public class CV7000Reader extends FormatReader
Modifier and Type | Class and Description |
---|---|
(package private) class |
CV7000Reader.Channel |
(package private) class |
CV7000Reader.LightSource |
(package private) class |
CV7000Reader.MeasurementDataHandler |
(package private) class |
CV7000Reader.MeasurementDetailHandler |
(package private) class |
CV7000Reader.MeasurementSettingsHandler |
(package private) class |
CV7000Reader.MinMax |
(package private) class |
CV7000Reader.Plane |
(package private) class |
CV7000Reader.WPIHandler |
Modifier and Type | Field and Description |
---|---|
private java.lang.String[] |
allFiles |
private java.util.ArrayList<CV7000Reader.Channel> |
channels |
private java.lang.String |
detailPath |
private java.lang.String |
endTime |
private java.util.ArrayList<java.lang.String> |
extraFiles |
private int |
fields |
private java.util.ArrayList<CV7000Reader.LightSource> |
lightSources |
private static org.slf4j.Logger |
LOGGER |
private static java.lang.String |
MEASUREMENT_DETAIL |
private static java.lang.String |
MEASUREMENT_FILE |
private java.lang.String |
measurementPath |
private loci.common.Location |
parent |
private java.util.ArrayList<CV7000Reader.Plane> |
planeData |
private static java.lang.String |
POST_PROCESS |
private MinimalTiffReader |
reader |
private int[][] |
reversePlaneLookup |
private java.lang.String |
settingsPath |
private java.lang.String |
startTime |
private java.lang.String |
wppPath |
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
CV7000Reader()
Constructs a new Yokogawa CV7000 reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
int |
fileGroupOption(java.lang.String id)
Returns an indication of whether the files in a multi-file dataset can
be handled individually.
|
int |
getRequiredDirectories(java.lang.String[] files)
Returns the number of parent directories that are important when
processing the given list of files.
|
java.lang.String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
java.lang.String[] |
getUsedFiles(boolean noPixels)
Returns an array of filenames needed to open this dataset.
|
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.
|
private boolean |
isWellAcquired(int row,
int col) |
private CV7000Reader.Plane |
lookupPlane(int series,
int no) |
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.
|
private java.lang.String |
readSanitizedXML(java.lang.String filename) |
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, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, 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, openThumbBytes, readPlane, readPlane, reopenFile, 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
private static final org.slf4j.Logger LOGGER
private static final java.lang.String MEASUREMENT_FILE
private static final java.lang.String MEASUREMENT_DETAIL
private static final java.lang.String POST_PROCESS
private java.lang.String[] allFiles
private loci.common.Location parent
private MinimalTiffReader reader
private java.lang.String wppPath
private java.lang.String detailPath
private java.lang.String measurementPath
private java.lang.String settingsPath
private java.util.ArrayList<CV7000Reader.Plane> planeData
private int[][] reversePlaneLookup
private java.util.ArrayList<CV7000Reader.LightSource> lightSources
private java.util.ArrayList<CV7000Reader.Channel> channels
private int fields
private java.lang.String startTime
private java.lang.String endTime
private java.util.ArrayList<java.lang.String> extraFiles
public int getRequiredDirectories(java.lang.String[] files) throws FormatException, java.io.IOException
IFormatReader
getRequiredDirectories
in interface IFormatReader
getRequiredDirectories
in class FormatReader
FormatException
java.io.IOException
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 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 java.lang.String[] getUsedFiles(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.getUsedFiles
in interface IFormatReader
getUsedFiles
in class FormatReader
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 void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
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)
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 java.lang.String readSanitizedXML(java.lang.String filename) throws java.io.IOException
java.io.IOException
private boolean isWellAcquired(int row, int col)
private CV7000Reader.Plane lookupPlane(int series, int no)
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