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/*******************************************************************************
* Copyright (c) 2015-2018 Skymind, Inc.
*
* This program and the accompanying materials are made available under the
* terms of the Apache License, Version 2.0 which is available at
* https://www.apache.org/licenses/LICENSE-2.0.
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
* WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
* License for the specific language governing permissions and limitations
* under the License.
*
* SPDX-License-Identifier: Apache-2.0
******************************************************************************/
package org.nd4j.linalg.dataset.api;
import lombok.NonNull;
import lombok.extern.slf4j.Slf4j;
import lombok.val;
import org.nd4j.common.base.Preconditions;
import org.nd4j.linalg.exception.ND4JIllegalStateException;
import org.nd4j.common.primitives.Pair;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.api.ops.impl.broadcast.BroadcastMulOp;
import org.nd4j.linalg.api.shape.Shape;
import org.nd4j.linalg.factory.Nd4j;
import org.nd4j.linalg.indexing.INDArrayIndex;
import org.nd4j.linalg.indexing.NDArrayIndex;
import java.util.Arrays;
/**
* Created by susaneraly on 9/20/16.
*/
@Slf4j
public class DataSetUtil {
public static INDArray tailor2d(@NonNull DataSet dataSet, boolean areFeatures) {
return tailor2d(areFeatures ? dataSet.getFeatures() : dataSet.getLabels(),
areFeatures ? dataSet.getFeaturesMaskArray() : dataSet.getLabelsMaskArray());
}
public static INDArray tailor2d(@NonNull INDArray data, INDArray mask) {
switch (data.rank()) {
case 1:
case 2:
return data;
case 3:
return tailor3d2d(data, mask);
case 4:
return tailor4d2d(data);
default:
throw new RuntimeException("Unsupported data rank");
}
}
/**
* @deprecated
*/
public static INDArray tailor3d2d(DataSet dataset, boolean areFeatures) {
INDArray data = areFeatures ? dataset.getFeatures() : dataset.getLabels();
INDArray mask = areFeatures ? dataset.getFeaturesMaskArray() : dataset.getLabelsMaskArray();
return tailor3d2d(data, mask);
}
public static INDArray tailor3d2d(@NonNull INDArray data, INDArray mask) {
//Check mask shapes:
if (mask != null) {
if (data.size(0) != mask.size(0) || data.size(2) != mask.size(1)) {
throw new IllegalArgumentException(
"Invalid mask array/data combination: got data with shape [minibatch, vectorSize, timeSeriesLength] = "
+ Arrays.toString(data.shape())
+ "; got mask with shape [minibatch,timeSeriesLength] = "
+ Arrays.toString(mask.shape())
+ "; minibatch and timeSeriesLength dimensions must match");
}
}
if (data.ordering() != 'f' || data.isView() || !Shape.strideDescendingCAscendingF(data)) {
data = data.dup('f');
}
//F order: strides are like [1, miniBatch, minibatch*size] - i.e., each time step array is contiguous in memory
//This can be reshaped to 2d with a no-copy op
//Same approach as RnnToFeedForwardPreProcessor in DL4J
//I.e., we're effectively stacking time steps for all examples
val shape = data.shape();
INDArray as2d;
if (shape[0] == 1) {
as2d = data.tensorAlongDimension(0, 1, 2).permutei(1, 0); //Edge case: miniBatchSize==1
} else if (shape[2] == 1) {
as2d = data.tensorAlongDimension(0, 1, 0); //Edge case: timeSeriesLength=1
} else {
INDArray permuted = data.permute(0, 2, 1); //Permute, so we get correct order after reshaping
as2d = permuted.reshape('f', shape[0] * shape[2], shape[1]);
}
