public class CellSensReader extends FormatReader
Modifier and Type | Class and Description |
---|---|
(package private) class |
CellSensReader.Pyramid |
(package private) class |
CellSensReader.TileCoordinate |
Modifier and Type | Field and Description |
---|---|
private static int |
ACCUMULATION |
private static int |
ACCUMULATION_MODE |
private static int |
ACQUISITION_PROPERTIES |
private static int |
ACTIVE_CHANNEL |
private static int |
ACTIVE_LAYER_INDEX_VECTOR |
private static int |
ACTIVE_LAYER_VECTOR |
private static int |
ACTIVE_STACK_DIMENSION |
private static int |
ANDOR_SHIFT_SPEED |
private static int |
AUTOEXPOSURE |
private static int |
AVERAGING |
private java.util.HashMap<java.lang.Integer,byte[]> |
backgroundColor |
private static int |
BASELINE_OFFSET_CLAMP |
private static int |
BGR |
private static int |
BIT_DEPTH |
private static int |
BLUE_GAIN |
private static int |
BLUE_OFFSET |
private static int |
BMP |
private static int |
BOOLEAN |
private static int |
BRIGHTNESS |
private static int |
C |
private static int |
CAMERA_GAIN |
private static int |
CAMERA_GAMMA |
private static int |
CAMERA_OFFSET |
private static int |
CANVAS_COLOR_1 |
private static int |
CANVAS_COLOR_2 |
private static int |
CCD_SENSITIVITY |
private static int |
CHAINED_LAYERS |
private static int |
CHANNEL_CONTRAST_BRIGHTNESS |
private static int |
CHANNEL_DIM |
private static int |
CHANNEL_GAMMA_CORRECTION |
private static int |
CHANNEL_INFO_PROPERTIES |
private static int |
CHANNEL_NAME |
private static int |
CHANNEL_OVERFLOW |
private static int |
CHANNEL_PROPERTIES |
private static int |
CHANNEL_TRANSPARENCY_VALUE |
private static int |
CHANNEL_VISIBLE |
private int |
channelCount |
private static int |
CHAR |
private static int |
CLIPPING |
private static int |
CLIPPING_STATE |
private static int |
COARSE_FRAME_IFD |
private static int |
COARSE_PYRAMID_LEVEL |
private static int |
COLLECTION_VOLUME |
private static int |
COLOR_SPACE |
private static int |
COLORSPACE |
private java.util.ArrayList<java.lang.Integer> |
cols |
private static int |
COMPLEX |
private java.util.ArrayList<java.lang.Integer> |
compressionType |
private static int |
CONTRAST |
private static int |
CONTRAST_BRIGHTNESS |
private static int |
CONTRAST_TARGET |
private static int |
COOLING_ON |
private static int |
CREATION_TIME |
private static int |
CUSTOM_GRAYSCALE |
private static int |
DATE |
private static int |
DEFAULT_BACKGROUND_COLOR |
private static int |
DEFAULT_IMAGE |
private static int |
DEFAULT_SAMPLE_IFD |
private static int |
DEVICE_ID |
private static int |
DEVICE_MANUFACTURER |
private static int |
DEVICE_NAME |
private static int |
DEVICE_SUBTYPE |
private static int |
DIM_INDEX_1 |
private static int |
DIM_INDEX_2 |
private static int |
DIMENSION_DESCRIPTION_VOLUME |
private static int |
DIMENSION_INCREMENT_ID |
private static int |
DIMENSION_MEANING |
private static int |
DIMENSION_NAME |
private static int |
DIMENSION_SIZE |
private static int |
DIMENSION_START_ID |
private static int |
DIMENSION_VALUE_ID |
private int |
dimensionTag |
private static int |
DISPLAY_COLOR |
private static int |
DISPLAY_CONTRAST_BRIGHTNESS |
private static int |
DISPLAY_GAMMA_CORRECTION |
private static int |
DISPLAY_LIMITS |
private static int |
DISPLAY_LUT |
private static int |
DISPLAY_MAPPING_VOLUME |
private static int |
