Nd4j refactoring (#109)

* refactoring.

Signed-off-by: Robert Altena <Rob@Ra-ai.com>

* wip

Signed-off-by: Robert Altena <Rob@Ra-ai.com>

* wip

Signed-off-by: Robert Altena <Rob@Ra-ai.com>

* wip

Signed-off-by: Robert Altena <Rob@Ra-ai.com>

* review feedback

Signed-off-by: Robert Altena <Rob@Ra-ai.com>

nd4j/nd4j-backends/nd4j-api-parent/nd4j-api/src/main/java/org/nd4j/linalg/factory/Nd4j.java

@@ -2222,7 +2222,6 @@ public class Nd4j {
      * Write an ndarray to a writer
      * @param writer the writer to write to
      * @param write the ndarray to write
-     * @throws IOException
      */
     public static void write(OutputStream writer, INDArray write) throws IOException {
         DataOutputStream stream = new DataOutputStream(writer);
@@ -2230,14 +2229,12 @@ public class Nd4j {
         stream.close();
     }
 
-
     /**
      * Convert an ndarray to a byte array
      * @param arr the array to convert
      * @return the converted byte array
-     * @throws IOException
      */
-    public static byte[] toByteArray(INDArray arr) throws IOException {
+    public static byte[] toByteArray(@NonNull  INDArray arr) throws IOException {
         if (arr.length() * arr.data().getElementSize() >  Integer.MAX_VALUE)
             throw new ND4JIllegalStateException("");
 
@@ -2252,15 +2249,13 @@ public class Nd4j {
      * Read an ndarray from a byte array
      * @param arr the array to read from
      * @return the deserialized ndarray
-     * @throws IOException
      */
-    public static INDArray fromByteArray(byte[] arr) throws IOException {
+    public static INDArray fromByteArray(@NonNull  byte[] arr) throws IOException {
         ByteArrayInputStream bis = new ByteArrayInputStream(arr);
         INDArray ret = read(bis);
         return ret;
     }
 
-
     /**
      * Read line via input streams
      *
@@ -2280,7 +2275,6 @@ public class Nd4j {
      * @param split    the split separator
      * @param charset the  charset
      * @return the deserialized array.
-     * @throws IOException
      */
     public static INDArray readNumpy(@NonNull DataType dataType, @NonNull InputStream filePath, @NonNull String split, @NonNull Charset charset) throws IOException {
         BufferedReader reader = new BufferedReader(new InputStreamReader(filePath, charset));
@@ -2449,7 +2443,7 @@ public class Nd4j {
                 }
                 //parse data
                 if (lineNum > 5) {
-                    String[] entries = line.replace("\\],", "").replaceAll("\\]", "").replaceAll("\\[", "").split(sep);
+                    String[] entries = line.replace("\\],", "").replaceAll("]", "").replaceAll("\\[", "").split(sep);
                     if (rank == 0) {
                         try {
                             newArr.addi((format.parse(entries[0])).doubleValue());
@@ -2496,7 +2490,6 @@ public class Nd4j {
      * @return NDArray
      */
     public static INDArray readTxt(String filePath) {
-        String sep = ",";
         File file = new File(filePath);
         InputStream is = null;
         try {
@@ -2505,13 +2498,7 @@ public class Nd4j {
         } catch (FileNotFoundException e) {
             throw new RuntimeException(e);
         } finally {
-            if (is != null) {
+            IOUtils.closeQuietly(is);
-                try {
-                    is.close();
-                } catch (IOException e) {
-                    e.printStackTrace();
-                }
-            }
         }
     }
 
@@ -2552,9 +2539,9 @@ public class Nd4j {
      */
     public static INDArray createArrayFromShapeBuffer(DataBuffer data, Pair<DataBuffer, long[]> shapeInfo) {
         int rank = Shape.rank(shapeInfo.getFirst());
-        long offset = Shape.offset(shapeInfo.getFirst());
+        // removed offset parameter that called a deprecated method which always returns 0.
         INDArray result = Nd4j.create(data, toIntArray(rank, Shape.shapeOf(shapeInfo.getFirst())),
-                toIntArray(rank, Shape.stride(shapeInfo.getFirst())), offset, Shape.order(shapeInfo.getFirst()));
+                toIntArray(rank, Shape.stride(shapeInfo.getFirst())), 0, Shape.order(shapeInfo.getFirst()));
         if (data instanceof CompressedDataBuffer)
             result.markAsCompressed(true);
 
