def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImagesMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Initialize array of metadata entries
metaData = []
# Iterate over all image identifiers
for id in imageIdentifiers:
# Extract the info from the image identifier
ch = int(id.colorChannelIndex)
plane = int(id.focalPlaneIndex)
series = int(id.seriesIndex)
timepoint = int(id.timeSeriesIndex)
# Make sure to process only the relevant series
if self._seriesNum != -1 and series != self._seriesNum:
continue
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(ch)
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata()
# Fill in all information
imageMetadata.imageIdentifier = id
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timepoint
imageMetadata.depth = plane
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = 1 # + self._seriesNum
imageMetadata.well = "IGNORED"
# Append metadata for current image
metaData.append(imageMetadata)
# Log image geometry information
if self._DEBUG:
self._logger.info(
"MICROSCOPYSINGLEDATASETCONFIG::extractImagesMetadata(): " +
"Current image: series = " + str(series) + " channel = " +
str(ch) + " plane = " + str(plane) + " timepoint = " +
str(timepoint) + " channel code = " + str(channelCode))
# Now return the metaData array
return metaData
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImagesMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Initialize array of metadata entries
metaData = []
# Iterate over all image identifiers
for id in imageIdentifiers:
# Extract the info from the image identifier
ch = int(id.colorChannelIndex)
plane = int(id.focalPlaneIndex)
series = int(id.seriesIndex)
timepoint = int(id.timeSeriesIndex)
# Make sure to process only the relevant series
if self._seriesNum != -1 and series != self._seriesNum:
continue
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(ch)
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata();
# Fill in all information
imageMetadata.imageIdentifier = id
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timepoint
imageMetadata.depth = plane
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = 1 # + self._seriesNum
imageMetadata.well = "IGNORED"
# Append metadata for current image
metaData.append(imageMetadata)
# Log image geometry information
if self._DEBUG:
self._logger.info("MICROSCOPYSINGLEDATASETCONFIG::extractImagesMetadata(): " +
"Current image: series = " + str(series) +
" channel = " + str(ch) +
" plane = " + str(plane) +
" timepoint = " + str(timepoint) +
" channel code = " + str(channelCode))
# Now return the metaData array
return metaData
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImageMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Info
self._logger.info("Processing file " + str(imagePath) +
" with identifiers " + str(imageIdentifiers))
# Find the file in the csvTable hashmap
row = self._csvTable[imagePath]
self._logger.info("File " + imagePath + " was found in the CSV table.")
self._logger.info("The corresponding row is " + str(row))
# Coordinates
position = -1
tileX = -1
tileY = -1
planeNum = -1
timeNum = -1
well = ""
# Get the well
well = row[4]
# Test position string
self._logger.info("Position string is " + str(row[5]))
# Get the positions from the Position column
m_pos = self._pattern_pos.match(row[5])
if m_pos is not None:
if m_pos.group("position") is not None:
position = int(m_pos.group("position"))
if m_pos.group("x") is not None:
tileX = int(m_pos.group("x"))
if m_pos.group("y") is not None:
tileY = int(m_pos.group("y"))
if m_pos.group("z") is not None:
planeNum = int(m_pos.group("z"))
# Try the fallback option
m_pos_name_fb = self._pattern_pos_name_fb.match(row[6])
if m_pos_name_fb is not None:
if m_pos_name_fb.group("pos") is not None:
pos = m_pos_name_fb.group("pos")
tileX = int(pos[0:2])
tileY = int(pos[2:4])
# Then, get time information
m_time = self._pattern_time_name.match(row[6])
if m_time is not None:
if m_time.group("time") is not None:
timeNum = int(m_time.group("time"))
else:
# Try the fallback option
m_time_fb = self._pattern_time_name_fb.match(row[6])
if m_time_fb is not None:
if m_time_fb.group("time") is not None:
timeNum = int(m_time_fb.group("time"))
# Fallback
if position == -1:
position = 1
if tileX == -1:
tileX = 1
if tileY == -1:
tileY = 1
if planeNum == -1:
planeNum = 1
if timeNum == -1:
timeNum = 1
# Channel name
channelName = self._buildChannelName(row)
# Build series ID from row (if present, use path information to build a unique id)
seriesID = "Well_" + well + "_Pos_" + str(position) + "_" + str(tileX) + "_" + str(tileY) + "_Path_" + \
self._pathInfoAsID(row[6])
# Find the series number that correspond to seriesID
series = self._seriesNumFromSeriesID(seriesID)
# Inform
if series == -1:
err = "Series with ID " + seriesID + " could not be found!"
