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Remove example_processing_code.py

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bertoz_b
2025-09-11 12:01:39 +02:00
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example_processing_code.py
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# -*- coding: utf-8 -*-
"""
Created on Mon May 27 11:45:19 2024
@author: bertoz_b
"""
import time
import pandas as pd
import dask.dataframe as dd
import dask
from dask.distributed import Client
from dask_jobqueue import SLURMCluster
import gc
from SP2XR_toolkit import (
find_files,
read_and_process_sp2b,
read_csv_files_with_dask_2,
process_sp2b_parquet,
resample_to_dt,
chunks,
list_first_level_subdirs,
process_pbp_parquet,
get_file_dict,
)
# %% Define directories and folders
parent_directory = "/data/user/bertoz_b/SP2XR/data/NyA"
source_directory = parent_directory + "/SP2XR_files"
target_directory_pbp_parquet = parent_directory + "/SP2XR_pbp_parquet"
filter_string_pbp = "PbP"
target_directory_sp2b_parquet = parent_directory + "/SP2XR_sp2b_parquet"
filter_string_sp2b = "sp2b"
target_directory_hk_parquet = parent_directory + "/SP2XR_hk_parquet"
filter_string_hk = "hk"
meta_file_pbp = pd.read_parquet(
"/data/user/bertoz_b/SP2XR/final_test_script_and_data/meta_files/pbp_meta.parquet",
engine="fastparquet",
)
meta_file_hk = pd.read_parquet(
"/data/user/bertoz_b/SP2XR/final_test_script_and_data/meta_files/hk_meta.parquet",
engine="fastparquet",
)
meta_file_sp2b = pd.read_parquet(
"/data/user/bertoz_b/SP2XR/final_test_script_and_data/meta_files/meta_sp2b_20240619.parquet",
engine="pyarrow",
)
matching_files_pbp = find_files(source_directory, filter_string_pbp)
matching_files_hk = find_files(source_directory, filter_string_hk)
matching_files_sp2b = find_files(source_directory, filter_string_sp2b)[10000:50000]
# %% PBP: From csv/zip to parquet
start_time = time.time()
cluster = SLURMCluster(
cores=64,
processes=64,
memory="128GB",
walltime="05:59:00",
job_extra_directives=["--partition=daily"],
)
cluster.scale(1)
client = Client(cluster)
print(client.dashboard_link)
i = 0
for chunk_pbp in chunks(matching_files_pbp, 100):
print(f"chunk: {i}")
dask.compute(
*[
read_csv_files_with_dask_2(
f, meta_file_pbp, meta_file_hk, target_directory_pbp_parquet
)
for f in chunk_pbp
]
)
gc.collect()
i += 1
client.close()
cluster.close()
print("--- %s seconds ---" % (time.time() - start_time))
# %% HK: From csv/zip to parquet
start_time = time.time()
cluster = SLURMCluster(
cores=16,
processes=16,
memory="128GB",
walltime="07:59:00",
job_extra_directives=["--partition=daily"],
)
cluster.scale(1)
client = Client(cluster)
print(client.dashboard_link)
i = 0
for chunk_hk in chunks(matching_files_hk, 100):
print(f"chunk: {i}")
dask.compute(
*[
read_csv_files_with_dask_2(
f, meta_file_pbp, meta_file_hk, target_directory_hk_parquet
)
for f in chunk_hk
]
)
gc.collect()
i += 1
client.close()
cluster.close()
print("--- %s seconds ---" % (time.time() - start_time))
# %% SP2B: From csv/zip to parquet
start_time = time.time()
cluster = SLURMCluster(
cores=64,
processes=64,
memory="128GB", # 2GB/process should sufficient
walltime="02:59:00",
job_extra_directives=["--partition=daily"],
)
cluster.scale(1)
client = Client(cluster)
print(client.dashboard_link)
sp2b_orig = read_and_process_sp2b(
matching_files_sp2b, target_directory_sp2b_parquet, meta_file_sp2b
)
client.close()
cluster.close()
print("--- %s seconds ---" % (time.time() - start_time))
