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 serve_blob_image(parsed, mimetype, outline=False, target_img=None):
# first, read the blob from the zipfile
blob_zip = get_product_file(parsed, 'blobs')
png_name = parsed['lid'] + '.png' # name is target LID + png extension
png_data = get_zip_entry_bytes(blob_zip, png_name)
# if we want a blob png, then pass it through without conversion
if not outline and mimetype == 'image/png':
return Response(png_data, mimetype='image/png')
else:
# read the png-formatted blob image into a PIL image
pil_img = PIL.Image.open(StringIO(png_data))
blob = np.array(pil_img.convert('L')) # convert to 8-bit grayscale
if not outline: # unless we are drawing the outline
return Response(as_bytes(blob), mimetype=mimetype) # format and serve
else:
blob_outline = find_boundaries(blob)
roi = target_img
blob = np.dstack([roi,roi,roi])
blob[blob_outline] = [255,0,0]
return Response(as_bytes(blob, mimetype), mimetype=mimetype)
def serve_mosaic_image(time_series=None, pid=None, params='/'):
"""Generate a mosaic of ROIs from a sample bin.
params include the following, with default values
- series (mvco) - time series (FIXME: handle with resolver, clarify difference between namespace, time series, pid, lid)
- size (1024x1024) - size of the mosaic image
- page (1) - page. for typical image sizes the entire bin does not fit and so is split into pages.
- scale - scaling factor for image dimensions """
# parse params
size, scale, page = parse_mosaic_params(params)
(w,h) = size
parsed = parse_pid(pid)
schema_version = parsed['schema_version']
try:
paths = get_fileset(parsed)
except NotFound:
abort(404)
adc_path = paths['adc_path']
roi_path = paths['roi_path']
bin_pid = canonicalize(get_url_root(), time_series, parsed['bin_lid'])
# perform layout operation
scaled_size = (int(w/scale), int(h/scale))
layout = list(get_mosaic_layout(adc_path, schema_version, bin_pid, scaled_size, page))
extension = parsed['extension']
# serve JSON on request
if extension == 'json':
return Response(json.dumps(list(layout2json(layout, scale))), mimetype=MIME_JSON)
mimetype = mimetypes.types_map['.' + extension]
# read all images needed for compositing and inject into Tiles
image_layout = []
with open(roi_path,'rb') as roi_file:
for tile in layout:
target = tile.image # in mosaic API, the record is called 'image'
# FIXME 1. replace PIL
image = get_target_image(parsed, target, file=roi_file, raw_stitch=True)
image_layout.append(Tile(PIL.Image.fromarray(image), tile.size, tile.position))
# produce and serve composite image
mosaic_image = thumbnail(mosaic.composite(image_layout, scaled_size, mode='L', bgcolor=160), (w,h))
#pil_format = filename2format('foo.%s' % extension)
return Response(as_bytes(mosaic_image), mimetype=mimetype)
def serve_pid(pid):
req = DashboardRequest(pid, request)
try:
paths = get_fileset(req.parsed)
except NotFound:
abort(404)
hdr_path = paths['hdr_path']
adc_path = paths['adc_path']
roi_path = paths['roi_path']
adc = Adc(adc_path, req.schema_version)
heft = 'full' # heft is either short, medium, or full
if 'extension' in req.parsed:
extension = req.parsed['extension']
if 'target' in req.parsed:
canonical_bin_pid = canonicalize(req.url_root, req.time_series, req.bin_lid)
target_no = int(req.parsed['target'])
# pull three targets, then find any stitched pair
targets = adc.get_some_targets(target_no-1, 3)
targets = list_stitched_targets(targets)
for t in targets:
if t[TARGET_NUMBER] == target_no:
target = t
add_pid(target, canonical_bin_pid)
# check for image
mimetype = mimetypes.types_map['.' + extension]
if mimetype.startswith('image/'):
if req.product=='raw':
img = get_target_image(req.parsed, target, roi_path)