self._logger.error(err)
raise (Exception(err))
else:
self._logger.info("Series with ID " + seriesID +
" corresponds to series number " + str(series))
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# Get channel index from channel name
channel = self._getChannelNumber(self._allSeriesMetadata[series],
channelName)
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(channel)
if self._DEBUG:
msg = "Current file = " + imagePath + " has series = " + \
str(series) + " timepoint = " + str(timeNum) + " plane = " + \
str(planeNum) + " channel = " + str(channel) + " channelCode = " + \
str(channelCode)
self._logger.info(msg)
# Initialize Metadata array
Metadata = []
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata()
# Build a tile number from tileX and tileY
tileNum = 1000 * tileX + tileY
if tileNum < 1:
tileNum = 1
self._logger.info("Tile number is " + str(tileNum))
# Fill in all information
imageMetadata.imageIdentifier = imageIdentifiers.get(0)
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timeNum
imageMetadata.depth = planeNum
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = tileNum
imageMetadata.well = well
# Now return the image metadata object in an array
Metadata.append(imageMetadata)
return Metadata
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImageMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Info
self._logger.info("Processing file " + str(imagePath) +
" with identifiers " + str(imageIdentifiers))
# Extract the relevant information from the file name - the image
# identifiers in this case do not carry any useful information.
m = self._pattern.match(imagePath)
if m is None:
err = "VISITRONNDCOMPOSITEDATASETCONFIG::extractImageMetadata(): " + \
"unexpected file name " + str(imagePath)
self._logger.error(err)
raise Exception(err)
# Get the extracted info
fileinfo = m.groupdict()
# Get and store the base name
basename = fileinfo['basename']
# Extract the series number
series = self._seriesNumFromFileName(imagePath)
if series == -1:
raise Exception("Could not find any series containing file " +
imagePath + "!")
if self._DEBUG:
self._logger.info("Found file " + imagePath + " in series " +
str(series))
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# Get current metadata
currentMetaData = self._allSeriesMetadata[series]
# Compare the basename extracted from the file name with
# the one stored in the attributes
if basename != currentMetaData["basename"]:
self._logger.error("Basename mismatch: " + basename +
"(from filename) vs. " +
currentMetaData["basename"] +
"(from attributes).")
# Extract the channel number
# The channel number in the file name is 1-based
if fileinfo["channel"] is not None:
channelNumberFromFile = int(fileinfo['channel']) - 1
if self._DEBUG:
self._logger.info("Found channel number " +
str(channelNumberFromFile) +
" in file name.")
else:
self._logger.info(
"Channel number not found: fall back to image identifiers.")
channelNumberFromFile = -1
if fileinfo["channelname"] is not None:
channelName = fileinfo['channelname']
if self._DEBUG:
self._logger.info("Found channel name " + channelName +
" in file name.")
else:
if channelNumberFromFile != -1:
keyName = "channelName" + channelNumberFromFile
if keyName in currentMetadata:
channelName = currentMetadata[keyName]
self._logger.info("Channel name from metadata: " +
channelName)
else:
self._logger.info(
"Channel name not found: falling back to ''.")
channelName = ""
self._logger.info("Channel name not found: falling back to ''.")
channelName = ""
# Extract the timepoint
# The timepoint number in the file (if defined) is 1-based
if fileinfo["timepoint"] is not None:
timepointFromFile = int(fileinfo['timepoint']) - 1
if self._DEBUG:
self._logger.info("Found timepoint " + str(timepointFromFile) +
" in file name.")
