/// <summary>
/// Marks a imaging as completed.
/// </summary>
public void ImagedPlate(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, string imagingID)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
if (null == imagingID)
{
throw new System.NullReferenceException("imagingID must not be null");
}
ImagingTask task;
bool ok = _tasks.TryGetValue(imagingID, out task);
if (ok)
{
task.SetInQueue(false);
task.SetState(ImagingState.Completed);
}
return;
}
/// <summary>
/// Marks an imaging as skipped.
/// </summary>
public void SkippedImaging(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, DateTime dateToImage)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
string imagingID = DummyImagingTaskProvider.GetImagingID(plateID, dateToImage);
ImagingTask task;
bool ok = _tasks.TryGetValue(imagingID, out task);
if (ok)
{
task.SetInQueue(false);
task.SetState(ImagingState.Skipped);
}
return;
}
/// <summary>
/// Construct an IImageProcessor instance for the specified IRobot and IProcessingInfo.
/// </summary>
/// <param name="robot">The Robot that took the images to be processed by this IImageProcessor instance</param>
/// <param name="processingInfo">The description of the images to be processed by this IImageProcessor instance</param>
public ImageProcessor2(IRobot robot, IProcessingInfo processingInfo, IPlateInfo plateInfo, IPlateType plateType)
{
// Get Logger.
_log = LogManager.GetLogger(this.GetType());
_dateImaged = DateTime.MinValue;
_lightPath = 0;
_robot = robot;
_processingInfo = processingInfo;
_plateInfo = plateInfo;
_plateType = plateType;
_captureInfo = null;
SetRegionName(_processingInfo.RegionID);
SetProfileName(_processingInfo.ProfileID);
_log.Info(
"DropNumber=" + processingInfo.DropNumber +
";ImagingID=\"" + processingInfo.ImagingID + "\"" +
";PlatedID=\"" + processingInfo.PlateID + "\"" +
";ProfileID=\"" + processingInfo.ProfileID + "\"" +
";RegionID=\"" + processingInfo.RegionID + "\"" +
";RegionType=" + processingInfo.RegionType.ToString() +
";WellNumber=" + processingInfo.WellNumber +
";Robot.Name=\"" + _robot.Name + "\"");
}
/// <summary>
/// Marks a imaging as completed.
/// </summary>
void IImagingTaskProvider.ImagedPlate(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, string imagingID)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
if (null == imagingID)
{
throw new System.NullReferenceException("imagingID must not be null");
}
// Log the call to the method
if (_log.IsDebugEnabled)
{
string msg = "Called " + this + ".ImagedPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", imagingID=\"" + imagingID + "\")";
_log.Debug(msg);
}
// Set the request
imagedPlate request = new imagedPlate();
request.robot = OPPF.Utilities.RobotUtils.createProxy(robot);
request.plateID = plateID;
request.imagingID = imagingID;
// Make the call
WSPlate wsPlate = new WSPlate();
imagedPlateResponse response = null;
try
{
response = wsPlate.imagedPlate(request);
}
catch (Exception e)
{
// Log it
string msg = "WSPlate.imagedPlate threw " + e.GetType() + ": " + e.Message + " - panic!";
msg = msg + "\nin " + this + ".ImagedPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", imagingID=\"" + imagingID + "\")";
if (e is System.Web.Services.Protocols.SoapException)
{
System.Web.Services.Protocols.SoapException ee = (System.Web.Services.Protocols.SoapException)e;
msg = msg + "\n\n" + ee.Detail.InnerXml;
}
_log.Fatal(msg, e);
// Panic
throw e;
}
// Webservice always returns true if it doesn't throw an exception
return;
}
/// <summary>
/// Gets the capture profile for the plate under the microscope.
/// </summary>
/// <param name="plateID">The plateID to retrieve the capture profile for.</param>
/// <returns>The default <c>ICaptureProfile</c> for this plateID, or <c>null</c> if the default imager configuration should be used.</returns>
ICaptureProfile ICaptureProvider.GetDefaultCaptureProfile(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID)
{
// TODO: Add CaptureProvider.GetDefaultCaptureProfile implementation
if (_log.IsInfoEnabled)
{
_log.Info("Called ICaptureProvider.GetDefaultCaptureProfile(" + Robot.ToString(robot) + ", \"" + plateID + "\") - returning null");
}
return(null);
}
/*
* Added in Formulatrix.Integrations.ImagerLink.dll v2.0.0.73 (RockImager v2.0.3.18),
* which is supposed to be more recent than v2.0.1.136 (RockImager v2.0.1.136).
*/
/// <summary>
/// Gets an <c>ICapturePointList</c> to image for this plateID on the specified <c>imagingID</c>.
