def read_rsml(file_name:str, verbose=True):
""" reads an RSML file and converts to MappedSegments with units [cm]
@file_name the file name of the rsml, including file extension (e.g. "test.rsml" )
@return a CPlantBox MappedSegments object
"""
polylines, props, funcs = rsml.read_rsml(file_name)
bn = 0 # count base roots
for i, _ in enumerate(polylines):
if props["parent-poly"][i] < 0:
bn += 1
if bn > 1:
polylines, props, funcs = rsml.artificial_shoot(polylines, props, funcs)
if verbose:
print("XylemFluxPython.read_rsml: added an artificial shoot")
nodes, segs = rsml.get_segments(polylines, props)
radii, seg_ct, types = rsml.get_parameter(polylines, funcs, props)
if verbose:
print("XylemFluxPython.read_rsml: read rsml with", len(nodes), "nodes and", len(segs), "segments")
nodes = np.array(nodes) # for slicing in the plots
nodes2 = [] # Conversions...
for n in nodes:
nodes2.append(pb.Vector3d(n[0] , n[1] , n[2]))
segs2 = []
nodeCTs = np.zeros((len(nodes), 1)) # we need node creation times
for i, s in enumerate(segs):
nodeCTs[s[1]] = seg_ct[i]
segs2.append(pb.Vector2i(int(s[0]), int(s[1])))
radii = np.array(radii)
types = np.array(types, dtype=np.int64) - 1 # index must start with 0
if verbose:
print(" nodeCTs [{:g}, {:g}] days".format(np.min(nodeCTs), np.max(nodeCTs)))
print(" raddii [{:g}, {:g}] cm".format(np.min(radii), np.max(radii)))
print(" subTypes [{:g}, {:g}] ".format(np.min(types), np.max(types)))
return pb.MappedSegments(nodes2, nodeCTs, segs2, radii, types) # root system grid
def convert_to_xylem_flux_(self):
""" converts the polylines to a SegmentAnalyser and a MappedSegments object, and stores max_ct
uses:
properties["parent-poly"], properties["parent-nodes"]
radii, cts, types
"""
nodes, segs = rsml_reader.get_segments(self.polylines, self.properties) # fetch nodes and segments
segRadii = np.zeros((segs.shape[0], 1)) # convert to paramter per segment
segCTs = np.zeros((segs.shape[0], 1))
subTypes = np.zeros((segs.shape[0], 1))
for i, s in enumerate(segs):
segRadii[i] = self.radii[s[1]] # seg to node index
segCTs[i] = self.cts[s[1]]
subTypes[i] = self.types[s[1]]
if np.isnan(subTypes[0]):
subTypes = np.ones((len(segs),), dtype=np.int64)
segs_ = [pb.Vector2i(s[0], s[1]) for s in segs] # convert to CPlantBox types
nodes_ = [pb.Vector3d(n[0], n[1], n[2]) for n in nodes]
self.analyser = pb.SegmentAnalyser(nodes_, segs_, segCTs, segRadii)
self.analyser.addData("subType", subTypes)
ms = pb.MappedSegments(self.analyser.nodes, np.array(self.cts), segs_, np.array(segRadii), np.array(subTypes))
self.xylem_flux = xylem_flux.XylemFluxPython(ms)
self.base_nodes = self.get_base_node_indices_()
self.xylem_flux.neumann_ind = self.base_nodes # needed for suf
self.xylem_flux.dirichlet_ind = self.base_nodes # needed for krs
self.base_segs = self.xylem_flux.find_base_segments()
def read_rsml(file_name: str):
"""
Reads an RSML file and converts to MappedSegments with units [cm]
"""
polylines, props, funcs = rsml.read_rsml(file_name)
assert len(polylines) == len(
props['parent-poly']
), "XylemFluxPython.read_rsml: wrong number of parent-poly tags"
if not 'parent-node' in props: # reconstruct...
print("parse_rsml: no parent-node tag found, reconstructing...")
props['parent-node'] = []
for i in range(0, len(polylines)):
if props['parent-poly'][i] >= 0:
pni = XylemFluxPython.connect(
np.array(polylines[i][0]),
polylines[props['parent-poly'][i]])
else:
pni = -1
# print("parent", props['parent-poly'][i], "pni", pni)
props['parent-node'].append(pni)
assert len(polylines) == len(
props['parent-node']
), "XylemFluxPython.read_rsml: wrong number of parent-node tags"
nodes, segs = rsml.get_segments(polylines, props)
print("Read rsml:", len(nodes), "segs", len(segs), "segs")
nodes2 = [pb.Vector3d(n[0], n[1], n[2])
for n in nodes] # convert to plantbox types
segs2 = [pb.Vector2i(int(s[0]), int(s[1])) for s in segs]
radii_, nodeCTs_, types_ = [], [], []
for i, p in enumerate(polylines):
for j in range(0, len(p)):
if 'diameter' in funcs:
radii_.append(funcs['diameter'][i][j] / 2)
else:
print("XylemFluxPython.read_rsml: no diameter tag found")
radii_.append(0.)
