def makeImg(filepaths, pixelType, loadImg, img_dimensions, matrices,
cropInterval, preload):
dims = Intervals.dimensionsAsLongArray(cropInterval)
voldims = [dims[0], dims[1], len(filepaths)]
cell_dimensions = [dims[0], dims[1], 1]
grid = CellGrid(voldims, cell_dimensions)
cellGet = TranslatedSectionGet(filepaths,
loadImg,
matrices,
img_dimensions,
cell_dimensions,
cropInterval,
preload=preload)
return LazyCellImg(grid, pixelType(), cellGet), cellGet
def lazyCachedCellImg(loader, volume_dimensions, cell_dimensions, pixelType, primitiveType):
""" Create a lazy CachedCellImg, backed by a SoftRefLoaderCache,
which can be used to e.g. create the equivalent of ij.VirtualStack but with ImgLib2,
with the added benefit of a cache based on SoftReference (i.e. no need to manage memory).
loader: a CacheLoader that returns a single Cell for each index (like the Z index in a VirtualStack).
volume_dimensions: a list of int or long numbers, with the last dimension
being the number of Cell instances (i.e. the number of file paths).
cell_dimensions: a list of int or long numbers, whose last dimension is 1.
pixelType: e.g. UnsignedByteType
primitiveType: e.g. BYTE
Returns a CachedCellImg.
"""
return CachedCellImg(CellGrid(volume_dimensions, cell_dimensions),
pixelType(),
SoftRefLoaderCache().withLoader(loader),
ArrayDataAccessFactory.get(primitiveType, AccessFlags.setOf(AccessFlags.VOLATILE)))
os.path.join(folderpath, filename)
for filename in sorted(os.listdir(folderpath))
]
# Desired dimensions for reading in chunks of a single section
#cell_width, cell_height = 1024, 1024 # one megabyte
cell_width, cell_height = 256, 256
# Each Cell is a chunk of a single section, hence 3rd dimension is 1
cell_dimensions = [cell_width, cell_height, 1]
# Volume dimensions
dimensions = [section_width, section_height, len(filepaths)]
# The grid of the CellImg
grid = CellGrid(dimensions, cell_dimensions)
def createAccess(bytes, bytesPerPixel):
""" Return a new volatile access instance for the appropriate pixel type.
Supports byte, short, float and long. """
if 1 == bytesPerPixel: # BYTE
return VolatileByteArray(bytes, True)
# Transform bytes into another type
bb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN)
if 2 == bytesPerPixel: # SHORT
pixels = zeros(len(bytes) / 2, 's')
bb.asShortBuffer().get(pixels)
return VolatileShortArray(pixels, True)
if 4 == bytesPerPixel: # FLOAT
pixels = zeros(len(bytes) / 4, 'f')
filepaths = [
os.path.join(folderpath, filename)
for filename in sorted(os.listdir(folderpath))
]
# Desired dimensions for reaching chunks of a single section
cell_width, cell_height = 1024, 1024 # one megabyte
# Each Cell is a chunk of a single section, hence 3rd dimension is 1
cell_dimensions = [cell_width, cell_height, 1]
# Volume dimensions
dimensions = [section_width, section_height, len(filepaths)]
# The grid of the CellImg
grid = CellGrid(dimensions, cell_dimensions)
nX, nY, nZ = grid.getGridDimensions()
cells_per_section = nX * nY
def createAccess(bytes, bytesPerPixel):
""" Return a new access instance for the appropriate pixel type.
