public MOTMasterSequence GetSequence()
{
MOTMasterSequence s = new MOTMasterSequence();
s.DigitalPattern = GetDigitalPattern();
s.AnalogPattern = GetAnalogPattern();
return s;
}
public MOTMasterSequence GetSequence()
{
MOTMasterSequence s = new MOTMasterSequence();
s.DigitalPattern = GetDigitalPattern();
s.AnalogPattern = GetAnalogPattern();
return(s);
}
public void StoreRun(string saveFolder, int batchNumber, string pathToPattern, string pathToHardwareClass,
MOTMasterSequence sequence, Dictionary <String, Object> dict, Dictionary <String, Object> report, string externalFilesPath, string externalFilePattern)
{
string fileTag = getDataID(element, batchNumber);
saveToFiles(fileTag, saveFolder, batchNumber, pathToPattern, pathToHardwareClass, dict, report, sequence);
string[] files = putCopiesOfFilesToZip(saveFolder, fileTag, externalFilesPath, externalFilePattern);
deleteFiles(files);
}
public void Run(Dictionary <String, Object> dict)
{
Stopwatch watch = new Stopwatch();
MOTMasterScript script = prepareScript(scriptPath, dict);
if (script != null)
{
MOTMasterSequence sequence = getSequenceFromScript(script);
try
{
prepareCameraControl();
armTranslationStageForTimedMotion(script);
GrabImage((int)script.Parameters["NumberOfFrames"]);
buildPattern(sequence, (int)script.Parameters["PatternLength"]);
waitUntilCameraIsReadyForAcquisition();
watch.Start();
runPattern(sequence);
watch.Stop();
//MessageBox.Show(watch.ElapsedMilliseconds.ToString());
if (saveEnable)
{
waitUntilCameraAquisitionIsDone();
try
{
checkDataArrived();
}
catch (DataNotArrivedFromHardwareControllerException)
{
return;
}
Dictionary <String, Object> report = GetExperimentReport();
save(script, scriptPath, imageData, report);
}
finishCameraControl();
disarmAndReturnTranslationStage();
}
catch (System.Net.Sockets.SocketException e)
{
MessageBox.Show("CameraControllable not found. \n Is there a hardware controller running? \n \n" + e.Message, "Remoting Error");
}
}
else
{
MessageBox.Show("Unable to load pattern. \n Check that the script file exists and that it compiled successfully");
}
}
private void initializeHardware(MOTMasterSequence sequence)
{
if (triggered == true)
{
pg.Configure(config.DigitalPatternClockFrequency, false, true, true, sequence.DigitalPattern.Pattern.Length, true, true);
}
else
{
pg.Configure(config.DigitalPatternClockFrequency, false, true, true, sequence.DigitalPattern.Pattern.Length, true, false);
}
apg.Configure(sequence.AnalogPattern, config.AnalogPatternClockFrequency, false);
}
private void storeAnalogPattern(string dataStoreFilePath, MOTMasterSequence sequence)
{
Dictionary <String, Dictionary <Int32, Double> > analogPatterns = sequence.AnalogPattern.AnalogPatterns;
var settings = new DataContractJsonSerializerSettings();
settings.UseSimpleDictionaryFormat = true; // Make format of json file {key : value} instead of {"Key": key, "Value": value}
DataContractJsonSerializer serializer = new DataContractJsonSerializer(typeof(Dictionary <String, Dictionary <Int32, Double> >), settings);
TextWriter output = File.CreateText(dataStoreFilePath);
using (MemoryStream ms = new MemoryStream())
{
serializer.WriteObject(ms, analogPatterns);
output.Write(Encoding.Default.GetString(ms.ToArray()));
output.Close();
}
}
private void storeDigitalPattern(string dataStoreFilePath, MOTMasterSequence sequence)
{
Hashtable digitalChannelsHash = DAQ.Environment.Environs.Hardware.DigitalOutputChannels;
Dictionary <string, int> digitalChannels = new Dictionary <string, int>();
foreach (DictionaryEntry pair in digitalChannelsHash)
{
string patternGeneratorBoard = (string)DAQ.Environment.Environs.Hardware.GetInfo("PatternGeneratorBoard");
if (((DigitalOutputChannel)pair.Value).Device == patternGeneratorBoard)
{
digitalChannels.Add((string)pair.Key, ((DigitalOutputChannel)pair.Value).BitNumber);
}
}
var settings = new DataContractJsonSerializerSettings();
settings.UseSimpleDictionaryFormat = true; // Make format of json file {key : value} instead of {"Key": key, "Value": value}
DataContractJsonSerializer serializer = new DataContractJsonSerializer(typeof(Dictionary <string, int>), settings);
