus the final list of detections highlighted, along with the detection and growth thresholds. This plot will also be written to the "detectionMap" image. * All spectral plots will now show the detection (and growth, if applicable) thresholds when plotting the peak flux spectrum. * Accessing FITS files when a subsection string is provided has been streamlined. The cfitsio package, which handles the FITS access, creates a temporary file containing this image section, and this meant the previous approach was slow, particularly for large files/sections. Now the file is only opened once and the overhead of creating the temporary file is only encountered once. * Several aspects of the processing & output did not handle a non-existent WCS well. This has been improved, so that all stages of execution will proceed without errors. Bug fixes: * The absence of a BLANK keyword when trimming will now not trigger a failure, only a warning message. * The flux unit conversion (eg. from Jy/beam to mJy/beam) was not being applied correctly when an existing reconstructed or smoothed array was being read in. This is now applied properly. * When saving reconstructed or smoothed arrays, the data type is now set to FLOAT, so that the correct values are written (and subsequently read in). The previous version was potentially saving to a FITS file with integer data type (this depended on the type of the input array). In this case, the full precision of data values would not be preserved, so reading back in and doing an identical search could yield different sources. * For certain cases, the reconstruction attempted to use a very large number of scales. This has been fixed. * The maximum scale for the reconstruction was not always being applied. The scale ranges are now enforced for all types of reconstructions. * When saving a mask image while using a subsection of a cube, the offsets for the subsection were not being accounted for correctly. This is now fixed. * The detection map plots were not recording pixels added from the growing stage. This has been fixed. * The RA & Dec now have appropriate precision, rather than an arbitrary 2 decimal places on the seconds value. The RA will be one decimal place more than the Dec, and they will reflect the degree of precision in the image pixels. * A number of data type conversions (typically ints to floats) led to errors in some calculations, such as WCS conversions. Care has been taken to make sure all indexing is done appropriately with no overflow, and that all conversions (where necessary) are done appropriately. * It was possible to get world positions looking like 11:59:60.0! Not any more. * Reading previous detections from the log file (via the use of the usePrevious parameter) did result in error messages due to slightly incompatible formats. These have been fixed, and all graphical output should work properly. * When using a spectral search, having a blank pixel in the first channel could lead to that entire spectrum being ignored, leading to inconsistent results between spectral and spatial searches. This issue has been fixed, with both types of searches returning the same catalogue. Code base development notes: * Most instances of integer overflow due to insufficient precision have been tracked down - many of these were indexing variables of type int, which have been changed to size_t. * Importantly, for code interfacing with the duchamp::Cube and related classes, axisDim is now an array of size_t elements, rather than long. * Object3D now carries its spatial map with it, rather than calculating it on the fly when requested. This saves a lot of unnecessary computational effort. * The warning/error interface has improved, making use of C++ exception handling. This should be compatible with external logging infrastructure (such as log4cxx). * The interface to the FitsHeader & WCS structures for external code has been improved, so that the WCS can be set up via function calls. Duchamp version 1.1.13 (2011/04/10) ------------------------------------- Bug fixes: * The median statistics calculations had a bug in the test for whether the array under consideration was of even size. The correction for this can mean small differences in the resulting values. This can flow through to calculated detection thresholds - please check this with your data if you use this mode! * The reconstruction code had a bug where the incorrect number of scales was being used. This occurred when the blank pixel flag was set, and when the spectral dimension was smaller than both the spatial dimensions. Other: * The default value of the blank pixel flag has been set to false, rather than true. For Duchamp, this should not matter, as it is set when the FITS file is read in. For external code using, for instance, the reconstruction algorithms, this default may be important. Having it true was contributing to the second bug listed above. It also makes more sense for it to be false unless explicitly set in some way. * The reconstruction code has been streamlined a little, reducing its memory impact and using more appropriate variable types (eg. unsigned ints instead of ints and so forth). * For those who care about the actual code base, the statistics functions have been expanded, and separated from getStats.cc into "normal" and "robust" versions. Duchamp version 1.1.12 (2011/03/18) ------------------------------------- Bug fixes: * The velocity width calculations had a bug that occasionally led to very large values. The widths are calculated using the integrated spectrum, using a threshold relative to its peak. In v.1.1.10 and 1.1.11, however, the peak was searched for over the entire spectral range, rather than just the range for the current object. This led to spurious values. This has been fixed, so that the peak is only searched for within the detected ranage of the object. * Both the pixel and statistics subsections are now more carefully examined, with errors reported if there are no valid pixels in the pixel subsection, or if the statistics subsection does not intersect with the pixel subsection. Other: * The configure script has been slightly improved so that the pgsbox library is only added if PGPlot has been enabled - this is particularly