#!/usr/bin/env python3 # -*- coding: utf-8 -*- # import vtk import sys import time from pathlib import Path from sys import getsizeof import h5py import numba import numpy as np import scipy.spatial @numba.njit() def determine_desired_range(offset, minimum, upper_limit_bottom, lower_limit_top, maximum): a = minimum b = maximum if offset < 0: a = lower_limit_top elif offset > 0: b = upper_limit_bottom return a, b @numba.njit() def find_coordinates_to_move(minimum, maximum, ratio, x_offset, y_offset, z_offset, move_candidates): coordinates_to_move = [] x_start, x_end = determine_desired_range(x_offset, minimum, upper_limit_bottom, lower_limit_top, maximum) y_start, y_end = determine_desired_range(y_offset, minimum, upper_limit_bottom, lower_limit_top, maximum) z_start, z_end = determine_desired_range(z_offset, minimum, upper_limit_bottom, lower_limit_top, maximum) for particle in move_candidates: point = particle[0:3] if x_start <= point[0] <= x_end and y_start <= point[1] <= y_end and z_start <= point[2] <= z_end: coordinates_to_move.append(particle) return coordinates_to_move # directory = Path(r"/home/ben/sims/swiftsim/examples/zoom_tests/auriga6_halo7_8_10/") directory = Path(r"/home/ben/sims/data_swift/monofonic_tests/DB2_128_100/") # file = h5py.File(directory / "auriga6_halo7_8_9.hdf5", "r") # for filename in sorted(directory.glob("output_*.hdf5")): for filename in sorted(directory.glob("output_0004.hdf5")): print(filename) file = h5py.File(str(filename), "r") Header = file['Header'] highres_coordinates = file["PartType1"]["Coordinates"][:] # for highres particles highres_names = file["PartType1"]["ParticleIDs"][:] highres_velocities = file["PartType1"]["Velocities"][:] highres_masses = file['PartType1']['Masses'][:] highres_group_ids = file['PartType1']['FOFGroupIDs'][:] highres_absolute_velo = np.sqrt(np.sum(highres_velocities ** 2, axis=1)) lowres_coordinates = file["PartType2"]["Coordinates"][:] # for lowres particles lowres_names = file["PartType2"]["ParticleIDs"][:] lowres_velocities = file["PartType2"]["Velocities"][:] lowres_masses = file['PartType2']['Masses'][:] lowres_group_ids = file['PartType2']['FOFGroupIDs'][:] lowres_absolute_velo = np.sqrt(np.sum(lowres_velocities ** 2, axis=1)) original_coordinates = np.concatenate((highres_coordinates, lowres_coordinates)) # if "auriga" in str(filename): # original_coordinates /= 1000 # print(original_coordinates.mean()) # print(original_coordinates.min()) # print(original_coordinates.max()) # print(file['Header']) # print(list(file['Units'].attrs.items())) # exit() names = np.concatenate((highres_names, lowres_names)) velocities = np.concatenate((highres_velocities, lowres_velocities)) masses = np.concatenate((highres_masses, lowres_masses)) group_ids = np.concatenate((highres_group_ids, lowres_group_ids)) absolute_velo = np.concatenate((highres_absolute_velo, lowres_absolute_velo)) # for bla in [original_coordinates, names, velocities, masses, absolute_velo]: # print(bla.shape) original_data = np.vstack([ original_coordinates[::, 0], original_coordinates[::, 1], original_coordinates[::, 2], names, velocities[::, 0], velocities[::, 1], velocities[::, 2], masses, group_ids, absolute_velo, ]).T print(original_data.shape) assert (original_coordinates == original_data[::, 0:3]).all() boundaries = Header.attrs['BoxSize'] # BoxLength for e5 boxes depends on Nres, 2.36438 for 256, 4.72876 for 512. print(boundaries, len(highres_names)) if not boundaries.shape: boundaries = np.array([boundaries] * 3) offsets = [-1, 0, 1] transformed_data = original_data[:] number_of_time_that_points_have_been_found = 0 # assumes cube form and 0.1 as desired ratio to move minimum = 0.0 maximum = max(boundaries) ratio = 0.1 box_length = maximum - minimum range_to_move = 0.1 * box_length upper_limit_bottom = minimum + range_to_move lower_limit_top = maximum - range_to_move print("Find candidates to move...") @numba.njit() def find_move_candidates(): move_candidates = [] print("finding move candidates") for particle in original_data: point = particle[0:3] if ( minimum <= point[0] <= upper_limit_bottom or lower_limit_top <= point[0] <= maximum or minimum <= point[1] <= upper_limit_bottom or lower_limit_top <= point[1] <= maximum or minimum <= point[2] <= upper_limit_bottom or lower_limit_top <= point[2] <= maximum ): move_candidates.append(particle) # print(point) return move_candidates move_candidates = find_move_candidates() move_candidates = np.array(move_candidates) print("...done.") for x in offsets: for y in offsets: for z in offsets: if (x, y, z) == (0, 0, 0): continue moved_coordinates = find_coordinates_to_move(minimum, maximum, ratio, x, y, z, move_candidates) # print(moved_coordinates) moved_coordinates = np.array(moved_coordinates) # if not moved_coordinates: # print(f"nothing moved in {(x,y,z)}") # continue moved_coordinates[::, 0] += x * boundaries[0] moved_coordinates[::, 1] += y * boundaries[1] moved_coordinates[::, 2] += z * boundaries[2] transformed_data = np.vstack((transformed_data, moved_coordinates)) number_of_time_that_points_have_been_found += 1 print(f"Points found: {number_of_time_that_points_have_been_found}/26...") # assert coordinates.shape[0] == original_coordinates.shape[0] * 3 ** 3 #check that the new space has the shape we want it to have num_nearest_neighbors = 40 print("Building 3d-Tree for all particles...") coordinates = transformed_data[::, 0:3] print(coordinates.shape) tree = scipy.spatial.KDTree(coordinates) print(getsizeof(tree) / 1024, "KB") print("...done.") print("Searching neighbours...") a = time.perf_counter_ns() distances, indices = tree.query([coordinates], k=num_nearest_neighbors, workers=6) # shape of closest_neighbours: (1, xxxx, 40) b = time.perf_counter_ns() print("...found neighbours.") print(f"took {(b - a) / 1000 / 1000:.2f} ms") distances = distances[0] # to (xxxx, 40) indices = indices[0] # to (xxxx, 40) print(distances.shape) print(indices.shape) print(indices) mass_array = [] print("fetching masses") for subindices in indices: # subindices is (40) # can maybe be optimized to remove loop masses = transformed_data[subindices, 7] mass_array.append(masses) mass_array = np.array(mass_array) print("finished fetching masses") # print(closest_neighbours, indices) # print(indices) # densities = num_nearest_neighbors * mass_per_particle / np.mean(closest_neighbours, axis=1) ** 3 total_masses = np.sum(mass_array, axis=1) densities = total_masses / np.mean(distances, axis=1) ** 3 alt_densities = total_masses / np.max(distances, axis=1) ** 3 # print(closest_neighbours.shape) # print(densities) # print(densities.shape) all_data = np.column_stack([list(range(densities.shape[0])), transformed_data, densities, alt_densities]) # print(all_data.shape) # print(original_data.shape[0]) export_data = all_data[:original_data.shape[0]] # print(export_data.shape) # all_data = np.append(coordinates, velocities, axis=1) # all_data = np.column_stack((all_data, absolute_velo, names, densities)) # sorted_index = np.argsort(all_data[::, 7], kind="stable") # all_data = all_data[sorted_index, :] # np.savetxt("out_"+filename.with_suffix(".csv").name, all_data[indices], delimiter=",", fmt="%.3f", header="x,y,z,vx,vy,vz,v,name") #if indices are needed np.savetxt(directory / f"out_{filename.with_suffix('.csv').name}", export_data, delimiter=",", fmt="%.3f", header="num,x,y,z,name,vx,vy,vz,masse,groupid,v,density,density_alt") file.close()