def xySlice ( self, fileobj ):
zdim,ydim,xdim = self.data.shape
imagemap = np.zeros ( [ ydim, xdim ], dtype=np.uint32 )
# false color redrawing of the region
recolor_cy ( self.data.reshape((imagemap.shape[0],imagemap.shape[1])), imagemap )
outimage = Image.frombuffer ( 'RGBA', (xdim,ydim), imagemap, 'raw', 'RGBA', 0, 1 )
outimage.save ( fileobj, "PNG" )
def yzSlice ( self, scale, fileobj ):
zdim,ydim,xdim = self.data.shape
imagemap = np.zeros ( [ zdim, ydim ], dtype=np.uint32 )
# false color redrawing of the region
recolor_cy ( self.data.reshape((imagemap.shape[0],imagemap.shape[1])), imagemap )
outimage = Image.frombuffer ( 'RGBA', (ydim,zdim), imagemap, 'raw', 'RGBA', 0, 1 )
newimage = outimage.resize ( [ydim, int(zdim*scale)] )
newimage.save ( fileobj, "PNG" )
def tile2WebPNG ( self, xdim, ydim, tile ):
"""Create PNG Images and write to cache for the specified tile"""
# write it as a png file
if self.dbtype == dbtype.IMAGES_8bit :
return Image.frombuffer ( 'L', [xdim,ydim], tile.flatten(), 'raw', 'L', 0, 1 )
elif self.dbtype == dbtype.ANNOTATIONS :
recolor_cy (tile, tile)
return Image.frombuffer ( 'RGBA', [xdim,ydim], tile.flatten(), 'raw', 'RGBA', 0, 1 )
elif self.dbtype == dbtype.IMAGES_16bit :
outimage = Image.frombuffer ( 'I;16', [xdim,ydim], tile.flatten(), 'raw', 'I;16', 0, 1)
outimage = outimage.point(lambda i:i*(1./256)).convert('L')
elif self.dbtype == dbtype.RGB_32bit :
outimage = Image.fromarray( tile, 'RGBA')
else :
logger.warning ( "Datatype not yet supported".format(self.dbtype) )
return outimage
def cacheMiss ( self, resolution, xtile, ytile, zslice ):
"""On a miss. Cutout, return the image and load the cache in a background thread"""
# make sure that the tile size is aligned with the cubedim
if self.tilesz % self.proj.datasetcfg.cubedim[resolution][0] != 0 or self.tilesz % self.proj.datasetcfg.cubedim[resolution][1]:
raise("Illegal tile size. Not aligned")
# figure out the cutout (limit to max image size)
xstart = xtile*self.tilesz
ystart = ytile*self.tilesz
xend = min ((xtile+1)*self.tilesz,self.proj.datasetcfg.imagesz[resolution][0])
yend = min ((ytile+1)*self.tilesz,self.proj.datasetcfg.imagesz[resolution][1])
# get an xy image slice
imageargs = '{}/{},{}/{},{}/{}/'.format(resolution,xstart,xend,ystart,yend,zslice)
cb = ocpcarest.xySlice ( imageargs, self.proj, self.db )
if cb.data.shape != (1,self.tilesz,self.tilesz):
tiledata = np.zeros((self.tilesz,self.tilesz), cb.data.dtype )
tiledata[0:((yend-1)%self.tilesz+1),0:((xend-1)%self.tilesz+1)] = cb.data[0,:,:]
else:
tiledata = cb.data
# need to make polymorphic for different image types
if tiledata.dtype == np.uint8:
outimage = Image.frombuffer ( 'L', (self.tilesz,self.tilesz), tiledata, 'raw', 'L', 0, 1 )
elif tiledata.dtype == np.uint32:
tiledata = tiledata.reshape([self.tilesz,self.tilesz])
recolor_cy (tiledata, tiledata)
outimage = Image.frombuffer ( 'RGBA', [self.tilesz,self.tilesz], tiledata, 'raw', 'RGBA', 0, 1 )
else:
#added by PJM to support probmap type.
tiledata = np.uint8(tiledata*256)
outimage = Image.frombuffer ( 'L', (self.tilesz,self.tilesz), tiledata, 'raw', 'L', 0, 1 )
#assert 0
# need to fix here and add falsecolor args
return outimage
def tile2WebPNG ( self, tile, color, brightness ):
"""Create PNG Images for the specified tile"""
if color != None:
# 16 bit images map down to 8 bits
if tile.dtype == np.uint16:
tile = np.uint8(tile/256)
# false color the image
if tile.dtype != np.uint8:
raise ("Illegal color option for data type %s" % ( tile.dtype ))
else:
tile = self.falseColor ( tile, color )
img = Image.frombuffer ( 'RGBA', [self.tilesz,self.tilesz], tile.flatten(), 'raw', 'RGBA', 0, 1 )
# enhance false color images when requested
if brightness != None:
# Enhance the image
from PIL import ImageEnhance
enhancer = ImageEnhance.Brightness(img)
img = enhancer.enhance(brightness)
return img
else:
# write it as a png file
if tile.dtype==np.uint8:
return Image.frombuffer ( 'L', [self.tilesz,self.tilesz], tile.flatten(), 'raw', 'L', 0, 1 )
elif tile.dtype==np.uint32:
recolor_cy (tile, tile)
return Image.frombuffer ( 'RGBA', [self.tilesz,self.tilesz], tile.flatten(), 'raw', 'RGBA', 0, 1 )
elif tile.dtype==np.uint16:
outimage = Image.frombuffer ( 'I;16', [self.tilesz,self.tilesz], tile.flatten(), 'raw', 'I;16', 0, 1)
outimage = outimage.point(lambda i:i*(1./256)).convert('L')
return outimage
def catmaidSlice( self ):
cmtilesz = self.data.shape[0]
recolor_cy( self.data, self.data )
self.data = Image.frombuffer ( 'L', [cmtilesz,cmtilesz], self.data, 'raw', 'RGBA', 0, 1 )
