v0.5.0

What's Changed

• update for python 3.9 etc by @tlambert03 in #35
• fix tests, general reformat, pre-commit, etc... by @tlambert03 in #36

Full Changelog: 0.4.9...v0.5.0

v0.4.8

• fixes a reversion introduced in e14d8ff wherein selection of the default OTF would fail, (yielding the PSF file instead). This in turn caused a crash in cudaDeconv RLgpuImpl.cu(86) : cudaSafeCall() Runtime API error 1: invalid argument. that would crash the entire program.
• decreases the size of the icon files. The large files were causing crashes on some X windows setups (#24, thanks @VolkerH )
• updates napari preview function to use the newer add_image API introduced in v0.2.4. (napari must be updated to ≥v0.2.4
• added more documentation about how OTFs are selected, and assumptions about OTF acquisition

v0.4.7

• added alpha support for napari viewer. If napari is installed in the environment, it will be enabled as an option in the config "preview type" section. napari is in rapid development, so this should be considered experimental, and you should aim to keep napari up to date.

  To install the most recent napari release:
  pip install napari
  To install the bleeding edge master branch on github:
  pip install git+git://github.com/napari/napari.git

• allow for no compression binaries to be installed, but deactivate compression checkbox if so

• fix OTF filepattern searching, (otf search was missing OTFs named according to the documentation)

• change behavior of "ditch partial files"... should decrease frequency of confusing error message.

• (hopefully) fixed issue on OSX, where cudaDeconv could not find shared libraries.

v0.4.5

various changes to accommodate new settings.txt file formats from updated versions of Dan's software.

v0.4.4

fixes Issue #22 where MIP merging fails with different filename patterns

v0.4.3

fixes a bug in channel registration that caused the registered channels to be translated 0.5 pixels in XYZ relative to the target channel.

v0.4.2

cudaDeconv and libCudaDeconv should now be installed automatically by the conda installer

v0.4.0

long overdue "refresh" to improve LLSpy/cudaDeconv compatibility.

I recommend creating a new conda environment just to be safe... for example, install at a conda prompt:
conda create -n llsenv04 llspy

please note, you must use the cudaDeconv packaged in llspy_extra (in Janelia dropbox) in order for LLSpy to work. do not update cudaDeconv in your llspy environment

Added:

• new Decon option "dupRevStack" to reduce axial ringing
• enabled LZW compression in saved Tiffs (reduces file size, but increases time to open files)
• customizable pad value when deskewing
• integrated Lin's improvements to the matplotlib preview window (added gamma, and FFTs)
• Lin's updated rotation method in cudaDeconv (no cropping)

Fixed:

• "reverse" checkbox now actually works when rotating a stack to coverslip coords (changes sign of the sheet angle)
• relax filename parsing pattern to fix bug when number of reltime digits > 7
• updated dependency chains for conda builds
• fix reg-file date parsing
• fixed a bug that caused a failure when the number of GPUs was greater than the number of timepoints in the experiment.
• don't show library load errors when using lls install

Changed:

• drop support for python 2.7 and 3.5 ... currently python 3.6 only
• slightly more verbose errors when subprocess cudaDeconv fails
• llspy_extra can be installed directly as a zip file with lls install

v0.3.8

Fixed:

• bug: 'TiffPage' object has no attribute 'bits_per_sample' (tifffile update broke ability to read tiff bit depth)
• dependency versions now explicitly listed.

v0.3.7

Hotfix:

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