{5} Assigned, Active Tickets by Owner (Full Description) (28 matches)

It would be good to have the threshold depend on what the local noise is. For instance, with 2D images, there might be regions of lower noise, where you want to search deeper, compared to other regions that might be affected by artifacts where the threshold will be higher.

There might be a need to output an image showing the detection threshold as a function of position.

This is related to #59.

It would be good to have (IWBGTH) the ability to select either a single threshold (this is the current functionality) or an adaptive threshold.

The latter case could either be:

• a S/N cut depending on the noise in a given 2D image
• a S/N cut depending on the noise in a given 1D spectrum
• a spatial filter (in the style of the ASKAPsoft continuum case) to determine the local noise
• a spectral equivalent
• a "3D" equivalent, looking at a bunch of channels over a small range of frequencies.

Where the stats are calculated would depend on the single/adaptive nature of the threshold, and on what the adaptive case was.

Suggestion from Mary Putman:

Has anyone else been interested in pulling out the peak column density of the objects? Maybe not since most people are cataloging galaxies. I was trying to figure out the easiest way to extract that for each object and if there is anything from Duchamp that would help.

This was prompted by ticket #33. It would be nice to have the ability to specify which output columns are written. If the peak column density is included, it will not be of interest a lot of the time. The way around that would be to have an input parameter specify a list of quantities to be written. e.g.

outputParams ra,dec,f_int,w50,col_dens,s/n

This would impact on the output functions -- each parameter would need a check to see whether it appeared in the list before it was written out.

It would be useful from the ASKAP cduchamp point of view to have the Detection class store the moment map and spectrum. This would enable us to access them separately and potentially output as FITS files or whatever as needed.

It would make the plotting of them relatively straightforward too!

There are a lot of functions that do not have doxygen comments associated with them. Do a large update before the next major release!

It would be good if the code developed for ASKAP - the Gaussian fitting and the variable threshold stuff - could be incorporated into the standalone Duchamp package.

This would mean:

• Importing the relevant files
• Purging ASKAP-related stuff (logging, parallel/distributed processing, ...)
• Updating the build requirements to allow for casacore
  • This could be an optional thing, much like pgplot, where if someone doesn't have casacore it is still possible to build Duchamp.

The impact of doing this should be evaluated.

These flags (such as arrayAllocated) in the Cube classes are unnecessary. Should just test for the pointer being zero - this will clean things up a bit.

The way the getStats functions report / deal with errors is not terribly useful. It would be better to make use of a return value so that the calling function knows if something went wrong.

Here's the example that I had: I was calling findMedianStats with a mask, but had the wrong size provided - instead of the size of the array, it was the number of good points in the mask. findMedianStats then looks at only the first 'size' points in the mask array, but in this case they were invalid, and so no good points were found.

Might also want to improve the documentation so that the nature of the "size" parameter is explicitly identified.

The mask optimisation routine used in Selavy should be added to Duchamp. It uses no new code/libraries other than the ASKAP logging and the parameter set interface (which can easily be changed to a Param interface).

This would be a worthwhile inclusion in 1.6, and would address a few concerns people have about using Duchamp. The User Guide should detail what is being done, and cite Westmeier (I think) for the reason you want this (ie. to get total integrated flux).

In the User Guide, the only place the UCDs used for the output parameters are listed is in Appendix E where they are buried in the VOTable header.

It would be good to have a simple table somewhere (in the appendix, perhaps), that lists the Duchamp parameter and its corresponding UCD.

It would be good to have a specific absorption-line mode, that does both negative searching and baseline-subtraction.

Together with this, it would be good to have absorption-line-specific parameterisation: peak optical depth, integrated optical depth, peak (& mean?) continuum level.

See notes in #219.