/// </summary>
/// <param name="robot"></param>
/// <param name="plateID"></param>
/// <param name="imagingID">The imaging ID started for this run.</param>
/// <param name="includeOverview"></param>
/// <param name="userSelectionCaptureProfileID"></param>
/// <returns></returns>
/// <remarks>
/// Added in Formulatrix.Integrations.ImagerLink.dll v2.0.0.73 (RockImager v2.0.3.18),
/// which is supposed to be more recent than v2.0.1.136 (RockImager v2.0.1.136).
/// </remarks>
ICapturePointList ICaptureProvider.GetCapturePoints(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, string imagingID, bool includeOverview, int userSelectionCaptureProfileID)
{
// TODO: Add CaptureProvider.GetCapturePoints implementation
//return null;
if (_log.IsInfoEnabled)
{
_log.Info("Called ICaptureProvider.GetCapturePoints(" + Robot.ToString(robot) + ", \"" + plateID + "\", \"" + imagingID + "\", " + includeOverview + ", " + userSelectionCaptureProfileID + ")");
}
CapturePointList capturePointList = null;
// OPPF Vis
if (1 == userSelectionCaptureProfileID)
{
_log.Info("Returning empty ICapturePointList");
capturePointList = new CapturePointList();
}
// OPPF UV
else if (2 == userSelectionCaptureProfileID)
{
_log.Info("Returning ICapturePointList with PlateCaptureProfile and CapturePoints set to an ICaptureProfile with one IProperty of \"LightPath\" = \"1\"");
// Create the property array containing the UV LightPath property
IProperty[] properties = new OPPF.Integrations.ImagerLink.Property[1];
properties[0] = new OPPF.Integrations.ImagerLink.Property("LightPath", "1");
// Create a new CaptureProfile and apply the UV LightPath property
CaptureProfile captureProfile = new CaptureProfile();
captureProfile.SetProfileID("2");
captureProfile.SetProperties(properties);
// Create the array of capture profiles to be used for each drop - in this case only one
CaptureProfile[] captureProfiles = new CaptureProfile[1];
captureProfiles[0] = captureProfile;
// Create a CapturePoint for each drop using RockImager's default drop position and the UV LightPath
// TODO: Get number of wells and drops from plate type
int wells = 96;
CapturePoint[] capturePoints = new CapturePoint[wells];
for (int i = 0; i < wells; i++)
{
// TODO: Loop over drops - currently assumes one drop per well
capturePoints[i] = new CapturePoint(i + 1, 1, captureProfiles, null, null, "1", RegionType.Drop);
}
// Create the CapturePointList and set the PlateCaptureProfile and CapturePoints
// NB I don't think RockImager actually uses the PlateCaptureProfile
capturePointList = new CapturePointList();
capturePointList.SetPlateCaptureProfile(captureProfile);
capturePointList.SetCapturePoints(capturePoints);
}
return(capturePointList);
}
/// <summary>
/// This method is intended to cause any resources that are no
/// longer necessary to be released
/// </summary>
void IDisposable.Dispose()
{
_regionName = null;
_profileName = null;
_captureInfo = null;
_robot = null;
_processingInfo = null;
_plateInfo = null;
_plateType = null;
}
/// <summary>
/// If this <c>IImagingTaskProvider</c> supports changing priority,
/// changes the priority of the IImagingTask with this <c>dateToImage</c>.
/// </summary>
void IImagingTaskProvider.UpdatedPriority(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, DateTime dateToImage, int priority)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
// Log the call to the method
if (_log.IsDebugEnabled)
{
string msg = "Called " + this + ".UpdatedPriority(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, priority=" + priority + ")";
_log.Debug(msg);
}
// Set the request
updatedPriority request = new updatedPriority();
request.robot = OPPF.Utilities.RobotUtils.createProxy(robot);
request.plateID = plateID;
// .NET < 2.0
//request.dateToImage = dateToImage;
// .NET >= 2.0
request.dateToImage = dateToImage.ToUniversalTime();
request.priority = priority;
// Make the call
WSPlate wsPlate = new WSPlate();
try
{
wsPlate.updatedPriority(request);
}
catch (Exception e)
{
// Log it
string msg = "WSPlate.updatedPriority threw " + e.GetType() + ": " + e.Message + " - ignoring";
if (e is System.Web.Services.Protocols.SoapException)
{
System.Web.Services.Protocols.SoapException ee = (System.Web.Services.Protocols.SoapException)e;
msg = msg + "\n\n" + ee.Detail.InnerXml;
}
_log.Warn(msg, e);
// Don't rethrow - just return - don't really care if this didn't work
return;
}
// Webservice always returns true if there is no exception
return;
}
/// <summary>
/// Plate is starting to image. Returns an imaging identifier that will be
/// embedded in the image names, and returned in ImagedPlate or null if
/// the ImagingID is unavailable.
