/*-
* #%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>.
* #L%
*/
package spim.fiji.spimdata.imgloaders;
import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.GenericDialog;
import ij.io.Opener;
import ij.process.ImageProcessor;
import java.io.File;
import java.util.Date;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.sequence.ViewId;
import mpicbg.spim.io.IOFunctions;
import net.imglib2.Cursor;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.converter.RealUnsignedShortConverter;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImg;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.img.planar.PlanarImg;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.view.Views;
import spim.fiji.datasetmanager.StackListImageJ;
import spim.fiji.plugin.resave.Generic_Resave_HDF5;
import spim.fiji.plugin.resave.Generic_Resave_HDF5.Parameters;
import spim.fiji.plugin.util.GUIHelper;
import spim.process.fusion.export.ExportSpimData2HDF5;
public class LegacyStackImgLoaderIJ extends LegacyStackImgLoader
{
Parameters params = null;
public LegacyStackImgLoaderIJ(
final File path, final String fileNamePattern, final ImgFactory< ? extends NativeType< ? > > imgFactory,
final int layoutTP, final int layoutChannels, final int layoutIllum, final int layoutAngles,
final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
super( path, fileNamePattern, imgFactory, layoutTP, layoutChannels, layoutIllum, layoutAngles, sequenceDescription );
}
public static ImagePlus open( File file )
{
final ImagePlus imp = new Opener().openImage( file.getAbsolutePath() );
if ( imp == null )
{
IOFunctions.printlnSafe( "Could not open file with ImageJ TIFF reader: '" + file.getAbsolutePath() + "'" );
return null;
}
return imp;
}
/**
* Get {@link FloatType} image normalized to the range [0,1].
*
* @param view
* timepoint and setup for which to retrieve the image.
* @param normalize
* if the image should be normalized to [0,1] or not
* @return {@link FloatType} image normalized to range [0,1]
*/
@Override
public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
{
final File file = getFile( view );
if ( file == null )
throw new RuntimeException( "Could not find file '" + file + "'." );
IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Loading '" + file + "' ..." );
final ImagePlus imp = open( file );
if ( imp == null )
throw new RuntimeException( "Could not load '" + file + "'." );
final long[] dim = new long[]{ imp.getWidth(), imp.getHeight(), imp.getStack().getSize() };
final Img< FloatType > img = this.instantiateImg( dim, new FloatType() );
if ( img == null )
throw new RuntimeException( "Could not instantiate " + getImgFactory().getClass().getSimpleName() + " for '" + file + "', most likely out of memory." );
else
IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Opened '" + file + "' [" + dim[ 0 ] + "x" + dim[ 1 ] + "x" + dim[ 2 ] + " image=" + img.getClass().getSimpleName() + "<FloatType>]" );
imagePlus2ImgLib2Img( imp, img, normalize );
// update the MetaDataCache of the AbstractImgLoader
// this does not update the XML ViewSetup but has to be called explicitly before saving
updateMetaDataCache( view, imp.getWidth(), imp.getHeight(), imp.getStack().getSize(),
imp.getCalibration().pixelWidth, imp.getCalibration().pixelHeight, imp.getCalibration().pixelDepth );
imp.close();
return img;
}
public static void imagePlus2ImgLib2Img( final ImagePlus imp, final Img< FloatType > img, final boolean normalize )
{
final ImageStack stack = imp.getStack();
final int sizeZ = imp.getStack().getSize();
if ( img instanceof ArrayImg || img instanceof PlanarImg )
{
final Cursor< FloatType > cursor = img.cursor();
final int sizeXY = imp.getWidth() * imp.getHeight();
if ( normalize )
{