# %% PBP: from single particle to specified dt
# config_path = '/data/user/bertoz_b/SP2XR/data/Granada/SP2XR_files/20240612/20240612061852'
config_path = "/data/user/bertoz_b/SP2XR/data/NyA/SP2XR_files/20200922/20200922064903"
# The level keyword has been added to control the partitioning columns of the processed pbp files,
# this level has to match the partition_on keyword in the process_pbp_parquet function below
files_pbp = get_file_dict(target_directory_pbp_parquet, "PbP", level="date")
files_hk = get_file_dict(target_directory_hk_parquet, "HK", level="date")
list_pbp = []
list_hk = []
for key in files_pbp:
if key in files_hk:
list_pbp.append(files_pbp[key])
list_hk.append(files_hk[key])
start_time = time.time()
cluster = SLURMCluster(
cores=8,
processes=8,
memory="128GB",
walltime="11:59:00",
job_extra_directives=["--partition=daily"],
)
cluster.scale(1)
client = Client(cluster)
print(client.dashboard_link)
# when at hour level the chunks can also be of 50 (hours), when level is day the chuncks should be max 25 (days)
# when using the cluster settings above (8cores, 128GB)
i = 0
for chunk_pbp, chunk_hk in zip(chunks(list_pbp, 25), chunks(list_hk, 25)):
print(f"chunk: {i}")
dask.compute(
*[
process_pbp_parquet(
dir_path_pbp,
dir_path_hk,
dt=60,
rho_eff=1800,
BC_type="constant_effective_density",
inc_calib_curve="polynomial",
inc_calib_params=[0.05, 2.0470000507725255e-07],
scatt_calib_curve="powerlaw",
scatt_calib_params=[17.21724257, 0.16908516, -1.49431104],
config_file_dir=config_path,
minM=0.3,
maxM=400,
n_incbins=50,
minOptD=100,
maxOptD=500,
n_scattbins=20,
minTL=-10,
maxTL=400,
n_timelag=100,
path_parquet="/data/user/bertoz_b/SP2XR/data/NyA/SP2XR_pbp_processed_20250212/",
partition_on=["date"],
save_final_data=True,
)
for dir_path_pbp, dir_path_hk in zip(chunk_pbp, chunk_hk)
]
)
gc.collect()
i += 1
client.close()
cluster.close()
print("--- %s seconds ---" % (time.time() - start_time))
# %% PBP: Resample
dir_pbp_1s = list_first_level_subdirs(
"/data/user/bertoz_b/SP2XR/data/NyA/SP2XR_pbp_processed_new"
)
start_time = time.time()
cluster = SLURMCluster(
cores=8,
processes=8,
memory="32GB",
walltime="00:20:00",
job_extra_directives=["--partition=hourly"],
)
cluster.scale(1)
client = Client(cluster)
print(client.dashboard_link)
i = 0
for chunk_pbp in chunks(dir_pbp_1s, 50):
print(f"chunk: {i}")
dask.compute(
*[
resample_to_dt(
dir_path_pbp,
dt=60,
path_parquet="/data/user/bertoz_b/SP2XR/data/NyA/SP2XR_pbp_processed_new_1min/",
save_final_data=True,
)
for dir_path_pbp in chunk_pbp
]
)
gc.collect()
i += 1
client.close()
cluster.close()
print("--- %s seconds ---" % (time.time() - start_time))
# %% SP2B: Process parquet files
# This is a very old function, it might need revisiting
start_time = time.time()
cluster = SLURMCluster(
cores=8,
processes=8,
memory="16GB",
walltime="00:30:00",
job_extra_directives=["--partition=hourly"],
)
cluster.scale(1)
client = Client(cluster)
print(client.dashboard_link)
sp2_raw_traces = dd.read_parquet(
"/data/user/bertoz_b/SP2XR/data/NyA/SP2XR_sp2b_parquet", calculate_divisions=True
) # .repartition(freq='1h')
test2 = process_sp2b_parquet(
sp2_raw_traces,
scatt_sat_threshold=1e9,
inc_sat_threshold=1e8,
scatt_noise_threshold=1e4,
end_bkgr_ch0=100,
end_bkgr_ch1=350,
output_path="/data/user/bertoz_b/SP2XR/data/NyA/SP2XR_sp2b_processed",
)
client.close()
cluster.close()
print("--- %s seconds ---" % (time.time() - start_time))