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Merge c028fee into 6f2e752
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@ritchieGitHub
ritchieGitHub committed May 29, 2016
2 parents 6f2e752 + c028fee commit e05579e
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Showing 3 changed files with 32 additions and 34 deletions.
38 changes: 26 additions & 12 deletions src/main/java/nom/tam/fits/BinaryTable.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,7 @@
import nom.tam.util.FitsIO;
import nom.tam.util.RandomAccess;
import nom.tam.util.TableException;
import nom.tam.util.type.PrimitiveTypeHandler;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;

/**
Expand Down Expand Up @@ -141,6 +142,20 @@ public int[] getDimens() {
return this.dimens;
}

/**
* @return new instance of the array with space for the specified number
* of rows.
* @param nRow
* the number of rows to allocate the array for
*/
public Object newInstance(int nRow) {
return ArrayFuncs.newInstance(ArrayFuncs.getBaseClass(this.model), this.size * nRow);
}

public int rowLen() {
return this.size * PrimitiveTypeHandler.valueOf(this.base).size();
}

/**
* @return Is this a variable length column using longs? [Must have
* isVarying true too]
Expand Down Expand Up @@ -538,10 +553,12 @@ public int addRow(Object[] o) throws FitsException {
public void deleteColumns(int start, int len) throws FitsException {
ensureData();
try {
this.rowLen = this.table.deleteColumns(start, len);
this.table.deleteColumns(start, len);
// Need to get rid of the column level metadata.
for (int i = start + len - 1; i >= start; i -= 1) {
if (i >= 0 && i <= this.columnList.size()) {
ColumnDesc columnDesc = this.columnList.get(i);
this.rowLen -= columnDesc.rowLen();
this.columnList.remove(i);
}
}
Expand Down Expand Up @@ -1286,7 +1303,7 @@ private ColumnTable<SaveState> createTable() throws FitsException {
arrCol[i] = desc.column;
desc.column = null;
} else {
arrCol[i] = ArrayFuncs.newInstance(ArrayFuncs.getBaseClass(desc.model), desc.size * this.nRow);
arrCol[i] = desc.newInstance(this.nRow);
}
}
this.table = createColumnTable(arrCol, sizes);
Expand Down Expand Up @@ -1352,8 +1369,9 @@ private void ensureDataSilent() {
}

/**
* @return row from the file. * @throws FitsException if the operation
* failed
* @return row from the file.
* @throws FitsException
* if the operation failed
*/
private Object[] getFileRow(int row) throws FitsException {

Expand All @@ -1363,7 +1381,7 @@ private Object[] getFileRow(int row) throws FitsException {
Object[] data = new Object[this.columnList.size()];
for (int col = 0; col < data.length; col++) {
ColumnDesc colDesc = this.columnList.get(col);
data[col] = ArrayFuncs.newInstance(ArrayFuncs.getBaseClass(colDesc.model), colDesc.size);
data[col] = colDesc.newInstance(1);
}

try {
Expand Down Expand Up @@ -1565,7 +1583,7 @@ private int processCol(Header header, int col) throws FitsException {
}
if (colDesc.isVarying) {
dims = new int[]{
2
2
};
colBase = int.class;
bSize = FitsIO.BYTES_IN_INTEGER * 2;
Expand Down Expand Up @@ -1763,22 +1781,18 @@ int addFlattenedColumn(Object o, int[] dims, boolean allocated) throws FitsExcep
* FitsException if the operation failed
*/
void fillForColumn(Header h, int col, Cursor<String, HeaderCard> iter) throws FitsException {

String tform;
ColumnDesc colDesc = this.columnList.get(col);

String tform;
if (colDesc.isVarying) {
if (colDesc.isLongVary) {
tform = "1Q";
} else {
tform = "1P";
}