if (mask == null) {
return as2d;
}
//With stride 1 along the examples (dimension 0), we are concatenating time series - same as the
if (mask.ordering() != 'f' || mask.isView() || !Shape.strideDescendingCAscendingF(mask)) {
mask = mask.dup('f');
}
INDArray mask1d = mask.reshape('f', new long[] {mask.length(), 1});
//Assume masks are 0s and 1s: then sum == number of elements
int numElements = mask.sumNumber().intValue();
if (numElements == mask.length()) {
return as2d; //All are 1s
}
if (numElements == 0) {
return null;
}
int[] rowsToPull = new int[numElements];
float[] floatMask1d = mask1d.data().asFloat();
int currCount = 0;
for (int i = 0; i < floatMask1d.length; i++) {
if (floatMask1d[i] != 0.0f) {
rowsToPull[currCount++] = i;
}
}
INDArray subset = Nd4j.pullRows(as2d, 1, rowsToPull); //Tensor along dimension 1 == rows
return subset;
}
public static INDArray tailor4d2d(DataSet dataset, boolean areFeatures) {
return tailor4d2d(areFeatures ? dataset.getFeatures() : dataset.getLabels());
}
public static INDArray tailor4d2d(@NonNull INDArray data) {
long instances = data.size(0);
long channels = data.size(1);
long height = data.size(2);
long width = data.size(3);
INDArray in2d = Nd4j.create(channels, height * width * instances);
long tads = data.tensorsAlongDimension(3, 2, 0);
for (int i = 0; i < tads; i++) {
INDArray thisTAD = data.tensorAlongDimension(i, 3, 2, 0);
in2d.putRow(i, Nd4j.toFlattened(thisTAD));
}
return in2d.transposei();
}
public static void setMaskedValuesToZero(INDArray data, INDArray mask) {
if (mask == null || data.rank() != 3)
return;
Nd4j.getExecutioner().exec(new BroadcastMulOp(data, mask, data, 0, 2));
}
/**
* Merge all of the features arrays into one minibatch.
*
* @param featuresToMerge features to merge. Note that first index is the input array (example) index, the second
* index is the input array.
* Thus to merge 10 examples with 3 input arrays each, featuresToMerge will be indexed
* like featuresToMerge[0..9][0..2]
* @param featureMasksToMerge May be null. If non-null: feature masks to merge
* @return Merged features, and feature masks. Note that feature masks may be added automatically, if required - even
* if no feature masks were present originally
*/
public static Pair mergeFeatures(@NonNull INDArray[][] featuresToMerge, INDArray[][] featureMasksToMerge) {
int nInArrs = featuresToMerge[0].length;
INDArray[] outF = new INDArray[nInArrs];
INDArray[] outM = null;
for (int i = 0; i < nInArrs; i++) {
Pair p = mergeFeatures(featuresToMerge, featureMasksToMerge, i);
outF[i] = p.getFirst();
if (p.getSecond() != null) {
if (outM == null) {
outM = new INDArray[nInArrs];
}
outM[i] = p.getSecond();
}
}
return new Pair<>(outF, outM);
}
/**
* Merge the specified features and mask arrays (i.e., concatenate the examples)
*
* @param featuresToMerge Features to merge
* @param featureMasksToMerge Mask arrays to merge. May be null
* @return Merged features and mask. Mask may be null
*/
public static Pair mergeFeatures(@NonNull INDArray[] featuresToMerge,
INDArray[] featureMasksToMerge) {
Preconditions.checkNotNull(featuresToMerge[0], "Encountered null feature array when merging");
int rankFeatures = featuresToMerge[0].rank();
switch (rankFeatures) {
case 2:
return DataSetUtil.merge2d(featuresToMerge, featureMasksToMerge);
case 3:
return DataSetUtil.mergeTimeSeries(featuresToMerge, featureMasksToMerge);
case 4:
return DataSetUtil.merge4d(featuresToMerge, featureMasksToMerge);
