/*
*------------------------------------------------------------------------------
* Copyright (C) 2006-2015 University of Dundee. All rights reserved.
*
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
*------------------------------------------------------------------------------
*/
package omero.gateway.model;
import ome.formats.model.UnitsFactory;
import ome.model.units.BigResult;
import omero.RDouble;
import omero.model.AcquisitionMode;
import omero.model.Binning;
import omero.model.ContrastMethod;
import omero.model.DetectorSettings;
import omero.model.DetectorSettingsI;
import omero.model.ElectricPotential;
import omero.model.ElectricPotentialI;
import omero.model.FilterSet;
import omero.model.Frequency;
import omero.model.FrequencyI;
import omero.model.Illumination;
import omero.model.Length;
import omero.model.LengthI;
import omero.model.LightPath;
import omero.model.LightSettings;
import omero.model.LightSettingsI;
import omero.model.LightSource;
import omero.model.LogicalChannel;
import omero.model.enums.UnitsElectricPotential;
import omero.model.enums.UnitsFrequency;
import omero.model.enums.UnitsLength;
/**
* Object hosting the acquisition related to a logical channel.
*
* @author Jean-Marie Burel
* <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @author Donald MacDonald
* <a href="mailto:donald@lifesci.dundee.ac.uk">donald@lifesci.dundee.ac.uk</a>
* @version 3.0
* @since 3.0-Beta4
*/
public class ChannelAcquisitionData
extends DataObject
{
/** The settings of the detector. */
private DetectorSettings detectorSettings;
/** The settings of the light source. */
private LightSettings lightSettings;
/** The filterSet used. */
private FilterSetData filterSet;
/** The light path described. */
private LightPathData lightPath;
/** The light source. */
private LightSourceData lightSource;
/** Flag indicating if the detector settings is dirty. */
private boolean detectorSettingsDirty;
/** Flag indicating if the detector settings is dirty. */
private boolean lightSourceSettingsDirty;
/** The detector used. */
private DetectorData detector;
/** The otf used. */
private OTFData otf;
/** The binning factor. */
private Binning binning;
/**
* Creates a new instance.
*
* @param channel The image the acquisition data is related to.
* Mustn't be <code>null</code>.
*/
public ChannelAcquisitionData(LogicalChannel channel)
{
if (channel == null)
throw new IllegalArgumentException("Object cannot null.");
setValue(channel);
detectorSettings = channel.getDetectorSettings();
lightSettings = channel.getLightSourceSettings();
FilterSet set = channel.getFilterSet();
if (set != null) filterSet = new FilterSetData(set);
LightPath path = channel.getLightPath();
if (path != null) lightPath = new LightPathData(path);
if (channel.getOtf() != null)
otf = new OTFData(channel.getOtf());
}
/**
* Returns the detector used for that channel.
*
* @return See above.
*/
public DetectorData getDetector()
{
if (detectorSettings == null) return null;
if (detector == null)
detector = new DetectorData(detectorSettings.getDetector());
return detector;
}
/**
* Returns the OTF used for that channel.
*
* @return See above.
*/
public OTFData getOTF() { return otf; }
/**
* Returns the offset set on the detector.
*
* @return See above.
*/
public Double getDetectorSettingsOffset()
{
if (detectorSettings == null) return null;
RDouble value = detectorSettings.getOffsetValue();
if (value == null) return null;
return value.getValue();
}
/**
* Returns the gain set on the detector.
*
* @return See above.
*/
public Double getDetectorSettingsGain()
{
if (detectorSettings == null) return null;
RDouble value = detectorSettings.getGain();
if (value == null) return null;
return value.getValue();
}
/**
* Returns the voltage set on the detector.
*
* @param unit
* The unit (may be null, in which case no conversion will be
* performed)
* @return See above.
* @throws BigResult If an arithmetic under-/overflow occurred
*/
public ElectricPotential getDetectorSettingsVoltage(UnitsElectricPotential unit) throws BigResult
{
if (detectorSettings == null)
return null;
ElectricPotential e = detectorSettings.getVoltage();
if (e == null)
return null;
return unit == null ? e : new ElectricPotentialI(e, unit);
}
/**
* Returns the voltage set on the detector.
*
* @return See above.
