def get_formats(cls):
'''inits supported file formats'''
if cls.installed_formats is None:
cls.installed_formats = OrderedDict()
formats_xml = cls.run_command( [cls.BFORMATS, '-xml'] )
if formats_xml is None:
return
formats = etree.fromstring( formats_xml )
codecs = formats.xpath('//format')
for c in codecs:
try:
ext=c.xpath('tag[@name="extensions"]')[0].get('value', '').split('|')
name = c.get('name')
cls.installed_formats[name.lower()] = Format(
name=name,
fullname=c.get('name'),
ext=ext,
reading=len(c.xpath('tag[@name="support" and @value="reading"]'))>0,
writing=len(c.xpath('tag[@name="support" and @value="writing"]'))>0,
multipage=len(c.xpath('tag[@name="support" and @value="writing multiple pages"]'))>0,
metadata=True,
)
except IndexError:
continue
def load_default_drivers():
stores = OrderedDict()
store_list = [
x.strip()
for x in config.get('bisque.blob_service.stores', '').split(',')
]
log.debug('requested stores = %s', store_list)
for store in store_list:
# pull out store related params from config
params = dict((x[0].replace('bisque.stores.%s.' % store, ''), x[1])
for x in config.items()
if x[0].startswith('bisque.stores.%s.' % store))
if 'mounturl' not in params:
if 'path' in params:
path = params.pop('path')
params['mounturl'] = string.Template(path).safe_substitute(
OLDPARMS)
log.warn(
"Use of deprecated path (%s) in %s driver . Please change to mounturl and remove any from %s",
path, store, OLDPARMS.keys())
log.info("using mounturl = %s", params['mounturl'])
else:
log.error('cannot configure %s without the mounturl parameter',
store)
continue
#if 'top' not in params:
# params['top'] = params['mounturl'].split ('$user')[0]
# log.warn ("top for %s was not set. Using %s", params['mounturl'], params['top'])
log.debug("params = %s", params)
#driver = make_storage_driver(params.pop('path'), **params)
#if driver is None:
# log.error ("failed to configure %s. Please check log for errors " , str(store))
# continue
stores[store] = params
return stores
def get_formats(cls):
'''inits supported file formats'''
if cls.installed_formats is None:
formats_xml = cls.run_command([cls.CONVERTERCOMMAND, '-fmtxml'])
formats = etree.fromstring('<formats>%s</formats>' % formats_xml)
cls.installed_formats = OrderedDict()
codecs = formats.xpath('//codec')
for c in codecs:
try:
name = c.get('name')
fullname = c.xpath('tag[@name="fullname"]')[0].get(
'value', '')
exts = c.xpath('tag[@name="extensions"]')[0].get(
'value', '').split('|')
reading = len(
c.xpath(
'tag[@name="support" and @value="reading"]')) > 0
writing = len(
c.xpath(
'tag[@name="support" and @value="writing"]')) > 0
multipage = len(
c.xpath(
'tag[@name="support" and @value="writing multiple pages"]'
)) > 0
metadata = len(
c.xpath(
'tag[@name="support" and @value="reading metadata"]'
)
) > 0 or len(
c.xpath(
'tag[@name="support" and @value="writing metadata"]'
)) > 0
samples_min = misc.safeint(
c.xpath('tag[@name="min-samples-per-pixel"]')[0].get(
'value', '0'))
samples_max = misc.safeint(
c.xpath('tag[@name="max-samples-per-pixel"]')[0].get(
'value', '0'))
bits_min = misc.safeint(
c.xpath('tag[@name="min-bits-per-sample"]')[0].get(
'value', '0'))
bits_max = misc.safeint(
c.xpath('tag[@name="max-bits-per-sample"]')[0].get(
'value', '0'))
except IndexError:
continue
cls.installed_formats[name.lower()] = Format(
name=name,
fullname=fullname,
ext=exts,
reading=reading,
writing=writing,
multipage=multipage,
metadata=metadata,
samples=(samples_min, samples_max),
bits=(bits_min, bits_max))
def load_storage_drivers():
stores = OrderedDict()
store_list = [ x.strip() for x in config.get('bisque.blob_service.stores','').split(',') ]
log.debug ('requested stores = %s' , store_list)
for store in store_list:
# pull out store related params from config
params = dict ( (x[0].replace('bisque.stores.%s.' % store, ''), x[1])
for x in config.items() if x[0].startswith('bisque.stores.%s.' % store))
if 'path' not in params:
log.error ('cannot configure %s without the path parameter' , store)
continue
log.debug("params = %s" , str(params))
driver = make_storage_driver(params.pop('path'), **params)
if driver is None:
log.error ("failed to configure %s. Please check log for errors " , str(store))
continue
stores[store] = driver
return stores