necessary with the slightly changed build procedure for recent wcslib versions. * In a related note, one file - momentMap.cc - had some #include statements that failed when PGPlot (and hence pgsbox in WCSLIB) was not enabled. These were actually unnecesssary and have been removed. * There is a new input parameter - flagPlotSpectra - that allows the user to turn off the production of the spectral plots. It defaults to true (meaning the plots are produced). Duchamp version 1.1.11 (2011/03/01) ------------------------------------- Improvements: * The largest changes in this release involved improving the efficiency of the code, resulting in further speed-ups. The code affected was the low-level object-handling code, with the merging stages in particular showing good speed-ups. * The default value for the beam size, when the beam parameters are not in the FITS header, has been dropped. Now the default behaviour is to simply not make any beam corrections if the beam is not specified by either the FITS file or the input parameters. Thanks to Tobias Westemeier for the suggestion. * The reporting of the beam size has changed slightly to provide a bit more information. Bug Fixes: * The statistics section (statSec) could be larger than the image subsection (if provided), yet the pixels required would never be read in from the FITS file. The behaviour has been changed so that the statSec, if requested, is trimmed to be wholly within the image section. * It was possible to request, for instance, spectral smoothing on a 2D image. This resulted in a blank smoothed array, which led to problems in the calculations of statistics (and hence the threshold), as well as subsequent calculations. This has been fixed, so that in cases like this the smoothing is turned off (and a warning message is displayed). * There was a problem with using a MW range and subsectioning when growing objects, as a result of changes in 1.1.10. This has been fixed. * Inversion was failing when no array was allocated (not a problem for standard Duchamp, but affected its use as a library by other code). * Writing text spectra would only occur when PGPlot output was enabled in the build (it was combined with the plotting of the spectral graphs). This has been changed so that this output can be requested without requiring PGPlot. * The equation for the beam size in Sec.4.2 of the User Guide was incorrect and has been fixed. * Minor change to the configure script to improve the detection of the PGPlot library. Code development notes: * The main work has been additions and improvements to the interfaces for the Param and the Section classes, as well as new classes to manage the beam information. The efficiency changes mentioned above also affected the internals of some of the PixelInfo classes, and provided additional functions for judging the closeness of neighbouring objects. Duchamp version 1.1.10 (2010/11/15) ------------------------------------- Improvements: * The major change for this release is a greatly improved growing algorithm. The previous incarnation was very inefficient (testing all pixels in an object, most of which only have neighbours that are already in the object), and could take an unnecessarily large amount of time in the case of extended sources. The improved algorithm makes use of voxel flags to quickly identify those voxels not yet in an object and only examines them. For a certain test case (observations of extended Galactic HI), the time required reduced from about a day to about a minute! (Note that compact sources, such as HI galaxies, will not show this degree of speedup...) Many thanks to Tara Murphy for pointing out this bug and her help in diagnosing/fixing the problem. * There have been a number of further improvements to the code to speed it up, based on some profiling. The most important was the function to add pixels to a 2D object, but there were several other minor changes as well. * The minimum size of the detections can now also be specified in terms of the total number of voxels (in addition or instead of specifying the minimum spatial pixels or channels). * The way memory is allocated when reading the image has been streamlined. The amount of memory being allocated is also now reported - this is in an effort to allow users to identify problems with running out of memory. * The version number is now reported in the results and log files. * Only the filename of the input image (ie. not the leading directories) is now shown on the detection and moment-0 maps. This is to avoid problems with large directory paths being too wide for the plot. * The verification script was improved for readability (although no functional change was made). Bug fixes: * Growing was not being done when a single source was found. Now fixed. * For particular WCS setups, the RA can be interpreted as being negative, which corrupted the Source ID (ie. the IAU-format string). This has been fixed. * When the flux units were changed, problems had been seen when writing a reconstructed cube to a FITS file. Any unit change is now undone prior to writing and there should now be no problem. * Filenames with spaces in them were not handled well. New functions were included and moved to a more obvious location. These filenames now work as expected. * Spectral axes of type FREQ that had a rest frequency were not being put into velocity units. Now fixed. * Improvements to the output to screen, making sure everything is covered by the verbose flag. * Better management of the allocation of arrays. * The minSize parameter in Image was never initialised, leading to unpredictable behaviour. Now fixed. Code development notes: * New functionality includes: a function to return a vector list of voxels in an Object3D or Detection; a new generic Search function (basically a front-end to each of the individual functions); more complete copy constructors for the DataArray classes; new methods for finding the velocity widths. Duchamp version 1.1.9 (2010/03/26) ------------------------------------- Improvements: * There is now the ability to save the moment-0 map as a FITS file. This is controlled by the parameters flagOutputMomentMap and fileOutputMomentMap, which work in the same way for the mask