Variables
	p = optparse.OptionParser()

	action

	dest

	default

	help

	options

	args

	run_path = options.rundir

	buffsize = int(options.buffersize)

	format

	style

	datefmt

	level

	file_handler = logging.FileHandler("debug.log", mode="w", encoding="utf-8")

	logger = logging.getLogger(__name__)

	propagate

list	folders = [f for f in os.listdir(run_path) if os.path.isdir(os.path.join(run_path, f))]

	fold = options.outdir.replace(".hdf5","")

	basepath = run_path

bool	looping = True

	output_file = os.path.join(fold, folders[0]+".hdf5")

list	dirs = [d for d in os.listdir(run_path) if os.path.isdir(os.path.join(run_path, d)) and d != "network_data"]

	f_hdf = h5py.File(output_file, 'w')

bool	found = False

	data = wreader(os.path.join(run_path, d))

list	template_name = [f for f in os.listdir(os.path.join(run_path, d)) if f.endswith('.par')][0]

	t = template(os.path.join(run_path, d, template_name))

	net_source = options.sunet_path

	nuclei = np.loadtxt(net_source,dtype=str)

	nuclei_data = nucleus_multiple(nuclei)

	mainout_time = np.loadtxt(options.time_file, dtype=float, unpack=True)

	final_time = float(options.time_final)

	initial_time = float(options.time_initial)

	time_number = int(options.time_number)

list	possible_entries = []

dictionary	entry_dict = {}

bool	summarize_snapshots = False

	snapshot_time = np.loadtxt(os.path.join(t["snapshot_file"]),dtype=float)

	snapshot_data = np.zeros((len(nuclei),len(snapshot_time),buffsize))

	finab_data_Y = np.zeros((len(nuclei),buffsize))

	finab_data_X = np.zeros((len(nuclei),buffsize))

	dtype_nuclei = np.dtype([('A', int), ('Z', int)])

	nuclei_struct = np.array(list(zip(nuclei_data.A.astype(int), nuclei_data.Z.astype(int))), dtype=dtype_nuclei)

	nuclei_sorted_idx = np.argsort(nuclei_struct)

	sorted_nuclei_struct = nuclei_struct[nuclei_sorted_idx]

	run_names = np.zeros(buffsize,dtype="S100")

	run_ids = np.zeros(buffsize,dtype=int)

int	ind = -1

	maxshape
	Finab ####. More...

	finab_struct = np.array(list(zip(data.finab["A"].astype(int), data.finab["Z"].astype(int))), dtype=dtype_nuclei)

	matching_idx = np.searchsorted(sorted_nuclei_struct, finab_struct)

	indices = nuclei_sorted_idx[matching_idx]

	dtype

	snapstime = data.snapshot_time
	Custom snapshots ####. More...

	indexes = np.searchsorted(snapstime, snapshot_time)

	mask = np.zeros(len(snapshot_time),dtype=bool)

	axis

	indices_nuclei = nuclei_sorted_idx[matching_idx]

dictionary	dim = entry_dict[entry][key].ndim
	Other entries ####. More...

	value

Variable Documentation

◆ action

summarize.action

Definition at line 21 of file summarize.py.

◆ args

summarize.args

Definition at line 65 of file summarize.py.

◆ axis

summarize.axis

Definition at line 441 of file summarize.py.

◆ basepath

summarize.basepath = run_path

Definition at line 109 of file summarize.py.

◆ buffsize

summarize.buffsize = int(options.buffersize)

Definition at line 70 of file summarize.py.

◆ data

summarize.data = wreader(os.path.join(run_path, d))

Definition at line 159 of file summarize.py.

◆ datefmt

summarize.datefmt

Definition at line 79 of file summarize.py.

◆ default

summarize.default

Definition at line 21 of file summarize.py.

◆ dest

summarize.dest

Definition at line 21 of file summarize.py.

◆ dim

dictionary summarize.dim = entry_dict[entry][key].ndim

Other entries ####.

Definition at line 485 of file summarize.py.

