/*
*------------------------------------------------------------------------------
* 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 java.math.RoundingMode;
import ome.formats.model.UnitsFactory;
import ome.model.units.BigResult;
import omero.RDouble;
import omero.RInt;
import omero.RString;
import omero.model.AcquisitionMode;
import omero.model.Channel;
import omero.model.ChannelI;
import omero.model.ContrastMethod;
import omero.model.Illumination;
import omero.model.Length;
import omero.model.LengthI;
import omero.model.LogicalChannel;
import omero.model.StatsInfo;
import omero.model.enums.UnitsLength;
import org.apache.commons.lang.StringUtils;
import com.google.common.math.DoubleMath;
/**
* The data that makes up an <i>OME</i> Channel along with links to its 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 ChannelData
extends DataObject
{
/** Identifies the {@link ome.model.core.Channel#ANNOTATIONLINKS} field. */
public final static String ANNOTATIONS = ChannelI.ANNOTATIONLINKS;
/** The index of the channel. */
private int index;
/** The acquisition mode. */
private AcquisitionMode mode;
/** The illumination. */
private Illumination illumination;
/** The contrast method. */
private ContrastMethod contrastMethod;
/**
* Creates a new instance.
*
* @param index The index of the channel.
*/
public ChannelData(int index)
{
setDirty(false);
setValue(new ChannelI());
this.index = index;
}
/**
* Creates a new instance.
*
* @param index The index of the channel.
* @param channel Back pointer to the {@link Channel} model object.
* Mustn't be <code>null</code>.
* @throws IllegalArgumentException If the object is <code>null</code>.
*/
public ChannelData(int index, Channel channel)
{
if (channel == null)
throw new IllegalArgumentException("Object cannot null.");
this.index = index;
setValue(channel);
setDirty(false);
}
/**
* Returns the channel's index.
*
* @return See above.
*/
public int getIndex() { return index; }
/**
* Returns the label of the channel.
* Following the specification: Name>Fluor>Emission wavelength>index.
*
* @return See above.
*/
public String getChannelLabeling()
{
String value = getName();
if (StringUtils.isNotBlank(value)) return value;
value = getFluor();
if (StringUtils.isNotBlank(value)) return value;
Length v = null;
try {
v = getEmissionWavelength(null);
} catch (BigResult e) { }
if (v != null) {
return ""+ DoubleMath.roundToInt(v.getValue(), RoundingMode.DOWN);
}
return ""+index;
}
// Immutables
/**
* Sets the name of the logical channel.
*
* @param name The name of the channel.
*/
public void setName(String name)
{
if (name == null) return;
setDirty(true);
asChannel().getLogicalChannel().setName(omero.rtypes.rstring(name));
}
/**
* Returns the name of the channel.
*
* @return See above.
*/
public String getName()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return null;
omero.RString n = lc.getName();
if (n != null) return n.getValue();
return null;
}
/**
* Returns the emission wavelength of the channel.
*
* 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 getEmissionWavelength(UnitsLength unit) throws BigResult
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null)
return null;
Length l = lc.getEmissionWave();
if (l == null)
return null;
return unit == null ? l : new LengthI(l, unit);
}
/**
* Returns the emission wavelength of the channel.
*
* @return See above
* @deprecated Replaced by {@link #getEmissionWavelength(UnitsLength)}
*/
@Deprecated
public double getEmissionWavelength()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return index;
Length value = lc.getEmissionWave();
if (value != null) {
try {
return new LengthI(value,
UnitsFactory.Channel_EmissionWavelength).getValue();
} catch (BigResult e) {
return e.result.doubleValue();
}
}
return -1;
}
/**
* Returns the excitation wavelength of the channel.
*
* @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 getExcitationWavelength(UnitsLength unit) throws BigResult
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null)
return getEmissionWavelength(unit);
Length l = lc.getExcitationWave();
if (l == null)
return null;
return unit == null ? l : new LengthI(l, unit);
}
/**
* Returns the excitation wavelength of the channel.
*
* @return See above
* @deprecated Replaced by {@link #getExcitationWavelength(UnitsLength)}
*/
@Deprecated
public double getExcitationWavelength()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return getEmissionWavelength();
Length value = lc.getExcitationWave();
if (value != null) {
try {
return new LengthI(value,
UnitsFactory.Channel_ExcitationWavelength).getValue();
} catch (BigResult e) {
return e.result.doubleValue();
}
}
return -1;
}
/**
* Returns the pin hole size of the channel.
*
* @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 getPinholeSize(UnitsLength unit) throws BigResult
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null)
return null;
Length l = lc.getPinHoleSize();
if (l == null)
return null;
return unit == null ? l : new LengthI(l, unit);
}
/**
* Returns the pin hole size of the channel.
*
* @return See above
* @deprecated Replaced by {@link #getPinholeSize(UnitsLength)}
*/
@Deprecated
public double getPinholeSize()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return -1;
Length value = lc.getPinHoleSize();
if (value != null) {
try {
return new LengthI(value,
UnitsFactory.Channel_PinholeSize).getValue();
} catch (BigResult e) {
return e.result.doubleValue();
}
}
return -1;
}
/**
* Returns the ND filter wavelength of the channel.
*
* @return See above
*/
public double getNDFilter()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return -1;
RDouble value = lc.getNdFilter();
if (value != null) return value.getValue();
return -1;
}
/**
* Returns the Fluorophore used.
*
* @return See above.
