def bin_zip(hit, hdr_path, adc_path, roi_path, outfile):
"""hit should be the hit on the mvco resolver for pid=bin_pid on the 'pid' resolver.
outfile must be a filelike object open for writing, not a pathname. StringIO will work"""
props = read_hdr(LocalFileSource(hdr_path))
context = props[CONTEXT]
del props[CONTEXT]
props = [(k,props[k]) for k,_ in HDR_SCHEMA if k in props]
raw_targets = list(read_adc(LocalFileSource(adc_path), 1, -1, hit.schema_version))
raw_targets = add_bin_pid(raw_targets, hit.bin_pid)
stitched_targets = deepcopy(raw_targets)
stitched_targets = list_stitched_targets(stitched_targets)
stitched_targets = add_bin_pid(stitched_targets, hit.bin_pid)
target_pids = ['%s_%05d' % (hit.bin_pid, target['targetNumber']) for target in stitched_targets]
template = dict(hit=hit,context=context,properties=props,targets=stitched_targets,target_pids=target_pids)
with tempfile.SpooledTemporaryFile() as temp:
z = ZipFile(temp,'w',ZIP_DEFLATED)
csv_out = '\n'.join(bin2csv(stitched_targets, hit.schema_version))
z.writestr(hit.bin_lid + '.csv', csv_out)
# xml as well, including header info
z.writestr(hit.bin_lid + '.xml', bin2xml(template))
pairs = list(find_pairs(raw_targets))
with open(roi_path,'rb') as roi_file:
for target in stitched_targets:
im = None
for (a,b) in pairs:
if a[TARGET_NUMBER] == target[TARGET_NUMBER]:
images = list(read_rois((a,b),roi_file=roi_file)) # read the images
(im, _) = stitch((a,b), images) # stitch them
if im is None:
im = list(read_rois([target],roi_file=roi_file))[0] # read the image
# need LID here
target_lid = re.sub(r'.*/','',target[PID]) # FIXME resolver should do this
z.writestr(target_lid + '.png', im2bytes(im))
z.close()
temp.seek(0)
shutil.copyfileobj(temp, outfile)
return stitched_targets
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