def _get_stores(self):
"Return an OrderedDict of store resources in the users ordering"
#root = self._create_root_mount()
root = self._load_root_mount()
store_order = get_tag (root, 'order')
if store_order is None:
store_order = config.get('bisque.blob_service.stores','')
else:
store_order = store_order[0].get ('value')
log.debug ("using store order %s", store_order)
stores = OrderedDict()
for store_name in (x.strip() for x in store_order.split(',')):
store_el = root.xpath('./store[@name="%s"]' % store_name)
if not store_el or len(store_el) > 1:
log.warn ("store %s does not exist in %s", store_name, etree.tostring(root))
continue
store = store_el[0]
stores[store_name] = store
log.debug ("adding store '%s' at %s", store_name, len(stores))
return stores
def get_formats(cls):
'''inits supported file formats'''
if cls.installed_formats is not None:
return
fs = cls.run_command( [cls.CONVERTERCOMMAND, '-h'] )
if fs is None:
return ''
ins = [f.strip(' ') for f in misc.between('Input File Formats are:%s' % (os.linesep*2) , 'Output File Formats are:', fs).split(os.linesep) if f != '']
# version 8.0.0
if 'Exit Codes:' in fs:
ous = [f.strip(' ') for f in misc.between('Output File Formats are:%s' % (os.linesep*2), 'Exit Codes:', fs).split(os.linesep) if f != '']
else: # version 7.X
ous = [f.strip(' ') for f in misc.between('Output File Formats are:%s' % (os.linesep*2), 'Examples:', fs).split(os.linesep) if f != '']
ins = [parse_format(f) for f in ins]
ous = [parse_format(f) for f in ous]
# join lists
cls.installed_formats = OrderedDict()
for name,longname,ext in ins:
cls.installed_formats[name.lower()] = Format(name=name, fullname=longname, ext=ext, reading=True, multipage=True, metadata=True)
for name,longname,ext in ous:
cls.installed_formats[name.lower()] = Format(name=name, fullname=longname, ext=ext, reading=True, writing=True, multipage=True, metadata=True )
#log.debug("loading %s -> name/type (%s/%s)(%s) " , uri, name, str(dbcls), ida)
#resource = DBSession.query(dbcls).get (int (ida))
resource = DBSession.query(dbcls).filter(dbcls.id == int(ida))
if not query:
resource = resource.first()
#log.debug ("loaded %s" % resource)
return resource
except Exception:
log.exception("Failed to load uri %s", uri)
return None
converters = OrderedDict((
('object', load_uri),
('integer', int),
('float', float),
('number', float),
('string', unicode_safe),
))
def try_converters(value):
for ty_, converter in converters.items():
try:
v = converter(value)
if v is not None:
return v
except ValueError:
pass
# we should never get here
raise ValueError
def get_formats(cls):
'''inits supported file formats'''
if cls.installed_formats is not None:
return
cls.extensions = [
'.svs', '.ndpi', '.vms', '.vmu', '.scn', '.mrxs', '.svslide',
'.bif'
]
# Many extensions may unfortunately be .tif, we'll have to deal with that later
cls.installed_formats = OrderedDict()
cls.installed_formats['aperio'] = Format(name='aperio',
fullname='Aperio',
ext=['svs', 'tif', 'tiff'],
reading=True,
multipage=False,
metadata=True) # tif
cls.installed_formats['hamamatsu'] = Format(name='hamamatsu',
fullname='Hamamatsu',
ext=['ndpi', 'vms', 'vmu'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['leica'] = Format(name='leica',
fullname='Leica',
ext=['scn'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['mirax'] = Format(name='mirax',
fullname='MIRAX',
ext=['mrxs'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['philips'] = Format(name='philips',
fullname='Philips',
ext=['tiff'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['sakura'] = Format(name='sakura',
fullname='Sakura',
ext=['svslide'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['trestle'] = Format(name='trestle',
fullname='Trestle',
ext=['tif'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['ventana'] = Format(name='ventana',
fullname='Ventana',
ext=['bif', 'tif'],
reading=True,
multipage=False,
metadata=True)
cls.installed_formats['tiff'] = Format(name='tiff',
fullname='Generic tiled TIFF',
ext=['tif', 'tiff'],
reading=True,
multipage=False,
metadata=True)
def get_formats(cls):
'''inits supported file formats'''
if cls.installed_formats is None:
cls.installed_formats = OrderedDict() # OrderedDict containing Format and keyed by format name