def get(self, index):
ra = None
try:
# Read cell origin and dimensions for cell at index
cellMin = zeros(3, 'l') # long, 3 dimensions
cellDims = zeros(3, 'i') # integer, 3 dimensions
grid.getCellDimensions(index, cellMin, cellDims)
# Unpack Cell origin (in pixel coordinates)
x, y, z = cellMin
# Unpack Cell dimensions: at margins, may be smaller than cell_width, cell_height
width, height, _ = cellDims # ignore depth: it's 1
# Read cell from file into a byte array
ra = RandomAccessFile(filepaths[z], 'r')
read_width = width * bytesPerPixel
bytes = zeros(read_width * height, 'b')
# Initial offset to the Cell origin
offset = (section_width * y + x) * bytesPerPixel
n_read = 0
n_pixels = width * height
# Read line by line
while n_read < n_pixels:
ra.seek(offset)
ra.read(bytes, n_read, read_width)
n_read += read_width
offset += section_width * bytesPerPixel
# Create a new Cell of the right pixel type
return Cell(cellDims, cellMin, createAccess(bytes, bytesPerPixel))
except:
print sys.exc_info()
finally:
if ra:
ra.close()
def parse_TIFF_IFDs(filepath):
""" Returns a generator of dictionaries of tags for each IFD in the TIFF file,
as defined by the 'parseIFD' function above. """
ra = RandomAccessFile(filepath, 'r')
try:
# TIFF file format can have metadata at the end after the images, so the above approach can fail
# TIFF file header is 8-bytes long:
# (See: http://paulbourke.net/dataformats/tiff/tiff_summary.pdf )
#
# Bytes 1 and 2: identifier. Either the value 4949h (II) or 4D4Dh (MM),
# meaning little-endian and big-endian, respectively.
# All data encountered past the first two bytes in the file obey
# the byte-ordering scheme indicated by the identifier field.
b1, b2 = ra.read(), ra.read() # as two java int, each one byte sized
bigEndian = chr(b1) == 'M'
parseNextInt = parseNextIntBigEndian if bigEndian else parseNextIntLittleEndian
# Bytes 3 and 4: Version: Always 42
ra.skipBytes(2)
# Bytes 5,6,7,8: IFDOffset: offset to first image file directory (IFD), the metadata entry for the first image.
nextIFDoffset = parseNextInt(ra, 4) # offset to first IFD
while nextIFDoffset != 0:
ra.seek(nextIFDoffset)
tags, nextIFDoffset = parseIFD(ra, parseNextInt)
tags["bigEndian"] = bigEndian
yield tags
finally:
ra.close()
def readFIBSEMdat(path, channel_index=-1, header=1024, magic_number=3555587570, asImagePlus=False, toUnsigned=True):
""" Read a file from Shan Xu's FIBSEM software, where two or more channels are interleaved.
Assumes channels are stored in 16-bit.
path: the file path to the .dat file.
channel_index: the 0-based index of the channel to parse, or -1 (default) for all.
header: defaults to a length of 1024 bytes
magic_number: defaults to that for version 8 of Shan Xu's .dat image file format.
isSigned: defaults to True, will subtract the min value when negative.
asImagePlus: return a list of ImagePlus instead of ArrayImg which is the default.
