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CHANGELOG

0.4.3

  • Fixed issue #70 which affected windows builds only.

  • Dw will now give a error message if the log file can't be opened instead of quietly crashing.

  • Disabled some debug code that caused dw to write the file (one.tif) every time that is was run. It has been doing so since version 0.4.1.

0.4.2

  • VkFFT upgraded from v1.3.3 to v1.3.4.
  • Fixed an issue preventing anything than --bq 0 to be used on Windows (one array was not properly initialized to 0).

0.4.1

  • Fixes the GPU memory leak reported in issue #62.

0.4.0

TLDR New features and bug fixes. Update if you are on version 0.3.7 or below.

  • Added pre-generated header files under /src/kernels/ so that make kernels is not needed during the build process. Solves issue #55

Updates to dw dots:

  • Updated LoG filter and maxima finding routine gives a speedup > 2x.
  • Setting the filter sizes based on the optical parameters, assuming diffraction limited dots.
  • Addition: Can fit dots using a 3D Gaussian while minimizing the $-\log$ likelihood assuming Poissonian noise. For this purpose the Broyden-Fletcher-Goldfarb-Shanno algoritm (bfgs2 in GSL) is used.

0.3.9

  • Added the --offset option. This will add an offset to the image before the deconvolution start, which will be removed before saving the result to disk. Initial tests suggests that this can reduce the effect of detector noise (non-Poisson) by decreasing the relative weight of pixels with low values. See some numerical tests below, on the microtubules image:

    iterations vs mse

    The default value is set to 5 which should be safe in most situations, but it is suggested that it is set to the standard deviation of the detector noise. To revert to the old behaviour, use --offset 0.

  • Removed the --relax option since it made no sense.

  • Reverted the default start guess to flat, like it was before v 0.3.8. The --start_lp still seems to produce better images but takes a little too long to initialize for being a default method. Might still be the default in future version when there is a GPU implementation.

0.3.8

  • Fixed crashes when trying to read a non tif file.

  • For systems with multiple GPUs or OpenCL compatible devices it is now possible to select which to use with --cldevice. To figure out which that are available it is simplest to use clinfo. Alternatively call dw with --verbose 2 or above.

  • Removed depreciated makefile for freebsd as it is no longer needed.

  • Removed anything related to meson as it is no longer needed.

  • Using the PRI* macros from inttype.h, especially PRIu64 for uint64_t and PRId64 for int64_t to get rid of some warnings under MacOS.

  • Changed the initial guess for all methods. It is now set to be a low pass filtered version of the input image. Experiments suggests that this was better than the previous approach where a flat image was used. To use the previous default, please use --start_flat.

  • Added the option to start from the input image with the flag --start_id. This might be a good option when only a few iterations are used since but can lead to more shot noise.

  • Added a noise filter for the input image which can be enabled with --psigma s, where s controls the filter shape. This is implemented as follows: 1) the Anscombe transform is applied 2) the transformed image is filtered with a isotropic Gaussian kernel with sigma=s. 3) The inverse transform is applied. Using this with moderate values of s leads to better results on synthetic images. For example on the microtubules image the best results were achieved with --psigma 0.7. A value of 0 is the same as not using the filter.

Results when testing on the microtubules image shown below.

iterations vs mse

0.3.7

  • Deconwolf compiles as a native windows program using clang. So far the binaries are only smoke tested since the main target is linux.

  • dw_bw use OpenMP and does not rely on pthreads any more (for portability reasons).

  • Removed the AVE and EVE methods since they don't add anything over SHB.

  • Added a CMakeList.txt for building with cmake.

  • Added --gpu which at the moment is equivalent to --method shbcl2 but a little more mnemonic.

  • Added the --periodic option which turns on periodic boundary conditions, i.e. is equivalent to --bq 0.

0.3.6

  • The GPU code path uses in-place transformations as much as possible to save a little on the memory usage.

  • Switched to VkFFT (v1.3.3) as the default FFT backend on the GPU. Unless a big regression is found, the clFFT code path will most likely not be maintained in future versions and be removed.

    To build with GPU acceleration use:

    make kernels
make -B VKFFT=1

    As before, you need also to choose --method shbcl2 to use it over the CPU implementation.

    Initial tests show a speed up of about 10-30% depending on the image size. As a bonus VkFFT will process any sizes while clFFT simply refuse to process the tricky ones.

  • Identified that cl_idiv_kernel.c took a substantial amount of the iteration time and rewrote it.

  • Removed the "CUDA" backend since it does not make sense any more.

  • Checks that the min value of the image > 0. Aborts if not.

  • Checks that the max value of the image >= 1. Aborts if not.

0.3.5

  • dw maxproj There were problems reading the output in MATLAB. Updated so that the output image will be written as a single strip.

0.3.4

  • Minor bug fixes which gives a clean build with -fanalyzer.

0.3.3

  • Writing pixel size to output file also when tiling is used.

0.3.2

  • Tested on raspberry pi 4 using 64-bit bookworm.
  • Found a bug in fft.c where memcpy was used wrongly (replaced by memmove). Strangely that bug never manifested under Ubuntu/x86_64.
  • Added fim_realloc for aligned reallocs. This function could be branched depending on the OS since there are platform specific aligned reallocation functions.
  • Header files: Using #pragma once instead of the #ifndef file_h_ pattern.

0.3.1

  • Introduced fim_malloc for all allocations that might benefit from a stricter alignment than malloc provides by default. Tested with MADV_HUGEPAGE for the allocations but the results are inconclusive (but it uses more RAM when enabled). Cleared all uses of fftw_free and fftw_malloc.