./configure --prefix=/usr/local/ --with-wcslib=/usr/local/include --with-pgplot=/usr/local/lib
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configure: X-library search yielded X_CFLAGS= -I/usr/X11/include, X_LIBS= -L/usr/X11/lib, X_EXTRA_LIBS=, X_PRE_LIBS= -lSM -lICE
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configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/config.h
config.status: src/config.h is unchanged
joanne:duchamp mad134$ make
g++ -o Duchamp-1.6.1 ./src/mainDuchamp.o ./src/duchamp.o ./src/param.o ./src/fitsHeader.o ./src/PixelMap/Line.o ./src/PixelMap/Voxel.o ./src/PixelMap/Scan.o ./src/PixelMap/Object2D.o ./src/PixelMap/Object3D.o ./src/ATrous/filter.o ./src/ATrous/B3SplineFilter.o ./src/ATrous/TriangleFilter.o ./src/ATrous/HaarFilter.o ./src/ATrous/FilterFactory.o ./src/ATrous/atrous_1d_reconstruct.o ./src/ATrous/atrous_2d_reconstruct.o ./src/ATrous/atrous_3d_reconstruct.o ./src/ATrous/baselineSubtract.o ./src/ATrous/ReconSearch.o ./src/Detection/detection.o ./src/Detection/ObjectGrower.o ./src/Detection/areClose.o ./src/Detection/lutz_detect.o ./src/Detection/mergeIntoList.o ./src/Detection/outputDetection.o ./src/Detection/sorting.o ./src/Detection/spectrumDetect.o ./src/Cubes/cubes.o ./src/Cubes/cubes_extended.o ./src/Cubes/baseline.o ./src/Cubes/CubicSearch.o ./src/Cubes/detectionIO.o ./src/Cubes/existingDetections.o ./src/Cubes/getImage.o ./src/Cubes/invertCube.o ./src/Cubes/Merger.o ./src/Cubes/momentMap.o ./src/Cubes/smoothCube.o ./src/Cubes/spectraUtils.o ./src/Cubes/trimImage.o ./src/FitsIO/Beam.o ./src/FitsIO/DuchampBeam.o ./src/FitsIO/ReadExisting.o ./src/FitsIO/ReadExistingRecon.o ./src/FitsIO/ReadExistingSmooth.o ./src/FitsIO/WriteArray.o ./src/FitsIO/WriteBaselineArray.o ./src/FitsIO/WriteMaskArray.o ./src/FitsIO/WriteMomentMapArray.o ./src/FitsIO/WriteMomentMaskArray.o ./src/FitsIO/WriteReconArray.o ./src/FitsIO/WriteSmoothArray.o ./src/FitsIO/dataIO.o ./src/FitsIO/headerIO.o ./src/FitsIO/subsection.o ./src/FitsIO/wcsIO.o ./src/Utils/Section.o ./src/Utils/Statistics.o ./src/Utils/feedback.o ./src/Utils/GaussSmooth1D.o ./src/Utils/Hanning.o ./src/Utils/VOField.o ./src/Utils/VOParam.o ./src/Utils/getStats.o ./src/Utils/getNormalStats.o ./src/Utils/getRobustStats.o ./src/Utils/linear_regression.o ./src/Utils/medianBaseline.o ./src/Utils/position_related.o ./src/Utils/sort.o ./src/Utils/string_related.o ./src/Utils/wcsFunctions.o ./src/Utils/zscale.o ./src/Outputs/columns.o ./src/Outputs/CatalogueSpecification.o ./src/Outputs/CatalogueWriter.o ./src/Outputs/FileCatalogueWriter.o ./src/Outputs/ASCIICatalogueWriter.o ./src/Outputs/VOTableCatalogueWriter.o ./src/Outputs/AnnotationWriter.o ./src/Outputs/KarmaAnnotationWriter.o ./src/Outputs/DS9AnnotationWriter.o ./src/Outputs/CasaAnnotationWriter.o ./src/Cubes/drawBlankEdges.o ./src/Cubes/drawMomentCutout.o ./src/Cubes/outputSpectra.o ./src/Cubes/plotting.o ./src/Detection/drawBorders.o ./src/Plotting/DuchampPlot.o ./src/Plotting/MultipleDuchampPlot.o ./src/Plotting/ImagePlot.o ./src/Plotting/SpectralPlot.o ./src/Plotting/SimpleSpectralPlot.o ./src/Plotting/CutoutPlot.o ./src/Utils/mycpgplot.o ./src/Utils/PlottingUtilities.o ./src/Utils/pgplot_related.o -lwcs -L/usr/local/lib  -lcfitsio -L/usr/local/lib -lcpgplot -lpgplot  -L/usr/X11/lib  -lSM -lICE -lX11  -lz -lpng -lc++ -lstdc++ -lm  
Undefined symbols for architecture x86_64:
  "_cpgsbox", referenced from:
      wcsAxes(wcsprm*, unsigned long*, int, int) in PlottingUtilities.o
  "_pgwcsl_", referenced from:
      wcsAxes(wcsprm*, unsigned long*, int, int) in PlottingUtilities.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [duchamp] Error 1

The configure script is consistently finding that the linking for the X libraries should have:

X_LIBS= -L/usr/X11/lib -R/usr/X11/lib

This is annoying, as some compilers will not recognise the -R bit. While some will ignore it more or less happily, others will actually crash - this can lead to the pgplot library not being included properly in the linking command as well.

While this can be fixed by tinkering with the Makefile, this is not really acceptable.

The offending part of the configure.ac script appears to be

AC_PATH_XTRA