Merge branch 'development'

.gitignore

@@ -4,8 +4,7 @@ __pycache__
 /**/.ipynb_checkpoints
 **/*.ipynb_checkpoints/
 mesoSPIM/legacy/*
-tmp/*
-/tmp/*
+
 *.log
 mesoSPIM/src/devices/zoom/dynamixel/*
 mesoSPIM/PI_GCS2_DLL_x64.dll
@@ -23,6 +22,12 @@ mesoSPIM/src/devices/stages/galil/gclib/__init__\.py
 
 mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
 
+mesoSPIM/config/*.py
+!mesoSPIM/config/demo_config.py
+
+mesoSPIM/config/etl_parameters/*.*
+!mesoSPIM/config/etl_parameters/ETL-parameters.csv
+
 mesoSPIM/src/devices/stages/galil/gclib/gclib\.py
 
 mesoSPIM/src/devices/stages/galil/gclib\.py
@@ -34,15 +39,31 @@ mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
 
 mesoSPIM/src/mesoSPIM_DemoSerial\.py
 
-
-mesoSPIM/src/devices/stages/galil/gclib/gclib\.py
-
-mesoSPIM/src/devices/stages/galil/gclib\.py
-
-mesoSPIM/src/devices/stages/galil/gclib/__init__\.py
-
-mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
-
-*.log
-
-mesoSPIM/src/devices/zoom/dynamixel\.zip
+
+
+mesoSPIM/src/devices/stages/galil/gclib/gclib\.py
+
+
+
+mesoSPIM/src/devices/stages/galil/gclib\.py
+
+
+
+mesoSPIM/src/devices/stages/galil/gclib/__init__\.py
+
+
+
+mesoSPIM/config/etl_parameters/ETL-parameters - Fabian - DBE - H45\.csv
+
+
+
+*.log
+
+
+
+mesoSPIM/src/devices/zoom/dynamixel\.zip
+
+mesoSPIM/acq/
+
+mesoSPIM/tmp/
+!mesoSPIM/tmp/readme.txt

CHANGELOG.md

@@ -0,0 +1,38 @@
+## Version [0.1.3] - March 13, 2020
+* :warning: **Depending on your microscope configuration, this release breaks backward compatibility with previous configuration files. If necessary, update your configuration file using `demo_config.py` as an example.**
+* :warning: **There are new startup parameters in the config file - make sure to update your config files accordingly**. For example, `average_frame_rate` has been added.
+* :warning: **This release removes unnecessary configuration files from the public repository - make sure to back up your mesoSPIM & ETL configuration files beforehand. In addition, old example acquisition tables (in `mesoSPIM-control\mesoSPIM\acquisitions\`) are removed as well.** 
+* :gem: **New: Support for more cameras**: **Photometrics** cameras are now supported if `PyVCAM` and the PVCAM-SDK are installed. Only the Iris 15 has been tested so far. In addition, the **Hamamatsu Orca Fusion** is now supported.
+* :gem: **New: Multicolor tiling wizard**: The Tiling wizard can now support up to 3 color channels with different ETL parameters and focus tracking settings.
+* :gem: **New: Full demo mode - addresses #16**: `mesoSPIM-control` can now be run without any microscope hardware by using the `demo_config.py` configuration file. 
+* :gem: **New: Snap function** -- Single pictures can now be taken by clicking the snap button. The filename is autogenerated from the current time. Files are saved as `.tif` which requires `tifffile` as an additional library.
+* :gem: **New: Acquisition time prediction** -- `mesoSPIM-control` now measures the average framerate every 100 frames to predict the acquisition time. To have a correct initial estimate 
+in the `Acquisition Manager`, please update the `average_frame_rate` with the measured values 
+from your microscope (are now logged in the metadata files after an acquisition).
+* :gem: **New: Focus tracking** -- Different start and end focus positions can now be specified in the Acquisition Manager. When moving the sample to acquire the stack, the microscope changes focus according to a linear interpolation between these values. At z_start, the microscope moves the detection path 
+to f_start and at z_end, the detection path focus is at z_end. This allows imaging a liquid-filled sample cuvette without an immersion cuvette. The `Mark current focus` button changes both values at once. 
+* :gem: **New: Improved acquisition previews** -- An additional checkbox allows to switch off Z axis movements when previewing acquisitions. This way, the field-of-view does not move outside of the sample which is especially helpful when updating ETL value for individual tiles/stacks in large acquisition tables. :warning: When previewing an acquistion requires a rotation, z movements still occur for safety reasons. 
+* :gem: **New: Image Processing Wizard**: `mesoSPIM-control` now has an Image Processing Wizard (accessible via a button in the `Acquisition Manager`). Currently, this allows maximum projections to be generated automatically after acquisitions.  
+* :sparkles: **Improvement:** `Acquisition Manager`: Naming of buttons has been improved, in addition, **tooltips** have been added to improve usability. 
+* :sparkles: **Improvement:** Removed unnecessary microscope and ETL configuration files cluttering the repository. Changed `.gitignore` correspondingly - future changes to configuration files. This addresses issue #16.
+* :sparkles: **Improvement:** The software now provides more verbose warnings when acquisitions cannot be started due to missing folders, duplicated filenames and already existing files.
+* :sparkles: **Improvement:** Better warnings if no row is selected while clicking Mark buttons.
+* :sparkles: **New:** Added a `CHANGELOG.md` file
+* :bug: **Bugfix:** Manually entering a value in a field in the Acquisition Manager table would change values in other rows as well if the row had been copied before.
+* :bug: **Bugfix:** Mark buttons and dropdown menus in the Acquisition Manager table slowed down the GUI when a lot of rows (>25) were present. As a fix, only the selected row shows the menu.
+* :bug: **Bugfix #26:** Fixed: First row is selected by mark buttons by default if only a single row exists in the Acquisition Manager Table
+* :bug: **Bugfix #27:** Fixed: Entering text into boxes is a bit buggy
+* :bug: **Bugfix #30:** Fixed: Zooming drop down menu often fails to update after a zoom
+* :bug: **Bugfix #31:** Fixed: `demo_config.py` now contains subsampling settings
+* :bug: **Bugfix #34:** Fixed: Last frame in a stack is blank due to an off-by-one error
+* :bug: **Bugfix #35:** Fixed: Software crashes when one folder (to save data in) in the acquisition list does not exist
+
+---
+
+## Version [0.1.2] - August 19th, 2019
+* **New:** Logging is now supported. Logfiles go in the `log` folder. 
+* **New:** Improved support for a specific mesoSPIM configuration using sample & focusing stages by Steinmayer Mechantronik and in combination with PI stages for sample rotation and z-movement.
+* **Fix:** Reduced the output to the command line
+* **Fix:** To decrease laggyness of the GUI in live mode and during acquisitions, display subsampling is now available. This way, less image data has to be rendered by the GUI. 
+* **Fix:** Fixed a variety of multithreading bugs.
+* **Fix:** Galvo amplitude and frequency in the startup part of the configuration file are now used to set startup parameters properly

