Adding new valves, components, and smaller fixes (#7)

* Update setup.cfg

* Cosmetic updates in autofish_gui.py

* Add templates for missing docstrings

* First clean up of error messages when initiating robot.

* changes to help that volume file is updated rather than always recreated

should close #4

* small updates in documentation

* small changes

* update gitignore

* remove not needed blanks

* some more cosmetic clean-ups

* correct bug with wrongly assigned feed for valve

* Add support for Longer pump

* cosmetic changes

* Update README.md

* update gitignore

* continue integration of Longer pump

* bug fixing for Longer control

* Smaller fixes for longer pump support

* clean up

* Started bug fix on reading csv file from french computers

Some cleanup

* Update README.md

* Correct bug for flow sensor, zero robot when closing interface

* New sync option via creation of text file

Smaller cosmetic changes
Corrected bug in demo mode

* Correction of bug with moving to zero and keeping old position in memory

* TTL trigger

* Update .DS_Store

* TTL cleanup

* Update autofish_manual.pdf

* Update imager.py

* remove tests

* Add control for outlet valve

* updated config files for outlet valve

* Updated docs

* Added control for pycromanager

Specify stage-speed and Core-timeout in config file.

* Update .gitignore

* Added code to test components

* Update pump-longer-bt100.py

* new valve added

* updates on documentation

* update readme and remove pdfs

* update bug when trying to open TTL without specified file

* Delete .DS_Store

* Various small bug fixes

.gitignore

@@ -86,4 +86,7 @@ env.bak/
 venv.bak/
 
 # mkdocs documentation
-/site
+/site
+.DS_Store
+.DS_Store
+.DS_Store

README.md

@@ -5,7 +5,15 @@
 
 Python library to control an automated fluidics system and perform microscope acquisition for iterative FISH experiments.
 
-See dedicated documentation [**here**](https://github.com/fish-quant/autofish/blob/master/docs/autofish_manual.pdf) for how to install and use this package.
+Documentation of this **package**:
+
+- [**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 to **build the fluidics system**:
+
+- [**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)
 
 **TESTED FOR WIN 10 only**: micromanager and most microscope controls work only under Windows.
 
@@ -15,10 +23,35 @@ See dedicated documentation [**here**](https://github.com/fish-quant/autofish/bl
 
 ### Installation
 
-1. Download latest version of miniconda from [**here**](https://docs.conda.io/en/latest/miniconda.html) (can also be Python 3.X).
+We recommend using a package manager (conda) to maintain a clean Python installation. This nees to be done only once.
+
+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 `pip install -i https://test.pypi.org/simple/ autofish`
+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`
+
+#### Installation for development
+
+If you want to further develop the package, several options exist. A simply one is local installation.
+
+Rather than performing the pip install from pypi (step 4 above), you can install it locally
+
+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`
+
+### Pycromanager
+
+One of the acquisition options is via 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
 
 ### Starting autofish
 
@@ -29,13 +62,10 @@ See dedicated documentation [**here**](https://github.com/fish-quant/autofish/bl
 
 The behavior of the fluidics and acquistion system is defined by several config files.
 
-* To test the installation of autofish, you can use demo configurations which require neither a microscope nor a fluidics systems: <https://github.com/fish-quant/autofish/tree/main/demo>
-
-* We provide config files that we use on our system (with a Nikon Ti): <https://github.com/fish-quant/autofish/tree/main/configs>
+- To test the installation of autofish, you can use demo configurations which require neither a microscope nor a fluidics systems: <https://github.com/fish-quant/autofish/tree/main/demo>
 
-### Building the Fluidics system
+- We provide config files that we use on our system (with a Nikon Ti): <https://github.com/fish-quant/autofish/tree/main/configs>
 
-See dedicated documentation [**here**](https://github.com/fish-quant/autofish/blob/master/docs/fluidics_construction.pdf) for how to build the fluidics system.
 
 ## Reporting a problem/suggestion
 

autofish/Arduino_TTL_sync/Arduino_TTL_sync.ino

@@ -0,0 +1,71 @@
+String serial_InBytes;
+
+
+// Define pins
+int TTL_start_OUT = 12;
+int TTL_finished_IN = 10;
+int val_TTL_finished_IN;
+
+void setup() {
+  pinMode(LED_BUILTIN, OUTPUT);
+  pinMode(TTL_start_OUT, OUTPUT);
+  pinMode(TTL_finished_IN, INPUT);
+
+  Serial.begin(9600);
+  Serial.setTimeout(1000);
+
+  // TTL signal for debugging
+  pinMode(7, OUTPUT);
+  pinMode(8, OUTPUT);
+
+}
+void loop() {
+
+  // TTL signal for debugging (pin 8 can be used to simulate incoming TTL)
+  digitalWrite(7, HIGH); 
+  digitalWrite(8, LOW); 
+
+
+  if (Serial.available() > 0){
+
+    /*
+    // DEBUGGIN : print TTL signal
+    val_TTL_in = digitalRead(TTL_in);   // read the input pin
+    Serial.println(val_TTL_in);
+    delay(10);
+    */
+
+    // Read from serial port
+    serial_InBytes = Serial.readStringUntil('\n');
+    //Serial.println(InBytes);
+
+    // Start acquisition
+    if (serial_InBytes == "start"){
+      Serial.println("Sending TTL trigger to launch acquisition");
+      digitalWrite(TTL_start_OUT, HIGH); 
+      digitalWrite(LED_BUILTIN, HIGH);
+
+      // Wait for trigger that acquisition is done
+      val_TTL_finished_IN = 0;
+      while (val_TTL_finished_IN==0) {
+        val_TTL_finished_IN = digitalRead(TTL_finished_IN);   // read the input pin
+        Serial.println(val_TTL_finished_IN);
+        delay(500);
+      }
+
+      // Signal received that acquisition is finished
+      Serial.println("finished");
+      digitalWrite(TTL_start_OUT, LOW);
+      digitalWrite(LED_BUILTIN, LOW);
+    }
+
+    // Unknown command
+    else{
+      Serial.println("Unknown command: " + serial_InBytes);
+    }
+
+  delay(500);
+
+  }
+}
+