Commit 7d4f35d3 authored by André Anjos's avatar André Anjos

Allow to view sample using a database name

parent 12b3da0c
......@@ -12,12 +12,13 @@ Usage: %(prog)s [-v...] [-s <path>] <database> <processed> <stem> [<stem>...]
Arguments:
<database> Path to the database with the image to be inspected
<database> Name of the database to use for creating the model (options are:
"fv3d" or "verafinger")
<processed> Path with the directory holding the preprocessed and extracted
sub-directories containing the processing results of a
bob.bio.vein toolchain
<stem> Name of the object on the database to display, with the root or
the extension
<stem> Name of the object on the database to display, without the root
or the extension
Options:
......@@ -31,13 +32,13 @@ Options:
Examples:
Visualize to processing toolchain over a single image
Visualize to processing toolchain over a single image of VERA finger vein:
$ %(prog)s /database /mc client/sample
$ %(prog)s verafinger /mc client/sample
Visualize multiple masks (like in a proof-sheet):
$ %(prog)s /database /mc client/sample1 client/sample2
$ %(prog)s verafinger /mc client/sample1 client/sample2
"""
......@@ -46,6 +47,10 @@ import os
import sys
import numpy
import schema
import docopt
import bob.core
logger = bob.core.log.setup("bob.bio.vein")
......@@ -148,6 +153,41 @@ def proof_figure(title, image, mask, image_pp, binary=None):
return fig
def validate(args):
'''Validates command-line arguments, returns parsed values
This function uses :py:mod:`schema` for validating :py:mod:`docopt`
arguments. Logging level is not checked by this procedure (actually, it is
ignored) and must be previously setup as some of the elements here may use
logging for outputing information.
Parameters:
args (dict): Dictionary of arguments as defined by the help message and
returned by :py:mod:`docopt`
Returns
dict: Validate dictionary with the same keys as the input and with values
possibly transformed by the validation procedure
Raises:
schema.SchemaError: in case one of the checked options does not validate.
'''
sch = schema.Schema({
'<database>': lambda n: n in ('fv3d', 'verafinger'),
str: object, #ignores strings we don't care about
}, ignore_extra_keys=True)
return sch.validate(args)
def main(user_input=None):
if user_input is not None:
......@@ -155,7 +195,6 @@ def main(user_input=None):
else:
argv = sys.argv[1:]
import docopt
import pkg_resources
completions = dict(
......@@ -169,22 +208,41 @@ def main(user_input=None):
version=completions['version'],
)
# Sets-up logging
verbosity = int(args['--verbose'])
bob.core.log.set_verbosity_level(logger, verbosity)
try:
from .validate import setup_logger
logger = setup_logger('bob.bio.vein', args['--verbose'])
args = validate(args)
except schema.SchemaError as e:
sys.exit(e)
if args['<database>'] == 'fv3d':
from ..configurations.fv3d import database as db
elif args['<database>'] == 'verafinger':
from ..configurations.verafinger import database as db
else:
raise schema.SchemaError('Database %s is not supported' % \
args['<database>'])
database_replacement = "%s/.bob_bio_databases.txt" % os.environ["HOME"]
db.replace_directories(database_replacement)
all_files = db.objects()
# Loads the image, the mask and save it to a PNG file
for stem in args['<stem>']:
image = bob.bio.base.load(os.path.join(args['<database>'], stem + '.png'))
image = numpy.rot90(image, k=-1)
pp = bob.io.base.HDF5File(os.path.join(args['<processed>'],
'preprocessed', stem + '.hdf5'))
f = [k for k in all_files if k.path == stem]
if len(f) == 0:
raise RuntimeError('File with stem "%s" does not exist on "%s"' % \
stem, args['<database>'])
f = f[0]
image = f.load(db.original_directory, db.original_extension)
pp_name = f.make_path(os.path.join(args['<processed>'], 'preprocessed'),
extension='.hdf5')
pp = bob.io.base.HDF5File(pp_name)
mask = pp.read('mask')
image_pp = pp.read('image')
binary_path = os.path.join(args['<processed>'], 'extracted', stem + '.hdf5')
if os.path.exists(binary_path):
binary = bob.io.base.load(binary_path)
else:
try:
binary = f.load(os.path.join(args['<processed>'], 'extracted'))
except:
binary = None
fig = proof_figure(stem, image, mask, image_pp, binary)
if args['--save']:
......
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