def main():
imp = IJ.getFilePath("Select DCIMG file")
if not imp:
return
root, ext = os.path.splitext(imp)
if ext.lower() != '.dcimg':
cFrame = PlugInFrame('ERR DLG')
MessageDialog(cFrame, 'ERROR', 'Expected extension .dcimg')
return
#Lets start
fID = open(imp, 'rb')
hdr_bytes = read_header_bytes(fID)
hdr = parse_header_bytes(fID, hdr_bytes)
metadataStr = beginMetadata()
for key, value in hdr.iteritems():
metadataStr += addMetadataEntry(key, str(value))
metadataStr += endMetadata()
metadataDlg = HTMLDialog("DCIMG metadata", metadataStr, 0)
size = metadataDlg.getSize()
if size.width < 300:
size.width = 300
if size.height < 500:
size.height = 500
metadataDlg.setSize(size)
finfo = FileInfo()
finfo.fileName = imp
#finfo.width = hdr['xsize_req']
finfo.width = hdr['xsize']
finfo.height = hdr['ysize']
finfo.nImages = hdr['nframes']
finfo.offset = 232
finfo.fileType = hdr['bitdepth'] / 8 - 1 #Ugh
finfo.intelByteOrder = 1
#finfo.gapBetweenImages = int(hdr['bytes_per_img']*(1-float(hdr['xsize_req'])/float(hdr['xsize'])))
finfo.gapBetweenImages = 0
finfo.fileFormat = 1
finfo.samplesPerPixel = 1
finfo.displayRanges = None
finfo.lutSize = 0
finfo.whiteIsZero = 0
vs = VirtualStack()
finfo.virtualStack = vs
FileInfoVirtualStack(finfo)
def unpackBits2(bytes_packedbits, tags, use_imagereader=False):
# Decompress a packBits-compressed image, returns an array of n_bytes.
# ra: a RandomAccessFile with the pointer at the right place to start reading.
# PackBits actually packages bytes: a byte-wise RLE most efficient at encoding runs of bytes
# 3 types of data packets:
# 1. two-byte encoded run packet:
# - first byte is the number of bytes in the run.
# Ranges from -127 to -1, meaning +1: from 2 to 128 (-count + 1)
# - second byte value of each byte in the run.
# 2. literal run packet: stores 1 to 128 bytes literally without compression.
# - first byte is the number of bytes in the run.
# Ranges from 0 to 127, indicating 1 to 128 values (count + 1)
# - then the sequence of literal bytes
# 3. no-op packet: never used, value -128.
# See documentation: http://paulbourke.net/dataformats/tiff/tiff_summary.pdf
# (note documentation PDF has its details flipped when it comes to the ranges for literal runs and packed runs)
# See also: ij.io.ImageReader.packBitsUncompress (a public method without side effects)
n_bytes = tags["width"] * tags["height"]
if use_imagereader:
return ImageReader(FileInfo()).packBitsUncompress(
bytes_packedbits, n_bytes)
bytes = zeros(n_bytes, 'b')
try:
indexP = 0 # packed
indexU = 0 # unpacked
while indexU < n_bytes:
count = bytes_packedbits[indexP]
if count >= 0:
# Literal run
System.arraycopy(bytes_packedbits, indexP + 1, bytes, indexU,
count + 1)
indexP += count + 2 # one extra for the 'count' byte
indexU += count + 1
else:
# Packed run
Arrays.fill(bytes, indexU, indexU - count + 1,
bytes_packedbits[indexP + 1])
indexP += 2
indexU += -count + 1
except:
print sys.exc_info()
finally:
return bytes
def unpackBits(ra, tags, use_imagereader=False):
