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Improved reading of fit pseudodata #1334

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Merged
siranipour merged 2 commits into from
Jul 21, 2021
Merged

Improved reading of fit pseudodata #1334

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eae2d96
Changing logic of reading pseudodata
Jul 19, 2021
4cf6d57
Removing os import
Jul 21, 2021
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68 changes: 28 additions & 40 deletions validphys2/src/validphys/pseudodata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@
"""
from collections import namedtuple
import logging
import os
import pathlib

import numpy as np
Expand All @@ -21,9 +20,11 @@
DataTrValSpec = namedtuple('DataTrValSpec', ['pseudodata', 'tr_idx', 'val_idx'])

context_index = collect("groups_index", ("fitcontext",))
read_fit_pseudodata = collect('read_replica_pseudodata', ('fitreplicas',))
read_pdf_pseudodata = collect('read_replica_pseudodata', ('pdfreplicas',))

@check_cuts_fromfit
def read_fit_pseudodata(fitcontext, context_index):
def read_replica_pseudodata(fit, context_index, replica):
"""Function to handle the reading of training and validation splits for a fit that has been
produced with the ``savepseudodata`` flag set to ``True``.

Expand Down Expand Up @@ -68,45 +69,32 @@ def read_fit_pseudodata(fitcontext, context_index):
# The [0] is because of how pandas handles sorting a MultiIndex
sorted_index = context_index.sortlevel(level=range(1,3))[0]

pdf = fitcontext["pdf"]
log.debug(f"Using same pseudodata & training/validation splits as {pdf.name}.")
nrep = len(pdf)
path = pathlib.Path(pdf.infopath)

data_indices_list = []
for rep_number in range(1, nrep):
# This is a symlink (usually).
replica = path.with_name(pdf.name + "_" + str(rep_number).zfill(4) + ".dat")
# we resolve the symlink
if replica.parent.is_symlink():
replica = pathlib.Path(os.path.realpath(replica))

training_path = replica.with_name("training.dat")
validation_path = replica.with_name("validation.dat")

try:
tr = pd.read_csv(training_path, index_col=[0, 1, 2], sep="\t", names=["data"])
val = pd.read_csv(validation_path, index_col=[0, 1, 2], sep="\t", names=["data"])
except FileNotFoundError as e:
raise FileNotFoundError(
"Could not find saved training and validation data files. "
f"Please ensure {pdf} was generated with the savepseudodata flag set to true"
) from e
tr["type"], val["type"] = "training", "validation"

pseudodata = pd.concat((tr, val))
pseudodata.sort_index(level=range(1,3), inplace=True)

pseudodata.index = sorted_index

tr = pseudodata[pseudodata["type"]=="training"]
val = pseudodata[pseudodata["type"]=="validation"]

data_indices_list.append(
DataTrValSpec(pseudodata.drop("type", axis=1), tr.index, val.index)
)
log.debug(f"Reading pseudodata & training/validation splits from {fit.name}.")
path = pathlib.Path(fit.path) / 'nnfit'
replica_path = path / ("replica_" + str(replica))

training_path = replica_path / "training.dat"
validation_path = replica_path / "validation.dat"

try:
tr = pd.read_csv(training_path, index_col=[0, 1, 2], sep="\t", names=[f"replica {replica}"])
val = pd.read_csv(validation_path, index_col=[0, 1, 2], sep="\t", names=[f"replica {replica}"])
except FileNotFoundError as e:
raise FileNotFoundError(
"Could not find saved training and validation data files. "
f"Please ensure {fit} was generated with the savepseudodata flag set to true"
) from e
tr["type"], val["type"] = "training", "validation"

pseudodata = pd.concat((tr, val))
pseudodata.sort_index(level=range(1,3), inplace=True)

pseudodata.index = sorted_index

tr = pseudodata[pseudodata["type"]=="training"]
val = pseudodata[pseudodata["type"]=="validation"]

return data_indices_list
return DataTrValSpec(pseudodata.drop("type", axis=1), tr.index, val.index)


def make_replica(dataset_inputs_loaded_cd_with_cuts, replica_mcseed):
Expand Down