DISPLAY_PROCESSOR_TYPE |
private static int |
DISPLAY_STACK_ID |
private static int |
DISPLAY_STACK_INDEX |
private static int |
DISPLAY_VISIBLE |
private static int |
DISPLAYED_LUT_ID |
private static int |
DOCUMENT_AUTHOR |
private static int |
DOCUMENT_COMPANY |
private static int |
DOCUMENT_CREATOR_BUILD_NUMBER |
private static int |
DOCUMENT_CREATOR_MAJOR_VERSION |
private static int |
DOCUMENT_CREATOR_MINOR_VERSION |
private static int |
DOCUMENT_CREATOR_NAME |
private static int |
DOCUMENT_CREATOR_PACKAGE |
private static int |
DOCUMENT_CREATOR_SUB_VERSION |
private static int |
DOCUMENT_NAME |
private static int |
DOCUMENT_NOTE |
private static int |
DOCUMENT_PRODUCT |
private static int |
DOCUMENT_PRODUCT_NAME |
private static int |
DOCUMENT_PRODUCT_VERSION |
private static int |
DOCUMENT_PROPERTIES |
private static int |
DOCUMENT_THUMB |
private static int |
DOCUMENT_TIME |
private static int |
DOCUMENT_TYPE_HINT |
private static int |
DOUBLE |
private static int |
DOUBLE_2 |
private static int |
DOUBLE_2_2 |
private static int |
DOUBLE_3 |
private static int |
DOUBLE_3_3 |
private static int |
DOUBLE_4 |
private static int |
DOUBLE_4_4 |
private static int |
DOUBLE_ARRAY_2 |
private static int |
DOUBLE_ARRAY_3 |
private static int |
DOUBLE_INTERVAL |
private static int |
DOUBLE_RECT |
private static int |
DP80_FRAME_CENTERING |
private static int |
DWORD |
private static int |
DYNAMIC_PROPERTIES |
private static int |
EFI_HEIGHT_MAP |
private static int |
EFI_SHARPNESS_MAP |
private static int |
EFI_STACK |
private static int |
EFI_TEXTURE_MAP |
private static int |
EM_GAIN |
private static int |
ENHANCED_DYNAMIC_RANGE |
private boolean |
expectETS |
private static int |
EXPOSURE_METERING_MODE |
private static int |
EXPOSURE_TIME |
private static int |
EXTERNAL_DATA_VOLUME |
private static int |
EXTERNAL_FILE_PROPERTIES |
private static int |
EXTRA_SAMPLES |
private static int |
EXTRA_SAMPLES_PROPERTIES |
static boolean |
FAIL_ON_MISSING_DEFAULT |
static java.lang.String |
FAIL_ON_MISSING_KEY |
private static int |
FAN_SPEED |
private static int |
FIELD_TYPE |
private java.util.HashMap<java.lang.Integer,java.lang.String> |
fileMap |
private static int |
FLOAT |
private static int |
FOCUS_IMAGE |
private boolean |
foundChannelTag |
private static int |
FRAME_ORIGIN |
private static int |
FRAME_PROPERTIES |
private static int |
FRAME_SCALE |
private static int |
FRAME_SIZE |
private static int |
FRAME_TRANSFER |
private static int |
FRAME_TYPE |
private static int |
GAIN_UNIT |
private static int |
GAMMA_CORRECTION |
private static int |
GRADIENT_LUT |
private static int |
GREEN_GAIN |
private static int |
GREEN_OFFSET |
private static int |
HAS_EXTERNAL_FILE |
private static int |
HDRI_EXPOSURE_RANGE |
private static int |
HDRI_FRAMES |
private static int |
HDRI_MAP_MODE |
private static int |
HDRI_ON |
private static int |
HIDDEN_LAYER |
private static int |
HOT_PIXEL_CORRECTION |
private static int |
ICC_ENABLED |
private IFDList |
ifds |
private static int |
IMAGE_BOUNDARY |
private static int |
IMAGE_COLLECTION_PROPERTIES |
private static int |
IMAGE_FRAME_VOLUME |
private boolean |
inDimensionProperties |
private static int |
INT |
private static int |
INT_2 |
private static int |
INT_3 |
private static int |
INT_4 |
private static int |
INT_ARRAY_2 |
private static int |
INT_ARRAY_3 |
