def _run_keep(arrays_dict, buffers, buffers_to_infiles, buffer_to_outfiles):
"""
Arguments:
----------
arrays_dict: dictionary mapping each output block index to its list of write blocks
buffers: list of Volume objects (see utils.py) representing the read buffers. Each volume contains the coordinates of the buffer in the original image.
buffers_to_infiles: maps each read buffer index to the list of input blocks it crosses -> to know which input block to read
buffer_to_outfiles: maps each read buffer index to the list of output blocks it crosses -> to only search for the write buffers linked to that read buffer
"""
cache = dict()
voxel_tracker = VoxelTracker()
nb_infile_openings = 0
nb_infile_inside_seeks = 0
nb_buffers = len(buffers.keys())
read_time = 0
write_time = 0
from monitor.monitor import Monitor
_monitor = Monitor(enable_print=False, enable_log=False, save_data=True)
_monitor.disable_clearconsole()
_monitor.set_delay(5)
_monitor.start()
buffer_shape = buffers[0].get_shape()
buffer_size = buffer_shape[0] * buffer_shape[1] * buffer_shape[2] * 2
buffer_data = np.empty(copy.deepcopy(buffer_shape), dtype=np.float16)
voxel_tracker.add_voxels(buffer_size)
# for each read buffer
for buffer_index in range(nb_buffers):
print("\nBUFFER ", buffer_index, '/', nb_buffers)
if DEBUG:
print_mem_info()
buffer = buffers[buffer_index]
nb_opening_seeks_tmp, nb_inside_seeks_tmp, t1, t2 = process_buffer(buffer_data, arrays_dict, buffers, buffer, voxel_tracker, buffers_to_infiles, buffer_to_outfiles, cache)
read_time += t1
write_time += t2
nb_infile_openings += nb_opening_seeks_tmp
nb_infile_inside_seeks += nb_inside_seeks_tmp
if DEBUG:
print("End of buffer - Memory info:")
print_mem_info()
if buffer_index == 1:
sys.exit()
buffer_data = np.empty(copy.deepcopy(buffer_shape), dtype=np.float16)
file_manager.close_infiles()
_monitor.stop()
ram_pile, swap_pile = _monitor.get_mem_piles()
return [read_time, write_time], ram_pile, swap_pile, nb_infile_openings, nb_infile_inside_seeks, voxel_tracker
def experiment(args):
"""
Note:
- data type is np.float16
"""
paths = load_json(args.paths_config)
for k, v in paths.items():
if "PYTHONPATH" in k:
sys.path.insert(0, v)
from monitor.monitor import Monitor
from repartition_experiments.scripts_exp.exp_utils import create_empty_dir, verify_results
from repartition_experiments.algorithms.baseline_algorithm import baseline_rechunk
from repartition_experiments.algorithms.keep_algorithm import keep_algorithm, get_input_aggregate
from repartition_experiments.algorithms.utils import get_file_manager
from repartition_experiments.algorithms.clustered_reads import clustered_reads
# setting
paths = load_json(args.paths_config)
cases = load_json(args.cases_config)
bpv = 2
indir_path, outdir_path = os.path.join(paths["ssd_path"],
'indir'), os.path.join(
paths["ssd_path"], 'outdir')
# creating empty output directories
create_empty_dir(outdir_path)
if args.distributed:
print(f"Distributed mode -> creating the output directories")
for i in range(6):
dirpath = '/disk' + str(i) + '/gtimothee'
create_empty_dir(os.path.join(dirpath, 'output'))
fm = get_file_manager(args.file_format)
if args.overwrite:
fm.remove_all(paths["ssd_path"])
# transform cases into tuples + perform sanity check
case = cases[args.case_name]
for run in case:
R, O, I, B, volumestokeep = tuple(run["R"]), tuple(run["O"]), tuple(
run["I"]), tuple(run["B"]), run["volumestokeep"]
if args.case_name.split('_')[0] == "case 1":
lambd = get_input_aggregate(O, I)
B, volumestokeep = (lambd[0], lambd[1],
lambd[2]), list(range(1, 8))
run["volumestokeep"] = volumestokeep
run["R"] = R
run["O"] = O
run["I"] = I
run["B"] = B
for shape_to_test in [O, I, B]:
for dim in range(3):
try:
assert R[dim] % shape_to_test[dim] == 0
except Exception as e:
print(R, shape_to_test)
print(e)
random.shuffle(case)
results = list()
R_prev, I_prev = (0, 0, 0), (0, 0, 0)
for run in case:
R, O, I, B, volumestokeep = run["R"], run["O"], run["I"], run[
"B"], run["volumestokeep"]
ref = run["ref"]
print(
f'Case being processed: (ref: {ref}) {R}, {I}, {O}, {B}, {volumestokeep}'
)
filename = f'{R[0]}_{R[1]}_{R[2]}_original.hdf5'
origarr_filepath = os.path.join(paths["ssd_path"], filename)
# resplit
print("processing...")
flush_cache()
print(f"cache flushed")
if args.model == "baseline":
_monitor = Monitor(enable_print=False,
enable_log=False,
save_data=True)
_monitor.disable_clearconsole()
_monitor.set_delay(15)
_monitor.start()
t = time.time()
tread, twrite, seeks_data = baseline_rechunk(
indir_path, outdir_path, O, I, R, args.file_format,
args.addition, args.distributed)
t = time.time() - t
_monitor.stop()
piles = _monitor.get_mem_piles()
max_voxels = 0
print(f"Processing time: {t}")
print(f"Read time: {tread}")
print(f"Write time: {twrite}")
tpp = 0
voxel_tracker = None
elif args.model == "keep":
print(f"Running keep...")
t = time.time()
tpp, tread, twrite, seeks_data, voxel_tracker, piles = keep_algorithm(
R, O, I, B, volumestokeep, args.file_format, outdir_path,
indir_path, args.addition, args.distributed)
t = time.time() - t - tpp
max_voxels = voxel_tracker.get_max()
print(f"Processing time: {t}")
print(f"Read time: {tread}")
print(f"Write time: {twrite}")
elif args.model == "clustered":
tpp = 0
m = args.clustered_mem * 1000000000 # one GIG
_monitor = Monitor(enable_print=False,
enable_log=False,
save_data=True)
_monitor.disable_clearconsole()
_monitor.set_delay(15)
_monitor.start()
t = time.time()
tread, twrite, seeks_data = clustered_reads(
outdir_path, R, I, bpv, m, args.file_format, indir_path)
t = time.time() - t - tpp
_monitor.stop()
piles = _monitor.get_mem_piles()
voxel_tracker = None
max_voxels = 0
print(f"Processing time: {t}")
print(f"Read time: {tread}")
print(f"Write time: {twrite}")
else:
raise ValueError("Bad model name")
# verify and clean output
print("verifying results....")
if args.verify:
split_merge = False
if args.case_name == "case 3":
split_merge = True
success = verify_results(outdir_path, origarr_filepath, R, O,
args.file_format, args.addition,
split_merge)
else:
success = True
print("successful run: ", success)
results.append([
args.case_name, run["ref"], args.model, t, tpp, tread, twrite,
seeks_data[0], seeks_data[1], seeks_data[2], seeks_data[3],
max_voxels, success
])
create_empty_dir(outdir_path)
R_prev, I_prev = R, I
write_memory_pile(piles[0], piles[1], run["ref"], args)
if voxel_tracker != None:
write_voxel_history(voxel_tracker, run["ref"], args)
return results