default:
throw new IllegalStateException("Cannot merge examples: features rank must be in range 2 to 4"
+ " inclusive. First example features shape: "
+ Arrays.toString(featuresToMerge[0].shape()));
}
}
/**
* Extract out the specified column, and merge the specified features and mask arrays (i.e., concatenate the examples)
*
* @param featuresToMerge Features to merge. Will use featuresToMerge[all][inOutIdx]
* @param featureMasksToMerge Mask arrays to merge. May be null
* @return Merged features and mask. Mask may be null
*/
public static Pair mergeFeatures(INDArray[][] featuresToMerge, INDArray[][] featureMasksToMerge,
int inOutIdx) {
Pair p = selectColumnFromMDSData(featuresToMerge, featureMasksToMerge, inOutIdx);
return mergeFeatures(p.getFirst(), p.getSecond());
}
/**
* Merge the specified labels and label mask arrays (i.e., concatenate the examples)
*
* @param labelsToMerge Features to merge
* @param labelMasksToMerge Mask arrays to merge. May be null
* @return Merged features and mask. Mask may be null
*/
public static Pair mergeLabels(INDArray[] labelsToMerge, INDArray[] labelMasksToMerge) {
Preconditions.checkNotNull(labelsToMerge[0], "Cannot merge data: Encountered null labels array");
int rankFeatures = labelsToMerge[0].rank();
switch (rankFeatures) {
case 2:
return DataSetUtil.merge2d(labelsToMerge, labelMasksToMerge);
case 3:
return DataSetUtil.mergeTimeSeries(labelsToMerge, labelMasksToMerge);
case 4:
return DataSetUtil.merge4d(labelsToMerge, labelMasksToMerge);
default:
throw new ND4JIllegalStateException("Cannot merge examples: labels rank must be in range 2 to 4"
+ " inclusive. First example features shape: "
+ Arrays.toString(labelsToMerge[0].shape()));
}
}
/**
* Extract out the specified column, and merge the specified label and label mask arrays
* (i.e., concatenate the examples)
*
* @param labelsToMerge Features to merge. Will use featuresToMerge[all][inOutIdx]
* @param labelMasksToMerge Mask arrays to merge. May be null
* @return Merged features and mask. Mask may be null
*/
public static Pair mergeLabels(@NonNull INDArray[][] labelsToMerge,
INDArray[][] labelMasksToMerge, int inOutIdx) {
Pair p = selectColumnFromMDSData(labelsToMerge, labelMasksToMerge, inOutIdx);
return mergeLabels(p.getFirst(), p.getSecond());
}
private static Pair selectColumnFromMDSData(@NonNull INDArray[][] arrays,
INDArray[][] masks, int inOutIdx) {
INDArray[] a = new INDArray[arrays.length];
INDArray[] m = new INDArray[a.length];
for (int i = 0; i < a.length; i++) {
a[i] = arrays[i][inOutIdx];
if (masks != null && masks[i] != null) {
m[i] = masks[i][inOutIdx];
}
}
return new Pair<>(a, m);
}
/**
* Merge the specified 2d arrays and masks. See {@link #mergeFeatures(INDArray[], INDArray[])}
* and {@link #mergeLabels(INDArray[], INDArray[])}
*
* @param arrays Arrays to merge
* @param masks Mask arrays to merge
* @param inOutIdx Index to extract out before merging
* @return Merged arrays and mask
*/
public static Pair merge2d(@NonNull INDArray[][] arrays, INDArray[][] masks, int inOutIdx) {
Pair p = selectColumnFromMDSData(arrays, masks, inOutIdx);
return merge2d(p.getFirst(), p.getSecond());
}
/**
* Merge the specified 2d arrays and masks. See {@link #mergeFeatures(INDArray[], INDArray[])}
* and {@link #mergeLabels(INDArray[], INDArray[])}
*
* @param arrays Arrays to merge
* @param masks Mask arrays to merge
* @return Merged arrays and mask
*/