README.md

@@ -1,20 +1,25 @@
 # mesoSPIM-control
-Code and documentation for the mesoSPIM light-sheet microscope software.
-The documentation of the microscope hardware information can be found [here](https://github.com/mesoSPIM/mesoSPIM-hardware-documentation).
+Image acquisition software for [mesoSPIM](http://mesospim.org/) light-sheet microscopes. A mesoSPIM (mesoscale selective plane illumination microscope) is optimized for fast imaging of large (many cm³) cleared tissue samples at near-isotropic resolution. Currently, more than 10 mesoSPIM setups are operational [around the world](http://mesospim.org/setups/).
+
+Parts lists, drawings, and instructions for building a mesoSPIM can be found in the [mesoSPIM wiki](https://github.com/mesoSPIM/mesoSPIM-hardware-documentation).
 
 ## Overview
-The Swiss mesoSPIM is a versatile light-sheet microscope for imaging
+The mesoSPIM is a versatile light-sheet microscope for imaging
 cleared tissue samples. It is compatible with all major clearing approaches - including CLARITY - and optimized for quickly creating large-field-of-view overview datasets of whole mouse brains.
 
 ## Installation
 
+### :warning: Warning
+If you are updating `mesoSPIM-control` from a previous version: Please have a close look at the [Changelog](CHANGELOG.md) to avoid overwriting your configuration files.
+
 ### Prerequisites
 * Windows 7 or Windows 10
 * Python >3.6
 
 #### Device drivers
 * [Hamamatsu DCAM API](https://dcam-api.com/) when using Hamamatsu Orca Flash 4.0 V2 or V3 sCMOS cameras. To test camera functionality, [HCImage](https://dcam-api.com/hamamatsu-software/) can be used.
-* [Software for Physik Instrumente stages](https://www.physikinstrumente.com/en/products/motion-control-software/) if a PI stage is used. To test the stages, PI MicroMove can be used.
+* [PVCAM and PVCAM-SDK](https://www.photometrics.com/support/software/) when using Photometrics cameras (under development). In addition, the `PyVCAM` Python package is necessary ([Link](https://github.com/Photometrics/PyVCAM)).
+* [Software for Physik Instrumente stages](https://www.physikinstrumente.com/en/products/motion-control-software/) if a PI stage is used. To test the stages, PI MicroMove can be used. 
 * [Software for Steinmeyer Mechatronics / Feinmess stages using Galil drivers](http://www.galilmc.com/downloads/api) if such a stage is used. To test the stages, GalilTools can be used.
 * [Robotis DynamixelSDK](https://github.com/ROBOTIS-GIT/DynamixelSDK/releases) for Dynamixel Zoom servos. Make sure you download version 3.5.4 of the SDK.
 
@@ -28,15 +33,17 @@ mesoSPIM-control is usually running with [Anaconda](https://www.anaconda.com/dow
 * scipy
 * ctypes
 * importlib
-* PyQt5
+* PyQt5 (if there are problems with PyQt5 such as `ModuleNotFoundError: No module named 'PyQt5.QtWinExtras` after starting `mesoSPIM-control`, try reinstalling PyQt5 by: `python -m pip install --user -I PyQt5` and `python -m pip install --user -I PyQt5-sip`)
 
 In addition (for Anaconda), the following packages need to be installed:
 * nidaqmx (`python -m pip install nidaqmx`)
 * indexed (`python -m pip install indexed.py`)
 * serial (`python -m pip install pyserial`)
 * pyqtgraph  (`python -m pip install pyqtgraph`)
 * pywinusb  (`python -m pip install pywinusb`)
-* PIPython (part of the Physik Instrumente software collection. Unzip it, `cd` to the directory with the Anaconda terminal as an admin user, then install with `python setup.py install`. Test install with  test installation with `import pipython`)
+* PIPython (part of the Physik Instrumente software collection. Unzip it, `cd` to the directory with the Anaconda terminal as an admin user, then install with `python setup.py install`. Test install with  test installation with `import pipython`). You can also download PIPython [here](https://github.com/royerlab/pipython)
+* tifffile (`python -m pip install tifffile`)
+* ([PyVCAM when using Photometrics cameras](https://github.com/Photometrics/PyVCAM)
 
 #### Preparing python bindings for device drivers
 * For PI stages, copy `C:\ProgramData\PI\GCSTranslator\PI_GCS2_DLL_x64.dll` in the main mesoSPIM folder: `PI_GCS2_DLL_x64.dll`