private void testIsNotRemovedAndRetainsValue(
String description,
AttributeTag creatorTag,
String creator,
Attribute privateAttribute,
String expectValue)
throws DicomException {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(creatorTag);
a.addValue(creator);
list.put(a);
}
list.put(privateAttribute);
AttributeTag privateTag = privateAttribute.getTag();
list.removeUnsafePrivateAttributes();
assertTrue("Checking Creator is not removed", list.get(creatorTag) != null);
assertEquals(
"Checking Creator retains value",
creator,
Attribute.getDelimitedStringValuesOrEmptyString(list, creatorTag));
assertTrue("Checking " + description + " is not removed", list.get(privateTag) != null);
assertEquals(
"Checking " + description + " retains value",
expectValue,
Attribute.getDelimitedStringValuesOrEmptyString(list, privateTag));
}
public void readByte2Short() throws Exception {
Variable t2 = null;
assert (null != (t2 = ncfileRead.findVariable("t2")));
assert (t2.getDataType() == DataType.BYTE);
Attribute att = t2.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2 == att.getNumericValue().doubleValue());
assert (DataType.SHORT == att.getDataType());
assert (null != (t2 = dsRead.findVariable("t2")));
assert t2 instanceof VariableEnhanced;
VariableDS vs = (VariableDS) t2;
assert (vs.getDataType() == DataType.SHORT) : vs.getDataType();
assert (!vs.hasMissing());
Array A = vs.read();
assert (A.getElementType() == short.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getShort(ima.set(i, j)) == (2 * (i * 10 + j) + 77));
}
}
System.out.println("**************TestStandardVar readByte2Short");
}
public void TestSafePrivateGEPACSRelated_CreatorFromList() throws Exception {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0903, 0x0010));
a.addValue("GEIIS PACS");
list.put(a);
}
assertTrue(
"Checking Reject Image Flag is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0903, 0x1010), list));
}
public void TestSafePrivatePhilipsPETRelated_ScaleFactors_FromList() throws Exception {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x7053, 0x0010));
a.addValue("Philips PET Private Group");
list.put(a);
}
assertTrue(
"Checking SUV Factor is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x7053, 0x1000), list));
assertTrue(
"Checking Activity Concentration Factor is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x7053, 0x1009), list));
}
public void readDouble() throws Exception {
Variable t1 = null;
assert (null != (t1 = ncfileRead.findVariable("t1")));
assert (t1.getDataType() == DataType.DOUBLE);
Attribute att = t1.findAttribute(CDM.SCALE_FACTOR);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
assert (2.0 == att.getNumericValue().doubleValue());
assert (DataType.DOUBLE == att.getDataType());
// read
Array A = t1.read();
int i, j;
Index ima = A.getIndex();
int[] shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (double) (i * 10.0 + j));
}
}
assert (null != (t1 = dsRead.findVariable("t1")));
assert t1 instanceof VariableEnhanced;
VariableEnhanced dsVar = (VariableEnhanced) t1;
assert (dsVar.getDataType() == DataType.DOUBLE);
A = dsVar.read();
ima = A.getIndex();
shape = A.getShape();
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getDouble(ima.set(i, j)) == (2.0 * (i * 10.0 + j) + 77.0));
}
}
assert (null == t1.findAttribute(CDM.SCALE_FACTOR));
assert (null == t1.findAttribute("add_offset"));
System.out.println("**************TestStandardVar ReadDouble");
}
public void TestSafePrivateGEMRRelated_AddedToList() throws Exception {
{
String value = "MySequence";
Attribute a = new LongStringAttribute(new AttributeTag(0x0019, 0x109E));
a.addValue(value);
testIsNotRemovedAndRetainsValue(
"Internal Pulse Sequence Name",
new AttributeTag(0x0019, 0x0010),
"GEMS_ACQU_01",
a,
value);
}
{
String value = "35";
Attribute a = new SignedLongAttribute(new AttributeTag(0x0025, 0x1007));
a.addValue(value);
testIsNotRemovedAndRetainsValue(
"Images In Series", new AttributeTag(0x0025, 0x0010), "GEMS_SERS_01", a, value);
}
{
String expectValue = "0\\0\\0\\2";
Attribute a = new DecimalStringAttribute(new AttributeTag(0x0043, 0x106F));
a.addValue("0");
a.addValue("0");
a.addValue("0");
a.addValue("2");
testIsNotRemovedAndRetainsValue(
"Scanner Table Entry + Gradient Coil Selected",
new AttributeTag(0x0043, 0x0010),
"GEMS_PARM_01",
a,
expectValue);
}
}
public void TestSafePrivateGEPACSRelated_AddedToList() throws Exception {
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0903, 0x0010));
a.addValue("GEIIS PACS");
list.put(a);
}
{
Attribute a = new UnsignedShortAttribute(new AttributeTag(0x0903, 0x1010));
