def readblockfromtif(pidxbidx_):
planeidx, blockidx = pidxbidx_
blocks = []
planeshape = None
blockstart = None
blockend = None
for fname in filenames:
reader_ = getFileReaderForPath(fname)()
fp = reader_.open(fname)
try:
if minimize_reads:
# use multitif module to generate a fake, in-memory one-page tif file
# the advantage of this is that it cuts way down on the many small reads
# that PIL/pillow will make otherwise, which would be a problem for s3
tiffparser_ = multitif.TiffParser(fp, debug=False)
tiffilebuffer = multitif.packSinglePage(
tiffparser_, page_idx=planeidx)
bytebuf = io.BytesIO(tiffilebuffer)
try:
pilimg = Image.open(bytebuf)
ary = pil_to_array(pilimg).T
finally:
bytebuf.close()
del tiffilebuffer, tiffparser_, pilimg, bytebuf
else:
# read tif using PIL directly
pilimg = Image.open(fp)
pilimg.seek(planeidx)
ary = pil_to_array(pilimg).T
del pilimg
if not planeshape:
planeshape = ary.shape[:]
blockstart = blockidx * blocklenPixels
blockend = min(blockstart + blocklenPixels,
planeshape[0] * planeshape[1])
blocks.append(ary.ravel(order='C')[blockstart:blockend])
del ary
finally:
fp.close()
buf = vstack(
blocks).T # dimensions are now linindex x time (images)
del blocks
buf = buf.astype(newdtype, casting=casting, copy=False)
# append subscript keys based on dimensions
linindx = arange(blockstart, blockend) # zero-based
serieskeys = zip(
*map(tuple, unravel_index(linindx, planeshape, order='C')))
# add plane index to end of keys
serieskeys = [
tuple(list(keys_)[::-1] + [planeidx]) for keys_ in serieskeys
]
return zip(serieskeys, buf)
def __readMetadataFromFirstPageOfMultiTif(reader, filePath):
import thunder.rdds.fileio.multitif as multitif
# read first page of first file to get expected image size
tiffFP = reader.open(filePath)
tiffParser = multitif.TiffParser(tiffFP, debug=False)
tiffHeaders = multitif.TiffData()
tiffParser.parseFileHeader(destinationTiff=tiffHeaders)
firstIfd = tiffParser.parseNextImageFileDirectory(
destinationTiff=tiffHeaders)
if not firstIfd.isLuminanceImage():
raise ValueError(("File %s does not appear to be a luminance " %
filePath) +
"(greyscale or bilevel) TIF image, " +
"which are the only types currently supported")
# keep reading pages until we reach the end of the file, in order to get number of planes:
while tiffParser.parseNextImageFileDirectory(
destinationTiff=tiffHeaders):
pass
# get dimensions
npages = len(tiffHeaders.ifds)
height = firstIfd.getImageHeight()
width = firstIfd.getImageWidth()
# get datatype
bitsPerSample = firstIfd.getBitsPerSample()
if not (bitsPerSample in (8, 16, 32, 64)):
raise ValueError(
"Only 8, 16, 32, or 64 bit per pixel TIF images are supported, got %d"
% bitsPerSample)
sampleFormat = firstIfd.getSampleFormat()
if sampleFormat == multitif.SAMPLE_FORMAT_UINT:
dtStr = 'uint'
elif sampleFormat == multitif.SAMPLE_FORMAT_INT:
dtStr = 'int'
elif sampleFormat == multitif.SAMPLE_FORMAT_FLOAT:
dtStr = 'float'
else:
raise ValueError(
"Unknown TIF SampleFormat tag value %d, should be 1, 2, or 3 for uint, int, or float"
% sampleFormat)
dtype = dtStr + str(bitsPerSample)
return height, width, npages, dtype