Supports byte, short, float and long. """
if 1 == bytesPerPixel: # BYTE
return ByteArray(bytes)
# Transform bytes into another type
bb = ByteBuffer.wrap(bytes).order(ByteOrder.BIG_ENDIAN)
if 2 == bytesPerPixel: # SHORT
pixels = zeros(len(bytes) / 2, 's')
bb.asShortBuffer().get(pixels)
return ShortArray(pixels)
img.dimension(0),
img.dimension(1),
img.dimension(2), 1
]
return Cell(self.cell_dimensions, [0, 0, 0, index],
extractDataAccess(img, self.cell_dimensions))
first = getStack(timepoint_paths[0])
# One cell per time point
dimensions = [
1 * first.dimension(0), 1 * first.dimension(1), 1 * first.dimension(2),
len(timepoint_paths)
]
grid = CellGrid(dimensions, dimensions[0:3] + [1])
vol4d = LazyCellImg(grid,
first.randomAccess().get().createVariable(),
TimePointGet(timepoint_paths))
print dimensions
# Visualization option 2:
# Create a 4D VirtualStack manually
# Need a fast way to copy pixel-wise
w = Weaver.method(
"""
static public final void copy(final Cursor src, final Cursor tgt) {
while (src.hasNext()) {
img.dimension(d) - 1 + self.cell_padding
for d in xrange(img.numDimensions())
]
imgP = Views.interval(imgE, minC, maxC)
return Cell(cell_dimensions, [x0, y0],
ProxyByteAccess(imgP, self.grid))
n_cols = 10
n_rows = 12
cell_padding = 5 # pixels, effective cell dimensions are 5+width+5, 5+height+5
cell_width = imp.getWidth() + cell_padding * 2
cell_height = imp.getHeight() + cell_padding * 2
grid = CellGrid([n_cols * cell_width, n_rows * cell_height],
[cell_width, cell_height])
print grid # shows: CellGrid( dims = (1572, 1640), cellDims = (131, 164) )
print "numDim:", grid.numDimensions()
print "gridDim:", grid.getGridDimensions()
print "x, y", grid.gridDimension(0), grid.gridDimension(1)
print "imgDim:", grid.getImgDimensions()
print "cellDim", grid.cellDimension(0), grid.cellDimension(1)
cellMin = zeros(2, 'l')
cellDims = zeros(2, 'i')
grid.getCellDimensions(0, cellMin, cellDims)
print "cellDim 0", cellMin, cellDims
grid.getCellDimensions(5, cellMin, cellDims)
print "cellDim 5", cellMin, cellDims
grid.getCellDimensions(10, cellMin, cellDims)
print "cellDim 10", cellMin, cellDims
slices = TIFFSlices(filepath)
for IFD in slices.IFDs:
print IFD
firstIFD = slices.IFDs[0]
print firstIFD
width, height = firstIFD["width"], firstIFD["height"]
bitDepth = firstIFD["bitDepth"]
pixel_type = {
8: UnsignedByteType,
16: UnsignedShortType,
32: FloatType
}[bitDepth]
grid = CellGrid([width, height, len(slices.IFDs)], [width, height, 1])
# The whole TIFF file as one Cell per slice, independently loadable
imgTIFF = LazyCellImg(grid, pixel_type(), slices)
# The whole file
#imp = IL.wrap(imgTIFF, os.path.basename(filepath))
#imp.show()
# Pick only from slices 3 to 6
view_3_to_6 = Views.interval(imgTIFF, [0, 0, 0], [width - 1, height - 1, 5])
imp_3_to_6 = IL.wrap(view_3_to_6, "3 to 6")
imp_3_to_6.show()
# Pick only every 3rd slice
#view_every_3 = Views.subsample(imgTIFF, [1, 1, 3])
cache_loader = SoftRefLoaderCache().withLoader(loader) # SoftReference
# Load the first image via the loader so that it's cached
# and read the dimensions
first = cache_loader.get(
0
) # a Cell that wraps the ShortArray for the image pixels of the slice at index 0
width = first.dimension(0)
height = first.dimension(1)
depth = len(
filepaths) # assumption: all files have the same dimensions and pixel type
volume_dimensions = [width, height, depth]
cell_dimensions = [width, height, 1] # just one image, one stack slice
# The layout of cells: in this case, each Cell is a stack slice
grid = CellGrid(volume_dimensions, cell_dimensions)
img = CachedCellImg(
grid, # the data layout
UnsignedShortType(
), # for 16-bit images, each with a short[] native arrays
cache_loader, # the loader, with a SoftReference cache
ArrayDataAccessFactory.get(PrimitiveType.SHORT,
AccessFlags.setOf(AccessFlags.VOLATILE)))
IL.show(
img,
"Virtual stack: lazy-loading cached CellImg of a whole directory of images"
)
def makeCell(self, index):
n_cols = self.grid.imgDimension(0) / self.grid.cellDimension(0)
x0 = (index % n_cols) * self.grid.cellDimension(0)
y0 = (index / n_cols) * self.grid.cellDimension(1)
index += 1 # 1-based slice indices in ij.ImageStack
if index < 1 or index > self.imp.getStack().size():
# Return blank image: a ByteAccess that always returns 255
return Cell(
self.cell_dimensions, [x0, y0],
type('ConstantValue', (ByteAccess, ), {
'getValue': lambda self, index: 255
})())
else:
return Cell(
self.cell_dimensions, [x0, y0],
ByteArray(self.imp.getStack().getProcessor(index).getPixels()))
n_cols = 12
n_rows = 10
cell_width = imp.getWidth()
cell_height = imp.getHeight()
grid = CellGrid([n_cols * cell_width, n_rows * cell_height],
[cell_width, cell_height])
montage = LazyCellImg(grid,
img.cursor().next().createVariable(),
SliceGet(imp, grid))
IL.show(montage, "Montage")