file. * There is a new parameter flagRejectBeforeMerge that, when true, rejects sources according to the minPix/minChannels requirements before the merging and growing is done. This defaults to false (so default behaviour is as before). Thanks to Tobias Westmeier for suggesting this and the above improvement. * There is also a new parameter flagTwoStageMerging. When true (the default), newly-detected objects are merged with the first close object in the list. When false, they are simply added to the end of the list. In both cases, a second round of merging is done to pick up all close matches. * The way the beam is specified in the absence of the BMAJ/BMIN/BPA parameters has been slightly changed. The use of "beamSize" was somewhat ambiguous (it meant the number of pixels covered by the beam, not the FWHM), so new parameters have been introduced. The beam can be specified by beamArea (which replaces beamSize), or beamFWHM (the FWHM of the beam in pixels). If beamFWHM is provided, it will be used, else the beamArea will be. * There is a new parameter searchType that allows the user to choose how the searching is done. The behaviour up till now has been to search the 2D channel maps one at a time to build up the 3D detections. This is the default, and can be obtained by setting searchType=spatial. Alternatively, you can set searchType=spectral to do the searching in the 1D spectra. * Profiling of the code has led to a few changes that have sped up some calculations, particularly those involving the median. Rather than using std::sort, the code now simply uses std::nth_element, which shows a substantial speedup factor. * When using the objectList parameter, the maps will now only show the selected objects, rather than all detected objects. * There is a new verification test that looks at the "growing" functionality. Bug fixes: * When saving a mask FITS file, there was an occasional memory leak that caused Duchamp to crash (only when the cube was suitably large). This has been fixed. * The median calculation had a bug that led to an incorrect value being reported. The difference will not be great (the element of an array being reported as the median was out by one), but could be noticeable depending on the dataset. * The MW range parameters did not respond to the use of a subsection. They should refer to channel ranges in the original cube, and changes have been made to the code to reflect this. * There was an occasional error in writing out FITS keywords, due to the way comment strings were intialised. This has been improved and made more robust. * Testing with gcc-4.3.2 showed a number of compilation warnings & errors, which have been fixed. * The Gaussian smoothing kernel was too small - it is now made big enough to encompass all possible values. It was also being incorrectly scaled. This had no functional effect on the detection of objects, but for other uses was incorrect. This has been rectified. * Some outputs that weren't caught by the verbose flag now are. Code development notes: The following notes only apply if you want to use the code as a library, rather than the stand-alone package. These have generally come out of the ASKAP software development. If you just use the stand-alone package, they won't be a concern. * The API for storing detected objects has changed, making it more robust from a programming point of view. * Additional versions of some functions (and the Gaussian smoothing class) have been added - this has come out of the ASKAP development work. * A number of instances of "unsigned int" being used for loops have been changed to iterators or "size_t". There shouldn't be any functional change from this -- the code should just build more cleanly. * The Detection class now records whether the parameters have been set, and unsets that flag when objects are merged. This allows external programs to track which objects have been merged and deal with them appropriately. Duchamp version 1.1.8 (2009/07/20) ---------------------------------- Improvements: * The final source list can now be sorted on one of a range of object parameters: x-value, y-value, z-value, ra, dec, vel, w50, iflux, pflux (integrated and peak flux respectively), or snr. Simply use the new input parameter sortingParam. Its default value is vel, so the default behaviour stays the same. * The FDR method involves calculating how many pixels are correlated. This previously involved multiplying the beam area by 2, implying that 2 neighbouring channels were correlated. This factor is now a user-selectable parameter, so that if you know how many spectral channels should be correlated, you can set the parameter FDRnumCorChan and the FDR calculation will be done correctly. * Screen output now has more information on the growing threshold when the cube statistics are printed. Bug fixes: * When reading in previous detections, there was a bug causing a segmentation fault. This has been fixed and made more robust. * There was an apparent bug when writing out the reconstructed cubes to a FITS file that caused the new file to be very large. Changing the cfitsio function used has fixed this. * Using NCP projections near the equator could result in a large stream of error messages, due to coordinate transformations being done in blank regions outside of the acceptable range of world coordinates. This has been fixed. * The function that grows objects had a major bug, that stopped it working when flagAdjacent=false. This has been fixed and should work fine. * The input parameter spectraTextFile was not being read properly. This has been remedied. * The units for the integrated flux were wrong for some types of pixel flux units. This has been fixed. * A minor bug caused incorrect calculation of the 20% widths. * All calls to uint were changed to unsigned int, as some compilers had problems recognising that they were the same thing. * src/fitsHeader.cc was missing an include statement for stdlib.h, again causing some compilers to fail. Duchamp version 1.1.7 (2009/01/16) ---------------------------------- Improvements: * The mask file that can be created with flagMask can now specify which object a given detected pixel belongs to, by taking the object ID as its value. This applies if