Merge pull request #546 from jungmannlab/development

v0.8.5

- Sound notifications when long processes finish, see `here <https://picassosr.readthedocs.io/en/latest/others.html>`_
- Several dialogs in Render, Localize and Simulate are now scrollable (*experimental*)
- SPINNA fix automatic area detection from picked localizations
- Render add dependency ``imageio[ffmpeg]`` for building animations
- Render allow for loading pick regions by dropping a .yaml file onto the window
- Render improve zooming with mouse wheel (Ctrl/Cmd + wheel)
- Fast rendering automatically adjusts constrast
- Localize show scale bar function added
- Localize plotted ROI remains the same when zooming in/out and panning
- Localize Gauss MLE saves number of iterations and fit log-likelihood
- DBSCAN accepts min. no. of localizations per cluster
- Cluster center calculations calculate arithmetic mean, not weighted mean
- Other bug fixes and minor improvements

Author: rafalkowalewski1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.4
+current_version = 0.8.5
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

.gitignore

@@ -28,9 +28,15 @@ wheels/
 # Plugins
 picasso/gui/plugins/
 
+# Sound notifications
+resources/notification_sounds/
+
 # Camera configuration
 picasso/config.yaml
 
+# One-click-installer output
+release/one_click_windows_gui/Output/
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

changelog.rst

@@ -1,7 +1,23 @@
 Changelog
 =========
 
-Last change: 08-SEP-2025 MTS
+Last change: 30-SEP-2025 CEST
+
+0.8.5
+-----
+- Sound notifications when long processes finish, see `here <https://picassosr.readthedocs.io/en/latest/others.html>`_
+- Several dialogs in Render, Localize and Simulate are now scrollable (*experimental*)
+- SPINNA fix automatic area detection from picked localizations
+- Render add dependency ``imageio[ffmpeg]`` for building animations
+- Render allow for loading pick regions by dropping a .yaml file onto the window
+- Render improve zooming with mouse wheel (Ctrl/Cmd + wheel)
+- Fast rendering automatically adjusts constrast
+- Localize show scale bar function added
+- Localize plotted ROI remains the same when zooming in/out and panning
+- Localize Gauss MLE saves number of iterations and fit log-likelihood
+- DBSCAN accepts min. no. of localizations per cluster
+- Cluster center calculations calculate arithmetic mean, not weighted mean
+- Other bug fixes and minor improvements
 
 0.8.4
 -----

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.8.4
+AppVersion=0.8.5
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.8.4"
+OutputBaseFilename="Picasso-Windows-64bit-0.8.5"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.8.4"
+release = "0.8.5"
 
 # -- General configuration ---------------------------------------------------
 

docs/files.rst

@@ -27,7 +27,7 @@ In MATLAB, execute the command ``locs = h5read(filename, dataset)``. Replace dat
 
 In Origin, select ``File > Import > HDF5`` or drag and drop the file into the main window.
 
-Picasso uses ``h5py``. To load localizations, Picasso uses the function ``load_locs(filename)``` located in the ``io.py`` package of Picasso.
+Picasso uses ``h5py``. To load localizations, Picasso uses the function ``load_locs(filename)`` located in the ``io.py`` package of Picasso.
 
 Localization HDF5 Files
 -----------------------

docs/index.rst

@@ -26,6 +26,7 @@ This documentation is based on the `Nature Protocols publication <https://www.na
    postprocessing
    nanotron
    plugins
+   others
    faq
 
 Indices and tables

docs/others.rst

@@ -0,0 +1,35 @@
+=====
+Other
+=====
+
+Sound notifications
+-------------------
+Starting in version 0.8.5, Picasso supports sound notifications. In Render and SPINNA, these can be selected in the ``File`` menu in the menu bar. The available files are read from the ``resources/notification_sounds`` folder. ``.mp3`` and ``.wav`` files are supported. Default sound notification is saved automatically when manually changed.
+
+Custom notifications
+~~~~~~~~~~~~~~~~~~~~
+To add custom notification sounds, copy the sound files (``.mp3`` or ``.wav``) to the  ``resources/notification_sounds`` folder. Depending on how you installed Picasso, this folder can be found in different locations:
+
+GitHub
+------
+If you cloned the GitHub repository, you can add sound notifications by following these steps:
+
+- Find the directory where you cloned the GitHub repository with Picasso.
+- Go to ``picasso/resources/notification_sounds``.
+- Copy the sound files to this folder.
+
+PyPI
+----
+If you installed Picasso using ``pip install picassosr``, you can add sound notifications by following these steps:
+
+- To find the location of the environment where ``picassosr`` is installed, type ``conda env list``.
+- If your environment can be found under ``YOUR_ENVIRONMENT``, go to ``YOUR_ENVIRONMENT/Lib/site-packages/picasso/resources/notification_sounds``.
+- Copy the sound files to this folder.
+
+One click installer
+-------------------
+If you installed Picasso using the one click installer from `the Picasso release page <https://github.com/jungmannlab/picasso/releases/>`__ , you can add sound notifications by following these steps:
+
+- Find the location where you installed Picasso. By default, it is ``C:/Picasso``.
+- Go to the following subfolder in the `Picasso` directory: ``picasso/resources/notification_sounds``.
+- Copy the sound files to this folder.

