def list_targets(hit, target_no=1, limit=-1, adc_path=None, stitch_targets=None):
if stitch_targets is None:
stitch_targets = app.config[STITCH]
if adc_path is None:
adc_path = resolve_adc(hit.bin_pid)
targets = read_targets(adc_path, target_no, limit, hit.schema_version)
if stitch_targets:
targets = list_stitched_targets(targets)
targets = add_bin_pid(targets, hit.bin_pid)
return targets
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
