/*-
* #%L
* Fiji distribution of ImageJ for the life sciences.
* %%
* Copyright (C) 2007 - 2017 Fiji developers.
* %%
* 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, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
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*/
package spim.fiji.datasetmanager;
import fiji.util.gui.GenericDialogPlus;
import ij.gui.GenericDialog;
import java.awt.Color;
import java.awt.Font;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import mpicbg.spim.data.SpimData;
import mpicbg.spim.data.registration.ViewRegistrations;
import mpicbg.spim.data.sequence.Angle;
import mpicbg.spim.data.sequence.Channel;
import mpicbg.spim.data.sequence.FinalVoxelDimensions;
import mpicbg.spim.data.sequence.Illumination;
import mpicbg.spim.data.sequence.ImgLoader;
import mpicbg.spim.data.sequence.MissingViews;
import mpicbg.spim.data.sequence.SequenceDescription;
import mpicbg.spim.data.sequence.TimePoint;
import mpicbg.spim.data.sequence.TimePoints;
import mpicbg.spim.data.sequence.ViewDescription;
import mpicbg.spim.data.sequence.ViewSetup;
import mpicbg.spim.data.sequence.VoxelDimensions;
import mpicbg.spim.io.IOFunctions;
import net.imglib2.Cursor;
import net.imglib2.Dimensions;
import net.imglib2.FinalDimensions;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.img.cell.CellImgFactory;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Util;
import spim.fiji.plugin.Apply_Transformation;
import spim.fiji.plugin.util.GUIHelper;
import spim.fiji.spimdata.SpimData2;
import spim.fiji.spimdata.boundingbox.BoundingBoxes;
import spim.fiji.spimdata.imgloaders.LegacyLightSheetZ1ImgLoader;
import spim.fiji.spimdata.imgloaders.LightSheetZ1ImgLoader;
import spim.fiji.spimdata.interestpoints.ViewInterestPoints;
public class LightSheetZ1 implements MultiViewDatasetDefinition
{
public static String[] rotAxes = new String[] { "X-Axis", "Y-Axis", "Z-Axis" };
public static String defaultFirstFile = "";
public static boolean defaultModifyCal = false;
public static boolean defaultRotAxis = false;
public static boolean defaultApplyRotAxis = true;
public static boolean defaultFixBioformats = false;
private boolean fixBioformats = false;
@Override
public String getTitle() { return "Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)"; }
@Override
public String getExtendedDescription()
{
return "This datset definition supports files saved by the Zeiss Lightsheet Z.1\n" +
"microscope. By default, one file per time-point is saved by Zen, which includes\n" +
"all angles, channels and illumination directions. We support this format and\n" +
"most other combinations that can be saved.\n" +
"\n" +
"Note: if you want to process multiple CZI datasets that are actually one experi-\n" +
"ment (e.g. two channels individually acquired), please re-save them in Zen as\n" +
"CZI files containing only one 3d stack per file and use the dataset definition\n" +
"'3d Image Stacks (LOCI Bioformats)'";
}
@Override
public SpimData2 createDataset()
{
final File cziFile = queryCZIFile();
if ( cziFile == null )
return null;
final LightSheetZ1MetaData meta = new LightSheetZ1MetaData();
if ( !meta.loadMetaData( cziFile ) )
{
IOFunctions.println( "Failed to analyze file." );
return null;
}
if ( !showDialogs( meta ) )
return null;
final String directory = cziFile.getParent();
final ImgFactory< ? extends NativeType< ? > > imgFactory = selectImgFactory( meta );
// assemble timepints, viewsetups, missingviews and the imgloader
final TimePoints timepoints = this.createTimePoints( meta );
final ArrayList< ViewSetup > setups = this.createViewSetups( meta );
final MissingViews missingViews = null;
// instantiate the sequencedescription
final SequenceDescription sequenceDescription = new SequenceDescription( timepoints, setups, null, missingViews );
final ImgLoader imgLoader = new LightSheetZ1ImgLoader( cziFile, imgFactory, sequenceDescription );
sequenceDescription.setImgLoader( imgLoader );
// get the minimal resolution of all calibrations
final double minResolution = Math.min( Math.min( meta.calX(), meta.calY() ), meta.calZ() );
IOFunctions.println( "Minimal resolution in all dimensions is: " + minResolution );
IOFunctions.println( "(The smallest resolution in any dimension; the distance between two pixels in the output image will be that wide)" );
// create the initial view registrations (they are all the identity transform)
final ViewRegistrations viewRegistrations = StackList.createViewRegistrations( sequenceDescription.getViewDescriptions(), minResolution );
// create the initial view interest point object
final ViewInterestPoints viewInterestPoints = new ViewInterestPoints();
viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
// finally create the SpimData itself based on the sequence description and the view registration
final SpimData2 spimData = new SpimData2( new File( directory ), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes() );
if ( meta.applyAxis() )
Apply_Transformation.applyAxis( spimData );
// TODO: Remove BIOFORMATS bug workaround
if ( fixBioformats )
fixBioformats( spimData, cziFile, meta );
return spimData;
}
/**
* Creates the List of {@link ViewSetup} for the {@link SpimData} object.