private static int |
INT_ARRAY_4 |
private static int |
INT_ARRAY_5 |
private static int |
INT_INTERVAL |
private static int |
INT_RECT |
private static int |
IS_TRANSMISSION |
private static int |
ISO_SENSITIVITY |
private boolean |
jpeg |
private static int |
JPEG |
private static int |
JPEG_2000 |
private static int |
JPEG_LOSSLESS |
private static int |
LAMBDA |
private static int |
LAMBDA_INCREMENT |
private static int |
LAMBDA_START |
private static int |
LAMBDA_VALUE |
private static int |
LAYER_INFO_PROPERTIES |
private static int |
LAYER_SELECTION |
private static int |
LAYER_SELECTION_INDEX |
private static int |
LAYER_XY_FIXED |
private static int |
LIVE_OVERFLOW |
private static int |
LONG |
private static int |
MACRO_IMAGE |
private static int |
MAGNIFICATION |
private static int |
MEM_MODEL |
private int |
metadataIndex |
private static int |
MIRROR_H |
private static int |
MIRROR_V |
private static int |
MULTIDIM_IMAGE_VOLUME |
private static int |
MULTIDIM_STACK_PROPERTIES |
private java.util.ArrayList<java.lang.Integer> |
nDimensions |
private static int |
NEW_MDIM_VOLUME_HEADER |
private static int |
NEW_VOLUME_HEADER |
private static int |
NOISE_REDUCTION |
private static int |
NUMERICAL_APERTURE |
private static int |
OBJECTIVE_MAG |
private static int |
OBJECTIVE_NAME |
private static int |
OBJECTIVE_TYPE |
private static int |
OPTICAL_PATH |
private static int |
ORIGINAL_FRAME_RATE |
private static int |
OVERVIEW_IMAGE |
private TiffParser |
parser |
private static int |
PHASE |
private static int |
PHOTOBLEACHING |
private static int |
PHOTON_IMAGING_MODE |
private static int |
PIXEL_CLOCK |
private static int |
PIXEL_INFO_TYPE |
private static int |
PLANE_ORIGIN_RWC |
private static int |
PLANE_SCALE_RWC |
private static int |
PLANE_UNIT |
private static int |
PNG |
private static int |
PREAMP_GAIN_VALUE |
private int |
previousTag |
private static int |
PROPERTY_SET_VOLUME |
private java.util.ArrayList<CellSensReader.Pyramid> |
pyramids |
private static int |
RAW |
private static int |
RED_GAIN |
private static int |
RED_OFFSET |
private static int |
REFRACTIVE_INDEX |
private static int |
RENDER_OPERATION_ID |
private static int |
RGB |
private java.util.ArrayList<java.lang.Integer> |
rows |
private static int |
RWC_FRAME_ORIGIN |
private static int |
RWC_FRAME_SCALE |
private static int |
RWC_FRAME_UNIT |
private static int |
SAMPLE_FLAGS_LIST |
private static int |
SAMPLE_ID_LIST |
private static int |
SAMPLE_MASK |
private static int |
SATURATION |
private static int |
SELECTED_CHANNELS |
private static int |
SELECTED_FRAMES |
private static int |
SERIALIZED_MASK |
private static int |
SHADING_MUL |
private static int |
SHADING_SUB |
private static int |
SHARPNESS |
private static int |
SHORT |
private static int |
SIGNAL_OUTPUT |
private static int |
SLIDE_INFO |
private static int |
SLIDE_NAME |
private static int |
SLIDE_PREPARATION |
private static int |
SLIDE_PROPERTIES |
private static int |
SLIDE_SPECIMEN |
private static int |
SLIDE_STAINING |
private static int |
SLIDE_TISSUE |
private static int |
SPURIOUS_NOISE_REMOVAL |
private static int |
STACK_DISPLAY_LUT |
private static int |
STACK_NAME |
private static int |
STACK_TYPE |
private static int |
T |
private static int |
TCHAR |
private static int |
TEMPERATURE_TARGET |
private static int |
THIRD_ID |
private static int |