/// </summary>
public string ImagingPlate(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, bool scheduled, DateTime dateToImage, DateTime dateImaged)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
string imagingID = DummyImagingTaskProvider.GetImagingID(plateID, dateToImage);
/*
* Unnecessary code
*
* bool exists = true;
* if (!scheduled)
* {
* ImagingTask task = new ImagingTask();
* task.SetDateImaged(dateImaged);
* task.SetDateToImage(dateToImage);
* task.SetInQueue(true);
* task.SetPriority(5);
* task.SetState(ImagingState.Imaging);
*
* lock (_tasks)
* {
* if (! _tasks.ContainsKey(imagingID))
* {
* exists = false;
* _tasks.Add(imagingID, task);
* }
* }
* }
*
*
* if (scheduled || exists)
*/
if (scheduled)
{
ImagingTask task;
bool ok = _tasks.TryGetValue(imagingID, out task);
if (ok)
{
task.SetDateImaged(dateImaged);
task.SetState(ImagingState.Imaging);
}
}
return(DummyImagingTaskProvider.GetImagingID(plateID, dateToImage));
}
/// <summary>
/// Marks an imaging as skipped.
/// </summary>
void IImagingTaskProvider.SkippedImaging(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, DateTime dateToImage)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
// Log the call to the method
if (_log.IsDebugEnabled)
{
string msg = "Called " + this + ".SkippedImaging(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC)";
_log.Debug(msg);
}
// Set the request
skippedImaging request = new skippedImaging();
request.robot = OPPF.Utilities.Robot2Utils.createProxy(robot);
request.plateID = plateID;
request.dateToImage = dateToImage.ToUniversalTime();
// Make the call
WSPlate wsPlate = WSPlateFactory.getWSPlate2();
skippedImagingResponse response = null;
try
{
response = wsPlate.skippedImaging(request);
}
catch (Exception e)
{
// Log it
string msg = "WSPlate.skippedImaging threw " + e.GetType() + ": " + e.Message + " - ignoring";
msg = msg + "\nin " + this + ".SkippedImaging(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC)";
if (e is System.Web.Services.Protocols.SoapException)
{
System.Web.Services.Protocols.SoapException ee = (System.Web.Services.Protocols.SoapException)e;
msg = msg + "\n\n" + ee.Detail.InnerXml;
}
_log.Warn(msg, e);
// Don't rethrow - just return - don't really care if this didn't work
return;
}
// Webservice always returns true if it doesn't throw an exception
return;
}
public ImageProcessor(Formulatrix.Integrations.ImagerLink.IRobot robot, IProcessingInfo processingInfo)
{
// Get Logger.
_log = LogManager.GetLogger(this.GetType());
SetRegionName("");
SetProfileName("");
_captureInfo = null;
_imageInfo = null;
_robot = robot;
_processingInfo = processingInfo;
}
/// <summary>
/// Return <c>true</c> if this provider supplies <c>IImagingTask.Priority</c>.
/// Otherwise the imager should manage individual task priority.
/// </summary>
bool IImagingTaskProvider.SupportsPriority(Formulatrix.Integrations.ImagerLink.IRobot robot)
{
// OPPF PERFORMANCE BODGE - Actually this method should always return true!
return(true);
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
// Log the call to the method
if (_log.IsDebugEnabled)
{
string msg = "Called " + this + ".SupportsPriority(robot=" + RobotUtils.iRobotToString(robot) + ")";
_log.Debug(msg);
}
// Set the request
supportsPriority request = new supportsPriority();
request.robot = OPPF.Utilities.RobotUtils.createProxy(robot);
// Make the call
WSPlate wsPlate = new WSPlate();
supportsPriorityResponse response = null;
try
{
response = wsPlate.supportsPriority(request);
}
catch (Exception e)
{
// Log it
string msg = "WSPlate.supportsPriority threw " + e.GetType() + ": " + e.Message + " - ignoring";
if (e is System.Web.Services.Protocols.SoapException)
{
System.Web.Services.Protocols.SoapException ee = (System.Web.Services.Protocols.SoapException)e;
msg = msg + "\n\n" + ee.Detail.InnerXml;
}
_log.Warn(msg, e);
// Don't rethrow - just return false
return(false);
}
// Return the response's value
//_log.Debug("supportsPriority returned " + response.supportsPriorityReturn);
return(response.supportsPriorityReturn);
}
protected virtual void Dispose(bool disposing)
{
if (!this.disposed)
{
if (disposing)
{
// dispose managed resources
}
// free native resources
_regionName = null;
_profileName = null;
_captureInfo = null;
_robot = null;
_processingInfo = null;
_plateInfo = null;
_plateType = null;
disposed = true;
}
}
/// <summary>
/// If this <c>IImagingTaskProvider</c> supports changing priority,
/// changes the priority of the IImagingTask with this <c>dateToImage</c>.
