FormatReaderTest (Bio-Formats API)

java.lang.Object
- loci.tests.testng.FormatReaderTest

```
public class FormatReaderTest
extends Object
```
TestNG tester for Bio-Formats file format readers. Details on failed tests are written to a log file, for easier processing. NB: loci.formats.ome and ome-xml.jar are required for some of the tests. To run tests: ant -Dtestng.directory="/path" -Dtestng.multiplier="1.0" test-all

Field Summary

Fields
Modifier and Type	Field and Description
`private Configuration`	`config`
`static ConfigurationTree`	`configTree` Configuration tree structure containing dataset metadata.
`private String`	`id`
`private boolean`	`inMemory`
`private static org.slf4j.Logger`	`LOGGER`
`private String`	`omexmlDir`
`private OMEXMLService`	`omexmlService`
`private BufferedImageReader`	`reader` Global shared jeader for use in all tests.
`private boolean`	`skip`
`private static String`	`SKIP_MESSAGE` Message to give for why a test was skipped.
`private static List<String>`	`skipFiles` List of files to skip.
`private float`	`timeMultiplier` Multiplier for use adjusting timing values.

Constructor Summary

Constructors
Constructor and Description

FormatReaderTest(String filename, float multiplier, boolean inMemory)

Constructors
Constructor and Description
`FormatReaderTest(String filename, float multiplier, boolean inMemory)`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`close()`
`String`	`getID()`
`private boolean`	`initFile()` Initializes the reader and configuration tree.
`private boolean`	`initFile(boolean removeDuplicateFiles)`
`private boolean`	`isAlmostEqual(Quantity q1, Quantity q2)`
`private static void`	`result(String testName, boolean success)` Outputs test result and generates appropriate assertion.
`private static void`	`result(String testName, boolean success, String msg)` Outputs test result with optional extra message and generates appropriate assertion.
`void`	`setup()`
`private void`	`setupReader()` Sets up the current IFormatReader.
`void`	`testBufferedImageDimensions()`
`void`	`testByteArrayDimensions()`
`void`	`testChannelNames()`
`void`	`testConsistentReader()`
`void`	`testDeltaT()`
`void`	`testDetectors()`
`void`	`testDimensionOrder()`
`void`	`testEmissionWavelengths()`
`void`	`testEqualOMEXML()`
`void`	`testExcitationWavelengths()`
`void`	`testExposureTimes()`
`void`	`testFalseColor()`
`void`	`testImageCount()`
`void`	`testImageDescriptions()`
`void`	`testImageNames()`
`void`	`testIndexed()`
`void`	`testIsInterleaved()`
`void`	`testIsThisType()`
`void`	`testIsThisTypeConsistent()`
`void`	`testLightSources()`
`void`	`testLittleEndian()`
`void`	`testMemoFileUsage()`
`void`	`testOMEXML()`
`void`	`testPerformance()`
`void`	`testPhysicalSizeX()`
`void`	`testPhysicalSizeY()`
`void`	`testPhysicalSizeZ()`
`void`	`testPixelsHashes()`
`void`	`testPixelType()`
`void`	`testPlanePositions()`
`void`	`testRequiredDirectories()`
`void`	`testRGB()`
`void`	`testSaneOMEXML()`
`void`	`testSaneUsedFiles()`
`void`	`testSeriesCount()`
`void`	`testSizeC()`
`void`	`testSizeT()`
`void`	`testSizeX()`
`void`	`testSizeY()`
`void`	`testSizeZ()`
`void`	`testSubimagePixelsHashes()`
`void`	`testThumbnailByteArrayDimensions()`
`void`	`testThumbnailImageDimensions()`
`void`	`testThumbSizeX()`
`void`	`testThumbSizeY()`
`void`	`testTileHeight()`
`void`	`testTileWidth()`
`void`	`testTimeIncrement()`
`void`	`testUnflattenedPixelsHashes()`
`void`	`testUnflattenedSubimagePixelsHashes()`
`void`	`testValidXML()`
`void`	`writeConfigFile()`
`void`	`writeXML()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- LOGGER
```
private static final org.slf4j.Logger LOGGER
```
- SKIP_MESSAGE
```
private static final String SKIP_MESSAGE
```
  Message to give for why a test was skipped.
  
  See Also:
  Constant Field Values
- configTree
```
public static ConfigurationTree configTree
```
  Configuration tree structure containing dataset metadata.
- skipFiles
```
private static List<String> skipFiles
```
  List of files to skip.
- reader
```
private BufferedImageReader reader
```
  Global shared jeader for use in all tests.
- id
```
private String id
```
- skip
```
private boolean skip
```
- config
```
private Configuration config
```
- omexmlDir
```
private String omexmlDir
```
- timeMultiplier
```
private float timeMultiplier
```
  Multiplier for use adjusting timing values. Slower machines take longer to complete the timing test, and thus need to set a higher (>1) multiplier to avoid triggering false timing test failures. Conversely, faster machines should set a lower (<1) multipler to ensure things finish as quickly as expected.
- inMemory
```
private boolean inMemory
```
- omexmlService
```
private OMEXMLService omexmlService
```

Constructor Detail

FormatReaderTest

public FormatReaderTest(String filename,
                float multiplier,
                boolean inMemory)