@@ -2566,7 +2553,6 @@ public class Nd4j {
      *
      * @param dis the data input stream to read from
      * @return the ndarray
-     * @throws IOException
      */
     public static INDArray read(DataInputStream dis) throws IOException {
         val headerShape = BaseDataBuffer.readHeader(dis);
@@ -2597,7 +2583,6 @@ public class Nd4j {
      *
      * @param arr              the array to write
      * @param dataOutputStream the data output stream to write to
-     * @throws IOException
      */
     public static void write(INDArray arr, DataOutputStream dataOutputStream) throws IOException {
         //BaseDataBuffer.write(...) doesn't know about strides etc, so dup (or equiv. strategy) is necessary here
@@ -2614,7 +2599,6 @@ public class Nd4j {
      * Save an ndarray to the given file
      * @param arr the array to save
      * @param saveTo the file to save to
-     * @throws IOException
      */
     public static void saveBinary(INDArray arr, File saveTo) throws IOException {
         BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(saveTo));
@@ -2629,7 +2613,6 @@ public class Nd4j {
      * Read a binary ndarray from the given file
      * @param read the nd array to read
      * @return the loaded ndarray
-     * @throws IOException
      */
     public static INDArray readBinary(File read) throws IOException {
         BufferedInputStream bis = new BufferedInputStream(new FileInputStream(read));
@@ -2645,21 +2628,9 @@ public class Nd4j {
      * @param arr the array to clear
      */
     public static void clearNans(INDArray arr) {
-        //BooleanIndexing.applyWhere(arr, Conditions.isNan(), new Value(Nd4j.EPS_THRESHOLD));
         getExecutioner().exec(new ReplaceNans(arr, Nd4j.EPS_THRESHOLD));
     }
     
-    /**
-     * Reverses the passed in matrix such that m[0] becomes m[m.length - 1] etc
-     *
-     * @param reverse the matrix to reverse
-     * @return the reversed matrix
-     */
-    public static INDArray rot(INDArray reverse) {
-        INDArray ret = INSTANCE.rot(reverse);
-        return ret;
-    }
-
     /**
      * Reverses the passed in matrix such that m[0] becomes m[m.length - 1] etc
      *
@@ -2667,8 +2638,6 @@ public class Nd4j {
      * @return the reversed matrix
      */
     public static INDArray reverse(INDArray reverse) {
-        //INDArray ret = INSTANCE.reverse(reverse);
-        //logCreationIfNecessary(ret);
         return Nd4j.getExecutioner().exec(new OldReverse(reverse));
     }
 
@@ -2682,8 +2651,7 @@ public class Nd4j {
      * @return the 1D range vector
      */
     public static INDArray arange(double begin, double end, double step) {
-        INDArray ret = INSTANCE.arange(begin, end, step);
+        return INSTANCE.arange(begin, end, step);
-        return ret;
     }
 
     /**
@@ -2693,8 +2661,7 @@ public class Nd4j {
      * See {@link #arange(double, double, double)} with step size 1.
      */
     public static INDArray arange(double begin, double end) {
-        INDArray ret = INSTANCE.arange(begin, end, 1);
+        return INSTANCE.arange(begin, end, 1);
-        return ret;
     }
 
     /**
@@ -2717,27 +2684,6 @@ public class Nd4j {
         INSTANCE.copy(a, b);
     }
 
-    /**
-     * Creates a new matrix where the values of the given vector are the diagonal values of
-     * the matrix if a vector is passed in, if a matrix is returns the kth diagonal
-     * in the matrix
-     *
-     * @param x the diagonal values
-     * @param k the kth diagonal to get
-     * @return new matrix
-     */
-    public static INDArray diag(INDArray x, int k) {
-        INDArray ret;
-        if(x.isVectorOrScalar() || x.isRowVector() || x.isColumnVector()) {
-            ret = Nd4j.create(new long[]{x.length(), x.length()});
-            Nd4j.getExecutioner().execAndReturn(new Diag(new INDArray[]{x},new INDArray[]{ret}));
-        } else {
-            ret = Nd4j.createUninitialized(new long[]{Math.min(x.size(0), x.size(1))});
-            Nd4j.getExecutioner().execAndReturn(new DiagPart(x,ret));
-        }
-        return ret;
-    }
-
     /**
      * Creates a new matrix where the values of the given vector are the diagonal values of
      * the matrix if a vector is passed in, if a matrix is returns the kth diagonal
@@ -2747,7 +2693,15 @@ public class Nd4j {
      * @return new matrix
      */
     public static INDArray diag(INDArray x) {
-        return diag(x, 0);
+        INDArray ret;
+        if(x.isVectorOrScalar() || x.isRowVector() || x.isColumnVector()) {
+            ret = Nd4j.create(x.dataType(), x.length(), x.length());
+            Nd4j.getExecutioner().execAndReturn(new Diag(new INDArray[]{x},new INDArray[]{ret}));
+        } else {
+            ret = Nd4j.createUninitialized(x.dataType(), Math.min(x.size(0), x.size(1)));
+            Nd4j.getExecutioner().execAndReturn(new DiagPart(x,ret));
+        }
+        return ret;
     }
 
     /**