def manage_reconstruction(proc, experiment_dir, rec_id=None):
"""
This function starts the interruption discovery process and continues the recontruction processing.
It reads configuration file defined as <experiment_dir>/conf/config_rec.
If multiple generations are configured, or separate scans are discovered, it will start concurrent reconstructions.
It creates image.npy file for each successful reconstruction.
Parameters
----------
proc : str
processing library, choices are: cpu, cuda, opencl
experiment_dir : str
directory where the experiment files are loacted
rec_id : str
optional, if given, alternate configuration file will be used for reconstruction, (i.e. <rec_id>_config_rec)
Returns
-------
nothing
"""
if os.path.exists('stopfile'):
os.remove('stopfile')
print('starting reconstruction')
# the rec_id is a postfix added to config_rec configuration file. If defined, use this configuration.
conf_dir = os.path.join(experiment_dir, 'conf')
if rec_id is None:
conf_file = os.path.join(conf_dir, 'config_rec')
else:
conf_file = os.path.join(conf_dir, rec_id + '_config_rec')
# check if file exists
if not os.path.isfile(conf_file):
print('no configuration file ' + conf_file + ' found')
return
# verify the configuration file
if not ver.ver_config_rec(conf_file):
# if not verified, the ver will print message
return
try:
config_map = ut.read_config(conf_file)
if config_map is None:
print("can't read configuration file " + conf_file)
return
except Exception as e:
print('Cannot parse configuration file ' + conf_file +
' , check for matching parenthesis and quotations')
print(str(e))
return
# exp_dirs_data list hold pairs of data and directory, where the directory is the root of data/data.tif file, and
# data is the data.tif file in this directory.
exp_dirs_data = []
# experiment may be multi-scan in which case reconstruction will run for each scan
for dir in os.listdir(experiment_dir):
if dir.startswith('scan'):
datafile = os.path.join(experiment_dir, dir, 'data', 'data.tif')
if os.path.isfile(datafile):
exp_dirs_data.append(
(datafile, os.path.join(experiment_dir, dir)))
# if there are no scan directories, assume it is combined scans experiment
if len(exp_dirs_data) == 0:
# in typical scenario data_dir is not configured, and it is defaulted to <experiment_dir>/data
# the data_dir is ignored in multi-scan scenario
try:
data_dir = config_map.data_dir
except AttributeError:
data_dir = os.path.join(experiment_dir, 'data')
datafile = os.path.join(data_dir, 'data.tif')
if os.path.isfile(datafile):
exp_dirs_data.append((datafile, experiment_dir))
no_runs = len(exp_dirs_data)
if no_runs == 0:
print('did not find data.tif file(s). ')
return
try:
generations = config_map.generations
except:
generations = 0
try:
reconstructions = config_map.reconstructions
except:
reconstructions = 1
device_use = []
if proc == 'cpu':
cpu_use = [-1] * reconstructions
if no_runs > 1:
for _ in range(no_runs):
device_use.append(cpu_use)
else:
device_use = cpu_use
else:
try:
devices = config_map.device
except:
devices = [-1]
if no_runs * reconstructions > 1:
data_shape = ut.read_tif(exp_dirs_data[0][0]).shape
device_use = get_gpu_use(devices, no_runs, reconstructions,
data_shape)
else:
device_use = devices
# start the interrupt process
interrupt_process = Process(target=interrupt_thread, args=())
interrupt_process.start()
if no_runs == 1:
if len(device_use) == 0:
device_use = [-1]
dir_data = exp_dirs_data[0]
datafile = dir_data[0]
dir = dir_data[1]
if generations > 1:
gen_rec.reconstruction(proc, conf_file, datafile, dir, device_use)
elif reconstructions > 1:
mult_rec.reconstruction(proc, conf_file, datafile, dir, device_use)
else:
rec.reconstruction(proc, conf_file, datafile, dir, device_use)
else:
if len(device_use) == 0:
device_use = [[-1]]
else:
# check if is it worth to use last chunk
if proc != 'cpu' and len(device_use[0]) > len(device_use[-1]) * 2:
device_use = device_use[0:-1]
if generations > 1:
r = 'g'
elif reconstructions > 1:
r = 'm'
else:
r = 's'
q = Queue()
for gpus in device_use:
q.put((None, gpus))
# index keeps track of the multiple directories
index = 0
processes = {}
while index < no_runs:
pid, gpus = q.get()
if pid is not None:
os.kill(pid, signal.SIGKILL)
del processes[pid]
datafile = exp_dirs_data[index][0]
dir = exp_dirs_data[index][1]
p = Process(target=rec_process,
args=(proc, conf_file, datafile, dir, gpus, r, q))
p.start()
processes[p.pid] = index
index += 1
# close the queue
while len(processes.items()) > 0:
pid, gpus = q.get()
os.kill(pid, signal.SIGKILL)
del processes[pid]
q.close()
interrupt_process.terminate()
print('finished reconstruction')
def write_conf(conf_map, dir, file):
"""
It creates configuration file from the parameters included in dictionary, verifies, and saves in the configuration directory.
Parameters
----------
conf_map : dict
dictionary containing configuration parameters
dir : str
a directory where the configuration file will be saved
file : str
name of the configuration file to save
Returns
-------
nothing
"""
# create "temp" file first, verify it, and if ok, copy to a configuration file
if not os.path.exists(dir):
os.makedirs(dir)
conf_file = os.path.join(dir, file)
temp_file = os.path.join(dir, 'temp')
if os.path.isfile(temp_file):
os.remove(temp_file)
with open(temp_file, 'a') as f:
for key in conf_map:
value = conf_map[key]
if len(value) > 0:
f.write(key + ' = ' + conf_map[key] + '\n')
f.close()
if file == 'config':
if not ver.ver_config(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the main window. Cannot save this format'
)
return False
elif file == 'config_prep':
if not ver.ver_config_prep(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Data prep tab. Cannot save this format'
)
return False
elif file == 'config_data':
if not ver.ver_config_data(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Data tab. Cannot save this format'
)
return False
elif file.endswith('config_rec'):
if not ver.ver_config_rec(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Reconstruction tab. Cannot save this format'
)
return False
elif file == 'config_disp':
if not ver.ver_config_disp(temp_file):
os.remove(temp_file)
msg_window(
'please check the entries in the Display tab. Cannot save this format'
)
return False
# copy if verified
shutil.copy(temp_file, conf_file)
os.remove(temp_file)
return True