/// </summary>
void IImagingTaskProvider.UpdatedPriority(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, DateTime dateToImage, int priority)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
string imagingID = DummyImagingTaskProvider.GetImagingID(plateID, dateToImage);
ImagingTask task;
bool ok = _tasks.TryGetValue(imagingID, out task);
if (ok)
{
task.SetPriority(priority);
}
return;
}
/// <summary>
/// Plate is starting to image. Returns an imaging identifier that will be
/// embedded in the image names, and returned in ImagedPlate or null if
/// the ImagingID is unavailable.
/// </summary>
public string ImagingPlate(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, bool scheduled, DateTime dateToImage, DateTime dateImaged)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
// Log the call to the method
if (_log.IsInfoEnabled)
{
string msg = "Called " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", scheduled=\"" + scheduled + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
_log.Info(msg);
}
// Set the request
imagingPlate request = new imagingPlate();
request.robot = global::OPPF.Utilities.Robot2Utils.createProxy(robot);
request.plateID = plateID;
request.scheduled = scheduled;
//request.dateToImage = dateToImage.ToUniversalTime();
// Is this a fix for the date collision problem?
if (scheduled)
{
request.dateToImage = dateToImage.ToUniversalTime();
}
else
{
request.dateToImage = dateImaged.ToUniversalTime();
}
request.dateImaged = dateImaged.ToUniversalTime();
// Make the call
WSPlate wsPlate = WSPlateFactory.getWSPlate2();
imagingPlateResponse response = null;
try
{
response = wsPlate.imagingPlate(request);
}
catch (Exception e)
{
string msg = "WSPlate.imagingPlate threw " + e.GetType() + ": " + e.Message + " - panic!";
msg = msg + "\nin " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
msg = msg + WSPlateFactory.SoapExceptionToString(e);
_log.Fatal(msg, e);
// Panic
throw;
}
// If we got no response
if (null == response)
{
string msg = "WSPlate.imagingPlate returned null - panic!";
msg = msg + "\nin " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
_log.Fatal(msg);
// Panic
throw new System.NullReferenceException(msg);
}
// If we got a null imagingID
if (null == response.imagingPlateReturn)
{
string msg = "WSPlate.imagingPlate returned a null imagingID - panic!";
msg = msg + "\nin " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
_log.Fatal(msg);
// Panic
throw new System.NullReferenceException(msg);
}
// Return the imagingID
return(response.imagingPlateReturn);
}
/// <summary>
/// Returns all scheduled <c>IImagingTask</c>s for the <c>plateID</c>.
/// </summary>
public IImagingTask[] GetImagingTasks(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
// Log the call to the method
if (_log.IsDebugEnabled)
{
string msg = "Called " + this + ".GetImagingTasks(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\")";
_log.Debug(msg);
}
// Declare the array that will be populated and returned - default to a zero-length array
IImagingTask[] iImagingTasks = new IImagingTask[0];
// Bail out on test plates
if ("ReliabilityTestPlate".Equals(plateID) || "ReservedSlot".Equals(plateID))
{
return(iImagingTasks);
}
// Ensure connected to database - may throw an exception but we don't need/want to catch it
if ((null == _dbConnection) || (System.Data.ConnectionState.Closed.Equals(_dbConnection.State)))
{
//connectToDB();
}
// Try and read the imaging tasks from the db
OdbcDataReader dataReader = null;
try
{
// TODO - unnecessary check? Can connectToDB fail without throwing an exception?
if (System.Data.ConnectionState.Open.Equals(_dbConnection.State))
{
// Update the parameters
_command.Parameters["@p1"].Value = plateID;
// If we care which imager
if (2 == _command.Parameters.Count)
{
_command.Parameters["@p2"].Value = robot.Name;
}
// Execute the select
dataReader = _command.ExecuteReader();
// Read the data reader's rows into the ProjectList
if (dataReader.HasRows)
{
// Get an ArrayList to hold the tasks
System.Collections.ArrayList tasks = new System.Collections.ArrayList();
// Loop over all the returned rows
while (dataReader.Read())
{
// Create and populate a new ImagingTask
global::OPPF.Integrations.ImagerLink.Scheduling.ImagingTask task = new global::OPPF.Integrations.ImagerLink.Scheduling.ImagingTask();
// .NET < 2.0
//task.DateToImage = dataReader.GetDateTime(0);
// .NET >= 2.0 Only!
