def write_fused(output_path,channel,sizeZ,theC,physX,physY,physZ):
IJ.log("Writing fused data")
# number of slices will determine filename format
digits = "00"
if sizeZ < 100:
digits = "0"
if sizeZ < 10:
digits = ""
# get the base metadata from the first fused image
meta = MetadataTools.createOMEXMLMetadata()
reader = get_reader(output_path+"img_t1_z%s1_c1"%digits,meta)
reader.close()
# reset some metadata
meta.setPixelsPhysicalSizeX(physX,0)
meta.setPixelsPhysicalSizeY(physY,0)
meta.setPixelsPhysicalSizeZ(physZ,0)
meta.setPixelsSizeZ(PositiveInteger(sizeZ),0)
meta.setChannelID("Channel:0:" + str(0), 0, 0)
spp = channel['spp']
meta.setChannelSamplesPerPixel(spp, 0, 0)
name = channel['name']
color = channel['color']
meta.setChannelName(name,0,0)
meta.setChannelColor(color,0,0)
# determine the number of subsets that need to be written
slices_per_subset = 200
num_output_files = divmod(sizeZ,slices_per_subset)
fpaths = []
if num_output_files[0] == 0:
nslices = [sizeZ]
num_output_files = 1
fpaths.append("%sfused_C%s.ome.tif"%(output_path,str(theC-1)))
else:
nslices = []
for n in range(num_output_files[0]):
nslices.append(slices_per_subset)
if num_output_files[1] > 0:
nslices.append(num_output_files[1])
for s in range(len(nslices)):
fpaths.append("%sfused_C%s_subset%s.ome.tif"%(output_path,str(theC-1),str(s)))
# setup a writer
writer = ImageWriter()
writer.setCompression('LZW')
writer.setMetadataRetrieve(meta)
writer.setId(fpaths[0])
# write the slices, changing the output file when necessary
theZ = 0
for f in range(len(fpaths)):
meta.setImageName(os.path.basename(fpaths[f]),0)
writer.changeOutputFile(fpaths[f])
for s in range(nslices[f]):
fpath = output_path+"img_t1_z%s%s_c1"%(digits,str(theZ+1))
if (len(digits) == 1) and (theZ+1 > 9):
fpath = output_path+"img_t1_z%s_c1"%(str(theZ+1))
if (len(digits) == 2) and (theZ+1 > 9):
fpath = output_path+"img_t1_z0%s_c1"%(str(theZ+1))
if (len(digits) == 2) and (theZ+1 > 99):
fpath = output_path+"img_t1_z%s_c1"%(str(theZ+1))
IJ.log("writing slice %s"%os.path.basename(fpath))
m = MetadataTools.createOMEXMLMetadata()
r = get_reader(fpath,m)
m.setPixelsPhysicalSizeX(physX,0)
m.setPixelsPhysicalSizeY(physY,0)
m.setPixelsPhysicalSizeZ(physZ,0)
m.setChannelID("Channel:0:" + str(0), 0, 0)
spp = channel['spp']
m.setChannelSamplesPerPixel(spp, 0, 0)
name = channel['name']
color = channel['color']
m.setChannelName(name,0,0)
m.setChannelColor(color,0,0)
writer.saveBytes(theZ,r.openBytes(0))
r.close()
theZ += 1
writer.close()
def save_ome_tiff(filename, image, metadata):
reader = ImageReader()
writer = ImageWriter()
writer.setMetadataRetrieve(metadata)
writer.setId(filename)
nchan = image.getNChannels()
stack = image.getImageStack()
print(image.getStackSize())
for i in range(nchan):
writer.setSeries(0)
process = stack.getProcessor(i + 1)
pixels = process.getPixels()
pixels = DataTools.floatsToBytes(pixels, True)
writer.saveBytes(i, pixels)
writer.close()
def run():
t_start = datetime.now()
image_paths = glob(os.path.join(str(import_dir.getPath()), '*tif'))
print '\tread image metadata'
reader = ImageReader()
in_meta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(in_meta)
x_dims = []
y_dims = []
z_dims = []
c_dims = []
t_dims = []
eff = []
spp = []
for image_path in image_paths:
print '\t parse %s' % (image_path)
reader.setId(image_path)
x_dims.append(reader.getSizeX())
y_dims.append(reader.getSizeY())
z_dims.append(reader.getSizeZ())
c_dims.append(reader.getSizeC())
t_dims.append(reader.getSizeT())
eff.append(reader.imageCount / z_dims[-1] / t_dims[-1])
spp.append(reader.getSizeC() / eff[-1])
format = FormatTools.getPixelTypeString(reader.getPixelType())
series = reader.getSeries()
big_endian = Boolean.FALSE
order = reader.getDimensionOrder()
reader.close()
# Compute the dimensions of the output file
x_dim = max(x_dims)
y_dim = max(y_dims)
z_dim = max(z_dims)
c_dim = max(c_dims)
t_dim = max(t_dims)
print '\t series: %i' % series
print '\t format: %s' % format
print '\t dimension order: %s' % order
print '\t x: %s -> %i' % (x_dims, x_dim)
print '\t y: %s -> %i' % (y_dims, y_dim)
print '\t z: %s -> %i' % (z_dims, z_dim)
print '\t c: %s -> %i' % (c_dims, c_dim)
print '\t t: %s -> %i' % (t_dims, t_dim)
print '\t effective size c: %s' % eff
print '\t samples per pixel: %s' % spp
# Get the time dimension from the number of input files
t_dim = len(image_paths)