* The {@link ViewSetup} are defined independent of the {@link TimePoint},
* each {@link TimePoint} should have the same {@link ViewSetup}s. The {@link MissingViews}
* class defines if some of them are missing for some of the {@link TimePoint}s
*
* @return
*/
protected ArrayList< ViewSetup > createViewSetups( final LightSheetZ1MetaData meta )
{
final ArrayList< Channel > channels = new ArrayList< Channel >();
for ( int c = 0; c < meta.numChannels(); ++c )
channels.add( new Channel( c, meta.channels()[ c ] ) );
final ArrayList< Illumination > illuminations = new ArrayList< Illumination >();
for ( int i = 0; i < meta.numIlluminations(); ++i )
illuminations.add( new Illumination( i, meta.illuminations()[ i ] ) );
final ArrayList< Angle > angles = new ArrayList< Angle >();
for ( int a = 0; a < meta.numAngles(); ++a )
{
final Angle angle = new Angle( a, meta.angles()[ a ] );
try
{
final double degrees = Double.parseDouble( meta.angles()[ a ] );
double[] axis = null;
if ( meta.rotationAxis() == 0 )
axis = new double[]{ 1, 0, 0 };
else if ( meta.rotationAxis() == 1 )
axis = new double[]{ 0, 1, 0 };
else if ( meta.rotationAxis() == 2 )
axis = new double[]{ 0, 0, 1 };
if ( axis != null && !Double.isNaN( degrees ) && !Double.isInfinite( degrees ) )
angle.setRotation( axis, degrees );
}
catch ( Exception e ) {};
angles.add( angle );
}
final ArrayList< ViewSetup > viewSetups = new ArrayList< ViewSetup >();
for ( final Channel c : channels )
for ( final Illumination i : illuminations )
for ( final Angle a : angles )
{
final VoxelDimensions voxelSize = new FinalVoxelDimensions( meta.calUnit(), meta.calX(), meta.calY(), meta.calZ() );
final Dimensions dim = new FinalDimensions( meta.imageSizes().get( a.getId() ) );
viewSetups.add( new ViewSetup( viewSetups.size(), null, dim, voxelSize, c, a, i ) );
}
return viewSetups;
}
/**
* Creates the {@link TimePoints} for the {@link SpimData} object
*/
protected TimePoints createTimePoints( final LightSheetZ1MetaData meta )
{
final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >();
for ( int t = 0; t < meta.numTimepoints(); ++t )
timepoints.add( new TimePoint( t ) );
return new TimePoints( timepoints );
}
protected ImgFactory< ? extends NativeType< ? > > selectImgFactory( final LightSheetZ1MetaData meta )
{
long maxNumPixels = 0;
for ( int a = 0; a < meta.numAngles(); ++a )
{
final int[] dim = meta.imageSizes().get( a );
long n = 1;
for ( int d = 0; d < dim.length; ++d )
{
n *= (long)dim[ d ];
if ( dim[ d ] <= 0 )
{
IOFunctions.println( "Dimensions couldn't be read from metadata, using CellImg(256)." );
return new CellImgFactory< FloatType >( 256 );
}
}
maxNumPixels = Math.max( n, maxNumPixels );
}
int smallerLog2 = (int)Math.ceil( Math.log( maxNumPixels ) / Math.log( 2 ) );
String s = "Maximum number of pixels in any view: n=" + maxNumPixels +
" (2^" + (smallerLog2-1) + " < n < 2^" + smallerLog2 + " px), ";
if ( smallerLog2 <= 31 )
{
IOFunctions.println( s + "using ArrayImg." );
return new ArrayImgFactory< FloatType >();
}
else
{
IOFunctions.println( s + "using CellImg(256)." );
return new CellImgFactory< FloatType >( 256 );
}
}
protected boolean fixBioformats( final SpimData2 spimData, final File cziFile, final LightSheetZ1MetaData meta )
{
final IFormatReader r;
// if we already loaded the metadata in this run, use the opened file
