def generate_xml_from_all_seq(self):
clear_scene_file_startswith(self.seq_name)
SceneGenerate.write_range_num_for_RT(self._cfgFile)
self.readParameterFileList()
for filename in self.parameter_file_list:
tcfgfile = os.path.join(session.get_input_dir(), filename)
prifix = os.path.splitext(filename)[0] + "_"
SceneGenerate.terr_generate(tcfgfile, prifix)
SceneGenerate.generate_objects_file(tcfgfile, prifix)
SceneGenerate.forest_generate(tcfgfile, prifix)
# if len(self.parameter_file_list) > 0:
# SceneGenerate.generate_objects_file(self._cfgFile, self.seq_name + "_")
# SceneGenerate.forest_generate(self._cfgFile, self.seq_name + "_")
# log("INFO: Generating view and illuminations.")
# 输出irridiance
fi = open(
os.path.join(session.get_output_dir(),
self.seq_name + "_" + irradiance_file), 'w')
sp = SceneParser()
for filename in self.parameter_file_list:
tcfgfile = os.path.join(session.get_input_dir(), filename)
prifix = os.path.splitext(filename)[0] + "_"
irrstr = sp.parse(tcfgfile, prifix, prifix)
fi.write(os.path.splitext(filename)[0] + "\n" + irrstr + "\n")
log("INFO: view and illuminations generated.")
fi.close()
def run_seq(self):
currdir = os.path.split(os.path.realpath(__file__))[0]
os.environ[
'PATH'] = currdir + '/bin/rt/' + current_rt_program + os.pathsep + os.environ[
'PATH']
self.readParameterFileList()
for filename in self.parameter_file_list:
log("INFO: " + filename)
tcfgfile = os.path.join(session.get_input_dir(), filename)
prifix = os.path.splitext(filename)[0]
f = open(tcfgfile, 'r')
cfg = json.load(f)
excuable = "lessrt"
scene_path = session.get_scenefile_path()
distFile = os.path.join(session.get_output_dir(), prifix)
# parameter = " -o " + distFile
scene_file_path = os.path.join(scene_path,
prifix + "_" + main_scene_xml_file)
# cmd = excuable + " " + os.path.join(scene_path, prifix+"_"+main_scene_xml_file) + parameter
# os.system(cmd)
cores = cfg["Advanced"]["number_of_cores"]
if cfg["Advanced"]["network_sim"]:
subprocess.call([
excuable, scene_file_path, "-o", distFile, "-p",
str(cores), "-s",
os.path.join(session.get_input_dir(), "server.txt")
])
else:
subprocess.call([
excuable, scene_file_path, "-o", distFile, "-p",
str(cores)
])
# os.system(excuable + " " + scene_file_path + " " + "-o " + distFile + " -p " + str(cores))
time.sleep(0.5)
if output_format not in ("npy", "NPY"):
if os.path.exists(distFile + ".npy"):
self.convert_npy_to_envi(cfg, distFile, output_format)
if os.path.exists(distFile + "_downwelling.npy"):
self.convert_npy_to_envi(cfg, distFile + "_downwelling",
output_format)
if os.path.exists(distFile + "_upwelling.npy"):
self.convert_npy_to_envi(cfg, distFile + "_upwelling",
output_format)
if os.path.exists(distFile + "_4Components.npy"):
data = np.load(distFile + "_4Components.npy")
dshape = data.shape
if len(dshape) == 3:
if dshape[2] <= 4:
data = data[:, :, 0]
else:
data = data[:, :, 0:5]
bandlist = []
RasterHelper.saveToHdr_no_transform(
data, distFile + "_4Components", bandlist,
output_format)
os.remove(distFile + "_4Components.npy")
def readParameterFileList(self):
if self.parameter_file_list is None:
self.parameter_file_list = []
for filename in os.listdir(session.get_input_dir()):
if filename.startswith(self.seq_name):
self.parameter_file_list.append(filename)
self.parameter_file_list = self.sort_list(self.parameter_file_list)
