def serve_bin(hit,mimetype):
"""Serve a sample bin in some format"""
# for raw files, simply pass the file through
if hit.extension == ADC:
return Response(file(resolve_adc(hit.bin_pid)), direct_passthrough=True, mimetype='text/csv')
elif hit.extension == ROI:
return Response(file(resolve_roi(hit.bin_pid)), direct_passthrough=True, mimetype='application/octet-stream')
# at this point we need to resolve the HDR file
hdr_path = resolve_hdr(hit.bin_pid)
if hit.extension == HDR:
return Response(file(hdr_path), direct_passthrough=True, mimetype='text/plain')
props = read_hdr(LocalFileSource(hdr_path))
bin_props = get_bin_props(hit.time_series).get_props(hit.bin_lid)
context = props[CONTEXT]
del props[CONTEXT]
# sort properties according to their order in the header schema
props = [(k,props[k]) for k,_ in HDR_SCHEMA if k in props]
# then add database props
props += [(k,bin_props[k]) for k in sorted(bin_props.keys())]
# get a list of all targets, taking into account stitching
if hit.product != 'short':
targets = list_targets(hit)
target_pids = ['%s_%05d' % (hit.bin_pid, target['targetNumber']) for target in targets]
else:
targets = []
target_pids = []
template = dict(hit=hit,context=context,properties=props,targets=targets,target_pids=target_pids,static=app.config[STATIC])
if minor_type(mimetype) == 'xml':
return template_response('bin.xml', **template)
elif minor_type(mimetype) == 'rdf+xml':
return template_response('bin.rdf', mimetype='text/xml', **template)
elif minor_type(mimetype) == 'csv':
return bin2csv_response(hit, targets)
elif mimetype == 'text/html':
return template_response('bin.html', **template)
elif mimetype == 'application/json':
properties = dict(props)
properties['context'] = context
properties['targets'] = targets
properties['date'] = hit.date
if hit.product == 'short':
del properties['targets']
if hit.product == 'medium':
properties['targets'] = target_pids
return jsonr(properties)
elif mimetype == 'application/zip':
return Response(bin_zip(hit,targets,template), mimetype=mimetype, headers=max_age())
else:
abort(404)
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 check_hdr(hdr_source):
try:
read_hdr(hdr_source)
except Exception, e:
raise IntegrityException('.hdr failed: ' + str(e)), None, sys.exc_info()[2]
