Various bug fixes (#11)

* Update version, change name of GRBL robot

* Update system_config__demo.json

* Provide autofish version in log file

* Various smaller fixes in the logger

* Update README.md

* Update automator.py

* Update README.md

add information about LEICA Thunder

* Update README.md

README.md

@@ -3,21 +3,27 @@
 
 # autoFISH - automated FISH experiments
 
-Python library to control an automated fluidics system and perform microscope acquisition for iterative FISH experiments.
+Python library to control an automated fluidics system and perform acquisition on a microscope for sequential FISH experiments.
 
-Documentation of this **package**:
+**TESTED FOR WIN 10 only**: micromanager and most microscope controls work only under Windows.
 
-- [**PDF**](https://drive.google.com/file/d/1BJOog03O_1Qd0z9-Iew3j0tdCUELFUi3/view?usp=drive_link)
-- [**WORD**](https://docs.google.com/document/d/1TDRwhDQSY43seuwou7y4bqMeq4aE-g-U/edit?usp=drive_link&ouid=115789064117209337821&rtpof=true&sd=true)
+## Documentation
 
-Documentation to **build the fluidics system**:
+We provide details documentation for the fluidics system and the experimental workflows with the links below:
 
-- [**PDF**](https://drive.google.com/file/d/1uwClR1c6G9sGJg4e6qd6qb3mEDM5nUBS/view?usp=drive_link)
-- [**WORD**](https://docs.google.com/document/d/1WErUkE9Bn6kUm9p4lFHiR1-yyyQqX7Lv/edit?usp=drive_link&ouid=115789064117209337821&rtpof=true&sd=true)
+### Fluidics system and software usage
 
-**TESTED FOR WIN 10 only**: micromanager and most microscope controls work only under Windows.
+- Documentation of this **package**: 
+  [**PDF**](https://drive.google.com/open?id=1-Fr_Dbg0eQDSbhBmq2gmJ1FDb4Uy_ToI&usp=drive_fs)  or 
+  [**WORD**](https://docs.google.com/document/d/1-IA6f02elFrF7JSLvXx199cNjnm8ciBB?rtpof=true&usp=drive_fs)
+
+- Documentation to **build the fluidics system**:
+  [**PDF**](https://drive.google.com/open?id=1-3anf7ieKRPeKJ387K1XaBH0heWWIocm&usp=drive_fs) or 
+  [**WORD**](https://docs.google.com/document/d/1-NUsaEacdTHfEi9gJ_SppbXEfD7z9-im?rtpof=true&usp=drive_fs)
 
-![fluidics-system](docs/fluidics-overview.png)
+- Documentation to **use a TTL trigger with the LEICA Thunder**:
+  [**PDF**](https://drive.google.com/open?id=1-bkihEoPfgZdNXIDN6bbxiwU0kXM9xOt&usp=drive_fs) or 
+  [**WORD**](https://docs.google.com/document/d/1-ZXZ6kcjAJHre7fJ8rNfXpDT03TYYEI-?rtpof=true&usp=drive_fs)
 
 ## Getting started
 
@@ -28,35 +34,32 @@ We recommend using a package manager (conda) to maintain a clean Python installa
 1. Download latest version of miniconda from [**here**](https://docs.conda.io/en/latest/miniconda.html).
 2. Open Anaconda terminal and create dedicated environment: `conda create --name autofish python=3.9`
 3. Activate environment: `conda activate autofish`
-4. Pip install autofish (as an alternative see development installation below)
+4. Pip install **autofish** (as an alternative see development installation below)
    - Base version (without pycromanager) : `pip install -i https://test.pypi.org/simple/autofish`
-   - Install pycromanager : `pip install pycromanager`
+   - [Optional] Install pycromanager : `pip install pycromanager`
 
-#### Installation for development
-
-If you want to further develop the package, several options exist. A simply one is local installation.
+### Starting autofish
 
-Rather than performing the pip install from pypi (step 4 above), you can install it locally
+1. Open Anaconda terminal and activate environment: `conda activate autofish`
+2. Start user interface with command `autofish`
 
-1. Download the zip archive of the branch you are interested in.
-2. Unzip on your machine.
-3. Open Anaconda terminal at location of the autofish package.
-4. Activate environment: `conda activate autofish`
-5. Editable install `pip install . -e`
+### Upgrading to a new version
 
-### Pycromanager
+1. Open Anaconda terminal and activate environment: `conda activate autofish`
+2. Upgrade autoFISH `pip install --upgrade https://test.pypi.org/simple/autofish`
 
-One of the acquisition options is via Pycromanager. We found that keeping both micromanager and Pycromanager up-to-date can help to prevent problems.
+### Development installation
 
-**Last tested, compatible versions**:
+If you want to modify develop the package, several options exist. 
 