if ( meta.getReader() == null )
r = LegacyLightSheetZ1ImgLoader.instantiateImageReader();
else
r = meta.getReader();
try
{
final boolean isLittleEndian = meta.isLittleEndian();
final int pixelType = meta.pixelType();
// open the file if not already done
try
{
if ( meta.getReader() == null )
{
IOFunctions.println( new Date( System.currentTimeMillis() ) + ": Opening '" + cziFile.getName() + "' for reading image data." );
r.setId( cziFile.getAbsolutePath() );
}
}
catch ( IllegalStateException e )
{
r.setId( cziFile.getAbsolutePath() );
}
// collect all Angles as their id defines the seriesId of Bioformats
final HashMap< Angle, ViewDescription > map = new HashMap<>();
final SequenceDescription sd = spimData.getSequenceDescription();
for ( final ViewSetup vs : sd.getViewSetupsOrdered() )
{
for ( final TimePoint t : sd.getTimePoints().getTimePointsOrdered() )
{
final ViewDescription vd = sd.getViewDescription( t.getId(), vs.getId() );
if ( vd.isPresent() )
map.put( vd.getViewSetup().getAngle(), vd );
}
}
for ( final Angle a : map.keySet() )
{
final ViewDescription vd = map.get( a );
final int width = (int)vd.getViewSetup().getSize().dimension( 0 );
final int height = (int)vd.getViewSetup().getSize().dimension( 1 );
final int depth = (int)vd.getViewSetup().getSize().dimension( 2 );
final int numPx = width * height;
// set the right angle
r.setSeries( a.getId() );
final byte[] b = new byte[ numPx * meta.bytesPerPixel() ];
final Img< FloatType > slice = ArrayImgs.floats( width, height );
int z;
if ( depth <= 0 )
{
IOFunctions.println( "Size couldn't be read from metadata, trying the hard way ... this is slow as it opens everything, but might solve the problem" );
z = 0;
do
{
final Cursor< FloatType > cursor = slice.localizingCursor();
try
{
r.openBytes( r.getIndex( z, 0, vd.getTimePointId() ), b );
if ( pixelType == FormatTools.UINT8 )
LegacyLightSheetZ1ImgLoader.readBytesArray( b, cursor, numPx );
else if ( pixelType == FormatTools.UINT16 )
LegacyLightSheetZ1ImgLoader.readUnsignedShortsArray( b, cursor, numPx, isLittleEndian );
else if ( pixelType == FormatTools.INT16 )
LegacyLightSheetZ1ImgLoader.readSignedShortsArray( b, cursor, numPx, isLittleEndian );
else if ( pixelType == FormatTools.UINT32 )
LegacyLightSheetZ1ImgLoader.readUnsignedIntsArray( b, cursor, numPx, isLittleEndian );
else if ( pixelType == FormatTools.FLOAT )
LegacyLightSheetZ1ImgLoader.readFloatsArray( b, cursor, numPx, isLittleEndian );
++z;
}
catch ( IllegalArgumentException e )
{
++z;
break;
}
}
while ( !allZero( slice ) );
--z;
}
else
{
z = depth - 1;
for ( z = depth - 1; z >= 0; --z )
{
final Cursor< FloatType > cursor = slice.localizingCursor();
r.openBytes( r.getIndex( z, 0, vd.getTimePointId() ), b );
if ( pixelType == FormatTools.UINT8 )
LegacyLightSheetZ1ImgLoader.readBytesArray( b, cursor, numPx );
else if ( pixelType == FormatTools.UINT16 )
LegacyLightSheetZ1ImgLoader.readUnsignedShortsArray( b, cursor, numPx, isLittleEndian );
else if ( pixelType == FormatTools.INT16 )
LegacyLightSheetZ1ImgLoader.readSignedShortsArray( b, cursor, numPx, isLittleEndian );
else if ( pixelType == FormatTools.UINT32 )
LegacyLightSheetZ1ImgLoader.readUnsignedIntsArray( b, cursor, numPx, isLittleEndian );
else if ( pixelType == FormatTools.FLOAT )
LegacyLightSheetZ1ImgLoader.readFloatsArray( b, cursor, numPx, isLittleEndian );