else:
timepointFromFile = -1
# Inform
if self._DEBUG:
self._logger.info("Parsing of file " + str(imagePath) + " gives: " + \
"basename = " + str(basename) + "; " + \
"channelNumber = " + str(channelNumberFromFile) + "; " + \
"channelName = " + channelName + "; " + \
"seriesNum = " + str(series) + "; " + \
"timepoint = " + str(timepointFromFile))
# Initialize array of metadata entries
metaData = []
# Now process the file indentifiers for this file
# Iterate over all image identifiers
for id in imageIdentifiers:
# Extract the relevant info from the image identifier
plane = id.focalPlaneIndex
# Fallback
if channelNumberFromFile == -1:
channelNumber = int(id.colorChannelIndex)
else:
channelNumber = channelNumberFromFile
if timepointFromFile == -1:
timepoint = id.timeSeriesIndex
else:
timepoint = timepointFromFile
if self._DEBUG:
self._logger.info("Image identifiers for image " +
str(imagePath) + ": " + str(id) +
" map to " + "channel = " +
str(id.colorChannelIndex) + "; plane = " +
str(id.focalPlaneIndex) + "; series = " +
str(id.seriesIndex) + "; timepoint = " +
str(id.timeSeriesIndex))
self._logger.info(
"Geometry after integrating image identifiers: " +
"channel = " + str(channelNumber) + "; plane = " +
str(plane) + "; series = " + str(series) +
"; timepoint = " + str(timepoint))
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(
channelNumber)
if self._DEBUG:
self._logger.info(
"Adding image to channel with channel code " + channelCode)
# Attempt to work around a geometry-parsing issue in imageIdentifiers
expectedNumPlanes = int(currentMetaData["sizeZ"])
expectedNumTimepoints = int(currentMetaData["sizeT"])
if (timepoint > (expectedNumTimepoints - 1) and expectedNumPlanes > 1) or \
(plane > (expectedNumPlanes - 1) and expectedNumTimepoints > 1):
self._logger.info("Swapping Z and T")
timepoint, plane = plane, timepoint
# Update the ImageIdentifier
id = ImageIdentifier(series, timepoint, plane, channelNumber)
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata()
# Fill in all information
imageMetadata.imageIdentifier = id
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timepoint
imageMetadata.depth = plane
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = 1 # + self._seriesNum
imageMetadata.well = "IGNORED"
# Append metadata for current image
metaData.append(imageMetadata)
# Now return the image metadata object in an array
return metaData
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImageMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Info
self._logger.info("Processing file " + str(imagePath) +
" with identifiers " + str(imageIdentifiers))
# Extract the relevant information from the file name - the image
# identifiers in this case do not carry any useful information.
m = self._pattern.match(imagePath)
if m is None:
err = "VISITRONNDCOMPOSITEDATASETCONFIG::extractImageMetadata(): " + \
"unexpected file name " + str(imagePath)
self._logger.error(err)
raise Exception(err)
# Get the extracted info
fileinfo = m.groupdict()
# Get and store the base name
basename = fileinfo['basename']
# Extract the series number
series = self._seriesNumFromFileName(imagePath)
if series == -1:
raise Exception("Could not find any series containing file " + imagePath + "!")
if self._DEBUG:
self._logger.info("Found file " + imagePath + " in series " + str(series))
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# Get current metadata
currentMetaData = self._allSeriesMetadata[series]
# Compare the basename extracted from the file name with
# the one stored in the attributes
if basename != currentMetaData["basename"]:
self._logger.error("Basename mismatch: " +
basename + "(from filename) vs. " +
currentMetaData["basename"] +
"(from attributes).")