◆ dirs

list summarize.dirs = [d for d in os.listdir(run_path) if os.path.isdir(os.path.join(run_path, d)) and d != "network_data"]

Definition at line 140 of file summarize.py.

◆ dtype

summarize.dtype

Definition at line 399 of file summarize.py.

◆ dtype_nuclei

summarize.dtype_nuclei = np.dtype([('A', int), ('Z', int)])

Definition at line 331 of file summarize.py.

◆ entry_dict

dictionary summarize.entry_dict = {}

Definition at line 246 of file summarize.py.

◆ f_hdf

summarize.f_hdf = h5py.File(output_file, 'w')

Definition at line 152 of file summarize.py.

◆ file_handler

summarize.file_handler = logging.FileHandler("debug.log", mode="w", encoding="utf-8")

Definition at line 82 of file summarize.py.

◆ finab_data_X

summarize.finab_data_X = np.zeros((len(nuclei),buffsize))

Definition at line 323 of file summarize.py.

◆ finab_data_Y

summarize.finab_data_Y = np.zeros((len(nuclei),buffsize))

Definition at line 322 of file summarize.py.

◆ finab_struct

summarize.finab_struct = np.array(list(zip(data.finab["A"].astype(int), data.finab["Z"].astype(int))), dtype=dtype_nuclei)

Definition at line 379 of file summarize.py.

◆ final_time

float summarize.final_time = float(options.time_final)

Definition at line 199 of file summarize.py.

◆ fold

summarize.fold = options.outdir.replace(".hdf5","")

Definition at line 108 of file summarize.py.

◆ folders

list summarize.folders = [f for f in os.listdir(run_path) if os.path.isdir(os.path.join(run_path, f))]

Definition at line 104 of file summarize.py.

◆ format

summarize.format

Definition at line 77 of file summarize.py.

◆ found

bool summarize.found = False

Definition at line 157 of file summarize.py.

◆ help

summarize.help

Definition at line 22 of file summarize.py.

◆ ind

int summarize.ind = -1

Definition at line 343 of file summarize.py.

◆ indexes

summarize.indexes = np.searchsorted(snapstime, snapshot_time)

Definition at line 435 of file summarize.py.

◆ indices

summarize.indices = nuclei_sorted_idx[matching_idx]

Definition at line 384 of file summarize.py.

◆ indices_nuclei

summarize.indices_nuclei = nuclei_sorted_idx[matching_idx]

Definition at line 452 of file summarize.py.

◆ initial_time

int summarize.initial_time = float(options.time_initial)

Definition at line 210 of file summarize.py.

◆ level

summarize.level

Definition at line 80 of file summarize.py.

◆ logger

summarize.logger = logging.getLogger(__name__)

Definition at line 83 of file summarize.py.

◆ looping

bool summarize.looping = True

Definition at line 123 of file summarize.py.

◆ mainout_time

summarize.mainout_time = np.loadtxt(options.time_file, dtype=float, unpack=True)

Definition at line 196 of file summarize.py.

◆ mask

summarize.mask = np.zeros(len(snapshot_time),dtype=bool)

Definition at line 439 of file summarize.py.

◆ matching_idx

summarize.matching_idx = np.searchsorted(sorted_nuclei_struct, finab_struct)

Definition at line 382 of file summarize.py.

◆ maxshape

summarize.maxshape

Finab ####.

Custom snapshots ####.

Run name ####.

Put the data in the finab_data, Notice that it should be at the right A and Z position A is contained in data.finab["A"] and Z in data.finab["Z"]. It should fit to the nuclei_data.A and nuclei_data.Z All of them are 1D arrays Getting indices where match occurs indices = [(np.where((nuclei_data.A.astype(int) == A) & (nuclei_data.Z.astype(int) == Z))[0][0]) for A, Z in zip(data.finab["A"].astype(int), data.finab["Z"].astype(int))]

Definition at line 368 of file summarize.py.

◆ net_source

summarize.net_source = options.sunet_path

Definition at line 178 of file summarize.py.

◆ nuclei

summarize.nuclei = np.loadtxt(net_source,dtype=str)

Definition at line 189 of file summarize.py.

