def createMorph(selectedImages,selectedPMs):
"""
Translates and rotate the bitmaps based on the shapedefining landmarks (selectedPMs)
of the associated image to the target image (first image).
Morphs the result so that the bitmap overlay on the first image is valid for the first image.
"""
#save the temporary results here later:
os_temp_path = tempfile.gettempdir()
#get the measurements for the first image (our targets)
mainImage = OriginalImage.objects.all().get(id=selectedImages[0])
potentialids = []
#now get the associated measurements
measures = Measurement.objects.all().filter(id__in=selectedPMs[0]).filter(mogelijkemeting__shapedefining=True)
measures = [j for j in measures]
measures.sort(key=lambda x: x.mogelijkemeting.name)
coordsx = []
coordsy = []
for k, measurement in enumerate(measures):
coordsx.append(float(measurement.x))
coordsy.append(float(measurement.y))
potentialids.append(measurement.mogelijkemeting.id)
r1 = vtk.vtkJPEGReader()
r1.SetFileName(settings.DATADIR + mainImage.id + ".jpg")
r1.Update()
# flip y coord (VTK has opposite convention), create 3-d coords (z=0)
ydim = r1.GetOutput().GetDimensions()[1]
coords = [(x, ydim - y, 0) for (x,y) in zip(coordsx, coordsy)]
# convert everything to vtkPoints
lmt = vtk.vtkPoints()
lmt.SetNumberOfPoints(len(coords))
for i, coord in enumerate(coords):
lmt.SetPoint(i,coord)
#The target is clear, let's get to work, get the source images...
images = []
#we don't need the first image or its measures anymore, because they don't need to be transformed or morphed
selectedImages.pop(0)
selectedPMs.pop(0)
for id in selectedImages:
images.append(OriginalImage.objects.all().get(id=id))
transformations = []
morphtransformations = []
#Create a new database object for the target image to associate the bitmaps with
img = OriginalImage(project=mainImage.project, name='MorphedImage')
img.save()
imp = Image.open(settings.DATADIR + mainImage.id + '.jpg')
imp.save(settings.DATADIR + img.id + '.jpg', 'JPEG')
orig_bitmaps = Bitmap.objects.all().filter(image=mainImage)
for bm in orig_bitmaps:
#store bitmaps of mainImage as sub of img
bitmap = Bitmap(project=img.project, name='warpedbitmap', image=img,
mogelijkemeting=bm.mogelijkemeting, imagewidth=bm.imagewidth,
imageheight=bm.imageheight, minx=bm.minx, miny=bm.miny, maxx=bm.maxx, maxy=bm.maxy)
bitmap.save()
bitmap_image = Image.open(settings.DATADIR + bm.id + '.gif')
bitmap_image = bitmap_image.convert("RGBA")
bitmap_image.save(settings.DATADIR + bitmap.id + '.gif', transparency=0)
#now get the other images and perform our transformations
for i in range(len(images)):
measures = Measurement.objects.all().filter(id__in=selectedPMs[i]).filter(mogelijkemeting__shapedefining=True)#get measurements
measures = [j for j in measures]
measures.sort(key=lambda x: x.mogelijkemeting.name)
coordsx = []
coordsy = []
for k, measurement in enumerate(measures):
coordsx.append(float(measurement.x))
coordsy.append(float(measurement.y))
if potentialids[k] != measurement.mogelijkemeting.id: #the potentialmeasurements do not match up to the ones in the target image
return img, 0
r = vtk.vtkJPEGReader()
r.SetFileName(settings.DATADIR + images[i].id + ".jpg")
r.Update()
ydim = r.GetOutput().GetDimensions()[1]
coordso = [(x, ydim - y, 0) for (x,y) in zip(coordsx, coordsy)]
lms = vtk.vtkPoints()
lms.SetNumberOfPoints(len(coordso))
for k, coord in enumerate(coordso):
lms.SetPoint(k,coord)
transformation = vtk.vtkLandmarkTransform()
transformation.SetTargetLandmarks(lmt)
lmt.Modified()
transformation.SetSourceLandmarks(lms)
lms.Modified()
#size matters, so set the mode to Rigid Body (also known as do not scale please)
transformation.SetModeToRigidBody()
transformation.Inverse()
transformation.Update()
out = vtk.vtkPoints()#this will be the source of our morph transform
transformation.TransformPoints(lms,out)
transformations.append(transformation)
ir = vtk.vtkImageReslice()
# we're not using linear, because we want to improve the quality of the bitmaps
ir.SetInterpolationModeToNearestNeighbor()
ir.SetResliceTransform(transformation)
ir.SetInput(r.GetOutput())
ir.SetInformationInput(r1.GetOutput())
w = vtk.vtkJPEGWriter()
w.SetFileName(os_temp_path+'/translated'+images[i].id+'.jpg')
w.SetInput(ir.GetOutput())
w.Write()
r2 = vtk.vtkJPEGReader()
r2.SetFileName(os_temp_path+'/translated'+images[i].id+'.jpg')
r2.Update()
# the mighty morphing ThinPlateSplineTransform
morphtransform = vtk.vtkThinPlateSplineTransform()
morphtransform.SetBasisToR2LogR()
morphtransform.SetSourceLandmarks(lms)
lms.Modified()
morphtransform.SetTargetLandmarks(lmt)
lmt.Modified()
morphtransform.Inverse()
morphtransform.Update()
morphtransformations.append(morphtransform)
#ir.SetInput(r2.GetOutput())
#ir.SetInformationInput(r1.GetOutput())
bitmaps = Bitmap.objects.all().filter(image=images[i])
#now perform the total transformation on all bitmaps
for bm in bitmaps:
location = settings.DATADIR + bm.id + ".gif"
im = Image.open(location)
im = im.convert("RGBA")
im.save(settings.DATADIR + bm.id + ".png", "PNG")
r3 = vtk.vtkPNGReader()
r3.SetFileName(settings.DATADIR + bm.id + '.png')
r3.Update()
ir2 = vtk.vtkImageReslice()
ir2.SetInterpolationModeToNearestNeighbor()
ir2.SetResliceTransform(morphtransform)
ir2.SetInput(r3.GetOutput())
ir2.SetInformationInput(r2.GetOutput())
w3 = vtk.vtkPNGWriter()
w3.SetFileName(os_temp_path+'/morphed'+bm.id+'.png')
w3.SetInput(ir2.GetOutput())
w3.Write()
bitmap = Bitmap(project=img.project, name='warpedbitmap', image=img,
mogelijkemeting=bm.mogelijkemeting, imagewidth=bm.imagewidth,
imageheight=bm.imageheight, minx=bm.minx, miny=bm.miny, maxx=bm.maxx, maxy=bm.maxy)
bitmap.save()
im = Image.open(os_temp_path+'/morphed'+bm.id+'.png')
im = im.convert("RGBA")
im.save(settings.DATADIR + bitmap.id + '.gif', transparency=0)
return img, 1
def handle_bitmap_stream(dump,original_image,previous_id,r,g,b,mm):
""" With the string representation of a bitmap; the original_image
this bitmap is painted over; the id of the previous bitmap;
the color information and the id of the possible measurement
this function saves the dump as a .gif-file and puts it in the db.