public static Pair merge2d(INDArray[] arrays, INDArray[] masks) {
long cols = arrays[0].columns();
INDArray[] temp = new INDArray[arrays.length];
boolean hasMasks = false;
for (int i = 0; i < arrays.length; i++) {
Preconditions.checkNotNull(arrays[i], "Encountered null array at position %s when merging data", i);
if (arrays[i].columns() != cols) {
throw new IllegalStateException("Cannot merge 2d arrays with different numbers of columns (firstNCols="
+ cols + ", ithNCols=" + arrays[i].columns() + ")");
}
temp[i] = arrays[i];
if (masks != null && masks[i] != null && masks[i] != null) {
hasMasks = true;
}
}
INDArray out = Nd4j.specialConcat(0, temp);
INDArray outMask = null;
if (hasMasks) {
outMask = DataSetUtil.mergePerOutputMasks2d(out.shape(), arrays, masks);
}
return new Pair<>(out, outMask);
}
public static INDArray mergePerOutputMasks2d(long[] outShape, INDArray[][] arrays, INDArray[][] masks, int inOutIdx) {
Pair p = selectColumnFromMDSData(arrays, masks, inOutIdx);
return mergePerOutputMasks2d(outShape, p.getFirst(), p.getSecond());
}
/**
* @deprecated USe {@link #mergeMasks2d(long[], INDArray[], INDArray[])}
*/
@Deprecated
public static INDArray mergePerOutputMasks2d(long[] outShape, INDArray[] arrays, INDArray[] masks) {
return mergeMasks2d(outShape, arrays, masks);
}
public static INDArray mergeMasks2d(long[] outShape, INDArray[] arrays, INDArray[] masks) {
val numExamplesPerArr = new long[arrays.length];
for (int i = 0; i < numExamplesPerArr.length; i++) {
numExamplesPerArr[i] = arrays[i].size(0);
}
INDArray outMask = Nd4j.ones(arrays[0].dataType(), outShape); //Initialize to 'all present' (1s)
int rowsSoFar = 0;
for (int i = 0; i < masks.length; i++) {
long thisRows = numExamplesPerArr[i]; //Mask itself may be null -> all present, but may include multiple examples
if (masks[i] == null) {
continue;
}
outMask.put(new INDArrayIndex[] {NDArrayIndex.interval(rowsSoFar, rowsSoFar + thisRows),
NDArrayIndex.all()}, masks[i]);
rowsSoFar += thisRows;
}
return outMask;
}
public static INDArray mergeMasks4d(INDArray[] featuresOrLabels, INDArray[] masks) {
long[] outShape = null;
long mbCountNoMask = 0;
for (int i = 0; i < masks.length; i++) {
if(masks[i] == null) {
mbCountNoMask += featuresOrLabels[i].size(0);
continue;
}
if(masks[i].rank() != 4)
throw new IllegalStateException("Cannot merge mask arrays: expected mask array of rank 4. Got mask array of rank " + masks[i].rank()
+ " with shape " + Arrays.toString(masks[i].shape()));
if(outShape == null)
outShape = masks[i].shape().clone();
else {
INDArray m = masks[i];
if(m.size(1) != outShape[1] || m.size(2) != outShape[2] || m.size(3) != outShape[3]){
throw new IllegalStateException("Mismatched mask shapes: masks should have same depth/height/width for all examples." +
" Prior examples had shape [mb," + masks[1] + "," + masks[2] + "," + masks[3] + "], next example has shape " +
Arrays.toString(m.shape()));
}
outShape[0] += m.size(0);
}
}
if(outShape == null)
return null; //No masks to merge
outShape[0] += mbCountNoMask;
INDArray outMask = Nd4j.ones(outShape); //Initialize to 'all present' (1s)
int exSoFar = 0;
for (int i = 0; i < masks.length; i++) {
if (masks[i] == null) {
exSoFar += featuresOrLabels[i].size(0);
continue;
}
long nEx = masks[i].size(0);
outMask.put(new INDArrayIndex[] {NDArrayIndex.interval(exSoFar, exSoFar + nEx),
NDArrayIndex.all()}, masks[i]);
exSoFar += nEx;
}
return outMask;
}
/**
