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MaskFactory.java
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Wed, May 8, 13:31

MaskFactory.java
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/*-
* #%L
* Fiji's plugin for colocalization analysis.
* %%
* Copyright (C) 2009 - 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 3 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-3.0.html>.
* #L%
*/
package sc.fiji.coloc.gadgets;
import java.util.Arrays;
import net.imglib2.Cursor;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.view.Views;
import sc.fiji.coloc.algorithms.MissingPreconditionException;
public class MaskFactory {
public enum CombinationMode {
AND, OR, NONE
}
/**
* Create a new mask image without any specific content, but with
* a defined size.
*/
public static RandomAccessibleInterval<BitType> createMask(long[] dim) {
ImgFactory< BitType > imgFactory = new ArrayImgFactory< BitType >();
return imgFactory.create(dim, new BitType());
}
/**
* Create a new mask image with a defined size and preset content.
*/
public static RandomAccessibleInterval<BitType> createMask(long[] dim, boolean val) {
RandomAccessibleInterval<BitType> mask = createMask(dim);
for (BitType t : Views.iterable(mask))
t.set(val);
return mask;
}
/**
* Create a new mask image with a defined size and preset content.
* @throws MissingPreconditionException
*/
public static RandomAccessibleInterval<BitType> createMask(long[] dim, long[] roiOffset, long[] roiDim)
throws MissingPreconditionException {
if (dim.length != roiOffset.length || dim.length != roiDim.length) {
throw new MissingPreconditionException("The dimensions of the mask as well as the ROIs and his offset must be the same.");
}
final RandomAccessibleInterval<BitType> mask = createMask(dim);
final int dims = mask.numDimensions();
final long[] pos = new long[dims];
// create an array with the max corner of the ROI
final long[] roiOffsetMax = new long[dims];
for (int i=0; i<dims; ++i)
roiOffsetMax[i] = roiOffset[i] + roiDim[i];
// go through the mask and mask points as valid that are in the ROI
Cursor<BitType> cursor = Views.iterable(mask).localizingCursor();
while ( cursor.hasNext() ) {
cursor.fwd();
cursor.localize(pos);
boolean valid = true;
// test if the current position is contained in the ROI
for(int i=0; i<dims; ++i)
valid &= pos[i] >= roiOffset[i] && pos[i] < roiOffsetMax[i];
cursor.get().set(valid);
}
return mask;
}
/**
* Create a new mask based on a threshold condition for two images.
*/
public static<T extends RealType< T >> RandomAccessibleInterval<BitType> createMask(
RandomAccessibleInterval<T> ch1, RandomAccessibleInterval<T> ch2,
T threshold1, T threshold2, ThresholdMode tMode, CombinationMode cMode) {
final long[] dims = new long[ ch1.numDimensions() ];
ch1.dimensions(dims);
RandomAccessibleInterval<BitType> mask = createMask(dims);
Cursor<T> cursor1 = Views.iterable(ch1).cursor();
Cursor<T> cursor2 = Views.iterable(ch2).cursor();
Cursor<BitType> maskCursor = Views.iterable(mask).cursor();
while (cursor1.hasNext() && cursor2.hasNext() && maskCursor.hasNext()) {
cursor1.fwd();
cursor2.fwd();
maskCursor.fwd();
boolean ch1Valid, ch2Valid;
T data1 = cursor1.get();
T data2 = cursor2.get();
// get relation to threshold
if (tMode == ThresholdMode.Above) {
ch1Valid = data1.compareTo(threshold1) > 0;
ch2Valid = data2.compareTo(threshold2) > 0;
} else if (tMode == ThresholdMode.Below) {
ch1Valid = data1.compareTo(threshold1) < 0;
ch2Valid = data2.compareTo(threshold2) < 0;
} else {
throw new UnsupportedOperationException();
}
BitType maskData = maskCursor.get();
// combine the results into mask
if (cMode == CombinationMode.AND) {
maskData.set( ch1Valid && ch2Valid );
} else if (cMode == CombinationMode.OR) {
maskData.set( ch1Valid || ch2Valid );
} else if (cMode == CombinationMode.NONE) {
maskData.set( !(ch1Valid || ch2Valid) );
} else {
throw new UnsupportedOperationException();
}
}
return mask;
}
/**
* Creates a new mask of the given dimensions, based on the image data
* in the passed image. If the requested dimensionality is higher than
* what is available in the data, the data gets repeated in the higher
* dimensions.
*
* @param dim The dimensions of the new mask image
* @param origMask The image from which the mask should be created from
*/
public static<T extends RealType< T >> RandomAccessibleInterval<BitType> createMask(
final long[] dim, final RandomAccessibleInterval<T> origMask) {
final RandomAccessibleInterval<BitType> mask = createMask(dim);
final long[] origDim = new long[ origMask.numDimensions() ];
origMask.dimensions(origDim);
// test if original mask and new mask have same dimensions
if (Arrays.equals(dim, origDim)) {
// copy the input image to the mask output image
Cursor<T> origCursor = Views.iterable(origMask).localizingCursor();
RandomAccess<BitType> maskCursor = mask.randomAccess();
while (origCursor.hasNext()) {
origCursor.fwd();
maskCursor.setPosition(origCursor);
boolean value = origCursor.get().getRealDouble() > 0.001;
maskCursor.get().set(value);
}
} else if (dim.length > origDim.length) {
// sanity check
for (int i=0; i<origDim.length; i++) {
if (origDim[i] != dim[i])
throw new UnsupportedOperationException("Masks with lower dimensionality than the image, "
+ " but a different extent are not yet supported.");
}
// mask and image have different dimensionality and maybe even a different extent
Cursor<T> origCursor = Views.iterable(origMask).localizingCursor();
RandomAccess<BitType> maskCursor = mask.randomAccess();
final long[] pos = new long[ origMask.numDimensions() ];
// iterate over the original mask
while (origCursor.hasNext()) {
origCursor.fwd();
origCursor.localize(pos);
boolean value = origCursor.get().getRealDouble() > 0.001;
// set available (lower dimensional) position information
for (int i=0; i<origDim.length; i++)
// setPosition requires first the position and then the dimension
maskCursor.setPosition(pos[i], i);
// go through the missing dimensions and set the value
for (int i=origDim.length; i<dim.length; i++)
for (int j=0; j<dim[i]; j++) {
// setPosition requires first the position and then the dimension
maskCursor.setPosition(j, i);
maskCursor.get().set(value);
}
}
} else if (dim.length < origDim.length) {
// mask has more dimensions than image
throw new UnsupportedOperationException("Masks with more dimensions than the image are not supported, yet.");
} else {
// mask and image have a different extent, but are equal in dimensionality. Scale it?
throw new UnsupportedOperationException("Masks with same dimensionality, but a different extent than the image are not supported, yet.");
}
return mask;
}
}

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