Java tutorial
/* * pojos.ChannelData * *------------------------------------------------------------------------------ * 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 pojos; 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 * <small> * (<b>Internal version:</b> $Revision: $Date: $) * </small> * @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; } }