return Response(as_bytes(img,mimetype),mimetype=mimetype)
if req.product=='blob':
return serve_blob_image(req.parsed, mimetype)
if req.product=='blob_outline':
img = get_target_image(req.parsed, target, roi_path)
return serve_blob_image(req.parsed, mimetype, outline=True, target_img=img)
# not an image, so get more metadata
targets = get_targets(adc, canonical_bin_pid)
# not an image, check for JSON
if extension == 'json':
return Response(json.dumps(target),mimetype=MIME_JSON)
target = get_target_metadata(target,targets)
# more metadata representations. we'll need the header
hdr = parse_hdr_file(hdr_path)
if extension == 'xml':
return Response(target2xml(req.canonical_pid, target, req.timestamp, canonical_bin_pid), mimetype='text/xml')
if extension == 'rdf':
return Response(target2rdf(req.canonical_pid, target, req.timestamp, canonical_bin_pid), mimetype='text/xml')
if extension in ['html', 'htm']:
template = {
'static': STATIC,
'target_pid': req.canonical_pid,
'bin_pid': canonical_bin_pid,
'properties': target,
'target': target.items(), # FIXME use order_keys
'date': req.timestamp
}
return template_response('target.html',**template)
else: # bin
if req.extension in ['hdr', 'adc', 'roi']:
path = dict(hdr=hdr_path, adc=adc_path, roi=roi_path)[req.extension]
mimetype = dict(hdr='text/plain', adc='text/csv', roi='application/octet-stream')[req.extension]
return Response(file(path,'rb'), direct_passthrough=True, mimetype=mimetype)
try:
if req.product in ['blobs','blob']: # accept old url pattern
return serve_blob_bin(req.parsed)
if req.product=='features':
return serve_features_bin(req.parsed)
if req.product=='class_scores':
return serve_class_scores_bin(req.parsed)
except NotFound:
abort(404)
# gonna need targets unless heft is medium or below
targets = []
if req.product != 'short':
targets = get_targets(adc, req.canonical_pid)
# end of views
# not a special view, handle representations of targets
if req.extension=='csv':
adc_cols = req.parsed[ADC_COLS].split(' ')
lines = targets2csv(targets,adc_cols)
return Response('\n'.join(lines)+'\n',mimetype='text/csv')
# we'll need the header for the other representations
hdr = parse_hdr_file(hdr_path)
if req.extension in ['html', 'htm']:
targets = list(targets)
context, props = split_hdr(hdr)
template = {
'static': STATIC,
'bin_pid': req.canonical_pid,
'time_series': req.time_series,
'context': context,
'properties': props,
'targets': targets,
'target_pids': [t['pid'] for t in targets],
'date': req.timestamp,
'files': get_files(req.parsed,check=True) # note: ORM call!
}
print get_files(req.parsed)
return template_response('bin.html', **template)
if req.extension=='json':
if req.product=='short':
return Response(bin2json_short(req.canonical_pid,hdr,req.timestamp),mimetype=MIME_JSON)
if req.product=='medium':
return Response(bin2json_medium(req.canonical_pid,hdr,targets,req.timestamp),mimetype=MIME_JSON)
return Response(bin2json(req.canonical_pid,hdr,targets,req.timestamp),mimetype=MIME_JSON)
if req.extension=='xml':
return Response(bin2xml(req.canonical_pid,hdr,targets,req.timestamp),mimetype='text/xml')
if req.extension=='rdf':
return Response(bin2rdf(req.canonical_pid,hdr,targets,req.timestamp),mimetype='text/xml')
if req.extension=='zip':
# look to see if the zipfile is resolvable
try:
zip_path = get_product_file(req.parsed, 'binzip')
if os.path.exists(zip_path):
return Response(file(zip_path), direct_passthrough=True, mimetype='application/zip')
except NotFound:
pass
except:
raise
buffer = BytesIO()
bin2zip(req.parsed,req.canonical_pid,targets,hdr,req.timestamp,roi_path,buffer)
return Response(buffer.getvalue(), mimetype='application/zip')
return 'unimplemented'