# Extract the channel number
# The channel number in the file name is 1-based
if fileinfo["channel"] is not None:
channelNumberFromFile = int(fileinfo['channel']) - 1
if self._DEBUG:
self._logger.info("Found channel number " + str(channelNumberFromFile) + " in file name.")
else:
self._logger.info("Channel number not found: fall back to image identifiers.")
channelNumberFromFile = -1
if fileinfo["channelname"] is not None:
channelName = fileinfo['channelname']
if self._DEBUG:
self._logger.info("Found channel name " + channelName + " in file name.")
else:
if channelNumberFromFile != -1:
keyName = "channelName" + channelNumberFromFile
if keyName in currentMetadata:
channelName = currentMetadata[keyName]
self._logger.info("Channel name from metadata: " + channelName)
else:
self._logger.info("Channel name not found: falling back to ''.")
channelName = ""
self._logger.info("Channel name not found: falling back to ''.")
channelName = ""
# Extract the timepoint
# The timepoint number in the file (if defined) is 1-based
if fileinfo["timepoint"] is not None:
timepointFromFile = int(fileinfo['timepoint']) - 1
if self._DEBUG:
self._logger.info("Found timepoint " + str(timepointFromFile) + " in file name.")
else:
timepointFromFile = -1
# Inform
if self._DEBUG:
self._logger.info("Parsing of file " + str(imagePath) + " gives: " + \
"basename = " + str(basename) + "; " + \
"channelNumber = " + str(channelNumberFromFile) + "; " + \
"channelName = " + channelName + "; " + \
"seriesNum = " + str(series) + "; " + \
"timepoint = " + str(timepointFromFile))
# Initialize array of metadata entries
metaData = []
# Now process the file indentifiers for this file
# Iterate over all image identifiers
for id in imageIdentifiers:
# Extract the relevant info from the image identifier
plane = id.focalPlaneIndex
# Fallback
if channelNumberFromFile == -1:
channelNumber = int(id.colorChannelIndex)
else:
channelNumber = channelNumberFromFile
if timepointFromFile == -1:
timepoint = id.timeSeriesIndex
else:
timepoint = timepointFromFile
if self._DEBUG:
self._logger.info("Image identifiers for image " + str(imagePath) +
": " + str(id) + " map to " +
"channel = " + str(id.colorChannelIndex) +
"; plane = " + str(id.focalPlaneIndex) +
"; series = " + str(id.seriesIndex) +
"; timepoint = " + str(id.timeSeriesIndex))
self._logger.info("Geometry after integrating image identifiers: " +
"channel = " + str(channelNumber) +
"; plane = " + str(plane) +
"; series = " + str(series) +
"; timepoint = " + str(timepoint))
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(channelNumber)
if self._DEBUG:
self._logger.info("Adding image to channel with channel code " + channelCode)
# Attempt to work around a geometry-parsing issue in imageIdentifiers
expectedNumPlanes = int(currentMetaData["sizeZ"])
expectedNumTimepoints = int(currentMetaData["sizeT"])
if (timepoint > (expectedNumTimepoints - 1) and expectedNumPlanes > 1) or \
(plane > (expectedNumPlanes - 1) and expectedNumTimepoints > 1):
self._logger.info("Swapping Z and T")
timepoint, plane = plane, timepoint
# Update the ImageIdentifier
id = ImageIdentifier(series, timepoint, plane, channelNumber)
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata();
# Fill in all information
imageMetadata.imageIdentifier = id
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timepoint
imageMetadata.depth = plane
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = 1 # + self._seriesNum
imageMetadata.well = "IGNORED"
# Append metadata for current image
metaData.append(imageMetadata)
# Now return the image metadata object in an array
return metaData
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImageMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Extract the relevant information from the file name - the image
# identifiers in this case do not carry any useful information.
m = self._pattern.match(imagePath)
simple_m = self._pattern_simple.match(imagePath)
# First we try the more complex regex
if m is not None:
# Get and store the base name
basename = m.group("basename")
if self._basename == "" or self._basename != basename:
self._basename = basename
# The series number is not always defined in the file name.
if m.group("series") is None:
series = 0
else:
series = int(m.group("series"))
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# The time index is also not always specified.