if 'emergence_time' in funcs:
nodeCTs_.append(funcs['emergence_time'][i][j])
else:
print(
"XylemFluxPython.read_rsml: no emergence_time tag found"
)
nodeCTs_.append(0.)
if 'type' in funcs:
types_.append(funcs["type"][i][j])
elif 'type' in props:
types_.append(props["type"][i])
else:
print("XylemFluxPython.read_rsml: no type tag found")
types_.append(0)
nodeCTs = np.array(nodeCTs_) # creation times per node
radii = np.zeros((len(segs), 1)) # radii per segment
types = np.ones((len(segs), 1), dtype=np.int64) # types per semgent
for i, s in enumerate(segs):
radii[i] = radii_[s[1]]
types[i] = types_[s[1]] - 1 # index must start with 0
return pb.MappedSegments(nodes2, nodeCTs, segs2, radii,
types) # root system grid
def read_rsml(file_name: str, verbose=True):
""" reads an RSML file and converts to MappedSegments with units [cm]
@file_name the file name of the rsml, including file extension (e.g. "test.rsml" )
@return a CPlantBox MappedSegments object
"""
polylines, props, funcs, _ = rsml.read_rsml(file_name)
bn = 0 # count base roots
for i, _ in enumerate(polylines):
if props["parent-poly"][i] < 0:
bn += 1
if bn > 1:
rsml.artificial_shoot(polylines, props, funcs)
if verbose:
print("XylemFluxPython.read_rsml: added an artificial shoot")
nodes, segs = rsml.get_segments(polylines, props)
if verbose:
print("XylemFluxPython.read_rsml: read rsml with", len(nodes),
"nodes and", len(segs), "segments")
nodes2 = [pb.Vector3d(n[0], n[1], n[2])
for n in nodes] # Conversions to PlantBox types
segs2 = [pb.Vector2i(int(s[0]), int(s[1])) for s in segs]
radii, cts, types, tag_names = rsml.get_parameter(
polylines, funcs, props)
segRadii = np.zeros(
(segs.shape[0], 1)) # convert to paramter per segment
segTypes = np.zeros((segs.shape[0], 1))
for i, s in enumerate(segs):
segRadii[i] = radii[s[1]] # seg to node index
segTypes[i] = types[s[1]]
if verbose:
print(" cts [{:g}, {:g}] days".format(
np.min(cts), np.max(cts)))
print(" raddii [{:g}, {:g}] cm".format(
np.min(radii), np.max(radii)))
print(" subTypes [{:g}, {:g}] ".format(
np.min(types), np.max(types)))
print()
return pb.MappedSegments(nodes2, cts, segs2, segRadii,
segTypes) # root system grid
def read_rsml(file_name: str):
"""
Reads an RSML file and converts to MappedSegments with units [cm]
"""
polylines, props, funcs = rsml.read_rsml(file_name)
nodes, segs = rsml.get_segments(polylines, props)
radii, seg_ct, types = rsml.get_parameter(polylines, funcs, props)
print("Read rsml:", len(nodes), "nodes", len(radii), "radii")
nodes = np.array(nodes) # for slicing in the plots
nodes2 = [] # Conversions...
for n in nodes:
nodes2.append(pb.Vector3d(n[0], n[1], n[2]))
segs2 = []
nodeCTs = np.zeros((len(nodes), 1)) # we need node creation times
for i, s in enumerate(segs):
nodeCTs[s[1]] = seg_ct[i]
segs2.append(pb.Vector2i(int(s[0]), int(s[1])))
radii = np.array(radii)
types = np.array(types, dtype=np.int64) - 1 # index must start with 0
return pb.MappedSegments(nodes2, nodeCTs, segs2, radii,
types) # root system grid
def check_polylines_2d_(self, shift_z=False):
""" converts 2d image coordinates to 3d coordinates
shift_z determines if the roots system seed is shifted to -3 cm
"""
nodes, segs = rsml_reader.get_segments(self.polylines, self.properties) # fetch nodes and segments
maxz = np.max(nodes[:, 2])
minz = np.min(nodes[:, 2])
if maxz >= 0 and minz >= 0: # image coordinates in px often start in lower left corner
print("DataModel.check_polylines_2d_(): assuming image coordinates, y-centered and z-flipped ")
miny = np.min(nodes[:, 1])
yy = np.max(nodes[:, 1]) - miny
for pl in self.polylines: # both (pl and node) are references
for node in pl:
node[2] = -node[2]
node[1] = node[1] - miny - yy / 2
if shift_z:
print("DataModel.check_polylines_2d_(): root system seed is shifted to (x,y,-3) ")
z = self.polylines[0][0][2]
print("z", z)
for pl in self.polylines: # both (pl and node) are references
for node in pl:
node[2] = node[2] - z + (-3)