TIFF_IFD |
private static int |
TILE_ORIGIN |
private static int |
TILE_SYSTEM |
private java.util.ArrayList<java.util.ArrayList<CellSensReader.TileCoordinate>> |
tileMap |
private java.util.ArrayList<java.lang.Long[]> |
tileOffsets |
private java.util.ArrayList<java.lang.Integer> |
tileX |
private java.util.ArrayList<java.lang.Integer> |
tileY |
private static int |
TIME_INCREMENT |
private static int |
TIME_START |
private static int |
TIME_VALUE |
private static int |
TIMESTAMP |
private static int |
TRANSPARENCY_ID |
private static int |
TRANSPARENCY_VALUE |
private static int |
UCHAR |
private static int |
UINT |
private static int |
ULONG |
private static int |
UNICODE_TCHAR |
private static int |
UNKNOWN |
private static int |
UNKNOWN_BLOBS_VOLUME |
private static int |
USE_ORIGINAL_FRAME_RATE |
private java.lang.String[] |
usedFiles |
private static int |
USHORT |
private static int |
VALUE |
private static int |
VCLOCK_AMPLITUDE |
private static int |
VECTOR_DATA |
private static int |
VECTOR_LAYER_VOLUME |
private static int |
VERSION_NUMBER |
private static int |
VOLUME_INDEX |
private static int |
WB_MODE |
private static int |
WB_PRESET_ID |
private static int |
WB_PRESET_NAME |
private static int |
WIDER |
private static int |
WIDER_ENABLED |
private static int |
WORKING_DISTANCE |
private static int |
X_BINNING |
private static int |
Y_BINNING |
private static int |
Y_DIMENSION_UNIT |
private static int |
Y_PLANE_DIMENSION_UNIT |
private static int |
Z |
private static int |
Z_INCREMENT |
private static int |
Z_START |
private static int |
Z_VALUE |
private int |
zCount |
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
CellSensReader()
Constructs a new cellSens reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
private int |
convertPixelType(int pixelType) |
private byte[] |
decodeTile(int no,
int row,
int col) |
boolean |
failOnMissingETS() |
int |
fileGroupOption(java.lang.String id)
Returns an indication of whether the files in a multi-file dataset can
be handled individually.
|
private java.lang.String |
getDeviceSubtype(java.lang.String type) |
private int |
getIFDIndex() |
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
|
int |
getOptimalTileWidth()
Returns the optimal sub-image width for use with openBytes.
|
java.lang.String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
private java.lang.String |
getStackType(java.lang.String type) |
private java.lang.String |
getTagName(int tag) |
private int |
getTileSize() |
private java.lang.String |
getVolumeName(int tag) |
protected void |
initFile(java.lang.String id)
Initializes the given file (parsing header information, etc.).
|
boolean |
isSingleFile(java.lang.String id)
Returns true if the named file is expected to be the only
file in the dataset.
|
byte[] |
openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane
into a pre-allocated byte array.
|
byte[] |
openThumbBytes(int no)
Obtains a thumbnail for the specified image plane from the current file,
as a byte array.
|
private void |
parseETSFile(loci.common.RandomAccessInputStream etsFile,
java.lang.String file,
int s) |
private void |
readTags(loci.common.RandomAccessInputStream vsi,
boolean populateMetadata,
java.lang.String tagPrefix) |
void |
reopenFile()
Reopen any files that were closed, and which are expected to be open
while the reader is open.