task.SetDateToImage(DateTime.SpecifyKind(dataReader.GetDateTime(0), DateTimeKind.Utc));
if (dataReader.IsDBNull(1))
{
task.SetDateImaged(DateTime.MinValue);
}
else
{
// .NET < 2.0
//task.DateImaged = dataReader.GetDateTime(1);
// .NET >= 2.0 Only!
task.SetDateImaged(DateTime.SpecifyKind(dataReader.GetDateTime(1), DateTimeKind.Utc));
//task.DateImaged = dataReader.GetDateTime(1).ToLocalTime();
}
if (dataReader.IsDBNull(2))
{
_log.Warn("Got null priority for plateID: " + plateID + " task: " + task.DateToImage.ToLongTimeString());
task.SetPriority(5);
}
else
{
task.SetPriority(dataReader.GetInt32(2));
}
if (dataReader.IsDBNull(3))
{
_log.Warn("Got null state for plateID: " + plateID + " task: " + task.DateToImage.ToLongTimeString());
if (dataReader.IsDBNull(1))
{
task.SetState(Formulatrix.Integrations.ImagerLink.Scheduling.ImagingState.NotCompleted);
}
else
{
task.SetState(Formulatrix.Integrations.ImagerLink.Scheduling.ImagingState.Completed);
}
}
else
{
task.SetState((Formulatrix.Integrations.ImagerLink.Scheduling.ImagingState)dataReader.GetInt32(3));
}
task.SetInQueue(true);
// Store this task in the ArrayList
tasks.Add(task);
//_log.Debug("> Got task: DateToImage=" + task.DateToImage + ", Priority=" + task.Priority + ", State=" + task.State + ", InQueue= " + task.InQueue);
}
// Convert ArrayList to IImagingTask[]
iImagingTasks = (IImagingTask[])tasks.ToArray(typeof(IImagingTask));
}
// Close the dataReader
dataReader.Close();
}
}
catch (Exception e)
{
// Log it
string msg = "Exception " + e.Message + " during direct db part of getImagingTasks() for plate " + plateID + " - will fail down to webservice call";
_log.Error(msg, e);
try
{
// Clean up the dataReader
if ((null != dataReader) && (!dataReader.IsClosed))
{
dataReader.Close();
}
dataReader = null;
if (null != _dbConnection)
{
_dbConnection.Close();
}
}
catch (Exception e1)
{
// Log it
string msg1 = "Exception " + e1.Message + " while handling exception during direct db part of direct db part of getImagingTasks() for plate " + plateID + " - will fail down to webservice call";
_log.Error(msg1, e1);
}
// Don't rethrow - fail down to webservice call
}
// If we got no or not enough tasks
if ((null == iImagingTasks) || (iImagingTasks.GetLength(0) < MIN_IMAGING_TASKS))
{
// Hit the webservice, which may cause a schedule to be created
iImagingTasks = GetImagingTasksFromWebService(robot, plateID);
}
// Set an appropriate value for InQueue
setInQueue(iImagingTasks);
// Ensure we never return null
if (null == iImagingTasks)
{
// Fix it
iImagingTasks = new IImagingTask[0];
// Log it
_log.Warn("Fixed null iImagingTasks at end of WSPlate.getImagingTasks() for plate " + plateID);
}
// Return the array of IImagingTasks
return(iImagingTasks);
}
/// <summary>
/// Web service version of GetImagingTasks - useful because it will
/// cause a full schedule to be written if one doesn't already
/// exist.
///
/// Warning - this is a lot slower than going straight to platedb!
/// </summary>
/// <param name="robot">The robot</param>
/// <param name="plateID">The barcode of the plate</param>
/// <returns></returns>
public IImagingTask[] GetImagingTasksFromWebService(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
// Log the call
if (_log.IsInfoEnabled)
{
string msg = "Calling WSPlate.getImagingTasks() for plate " + plateID + ", robot " + RobotUtils.iRobotToString(robot);
_log.Info(msg);
}
// Declare the array that will be populated and returned
// - default to a zero-length array
IImagingTask[] iImagingTasks = new IImagingTask[0];
// Set the request
getImagingTasks request = new getImagingTasks();
request.robot = global::OPPF.Utilities.Robot2Utils.createProxy(robot);
request.plateID = plateID;
// Make the call
getImagingTasksResponse response = null;
try
{
WSPlate wsPlate = WSPlateFactory.getWSPlate2();
wsPlate.Timeout = 10000;
response = wsPlate.getImagingTasks(request);
}
catch (Exception e)
{
// Log it
string msg = "WSPlate.getImagingTasks threw " + e.GetType() + ": " + e.Message + " for plateid \"" + plateID + "\" in robot \"" + robot.Name + "\" - returning empty IImagingTask[]";
msg = msg + WSPlateFactory.SoapExceptionToString(e);
_log.Error(msg, e);
// Don't rethrow - just return empty array
return(iImagingTasks);
}
// If we got a response
if (null != response)
{
// Get the array of ImagingTasks from the response
global::OPPF.Proxies2.ImagingTask[] wrapper = response.wrapper;
// Convert to IImagingTasks
iImagingTasks = new IImagingTask[wrapper.GetLength(0)];
for (int i = 0; i < wrapper.GetLength(0); i++)
{
global::OPPF.Integrations.ImagerLink.Scheduling.ImagingTask task = new global::OPPF.Integrations.ImagerLink.Scheduling.ImagingTask();
if (wrapper[i].dateImaged.HasValue)
{
task.SetDateImaged(wrapper[i].dateImaged.Value);
}
task.SetDateToImage(wrapper[i].dateToImage);
task.SetInQueue(wrapper[i].inQueue);
task.SetPriority(wrapper[i].priority);
task.SetState((Formulatrix.Integrations.ImagerLink.Scheduling.ImagingState)wrapper[i].state);
iImagingTasks[i] = task;
}
}
// Return the IImagingTask array
return(iImagingTasks);
}
/*
* Added in Formulatrix.Integrations.ImagerLink.dll v2.0.0.73 (RockImager v2.0.3.18),
* which is supposed to be more recent than v2.0.1.136 (RockImager v2.0.1.136).