def parse_seq(self):
clear_param_file_startswith(self.seq_name)
# write seq info
finfo = open(
os.path.join(session.get_output_dir(),
self.seq_name + BATCH_INFO_FILE), 'w')
params = []
f = open(self.seqPath, 'r')
seq = json.load(f, object_pairs_hook=OrderedDict)
groupNames = []
for groupName in seq:
groupParam = dict()
groupNames.append(groupName)
for paramName in seq[groupName]: # in each group
paramValue = seq[groupName][paramName]
if paramValue.startswith(batch_List_name):
arr = paramValue.split(":", 1)
arr = arr[1].split("/")
index = 0
for data in arr:
if index not in groupParam:
groupParam[index] = dict()
groupParam[index][paramName] = data
index += 1
# print groupParam
params.append(groupParam)
# mixture between group
indexList = []
for i in range(0, len(params)):
groupLen = len(params[i])
indexList.append(range(0, groupLen))
totalIndex = 0
combinations = list(itertools.product(*indexList))
for combination in combinations:
if len(combination) > 0:
groupIndex = 0
seq_input_file = os.path.join(
session.get_input_dir(),
self.seq_name + "_" + str(totalIndex) + ".json")
finfo.write(self.seq_name + "_" + str(totalIndex) + " ")
cfg = self.read_config_file()
totalIndex += 1
for paramValueIndex in combination:
for paramName in params[groupIndex][paramValueIndex]:
paraVal = params[groupIndex][paramValueIndex][
paramName]
print("INFO: --", paramName)
self.writeKey(cfg, paramName,
self.getTypedValue(paramName, paraVal))
finfo.write(paramName + " " + paraVal + " ")
groupIndex += 1
# write batch config file
self.writeCfgFile(cfg, seq_input_file)
finfo.write("\n")
finfo.close()
log("INFO: Sub region trees:", area_max)
log("INFO: Start parallel computing...")
# temp file
folder = tempfile.mkdtemp()
detected_trees_pos = np.memmap(os.path.join(folder, 'treedetect'), dtype=float, shape=(area_max, 5),
mode='w+')
detected_trees_pos += -1
joblib.Parallel(n_jobs=joblib.cpu_count()-1, max_nbytes=None)(
joblib.delayed(sub_fun)(nuclear, areas, detected_trees_pos, i,
real_coordinate, offset_x, offset_y,
pixel_size, obj_num, seg_size, crownDiameterList,crownHeightsList) for i in range(0, seg_num))
if out_file == "":
from session import session
out_file = os.path.join(session.get_input_dir(), "instances.txt")
if num_r == 0 and num_c == 0:
fw = open(out_file, 'w')
else:
fw = open(out_file, 'a')
for i in range(0, len(detected_trees_pos)):
if detected_trees_pos[i][0] >= 0:
outstr = objList[int(detected_trees_pos[i][0])] + " " + str(detected_trees_pos[i][1]) + " " + str(
detected_trees_pos[i][2])+" 0 "+str(detected_trees_pos[i][3])+" "+str(detected_trees_pos[i][4])
# if detected_trees_pos[i][0] >= 0:
# outstr = objList[int(detected_trees_pos[i][0])] + " " + str(detected_trees_pos[i][1]) + " " + str(
# detected_trees_pos[i][2]) + " 0"
fw.write(outstr + "\n")
fw.close()
del detected_trees_pos
detected_trees_pos = np.memmap(os.path.join(folder, 'treedetect'),
dtype=float,
shape=(area_max, 5),
mode='w+')
detected_trees_pos += -1
joblib.Parallel(n_jobs=joblib.cpu_count() - 1, max_nbytes=None)(
joblib.delayed(sub_fun)
(nuclear, areas, detected_trees_pos, i, real_coordinate,
offset_x, offset_y, pixel_size, obj_num, seg_size,
crownDiameterList, crownHeightsList)
for i in range(0, seg_num))
if out_file == "":
from session import session
out_file = os.path.join(session.get_input_dir(),
"instances.txt")
