Skip to content

Send thread #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jbowler06 wants to merge 3 commits into
base: main
Choose a base branch
from
Open

Send thread #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
49293a5
allow for non-lickport reward pins
jbowler06 Mar 18, 2024
c468945
fixed random iti for timed iti decorator
jbowler06 Aug 26, 2024
940334f
updated UDP message sending and file writing logic
jbowler06 Oct 31, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
57 changes: 0 additions & 57 deletions readme.md
View file
Open in desktop

This file was deleted.

4 changes: 2 additions & 2 deletions src/BasicContextList.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -224,7 +224,7 @@ public UdpClient getComm() {
* ?
*/
public void sendCreateMessages() {
// comm may be null for certian subclasses of ContextList which to not
// comm may be null for certain subclasses of ContextList which to not
// need to talk to the behavior arduino
if (comm != null) {
context_info.setString("action", "create");
Expand All @@ -242,7 +242,7 @@ public void sendCreateMessages() {
int valve_pin = valves.getInt(i);
JSONObject valve_json;

// frequency causes this singal to oscillate in order to play a
// frequency causes this signal to oscillate in order to play a
// tone
if (!context_info.isNull("frequency")) {
valve_json = TreadmillController.setup_valve_json(valve_pin,
Expand Down
14 changes: 10 additions & 4 deletions src/FileWriter.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -148,7 +148,7 @@ public class WriterThread extends Thread {
* Placeholder
*/
public void run() {
messageBuffer = writeQueue.poll();
messageBuffer = writeQueue.peek();
while (this.run || messageBuffer != null) {
if (messageBuffer != null) {
try {
Expand All @@ -173,11 +173,17 @@ public void run() {
alert += ("\n" + elements[i].toString());
}
if (tl != null) {
tl.exception(alert);
//tl.exception(alert);
tl.alert("FileWriter: Error logging message:\n"
+ messageBuffer);
try {
Thread.sleep(25);
} catch (InterruptedException ie) {}
}
break;
}
messageBuffer = writeQueue.poll();
writeQueue.poll();
messageBuffer = writeQueue.peek();
}

try {
Expand All @@ -194,7 +200,7 @@ public void run() {
Thread.sleep(25);
} catch (InterruptedException e) {}

messageBuffer = writeQueue.poll();
messageBuffer = writeQueue.peek();
}
}

Expand Down
9 changes: 5 additions & 4 deletions src/TimedITIContextDecorator.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,12 +27,12 @@ public class TimedITIContextDecorator extends SuspendableContextDecorator {
/**
* ?
*/
protected int iti_time_min;
protected float iti_time_min;

/**
* ?
*/
protected int iti_time_max;
protected float iti_time_max;

/**
* ?
Expand Down Expand Up @@ -73,6 +73,7 @@ public TimedITIContextDecorator(TreadmillController tc,
this.random_iti = context_info.getBoolean("random_iti", false);

if (this.random_iti) {
this.random = new Random();
this.iti_time_min = context_info.getInt("iti_time_min");
this.iti_time_max = context_info.getInt("iti_time_max");
} else {
Expand Down Expand Up @@ -134,8 +135,8 @@ public boolean check_suspend(float position, float time, int lap, int lick_count
if (this.long_delay_laps.contains(this.start_lap)) {
this.next_start = time + this.long_delay;
} else if (this.random_iti) {
this.next_start = time + random.nextInt(
(this.iti_time_max - this.iti_time_min + 1)) + this.iti_time_min;
this.next_start = time + this.random.nextFloat() *
(this.iti_time_max - this.iti_time_min) + this.iti_time_min;
} else {
this.next_start = time + this.iti_time;
}
Expand Down
52 changes: 40 additions & 12 deletions src/TreadmillController.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,10 @@ public class TreadmillController extends PApplet {
*/
ArrayList<UdpClient> comms;

// List to store behavior comms that haven't confirmed creation. Used to verify
// system is ready to start an experiment
ArrayList<String> unset_contexts;