|
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions
public static final java.lang.String FAIL_ON_MISSING_KEY
public static final boolean FAIL_ON_MISSING_DEFAULT
private static final int RAW
private static final int JPEG
private static final int JPEG_2000
private static final int JPEG_LOSSLESS
private static final int PNG
private static final int BMP
private static final int CHAR
private static final int UCHAR
private static final int SHORT
private static final int USHORT
private static final int INT
private static final int UINT
private static final int LONG
private static final int ULONG
private static final int FLOAT
private static final int DOUBLE
private static final int COMPLEX
private static final int BOOLEAN
private static final int TCHAR
private static final int DWORD
private static final int TIMESTAMP
private static final int DATE
private static final int INT_2
private static final int INT_3
private static final int INT_4
private static final int INT_RECT
private static final int DOUBLE_2
private static final int DOUBLE_3
private static final int DOUBLE_4
private static final int DOUBLE_RECT
private static final int DOUBLE_2_2
private static final int DOUBLE_3_3
private static final int DOUBLE_4_4
private static final int INT_INTERVAL
private static final int DOUBLE_INTERVAL
private static final int RGB
private static final int BGR
private static final int FIELD_TYPE
private static final int MEM_MODEL
private static final int COLOR_SPACE
private static final int INT_ARRAY_2
private static final int INT_ARRAY_3
private static final int INT_ARRAY_4
private static final int INT_ARRAY_5
private static final int DOUBLE_ARRAY_2
private static final int DOUBLE_ARRAY_3
private static final int UNICODE_TCHAR
private static final int DIM_INDEX_1
private static final int DIM_INDEX_2
private static final int VOLUME_INDEX
private static final int PIXEL_INFO_TYPE
private static final int NEW_VOLUME_HEADER
private static final int PROPERTY_SET_VOLUME
private static final int NEW_MDIM_VOLUME_HEADER
private static final int TIFF_IFD
private static final int VECTOR_DATA
private static final int COLLECTION_VOLUME
private static final int MULTIDIM_IMAGE_VOLUME
private static final int IMAGE_FRAME_VOLUME
private static final int DIMENSION_SIZE
private static final int IMAGE_COLLECTION_PROPERTIES
private static final int MULTIDIM_STACK_PROPERTIES
private static final int FRAME_PROPERTIES
private static final int DIMENSION_DESCRIPTION_VOLUME
private static final int CHANNEL_PROPERTIES
private static final int DISPLAY_MAPPING_VOLUME
private static final int LAYER_INFO_PROPERTIES
private static final int CHANNEL_INFO_PROPERTIES
private static final int DEFAULT_SAMPLE_IFD
private static final int VECTOR_LAYER_VOLUME
private static final int EXTERNAL_FILE_PROPERTIES
private static final int COARSE_FRAME_IFD
private static final int COARSE_PYRAMID_LEVEL
private static final int SERIALIZED_MASK
private static final int UNKNOWN_BLOBS_VOLUME
private static final int SAMPLE_ID_LIST
private static final int EXTRA_SAMPLES
private static final int EXTRA_SAMPLES_PROPERTIES
private static final int SAMPLE_FLAGS_LIST
private static final int FRAME_TYPE
private static final int DEFAULT_BACKGROUND_COLOR
private static final int VERSION_NUMBER
private static final int DOCUMENT_PROPERTIES
private static final int DOCUMENT_NAME
private static final int DOCUMENT_NOTE
private static final int DOCUMENT_TIME
private static final int DOCUMENT_AUTHOR
private static final int DOCUMENT_COMPANY
private static final int DOCUMENT_CREATOR_NAME
private static final int DOCUMENT_CREATOR_MAJOR_VERSION
private static final int DOCUMENT_CREATOR_MINOR_VERSION
private static final int DOCUMENT_CREATOR_SUB_VERSION
private static final int DOCUMENT_CREATOR_BUILD_NUMBER
private static final int DOCUMENT_CREATOR_PACKAGE