if num_r == 0 and num_c == 0:
fw = open(out_file, 'w')
else:
fw = open(out_file, 'a')
for i in range(0, len(detected_trees_pos)):
if detected_trees_pos[i][0] >= 0:
outstr = objList[int(
detected_trees_pos[i][0])] + " " + str(
detected_trees_pos[i][1]) + " " + str(
detected_trees_pos[i][2]) + " 0 " + str(
detected_trees_pos[i][3]) + " " + str(
detected_trees_pos[i][4])
# if detected_trees_pos[i][0] >= 0:
# outstr = objList[int(detected_trees_pos[i][0])] + " " + str(detected_trees_pos[i][1]) + " " + str(
def clear_json_file(self):
self.readParameterFileList()
for filename in self.parameter_file_list:
filepath = os.path.join(session.get_input_dir(), filename)
os.remove(filepath)
def getTreeLocAndHeight(chm_hdr_path,
out_file,
obj_list,
subregion=0,
real_coordinate=True):
idata_set = gdal.Open(chm_hdr_path)
transform = idata_set.GetGeoTransform()
if transform is None:
log("ERROR: No geotransform found for file ", chm_hdr_path)
return
objList = obj_list.strip().split("*")
obj_num = len(objList)
pixel_size = abs(transform[1])
band = idata_set.GetRasterBand(1)
banddata = band.ReadAsArray(0, 0, band.XSize, band.YSize)
width = band.XSize # XSize是列数, YSize是行数
height = band.YSize
if (subregion == 0):
subregion = max(width, height)
num_width = int(math.ceil(width / float(subregion)))
num_height = int(math.ceil(height / float(subregion)))
result = []
treeCount = 0
for num_r in range(0, num_height): # row
for num_c in range(0, num_width): #col
log("INFO: Region: " + str(num_r) + " " + str(num_c))
row_start = num_r * subregion
row_end = min((num_r + 1) * subregion, height)
col_start = num_c * subregion
col_end = min((num_c + 1) * subregion, width)
offset_x = num_c * subregion * pixel_size
offset_y = num_r * subregion * pixel_size
nuclear = banddata[row_start:row_end, col_start:col_end]
threshed = (nuclear > 3)
nuclear *= threshed
bc = np.ones((3, 3))
maxima = mahotas.morph.regmax(nuclear, Bc=bc)
spots, n_spots = mahotas.label(maxima)
surface = (nuclear.max() - nuclear)
areas = mahotas.cwatershed(surface, spots)
areas *= threshed
area_max = areas.max()
# seg_size = args.seg_size # 500000 points for each core, parallel
# seg_num = int(math.ceil(area_max / float(seg_size)))
print(area_max)
# 每棵树用不用的数值标记
for i in range(1, areas.max()):
if i % 1000 == 0:
log("INFO: Detected Trees: " + str(i))
treepixel = np.where(areas == i)
tmpmax = 0
tx, ty = 0, 0
tmp = 0
# crown = math.sqrt(len(treepixel[0]) * pixel_size * pixel_size) * 2
# tx,ty = sum(treepixel[0])/float(len(treepixel[0])),sum(treepixel[1])/float(len(treepixel[1]))
for m in range(0, len(treepixel[0])):
tmp += 1
if nuclear[treepixel[0][m]][treepixel[1][m]] > tmpmax:
tmpmax = nuclear[treepixel[0][m]][treepixel[1][m]]
tx, ty = treepixel[0][m], treepixel[1][m]
# maxHeight = nuclear[tx, ty]
if real_coordinate:
x = offset_x + ty * pixel_size
y = offset_y + tx * pixel_size
result.append([random.randint(0, obj_num - 1), x, y])
else:
result.append([random.randint(0, obj_num - 1), tx, ty])
if out_file == "":
from session import session
import os
out_file = os.path.join(session.get_input_dir(), "instances.txt")
log("INFO: Total detected trees: ", treeCount)
fw = open(out_file, 'w')
for i in range(0, len(result)):
outstr = objList[result[i][0]] + " " + str(result[i][1]) + " " + str(
result[i][2])
fw.write(outstr + "\n")
fw.close()