Method Detail

getID
```
public String getID()
```

setup

public void setup()
           throws IOException

Throws:: IOException

close

public void close()
           throws IOException

Throws:: IOException

testBufferedImageDimensions

public void testBufferedImageDimensions()

testByteArrayDimensions
```
public void testByteArrayDimensions()
```

testThumbnailImageDimensions

public void testThumbnailImageDimensions()

testThumbnailByteArrayDimensions

public void testThumbnailByteArrayDimensions()

testImageCount
```
public void testImageCount()
```

testTileWidth
```
public void testTileWidth()
```

testTileHeight
```
public void testTileHeight()
```

testOMEXML
```
public void testOMEXML()
```

testConsistentReader
```
public void testConsistentReader()
```

testSaneOMEXML
```
public void testSaneOMEXML()
```

testSeriesCount
```
public void testSeriesCount()
```

testSizeX
```
public void testSizeX()
```

testSizeY
```
public void testSizeY()
```

testSizeZ
```
public void testSizeZ()
```

testSizeC
```
public void testSizeC()
```

testSizeT
```
public void testSizeT()
```

testDimensionOrder
```
public void testDimensionOrder()
```

testIsInterleaved
```
public void testIsInterleaved()
```

testIndexed
```
public void testIndexed()
```

testFalseColor
```
public void testFalseColor()
```

testRGB
```
public void testRGB()
```

testThumbSizeX
```
public void testThumbSizeX()
```

testThumbSizeY
```
public void testThumbSizeY()
```

testPixelType
```
public void testPixelType()
```

testLittleEndian
```
public void testLittleEndian()
```

isAlmostEqual

private boolean isAlmostEqual(Quantity q1,
                    Quantity q2)

testPhysicalSizeX
```
public void testPhysicalSizeX()
```

testPhysicalSizeY
```
public void testPhysicalSizeY()
```

testPhysicalSizeZ
```
public void testPhysicalSizeZ()
```

testTimeIncrement
```
public void testTimeIncrement()
```

testLightSources
```
public void testLightSources()
```

testChannelNames
```
public void testChannelNames()
```

testExposureTimes
```
public void testExposureTimes()
```

testDeltaT
```
public void testDeltaT()
```

testPlanePositions
```
public void testPlanePositions()
```

testEmissionWavelengths
```
public void testEmissionWavelengths()
```

testExcitationWavelengths

public void testExcitationWavelengths()

testDetectors
```
public void testDetectors()
```

testImageNames
```
public void testImageNames()
```

testImageDescriptions
```
public void testImageDescriptions()
```

testEqualOMEXML
```
public void testEqualOMEXML()
```

testPerformance
```
public void testPerformance()
```

testRequiredDirectories
```
public void testRequiredDirectories()
```

testSaneUsedFiles
```
public void testSaneUsedFiles()
```

testValidXML
```
public void testValidXML()
```

testUnflattenedPixelsHashes

public void testUnflattenedPixelsHashes()

testPixelsHashes
```
public void testPixelsHashes()
```

testUnflattenedSubimagePixelsHashes

public void testUnflattenedSubimagePixelsHashes()

testSubimagePixelsHashes

public void testSubimagePixelsHashes()

testIsThisTypeConsistent

public void testIsThisTypeConsistent()

testIsThisType
```
public void testIsThisType()
```

testMemoFileUsage
```
public void testMemoFileUsage()
```

writeConfigFile
```
public void writeConfigFile()
```

writeXML
```
public void writeXML()
```

setupReader
```
private void setupReader()
```
Sets up the current IFormatReader.

initFile
```
private boolean initFile()
```
Initializes the reader and configuration tree.

initFile

private boolean initFile(boolean removeDuplicateFiles)

result

private static void result(String testName,
          boolean success)

Outputs test result and generates appropriate assertion.

result

private static void result(String testName,
          boolean success,
          String msg)

Outputs test result with optional extra message and generates appropriate assertion.

Class FormatReaderTest

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LOGGER

SKIP_MESSAGE

configTree

skipFiles

reader

id

skip

config

omexmlDir

timeMultiplier

inMemory

omexmlService

Constructor Detail

FormatReaderTest

Method Detail

getID

setup

close

testBufferedImageDimensions

testByteArrayDimensions

testThumbnailImageDimensions

testThumbnailByteArrayDimensions

testImageCount

testTileWidth

testTileHeight

testOMEXML

testConsistentReader

testSaneOMEXML

testSeriesCount

testSizeX

testSizeY

testSizeZ

testSizeC

testSizeT

testDimensionOrder

testIsInterleaved

testIndexed

testFalseColor

testRGB

testThumbSizeX

testThumbSizeY

testPixelType

testLittleEndian

isAlmostEqual

testPhysicalSizeX

testPhysicalSizeY

testPhysicalSizeZ

testTimeIncrement

testLightSources

testChannelNames

testExposureTimes

testDeltaT

testPlanePositions

testEmissionWavelengths

testExcitationWavelengths

testDetectors

testImageNames

testImageDescriptions

testEqualOMEXML

testPerformance

testRequiredDirectories

testSaneUsedFiles

testValidXML

testUnflattenedPixelsHashes

testPixelsHashes

testUnflattenedSubimagePixelsHashes

testSubimagePixelsHashes

testIsThisTypeConsistent

testIsThisType

testMemoFileUsage

writeConfigFile

writeXML

setupReader

initFile