"""
# Check the header
if dump == "_empty":
print "Empty bitmap submitted"
return previous_id
# Initialise color information
if not (r >= 0 and r <= 255 and
g >= 0 and g <= 255 and
b >= 0 and b <= 255):
r = 255
g = 0
b = 0
#backgroundColor = ((r << 16) & 0xFF) + ((g << 8) & 0xFF) + (b & 0xFF);
# Split dump in header and body
dump = dump.split("#")
header = dump[0].split("x")
body = dump[1]
# Check the header
if header[0] != "_scanline:":
print "wrong dump"
return
# Load needed variables from header
total_width = int(header[1])
total_height = int(header[2])
min_x = int(header[3])
max_x = int(header[4])
min_y = int(header[5])
max_y = int(header[6])
# Derive needed variables from loaded variables
block_width = max_x - min_x + 1
block_height = max_y - min_y + 1
skip_before = min_y * total_width + min_x
skip_between = min_x + (total_width - 1 - max_x)
skip_after = (total_height - 1 - max_y) * total_width + (total_width - 1 - max_x)
# Create string to fill before and after block
fill_before = ''.zfill(skip_before).replace('0',chr(0))
fill_after = ''.zfill(skip_after).replace('0',chr(0))
# Keep track of the amount of pixels that is currently on the line
# in the block to be able to determine how often we need to add skip_between
line_fill = 0
# Make decode bit-stream
stream = fill_before
# Do as long as there is still data in body
while len(body) > 1:
# Find number of black pixels
end = body.find("b")
i = int(body[:end])
body = body[end+1:]
# We need at least to add i pixels
line_fill += i
# Each whole amount block_with fits in line_fill,
# we need to add skip_between
while line_fill > block_width:
i += skip_between
line_fill -= block_width
# Write i background pixels to the bit-stream
stream += ''.zfill(i).replace('0',chr(0))
# Stop if we now finished the end of the string data
if len(body) < 2: break;
# Now do the foreground
end = body.find("f")
i = int(body[:end])
body = body[end+1:]
# If we now need to add lines, it should
# also be background outside the block
if line_fill + i > block_width:
# First write foreground pixels to fill the current row in the block
stream += ''.zfill(block_width - line_fill).replace('0', chr(255))
# We still have this much pixels to write
line_fill = i - (block_width - line_fill)
# As long as we can fill full block lines
while line_fill > block_width:
# First write background line to get back to block
stream += ''.zfill(skip_between).replace('0', chr(0))
# Then write a full line foreground-data
stream += ''.zfill(block_width).replace('0', chr(255))
line_fill -= block_width
# Return to a new line (by filling space outside the block)
stream += ''.zfill(skip_between).replace('0', chr(0))
# We still have a number of pixels left to write
i = line_fill
# Otherwise we also need to remember this set of pixels
else:
line_fill += i
# Write to the bit-stream
stream += ''.zfill(i).replace('0',chr(255))
stream += fill_after
# Build image
im = Image.fromstring("L",(total_width,total_height), stream, "raw", "L")
# Attach palette
im.convert("P")
palette = []
for i in range(256):
palette.extend((0, 0, 0))
palette[0] = 0
palette[1] = 0
palette[2] = 0
palette[765] = r
palette[766] = g
palette[767] = b
assert len(palette) == 768
im.putpalette(palette)
# Make database insert
if previous_id == '0':
# Create associated measurement
properties = dict(
image = original_image,
mogelijkemeting = mm,
imagewidth = int(total_width),
imageheight = int(total_height),
minx = min_x,
maxx = max_x,
miny = min_y,
maxy = max_y,
project = original_image.project,
name = "bitmap",
)
db_bitmap = Bitmap(**properties)
db_bitmap.save()
img_path = os.path.join(settings.DATADIR, db_bitmap.id + ".gif")
im.save(img_path, transparency=0)
return db_bitmap.id
# Just overwrite previous image-file
else:
previous_image = Bitmap.objects.all().get(id=previous_id)
previous_image.minx = min_x
previous_image.maxx = max_x
previous_image.miny = min_y
previous_image.maxy = max_y
previous_image.save()
image_path = os.path.join(settings.DATADIR, previous_image.id + '.gif')
im.save(image_path, transparency=0)
return previous_id