# TODO: Tried to work out the order with Axes class, got something weird though.
dimensions = [Short(x_dim), Short(y_dim), Short(c_dim), Short(z_dim)]
pixels_per_plane = x_dim * y_dim
# Assemble the metadata for the output file
out_meta = MetadataTools.createOMEXMLMetadata()
out_meta.setImageID(MetadataTools.createLSID('Image', series), series)
out_meta.setPixelsID(MetadataTools.createLSID('Pixels', series), series)
out_meta.setPixelsBinDataBigEndian(Boolean.TRUE, 0, 0)
out_meta.setPixelsDimensionOrder(DimensionOrder.fromString(order), series)
out_meta.setPixelsType(PixelType.fromString(format), series)
out_meta.setPixelsSizeX(PositiveInteger(x_dim), series)
out_meta.setPixelsSizeY(PositiveInteger(y_dim), series)
out_meta.setPixelsSizeZ(PositiveInteger(z_dim), series)
out_meta.setPixelsSizeC(PositiveInteger(c_dim), series)
out_meta.setPixelsSizeT(PositiveInteger(t_dim), series)
for c in range(c_dim):
out_meta.setChannelID(MetadataTools.createLSID('Channel', series, c),
series, c)
out_meta.setChannelSamplesPerPixel(PositiveInteger(1), series, c)
# Initialize the BF writer
result_path = os.path.join(result_dir.getPath(), result_name)
writer = ImageWriter()
writer.setMetadataRetrieve(out_meta)
writer.setId(result_path)
print '\tcreated to %s' % (result_path)
# Write the stacks into the output file
N = len(image_paths)
for i, image_path in enumerate(image_paths):
status.showStatus(i, N, "catenating %i of %i time-points" % (i, N))
print '\t processing %s' % (image_path)
ds = io.open(image_path)
xi = ds.dimensionIndex(Axes.X)
xv = ds.dimension(xi)
yi = ds.dimensionIndex(Axes.Y)
yv = ds.dimension(yi)
zi = ds.dimensionIndex(Axes.Z)
zv = ds.dimension(zi)
ti = ds.dimensionIndex(Axes.TIME)
tv = ds.dimension(ti)
ci = ds.dimensionIndex(Axes.CHANNEL)
cv = ds.dimension(ci)
dx = float(x_dim - xv) / 2.0
dy = float(y_dim - yv) / 2.0
dz = float(z_dim - zv) / 2.0
print '\t translation vector (dx, dy, dz) = (%f, %f, %f)' % (
dx, dy, dz)
if (dx != 0) or (dy != 0) or (dz != 0):
stk = Views.translate(ds, long(dx), long(dy), long(0), long(dz))
stk = Views.extendZero(stk)
else:
stk = Views.extendZero(ds.getImgPlus().getImg())
print '\t writing planes ',
n = 0
plane = 1
byte_array = []
interval_view = Views.interval(stk, \
[Long(0), Long(0), Long(0), Long(0)], \
[Long(x_dim - 1), Long(y_dim - 1), Long(c_dim - 1), Long(z_dim - 1)])
cursor = interval_view.cursor()
while cursor.hasNext():
n += 1
cursor.fwd()
value = cursor.get().getInteger()
bytes = DataTools.shortToBytes(value, big_endian)
byte_array.extend(bytes)
if n == pixels_per_plane:
writer.saveBytes(plane - 1, byte_array)
print '.',
if ((plane) % 10) == 0:
print '\n\t ',
byte_array = []
plane += 1
n = 0
print ' '
writer.close()
t = datetime.now() - t_start
print '\twrote %i planes to %s in %i sec.' % (plane - 1, result_path,
t.total_seconds())
print '... done.'
def write_tiles(r,tiles_dir,theT,sizeC,sizeZ,meta):
writer = ImageWriter()
writer.setCompression('LZW')
writer.setMetadataRetrieve(meta)
writer.setId("%s/tile_%s.ome.tif"%(tiles_dir,theT))
planes = sizeZ * sizeC
p = 0
for theZ in range(sizeZ):
for theC in range(sizeC):
writer.saveBytes(p,r.openBytes(reader.getIndex(theZ, theC, theT)))
p += 1
writer.close()
def write_fused(output_path,meta):
imp = ij.WindowManager.getCurrentImage()
meta.setPixelsSizeX(PositiveInteger(imp.getWidth()),0)
meta.setPixelsSizeY(PositiveInteger(imp.getHeight()),0)
writer = ImageWriter()
writer.setCompression('LZW')
writer.setMetadataRetrieve(meta)
writer.setId("%s/fused.ome.tif"%output_path)
littleEndian = not writer.getMetadataRetrieve().getPixelsBinDataBigEndian(0, 0)
planes = imp.getStack()
for p in range(planes.getSize()):
proc = planes.getProcessor(p+1)
writer.saveBytes(p,DataTools.shortsToBytes(proc.getPixels(), littleEndian))
writer.close()
start = len(shape + " " + "points=") + 1
pts = omeMetaStr[start+prefix:stop]
new_pts_str =pts.replace(" ",",")
new_pts = [int(p) for p in new_pts_str.split(",")]
xs = new_pts[0::2]
ys = new_pts[1::2]
proi = PolygonRoi(xs, ys, len(xs), Roi.POLYGON)
imp = imps[0]
imp.setRoi(proi)
# create a writer and set metadata
writer = ImageWriter()
writer.setMetadataRetrieve(omeMeta)
writer.setId('%s')
# get the stack
planes = imp.getStack()
for p in range(planes.getSize()):
# get the plane
plane = planes.getProcessor(p+1)
# fill outside
plane.fillOutside(proi)
pixels = plane.convertToByte(True).getPixels()
writer.saveBytes(p,pixels)