if ( !allZero( slice ) )
break;
}
// size is one bigger than the last z-slice
z++;
}
meta.imageSizes().put( a.getId(), new int[]{ width, height, z } );
for ( final ViewSetup vs : sd.getViewSetupsOrdered() )
{
if ( vs.getAngle().getId() == a.getId() )
{
vs.setSize( new FinalDimensions( meta.imageSizes().get( a.getId() ) ) );
IOFunctions.println( "Resetting image size for viewSetup: " + vs.getId() + ", old: " + width + "x" + height + "x" + depth + ", new: " + width + "x" + height + "x" + z );
}
}
}
}
catch ( Exception e )
{
IOFunctions.println( "File '" + cziFile.getAbsolutePath() + "' could not be opened: " + e );
IOFunctions.println( "Stopping" );
e.printStackTrace();
try { r.close(); } catch (IOException e1) { e1.printStackTrace(); }
return false;
}
return true;
}
private final static boolean allZero( final Img< FloatType > slice )
{
for ( final FloatType t : slice )
if ( t.get() != 0.0f )
return false;
return true;
}
protected boolean showDialogs( final LightSheetZ1MetaData meta )
{
GenericDialog gd = new GenericDialog( "Lightsheet Z.1 Properties" );
gd.addMessage( "Angles (" + meta.numAngles() + " present)", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
gd.addMessage( "" );
for ( int a = 0; a < meta.numAngles(); ++a )
gd.addStringField( "Angle_" + (a+1) + ":", meta.angles()[ a ] );
gd.addMessage( "Channels (" + meta.numChannels() + " present)", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
gd.addMessage( "" );
for ( int c = 0; c < meta.numChannels(); ++c )
gd.addStringField( "Channel_" + (c+1) + ":", meta.channels()[ c ] );
gd.addMessage( "Illumination Directions (" + meta.numIlluminations() + " present)", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
gd.addMessage( "" );
for ( int i = 0; i < meta.numIlluminations(); ++i )
gd.addStringField( "_______Illumination_" + (i+1) + ":", meta.illuminations()[ i ] );
gd.addMessage( "Timepoints (" + meta.numTimepoints() + " present)", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
gd.addMessage( "Calibration", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
gd.addCheckbox( "Modify_calibration", defaultModifyCal );
gd.addMessage( "Pixel Distance X: " + meta.calX() + " " + meta.calUnit() );
gd.addMessage( "Pixel Distance Y: " + meta.calY() + " " + meta.calUnit() );
gd.addMessage( "Pixel Distance Z: " + meta.calZ() + " " + meta.calUnit() );
gd.addMessage( "Additional Meta Data", new Font( Font.SANS_SERIF, Font.BOLD, 13 ) );
gd.addMessage( "" );
gd.addCheckbox( "Modify_rotation_axis", defaultRotAxis );
gd.addCheckbox( "Apply_rotation_to_dataset", defaultApplyRotAxis );
// TODO: Remove BIOFORMATS bug workaround
if ( meta.allImageSizesEqual() )
{
gd.addMessage( "WARNING: All image stacks have the same size, this could be the Bioformats bug.", new Font( Font.SANS_SERIF, Font.BOLD, 13 ), Color.red );
defaultFixBioformats = true;
}
gd.addCheckbox( "Fix_Bioformats image stack size bug", defaultFixBioformats );
gd.addMessage( "Acquisition Objective: " + meta.objective(), new Font( Font.SANS_SERIF, Font.ITALIC, 11 ) );
gd.addMessage( "Rotation axis: " + meta.rotationAxisName() + " axis", new Font( Font.SANS_SERIF, Font.ITALIC, 11 ) );
gd.addMessage( (meta.lightsheetThickness() < 0 ? "" : "Lighsheet thickness: " + meta.lightsheetThickness() + " um"), new Font( Font.SANS_SERIF, Font.ITALIC, 11 ) );
