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Changelog.txt
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Changelog.txt
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Lasagna Changelog
What is Lasagna?
Lasagna is a Python-based image viewer for 3-D anatomy datasets. It was inspired by the "slicing viewer",
VV (https://www.creatis.insa-lyon.fr/rio/vv). Lasagna was originally written in 2015/2016 at the Mrsic-Flogel
laboratory, Basel, by Rob Campbell.
2022/01/12
- Rob Campbell
Bug fix: An apparently previously working version of PyQt5 started throwing namespace errors. Corrected these. Segfaults started happening on image load. Updated to PyQt 5.15.6 and all is good.
2020/04/08
- Rob Campbell
Bug fix: Axis flipping is now done using PyQtGraph's invert axis methods. Previously it just flipped the image stack, which of course caused all sorts of problems.
2020/03/04
- Rob Campbell
Bugfix: Lasagna now honors "defaultAxisRatios" setting in .yml file
defaultAxisRatios are now [1,1,1]
demo images hosted on mouse.vision replaced
2019/07/26
- Antonin Blot
Multiple files can be selected at once when loading new image stack
2019/06/27
- Rob Campbell
Improve display of ingredients in list.
Elastix plugin no longer crashes if the user presses "cancel" instead of loading a stack.
Elastix and Transformix plugins allow loading of TIFF stacks.
2019/07/26
- Antonin Blot
Add support for nii files. (Loads the data but not the aspect ratio)
2019/06/27
- Rob Campbell
Add nice interpolation on add_line lines and create a save method for the line itself.
2019/06/26
- Rob Campbell
Fix silly bug that was causing the flip along the Y axis (dorso-ventral for our samples) in the first image axis
(the coronal axis in our data)
Greatly speed up initial display of larger images by fixing slow histogram calculation.
Bug fix axis ratio boxes that were causing a crash.
2019/06/25
- Antonin Blot
Improve the embeded ipython console. Giving the -C argument will start an ipython session in the terminal with `app`
and `tasty` in the namespace.
2019/06/24
- Rob Campbell
IO plugins now all start without needing to be listed in the Lasagna preferences file.
2019/06/23
- Rob Campbell
tree class replaced with refactored version (see note froom 2019/06/12) and confirm ARA Explorer works.
2019/06/22
- Rob Campbell
General work on add_line_plugin. It now handles point insertion, 3D line fit works better, bug fixes.
Rename "Base stack" to "Image stack"
2019/06/18
- Rob Campbell
8f9bc0134c64a4d3a2e3d199f15c23a5c28c46f8
Move code that generates ingredient QStandardItem for list out for the points, lines, and imagestack
ingredients and into lasagna_ingredient. Remove orphan version of lasanga_ingredient in root dir.
0c43bac4171f48099d58c27f609a7b07e7f55cf6
Replace some instances of lasanga.initialiseAxes() with the the new lasagna.update_2D_plot_ingredients_in_axes
Changes made in lasagna_object.py, overlay_random_points_plugin.py, and add_line_plugin.py
Lasagna.axisClicked() now stores the button that generated that click in self.last_button_click_in_axis
1=left, 2=right, 4=middle
2019/06/18
- Rob Campbell
Start to apply Black (https://black.readthedocs.io/en/latest/) to all new commits.
2019/06/13
- Rob Campbell
Bugfixes and minor re-organisation.
Replace lasagna which (caused a crash) with shutils.which (since we now are on >>Python 3.3)
Bugfix in MHD header reader that was causing files to fail to load.
2019/06/12
- Rob Campbell
Very extensive changes have been made to the dev branch and many things currently don't start.
First goal is to get everything running again. Some things are partially refactored, like tree,
and so aren't working. The first goal is to get everything running and then we can go back and
refactor. To that end I will add a tag to 7c1d0a7b4437864d3d6cb9dd6518901dad627113 on GitHub.
This is tagged as refactorBreakPoint01 This is the last commit with partially refactored stuff.
I will revert stuff that's not working yet in order to get it working. We can later come back
to this commit and use it as the basis for refactoring.
291ffac8273b3609573075be6e3f44c795332f5f
Most modules now load. All this commit does is change module load paths. Mainly:
"import lasagna_helperFunctions as lasHelp" to "import lasagna.utils.preferences as lasPref"
"from lasagna_plugin import lasagna_plugin" to "from lasagna.plugins.lasagna_plugin import LasagnaPlugin"
1ee8bea3ed16d423d2938163f63f49f31c0ea8c9
Reverts partial refactoring of the tree class used for plotting neurite trees and also for the ARA tree view.
TODO: in future refactor tree. See Issue #192.
Bugfixes to plugins
FROM NOW ON ALL CHANGES SHOULD BE DESCRIBED. ESPECIALLY STUFF TO DO WITH REFACTORING THIS THING
2019/03/09 Transfer ownership of repository to Sainsbury Wellcome Centre 2p serial section team