def stitch(targets,images):
mask = rois_mask(targets) # True where image data is
gaps_mask = mask==False # True where infill needs to go
# compute bounds relative to the camera field
(x,y,w,h) = stitched_box(targets)
uroi = img_as_float(stitch_raw(targets,images,(x,y,w,h))) # stitch with black infill
# step 1: sparsely sample background mostly ignoring blob
# compute gradient on both axes
k = [[-3,-1,0,1,3],
[-3,-1,0,1,3],
[-3,-1,0,1,3],
[-3,-1,0,1,3]]
gy = convolve(uroi,k)
gx = convolve(uroi,np.rot90(k))
# ignore all but low-gradient areas
bg = (abs(gy+gx) < 0.2) & mask
# step 2: remove less contiguous areas
filter_size = max(2,int(max(h,w)/200))
mf = minimum_filter(bg*1,filter_size)
# step 3: interpolate between samples
z = inpaint(uroi*mf,mf==False)
# step 4: subsample and re-interpolate to degrade artifacts in fill region
random = RandomState(0)
(h,w)=z.shape
ng = random.rand(h,w) < 0.01
z2 = inpaint(z*ng,ng==False)
# step 5: final composite
roi = (z2 * gaps_mask) + uroi
return (roi * 255).astype(np.uint8), mask
def get_roi_image_from_files(schema_version, adc_path, roi_path, bin_pid, target_no, fast_stitching=False, mask=False, stitch_version=1):
to_stitch = app.config[STITCH]
if to_stitch:
offset=max(1,target_no-1)
limit=3 # read three targets, in case we need to stitch
else:
offset=target_no
limit=1 # just read one
targets = list(read_targets(adc_path, offset, limit, schema_version))
if len(targets) == 0: # no targets? return Not Found
return None
# open the ROI file as we may need to read more than one
with open(roi_path,'rb') as roi_file:
if to_stitch:
pairs = list(find_pairs(targets)) # look for stitched pairs
else:
pairs = targets
roi_image = None
if len(pairs) >= 1: # found one?
(a,b) = pairs[0] # split pair
if b[TARGET_NUMBER] == target_no: # second of a pair?
return None
images = list(read_rois((a,b),roi_file=roi_file)) # read the images
if mask:
roi_image = stitching.mask((a,b))
elif fast_stitching:
roi_image = stitch_raw((a,b), images, background=180)
elif stitch_version == 1:
(roi_image, mask) = stitch((a,b), images) # stitch them
elif stitch_version == 2:
(roi_image, mask) = joe_stitch((a,b), images)
else:
# now check that the target number is correct
for target in targets:
if target[TARGET_NUMBER] == target_no:
images = list(read_rois([target],roi_file=roi_file)) # read the image
roi_image = images[0]
return roi_image
