def construct_tree(d):
items = []
for idx in d:
x = X[self.index_map == idx]
y = Y[self.index_map == idx]
z = Z[self.index_map == idx]
f = self.data[self.index_map == idx]
if type(d[idx]) == tuple:
sub_items = construct_tree(d[idx][0])
b = Branch(sub_items, x[0], y[0], z[0], f[0], id=idx)
for i in range(1, len(x)):
b.add_point(x[i], y[i], z[i], f[i])
items.append(b)
else:
l = Leaf(x[0], y[0], z[0], f[0], id=idx)
for i in range(1, len(x)):
l.add_point(x[i], y[i], z[i], f[i])
items.append(l)
return items
def _compute(self, data, minimum_flux=-np.inf, minimum_npix=0, minimum_delta=0, verbose=True):
# Reset ID counter
self._reset_idx()
# Initialize list of ancestors
ancestor = {}
# If array is 2D, recast to 3D
if len(data.shape) == 2:
self.n_dim = 2
self.data = data.reshape(1, data.shape[0], data.shape[1])
else:
self.n_dim = 3
self.data = data
# Extract data shape
nz, ny, nx = self.data.shape
# Create arrays with pixel positions
x = np.arange(self.data.shape[2], dtype=np.int32)
y = np.arange(self.data.shape[1], dtype=np.int32)
z = np.arange(self.data.shape[0], dtype=np.int32)
X, Y, Z = meshgrid_nd(x, y, z)
# Convert to 1D
flux, X, Y, Z = self.data.ravel(), X.ravel(), Y.ravel(), Z.ravel()
# Keep only values above minimum required
keep = flux > minimum_flux
flux, X, Y, Z = flux[keep], X[keep], Y[keep], Z[keep]
if verbose:
print "Number of points above minimum: %i" % np.sum(keep)
# Sort by decreasing flux
order = np.argsort(flux)[::-1]
flux, X, Y, Z = flux[order], X[order], Y[order], Z[order]
# Define index array indicating what item each cell is part of
self.index_map = np.zeros(self.data.shape, dtype=np.int32)
# Loop from largest to smallest value. Each time, check if the pixel
# connects to any existing leaf. Otherwise, create new leaf.
items = {}
for i in range(len(flux)):
# Print stats
if verbose and i % 10000 == 0:
print "%i..." % i
# Check if point is adjacent to any leaf
adjacent = []
if X[i] > 0 and self.index_map[Z[i], Y[i], X[i] - 1] > 0:
adjacent.append(self.index_map[Z[i], Y[i], X[i] - 1])
if X[i] < nx - 1 and self.index_map[Z[i], Y[i], X[i] + 1] > 0:
adjacent.append(self.index_map[Z[i], Y[i], X[i] + 1])
if Y[i] > 0 and self.index_map[Z[i], Y[i] - 1, X[i]] > 0:
adjacent.append(self.index_map[Z[i], Y[i] - 1, X[i]])
if Y[i] < ny - 1 and self.index_map[Z[i], Y[i] + 1, X[i]] > 0:
adjacent.append(self.index_map[Z[i], Y[i] + 1, X[i]])
if Z[i] > 0 and self.index_map[Z[i] - 1, Y[i], X[i]] > 0:
adjacent.append(self.index_map[Z[i] - 1, Y[i], X[i]])
if Z[i] < nz - 1 and self.index_map[Z[i] + 1, Y[i], X[i]] > 0:
adjacent.append(self.index_map[Z[i] + 1, Y[i], X[i]])
# Replace adjacent elements by its ancestor
for j in range(len(adjacent)):
if ancestor[adjacent[j]] is not None:
adjacent[j] = ancestor[adjacent[j]]
# Remove duplicates
adjacent = list(set(adjacent))
# Find how many unique adjacent structures there are
n_adjacent = len(adjacent)
if n_adjacent == 0: # Create new leaf
# Set absolute index of the new element
idx = self._next_idx()
# Create leaf
leaf = Leaf(X[i], Y[i], Z[i], flux[i], id=idx)
# Add leaf to overall list
items[idx] = leaf
# Set absolute index of pixel in index map
self.index_map[Z[i], Y[i], X[i]] = idx
# Create new entry for ancestor
ancestor[idx] = None
elif n_adjacent == 1: # Add to existing leaf or branch
# Get absolute index of adjacent element
idx = adjacent[0]
# Get adjacent item
item = items[idx]
# Add point to item
item.add_point(X[i], Y[i], Z[i], flux[i])