string digitalPatternString = sequence.DigitalPattern.Layout.ToString();
TextWriter output = File.CreateText(dataStoreFilePath);
output.Write("{");
output.Write("\"channels\":");
using (MemoryStream ms = new MemoryStream())
{
serializer.WriteObject(ms, digitalChannels);
output.Write(Encoding.Default.GetString(ms.ToArray()));
}
output.Write(",");
output.Write("\"pattern\":");
output.Write("\"");
output.Write(System.Web.HttpUtility.JavaScriptStringEncode(digitalPatternString));
output.Write("\"");
output.Write("}");
output.Close();
}
private void buildPattern(MOTMasterSequence sequence, int patternLength)
{
sequence.DigitalPattern.BuildPattern(patternLength);
sequence.AnalogPattern.BuildPattern();
}
private void runPattern(MOTMasterSequence sequence)
{
initializeHardware(sequence);
run(sequence);
releaseHardwareAndClearDigitalPattern(sequence);
}
public void Run(Dictionary <String, Object> dict)
{
Stopwatch watch = new Stopwatch();
MOTMasterScript script = prepareScript(scriptPath, dict);
if (script != null)
{
MOTMasterSequence sequence = getSequenceFromScript(script);
try
{
prepareCameraControl();
Console.WriteLine("prepared Camera Control");
armTranslationStageForTimedMotion(script);
GrabImage((int)script.Parameters["NumberOfFrames"]);
Console.WriteLine("'grabbed image'");
buildPattern(sequence, (int)script.Parameters["PatternLength"]);
Console.WriteLine("built pattern");
waitUntilCameraIsReadyForAcquisition();
watch.Start();
Console.WriteLine("watch started");
runPattern(sequence);
Console.WriteLine("sequence finished");
watch.Stop();
Console.WriteLine("watch stopped");
//MessageBox.Show(watch.ElapsedMilliseconds.ToString());
if (saveEnable)
{
Console.WriteLine("waiting for camera acquisition to finish");
waitUntilCameraAquisitionIsDone();
Console.WriteLine("waited for camera acquisition to finish");
try
{
checkDataArrived();
}
catch (DataNotArrivedFromHardwareControllerException)
{
Console.WriteLine("Data not arrived from hardware controller");
return;
}
int[] ROIforImageProcessing = { (int)script.Parameters["ROIforImageProcessingx1"], (int)script.Parameters["ROIforImageProcessingx2"], (int)script.Parameters["ROIforImageProcessingy1"], (int)script.Parameters["ROIforImageProcessingy2"] };
processImages(ROIforImageProcessing);
Console.WriteLine("processed images");
Dictionary <String, Object> report = GetExperimentReport();
Console.WriteLine("got experiment report");
if (absImage == null)
{
save(script, scriptPath, imageData, report);
}
else
{
save(script, scriptPath, imageData, absImage, columnSum, rowSum, report);
}
Console.WriteLine("saved images");
}
else
{
Console.WriteLine("waiting for camera acquisition to finish");
waitUntilCameraAquisitionIsDone();
Console.WriteLine("waited for camera acquisition to finish");
}
finishCameraControl();
Console.WriteLine("finished camera control");
disarmAndReturnTranslationStage();
}
catch (System.Net.Sockets.SocketException e)
{
MessageBox.Show("CameraControllable not found. \n Is there a hardware controller running? \n \n" + e.Message, "Remoting Error");
}
}
else
{
MessageBox.Show("Unable to load pattern. \n Check that the script file exists and that it compiled successfully");
}
}
private void releaseHardwareAndClearDigitalPattern(MOTMasterSequence sequence)
{
sequence.DigitalPattern.Clear(); //No clearing required for analog (I think).
pg.StopPattern();
apg.StopPattern();
}
private void runPattern(MOTMasterSequence sequence)
{
initializeHardware(sequence);
run(sequence);
releaseHardwareAndClearDigitalPattern(sequence);
}
private void releaseHardwareAndClearDigitalPattern(MOTMasterSequence sequence)
{
clearDigitalPattern(sequence);
releaseHardware();
}
private void buildPattern(MOTMasterSequence sequence, int patternLength)
{
sequence.DigitalPattern.BuildPattern(patternLength);
sequence.AnalogPattern.BuildPattern();
}
private void releaseHardwareAndClearDigitalPattern(MOTMasterSequence sequence)
{
clearDigitalPattern(sequence);
releaseHardware();
}
private void clearDigitalPattern(MOTMasterSequence sequence)
{
sequence.DigitalPattern.Clear(); //No clearing required for analog (I think).
