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CHANGELOG.rst

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LLSpy Release History

0.3.8

Fixed:

  • tifffile update broke ability to read tiff bit depth.
  • dependency versions now explicity listed

0.3.7

Fixed:

  • hotfix: FlashParams filename roi was not getting correctly parsed, causing failure when the calibrated chip size was not 1024 x 512.

0.3.6

Added:

  • lots of documentation on the Flash camera artifact and LLSpy camera corrections.
  • CLI lls compress command now has folder recursion and filtering by experiment age. useful for data server maintenance: quickly compress/freeze old data.
  • option in gui to delete unregistered files when performing channel registration

Changed:

  • llspy/parse.py filter functions now allow exclusive filtering in addition to inclusive
  • better error message in rename_iters when there is only a single Iteration being processed
  • lls install now accepts llspy_extra.zip file as well as llspy_extra directory

Fixed:

  • fixed erroneous "each iteration the same number of tiffs" error in rename_iters
  • fixed "Cannot create a file" bug in rename_iters when there is only a single position in the acquisition script. (thanks Mathieu)
  • (hopefully) fix IndexError in rename_iters in cases where Iter_n does not start at Iter_0.
  • fixed IndexError when no dark.tif images are present in the camera calibration folder (thanks Mathieu)
  • registration was skipping timepoints when the reference wavelength string appeared in the filename (thanks Lin)

0.3.5

Added:

  • CLI `lls show` command: quickly preview LLSdir (MIPS or z-stack) from command line.

Fixed:

  • bug: reg-preview was not using the just-generated registration file
  • many bug fixes related to previewing registration results

0.3.4

Added:

  • new option (in config tab) to enable adding folders without settings.txt file. Pick default values for missing options, and ability to directly change dx/dz/angle in the process queue.
  • new Merge Mips option under Tools menu (merge folder of individual MIPs after processing)
  • reveal in finder/explorer option

Changed:

  • CLI `lls info` command now calculates sizes
  • CLI `lls info` recurses to specified depth
  • changed internals representing timepoints (tset) and channels (cset) in LLSdir. Should prevent unexpected bugs in long run, may introduce unexpected things in the short term.
  • internal change, GUI queue box now stores/updates LLSdir instances.
  • give more meaningful error when folder is added that has tiffs and a settings.txt file, but not with the recognized naming convention.

Fixed:

  • bug: napodize and nzblend parameters were not getting passed to cudaDeconv
  • memory leak when closing preview window (wasn't releasing RAM required for image)
  • bugs resulting when the base part of the filename is interpreted as a non-string integer. (such as unsupported operand type(s) for +: 'int' and 'str' during mipmerge)

0.3.3

Added:

  • exposed "min bead number" parameter for automated bead detection in the gui, as well as manual intensity threshold.
  • alert when automated bead detection gives suspicious results (dramatically different number of beads in each channel).
  • ability to undo "Rename Scriped" (rename_iters function), under Process Menu

Changed:

  • more robust settings.txt file parsing (thanks for sample Carlos!)
  • refactored the rename_iters function to be more robust
  • slightly stricter OTF file naming regex. updated docs accordingly

Fixed:

  • fixed "invalid literal for int() with base 10" bug in refRegWave validation
  • (hopefully) fixed bug that bugs you to update llspy_extra when you've already done it. If this still fails, consider reinstalling (deleting your 'llsenv' anaconda environment and starting again with a fresh one).

0.3.2

SLM pattern generator moved into seperate package: ```slmgen```. Multiple additions and changes to SLM Pattern generator. Please see https://github.com/tlambert03/llspy-slm for full changelog, and further development.

Added:

  • improved docs on registration

Changed:

  • removed confusing error seen when using `lls path/to/llspy_extra`
  • modifications made to LLSpy to move SLMgen into seperate package.

0.3.1

Fixed:

  • fixed SLM preview glitch on Windows

0.3.0

Added:

Changed:

  • many small changes implemented to take advantage of new regfile class
  • registration now defaults to world coordinates (should work on datasets with different voxel sizes from fiducials)

Fixed:

  • fixed "long division or modulo by zero" error that sometimes appeared in matplotlib viewer
  • fixed bug that prevented processing of a subset of channels when the channel number was > 0
  • fixed bug when joining MIPs on a dataset with only 1 timepoint
  • various other small bug fixes

0.2.4

Added:

  • gpuCheckboxes added to config tab (disabled for now, future version will support multiple gpus)

Changed:

  • camera calibration GUI calculates no longer requires dark_avg or dark_std... will calculate itself if *dark*.tifs present in selected folder.
  • better feedback during camera calibration gui (still can't abort)
  • disable acquisition watch mode until ready...

Fixed:

  • important: fixed bug that causes crash when pressing preview button, if it had already failed once before f715f92
  • improved robustness and error messages when looking for OTFs in OTFdir

0.2.3

Added:

  • intelligible warning when openCL and CUDA clash. Workaround for [Error -529697949] Windows Error 0xE06D7363 b19c9bb
  • option to disable spimagine import (and reenable easily) 39a761f
  • list detected GPUs in logs at startup
  • check for update on launch 41a8cb6

Fixed:

  • properly parse 24-hour timestamp in settings.txt 36d4ed0e
  • fixed "handle is invalid" error on pyinstaller version
  • fixed multi-argument parameters in the CLI
  • don't allow trim sum greater than num pixels
  • fixed bug: 'NoneType' object has no attribute 'text' when deleting items from queue 53e7fda

Changed:

  • improved image scaling in matplotlib preview window
  • better choosing of default binary for each platform
  • much more useful information in the logs

0.2.2

Changed:

  • much improved docs structure and rtd build
  • gui pngs added to conda.recipe

Fixed:

  • version not properly reported in command line interface

0.2.1

Added:

  • Allow cRange subset in Preview
  • spimagine preview option with fallback to matplotlib if not installed
  • Option to close all preview windows in View menu
  • Option to quit LLSpy without confirmation
  • Allow to preview a subset of a compressed dataset without decompressing the whole thing
  • Search path for available compression options in {lbzip2, pbzip2, pigz, gzip, bzip2}
  • much improved exception handling in gui
  • log to file

Changed:

  • Rewritten native pyqt matplotlib image previewer
  • pigz default compression for windows, lbzip2 default for mac/linux
  • Improved handling of compression binaries
  • Improved shared library detection
  • improved validation of OTF dir, cudaDeconv binary path, and Camera Params tiff
  • simplified otf search, including approximate wavelength search
  • logging module used instead of print statements
  • better log tab handling in the gui

Fixed:

  • Native pyqt previewer eliminates the 'App already exists' bug on image preview
  • bugfix in abspath search

0.1.0 | 2017-09-13

  • Initial Release