*/
/// <summary>
/// Gets an <c>ICapturePointList</c> to image for this plateID on the specified <c>imagingID</c>.
/// </summary>
/// <param name="robot"></param>
/// <param name="plateID"></param>
/// <param name="imagingID">The imaging ID started for this run.</param>
/// <param name="includeOverview"></param>
/// <param name="userSelectionCaptureProfileID"></param>
/// <returns></returns>
/// <remarks>
/// Added in Formulatrix.Integrations.ImagerLink.dll v2.0.0.73 (RockImager v2.0.3.18),
/// which is supposed to be more recent than v2.0.1.136 (RockImager v2.0.1.136).
/// </remarks>
public ICapturePointList GetCapturePoints(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, string imagingID, bool includeOverview, int userSelectionCaptureProfileID)
{
// TODO: Add CaptureProvider.GetCapturePoints implementation
//return null;
if (_log.IsInfoEnabled)
{
_log.Info("Called ICaptureProvider.GetCapturePoints(" + Robot.ToString(robot) + ", \"" + plateID + "\", \"" + imagingID + "\", " + includeOverview + ", " + userSelectionCaptureProfileID + ")");
}
CapturePointList capturePointList = null;
// If 0 then it is a scheduled imaging, need to find the inspection type (light path)
if (userSelectionCaptureProfileID == 0)
{
userSelectionCaptureProfileID = GetLightPathForScheduledImaging(imagingID);
}
IPlateType plateType = _pip.GetPlateType(robot, _pip.GetPlateInfo(robot, plateID).PlateTypeID);
int[] sampleLocations = GetSampleLocations(plateID);
// OPPF Vis
if (1 == userSelectionCaptureProfileID)
{
_log.Info("Returning ICapturePointList with CapturePoints for specific drops to be imaged, with a null ICaptureProfile (Should assume visible LightPath)");
capturePointList = new CapturePointList();
CapturePoint[] capturePoints = GetCapturePointsDetails(sampleLocations, plateType, null);
capturePointList.SetCapturePoints(capturePoints);
}
// OPPF UV
else if (2 == userSelectionCaptureProfileID)
{
_log.Info("Returning ICapturePointList with PlateCaptureProfile and CapturePoints set to an ICaptureProfile with one IProperty of \"LightPath\" = \"1\"");
// Create the property array containing the UV LightPath property
IProperty[] properties = new global::OPPF.Integrations.ImagerLink.Property[1];
properties[0] = new global::OPPF.Integrations.ImagerLink.Property("LightPath", "1");
// Create a new CaptureProfile and apply the UV LightPath property
CaptureProfile captureProfile = new CaptureProfile();
captureProfile.SetProfileID("2");
captureProfile.SetProperties(properties);
// Create the array of capture profiles to be used for each drop - in this case only one
CaptureProfile[] captureProfiles = new CaptureProfile[1];
captureProfiles[0] = captureProfile;
// Get specific well and drop numbers to be imaged
CapturePoint[] capturePoints = GetCapturePointsDetails(sampleLocations, plateType, captureProfiles);
// Create the CapturePointList and set the PlateCaptureProfile and CapturePoints
// NB I don't think RockImager actually uses the PlateCaptureProfile
capturePointList = new CapturePointList();
capturePointList.SetPlateCaptureProfile(captureProfile);
capturePointList.SetCapturePoints(capturePoints);
}
// OPPF Teach 1
else if (3 == userSelectionCaptureProfileID)
{
_log.Info("Returning ICapturePointList with PlateCaptureProfile and CapturePoints set to an ICaptureProfile that only images the corners");
// Create the property array containing the UV LightPath property
IProperty[] properties = new global::OPPF.Integrations.ImagerLink.Property[1];
properties[0] = new global::OPPF.Integrations.ImagerLink.Property("LightPath", "0");
// Create a new CaptureProfile and apply the UV LightPath property
CaptureProfile captureProfile = new CaptureProfile();
captureProfile.SetProfileID("3");
captureProfile.SetProperties(properties);
// Create the array of capture profiles to be used for each drop - in this case only one
CaptureProfile[] captureProfiles = new CaptureProfile[1];
captureProfiles[0] = captureProfile;
// Create a CapturePoint for each drop using RockImager's default drop position and the vis LightPath