*/
public String getFluor()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return null;
RString value = lc.getFluor();
if (value != null) return value.getValue();
return null;
}
/**
* Returns the Pockel cell settings.
*
* @return See above.
*/
public int getPockelCell()
{
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return -1;
RInt value = lc.getPockelCellSetting();
if (value != null) return value.getValue();
return -1;
}
/**
* Returns the illumination.
*
* @return See above.
*/
public String getIllumination()
{
if (illumination != null) return illumination.getValue().getValue();
LogicalChannel lc = asChannel().getLogicalChannel();
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()
{
if (contrastMethod != null) return contrastMethod.getValue().getValue();
LogicalChannel lc = asChannel().getLogicalChannel();
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()
{
if (mode != null) return mode.getValue().getValue();
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return null;
AcquisitionMode value = lc.getMode();
if (value != null) return value.getValue().getValue();
return null;
}
/**
* Returns the global minimum of the channel i.e. the minimum of all minima.
*
* @return See above.
*/
public double getGlobalMin()
{
StatsInfo stats = asChannel().getStatsInfo();
if (stats == null) return 0.0;
RDouble object = stats.getGlobalMin();
if (object != null) return object.getValue();
return 0.0;
}
/**
* Returns the global maximum of the channel i.e. the maximum of all maxima.
*
* @return See above.
*/
public double getGlobalMax()
{
StatsInfo stats = asChannel().getStatsInfo();
if (stats == null) return 0.0;
RDouble object = stats.getGlobalMax();
if (object != null) return object.getValue();
return 0.0;
}
/**
* Returns <code>true</code> if the channel has some channel information
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean hasStats() { return asChannel().getStatsInfo() != null; }
/**
* Sets the pinhole size.
*
* @param value The value to set.
*/
public void setPinholeSize(Length value)
{
if (value == null)
return;
setDirty(true);
asChannel().getLogicalChannel().setPinHoleSize(value);
}
/**
* Sets the pinhole size.
*
* @param value The value to set.
* @deprecated Replaced by {@link #setPinholeSize(Length)}
*/
@Deprecated
public void setPinholeSize(double value)
{
if (value < 0) return;
setDirty(true);
asChannel().getLogicalChannel().setPinHoleSize(
new LengthI(value, UnitsFactory.Channel_PinholeSize));
}
/**
* Sets the ND filter.
*
* @param value The value to set.
*/
public void setNDFilter(double value)
{
if (value < 0) return;
setDirty(true);
asChannel().getLogicalChannel().setNdFilter(omero.rtypes.rdouble(value));
}
/**
* Sets the fluor.
*
* @param value The value to set.
*/
public void setFluor(String value)
{
if (value == null) return;
setDirty(true);
asChannel().getLogicalChannel().setFluor(omero.rtypes.rstring(value));
}
/**
* Sets the emission wavelength.
*
* @param value The value to set.
*/
public void setEmissionWavelength(Length value)
{
if (value == null)
return;
setDirty(true);
asChannel().getLogicalChannel().setEmissionWave(value);
}
/**
* Sets the emission wavelength.
*
* @param value The value to set.
* @deprecated Replaced by {@link #setEmissionWavelength(Length)}
*/
@Deprecated
public void setEmissionWavelength(double value)
{
if (value < 0) return;
setDirty(true);
asChannel().getLogicalChannel().setEmissionWave(
new LengthI(value, UnitsFactory.Channel_EmissionWavelength));
}
/**
* Sets the excitation wavelength.
*
* @param value The value to set.
*/
public void setExcitationWavelength(Length value)
{
if (value == null)
return;
setDirty(true);
asChannel().getLogicalChannel().setExcitationWave(value);
}
/**
* Sets the excitation wavelength.
*
* @param value The value to set.
* @deprecated Replaced by {@link #setExcitationWavelength(Length)}
*/
@Deprecated
public void setExcitationWavelength(double value)
{
if (value < 0) return;
setDirty(true);
asChannel().getLogicalChannel().setExcitationWave(
new LengthI(value, UnitsFactory.Channel_ExcitationWavelength));
}
/**
* Sets the pockel cell.
*
* @param value The value to set.
*/
public void setPockelCell(int value)
{
if (value < 0) return;
LogicalChannel lc = asChannel().getLogicalChannel();
if (lc == null) return;
setDirty(true);
lc.setPockelCellSetting(omero.rtypes.rint(value));
}
/**
* Sets the illumination value.
*
* @param illumination The value to set.
*/
public void setIllumination(Illumination illumination)
{
setDirty(true);
this.illumination = illumination;
}
/**
* Sets the acquisition mode value.
*
* @param mode The value to set.
*/
public void setMode(AcquisitionMode mode)
{
setDirty(true);
this.mode = mode;
}
/**
* Sets the contrast method value.
*
* @param contrastMethod The value to set.
*/
public void setContrastMethod(ContrastMethod contrastMethod)
{
setDirty(true);
this.contrastMethod = contrastMethod;
}
/**
* Returns the acquisition enumeration value.
*
* @return See above.
*/
public AcquisitionMode getModeAsEnum() { return mode; }
/**
* Returns the illumination enumeration value.
*
* @return See above.
*/
public Illumination getIlluminationAsEnum() { return illumination; }
/**
* Returns the contrast method enumeration value.
*
* @return See above.
*/
public ContrastMethod getContrastMethodAsEnum() { return contrastMethod; }
}