} else {
tform = "" + colDesc.size;

tform = Integer.toString(colDesc.size);
}

if (colDesc.base == int.class) {
tform += "J";
} else if (colDesc.base == short.class || colDesc.base == char.class) {
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/nom/tam/image/compression/hdu/CompressedTableHDU.java
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Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,10 @@ public class CompressedTableHDU extends BinaryTableHDU {
* the binary table to compress
* @param tileRows
* the number of rows that should be compressed per tile.
* @param columnCompressionAlgorithms
* the compression algorithms to use for the columns (optional
* default compression will be used if a column has no
* compression specified)
* @return the prepared compressed binaary table hdu.
* @throws FitsException
* if the binary table could not be used to create a compressed
Expand Down
24 changes: 2 additions & 22 deletions src/main/java/nom/tam/util/ColumnTable.java
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Original file line number Diff line number Diff line change
Expand Up @@ -280,9 +280,6 @@ public void read(ColumnTable<?> table, ArrayDataInput is, int index, int arrOffs
/** The number of rows */
private int nrow;

/** The size of a row in bytes */
private int rowSize;

/**
* The base type of each row (using the second character of the [x class
* names of the arrays.
Expand Down Expand Up @@ -346,8 +343,6 @@ public void addColumn(Object newColumn, int size) throws TableException {
String classname = newColumn.getClass().getName();
this.nrow = checkColumnConsistency(newColumn, classname, this.nrow, size);

this.rowSize += this.nrow * ArrayFuncs.getBaseLength(newColumn);

int ncol = this.arrays.length;

Object[] newArrays = new Object[ncol + 1];
Expand Down Expand Up @@ -434,9 +429,6 @@ public void addRow(Object[] row) throws TableException {
}
initializePointers();
this.nrow += 1;
if (rowSize == 0) {
this.rowSize = this.nrow * ArrayFuncs.getBaseLength(getRow(this.nrow - 1));
}
}
}

Expand Down Expand Up @@ -485,7 +477,6 @@ protected void checkArrayConsistency(Object[] newArrays, int[] newSizes) throws
}

this.nrow = ratio;
this.rowSize = newRowSize;
this.arrays = newArrays;
this.sizes = newSizes;
}
Expand Down Expand Up @@ -531,7 +522,6 @@ public ColumnTable<T> copy() throws TableException {
/**
* Delete a contiguous set of columns from the table.
*
* @return the rowlength
* @param start
* The first column (0-indexed) to be deleted.
* @param len
Expand All @@ -540,16 +530,13 @@ public ColumnTable<T> copy() throws TableException {
* if the request goes outside the boundaries of the table or if
* the length is negative.
*/
public int deleteColumns(int start, int len) throws TableException {
public void deleteColumns(int start, int len) throws TableException {
int ncol = this.arrays.length;
if (start < 0 || len < 0 || start + len > ncol) {
throw new TableException("Invalid request to delete columns start: " + start + " length:" + len + " for table with " + ncol + " columns.");
}
if (len == 0) {
return this.rowSize;
}
for (int i = start; i < start + len; i += 1) {
this.rowSize -= this.sizes[i] * ArrayFuncs.getBaseLength(this.arrays[i]);
return;
}
int ocol = ncol;
ncol -= len;
Expand Down Expand Up @@ -577,7 +564,6 @@ public int deleteColumns(int start, int len) throws TableException {
this.types = newTypes;

initializePointers();
return this.rowSize;
}

/**
Expand Down Expand Up @@ -905,9 +891,6 @@ private void setup(Object[] newArrays, int[] newSizes) throws TableException {
* if the write operation failed
*/
public void write(ArrayDataOutput os) throws IOException {
if (this.rowSize == 0) {
return;
}
int[] columnIndex = new int[MAX_COLUMN_INDEXES];
for (int row = 0; row < this.nrow; row += 1) {
Arrays.fill(columnIndex, 0);
Expand Down Expand Up @@ -939,9 +922,6 @@ public void write(ArrayDataOutput os) throws IOException {
* if the write operation failed
*/
public void write(ArrayDataOutput os, int rowStart, int rowEnd, int columnNr) throws IOException {
if (this.rowSize == 0) {
return;
}
int[] columnIndex = new int[MAX_COLUMN_INDEXES];
for (int row = 0; row < this.nrow; row += 1) {
if (row >= rowStart && row < rowEnd) {
Expand Down

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