From f266683a748c8eeb48b48360fd26176ff9f0d5e5 Mon Sep 17 00:00:00 2001
From: Mark Polk <mark.polk@choderalab.org>
Date: Thu, 24 Oct 2024 02:51:01 -0400
Subject: [PATCH] Added i-control XML parsing to plate_reader module.

---
 fluorescence_assay/plate_reader.py | 106 +++++++++++++++++++++++++++++
 1 file changed, 106 insertions(+)

diff --git a/fluorescence_assay/plate_reader.py b/fluorescence_assay/plate_reader.py
index a3ce033..500121f 100644
--- a/fluorescence_assay/plate_reader.py
+++ b/fluorescence_assay/plate_reader.py
@@ -1 +1,107 @@
 """Comment."""
+
+import logging
+import xml.etree.ElementTree as ET
+from abc import ABC, abstractmethod
+from dataclasses import dataclass, field
+from typing import List
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class Measurements(ABC):
+    """"""
+
+    def read_file(self, filepath: str, sections: list[str] | None = None) -> None:
+        """"""
+        self._parse_file(filepath, sections)
+        return
+
+    @abstractmethod
+    def _get_data(self) -> dict:
+        """"""
+        ...
+
+    # steps taken in read_file(...)
+
+    @abstractmethod
+    def _parse_file(self, filepath: str, sections: list[str] | None = None) -> None:
+        """"""
+        ...
+
+
+@dataclass
+class IControlXML(Measurements):
+    _data: dict = field(default_factory=dict, init=False)
+
+    def _parse_file(self, filepath: str, sections: list[str] | None = None) -> None:
+        """"""
+
+        try:
+
+            tree = ET.parse(filepath)
+            root = tree.getroot()
+
+            # section > data > well > scan
+
+            for section in root.findall(".//Section"):
+
+                if sections is not None and section.get("Name") not in sections:
+                    continue
+                else:
+
+                    # create section
+
+                    self._data[section.get("Name")] = {"parameters": {}, "data": {}}
+
+                    for parameter in section.findall(".//Parameter"):
+                        parameter_name = parameter.get("Name")
+                        parameter_value = parameter.get("Value")
+                        parameter_unit = parameter.get("Unit")
+
+                        try:
+                            parameter_value = int(parameter_value)
+                        except:
+                            pass
+
+                        self._data[section.get("Name")]["parameters"][
+                            parameter_name
+                        ] = (parameter_value, parameter_unit)
+
+                    # create data
+
+                    for data in section.findall(".//Data"):
+                        cycle = int(data.get("Cycle"))
+                        temperature = int(data.get("Temperature"))
+
+                        self._data[section.get("Name")]["data"][
+                            (cycle, temperature)
+                        ] = {}
+
+                        for well in data.findall(".//Well"):
+                            pos = well.get("Pos")
+
+                            self._data[section.get("Name")]["data"][
+                                (cycle, temperature)
+                            ][pos] = {}
+
+                            for scan in well.findall(".//Scan"):
+                                wl = int(scan.get("WL"))
+                                value = float(scan.text)
+
+                                self._data[section.get("Name")]["data"][
+                                    (cycle, temperature)
+                                ][pos][wl] = value
+
+        except ET.ParseError as e:
+            logging.error(f"Failed to parse the file at {filepath}", exc_info=e)
+
+    def _get_data(self) -> dict:
+        return self._data
+
+    def get_parameter(self, section: str, parameter: str) -> tuple:
+        return self._data[section]["parameters"][parameter]
+
+    def get_value(self, section: str, data: tuple, pos: str, wl: int):
+        return self._data[section]["data"][data][pos][wl]