// TODO: Get number of wells and drops from plate type
CapturePoint[] capturePoints = new CapturePoint[4];
capturePoints[0] = new CapturePoint(1, 1, captureProfiles, null, null, "1", RegionType.Drop); // A1
capturePoints[1] = new CapturePoint(12, 1, captureProfiles, null, null, "1", RegionType.Drop); // A12
capturePoints[2] = new CapturePoint(85, 1, captureProfiles, null, null, "1", RegionType.Drop); // H1
capturePoints[3] = new CapturePoint(96, 1, captureProfiles, null, null, "1", RegionType.Drop); // H12
// Create the CapturePointList and set the PlateCaptureProfile and CapturePoints
// NB I don't think RockImager actually uses the PlateCaptureProfile
capturePointList = new CapturePointList();
capturePointList.SetPlateCaptureProfile(captureProfile);
capturePointList.SetCapturePoints(capturePoints);
}
// OPPF Teach 1-Full - Just to allow special handling in the IImageProcessor
else if (4 == userSelectionCaptureProfileID)
{
_log.Info("Returning ICapturePointList with PlateCaptureProfile and CapturePoints set to an ICaptureProfile that only images the corners");
// Create the property array containing the UV LightPath property
IProperty[] properties = new global::OPPF.Integrations.ImagerLink.Property[1];
properties[0] = new global::OPPF.Integrations.ImagerLink.Property("LightPath", "0");
// Create a new CaptureProfile and apply the UV LightPath property
CaptureProfile captureProfile = new CaptureProfile();
captureProfile.SetProfileID("4");
captureProfile.SetProperties(properties);
// Create the array of capture profiles to be used for each drop - in this case only one
CaptureProfile[] captureProfiles = new CaptureProfile[1];
captureProfiles[0] = captureProfile;
// Create a CapturePoint for each drop using RockImager's default drop position and the vis LightPath
// TODO: Get number of wells and drops from plate type
int wells = 96;
CapturePoint[] capturePoints = new CapturePoint[wells];
for (int i = 0; i < wells; i++)
{
// TODO: Loop over drops - currently assumes one drop per well
capturePoints[i] = new CapturePoint(i + 1, 1, captureProfiles, null, null, "1", RegionType.Drop);
}
// Create the CapturePointList and set the PlateCaptureProfile and CapturePoints
// NB I don't think RockImager actually uses the PlateCaptureProfile
capturePointList = new CapturePointList();
capturePointList.SetPlateCaptureProfile(captureProfile);
capturePointList.SetCapturePoints(capturePoints);
}
return(capturePointList);
}
/// <summary>
/// Gets the first drop to move the plate to under the microscope.
/// </summary>
/// <param name="plateID">The plateID uniquely identifying the plate.</param>
/// <param name="wellNumber">The first well number of the plate. The first well is <c>1</c>.</param>
/// <param name="dropNumber">The first drop number in the first well. The first drop is <c>1</c>.</param>
/// <param name="robot">The robot which the plate is under.</param>
void ICaptureProvider.GetFirstDrop(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, ref int wellNumber, ref int dropNumber)
{
// TODO: Add CaptureProvider.GetFirstDrop implementation
wellNumber = 1;
dropNumber = 1;
}
/// <summary>
/// Gets an <c>ICapturePointList</c> to image for this plateID on the specified <c>imagingID</c>.
/// </summary>
/// <param name="robot"></param>
/// <param name="plateID"></param>
/// <param name="imagingID">The imaging ID started for this run.</param>
/// <param name="includeOverview"></param>
/// <returns>The list of <c>ICapturePoint</c>s, with an optional <c>ICaptureProfile</c> for this imaging.</returns>
ICapturePointList ICaptureProvider.GetCapturePoints(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, string imagingID, bool includeOverview)
{
// TODO: Add CaptureProvider.GetCapturePoints implementation
_log.Debug("Called 4-arg ICaptureProvider.GetCapturePoints() - delegating to 5-arg version with userSelectionCaptureProfileID = 0");
return(((ICaptureProvider)this).GetCapturePoints(robot, plateID, imagingID, includeOverview, 0));
}
/// <summary>
/// Return <c>true</c> if this provider supplies <c>IImagingTask.Priority</c>.
