class RootTip(object):
def setup(self):
#if not os.path.exists(self.images):
# os.makedirs(self.images)
self.bq.update_mex('initializing')
results = fetch_image_planes(self.bq, self.resource_url, '.')
# extract gobject inputs
tips = self.bq.mex.find('inputs',
'tag').find('image_url',
'tag').find('tips', 'gobject')
with open('inputtips.csv', 'w') as TIPS:
for point in tips.gobjects:
print >> TIPS, "%(y)s, %(x)s" % dict(x=point.vertices[0].x,
y=point.vertices[0].y)
def start(self):
self.bq.update_mex('executing')
# Matlab requires trailing slash
subprocess.call([EXEC, './'])
def teardown(self):
# Post all submex for files and return xml list of results
gobjects = self._read_results()
tags = [{
'name':
'outputs',
'tag': [{
'name':
'rootimage',
'type':
'image',
'value':
self.resource_url,
'gobject': [{
'name': 'root_tips',
'type': 'root_tips',
'gobject': gobjects
}]
}]
}]
self.bq.finish_mex(tags=tags)
def _read_results(self, ):
results = []
#image = self.bq.load(self.resource_url, view='full')
#xmax, ymax, zmax, tmax, ch = image.geometry()
# each line is a time point, tracked points in line
tips = [t for t in csv.reader(open('tips.csv', 'rb'))]
# each line is a time point, tracked points per line pt1, pt2, pt2
angles = [a for a in csv.reader(open('angles.csv', 'rb'))]
# We want to generate lines in time to keep the tracked point in a single object
# <gobject name="Tip 1" >
# <gobject type=tipangle>
# <point x= y= t=1..N >
# <tag name="angle" value="" />
# <gobject>
# ...
# </gobject>
# <gobject name="Tip 2" >
#
planes = len(angles)
tip_count = planes and len(angles[0]) or 0
tracks = []
for pt in range(tip_count):
gobs = []
for t_plane in range(planes):
gobs.append({
'type':
'tipangle',
'tag': [{
'name': 'angle',
'value': angles[t_plane][pt]
}],
'point': [{
'vertex': [{
't': str(t_plane),
'x': str(tips[t_plane][pt * 2]),
'y': str(tips[t_plane][pt * 2 + 1])
}]
}]
})
tracks.append({
'name': 'tip-%s' % pt,
'type': 'roottip',
'gobject': gobs
})
return tracks
def run(self):
parser = optparse.OptionParser()
parser.add_option('-d', '--debug', action="store_true")
parser.add_option('-n', '--dryrun', action="store_true")
parser.add_option('--credentials')
parser.add_option('--image_url')
(options, args) = parser.parse_args()
named = AttrDict(bisque_token=None,
mex_url=None,
staging_path=None,
image_url=None)
for arg in list(args):
tag, sep, val = arg.partition('=')
if sep == '=':
named[tag] = val
args.remove(arg)
self.named_args = named
self.staging_path = named.get('staging_path')
if named.bisque_token:
self.bq = BQSession().init_mex(named.mex_url, named.bisque_token)
self.resource_url = self.bq.parameter_value('image_url')
elif options.credentials:
user, pwd = options.credentials.split(':')
self.bq = BQSession().init_local(user, pwd)
self.resource_url = named.image_url
else:
parser.error('need bisque_token or user credential')
if self.resource_url is None:
parser.error('Need a resource_url')
if not args:
commands = ['setup', 'start', 'teardown']
else:
commands = [args]
try:
for command in commands:
command = getattr(self, command)
r = command()
except Exception, e:
logging.exception("problem during %s" % command)
self.bq.fail_mex(msg="Exception during %s: %s" % (command, e))
sys.exit(1)
sys.exit(0)
class RootTip(object):
def setup(self):
#if not os.path.exists(self.images):
# os.makedirs(self.images)
self.status = 0
self.bq.update_mex('initializing')
results = fetch_image_planes(self.bq, self.resource_url, '.')
def start(self):
self.bq.update_mex('executing')
# Matlab requires trailing slash
self.status = subprocess.call([EXEC, './'])
def teardown(self):
# Post all submex for files and return xml list of results
self.bq.update_mex('checking results')
if self.status != 0:
self.bq.fail_mex ("Bad result code form analysis: %d" % self.status)
return
gobjects = self._read_results()
tags = [{ 'name': 'outputs',
'tag' : [{'name': 'roots', 'type':'image', 'value':self.resource_url,
'gobject' : [{ 'name': 'root_tips', 'type': 'root_tips', 'gobject' : gobjects }] }]
}]
self.bq.update_mex('saving results')
self.bq.finish_mex(tags = tags)
def _read_results(self, ):
results = []
image = self.bq.load(self.resource_url, view='full')
xmax, ymax, zmax, tmax, ch = image.geometry()
tips = csv.reader(open('tips.csv','rb'))
angles = csv.reader(open('angle.csv','rb'))
grates = csv.reader(open('gr.csv','rb'))
for index, (tip, angle, gr) in enumerate(itertools.izip(tips, angles, grates)):
results.append({
'type' : 'tipangle',
'tag' : [{ 'name': 'angle', 'value': angle[0]},
{ 'name': 'growth', 'value': gr[0]}, ],
'point' : {
'vertex' : [ { 'x': str(xmax - int(tip[1])), 'y':tip[0], 't':index } ] ,
}
})
return results
def run(self):
parser = optparse.OptionParser()
parser.add_option('-d','--debug', action="store_true")
parser.add_option('-n','--dryrun', action="store_true")
parser.add_option('--credentials')
parser.add_option('--image_url')
(options, args) = parser.parse_args()
named = AttrDict (bisque_token=None, mex_url=None, staging_path=None, image_url=None)
for arg in list(args):
tag, sep, val = arg.partition('=')
if sep == '=':
named[tag] = val
args.remove(arg)
if named.bisque_token:
self.bq = BQSession().init_mex(named.mex_url, named.bisque_token)
self.resource_url = self.bq.parameter_value ('image_url')
elif options.credentials:
user,pwd = options.credentials.split(':')
self.bq = BQSession().init_local(user,pwd)
self.resource_url = named.image_url
else:
parser.error('need bisque_token or user credential')
if self.resource_url is None:
parser.error('Need a resource_url')
if not args :
commands = ['setup', 'start', 'teardown']
else:
commands = [ args ]
try:
for command in commands:
command = getattr(self, command)
r = command()
except Exception, e:
logging.exception ("problem during %s" % command)
self.bq.fail_mex(msg = "Exception during %s: %s" % (command, e))
sys.exit(1)
sys.exit(0)