/**
* Time (ms) of the last comms check
*/
Expand Down Expand Up @@ -502,6 +506,10 @@ public boolean Start(String mouse_name, String experiment_group) {

testComms();

if (unset_contexts.size() > 0) {
trialListener.alert("Failed to create Contexts\n" + String.join(", ", unset_contexts));
}

trialListener.started(fWriter.getFile());

timer.startTimer();
Expand Down Expand Up @@ -922,6 +930,9 @@ void configure_rewards() throws Exception {
if (context.getString("id").equals(reward_context)) {
JSONArray valve_list = context.getJSONArray("valves");
reward_valve = valve_list.getInt(0);
if (context.getString("type").equals("operant")) {
lickport_pin = context.getInt("sensor");
}
return;
}
}
Expand All @@ -939,6 +950,10 @@ void configure_rewards() throws Exception {
reward_info.setJSONArray("valves", context_valves);
}

if (!reward_info.isNull("sensor")) {
lickport_pin = reward_info.getInt("sensor");
}

if (!reward_info.isNull("drop_size")) {
JSONArray context_duration = new JSONArray();
context_duration.append(reward_info.getInt("drop_size"));
Expand Down Expand Up @@ -1011,6 +1026,7 @@ void reload_settings(String filename, String tag) throws Exception {
*/
void startComms() throws Exception {
comms = new ArrayList<UdpClient>();
unset_contexts = new ArrayList<String>();
position_comm = null;
behavior_comm = null;
reset_comm = null;
Expand Down Expand Up @@ -1178,10 +1194,11 @@ void reconfigureExperiment() throws Exception {
}

if (!settings_json.isNull("contexts")) {
unset_contexts.clear();
delay(10);
VrContextList2 vr_context = null;
ArrayList<VrCueContextList3> cue_lists =
new ArrayList<VrCueContextList3>();
//VrContextList2 vr_context = null;
//ArrayList<VrCueContextList3> cue_lists =
// new ArrayList<VrCueContextList3>();

JSONArray contexts_array = settings_json.getJSONArray("contexts");
for (int i = 0; i < contexts_array.size(); i++) {
Expand All @@ -1199,6 +1216,10 @@ void reconfigureExperiment() throws Exception {
" failed to connect to comm");
}
display.setContextLocations(context_list);

if ((behavior_comm != null) && (context_list.getComm() == behavior_comm)) {
unset_contexts.add(context_list.getId());
}
}

for (ContextList context : this.contexts) {
Expand Down Expand Up @@ -1670,10 +1691,19 @@ protected void updateBehavior(float time) {
String action = sensorJson.getString("action", "stop");
if (action.equals("start")) {
display.setSensorState(sensor_pin, 1);
sensor_counts.put(sensor_pin,
sensor_counts.get(sensor_pin) + 1);
if (sensor_counts.containsKey(sensor_pin)) {
sensor_counts.put(sensor_pin,
sensor_counts.get(sensor_pin) + 1);
}
if (sensor_pin == lickport_pin) {
display.addLick(started);
lick_count++;
}
} else if (action.equals("stop")) {
display.setSensorState(sensor_pin, -1);
if (sensor_pin == lickport_pin) {
display.lickStop();
}
} else if (action.equals("created")) {
sensor_counts.put(sensor_pin, 0);
display.setSensorState(sensor_pin, -1);
Expand Down Expand Up @@ -1712,17 +1742,15 @@ protected void updateBehavior(float time) {
if (!context_json.isNull("id")) {
String context_id = context_json.getString("id");
if (!context_json.isNull("action")) {
String action = context_json.getString("action");
for (int j=0; j < contexts.size(); j++) {
if (contexts.get(j).getId().equals(context_id)) {
if (context_json.getString("action").equals(
"start")) {

if (action.equals("start")) {
contexts.get(j).setStatus("started");
} else if (
context_json.getString("action").equals(
"stop")) {

} else if (action.equals("stop")) {
contexts.get(j).setStatus("stopped");
} else if (action.equals("created")) {
unset_contexts.remove(context_id);
}

break;
Expand Down
Loading