def bin2zip(parsed_pid,canonical_pid,targets,hdr,timestamp,roi_path,outfile):
"""parsed_pid - result of parsing pid
canonical_pid - canonicalized with URL prefix
targets - list of (stitched) targets
hdr - result of parsing header file
timestamp - timestamp (FIXME in what format?)
roi_path - path to ROI file
outfile - where to write resulting zip file"""
bin_lid = parsed_pid['bin_lid']
adc_cols = parsed_pid['adc_cols'].split(' ')
targets = list(targets)
with tempfile.SpooledTemporaryFile() as temp:
z = ZipFile(temp,'w',ZIP_DEFLATED)
csv_out = '\n'.join(targets2csv(targets, adc_cols))+'\n'
z.writestr(bin_lid + '.csv', csv_out)
xml_out = bin2xml(canonical_pid,hdr,targets,timestamp)
z.writestr(bin_lid + '.xml', xml_out)
with open(roi_path,'rb') as roi_file:
for target in targets:
if STITCHED in target and target[STITCHED] != 0:
subRois = [read_target_image(t,file=roi_file) for t in target[PAIR]]
im,_ = stitch(target[PAIR], subRois)
else:
im = read_target_image(target, file=roi_file)
target_lid = os.path.basename(target['pid'])
z.writestr(target_lid + '.png', as_bytes(im, mimetype='image/png'))
z.close()
temp.seek(0)
shutil.copyfileobj(temp, outfile)
def get_target_image(parsed, target, path=None, file=None, raw_stitch=False):
if PAIR in target:
(a,b) = target[PAIR]
a_image = read_target_image(a, path=path, file=file)
b_image = read_target_image(b, path=path, file=file)
if raw_stitch:
return stitch_raw((a,b),(a_image,b_image),background=180)
else:
try:
bin_zip = get_product_file(parsed, BINZIP_PRODUCT)
if os.path.exists(bin_zip):
# name is target LID + png extension
png_name = os.path.basename(target[PID]) + '.png'
png_data = get_zip_entry_bytes(bin_zip, png_name)
pil_img = PIL.Image.open(StringIO(png_data))
return np.array(pil_img.convert('L')) # convert to 8-bit grayscale
except NotFound:
pass
im,_ = v1_stitching.stitch((a,b),(a_image,b_image))
return im
else:
return read_target_image(target, path=path, file=file)