}
public void Go(Dictionary <String, Object> dict)
{
status = RunningState.running;
Stopwatch watch = new Stopwatch();
MOTMasterScript script = prepareScript(scriptPath, dict);
if (script != null)
{
MOTMasterSequence sequence = getSequenceFromScript(script);
try
{
if (config.CameraUsed)
{
prepareCameraControl();
}
if (config.TranslationStageUsed)
{
armTranslationStageForTimedMotion(script);
}
if (config.CameraUsed)
{
GrabImage((int)script.Parameters["NumberOfFrames"]);
}
buildPattern(sequence, (int)script.Parameters["PatternLength"]);
if (config.CameraUsed)
{
waitUntilCameraIsReadyForAcquisition();
}
watch.Start();
if (controllerWindow.RunUntilStoppedState)
{
while (status == RunningState.running)
{
if (!config.Debug)
{
runPattern(sequence);
}
}
}
else
{
for (int i = 0; i < controllerWindow.GetIterations() && status == RunningState.running; i++)
{
if (!config.Debug)
{
runPattern(sequence);
}
}
}
if (!config.Debug)
{
clearDigitalPattern(sequence);
}
watch.Stop();
//MessageBox.Show(watch.ElapsedMilliseconds.ToString());
if (saveEnable)
{
if (config.CameraUsed)
{
waitUntilCameraAquisitionIsDone();
try
{
checkDataArrived();
}
catch (DataNotArrivedFromHardwareControllerException)
{
return;
}
Dictionary <String, Object> report = null;
if (config.ReporterUsed)
{
report = GetExperimentReport();
}
save(script, scriptPath, imageData, report);
}
else
{
Dictionary <String, Object> report = null;
if (config.ReporterUsed)
{
report = GetExperimentReport();
}
save(script, scriptPath, report);
}
}
if (config.CameraUsed)
{
finishCameraControl();
}
if (config.TranslationStageUsed)
{
disarmAndReturnTranslationStage();
}
}
catch (System.Net.Sockets.SocketException e)
{
MessageBox.Show("CameraControllable not found. \n Is there a hardware controller running? \n \n" + e.Message, "Remoting Error");
}
}
else
{
MessageBox.Show("Unable to load pattern. \n Check that the script file exists and that it compiled successfully");
}
status = RunningState.stopped;
}
private MOTMasterSequence getSequenceFromScript(MOTMasterScript script)
{
MOTMasterSequence sequence = script.GetSequence();
return(sequence);
}
private void releaseHardwareAndClearDigitalPattern(MOTMasterSequence sequence)
{
sequence.DigitalPattern.Clear(); //No clearing required for analog (I think).
pg.StopPattern();
apg.StopPattern();
}
private void clearDigitalPattern(MOTMasterSequence sequence)
{
sequence.DigitalPattern.Clear(); //No clearing required for analog (I think).
}
private void initializeHardware(MOTMasterSequence sequence)
{
pg.Configure(pgClockFrequency, false, true, true, sequence.DigitalPattern.Pattern.Length, true);
apg.Configure(sequence.AnalogPattern, apgClockFrequency);
}
private void saveToFiles(string fileTag, string saveFolder, int batchNumber, string pathToPattern, string pathToHardwareClass,
Dictionary <String, Object> dict, Dictionary <String, Object> report, MOTMasterSequence sequence)
{
storeDigitalPattern(saveFolder + fileTag + "_digitalPattern.json", sequence);
storeAnalogPattern(saveFolder + fileTag + "_analogPattern.json", sequence);
storeDictionary(saveFolder + fileTag + "_parameters.txt", dict);
File.Copy(pathToPattern, saveFolder + fileTag + "_script.cs");
File.Copy(pathToHardwareClass, saveFolder + fileTag + "_hardwareClass.cs");
storeDictionary(saveFolder + fileTag + "_hardwareReport.txt", report);
}
private void run(MOTMasterSequence sequence)
{
apg.OutputPatternAndWait(sequence.AnalogPattern.Pattern);
pg.OutputPattern(sequence.DigitalPattern.Pattern);
}
private void run(MOTMasterSequence sequence)
{
apg.OutputPatternAndWait(sequence.AnalogPattern.Pattern);
pg.OutputPattern(sequence.DigitalPattern.Pattern);
}
private void initializeHardware(MOTMasterSequence sequence)
{
pg.Configure(pgClockFrequency, false, true, true, sequence.DigitalPattern.Pattern.Length, true, false);
apg.Configure(sequence.AnalogPattern, apgClockFrequency);
}
private void save(MOTMasterSequence sequence, MOTMasterScript script, string pathToPattern, Dictionary <String, Object> report)
{
ioHelper.StoreRun(motMasterDataPath, controllerWindow.GetSaveBatchNumber(), pathToPattern, hardwareClassPath,
sequence, script.Parameters, report, externalFilesPath, config.ExternalFilePattern);
}