float min = Float.MAX_VALUE;
float max = -Float.MAX_VALUE;
for ( int z = 0; z < sizeZ; ++z )
{
final ImageProcessor ip = stack.getProcessor( z + 1 );
for ( int i = 0; i < sizeXY; ++i )
{
final float v = ip.getf( i );
if ( v < min )
min = v;
if ( v > max )
max = v;
cursor.next().set( v );
}
}
for ( final FloatType t : img )
t.set( ( t.get() - min ) / ( max - min ) );
}
else
{
for ( int z = 0; z < sizeZ; ++z )
{
final ImageProcessor ip = stack.getProcessor( z + 1 );
for ( int i = 0; i < sizeXY; ++i )
cursor.next().set( ip.getf( i ) );
}
}
}
else
{
final int width = imp.getWidth();
if ( normalize )
{
float min = Float.MAX_VALUE;
float max = -Float.MAX_VALUE;
for ( int z = 0; z < sizeZ; ++z )
{
final Cursor< FloatType > cursor = Views.iterable( Views.hyperSlice( img, 2, z ) ).localizingCursor();
final ImageProcessor ip = stack.getProcessor( z + 1 );
while ( cursor.hasNext() )
{
cursor.fwd();
final float v = ip.getf( cursor.getIntPosition( 0 ) + cursor.getIntPosition( 1 ) * width );
if ( v < min )
min = v;
if ( v > max )
max = v;
cursor.get().set( v );
}
}
for ( final FloatType t : img )
t.set( ( t.get() - min ) / ( max - min ) );
}
else
{
for ( int z = 0; z < sizeZ; ++z )
{
final Cursor< FloatType > cursor = Views.iterable( Views.hyperSlice( img, 2, z ) ).localizingCursor();
final ImageProcessor ip = stack.getProcessor( z + 1 );
while ( cursor.hasNext() )
{
cursor.fwd();
cursor.get().set( ip.getf( cursor.getIntPosition( 0 ) + cursor.getIntPosition( 1 ) * width ) );
}
}
}
}
}
/**
* Get {@link UnsignedShortType} un-normalized image.
*
* @param view
* timepoint and setup for which to retrieve the image.
* @return {@link UnsignedShortType} image.
*/
@Override
public RandomAccessibleInterval< UnsignedShortType > getImage( final ViewId view )
{
final File file = getFile( view );
if ( file == null )
throw new RuntimeException( "Could not find file '" + file + "'." );
IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Loading '" + file + "' ..." );
final ImagePlus imp = open( file );
if ( imp == null )
throw new RuntimeException( "Could not load '" + file + "'." );
final boolean is32bit;
final RealUnsignedShortConverter< FloatType > converter;
if ( imp.getType() == ImagePlus.GRAY32 )
{
is32bit = true;
IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Image '" + file + "' is 32bit, opening as 16bit with scaling" );
if ( params == null )
params = queryParameters();
if ( params == null )
return null;
final double[] minmax = ExportSpimData2HDF5.updateAndGetMinMax( ImageJFunctions.wrapFloat( imp ), params );
converter = new RealUnsignedShortConverter< FloatType >( minmax[ 0 ], minmax[ 1 ] );
}
else
{
is32bit = false;
converter = null;
}
final long[] dim = new long[]{ imp.getWidth(), imp.getHeight(), imp.getStack().getSize() };
final Img< UnsignedShortType > img = instantiateImg( dim, new UnsignedShortType() );
if ( img == null )
throw new RuntimeException( "Could not instantiate " + getImgFactory().getClass().getSimpleName() + " for '" + file + "', most likely out of memory." );
else
IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Opened '" + file + "' [" + dim[ 0 ] + "x" + dim[ 1 ] + "x" + dim[ 2 ] + " image=" + img.getClass().getSimpleName() + "<UnsignedShortType>]" );
final ImageStack stack = imp.getStack();
final int sizeZ = imp.getStack().getSize();
if ( img instanceof ArrayImg || img instanceof PlanarImg )
{
final Cursor< UnsignedShortType > cursor = img.cursor();
final int sizeXY = imp.getWidth() * imp.getHeight();
for ( int z = 0; z < sizeZ; ++z )
{
final ImageProcessor ip = stack.getProcessor( z + 1 );
if( is32bit )
{
final FloatType input = new FloatType();
final UnsignedShortType output = new UnsignedShortType();
for ( int i = 0; i < sizeXY; ++i )
{
input.set( ip.getf( i ) );