if m.group("timepoint") is None:
timepoint = 0
else:
timepoint = int(m.group("timepoint"))
# Plane number is always specified
if m.group("plane") is None:
plane = 0
else:
plane = int(m.group("plane"))
# Channel number is always specified
if m.group("channel") is None:
ch = 0
else:
ch = int(m.group("channel"))
else:
# Try with the simpler regex
if simple_m is None:
err = "MICROSCOPYCOMPOSITEDATASETCONFIG::extractImageMetadata(): " + \
"unexpected file name " + str(imagePath)
self._logger.error(err)
raise Exception(err)
# Get and store the base name
basename = simple_m.group("basename")
if self._basename == "" or self._basename != basename:
self._basename = basename
# Series number
series = 0
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# Timepoint
timepoint = 0
# Plane number is always specified
if simple_m.group("plane") is None:
plane = 0
else:
plane = int(simple_m.group("plane"))
# Channel number
ch = 0
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(ch)
if self._DEBUG:
msg = "Current file = " + imagePath + " has series = " + \
str(series) + " timepoint = " + str(timepoint) + " plane = " + \
str(plane) + " channel = " + str(ch) + "; channelCode = " + \
str(channelCode)
self._logger.info(msg)
# Initialize Metadata array
Metadata = []
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata()
# Fill in all information
imageMetadata.imageIdentifier = imageIdentifiers.get(0)
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timepoint
imageMetadata.depth = plane
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = 1 # + self._seriesNum
imageMetadata.well = "IGNORED"
# Now return the image metadata object in an array
Metadata.append(imageMetadata)
return Metadata
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImageMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Info
self._logger.info("Processing file " + str(imagePath) + " with identifiers " + str(imageIdentifiers))
# Find the file in the csvTable hashmap
row = self._csvTable[imagePath]
self._logger.info("File " + imagePath + " was found in the CSV table.")
self._logger.info("The corresponding row is " + str(row))
# Coordinates
position = -1
tileX = -1
tileY = -1
planeNum = -1
timeNum = -1
well = ""
# Get the well
well = row[4]
# Test position string
self._logger.info("Position string is " + str(row[5]))
# Get the positions from the Position column
m_pos = self._pattern_pos.match(row[5])
if m_pos is not None:
if m_pos.group("position") is not None:
position = int(m_pos.group("position"))
if m_pos.group("x") is not None:
tileX = int(m_pos.group("x"))
if m_pos.group("y") is not None:
tileY = int(m_pos.group("y"))
if m_pos.group("z") is not None:
planeNum = int(m_pos.group("z"))
# Try the fallback option
m_pos_name_fb = self._pattern_pos_name_fb.match(row[6])
if m_pos_name_fb is not None:
if m_pos_name_fb.group("pos") is not None:
pos = m_pos_name_fb.group("pos")
tileX = int(pos[0:2])
tileY = int(pos[2:4])
# Then, get time information
m_time = self._pattern_time_name.match(row[6])
if m_time is not None:
if m_time.group("time") is not None:
timeNum = int(m_time.group("time"))
else:
# Try the fallback option
m_time_fb = self._pattern_time_name_fb.match(row[6])
if m_time_fb is not None:
if m_time_fb.group("time") is not None:
timeNum = int(m_time_fb.group("time"))
# Fallback
if position == -1:
position = 1
if tileX == -1:
tileX = 1
if tileY == -1:
tileY = 1
if planeNum == -1:
planeNum = 1
if timeNum == -1:
timeNum = 1
# Channel name
channelName = self._buildChannelName(row)
# Build series ID from row (if present, use path information to build a unique id)
seriesID = "Well_" + well + "_Pos_" + str(position) + "_" + str(tileX) + "_" + str(tileY) + "_Path_" + \
self._pathInfoAsID(row[6])
# Find the series number that correspond to seriesID
series = self._seriesNumFromSeriesID(seriesID)
# Inform
if series == -1:
err = "Series with ID " + seriesID + " could not be found!"
