Merge branch 'development'

.gitignore

@@ -4,6 +4,7 @@ __pycache__
 /**/.ipynb_checkpoints
 **/*.ipynb_checkpoints/
 venv/
+mesoSPIM/test/fixtures/
 *.log
 *.bin
 .idea
@@ -16,14 +17,9 @@ prototypes/python-essentials/temp\.tif
 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/*
 mesoSPIM/config/*
 !mesoSPIM/config/demo_config.py
-
-mesoSPIM/config/etl_parameters/*.*
-!mesoSPIM/config/etl_parameters/ETL-parameters.csv
-mesoSPIM/src/mesoSPIM_DemoSerial\.py
 mesoSPIM/src/devices/zoom/dynamixel\.zip
 
 mesoSPIM/acq/

CHANGELOG.md

@@ -1,3 +1,55 @@
+## Latest version
+* :gem: Support of multiple PI single-axis controllers, thanks to #52 by @drchrisch. 
+Note the changes in config file: single multi-axis controller (C-884) is initialized by `'PI_1controllerNstages'`, 
+while multiple single-axis controllers (C-663) by `'PI_NcontrollersNstages'`.
+
+## Version [0.1.5] 
+* :gem: Improved Tiling Wizard: 
+    * buttons `x-start, x-end, y-start, y-end` added for easier navigation: 
+    no need to search for corners of imaginary box around the sample. 
+    * `left, then right` illuminations can be created automatically for each tile: no need for manual duplication 
+    and changing the illumination directions in the Acquisition Manager.
+
+* :gem: Improved saving options in Fiji/BigStitcher H5 format:
+     * `laser`, `illumination`, `angle` attributes are saved in the BigStitcher XML file.
+     * (optional) downsampling and compression are supported.
+* :gem: Image window got `Adjust levels` button for automatic intensity adjustment.
+* :gem: Image window got optional `Box overlay` to help measure sample dimensions.
+* :mag: Tests for tiling and serial communication are created.
+* :bug: **Bugfix:** long-standing `permission denied` issues with serial communication 
+to filter wheel and zoom servo are fixed.
+The fix opens serial ports once and keeps them open during the session.
+The root cause was due to laser control software polling serial ports regularly, thus blocking access to them.
+
+## Version [0.1.4] 
+### Features & updates
+* :warning: **Config files need to be updated** Please note: Updating to this version requires updating your microscope configuration file. Please copy the new configuration options from the `demo.cfg` file into your config files.
+* :warning: :gem: **New handling of config files** - If there is a single config file (without a 'demo' prefix in the filename and apart from the `demo_config.py`-file) in the config folder, the software will automatically load this file. Otherwise, the config selection GUI is opened. This is especially helpful when operating a mesoSPIM with multiple users. Thanks to @raacampbell for this feature! 
+* :gem: **New: Writing HDF5** - If all rows in the acquistion manager contain the same file name (ending in `.h5`), the entire acquisition list will be saved in a single hdf5 file and a XML created automatically. Both can then be loaded into [Bigstitcher](https://imagej.net/BigStitcher) for stitching & multiview fusion. 
+For this, the `npy2bdv` package by @nvladimus needs to be installed via `python -m pip install npy2bdv`
+* :gem: **New: Dark mode** - If the `dark_mode` option in the config file is set to `True`, the user interface appears in a dark mode. For this, the `qdarkstyle` package needs to be installed via `python -m pip install qdarkstyle`.
+* :gem: **New: Camera and Acquisition Manager Windows can be reopened** - A new menu allows the camera and acquisition manager windows to be reopened in case they get closed. The same menu bar allows exiting the program as well.
+* :gem: **New: Disabling arrow buttons** - To allow mesoSPIM configurations with less than 5 motorized stages, the arrow buttons in the main window can now be disabled in the configuration file. Typical examples are a mesoSPIM without a rotation stage or a mesoSPIM using only a single motorized z-stage. This feature can also be useful if the serial connection to the stages is too slow and pressing the arrow buttons leads to incorrect movements. 
+* :gem: **Interactive IPython console** - If the software is launched via `python mesoSPIM-control.py -C`, an interactive IPython console is launched for debugging. Feature by @raacampbell.
+* :gem: **Command-line demo mode option** - If the software is launched via `python mesoSPIM-control.py -D`, it launches automatically into demo mode. Feature by @raacampbell.
+* :gem: **New: Support for PCO cameras** - PCO cameras with lightsheet mode are now supported. For this the `pco` Python package needs to be installed via `python -m pip install pco`. Currently, the only tested camera is the PCO panda 4.2 bi with lightsheet firmware.
+* :gem: **New: Support for Sutter Lambda 10B Filter Controller** Thanks to Kevin Dean @AdvancedImagingUTSW, Sutter filter wheels are now supported.
+* :gem: **New: Support for Physik Instrumente stepper motor stages in a XYZ configuration** Thanks to @drchrisch, a mesoSPIM configuration ('PI_xyz') using stepper motor stages for sample movement is now supported. Please note that this is currently not supporting focus movements or sample rotations.
+* :gem: **New: Support for Physik Instrumente C-863 controller in a single-stage config** To allow setting up a simplified mesoSPIM using only a single motorized z-stage (all other stages need to be manually operated), the combination of the C-863 motor controller and L-509 stage is now supported ('PI_z')
+* :sparkles: **Improvement:** **Disabling movement buttons in the GUI** By modifying the `ui_options` dictionary in the configuration file, the X,Y,Z, focus, rotation, and load/unload buttons can be disabled. This allows modifing the UI for mesoSPIM setups which do not utilize the full set of 5 axes. Disabled buttons are greyed out.
+* :sparkles: **Improvement:** **Updated multicolor tiling wizard** The tiling wizard now displays the FOV size and calculates the X and Y FOV offsets using a percentage setting. For this, the pixel size settings in the configuration file need to be set correctly.
+* :sparkles: **Improvement:** **Physik Instrumente stages now report their referencing status after startup in the logfile** This allows for easier diagnosis of unreferenced stages during startup. Feature by @raacampbell.
+* :bug: **Bugfix:** Binning was not working properly with all cameras.
+* :bug: **Bugfix:** Removed unnecessary imports.
+* :bug: **Bugfix:** Laser power setting `max_laser_voltage` was always 10V, ignoring the config file. This can damage some lasers that operate on lower command voltage.
+
+### Contributors 
+* Fabian Voigt (@ffvoigt)
+* Nikita Vladimirov (@nvladimus)
+* Kevin Dean (@AdvancedImagingUTSW)
+* Christian Schulze (@drchrisch)
+* Rob Campbell (@raacampbell)
+
 ## 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.
@@ -27,7 +79,7 @@ to f_start and at z_end, the detection path focus is at z_end. This allows imagi
 * :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. 

