def _generate_mask(self, interval, r_id):
"""
Actually generates a mask for a given interval and region (r_id)
"""
# Get GRASS interface instance
g = grass.get_g()
# Generate a random map name
mapname = g.generate_map_name("mask")
if r_id in self.bins.keys():
bins = self.bins[r_id]
elif "__default" in self.bin.keys():
bins = self.bins["__default"]
else:
self.log.error(
"Could not find any phenology bins for generating mask")
# Find what bin the interval lies within
for d_range, mean in bins.items():
if interval >= d_range[0] and interval <= d_range[1]:
g.mapcalc(mapname, "if(%s>=%f,if(%s<=%f,1,0),0)" % (self.p_map_names[
r_id], d_range[0], self.p_map_names[r_id], d_range[1]))
grassmap_mask = GrassMap(mapname)
grassmap_mask.temporary = True
return grassmap_mask
self.log.debug(
"No appropriate interval range found for interval %d" % interval)
def _generate_mask(self, interval, r_id):
"""
Actually generates a mask for a given interval and region (r_id)
"""
# Get GRASS interface instance
g = grass.get_g()
# Generate a random map name
mapname = g.generate_map_name("mask")
if r_id in self.bins.keys():
bins = self.bins[r_id]
elif "__default" in self.bin.keys():
bins = self.bins["__default"]
else:
self.log.error("Could not find any phenology bins for generating mask")
# Find what bin the interval lies within
for d_range, mean in bins.items():
if interval >= d_range[0] and interval <= d_range[1]:
g.mapcalc(
mapname,
"if(%s>=%f,if(%s<=%f,1,0),0)"
% (self.p_map_names[r_id], d_range[0], self.p_map_names[r_id], d_range[1]),
)
grassmap_mask = GrassMap(mapname)
grassmap_mask.temporary = True
return grassmap_mask
self.log.debug("No appropriate interval range found for interval %d" % interval)
def _load_lifestage(self):
""" Loads details from XML into class """
# Load name
if "name" in self.xml_node.attrib.keys():
self.name = self.xml_node.attrib["name"]
else:
raise Exception("Can't find name of lifestage")
# Load whether population based or not
if "populationBased" in self.xml_node.attrib.keys():
if self.xml_node.attrib["populationBased"].upper().find("TRUE") != -1:
self.populationBased = True
# Load and construct event objects
event_nodes = self.xml_node.xpath("event")
for e_node in event_nodes:
e = Event(e_node)
self.events.append(e)
# Load the initial distribution maps
init_map_nodes = self.xml_node.xpath('initialDistribution')
for i_node in init_map_nodes:
r_id = i_node.attrib["region"]
# stupid way of ignoring comments
for i in i_node.iter(tag=lxml.etree.Element):
if i == i_node:
continue
m_node = i
break
self.initial_maps[r_id] = GrassMap(m_node)
# Init phenology bins
self.init_phenology_bins()
def init_from_xml(self):
if self.node.tag == "mfilter":
self.area = Event(self.node)
else:
# If it's not an mfilter it must be a map
self.area = GrassMap(self.node)
class TreatmentArea:
def __init__(self, node, treatment, a_index):
"""
node is the xml node defining the TreatmentArea.
treatment is the parent Treatment this area is for.
a_index is the area index used to create the temp map name.
"""
self.treatment = treatment
self.node = node
self.area = None
self.area_filter_output = None
self.index = a_index
# temporary map name
self.area_temp = "x_t___strategy_" + self.treatment.strategy.get_name() + \
"_area_t_" + str(self.treatment.index) + "_" + str(self.index)
self.init_from_xml()
def __del__(self):
if self.area_filter_output is not None:
grass.get_g().remove_map(self.area_filter_output)
def init_from_xml(self):
if self.node.tag == "mfilter":
self.area = Event(self.node)
else:
# If it's not an mfilter it must be a map
self.area = GrassMap(self.node)
def is_dynamic(self):
"""
Return whether this TreatmentArea changes each timestep or not. An area
if dynamic if it uses an event/mfilter or a GrassMap with refresh==True.