# Decompress a packBits-compressed image, write into bytes array starting at indexU.
# ra: a RandomAccessFile with the pointer at the right place to start reading.
# PackBits actually packages bytes: a byte-wise RLE most efficient at encoding runs of bytes
# 3 types of data packets:
# 1. two-byte encoded run packet:
# - first byte is the number of bytes in the run.
# Ranges from -127 to -1, meaning +1: from 2 to 128 (-count + 1)
# - second byte value of each byte in the run.
# 2. literal run packet: stores 1 to 128 bytes literally without compression.
# - first byte is the number of bytes in the run.
# Ranges from 0 to 127, indicating 1 to 128 values (count + 1)
# - then the sequence of literal bytes
# 3. no-op packet: never used, value -128.
# See documentation: http://paulbourke.net/dataformats/tiff/tiff_summary.pdf
# (note documentation PDF has its details flipped when it comes to the ranges for literal runs and packed runs)
# See also: ij.io.ImageReader.packBitsUncompress (a public method without side effects)
if use_imagereader:
return ImageReader(FileInfo()).packBitsUncompress(
getIFDImageBytes(ra, tags), tags["width"] * tags["height"])
try:
bytes = zeros(tags["width"] * tags["height"], 'b')
indexU = 0 # index over unpacked bytes
for strip_offset, strip_length in zip(tags["StripOffsets"],
tags["StripByteCounts"]):
ra.seek(strip_offset)
indexP = 0
while indexP < strip_length and indexU < len(bytes):
count = ra.readByte()
if count >= 0:
# Literal run
ra.read(bytes, indexU, count + 1)
indexP += count + 2 # one extra for the count byte
indexU += count + 1
else:
# Packed run
Arrays.fill(bytes, indexU, indexU - count + 1,
ra.readByte())
indexP += 2
indexU += -count + 1
except:
print sys.exc_info()
finally:
return bytes
cs = ChannelSeparator()
cs.setId(filepath)
bfvs = BFVirtualStack(filepath, cs, False, False, False)
stack = ImageStack(width, height)
for index in xrange(slice_index, slice_index + num_slices):
stack.addSlice(bfvs.getProcessor(index))
title = os.path.split(filepath)[1] + " from slice %i" % slice_index
imp = ImagePlus(title, stack)
imp.show()
finally:
cs.close()
# Approach 3: using low-level ImageJ libraries
from ij.io import FileInfo, FileOpener
fi = FileInfo()
fi.width = width
fi.height = height
fi.offset = headerSize + slice_offset
# ASSUMES images aren't ARGB, which would also have 32 as bit depth
# (There are other types: see FileInfo javadoc)
fi.fileType = {
8: FileInfo.GRAY8,
16: FileInfo.GRAY16_UNSIGNED,
24: FileInfo.RGB,
32: FileInfo.GRAY32_UNSIGNED
}[bitDepth]
fi.samplesPerPixel = 1
fi.nImages = num_slices
directory, filename = os.path.split(filepath)
fi.directory = directory
def read_TIFF_plane(ra, tags, handler=None):
""" ra: RandomAccessFile
tags: dicctionary of TIFF tags for the IFD of the plane to parse.
handler: defaults to Nobe; a function that reads the image data and returns an array.
For compressed image planes, takes advantage of the ij.io.ImageReader class
which contains methods that ought to be static (no side effects) and therefore
demand a dummy constructor just to invoke them.
"""
if handler:
return handler(ra, tags)
# Values of the "compressed" tag field (when present):
# 1: "uncompressed",
# 32773: "packbits",
# 5: "LZW",
# 6: "JPEG",
width, height = tags["width"], tags["height"]
bitDepth = tags["bitDepth"]
n_bytes = int(ceil(width * height *
(float(bitDepth) / 8))) # supports bitDepth < 8
compression = tags.get("compression", 1)
bytes = None
if 32773 == compression:
bytes = unpackBits(ra, tags, use_imagereader=True)
elif 5 == compression:
bytes = ImageReader(FileInfo()).lzwUncompress(
getIFDImageBytes(ra, tags), tags["width"] * tags["height"])
elif 32946 == compression or 8 == compression:
bytes = ImageReader(FileInfo()).zipUncompress(
getIFDImageBytes(ra, tags), tags["width"] * tags["height"])
elif 1 == compression:
bytes = zeros(n_bytes, 'b')
index = 0
for strip_offset, strip_length in zip(tags["StripOffsets"],
tags["StripByteCounts"]):
ra.seek(strip_offset)
ra.read(bytes, index, strip_length)
elif 6 == compression:
print "Unsupported compression: JPEG"
raise Exception("Can't handle JPEG compression of TIFF image planes")
else:
raise Exception("Can't deal with compression type " + str(compression))
# If read as bytes, parse to the appropriate primitive type
if 8 == bitDepth:
return bytes
bb = ByteBuffer.wrap(bytes)
if not tags["bigEndian"]:
bb = bb.order(ByteOrder.BIG_ENDIAN)
if 16 == bitDepth:
pixels = zeros(width * height, 'h')
bb.asShortBuffer().get(pixels)
return pixels
if 32 == bitDepth:
pixels = zeros(width * height, 'f')
bb.asFloatBuffer().get(pixels)
return pixels
if bitDepth < 8:
# Support for 1-bit, 2-bit, 3-bit, ... 12-bit, etc. images
pixels = zeros(int(ceil(width * height * bitDepth / 64.0)), 'l')
bb.asLongBuffer().get(pixels)
# Reverse bits from left to right to right to left for ImgLib2 LongArray
pixels = array(imap(Long.reverse, pixels), 'l')
return pixels
metadataStr += addMetadataEntry('nImages', str(frames))
metadataStr += addMetadataEntry('offset', str(offset+64))
metadataStr += addMetadataEntry('fileType', str(fileType))
metadataStr += addMetadataEntry('gapBetweenImages', str(gap+64))
if(metadataInconsistency > 0):
metadataStr += addMetadataEntry('Inconsistent METADATA', str(metadataInconsistency))
metadataStr += endMetadata()
metadataDlg = HTMLDialog("HIS parameters", metadataStr, 0)
size = metadataDlg.getSize()
if size.width < 300:
size.width = 300
if size.height < 300:
size.height = 300
metadataDlg.setSize(size)
finfo = FileInfo()
finfo.fileName = imp
finfo.width = width
finfo.height = height
finfo.nImages = frames
finfo.offset = offset+64
finfo.fileType = fileType-1
finfo.intelByteOrder = 1
finfo.gapBetweenImages = gap+64
finfo.fileFormat = 1
finfo.samplesPerPixel = 1
finfo.displayRanges = None
finfo.lutSize = 0
finfo.whiteIsZero = 0
vs = VirtualStack()
finfo.virtualStack = vs