"""
ra = RandomAccessFile(path, 'r')
try:
# Check the magic number
ra.seek(0)
magic = ra.readInt() & 0xffffffff
if magic != magic_number:
msg = "magic number mismatch: v8 magic " + str(magic_number) + " != " + str(magic) + " for path:\n" + path
System.out.println(msg)
print msg
# Continue: attempt to parse the file anyway
# Read the number of channels
ra.seek(32)
numChannels = ra.readByte() & 0xff # a single byte as unsigned integer
# Parse width and height
ra.seek(100)
width = ra.readInt()
ra.seek(104)
height = ra.readInt()
# Read the whole interleaved pixel array
ra.seek(header)
bytes = zeros(width * height * 2 * numChannels, 'b') # 2 for 16-bit
ra.read(bytes)
# Parse as 16-bit array
sb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN).asShortBuffer()
bytes = None
finally:
ra.close()
#
shorts = zeros(width * height * numChannels, 'h')
sb.get(shorts)
sb = None
# Deinterleave channels and convert to unsigned short
# Shockingly, these values are signed shorts, not unsigned! (for first popeye2 squid volume, December 2021)
# With ASM: fast
channels = DAT_handler.deinterleave(shorts, numChannels, channel_index)
shorts = None
#
if toUnsigned:
for s in channels:
DAT_handler.toUnsigned(s)
# With python array sampling: very slow, and not just from iterating whole array once per channel
#seq = xrange(numChannels) if -1 == channel_index else [channel_index]
#channels = [shorts[i::numChannels] for i in seq]
if asImagePlus:
return [ImagePlus(str(i), ShortProcessor(width, height, s, None)) for i, s in enumerate(channels)]
else:
return [ArrayImgs.unsignedShorts(s, [width, height]) for s in channels]
def readBinaryMaskImg(filepath, width, height, depth, header_size):
ra = RandomAccessFile(filepath, 'r')
try:
ra.skipBytes(header_size)
bytes = zeros(width * height * depth, 'b')
ra.read(bytes)
return ArrayImgs.unsignedBytes(bytes, [width, height, depth])
finally:
ra.close()
def readUnsignedBytes(path, dimensions, header=0):
""" Read a file as an ArrayImg of UnsignedShortType """
ra = RandomAccessFile(path, 'r')
try:
if header < 0:
# Interpret from the end: useful for files with variable header lengths
# such as some types of uncompressed TIFF formats
header = ra.length() + header
ra.skipBytes(header)
bytes = zeros(reduce(operator.mul, dimensions), 'b')
ra.read(bytes)
return ArrayImgs.unsignedBytes(bytes, dimensions)
finally:
ra.close()
def readFIBSEMdat(path, channel_index=-1, header=1024, magic_number=3555587570):
""" Read a file from Shan Xu's FIBSEM software, where two channels are interleaved.
Assumes channels are stored in 16-bit.
path: the file path to the .dat file.
channel_index: the 0-based index of the channel to parse, or -1 (default) for all.
header: defaults to a length of 1024 bytes
magic_number: defaults to that for version 8 of Shan Xu's .dat image file format.
"""
ra = RandomAccessFile(path, 'r')
try:
# Check the magic number
ra.seek(0)
if ra.readInt() & 0xffffffff != magic_number:
print "Magic number mismatch"
return None
# Read the number of channels
ra.seek(32)
numChannels = ra.readByte() & 0xff # a single byte as unsigned integer
# Parse width and height
ra.seek(100)
width = ra.readInt()
ra.seek(104)
height = ra.readInt()
print numChannels, width, height
# Read the whole interleaved pixel array
ra.seek(header)
bytes = zeros(width * height * 2 * numChannels, 'b') # 2 for 16-bit
ra.read(bytes)
print "read", len(bytes), "bytes" # takes ~2 seconds
# Parse as 16-bit array
sb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN).asShortBuffer()
shorts = zeros(width * height * numChannels, 'h')
sb.get(shorts)
# Deinterleave channels
# With Weaver: fast
channels = w.deinterleave(shorts, numChannels, channel_index)
# With python array sampling: very slow, and not just from iterating whole array once per channel
# seq = xrange(numChannels) if -1 == channel_index else [channel_index]
#channels = [shorts[i::numChannels] for i in seq]
# With clojure: extremely slow, may be using reflection unexpectedly
#channels = deinterleave.invoke(shorts, numChannels)
print len(channels)