/// Otherwise the imager should manage individual task priority.
/// </summary>
public bool SupportsPriority(Formulatrix.Integrations.ImagerLink.IRobot robot)
{
// OPPF PERFORMANCE BODGE - Actually this method should always return true!
return(true);
}
/// <summary>
/// Returns all scheduled <c>IImagingTask</c>s for the <c>plateID</c>.
/// </summary>
public IImagingTask[] GetImagingTasks(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
IImagingTask[] myTasks = null;
lock (_scheduled)
{
if (!_scheduled.Contains(plateID))
{
_scheduled.Add(plateID);
List <IImagingTask> myTaskList = new List <IImagingTask>();
DateTime now = DateTime.Now;
for (int i = 0; i < 25; i++)
{
DateTime dateToImage = now.AddHours(i);
string imagingID = DummyImagingTaskProvider.GetImagingID(plateID, dateToImage);
ImagingTask task = new ImagingTask();
task.SetDateToImage(dateToImage);
task.SetInQueue(true);
task.SetPriority(5);
task.SetState(ImagingState.NotCompleted);
myTaskList.Add(task);
try
{
_tasks.Add(imagingID, task);
}
catch (System.ArgumentException e)
{
// Swallow duplicate key errors
if (!e.Message.Contains("same key has already been added"))
{
throw;
}
}
}
myTasks = myTaskList.ToArray();
}
}
if (null == myTasks)
{
List <IImagingTask> myTaskList = new List <IImagingTask>();
Dictionary <string, ImagingTask> .Enumerator en = _tasks.GetEnumerator();
while (en.MoveNext())
{
if (en.Current.Key.StartsWith(plateID))
{
myTaskList.Add(en.Current.Value);
}
}
myTasks = myTaskList.ToArray();
setInQueue(myTasks);
}
return(myTasks);
}
/// <summary>
/// Plate is starting to image. Returns an imaging identifier that will be
/// embedded in the image names, and returned in ImagedPlate or null if
/// the ImagingID is unavailable.
/// </summary>
string IImagingTaskProvider.ImagingPlate(Formulatrix.Integrations.ImagerLink.IRobot robot, string plateID, bool scheduled, DateTime dateToImage, DateTime dateImaged)
{
// Check arguments - do it up front to avoid possible inconsistencies later
if (null == robot)
{
throw new System.NullReferenceException("robot must not be null");
}
if (null == plateID)
{
throw new System.NullReferenceException("plateID must not be null");
}
// Log the call to the method
if (_log.IsDebugEnabled)
{
string msg = "Called " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
_log.Debug(msg);
}
// Set the request
imagingPlate request = new imagingPlate();
request.robot = OPPF.Utilities.RobotUtils.createProxy(robot);
request.plateID = plateID;
request.scheduled = scheduled;
request.dateToImage = dateToImage.ToUniversalTime();
request.dateImaged = dateImaged.ToUniversalTime();
// Make the call
WSPlate wsPlate = new WSPlate();
imagingPlateResponse response = null;
try
{
response = wsPlate.imagingPlate(request);
}
catch (Exception e)
{
string msg = "WSPlate.imagingPlate threw " + e.GetType() + ": " + e.Message + " - panic!";
msg = msg + "\nin " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
if (e is System.Web.Services.Protocols.SoapException)
{
System.Web.Services.Protocols.SoapException ee = (System.Web.Services.Protocols.SoapException)e;
msg = msg + "\n\n" + ee.Detail.InnerXml;
}
_log.Fatal(msg, e);
// Panic
throw e;
}
// If we got no response
if (null == response)
{
string msg = "WSPlate.imagingPlate returned null - panic!";
msg = msg + "\nin " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
_log.Fatal(msg);
// Panic
throw new System.NullReferenceException(msg);
}
// If we got a null imagingID
if (null == response.imagingPlateReturn)
{
string msg = "WSPlate.imagingPlate returned a null imagingID - panic!";
msg = msg + "\nin " + this + ".ImagingPlate(robot=" + RobotUtils.iRobotToString(robot) + ", plateID=\"" + plateID + "\", dateToImage=" + dateToImage.ToUniversalTime().ToString() + " UTC, dateImaged=" + dateImaged.ToUniversalTime().ToString() + " UTC)";
_log.Fatal(msg);
// Panic
throw new System.NullReferenceException(msg);
}
// Return the imagingID
return(response.imagingPlateReturn);
}