a.addValue(0);
list.put(a);
}
list.removeUnsafePrivateAttributes();
assertTrue(
"Checking Creator is not removed", list.get(new AttributeTag(0x0903, 0x0010)) != null);
assertTrue(
"Checking Reject Image Flag is not removed",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0903, 0x1010), list));
}
public void TestSafePrivateGEMRRelated_CreatorFromList() throws Exception {
{
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0019, 0x0010));
a.addValue("GEMS_ACQU_01");
list.put(a);
}
assertTrue(
"Internal Pulse Sequence Name is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0019, 0x109E), list));
}
{
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0025, 0x0010));
a.addValue("GEMS_SERS_01");
list.put(a);
}
assertTrue(
"Images In Series is safe",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0025, 0x1007), list));
}
{
AttributeList list = new AttributeList();
{
Attribute a = new LongStringAttribute(new AttributeTag(0x0043, 0x0010));
a.addValue("GEMS_PARM_01");
list.put(a);
}
assertTrue(
"Scanner Table Entry + Gradient Coil Selected",
ClinicalTrialsAttributes.isSafePrivateAttribute(new AttributeTag(0x0043, 0x106F), list));
}
}
public void readShortMissing() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t4")));
assert (v.getDataType() == DataType.SHORT);
// default use of missing_value
assert (null != (v = dsRead.findVariable("t4")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.SHORT);
Attribute att = vs.findAttribute(CDM.MISSING_VALUE);
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("missing_value = " + att.getNumericValue().shortValue());
assert (((short) -9999) == att.getNumericValue().shortValue());
assert (DataType.SHORT == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasMissingValue());
assert (vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
Array A = vs.read();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
// turn off missing data
vs.setMissingDataIsMissing(false);
assert (vs.getDataType() == DataType.SHORT);
assert (!vs.hasMissing());
assert (vs.hasMissingValue());
assert (!vs.isMissing((double) ((short) -9999)));
assert (vs.isMissingValue((double) ((short) -9999)));
vs.setMissingDataIsMissing(true);
assert (vs.hasMissing());
assert (vs.isMissing((double) ((short) -9999)));
System.out.println("**************TestStandardVar Read readShortMissing");
}
public void testCoordVar(NetcdfFile ncfile) {
Variable lat = ncfile.findVariable("lat");
assert null != lat;
assert lat.getShortName().equals("lat");
assert lat.getRank() == 1;
assert lat.getSize() == 3;
assert lat.getShape()[0] == 3;
assert lat.getDataType() == DataType.FLOAT;
assert !lat.isUnlimited();
assert lat.getDimension(0).equals(ncfile.findDimension("lat"));
Attribute att = lat.findAttribute("units");
assert null != att;
assert !att.isArray();
assert att.isString();
assert att.getDataType() == DataType.STRING;
assert att.getStringValue().equals("degrees_north");
assert att.getNumericValue() == null;
assert att.getNumericValue(3) == null;
try {
Array data = lat.read();
assert data.getRank() == 1;
assert data.getSize() == 3;
assert data.getShape()[0] == 3;
assert data.getElementType() == float.class;
IndexIterator dataI = data.getIndexIterator();
assert TestUtils.close(dataI.getDoubleNext(), 41.0);
assert TestUtils.close(dataI.getDoubleNext(), 40.0);
assert TestUtils.close(dataI.getDoubleNext(), 39.0);
} catch (IOException io) {
}
}
public void readByte() throws Exception {
Variable v = null;
assert (null != (v = ncfileRead.findVariable("t3")));
assert (v.getDataType() == DataType.BYTE);
assert (null != (v = dsRead.findVariable("t3")));
assert v instanceof VariableEnhanced;
assert v instanceof VariableDS;
VariableDS vs = (VariableDS) v;
assert (vs.getDataType() == DataType.BYTE);
Attribute att = vs.findAttribute("_FillValue");
assert (null != att);
assert (!att.isArray());
assert (1 == att.getLength());
System.out.println("_FillValue = " + att.getNumericValue().byteValue());
assert (((byte) 255) == att.getNumericValue().byteValue());
assert (DataType.BYTE == att.getDataType());
assert (vs.hasMissing());
assert (vs.hasFillValue());
assert (vs.isMissing((double) ((byte) 255)));
assert (vs.isFillValue((double) ((byte) 255)));
Array A = vs.read();
assert (A.getElementType() == byte.class) : A.getElementType();
Index ima = A.getIndex();
int[] shape = A.getShape();
int i, j;
for (i = 0; i < shape[0]; i++) {
for (j = 0; j < shape[1]; j++) {
assert (A.getFloat(ima.set(i, j)) == (i * 10 + j));
}
}
System.out.println("**************TestStandardVar ReadByte");
}