* Merge the specified time series (3d) arrays and masks. See {@link #mergeFeatures(INDArray[], INDArray[])}
* and {@link #mergeLabels(INDArray[], INDArray[])}
*
* @param arrays Arrays to merge
* @param masks Mask arrays to merge
* @param inOutIdx Index to extract out before merging
* @return Merged arrays and mask
*/
public static Pair mergeTimeSeries(INDArray[][] arrays, INDArray[][] masks, int inOutIdx) {
Pair p = selectColumnFromMDSData(arrays, masks, inOutIdx);
return mergeTimeSeries(p.getFirst(), p.getSecond());
}
/**
* Merge the specified time series (3d) arrays and masks. See {@link #mergeFeatures(INDArray[], INDArray[])}
* and {@link #mergeLabels(INDArray[], INDArray[])}
*
* @param arrays Arrays to merge
* @param masks Mask arrays to merge
* @return Merged arrays and mask
*/
public static Pair mergeTimeSeries(INDArray[] arrays, INDArray[] masks) {
//Merge time series data, and handle masking etc for different length arrays
//Complications with time series:
//(a) They may have different lengths (if so: need input + output masking arrays)
//(b) Even if they are all the same length, they may have masking arrays (if so: merge the masking arrays too)
//(c) Furthermore: mask arrays can be per-time-step (2d) or per output (3d). Per-input masks (3d feature masks)
// are not supported, however
long firstLength = arrays[0].size(2);
long size = arrays[0].size(1);
long maxLength = firstLength;
boolean hasMask = false;
int maskRank = -1;
boolean lengthsDiffer = false;
int totalExamples = 0;
for (int i = 0; i < arrays.length; i++) {
totalExamples += arrays[i].size(0);
long thisLength = arrays[i].size(2);
maxLength = Math.max(maxLength, thisLength);
if (thisLength != firstLength)
lengthsDiffer = true;
if (masks != null && masks[i] != null && masks[i] != null) {
maskRank = masks[i].rank();
hasMask = true;
}
if (arrays[i].size(1) != size) {
throw new IllegalStateException(
"Cannot merge time series with different size for dimension 1 (first shape: "
+ Arrays.toString(arrays[0].shape()) + ", " + i + "th shape: "
+ Arrays.toString(arrays[i].shape()));
}
}
boolean needMask = hasMask || lengthsDiffer;
INDArray arr = Nd4j.create(arrays[0].dataType(), totalExamples, size, maxLength);
INDArray mask = (needMask && maskRank != 3 ? Nd4j.ones(arrays[0].dataType(), totalExamples, maxLength) : null);
//Now, merge the time series (and if necessary, mask arrays):
int examplesSoFar = 0;
if (!lengthsDiffer && !needMask) {
//Simplest case: same length, no mask arrays
for (int i = 0; i < arrays.length; i++) {
long thisNExamples = arrays[i].size(0);
arr.put(new INDArrayIndex[] {NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.all(), NDArrayIndex.all()}, arrays[i]);
examplesSoFar += thisNExamples;
}
return new Pair<>(arr, null);
} else {
//Either different length, or have mask arrays (or, both)
if ((lengthsDiffer && !hasMask) || maskRank == 2) {
//Standard per-example masking required
for (int i = 0; i < arrays.length; i++) {
INDArray a = arrays[i];
long thisNExamples = a.size(0);
long thisLength = a.size(2);
arr.put(new INDArrayIndex[] {NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.all(), NDArrayIndex.interval(0, thisLength)}, a);
if (masks != null && masks[i] != null && masks[i] != null) {
INDArray origMask = masks[i];
long maskLength = origMask.size(1);
mask.put(new INDArrayIndex[] {
NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.interval(0, maskLength)}, origMask);
if (maskLength < maxLength) {
//Set end mask array to zero...