README.md

@@ -14,7 +14,7 @@ If you are updating `mesoSPIM-control` from a previous version: Please have a cl
 
 ### Prerequisites
 * Windows 7 or Windows 10
-* Python >3.6
+* 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.
@@ -24,26 +24,31 @@ If you are updating `mesoSPIM-control` from a previous version: Please have a cl
 * [Robotis DynamixelSDK](https://github.com/ROBOTIS-GIT/DynamixelSDK/releases) for Dynamixel Zoom servos. Make sure you download version 3.5.4 of the SDK.
 
 #### Python
-mesoSPIM-control is usually running with [Anaconda](https://www.anaconda.com/download/) using a >3.6 Python. For a clean python install, the following packages are necessary (part of Anaconda):
-
-* csv
-* traceback
-* pprint
-* numpy
-* scipy
-* ctypes
-* importlib
-* 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`)
-* 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`). 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)
+mesoSPIM-control is usually running with [Anaconda](https://www.anaconda.com/download/) using a >=3.6 Python. 
+##### Anaconda 
+(optional) Create and activate a Python 3.6 environment from Anaconda prompt (you can use any name instead of `py36`):
+```
+conda create -n py36 python=3.6
+conda activate py36
+```
+The step above is optional because the latest Python 3.8 is backward compatible with Python 3.6 code.
+
+Many libraries are already included in Anaconda. 
+Install mesoSPIM-specific libraries: 
+```
+pip install -r requirements-anaconda.txt
+```
+
+##### Clean python 
+For a clean (non-Anaconda) python interpreter, install all required libraries: 
+```
+pip install -r requirements-clean-python.txt
+```
+
+##### Additional libraries
+Camera libraries are not hosted on PyPi and need to be installed manually:
+* [PyVCAM when using a Photometrics camera](https://github.com/Photometrics/PyVCAM)
+* pco (`python -m pip install pco`) when using a PCO camera ([Link](https://pypi.org/project/pco/)). A Version ≥0.1.3 is recommended.
 
