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 add_artificial_shoot(self):
""" adds a 1 cm shoot element, connecting all base roots
the type for looking up conductivities is set to 10
"""
nodes = self.analyser.nodes
bni = self.base_nodes
print("DataModel.add_artificial_shoot() base node indices are", bni)
mid = np.zeros((3,))
for i in bni:
mid += np.array([nodes[i].x, nodes[i].y, nodes[i].z])
mid /= len(bni)
print("DataModel.add_artificial_shoot() mid point is", mid)
rsml_reader.artificial_shoot(self.polylines, self.properties, self.functions) # append artifial shoot (default values)
radii, cts, types, tagnames = rsml_reader.get_parameter(self.polylines, self.functions, self.properties) # paramter per node
# change default values from artificial shoot
collar = mid.copy()
mid[2] += 0.1 # shift a bit up
collar[2] += 1.1 # 1 cm shoot length
self.polylines[0][0] = collar
self.polylines[0][1] = mid
self.set_selected(radii, cts, types, tagnames)
self.scale_selected_()
self.radii[0] = 0.1 # cm
self.radii[1] = 0.1 # cm
self.types[0] = 10
self.types[1] = 10
# print("after ADD SHOOT")
# print(self.polylines)
# print(self.properties["parent-poly"])
# print(self.properties["parent-node"])
# print("radii", radii)
# print("cts", cts)
# print("types", types)
self.convert_to_xylem_flux_()
def open_rsml(self, fname, shift_z=False):
""" opens an rsml file into self.data, using rsml_reader (in CPlantBox/src/python_modules)
converts units to cm and day
if necessary converts 2d -> 3d,
"""
polylines, properties, functions, metadata = rsml_reader.read_rsml(fname)
print("DataModel.open_rsml(): scale to cm", metadata.scale_to_cm)
self.set_rsml(polylines, properties, functions, metadata)
self.scale_polylines_() # converts units
self.check_polylines_2d_(shift_z) # 2d -> 3d
radii, cts, types, tagnames = rsml_reader.get_parameter(polylines, functions, properties) # paramter per node
self.set_selected(radii, cts, types, tagnames)
self.scale_selected_() # converts units of special fields radii, cts, types
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 add_creation_times(self):
""" lineary interpolates creation times assuming a lateral delay time of one day """
pl_ = self.polylines # rename
self.functions["creation_time"] = [None] * len(pl_)
for i, pl in enumerate(pl_):
if self.properties["parent-poly"][i] == -1:
self.functions["creation_time"][i] = np.zeros((len(pl,)))
if not (i == 0 and len(pl) == 2): # not artifical shoot, else [0,0] is fine
ct = self.functions["creation_time"][i] # rename
lt = self.get_length_(pl)
l = 0
ct[0] = 0
for j in range(0, len(pl) - 1):
l += np.linalg.norm(np.array(pl[j + 1]) - np.array(pl[j]))
ct[j + 1] = self.max_ct * (l / lt)
for i, pl in enumerate(pl_):
if self.functions["creation_time"][i] is None:
self.add_creation_times_(i)
radii, cts, types, tagnames = rsml_reader.get_parameter(self.polylines, self.functions, self.properties) # paramter per node
self.set_selected(radii, cts, types, tagnames)
self.scale_selected_()
self.convert_to_xylem_flux_()