mask.put(new INDArrayIndex[] {
NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.interval(maskLength, maxLength)},
Nd4j.zeros(thisNExamples, maxLength - maskLength));
}
} else {
if (thisLength < maxLength) {
//Mask the end
mask.put(new INDArrayIndex[] {
NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.interval(thisLength, maxLength)},
Nd4j.zeros(thisNExamples, maxLength - thisLength));
}
}
examplesSoFar += thisNExamples;
}
} else if (maskRank == 3) {
//Per output masking required. May also be variable length
mask = Nd4j.create(arr.dataType(), arr.shape());
for (int i = 0; i < arrays.length; i++) {
INDArray m = masks[i];
INDArray a = arrays[i];
long thisNExamples = a.size(0);
long thisLength = a.size(2);
arr.put(new INDArrayIndex[] {NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.all(), NDArrayIndex.interval(0, thisLength)}, a);
if (m == null) {
//This mask is null -> equivalent to "all present"
mask.get(NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.all(), NDArrayIndex.interval(0, thisLength)).assign(1);
} else {
mask.put(new INDArrayIndex[] {
NDArrayIndex.interval(examplesSoFar, examplesSoFar + thisNExamples),
NDArrayIndex.all(), NDArrayIndex.interval(0, thisLength)}, m);
}
examplesSoFar += thisNExamples;
}
} else {
throw new UnsupportedOperationException("Cannot merge time series with mask rank " + maskRank);
}
}
return new Pair<>(arr, mask);
}
/**
* Merge the specified 4d arrays and masks. See {@link #mergeFeatures(INDArray[], INDArray[])}
* and {@link #mergeLabels(INDArray[], INDArray[])}
*
* @param arrays Arrays to merge
* @param masks Mask arrays to merge
* @param inOutIdx Index to extract out before merging
* @return Merged arrays and mask
*/
public static Pair merge4d(INDArray[][] arrays, INDArray[][] masks, int inOutIdx) {
Pair p = selectColumnFromMDSData(arrays, masks, inOutIdx);
return merge4d(p.getFirst(), p.getSecond());
}
/**
* Merge the specified 4d arrays and masks. See {@link #mergeFeatures(INDArray[], INDArray[])}
* and {@link #mergeLabels(INDArray[], INDArray[])}
*
* @param arrays Arrays to merge
* @param masks Mask arrays to merge
* @return Merged arrays and mask
*/
public static Pair merge4d(INDArray[] arrays, INDArray[] masks) {
//4d -> images. In principle: could have 2d mask arrays (per-example masks)
int nExamples = 0;
long[] shape = arrays[0].shape();
INDArray[] temp = new INDArray[arrays.length];
boolean hasMasks = false;
int maskRank = -1;
for (int i = 0; i < arrays.length; i++) {
Preconditions.checkNotNull(arrays[i], "Encountered null array when merging data at position %s", i);
nExamples += arrays[i].size(0);
long[] thisShape = arrays[i].shape();
if (thisShape.length != 4) {
throw new IllegalStateException("Cannot merge 4d arrays with non 4d arrays");
}
for (int j = 1; j < 4; j++) {
if (thisShape[j] != shape[j])
throw new IllegalStateException(
"Cannot merge 4d arrays with different shape (other than # examples): "
+ " data[0].shape = " + Arrays.toString(shape) + ", data[" + i
+ "].shape = " + Arrays.toString(thisShape));
}
temp[i] = arrays[i];
if (masks != null && masks[i] != null ) {
hasMasks = true;
maskRank = masks[i].rank();
}
}
INDArray out = Nd4j.specialConcat(0, temp);
INDArray outMask = null;
if (hasMasks) {
if(maskRank == 2) {
outMask = DataSetUtil.mergeMasks2d(out.shape(), arrays, masks);
} else if(maskRank == 4){
outMask = DataSetUtil.mergeMasks4d(arrays, masks);
}
}
return new Pair<>(out, outMask);
}
}