* @deprecated Replaced by {@link #getDetectorSettingsVoltage(UnitsElectricPotential)}
*/
@Deprecated
public Double getDetectorSettingsVoltage()
{
if (detectorSettings == null) return null;
ElectricPotential value = detectorSettings.getVoltage();
if (value == null) return null;
return value.getValue();
}
/**
* Returns the Read out rate set on the detector.
*
* @param unit
* The unit (may be null, in which case no conversion will be
* performed)
* @return See above.
* @throws BigResult If an arithmetic under-/overflow occurred
*/
public Frequency getDetectorSettingsReadOutRate(UnitsFrequency unit) throws BigResult
{
if (detectorSettings == null) return null;
Frequency f = detectorSettings.getReadOutRate();
if (f == null)
return null;
return unit == null ? f : new FrequencyI(f, unit);
}
/**
* Returns the Read out rate set on the detector.
*
* @return See above.
* @deprecated Replaced by {@link #getDetectorSettingsReadOutRate(UnitsFrequency)}
*/
@Deprecated
public Double getDetectorSettingsReadOutRate()
{
if (detectorSettings == null) return null;
Frequency value = detectorSettings.getReadOutRate();
if (value == null) return null;
try {
return new FrequencyI(value, UnitsFactory.DetectorSettings_ReadOutRate)
.getValue();
} catch (BigResult e) {
return e.result.doubleValue();
}
}
/**
* Returns the Binning factor.
*
* @return See above.
*/
public String getDetectorSettingsBinning()
{
if (detectorSettings == null) return "";
Binning value = detectorSettings.getBinning();
if (value == null) return "";
return value.getValue().getValue();
}
/**
* Returns the attenuation of the light source, percent value
* between 0 and 1.
*
* @return See above.
*/
public Double getLightSettingsAttenuation()
{
if (lightSettings == null) return null;
RDouble value = lightSettings.getAttenuation();
if (value == null) return null;
return value.getValue();
}
/**
* Returns the wavelength of the light source.
*
* @param unit
* The unit (may be null, in which case no conversion will be
* performed)
* @return See above.
* @throws BigResult If an arithmetic under-/overflow occurred
*/
public Length getLightSettingsWavelength(UnitsLength unit) throws BigResult
{
if (lightSettings == null) return null;
Length l = lightSettings.getWavelength();
if (l == null)
return null;
return unit == null ? l : new LengthI(l, unit);
}
/**
* Returns the wavelength of the light source.
*
* @return See above.
* @deprecated Replaced by {@link #getLightSettingsWavelength(UnitsLength)}
*/
@Deprecated
public Double getLightSettingsWavelength()
{
if (lightSettings == null) return null;
Length value = lightSettings.getWavelength();
if (value == null) return null;
return value.getValue();
}
/**
* Returns <code>true</code> if there is a filter set linked to the channel
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean hasFilter() { return filterSet != null; }
/**
* Returns <code>true</code> if there is a light path described
* for that channel, <code>false</code> otherwise.
*
* @return See above.
*/
public boolean hasLightPath() { return lightPath != null; }
/**
* Returns <code>true</code> if there is a detector for that channel,
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean hasDectector() { return getDetector() != null; }
/**
* Sets the attenuation of the light settings.
*
* @param value The value to set.
*/
public void setLightSettingsAttenuation(double value)
{
lightSourceSettingsDirty = true;
if (lightSettings == null) lightSettings = new LightSettingsI();
lightSettings.setAttenuation(omero.rtypes.rdouble(value));
}
/**
* Sets the wavelength of the light source.
*
* @param value The value to set.
*/
public void setLightSettingsWavelength(Length value)
{
lightSourceSettingsDirty = true;
if (lightSettings == null) lightSettings = new LightSettingsI();
lightSettings.setWavelength(value);
}
/**
* Sets the wavelength of the light source.
*
* @param value The value to set.
* @deprecated Replaced by {@link #setLightSettingsWavelength(Length)}
*/
@Deprecated
public void setLightSettingsWavelength(double value)
{
lightSourceSettingsDirty = true;
if (lightSettings == null) lightSettings = new LightSettingsI();
lightSettings.setWavelength(new LengthI(value,
UnitsFactory.LightSourceSettings_Wavelength));
}
/**
* Sets the detector's setting offset.
*
* @param value The value to set.