 #### 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`
@@ -63,12 +68,30 @@ At time of writing that means the master trigger out (`PXI6259/port0/line1`) sho
 Use BNC T connectors to split each analog output line to both lasers.
 * You will need to set the ThorLabs shutter controllers to run on TTL input mode.
 
-#### Run the software.
+## Launching
+#### From Anaconda prompt
 ```
+conda activate py36
 python mesoSPIM_Control.py
 ```
-After launch, it will prompt you for a configuration file. Please choose a file
-with demo devices (e.g. `DemoStage`) for testing.
+The software will now start. If you have multiple configuration files you will be prompted to choose one. 
+
+#### From start_mesoSPIM.bat file
+Open the `start_mesoSPIM.bat` file in text editor and configure Anaconda and `py36` path to your own. 
+Once done, launch mesoSPIM by double-clicking the file. 
+Optionally, create a Windows shortcut (via right-click menu) and place it e.g. on your desktop. 
+Using shortcut saves a lot of time.
+
+#### Starting with interactive console
+You may also run the software with an interactive IPython console for de-bugging:
+```
+python mesoSPIM_Control.py -C
+```
+For example, executing `mSpim.state.__dict__` in this console will show the current mesoSPIM state. 
+
+## Troubleshooting
+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`)
 
-#### Documentation for users
+## Documentation for users
 For instructions on how to use mesoSPIM-control, please check out the documentation [here](https://github.com/mesoSPIM/mesoSPIM-powerpoint-documentation).

mesoSPIM/config/demo_config.py

@@ -8,6 +8,18 @@
 (The extension has to be .py).
 '''
 
+'''
+Dark mode: Renders the UI dark
+'''
+ui_options = {'dark_mode' : True, # Dark mode: Renders the UI dark if enabled
+              'enable_x_buttons' : True, # Here, specific sets of UI buttons can be disabled   
+              'enable_y_buttons' : True, 
+              'enable_z_buttons' : True,
+              'enable_f_buttons' : True,
+              'enable_rotation_buttons' : True,
+              'enable_loading_buttons' : True,
+               }
+
 '''
 Waveform output for Galvos, ETLs etc.
 '''
@@ -186,9 +198,12 @@
 and safety limits. The rotation position defines a XYZ position (in absolute coordinates)
 where sample rotation is safe. Additional hardware dictionaries (e.g. pi_parameters)
 define the stage configuration details.
+All positions are absolute.
+
+'stage_type' options: 'DemoStage', 'PI_1controllerNstages' (former 'PI'), 'PI_NcontrollersNstages' 
 '''
 
-stage_parameters = {'stage_type' : 'DemoStage', # 'DemoStage' or 'PI' or other configs found in mesoSPIM_serial.py
+stage_parameters = {'stage_type' : 'DemoStage', # 'DemoStage'. 'PI_1controllerNstages', 'PI_NcontrollersNstages', see below
                     'startfocus' : -10000,
                     'y_load_position': -86000,
                     'y_unload_position': -120000,
@@ -198,54 +213,40 @@
                     'y_min' : -160000,
                     'z_max' : 99000,
                     'z_min' : -99000,
-                    'f_max' : 99000,
-                    'f_min' : -99000,
+                    'f_max' : 10000,
+                    'f_min' : -10000,
                     'theta_max' : 999,
                     'theta_min' : -999,
                     'x_rot_position': 0,
                     'y_rot_position': -121000,
                     'z_rot_position': 66000,
                     }
 