private static final int DOCUMENT_PRODUCT
private static final int DOCUMENT_PRODUCT_NAME
private static final int DOCUMENT_PRODUCT_VERSION
private static final int DOCUMENT_TYPE_HINT
private static final int DOCUMENT_THUMB
private static final int SLIDE_PROPERTIES
private static final int SLIDE_SPECIMEN
private static final int SLIDE_TISSUE
private static final int SLIDE_PREPARATION
private static final int SLIDE_STAINING
private static final int SLIDE_INFO
private static final int SLIDE_NAME
private static final int DYNAMIC_PROPERTIES
private static final int MAGNIFICATION
private static final int IMAGE_BOUNDARY
private static final int TILE_SYSTEM
private static final int HAS_EXTERNAL_FILE
private static final int EXTERNAL_DATA_VOLUME
private static final int TILE_ORIGIN
private static final int EXPOSURE_TIME
private static final int CAMERA_GAIN
private static final int CAMERA_OFFSET
private static final int CAMERA_GAMMA
private static final int SHARPNESS
private static final int RED_GAIN
private static final int GREEN_GAIN
private static final int BLUE_GAIN
private static final int RED_OFFSET
private static final int GREEN_OFFSET
private static final int BLUE_OFFSET
private static final int SHADING_SUB
private static final int SHADING_MUL
private static final int X_BINNING
private static final int Y_BINNING
private static final int CLIPPING
private static final int MIRROR_H
private static final int MIRROR_V
private static final int CLIPPING_STATE
private static final int ICC_ENABLED
private static final int BRIGHTNESS
private static final int CONTRAST
private static final int CONTRAST_TARGET
private static final int ACCUMULATION
private static final int AVERAGING
private static final int ISO_SENSITIVITY
private static final int ACCUMULATION_MODE
private static final int AUTOEXPOSURE
private static final int EXPOSURE_METERING_MODE
private static final int FRAME_SIZE
private static final int BIT_DEPTH
private static final int HDRI_ON
private static final int HDRI_FRAMES
private static final int HDRI_EXPOSURE_RANGE
private static final int HDRI_MAP_MODE
private static final int CUSTOM_GRAYSCALE
private static final int SATURATION
private static final int WB_PRESET_ID
private static final int WB_PRESET_NAME
private static final int WB_MODE
private static final int CCD_SENSITIVITY
private static final int ENHANCED_DYNAMIC_RANGE
private static final int PIXEL_CLOCK
private static final int COLORSPACE
private static final int COOLING_ON
private static final int FAN_SPEED
private static final int TEMPERATURE_TARGET
private static final int GAIN_UNIT
private static final int EM_GAIN
private static final int PHOTON_IMAGING_MODE
private static final int FRAME_TRANSFER
private static final int ANDOR_SHIFT_SPEED
private static final int VCLOCK_AMPLITUDE
private static final int SPURIOUS_NOISE_REMOVAL
private static final int SIGNAL_OUTPUT
private static final int BASELINE_OFFSET_CLAMP
private static final int DP80_FRAME_CENTERING
private static final int HOT_PIXEL_CORRECTION
private static final int NOISE_REDUCTION
private static final int WIDER
private static final int PHOTOBLEACHING
private static final int PREAMP_GAIN_VALUE
private static final int WIDER_ENABLED
private static final int Z_START
private static final int Z_INCREMENT
private static final int Z_VALUE
private static final int TIME_START
private static final int TIME_INCREMENT
private static final int TIME_VALUE
private static final int LAMBDA_START
private static final int LAMBDA_INCREMENT
private static final int LAMBDA_VALUE
private static final int DIMENSION_NAME
private static final int DIMENSION_MEANING
private static final int DIMENSION_START_ID
private static final int DIMENSION_INCREMENT_ID
private static final int DIMENSION_VALUE_ID
private static final int CHANNEL_NAME
private static final int Z
private static final int T