you set flagMaskWithObjectNum=true (it defaults to false, which means each detected pixel has the value 1). Non-detected pixels still have the value 0. * The names of the output FITS files are now able to be specified directly by input parameters. These will override the default names that Duchamp provides. * The Karma annotation file now specifies a font - previously it did not and so was at the mercy of whatever was specified in other annotation files being viewed at the same time. Please let me know if the font I've chosen (lucidasans-12) is not suitable. * The default flag, used in the absence of 'E', 'S' or 'N', is now '-' rather than blank. This will ensure that each column in the results file has something in it. * The configure script is somewhat more robust to non-standard systems, particularly when the X11 libraries are in unusual places. It can also deal with the slightly different way that wcslib-4.3 installs itself. * The installation part of the Makefile was altered so that the symbolic link Duchamp that points to Duchamp-1.1.7 does not have the absolute path encoded in it. This will enable the files to be moved around at a later date. Bug Fixes: * Fixed a bug that caused problems when the flux units were less than 5 characters long (e.g. 'K') * The new velocity width values were not getting proper headers in the VOTable output. This has been remedied. * Minor improvements to help non-pgplot use * Minor fix in WCS functionality. * Minor fixes to the FitsHeader class. * Improved FITS data reading, that doesn't require a nullarray array. This will reduce memory usage. * Improved subsection parsing, particularly for non-standard WCS systems. * Improving the memory allocation of the Cube class. * Fixed a bug that meant the growthThreshold values were sometimes being lost. * Improving the way the growing and merging is done, particularly in the case of non-adjacent merging. * Fixed a scaling bug in the GaussSmooth function. Other: * Numerous changes to the code that do not affect how Duchamp itself runs, but were necessary for code development with the Duchamp libraries (primarily as a part of the ASKAP code development). Duchamp version 1.1.6 (2008/09/08) ---------------------------------- New features: * The velocity widths can now be quoted in two additional ways: the full width at 50% of the peak flux (ie. the FWHM) and the full width at 20% of the peak flux (w_50 and w_20 respectively). The w_50 parameter is now quoted in the results printed to the screen (instead of w_VEL), but all three are written to the results file. * The facility now exists to bypass the searching step and go straight to the output stage using a list of previously detected objects. The list is extracted from a previously-created log file. The user can change the way the spectra are plotted (e.g. choose to plot integrated rather than peak spectra), and select a subset of the detected objects to be printed to individual postscript files. Use the input parameter usePrevious (set to true) to use this facility, and provide a list of objects using the objectList parameter (eg. 1,2,4,7-10,15) * A new parameter "growthThreshold" has been created, that goes with "threshold". If you manually specify a threshold, and you wish to grow detections, you need to manually specify a growthThreshold (in flux units). Bug fixes: * Cubes that do not have a spectral axis (such as Stokes cubes) were causing memory leaks and crashing, due to some assumptions of the existence of the spectral axis. These bugs have been fixed, so that Duchamp will run on such cubes, although the WCS transforms may not always work appropriately. Please let me know via bug reports of difficulties you encounter! * The growing function has had a few bugs fixed and is now more efficient. * The FDR method was previously overriding any manually-specified threshold. This has been fixed so that if the user specifies threshold=X, then the FDR method is not called. * Some undefined things were happening with textual output when no objects were detected. This has been fixed. * Memory leaks caused by FITS WCS irregularities have been fixed (specifically, if a FITS header had NAXIS=2 but more than two WCS axes were defined). Duchamp version 1.1.5 (2008/03/20) ---------------------------------- Bug fixes: * A major bug was discovered in the calculation of integrated fluxes. The flux was incorrectly being weighted by the spatial size of the detection, resulting in a (often considerable) overestimation of the integrated flux. This has been corrected. * The beam size calculation was also incorrect, being out by a factor of 1/ln(2). * The "make install" command previously failed to work properly if the library had not been created. This has been fixed so that the installation works even if there is no library file. New Features: * You can now provide a new flux unit string, so that the pixel fluxes will be converted to these new fluxes before any calculations are done. This is done with the newFluxUnits input parameter. The new units should be directly convertible from the old ones (given by the BUNIT header -- e.g. if BUNIT = Jy/beam, you can give newFluxUnits as mJy/beam, but not mJy). * You can now specify the precision used in the output files for flux, velocity and S/N ratio columns, via new input parameters precFlux, precVel and precSNR. These will apply to the VOTable output as well as the text table and information on the spectral plots. * The Karma annotation files previously provided just a circle at the spatial location of the detected object. You now have the option to draw a border around the detected pixels (in a similar manner to the PGPLOT moment maps). Karma does not do this perfectly, so the lines may not line up exactly with the pixel borders, so the option remains to keep using the circles. This is controlled by the parameter "annotationType", with possible options being "borders" (the default) or "circles". * There is a new function getMetadata() that loads the header and WCS data, but no pixel information. This is only of interest if you are doing code development with the Duchamp library -- it does not affect the running of Duchamp itself. 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.