An example of the latter case is using r.mapcalc.
"""
if isinstance(self.area, Event):
return True
elif isinstance(self.area, GrassMap):
return self.area.refresh
else:
raise Exception("Unknown area type")
def get_map_resources(self):
maps = []
if isinstance(self.area, Event):
m = self.treatment.strategy.experiment
maps.extend(self.area.get_map_resources(m))
elif isinstance(self.area, GrassMap):
if self.area.xml_map_type == "name":
g = grass.get_g()
maps.append((self.area.filename, g.find_mapset(self.area.filename)))
return maps
def get_treatment_area(self, replicate, last_area=None):
"""
Get the map name representing the treatment area, generating it
dynamically if necessary.
"""
if isinstance(self.area, Event):
if self.area_filter_output is not None:
grass.get_g().remove_map(self.area_filter_output)
if last_area:
dist_map = last_area
else:
dist_map = replicate.temp_map_names[self.treatment.area_ls][0]
self.area.run(dist_map, self.area_temp, replicate, False)
self.area_filter_output = self.area_temp
return self.area_filter_output
elif isinstance(self.area, GrassMap):
replacements = {
"POP_MAP": replicate.temp_map_names[self.treatment.area_ls][0],
"START_MAP": replicate.initial_maps[self.treatment.area_ls].get_map_filename()
}
return self.area.get_map_filename(replacements)
def init_from_xml(self):
if self.node.tag == "mfilter":
self.area = Event(self.node)
else:
# If it's not an mfilter it must be a map
self.area = GrassMap(self.node)
class TreatmentArea:
def __init__(self, node, treatment, a_index):
"""
node is the xml node defining the TreatmentArea.
treatment is the parent Treatment this area is for.
a_index is the area index used to create the temp map name.
"""
self.treatment = treatment
self.node = node
self.area = None
self.area_filter_output = None
self.index = a_index
# temporary map name
self.area_temp = "x_t___strategy_" + self.treatment.strategy.get_name() + \
"_area_t_" + str(self.treatment.index) + "_" + str(self.index)
self.init_from_xml()
def __del__(self):
if self.area_filter_output is not None:
grass.get_g().remove_map(self.area_filter_output)
def init_from_xml(self):
if self.node.tag == "mfilter":
self.area = Event(self.node)
else:
# If it's not an mfilter it must be a map
self.area = GrassMap(self.node)
def is_dynamic(self):
"""
Return whether this TreatmentArea changes each timestep or not. An area
if dynamic if it uses an event/mfilter or a GrassMap with refresh==True.
An example of the latter case is using r.mapcalc.
"""
if isinstance(self.area, Event):
return True
elif isinstance(self.area, GrassMap):
return self.area.refresh
else:
raise Exception("Unknown area type")
def get_map_resources(self):
maps = []
if isinstance(self.area, Event):
m = self.treatment.strategy.experiment
maps.extend(self.area.get_map_resources(m))
elif isinstance(self.area, GrassMap):
if self.area.xml_map_type == "name":
g = grass.get_g()
maps.append(
(self.area.filename, g.find_mapset(self.area.filename)))
return maps
def get_treatment_area(self, replicate, last_area=None):
"""
Get the map name representing the treatment area, generating it
dynamically if necessary.
"""
if isinstance(self.area, Event):
if self.area_filter_output is not None:
grass.get_g().remove_map(self.area_filter_output)
if last_area:
dist_map = last_area
else:
dist_map = replicate.temp_map_names[self.treatment.area_ls][0]
self.area.run(dist_map, self.area_temp, replicate, False)
self.area_filter_output = self.area_temp
return self.area_filter_output
elif isinstance(self.area, GrassMap):
replacements = {
"POP_MAP":
replicate.temp_map_names[self.treatment.area_ls][0],
"START_MAP":
replicate.initial_maps[
self.treatment.area_ls].get_map_filename()
}
return self.area.get_map_filename(replacements)