-'''
-Depending on the stage hardware, further dictionaries define further details of the stage configuration
-
-For a standard mesoSPIM V4 with PI stages, the following pi_parameters are necessary (replace the
-serialnumber with the one of your controller):
-
+''''
+If 'stage_type' = 'PI_1controllerNstages' (vanilla mesoSPIM V5 with single 6-axis controller):
 pi_parameters = {'controllername' : 'C-884',
-                 'stages' : ('M-112K033','L-406.40DG10','M-112K033','M-116.DG','M-406.4PD','NOSTAGE'),
+                 'stages' : ('L-509.20DG10','L-509.40DG10','L-509.20DG10','M-060.DG','M-406.4PD','NOSTAGE'),
                  'refmode' : ('FRF',),
-                 'serialnum' : ('118015797'),
+                 'serialnum' : ('118075764'),
                  }
 
-For a standard mesoSPIM V5 with PI stages, the following pi_parameters are necessary (replace the
-serialnumber with the one of your controller):
-
-pi_parameters = {'controllername' : 'C-884',
-                 'stages' : ('L-509.20DG10','L-509.40DG10','L-509.20DG10','M-060.DG','M-406.4PD','NOSTAGE'),
-                 'refmode' : ('FRF',),
-                 'serialnum' : ('118015799'),
+If 'stage_type' = 'PI_NcontrollersNstages' (mesoSPIM V5 with multiple single-axis controllers):
+pi_parameters = {'axes_names': ('x', 'y', 'z', 'theta', 'f'),
+                'stages': ('L-509.20SD00', 'L-509.40SD00', 'L-509.20SD00', None, 'MESOSPIM_FOCUS'),
+                'controllername': ('C-663', 'C-663', 'C-663', None, 'C-663'),
+                'serialnum': ('**********', '**********', '**********', None, '**********'),
+                'refmode': ('FRF', 'FRF', 'FRF', None, 'RON')
+                }
 '''
 
 '''
 Filterwheel configuration
-'''
-
-'''
-For a DemoFilterWheel, no COMport needs to be specified, for a Ludl Filterwheel,
-a valid COMport is necessary.
+For a DemoFilterWheel, no COMport needs to be specified.
+For a Ludl Filterwheel, a valid COMport is necessary. Ludl marking 10 = position 0.
 '''
 filterwheel_parameters = {'filterwheel_type' : 'DemoFilterWheel', # 'DemoFilterWheel' or 'Ludl'
                           'COMport' : 'COM53'}
 
-# Ludl marking 10 = position 0
-
-'''
-
-A Ludl double filter wheel can be
-'''
-
 filterdict = {'Empty-Alignment' : 0, # Every config should contain this
               '405-488-647-Tripleblock' : 1,
               '405-488-561-640-Quadrupleblock' : 2,
@@ -259,9 +260,6 @@
 
 '''
 Zoom configuration
-'''
-
-'''
 For the DemoZoom, servo_id, COMport and baudrate do not matter. For a Dynamixel zoom,
 these values have to be there
 '''
@@ -302,10 +300,18 @@
             '6.3x' : 1.03}
 
 '''
-Initial acquisition parameters
+ HDF5 parameters, if this format is used for data saving (optional).
+Downsampling and compression slows down writing by 5x - 10x, use with caution.
+Imaris can open these files if no subsampling and no compression is used.
+'''
+hdf5 = {'subsamp': ((1, 1, 1),), #((1, 1, 1),) no subsamp, ((1, 1, 1), (1, 4, 4)) for 2-level (z,y,x) subsamp.
+        'compression': None, # None, 'gzip', 'lzf'
+        'flip_xyz': (True, True, False) # match BigStitcher coordinates to mesoSPIM axes.
+        }
 
+'''                                                                  
+Initial acquisition parameters
 Used as initial values after startup
-
 When setting up a new mesoSPIM, make sure that:
 * 'max_laser_voltage' is correct (5 V for Toptica MLEs, 10 V for Omicron SOLE)
 * 'galvo_l_amplitude' and 'galvo_r_amplitude' (in V) are correct (not above the max input allowed by your galvos)
@@ -369,4 +375,4 @@
 'camera_binning':'1x1',
 'camera_sensor_mode':'ASLM',
 'average_frame_rate': 4.969,
-}
+}