0.3.0

  • Respects the NO_COLOR environmental variable in accord with https://no-color.org/.
  • Fixed correct capping of pixel values when --scaling is used.

v 0.2.9

  • Added the command line option --scaling for setting bypassing the automatic image scaling in 16-bit output mode.

v 0.2.8

  • Switched from fftw3f_threads to fftw3f_omp. This reduced the run time by about 10% on a Intel i7-6700K. Can be reverted by commenting in/out the corresponding lines in the makefile.
  • Cleaned up the output of dw --version

0.2.7

  • Converted a few minor code paths to execute in parallel by OpenMP directives.

0.2.6

  • Using ISO 8601 in log files, e.g., 2023-02-14T11:14:14.

0.2.5

  • Added the --xyz option to dw maxproj, for creating max projections along the three axes and collecting them on a single 2D image.

0.2.4

  • dw --help now shows the additional commands/modules available.
  • Reading 16-bit tif files with TIFFReadEncodedStrip instead of TIFFReadRawStrip. Some programs saves tiff files in other ways :)
  • Added the command psf-STED for 3D STED PSFs. Use at your own risk.
  • Building with meson is temporarily broken and to be fixed.
  • Fixed dw chashing when combining --method rl with --iterdump
  • Setting the background level automatically to min(image) unless specified with --bg.

0.2.3

  • Fixed some errors introduced in v 0.2.2, especially the dw maxproj was broken.
  • added the subcommand dw merge. To be used to merge single z-planes into a 3D volume.

0.2.2

  • Can deconvolve using clFFT, when compiled with OPENCL=1 two new methods appear, --method shbcl and --shbcl2, the first using clFFT only for the Fourier transforms, the latter using OpenCL for the whole deconvolution procedure. Uses quite much GPU memory which is something to improve upon in future version, possibly by switching to vkFFT.

0.1.1

  • Added experimental dw imshift for shifting images, also shift estimation using normalized cross correlation with dw imshift --ref file.tif. Might be extended to basic tiling etc.

0.1.0

  • Implements the 'Scaled Heavy Ball'. More memory efficient than eve and about the same speed and image quality. Might become the default method.
  • Reorganization of code with one file per deconvolution method, RL is now separated to an own file which improves readability.
  • The --method argument can be used to switch between several methods, see --help or the man page.
  • Showing Idivergence after each iteration, switch back to MSE with --mse
  • Cleaned up the text written to the terminal, notably any warnings from libtiff now go to the log file.
  • OMP is set to use as many cores as FFTW.
  • Added OMP directives to a few more loops.
  • Using static OMP schedule.
  • Introduces the --tsv argument to save information per iteration to a separate tsv file for easier plotting and analysis.
  • Three different stopping criteria: Relative error (default) Fixed number of iterations or at an absolute error.

0.0.26

  • dw maxproj works with file that are not in the current folder.
  • Fixed --iterdump not always working.

0.0.25

  • Builds with cuFFT on Linux, use make CUFFT=1 -B, requires a CUDA compatible GPU and of course the cuFFT library installed.

0.0.24

  • Tested on CentOS, install both with make and meson.
  • Fixed a memory leak with the --tilesize option causing crashed sometimes.

0.0.23

  • Added 'meson.build' files in order for deconwolf to be built by The Meson Build system, tested to work on both Ubuntu 21.10 and MacOS (on x86_64 hardware).
  • Added a small test image under demo/ together with a makefile to deconvolve it.
  • Added pseudo code for the binaries hoping to planning to replace this by a properly typeset and more detailed document.
  • Aborting if the number of threads is set < 1.
  • The algorithm is still unchanged since v 0.0.20.

0.0.22

  • Fixed double free-bug in tiling mode.

0.0.21

  • Updated documentation and man-pages based on markdown files for easier updating.
  • Provides makefile-freebsd for building on FreeBSD 13.0
  • Changed behavior when too few input arguments are given to only give a two-line message.

0.0.20

  • Changing acceleration technique to use 'Exponential Vector Extrapolation' (EVE) described in Biggs PhD thesis. Deconvolved images get higher MSE but much lower I-div.
  • '--xyfactor 0' does not crash dw anymore.
  • Frees the PSF as soon as not needed to save some memory.
  • Changing the behavior of the progress dots to appear more linear in time
  • Changing the non-negative condition to strictly positive in order for pixel not to get stuck at 0.
  • Adding the option to turn off Biggs acceleration, i.e. run normal Richardson-Lucy with --biggs 0.
  • Will load PSFs that don't have an odd number of pixels in each dimension however that is not recommended.
  • Can be built against Intel MKL (make MKL=1 ...), consider that an experimental option. 14 percent faster on a small test image, varied results on larger images.

0.0.19

  • Using lanczos5 instead of lanczos3 for the PSF generation. As a result GSL_EROUND is not raised for the test cases.
  • Faster PSF generation, using more symmetries.
  • dw_bw can now use more than one thread (wrongly disabled in v 0.0.18).

0.0.18

  • Provided install instructions for Windows 10.
  • Fixed some mismatching fftwf_malloc/fftwf_free where they were mixed up with malloc/free causing crashes on Windows.
  • Added an experimental src/CMakeLists.txt that can be used when building with cmake. It is also possible to cross compile for Windows on Linux although it takes some effort to collect the DLL files for the dependencies.

0.0.17

  • Fixed some bugs in the PSF generation code that did affect the accuracy of the pixels in the PSF.
  • Stared to use GSL for numerical integration. It remains to change the double integral over x-y into something more dynamic.