From 39d3a6448a8be94a7805877f2339d0eb97f6fc06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 3 Jan 2023 14:51:12 +0000
Subject: [PATCH] fix(meta): allow metadata absence
---
src/agora/io/metadata.py | 43 ++++++++++++++++++++++++----------------
1 file changed, 26 insertions(+), 17 deletions(-)
diff --git a/src/agora/io/metadata.py b/src/agora/io/metadata.py
index 949a5ce6..cc047cc6 100644
--- a/src/agora/io/metadata.py
+++ b/src/agora/io/metadata.py
@@ -9,6 +9,7 @@ ALIBY decides on using different metadata parsers based on two elements:
If parameters is a string pointing to a metadata file, ALIBY picks a parser based on the file format.
If parameters is True (as a boolean), ALIBY searches for any available file and uses the first valid one.
If there are no metadata files, ALIBY requires indicating indices for tiler, segmentation and extraction.
+
"""
import glob
import os
@@ -67,7 +68,9 @@ def flatten_dict(nested_dict, separator="/"):
Flattens nested dictionary
"""
df = pd.json_normalize(nested_dict, sep=separator)
- return df.to_dict(orient="records")[0]
+
+ flattened = df.to_dict(orient="records") or {}
+ return flattened
# Needed because HDF5 attributes do not support datetime objects
@@ -109,22 +112,20 @@ def parse_logfiles(
# ACQ_FILE = 'flavin_htb2_glucose_long_ramp_DelftAcq.txt'
# LOG_FILE = 'flavin_htb2_glucose_long_ramp_Delftlog.txt'
log_parser = Parser(log_grammar)
- try:
- log_file = find_file(root_dir, "*log.txt")
- except FileNotFoundError:
- raise ValueError("Experiment log file not found.")
- with open(log_file, "r") as f:
- log_parsed = log_parser.parse(f)
-
acq_parser = Parser(acq_grammar)
- try:
- acq_file = find_file(root_dir, "*[Aa]cq.txt")
- except FileNotFoundError:
- raise ValueError("Experiment acq file not found.")
- with open(acq_file, "r") as f:
- acq_parsed = acq_parser.parse(f)
- parsed = {**acq_parsed, **log_parsed}
+ log_file = find_file(root_dir, "*log.txt")
+ acq_file = find_file(root_dir, "*[Aa]cq.txt")
+
+ parsed = {}
+ if log_file and acq_file:
+ with open(log_file, "r") as f:
+ log_parsed = log_parser.parse(f)
+
+ with open(acq_file, "r") as f:
+ acq_parsed = acq_parser.parse(f)
+
+ parsed = {**acq_parsed, **log_parsed}
for key, value in parsed.items():
if isinstance(value, datetime):
@@ -186,7 +187,9 @@ def parse_swainlab_metadata(filedir: t.Union[str, PosixPath]):
if filedir.is_file():
filedir = filedir.parent
legacy_parse = parse_logfiles(filedir)
- minimal_meta = get_meta_from_legacy(legacy_parse)
+ minimal_meta = (
+ get_meta_from_legacy(legacy_parse) if legacy_parse else {}
+ )
return minimal_meta
@@ -195,5 +198,11 @@ def dispatch_metadata_parser(filepath: t.Union[str, PosixPath]):
"""
Function to dispatch different metadata parsers that convert logfiles into a
basic metadata dictionary. Currently only contains the swainlab log parsers.
+
+ Input:
+ --------
+ filepath: str existing file containing metadata, or folder containing naming conventions
"""
- return parse_swainlab_metadata(filepath)
+ parsed_meta = parse_swainlab_metadata(filepath)
+
+ return parsed_meta
--
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