private static final int LAMBDA
private static final int C
private static final int UNKNOWN
private static final int PHASE
private static final int DISPLAY_LIMITS
private static final int STACK_DISPLAY_LUT
private static final int GAMMA_CORRECTION
private static final int FRAME_ORIGIN
private static final int FRAME_SCALE
private static final int DISPLAY_COLOR
private static final int CREATION_TIME
private static final int RWC_FRAME_ORIGIN
private static final int RWC_FRAME_SCALE
private static final int RWC_FRAME_UNIT
private static final int STACK_NAME
private static final int CHANNEL_DIM
private static final int OPTICAL_PATH
private static final int STACK_TYPE
private static final int LIVE_OVERFLOW
private static final int IS_TRANSMISSION
private static final int CONTRAST_BRIGHTNESS
private static final int ACQUISITION_PROPERTIES
private static final int GRADIENT_LUT
private static final int DEFAULT_IMAGE
private static final int OVERVIEW_IMAGE
private static final int SAMPLE_MASK
private static final int FOCUS_IMAGE
private static final int EFI_SHARPNESS_MAP
private static final int EFI_HEIGHT_MAP
private static final int EFI_TEXTURE_MAP
private static final int EFI_STACK
private static final int MACRO_IMAGE
private static final int DISPLAY_PROCESSOR_TYPE
private static final int RENDER_OPERATION_ID
private static final int DISPLAY_STACK_ID
private static final int TRANSPARENCY_ID
private static final int THIRD_ID
private static final int DISPLAY_VISIBLE
private static final int TRANSPARENCY_VALUE
private static final int DISPLAY_LUT
private static final int DISPLAY_STACK_INDEX
private static final int CHANNEL_TRANSPARENCY_VALUE
private static final int CHANNEL_VISIBLE
private static final int SELECTED_CHANNELS
private static final int DISPLAY_GAMMA_CORRECTION
private static final int CHANNEL_GAMMA_CORRECTION
private static final int DISPLAY_CONTRAST_BRIGHTNESS
private static final int CHANNEL_CONTRAST_BRIGHTNESS
private static final int ACTIVE_STACK_DIMENSION
private static final int SELECTED_FRAMES
private static final int DISPLAYED_LUT_ID
private static final int HIDDEN_LAYER
private static final int LAYER_XY_FIXED
private static final int ACTIVE_LAYER_VECTOR
private static final int ACTIVE_LAYER_INDEX_VECTOR
private static final int CHAINED_LAYERS
private static final int LAYER_SELECTION
private static final int LAYER_SELECTION_INDEX
private static final int CANVAS_COLOR_1
private static final int CANVAS_COLOR_2
private static final int ORIGINAL_FRAME_RATE
private static final int USE_ORIGINAL_FRAME_RATE
private static final int ACTIVE_CHANNEL
private static final int PLANE_UNIT
private static final int Y_PLANE_DIMENSION_UNIT
private static final int Y_DIMENSION_UNIT
private static final int PLANE_ORIGIN_RWC
private static final int PLANE_SCALE_RWC
private static final int CHANNEL_OVERFLOW
private static final int OBJECTIVE_MAG
private static final int NUMERICAL_APERTURE
private static final int WORKING_DISTANCE
private static final int OBJECTIVE_NAME
private static final int OBJECTIVE_TYPE
private static final int REFRACTIVE_INDEX
private static final int DEVICE_NAME
private static final int DEVICE_ID
private static final int DEVICE_SUBTYPE
private static final int DEVICE_MANUFACTURER
private static final int VALUE
private java.lang.String[] usedFiles
private java.util.HashMap<java.lang.Integer,java.lang.String> fileMap
private TiffParser parser
private IFDList ifds
private java.util.ArrayList<java.lang.Long[]> tileOffsets
private boolean jpeg
private java.util.ArrayList<java.lang.Integer> rows
private java.util.ArrayList<java.lang.Integer> cols
private java.util.ArrayList<java.lang.Integer> compressionType
private java.util.ArrayList<java.lang.Integer> tileX
private java.util.ArrayList<java.lang.Integer> tileY
private java.util.ArrayList<java.util.ArrayList<CellSensReader.TileCoordinate>> tileMap