gd.addMessage( "Pixel type: " + meta.pixelTypeString() + " (" + meta.bytesPerPixel() + " byte per pixel)", new Font( Font.SANS_SERIF, Font.ITALIC, 11 ) );
IOFunctions.println( "Dataset directory: " + new File( meta.files()[ 0 ] ).getParent() );
IOFunctions.println( "Dataset files:" );
for ( int i = 0; i < meta.files().length; ++i )
IOFunctions.println( new File( meta.files()[ i ] ).getName() );
IOFunctions.println( "Image sizes:" );
for ( int a = 0; a < meta.numAngles(); ++a )
IOFunctions.println( "Angle " + meta.angles()[ a ] + ": " + Util.printCoordinates( meta.imageSizes().get( a ) ) + " px." );
GUIHelper.addScrollBars( gd );
gd.showDialog();
if ( gd.wasCanceled() )
return false;
for ( int a = 0; a < meta.numAngles(); ++a )
meta.angles()[ a ] = gd.getNextString();
for ( int c = 0; c < meta.numChannels(); ++c )
meta.channels()[ c ] = gd.getNextString();
for ( int i = 0; i < meta.numIlluminations(); ++i )
meta.illuminations()[ i ] = gd.getNextString();
final boolean modifyCal = defaultModifyCal = gd.getNextBoolean();
final boolean modifyAxis = defaultRotAxis = gd.getNextBoolean();
meta.setApplyAxis( defaultApplyRotAxis = gd.getNextBoolean() );
// TODO: Remove BIOFORMATS bug workaround
fixBioformats = defaultFixBioformats = gd.getNextBoolean();
if ( modifyAxis || modifyCal )
{
gd = new GenericDialog( "Modify Meta Data" );
if ( modifyCal )
{
gd.addNumericField( "Pixel_distance_x", meta.calX(), 5 );
gd.addNumericField( "Pixel_distance_y", meta.calY(), 5 );
gd.addNumericField( "Pixel_distance_z", meta.calZ(), 5 );
gd.addStringField( "Pixel_unit", meta.calUnit() );
}
if ( modifyAxis )
{
if ( meta.rotationAxis() < 0 )
meta.setRotationAxis( 0 );
gd.addChoice( "Rotation_around", rotAxes, rotAxes[ meta.rotationAxis() ] );
}
gd.showDialog();
if ( gd.wasCanceled() )
return false;
if ( modifyCal )
{
meta.setCalX( gd.getNextNumber() );
meta.setCalY( gd.getNextNumber() );
meta.setCalZ( gd.getNextNumber() );
meta.setCalUnit( gd.getNextString() );
}
if ( modifyAxis )
meta.setRotationAxis( gd.getNextChoiceIndex() );
}
return true;
}
protected File queryCZIFile()
{
GenericDialogPlus gd = new GenericDialogPlus( "Define Lightsheet Z.1 Dataset" );
gd.addFileField( "First_CZI file of the dataset", defaultFirstFile, 50 );
gd.showDialog();
if ( gd.wasCanceled() )
return null;
final File firstFile = new File( defaultFirstFile = gd.getNextString() );
if ( !firstFile.exists() )
{
IOFunctions.println( "File '" + firstFile.getAbsolutePath() + "' does not exist. Stopping" );
return null;
}
else
{
IOFunctions.println( "Investigating file '" + firstFile.getAbsolutePath() + "'." );
return firstFile;
}
}
@Override
public LightSheetZ1 newInstance() { return new LightSheetZ1(); }
public static void main( String[] args )
{
//defaultFirstFile = "/Volumes/My Passport/worm7/Track1(3).czi";
//defaultFirstFile = "/Volumes/My Passport/Zeiss Olaf Lightsheet Z.1/130706_Aiptasia8.czi";
//defaultFirstFile = "/Volumes/My Passport/Zeiss Olaf Lightsheet Z.1/abe_Arabidopsis1.czi";
//defaultFirstFile = "/Volumes/My Passport/Zeiss Olaf Lightsheet Z.1/multiview.czi";
defaultFirstFile = "/Users/spreibi/Downloads/007-H2B-GFP-LA-mKate2-220min-E03_E04.czi";
//defaultFirstFile = "/Volumes/My Passport/Zeiss Olaf Lightsheet Z.1/worm7/Track1.czi";
new LightSheetZ1().createDataset();
}
}