docs/plugins.rst

@@ -4,34 +4,35 @@ Plugins
 
 Usage
 -----
-Starting in version 0.5.0, Picasso supports plugins. Please find the instructions on how to add them to your Picasso below. 
+Starting in version 0.5.0, Picasso supports plugins. Below are the instructions on how to install them.
 
-Please keep in mind that the ``__init__.py`` file in the ``picasso/picasso/gui/plugins`` folder must not be modified or deleted.
+*Keep in mind that the* ``__init__.py`` *file in the* ``picasso/picasso/gui/plugins`` *folder must not be modified or deleted.*
 
-GitHub
-~~~~~~
-If you cloned the GitHub repository, you can add plugins by following these steps:
-- Find the directory where you cloned the GitHub repository with Picasso.
-- Go to ``picasso/picasso/gui/plugins``.
+One click installer
+~~~~~~~~~~~~~~~~~~~
+**NOTE**: After uninstalling Picasso, ``Picasso`` folder needs to be deleted manually, as the uninstaller currently does not remove the plugins automatically.
+
+- Find the location where you installed Picasso. By default, it is ``C:/Picasso``. *Before version 0.8.3, the default location was* ``C:/Program Files/Picasso``.
+- Then go to the folder ``picasso/gui/plugins``.
 - Copy the plugin(s) to this folder.
 
+**NOTE**: Plugins added in this distribution will not be able to use packages that are not installed automatically (from the file ``requirements.txt``).
+
 PyPI
 ~~~~
 If you installed Picasso using ``pip install picassosr``, you can add plugins by following these steps:
-- To find the location of the environment where ``picassosr`` is installed, type ``conda env list``.
-- If your environment can be found under ``YOUR_ENVIRONMENT``, go to ``YOUR_ENVIRONMENT/Lib/site-packages/picasso/gui/plugins``.
+- Activate your conda environment where ``picassosr`` is installed by typing ``conda activate YOUR_ENVIRONMENT``.
+- To find the location of the package, type ``pip show picassosr`` and look for the line starting with ``Location:``.
+- Navigate to this location and go to ``picasso/gui/plugins``.
 - Copy the plugin(s) to this folder.
 
-One click installer
-~~~~~~~~~~~~~~~~~~~
-**NOTE**: After deinstalling Picasso, ``Program Files/Picasso`` folder needs to be deleted manually, as the uninstaller currently does not remove the plugins automatically.
-
-- Find the location where you installed Picasso. By default, it is ``C:/Program Files/Picasso``.
-- Go to the following subfolder in the `Picasso` directory: ``picasso/gui/plugins``.
+GitHub
+~~~~~~
+If you cloned the GitHub repository, you can add plugins by following these steps:
+- Find the directory where you cloned the GitHub repository with Picasso.
+- Go to ``picasso/picasso/gui/plugins``.
 - Copy the plugin(s) to this folder.
 
-.. **NOTE**: Plugins added in this distribution will not be able to use packages that are not installed automatically (from the file ``requirements.txt``).
-
 For developers
 --------------
 To create a plugin, you can use the template provided in ``picasso/plugin_template.py``, see below.

docs/spinna.rst

@@ -95,6 +95,7 @@ Plotting
 - *Plot settings* opens a new dialog that allows the user to show/hide plot legend, adjust the histogram bin size and min. and max. plotted distances, among others, see below.
 
 .. image:: ../docs/spinna_nnd_plot_settings.png
+   :scale: 40 %
    :alt: nnd_plot_settings
 
 If the loaded structures include several molecular target species, several NND histograms are plotted, one for each pair of molecular target species which can be explored by clicking left and right arrows in the *Plotting* box.