# Shockingly, these values are signed shorts, not unsigned!
return [ArrayImgs.shorts(s, [width, height]) for s in channels]
finally:
ra.close()
def readFloats(path, dimensions, header=0, byte_order=ByteOrder.LITTLE_ENDIAN):
""" Read a file as an ArrayImg of FloatType """
size = reduce(operator.mul, dimensions)
ra = RandomAccessFile(path, 'r')
try:
if header < 0:
# Interpret from the end: useful for files with variable header lengths
# such as some types of uncompressed TIFF formats
header = ra.length() + header
ra.skipBytes(header)
bytes = zeros(size * 4, 'b')
ra.read(bytes)
floats = zeros(size, 'f')
ByteBuffer.wrap(bytes).order(byte_order).asFloatBuffer().get(floats)
return ArrayImgs.floats(floats, dimensions)
finally:
ra.close()
def readUnsignedShorts(path, dimensions, header=0, return_array=False, byte_order=ByteOrder.LITTLE_ENDIAN):
""" Read a file as an ArrayImg of UnsignedShortType """
size = reduce(operator.mul, dimensions)
ra = RandomAccessFile(path, 'r')
try:
if header < 0:
# Interpret from the end: useful for files with variable header lengths
# such as some types of uncompressed TIFF formats
header = ra.length() + header
ra.skipBytes(header)
bytes = zeros(size * 2, 'b')
ra.read(bytes)
shorts = zeros(size, 'h') # h is for short
ByteBuffer.wrap(bytes).order(byte_order).asShortBuffer().get(shorts)
return shorts if return_array else ArrayImgs.unsignedShorts(shorts, dimensions)
finally:
ra.close()
def get(self, index):
ra = None
try:
# Read cell origin and dimensions for cell at index
cellMin = zeros(3, 'l') # long[3]
cellDims = zeros(3, 'i') # integer[3]
grid.getCellDimensions(index, cellMin, cellDims)
# Unpack Cell origin (in pixel coordinates)
x, y, z = cellMin
# Unpack Cell dimensions: at margins, may be smaller than cell_width, cell_height
width, height, _ = cellDims # ignore depth: it's 1
# Read cell from file into a byte array
ra = RandomAccessFile(filepaths[z], 'r')
read_width = width * bytesPerPixel
bytes = zeros(read_width * height,
'b') # will contain the entire Cell pixel data
# Initial offset to the Cell origin
offset = (section_width * y + x) * bytesPerPixel
n_pixels = width * height
if width == section_width:
# Read whole block in one go: cell data is continuous in the file
ra.seek(offset)
ra.read(bytes, 0, n_pixels * bytesPerPixel)
else:
# Read line by line
n_read = 0
while n_read < n_pixels:
ra.seek(offset)
ra.read(bytes, n_read, read_width)
n_read += read_width # ensure n_read advances in case file is truncated to avoid infinite loop
offset += section_width * bytesPerPixel
# Create a new Cell of the right pixel type
return Cell(cellDims, cellMin, createAccess(bytes, bytesPerPixel))
except:
print sys.exc_info()
finally:
if ra:
ra.close()
nextIFDoffset = parseNextInt(ra, 4)
return tags, nextIFDoffset
if filepath.endswith("tif"):
try:
ra = RandomAccessFile(filepath, 'r')
# TIFF file format can have metadata at the end after the images, so the above approach can fail
# TIFF file header is 8-bytes long:
# (See: http://paulbourke.net/dataformats/tiff/tiff_summary.pdf )
#
# Bytes 1 and 2: identifier. Either the value 4949h (II) or 4D4Dh (MM),
# meaning little-ending and big-endian, respectively.
# All data encountered past the first two bytes in the file obey
# the byte-ordering scheme indicated by the identifier field.
b1, b2 = ra.read(), ra.read() # as two java int, each one byte sized
bigEndian = chr(b1) == 'M'
parseNextInt = parseNextIntBigEndian if bigEndian else parseNextIntLittleEndian
# Bytes 3 and 4: Version: Always 42
ra.skipBytes(2)
# Bytes 5,6,7,8: IFDOffset: offset to first image file directory (IFD), the metadata entry for the first image.
firstIFDoffset = parseNextInt(ra, 4)
ra.skipBytes(firstIFDoffset - ra.getFilePointer()
) # minus the current position: all offsets are absolute
firstTags, _ = parseIFD(ra, parseNextInt)
# Correct headerSize for TIFF files (and then assuming images are contiguous and in order,
# which they don't have to be either in TIFF)
headerSize = firstTags["offset"]
# Sanity check:
if width != firstTags["width"] or height != firstTags[
"height"] or bitDepth != firstTags["samples_per_pixel"] * 8:
# Parse the test file
IFDs = list(parse_TIFF_IFDs(filepath)) # the tags of each IFD
firstIFD = IFDs[0]
print firstIFD
ra = RandomAccessFile(filepath, 'r')
try:
# Read the image plane, compressed with packbits
bytes_packedbits = zeros(sum(firstIFD["StripByteCounts"]), 'b')
index = 0
for strip_offset, strip_length in zip(firstIFD["StripOffsets"], firstIFD["StripByteCounts"]):
ra.seek(strip_offset)
ra.read(bytes_packedbits, index, strip_length)
index += strip_length
print "Compressed:", bytes_packedbits
# unpack
bytes1 = unpackBits2(bytes_packedbits, firstIFD)
bytes2 = unpackBits2(bytes_packedbits, firstIFD, use_imagereader=True)
print "Decompressed jython:", bytes1
print "Decompressed imagej:", bytes2
# Check:
if 0 == sum(a - b for a, b in zip(source_bytes, bytes1)):
print "Image decompressed successfully by jython."
if 0 == sum(a - b for a, b in zip(source_bytes, bytes2)):
print "Image decompressed successfully by imagej."
finally:
ra.close()