# Set absolute index of pixel in index map
self.index_map[Z[i], Y[i], X[i]] = idx
else: # Merge leaves
# At this stage, the adjacent items might consist of an arbitrary
# number of leaves and branches.
# Find all leaves that are not important enough to be kept
# separate. These leaves will now be treated the same as the pixel
# under consideration
merge = []
for idx in adjacent:
if type(items[idx]) == Leaf:
leaf = items[idx]
if leaf.npix < minimum_npix or leaf.fmax - flux[i] < minimum_delta:
merge.append(idx)
# Remove merges from list of adjacent items
for idx in merge:
adjacent.remove(idx)
# If there is only one item left, then if it is a leaf, add to the
# list to merge, and if it is a branch then add the merges to the
# branch.
if len(adjacent) == 0:
# There are no separate leaves left (and no branches), so pick the
# first one as the reference and merge all the others onto it
idx = merge[0]
leaf = items[idx]
# Add current point to the leaf
leaf.add_point(X[i], Y[i], Z[i], flux[i])
# Set absolute index of pixel in index map
self.index_map[Z[i], Y[i], X[i]] = idx
for i in merge[1:]:
# print "Merging leaf %i onto leaf %i" % (i, idx)
# Remove leaf
removed = items.pop(i)
# Merge old leaf onto reference leaf
leaf.merge(removed)
# Update index map
self.index_map = removed.add_footprint(self.index_map, idx)
elif len(adjacent) == 1:
if type(items[adjacent[0]]) == Leaf:
idx = adjacent[0]
leaf = items[idx]
# Add current point to the leaf
leaf.add_point(X[i], Y[i], Z[i], flux[i])
# Set absolute index of pixel in index map
self.index_map[Z[i], Y[i], X[i]] = idx
for i in merge:
# print "Merging leaf %i onto leaf %i" % (i, idx)
# Remove leaf
removed = items.pop(i)
# Merge old leaf onto reference leaf
leaf.merge(removed)
# Update index map
self.index_map = removed.add_footprint(self.index_map, idx)
else:
idx = adjacent[0]
branch = items[idx]
# Add current point to the branch
branch.add_point(X[i], Y[i], Z[i], flux[i])
# Set absolute index of pixel in index map
self.index_map[Z[i], Y[i], X[i]] = idx
for i in merge:
# print "Merging leaf %i onto branch %i" % (i, idx)
# Remove leaf
removed = items.pop(i)
# Merge old leaf onto reference leaf
branch.merge(removed)
# Update index map
self.index_map = removed.add_footprint(self.index_map, idx)
else:
# Set absolute index of the new element
idx = self._next_idx()
# Create branch
branch = Branch([items[j] for j in adjacent], \
X[i], Y[i], Z[i], flux[i], id=idx)
# Add branch to overall list
items[idx] = branch
# Set absolute index of pixel in index map
self.index_map[Z[i], Y[i], X[i]] = idx
# Create new entry for ancestor
ancestor[idx] = None
for i in merge:
# print "Merging leaf %i onto branch %i" % (i, idx)
# Remove leaf
removed = items.pop(i)
# Merge old leaf onto reference leaf
branch.merge(removed)
# Update index map
self.index_map = removed.add_footprint(self.index_map, idx)
for j in adjacent:
ancestor[j] = idx
for a in ancestor:
if ancestor[a] == j:
ancestor[a] = idx
if verbose and not i % 10000 == 0:
print "%i..." % i
# Remove orphan leaves that aren't large enough
remove = []
for idx in items:
item = items[idx]
if type(item) == Leaf:
if item.npix < minimum_npix or item.fmax - item.fmin < minimum_delta:
remove.append(idx)
for idx in remove:
items.pop(idx)
# Create trunk from objects with no ancestors
self.trunk = Trunk()
for idx in items:
if ancestor[idx] is None:
self.trunk.append(items[idx])
# Make map of leaves vs branches
self.item_type_map = np.zeros(self.data.shape, dtype=np.uint8)
for idx in items:
item = items[idx]
if type(item) == Leaf:
self.item_type_map = item.add_footprint(self.item_type_map, 2)
else:
self.item_type_map = item.add_footprint(self.item_type_map, 1, recursive=False)
# Re-cast to 2D if original dataset was 2D
if self.n_dim == 2:
self.data = self.data[0, :, :]
self.index_map = self.index_map[0, :, :]
self.item_type_map = self.item_type_map[0, :, :]