private java.util.ArrayList<java.lang.Integer> nDimensions
private boolean inDimensionProperties
private boolean foundChannelTag
private int dimensionTag
private java.util.HashMap<java.lang.Integer,byte[]> backgroundColor
private int metadataIndex
private int previousTag
private java.util.ArrayList<CellSensReader.Pyramid> pyramids
private transient boolean expectETS
private transient int channelCount
private transient int zCount
public boolean failOnMissingETS()
public int fileGroupOption(java.lang.String id) throws FormatException, java.io.IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
in class FormatReader
id
- a file in the multi-file datasetFormatTools.MUST_GROUP
indicates that the
files cannot be handled separately; the reader will always detect and
read all files in the dataset. FormatTools.CAN_GROUP
indicates
that the files may be handled separately, but file grouping must then
be disabled via IFormatReader.setGroupFiles(boolean)
.
FormatTools.CANNOT_GROUP
indicates that the files must be handled
separately; the reader will not attempt to read all files in the dataset
(this is rare).FormatException
java.io.IOException
FormatTools.MUST_GROUP
,
FormatTools.CAN_GROUP
,
FormatTools.CANNOT_GROUP
public boolean isSingleFile(java.lang.String id) throws FormatException, java.io.IOException
IFormatReader
isSingleFile
in interface IFormatReader
isSingleFile
in class FormatReader
FormatException
java.io.IOException
public java.lang.String[] getSeriesUsedFiles(boolean noPixels)
IFormatReader
IFormatHandler.setId(String)
, if appropriate based upon 'noPixels'.
The remaining elements are expected to be in a consistent order;
if a directory listing is necessary to build the list then it should
be sorted first.getSeriesUsedFiles
in interface IFormatReader
getSeriesUsedFiles
in class FormatReader
public int getOptimalTileWidth()
IFormatReader
getOptimalTileWidth
in interface IFormatReader
getOptimalTileWidth
in class FormatReader
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class FormatReader
public byte[] openThumbBytes(int no) throws FormatException, java.io.IOException
IFormatReader
openThumbBytes
in interface IFormatReader
openThumbBytes
in class FormatReader
FormatException
java.io.IOException
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class FormatReader
no
- the image index within the file.buf
- a pre-allocated buffer.x
- X coordinate of the upper-left corner of the sub-imagey
- Y coordinate of the upper-left corner of the sub-imagew
- width of the sub-imageh
- height of the sub-imagebuf
for convenience.FormatException
- if there was a problem parsing the metadata of the
file.java.io.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public void reopenFile() throws java.io.IOException
IFormatReader
IFormatHandler.setId(java.lang.String)
has been
called, but close(false) has not been called.reopenFile
in interface IFormatReader
reopenFile
in class FormatReader
java.io.IOException
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the fileprivate int getTileSize()
private byte[] decodeTile(int no, int row, int col) throws FormatException, java.io.IOException
FormatException
java.io.IOException
private void parseETSFile(loci.common.RandomAccessInputStream etsFile, java.lang.String file, int s) throws FormatException, java.io.IOException
FormatException
java.io.IOException
private int convertPixelType(int pixelType) throws FormatException
FormatException
private void readTags(loci.common.RandomAccessInputStream vsi, boolean populateMetadata, java.lang.String tagPrefix)
private java.lang.String getVolumeName(int tag)
private java.lang.String getTagName(int tag)
private java.lang.String getDeviceSubtype(java.lang.String type)
private java.lang.String getStackType(java.lang.String type)
private int getIFDIndex()
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