def compare_structure_sequence(vs, display=True, slices=slice(None), file_id_part=2, append_file=None):
"""
For all TreeCompare in `vs.tc_list` call compare_structure
"""
from os.path import sep
res = []
for i,tc in np.array(list(enumerate(vs.tc_list)))[slices]:
c = tc.get('cmp')
r = tc.get('ref')
tc.clear()
f = sep.join(c.get_file().get_url().split(sep)[-file_id_part:])
print '--- comparing file: ...', f, '---'
r.segment.radius = np.zeros(r.segment.number())
c.segment.radius = np.zeros(c.segment.number())
rmtg = tree_to_mtg(r)
cmtg = tree_to_mtg(c)
c = _split_mtg(cmtg)
r = _split_mtg(rmtg)
##return c,r
for j,(ci,ri) in enumerate(zip(c,r)):
print 'comparing image %2d root %2d' % (i,j)
print '----------------------------'
print 'max scale', ri.max_scale(), ci.max_scale()
##return ri,ci
try:
match_ratio, topo_ratio = compare_structure(ci,ri,display=display)
res.append((i,f,j+1, match_ratio, topo_ratio))
except:
print '********** error processing', i,j, '**********'
if display:
k = raw_input('continue(y/n):')
if k=='n': return
print '----------------', i, j, '----------------'
if append_file:
with open(append_file,'a') as f:
print s,e, len(res)
for re in results:
re = ' '.join(map(str,re[1:]))
f.write(r+'\n')
return res
def compare_structure(self, display=False):
"""
Call `compare_structure` function and store results as dictionaries in
attributes `comparison.geometry` and `comparison.topology`
"""
from rhizoscan.root.graph.mtg import tree_to_mtg
from os.path import sep
c = self.get('cmp')
r = self.get('ref')
f = sep.join(c.get_file().get_url().split(sep)[-1:])
print '--- comparing file: .../%s ---' % f
print '============================' + '='*len(f)
r.segment.radius = np.zeros(r.segment.number())
c.segment.radius = np.zeros(c.segment.number())
rmtg = tree_to_mtg(r)
cmtg = tree_to_mtg(c)
c = _split_mtg(cmtg)
r = _split_mtg(rmtg)
geom = {}
topo = {}
for i,(ci,ri) in enumerate(zip(c,r)):
print 'comparing image root %2d' % i
print '-----------------------'
try:
match_ratio, topo_ratio = compare_structure(ci,ri,display=display)
geom[i] = match_ratio
topo[i] = topo_ratio
if display:
k = raw_input('geo:%.2f, topo:%.2f - continue(y/n):' % (match_ratio,topo_ratio))
if k=='n': return
except:
print '********** error processing root %d **********' % i
print '------------ end of root %d fo file %s ------------' % (i,f)
self.add_comparison('geometry', geom)
self.add_comparison('topology', topo)
def append_reference(ds,
refds,
name='reference_rsa',
verbose=False,
dry_run=False):
"""
Append reference trees (as rsml mtg) from `refds` into `ds` Datasets
:Inputs:
ds
Dataset object. It is loaded then dumped after adding refds tree into
refds
Dataset object. Once loaded, it should contains a 'tree' attribute
name
Name of the attribute to use for storage into `ds`
verbose
If True, print a line for each element processed
dry_run
If True, don't dump `ds` elements
:Outputs:
- `ds`
- the list of __key__ of refds element without tree
"""
from rhizoscan.root.graph.mtg import tree_to_mtg
# remove extra element of 'compared'
def get_key(x):
return x.__key__.replace('/', '_')
ds_dict = dict([(get_key(d), d) for d in ds])
to_merge = [(ds_dict.get(get_key(r), None), r) for r in refds]
# find tree that are not found
missing = []
for d, r in to_merge:
rtree = r.copy().load().get('tree', None)
if rtree is not None:
if verbose: print 'adding trees for', r.__key__
d = d.copy().load()
rrsa = tree_to_mtg(rtree)
d.set(name, rrsa, store=not dry_run)
if not dry_run:
d.dump()
else:
if verbose: print ' *** unavailable trees for', r.__key__
missing.append(r.__key__)
return ds, missing
def _update_tree(self):
item = self.edited_item
# set tree, if exist
if item.has_key('mtg'):
self.tree_viewer.set_model(item.mtg)
self.set_edited_presenter('tree_viewer')
elif item.has_key('tree'): ##to check
from rhizoscan.root.graph.mtg import tree_to_mtg
self.show_message("dataset item has not 'mtg' attribute")
mtg = tree_to_mtg(item.tree)
self.tree_viewer.set_model(mtg)
self.set_edited_presenter('tree_viewer')
else:
self.show_message(
"dataset item has not 'mtg' not 'tree' attribute")
def run(image_filename, have_petri_plate=False, verbose=False):
# ==========================================================================
# Load image
image = cv2.imread(image_filename, flags=cv2.IMREAD_GRAYSCALE)
if verbose:
show_image(image, "original image")
# ==========================================================================
# Detect features (Petri plate)
border_width = 250 # Measure in pixel
plate_size = 120 # Useful just for pixel scale
fg_smooth = 1 # Dono
if have_petri_plate:
pmask, px_scale, hull = detect_petri_plate(image,
border_width=border_width,
plate_size=plate_size,
fg_smooth=fg_smooth)
if verbose:
show_image(pmask, "mask petri plate")
print "Pixel scale :", px_scale
else:
pmask = None
px_scale = None
# ==========================================================================
# Image Segmentation
root_max_radius = 13
rmask, bbox = segment_image(image,
pmask=pmask,
root_max_radius=root_max_radius,
min_dimension=50,
smooth=2,
verbose=True)
if verbose:
show_image(rmask, "segment mask")
# ==========================================================================
# Detect leaves and seed
root_min_radius = 3
plant_number = 5
seed_map = detect_leaves_with_kmeans(rmask,
erode_iteration=0,
bounding_box=[0.05, 0.06, 0.90, 0.10],
plant_number=plant_number)
if verbose:
show_image(seed_map + rmask, "seed_map+rmask")
# ==========================================================================
# Compute the graph corresponding to the RSA
graph = compute_graph(rmask, seed_map, bbox=bbox, verbose=False)
if verbose:
graph.plot()
matplotlib.pyplot.show()
# ==========================================================================
# Extract a tree from the graph
tree = compute_tree(graph, px_scale=px_scale, min_length=15)
if verbose:
tree.plot()
matplotlib.pyplot.show()
# ==========================================================================
# Save the RSA into an MTG
mtg = tree_to_mtg(tree)
rsml_serializer = RSMLSerializer()
rsml_serializer.dump(mtg, image_filename + '.rsml')