◆ nuclei_data

summarize.nuclei_data = nucleus_multiple(nuclei)

Definition at line 190 of file summarize.py.

◆ nuclei_sorted_idx

summarize.nuclei_sorted_idx = np.argsort(nuclei_struct)

Definition at line 334 of file summarize.py.

◆ nuclei_struct

summarize.nuclei_struct = np.array(list(zip(nuclei_data.A.astype(int), nuclei_data.Z.astype(int))), dtype=dtype_nuclei)

Definition at line 332 of file summarize.py.

◆ options

summarize.options

Definition at line 65 of file summarize.py.

◆ output_file

summarize.output_file = os.path.join(fold, folders[0]+".hdf5")

Definition at line 130 of file summarize.py.

◆ p

summarize.p = optparse.OptionParser()

Definition at line 20 of file summarize.py.

◆ possible_entries

list summarize.possible_entries = []

Definition at line 223 of file summarize.py.

◆ propagate

summarize.propagate

Definition at line 97 of file summarize.py.

◆ run_ids

summarize.run_ids = np.zeros(buffsize,dtype=int)

Definition at line 340 of file summarize.py.

◆ run_names

summarize.run_names = np.zeros(buffsize,dtype="S100")

Definition at line 339 of file summarize.py.

◆ run_path

summarize.run_path = options.rundir

Definition at line 66 of file summarize.py.

◆ snapshot_data

summarize.snapshot_data = np.zeros((len(nuclei),len(snapshot_time),buffsize))

Definition at line 311 of file summarize.py.

◆ snapshot_time

summarize.snapshot_time = np.loadtxt(os.path.join(t["snapshot_file"]),dtype=float)

Definition at line 301 of file summarize.py.

◆ snapstime

summarize.snapstime = data.snapshot_time

Custom snapshots ####.

Definition at line 432 of file summarize.py.

◆ sorted_nuclei_struct

summarize.sorted_nuclei_struct = nuclei_struct[nuclei_sorted_idx]

Definition at line 335 of file summarize.py.

◆ style

summarize.style

Definition at line 78 of file summarize.py.

◆ summarize_snapshots

bool summarize.summarize_snapshots = False

Definition at line 285 of file summarize.py.

◆ t

summarize.t = template(os.path.join(run_path, d, template_name))

Definition at line 174 of file summarize.py.

◆ template_name

list summarize.template_name = [f for f in os.listdir(os.path.join(run_path, d)) if f.endswith('.par')][0]

Definition at line 173 of file summarize.py.

◆ time_number

int summarize.time_number = int(options.time_number)

Definition at line 215 of file summarize.py.

◆ value

summarize.value

Initial value:

1 = interp1d(data[entry]["time"],data[entry][key],

2 bounds_error = False, fill_value = np.nan, axis = 0)(mainout_time)

Definition at line 506 of file summarize.py.

Variables

Variable Documentation

◆ action

◆ args

◆ axis

◆ basepath

◆ buffsize

◆ data

◆ datefmt

◆ default

◆ dest

◆ dim

◆ dirs

◆ dtype

◆ dtype_nuclei

◆ entry_dict

◆ f_hdf

◆ file_handler

◆ finab_data_X

◆ finab_data_Y

◆ finab_struct

◆ final_time

◆ fold

◆ folders

◆ format

◆ found

◆ help

◆ ind

◆ indexes

◆ indices

◆ indices_nuclei

◆ initial_time

◆ level

◆ logger

◆ looping

◆ mainout_time

◆ mask

◆ matching_idx

◆ maxshape

◆ net_source

◆ nuclei

◆ nuclei_data

◆ nuclei_sorted_idx

◆ nuclei_struct

◆ options

◆ output_file

◆ p

◆ possible_entries

◆ propagate

◆ run_ids

◆ run_names

◆ run_path

◆ snapshot_data

◆ snapshot_time

◆ snapstime

◆ sorted_nuclei_struct

◆ style

◆ summarize_snapshots

◆ t

◆ template_name

◆ time_number

◆ value