From 2088e9528ea56eaf90f1ec64aa47d65a7d6f6af0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 4 Jan 2023 13:58:00 +0000
Subject: [PATCH] feat(meta): add legacy parser
---
src/logfile_parser/legacy.py | 56 ++++++++++++++++++++++++++++++++++++
1 file changed, 56 insertions(+)
create mode 100644 src/logfile_parser/legacy.py
diff --git a/src/logfile_parser/legacy.py b/src/logfile_parser/legacy.py
new file mode 100644
index 00000000..dac2b700
--- /dev/null
+++ b/src/logfile_parser/legacy.py
@@ -0,0 +1,56 @@
+#!/usr/bin/env jupyter
+from importlib_resources import files
+from logfile_parser import Parser
+
+grammars_dir = files("logfile_parser") / "grammars"
+
+
+def get_examples_dir():
+ return files("aliby").parent.parent / "examples" / "logfile_parser"
+
+
+def get_logfile_grammars_dir():
+ return files("logfile_parser") / "grammars"
+
+
+def get_legacy_log_example_interface() -> dict:
+ parsed = {}
+ examples_dir = get_examples_dir()
+ grammars_dir = get_logfile_grammars_dir()
+
+ for gram in ("acq", "log"):
+ for gram_file in grammars_dir.glob(f"multiDGUI_{gram}_format.json"):
+ parser = Parser(gram_file)
+ for file_to_parse in examples_dir.glob(f"*{gram}.txt"):
+ with open(file_to_parse, "r") as f:
+ parsed = {**parsed, **parser.parse(f)}
+ return parsed
+
+
+def to_legacy(parsed_logfile: dict) -> dict:
+ """
+ Convert the output of the new logfile parsing to legacy to a minimal working set of metadata.
+ This converts the new more complex metadata structure to the previous one that did not have configuration profiles, but instead one configuration per channel.
+ This is a temporal solution as we transition into a more general metadata structure that accounts for heterogeneous groups.
+
+ We convert image configs to channels, and add general metadata to the root.
+ """
+ name_translation = {
+ "Microscope name": "microscope",
+ }
+ channel_name_translation = {
+ "Image config": "channel",
+ "Channel": "channel_hardware",
+ "Exposure (ms)": "exposure",
+ "Z spacing (um)": "zsect",
+ }
+
+ # Translate general data
+ general = {v: d["general"][k] for k, v in name_translation.items()}
+ # Translate and cast image configs
+ channels = {
+ v: list(map(_cast_type, parsed_logfile["image_config"][k]))
+ for k, v in channel_name_translation.items()
+ }
+ legacy_format = {"channels": channels, **general}
+ return legacy_format
--
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