-- Pycromanager: 0.27.2
-- Micromanager: nightly 20230224
+1. Recommended is to **`clone` the repository**. This will then also allow to propose your changes to the main autoFISH repository as a PullRequest. See for instance [here](https://codex.so/fork-and-pull-en) for an explanation for how this is done. This also allows to easier add changes from the main repository 
+2. An alternative is a **local installation**. While this might be easier in the short run, it will be challenig to integrate future changes on the main repository. Rather than performing the pip install (step 4 above), you 
 
-### Starting autofish
-
-1. Open Anaconda terminal and activate environment: `conda activate autofish`
-2. Start user interface with command `autofish`
+   1. Download the zip archive of the branch you are interested in.
+   2. Unzip on your machine.
+   3. Open Anaconda terminal at location of the autofish package.
+   4. Activate environment: `conda activate autofish`
+   5. Editable install `pip install . -e`
 
 ### Configuration files
 
@@ -67,6 +70,16 @@ The behavior of the fluidics and acquistion system is defined by several config
 - We provide config files that we use on our system (with a Nikon Ti): <https://github.com/fish-quant/autofish/tree/main/configs>
 
 
+## Pycromanager
+
+One of the acquisition options is by using Pycromanager. We found that keeping both micromanager and Pycromanager up-to-date can help to prevent problems.
+
+**Last tested, compatible versions**:
+
+- Pycromanager: 0.27.2
+- Micromanager: nightly 20230224
+
+
 ## Reporting a problem/suggestion
 
 If you encounter a problem or you have a suggestion, please file an [**issue**](https://github.com/fish-quant/autofish/issues).

autofish/autofish_gui.py

@@ -10,15 +10,16 @@
 import threading
 from datetime import datetime
 import pathlib
-
+import autofish
 from autofish.automator import Robot
 from autofish.imager import pycroManager, fileSync_write, fileSync_create, TTL_sync
 from autofish.coordinator import Controller
-
+from importlib.metadata import version
 # ---------------------------------------------------------------------------
 # Functions
 # ---------------------------------------------------------------------------
 
+
 sg.theme('DarkAmber')
 NAME_SIZE = 23
 microscope_options = ('pycromanager', 'TTL sync', 'file synce - create', 'file sync - write')
@@ -37,9 +38,10 @@ def make_window_control():
               [sg.HorizontalSeparator()],
               [sg.Button('Initiate controller', key='-INITIATE_CONTROL-', disabled=True)],
               [sg.HorizontalSeparator()],
-              [sg.Button('RUN all ROUNDS!', key='-RUN_ALL_ROUNDS-', disabled=True),
-               sg.Button('STOP sequential RUN', key='-STOP_SEQ-', disabled=True)],
-              [sg.Text('Save path'),      sg.Text('                                 ', key='-OUTPUT_DIR_SAVE_IMGS-')],
+              [sg.Button('RUN all ROUNDS!', key='-RUN_ALL_ROUNDS-', disabled=True)
+               #sg.Button('STOP sequential RUN', key='-STOP_SEQ-', disabled=True)
+               ],
+              [sg.Text(''),      sg.Text('                                 ', key='-OUTPUT_DIR_SAVE_IMGS-')],
               ]
 
     return sg.Window('Automator - automate sequential FISH', layout, location=(800, 600), finalize=True)
@@ -166,8 +168,9 @@ def make_window_fluidics():
         [sg.Text(' >>  Run sequences <<')],
         [sg.Text('Choose sequence: '),
          sg.Combo(['To-be-specified'], key='-SEQ_LIST-'),
-         sg.Button('RUN sequence', key='-RUN_SEQ-', disabled=True),
-         sg.Button('STOP sequence', key='-STOP_SEQ-', disabled=False)],
+         sg.Button('RUN sequence', key='-RUN_SEQ-', disabled=True)
+         #sg.Button('STOP sequence', key='-STOP_SEQ-', disabled=False)
+         ],
 
         #[sg.HorizontalSeparator()],
         #[sg.Text(' Pippette robot status'),
@@ -206,6 +209,10 @@ def main():
     handler.setFormatter(formatter)
     logger.addHandler(handler)
 
+    logger_stream.info(f'More detailed log file can be found here {handler.baseFilename}.')
+    logger_stream.info(f"Using autofish version {version('autofish')}.")
+    logger.info(f"Using autofish version {version('autofish')}.")
+
     # >>> Event Loop
     while True:
 
@@ -459,7 +466,6 @@ def main():
         # >> FLUIDICS system
         # ******************************************************************************************************
         elif event == '-INITIATE_SYSTEM-':
-            logger_stream.info(f'Initiate Robot & open serial ports. More info in log {f_log}')
 
             try:
                 R = Robot(values['-CONFIG_SYSTEM-'], logger=logger, logger_short=logger_stream)