self._logger.error(err)
raise(Exception(err))
else:
self._logger.info("Series with ID " + seriesID + " corresponds to series number " + str(series))
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# Get channel index from channel name
channel = self._getChannelNumber(self._allSeriesMetadata[series], channelName)
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(channel)
if self._DEBUG:
msg = "Current file = " + imagePath + " has series = " + \
str(series) + " timepoint = " + str(timeNum) + " plane = " + \
str(planeNum) + " channel = " + str(channel) + " channelCode = " + \
str(channelCode)
self._logger.info(msg)
# Initialize Metadata array
Metadata = []
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata()
# Build a tile number from tileX and tileY
tileNum = 1000 * tileX + tileY
if tileNum < 1:
tileNum = 1
self._logger.info("Tile number is " + str(tileNum))
# Fill in all information
imageMetadata.imageIdentifier = imageIdentifiers.get(0)
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timeNum
imageMetadata.depth = planeNum
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = tileNum
imageMetadata.well = well
# Now return the image metadata object in an array
Metadata.append(imageMetadata)
return Metadata
def extractImagesMetadata(self, imagePath, imageIdentifiers):
"""Overrides extractImageMetadata method making sure to store
both series and channel indices in the channel code to be reused
later to extract color information and other metadata.
The channel code is in the form SERIES-(\d+)_CHANNEL-(\d+).
Only metadata for the relevant series number is returned!
@param imagePath Full path to the file to process
@param imageIdentifiers Array of ImageIdentifier's
@see constructor.
"""
# Extract the relevant information from the file name - the image
# identifiers in this case do not carry any useful information.
m = self._pattern.match(imagePath)
simple_m = self._pattern_simple.match(imagePath)
# First we try the more complex regex
if m is not None:
# Get and store the base name
basename = m.group("basename")
if self._basename == "" or self._basename != basename:
self._basename = basename
# The series number is not always defined in the file name.
# In the regex, the group(2) optionally matches _s{digits};
# in case group(2) is not None, the actual series number is
# stored in group(4).
if m.group("series") is None:
series = 0
else:
series = int("series")
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# The time index is also not always specified.
if m.group("timepoint") is None:
timepoint = 0
else:
timepoint = int(m.group("timepoint"))
# Plane number is always specified
if m.group("plane") is None:
plane = 0
else:
plane = int(m.group("plane"))
# Channel number is always specified
if m.group("channel") is None:
ch = 0
else:
ch = int(m.group(8))
else:
# Try with the simpler regex
if simple_m is None:
err = "MICROSCOPYCOMPOSITEDATASETCONFIG::extractImageMetadata(): " + \
"unexpected file name " + str(imagePath)
self._logger.error(err)
raise Exception(err)
# Get and store the base name
basename = simple_m.group("basename")
if self._basename == "" or self._basename != basename:
self._basename = basename
# Series number
series = 0
# Make sure to process only the relevant series
if series != self._seriesNum:
return []
# Timepoint
timepoint = 0
# Plane number is always specified
if simple_m.group("plane") is None:
plane = 0
else:
plane = int(simple_m.group("plane"))
# Channel number
ch = 0
# Build the channel code
channelCode = "SERIES-" + str(series) + "_CHANNEL-" + str(ch)
if self._DEBUG:
msg = "Current file = " + imagePath + " has series = " + \
str(series) + " timepoint = " + str(timepoint) + " plane = " + \
str(plane) + " channel = " + str(ch) + "; channelCode = " + \
str(channelCode)
self._logger.info(msg)
# Initialize Metadata array
Metadata = []
# Initialize a new ImageMetadata object
imageMetadata = ImageMetadata();
# Fill in all information
imageMetadata.imageIdentifier = imageIdentifiers.get(0)
imageMetadata.seriesNumber = series
imageMetadata.timepoint = timepoint
imageMetadata.depth = plane
imageMetadata.channelCode = channelCode
imageMetadata.tileNumber = 1 # + self._seriesNum
imageMetadata.well = "IGNORED"
# Now return the image metadata object in an array
Metadata.append(imageMetadata)
return Metadata