*/
public void setDetectorSettingOffset(double value)
{
detectorSettingsDirty = true;
if (detectorSettings == null)
detectorSettings = new DetectorSettingsI();
detectorSettings.setOffsetValue(omero.rtypes.rdouble(value));
}
/**
* Sets the detector setting's gain.
*
* @param value The value to set.
*/
public void setDetectorSettingsGain(double value)
{
detectorSettingsDirty = true;
if (detectorSettings == null)
detectorSettings = new DetectorSettingsI();
detectorSettings.setGain(omero.rtypes.rdouble(value));
}
/**
* Sets the detector setting's read out rate.
*
* @param value The value to set.
*/
public void setDetectorSettingsReadOutRate(Frequency value)
{
detectorSettingsDirty = true;
if (detectorSettings == null)
detectorSettings = new DetectorSettingsI();
detectorSettings.setReadOutRate(value);
}
/**
* Sets the detector setting's read out rate.
*
* @param value The value to set.
* @deprecated Replaced by {@link #setDetectorSettingsReadOutRate(Frequency)}
*/
@Deprecated
public void setDetectorSettingsReadOutRate(double value)
{
detectorSettingsDirty = true;
if (detectorSettings == null)
detectorSettings = new DetectorSettingsI();
detectorSettings.setReadOutRate(new FrequencyI(value,
UnitsFactory.DetectorSettings_ReadOutRate));
}
/**
* Sets the detector setting's voltage.
*
* @param value The value to set.
*/
public void setDetectorSettingsVoltage(ElectricPotential value)
{
detectorSettingsDirty = true;
if (detectorSettings == null)
detectorSettings = new DetectorSettingsI();
detectorSettings.setVoltage(value);
}
/**
* Sets the detector setting's voltage.
*
* @param value The value to set.
* @deprecated Replaced by {@link #setDetectorSettingsVoltage(ElectricPotential)}
*/
@Deprecated
public void setDetectorSettingsVoltage(double value)
{
detectorSettingsDirty = true;
if (detectorSettings == null)
detectorSettings = new DetectorSettingsI();
detectorSettings.setVoltage(new ElectricPotentialI(value,
UnitsFactory.Detector_Voltage));
}
/**
* Sets the detector's binning.
*
* @param binning The value to set.
*/
public void setDetectorSettingBinning(Binning binning)
{
this.binning = binning;
}
/**
* Returns the binning enumeration value.
*
* @return See above.
*/
public Binning getDetectorBinningAsEnum() { return binning; }
/**
* Returns <code>true</code> if the detector settings has been updated,
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean isDetectorSettingsDirty() { return detectorSettingsDirty; }
/**
* Returns <code>true</code> if the light source settings has been updated,
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean isLightSourceSettingsDirty()
{
return lightSourceSettingsDirty;
}
/**
* Returns the source of light.
*
* @return See above.
*/
public LightSourceData getLightSource()
{
if (lightSettings == null) return null;
if (lightSource != null) return lightSource;
LightSource src = lightSettings.getLightSource();
if (src != null) lightSource = new LightSourceData(src);
return lightSource;
}
/**
* Sets the light source associated to the settings.
*
* @param lightSource The value to set.
*/
public void setLightSource(LightSourceData lightSource)
{
this.lightSource = lightSource;
}
/**
* Returns the light path or <code>null</code>.
*
* @return See above.
*/
public LightPathData getLightPath() { return lightPath; }
/**
* Returns the filter set or <code>null</code>.
*
* @return See above.
*/
public FilterSetData getFilterSet() { return filterSet; }
/**
* Returns the illumination.
*
* @return See above.
*/
public String getIllumination()
{
LogicalChannel lc = (LogicalChannel) asIObject();
if (lc == null) return null;
Illumination value = lc.getIllumination();
if (value != null) return value.getValue().getValue();
return null;
}
/**
* Returns the contrast method.
*
* @return See above.
*/
public String getContrastMethod()
{
LogicalChannel lc = (LogicalChannel) asIObject();
if (lc == null) return null;
ContrastMethod value = lc.getContrastMethod();
if (value != null) return value.getValue().getValue();
return null;
}
/**
* Returns the mode.
*
* @return See above.
*/
public String getMode()
{
LogicalChannel lc = (LogicalChannel) asIObject();
if (lc == null) return null;
AcquisitionMode value = lc.getMode();
if (value != null) return value.getValue().getValue();
return null;
}
}