converter.convert( input, output );
cursor.next().set( output.get() );
}
}
else
{
for ( int i = 0; i < sizeXY; ++i )
cursor.next().set( ip.get( i ) );
}
}
}
else
{
final int width = imp.getWidth();
for ( int z = 0; z < sizeZ; ++z )
{
final Cursor< UnsignedShortType > cursor = Views.iterable( Views.hyperSlice( img, 2, z ) ).localizingCursor();
final ImageProcessor ip = stack.getProcessor( z + 1 );
if ( is32bit )
{
final FloatType input = new FloatType();
final UnsignedShortType output = new UnsignedShortType();
while ( cursor.hasNext() )
{
cursor.fwd();
input.set( ip.getf( cursor.getIntPosition( 0 ) + cursor.getIntPosition( 1 ) * width ) );
converter.convert( input, output );
cursor.get().set( output );
}
}
else
{
while ( cursor.hasNext() )
{
cursor.fwd();
cursor.get().set( ip.get( cursor.getIntPosition( 0 ) + cursor.getIntPosition( 1 ) * width ) );
}
}
}
}
// update the MetaDataCache of the AbstractImgLoader
// this does not update the XML ViewSetup but has to be called explicitly before saving
updateMetaDataCache( view, imp.getWidth(), imp.getHeight(), imp.getStack().getSize(),
imp.getCalibration().pixelWidth, imp.getCalibration().pixelHeight, imp.getCalibration().pixelDepth );
imp.close();
return img;
}
@Override
protected void loadMetaData( final ViewId view )
{
final File file = getFile( view );
final ImagePlus imp = open( file );
if ( imp == null )
throw new RuntimeException( "Could not load '" + file + "'." );
// update the MetaDataCache of the AbstractImgLoader
// this does not update the XML ViewSetup but has to be called explicitly before saving
updateMetaDataCache( view, imp.getWidth(), imp.getHeight(), imp.getStack().getSize(),
imp.getCalibration().pixelWidth, imp.getCalibration().pixelHeight, imp.getCalibration().pixelDepth );
imp.close();
}
@Override
public String toString()
{
return new StackListImageJ().getTitle() + ", ImgFactory=" + imgFactory.getClass().getSimpleName();
}
protected static Parameters queryParameters()
{
final GenericDialog gd = new GenericDialog( "Opening 32bit TIFF as 16bit" );
gd.addMessage( "You are trying to open 32-bit images as 16-bit (resaving as HDF5 maybe). Please define how to convert to 16bit.", GUIHelper.mediumstatusfont );
gd.addMessage( "Note: This dialog will only show up once for the first image.", GUIHelper.mediumstatusfont );
gd.addChoice( "Convert_32bit", Generic_Resave_HDF5.convertChoices, Generic_Resave_HDF5.convertChoices[ Generic_Resave_HDF5.defaultConvertChoice ] );
gd.showDialog();
if ( gd.wasCanceled() )
return null;
Generic_Resave_HDF5.defaultConvertChoice = gd.getNextChoiceIndex();
if ( Generic_Resave_HDF5.defaultConvertChoice == 2 )
{
if ( Double.isNaN( Generic_Resave_HDF5.defaultMin ) )
Generic_Resave_HDF5.defaultMin = 0;
if ( Double.isNaN( Generic_Resave_HDF5.defaultMax ) )
Generic_Resave_HDF5.defaultMax = 5;
final GenericDialog gdMinMax = new GenericDialog( "Define min/max" );
gdMinMax.addNumericField( "Min_Intensity_for_16bit_conversion", Generic_Resave_HDF5.defaultMin, 1 );
gdMinMax.addNumericField( "Max_Intensity_for_16bit_conversion", Generic_Resave_HDF5.defaultMax, 1 );
gdMinMax.addMessage( "Note: the typical range for multiview deconvolution is [0 ... 10] & for fusion the same as the input intensities., ",GUIHelper.mediumstatusfont );
gdMinMax.showDialog();
if ( gdMinMax.wasCanceled() )
return null;
Generic_Resave_HDF5.defaultMin = gdMinMax.getNextNumber();
Generic_Resave_HDF5.defaultMax = gdMinMax.getNextNumber();
}
else
{
Generic_Resave_HDF5.defaultMin = Generic_Resave_HDF5.defaultMax = Double.NaN;
}
return new Parameters( false, null, null, null, null, false, false, 0, 0, false, 0, Generic_Resave_HDF5.defaultConvertChoice, Generic_Resave_HDF5.defaultMin, Generic_Resave_HDF5.defaultMax );
}
}
