fix: Fix Perkin Elmer Envision parser to recognize A450 labels as absorbance (#1152)

## Summary
- Fixed Perkin Elmer Envision parser incorrectly classifying absorbance
measurements with labels like "A450", "A562", etc. as fluorescence
- Added regex pattern matching for common "A###" absorbance wavelength
naming convention
- Added comprehensive test case with representative A450 absorbance data

## Problem
The parser's `get_read_type()` function was defaulting to fluorescence
for any unrecognized label. Absorbance measurements using the common
"A###" naming pattern (where ### is the wavelength, e.g., A450 for 450nm
absorbance) were not recognized by the existing pattern matching.

## Solution
Added a regex pattern check `r"^A\d{3}"` to identify labels starting
with 'A' followed by three digits as absorbance measurements.

## Test plan
- [x] Created new test file `PE_Envision_absorbance_A450_example.csv`
with representative A450 data
- [x] Verified the parser correctly identifies A450 labels as absorbance
(192 absorbance fields, 0 fluorescence fields in output)
- [x] All existing Perkin Elmer Envision tests pass
- [x] Tested various absorbance patterns (A450, A562, A280, A600, A405)
all correctly identified

🤖 Generated with [Claude Code](https://claude.com/claude-code)

---------

Co-authored-by: Claude Opus 4.1 <noreply@anthropic.com>

Author: nathan-stender

src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py

@@ -21,7 +21,7 @@
 from dataclasses import dataclass
 from enum import Enum
 from pathlib import Path
-from re import search
+from re import match, search
 from typing import Any
 
 import numpy as np
@@ -291,7 +291,7 @@ class Result:
     uuid: str
     col: str
     row: str
-    value: int
+    value: float
 
 
 def create_results(reader: CsvReader) -> list[Result]:
@@ -316,7 +316,7 @@ def create_results(reader: CsvReader) -> list[Result]:
             uuid=random_uuid_str(),
             col=col,
             row=row,
-            value=int(series.loc[col, row]),
+            value=float(series.loc[col, row]),
         )
         for col, row in series.stack().index
     ]
@@ -674,6 +674,10 @@ def get_read_type(self) -> ReadType:
             read_type for key, read_type in patterns.items() if key in self.label
         }
 
+        # Check for absorbance wavelength patterns like A450, A562, etc.
+        if not read_types and match(r"^A\d{3}", self.label):
+            read_types.add(ReadType.ABSORBANCE)
+
         if len(read_types) > 1:
             msg = f"Unable to determine unique read type from label: '{self.label}'"
             raise AllotropeConversionError(msg)

tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_A450_example.csv

@@ -0,0 +1,170 @@
+Plate information
+Plate,Repeat,Barcode,Measured height,Chamber temperature at start,Chamber temperature at end,Humidity at start,Humidity at end,Ambient temperature at start,Ambient temperature at end,Group,Label,ScanX,ScanY,Measinfo,Kinetics,Measurement date,
+1,1,="",14.35,22.00,22.10,42.0,41.5,22.5,22.6,1,A450(1),0,0,De=1st Ex=Btm Em=N/A Wdw=N/A (8),0,1/15/2024 10:30:00 AM,
+
+Background information
+Plate,Label,Result,Signal,Flashes/Time,Meastime,MeasInfo,
+1,A450,0,295000,300,00:00:00.000,De=1st Ex=Btm Em=N/A Wdw=N/A (8),
+
+Results for A450(1) - channel 1 (A)
+,01,02,03,04,05,06,07,08,09,10,11,12,
+A,0.1500,0.0850,0.1000,1.8500,1.8000,1.7500,0.6000,1.0000,0.7500,0.6500,0.6000,0.7000,
+B,0.1000,0.0700,0.1100,1.0000,1.0500,1.1000,0.2500,0.8000,0.3000,0.2800,0.2200,0.3100,
+C,0.0950,0.0650,0.0800,0.5500,0.5000,0.4800,0.1500,0.1000,0.1600,0.1200,0.1300,0.1800,
+D,0.0700,0.0600,0.1500,0.2000,0.2100,0.2200,0.1000,0.1600,0.1100,0.1400,0.0850,0.1400,
+E,0.0800,0.0750,0.0900,0.1500,0.2800,0.1100,0.0800,0.1500,0.0900,0.4800,0.1000,0.1100,
+F,0.0750,0.0800,0.0780,0.0800,0.0820,0.1300,0.1050,0.0650,0.1400,0.0950,0.1100,0.0950,
+G,0.1000,0.1500,0.0750,0.0900,0.0780,0.1000,0.0850,0.4500,0.1050,0.0850,0.1100,0.1200,
+H,0.1800,0.0900,0.0950,0.0750,0.1050,0.0900,0.0800,0.0800,0.0950,0.1100,0.0950,0.0950,
+
+Plate information
+Plate,Repeat,Barcode,Measured height,Chamber temperature at start,Chamber temperature at end,Humidity at start,Humidity at end,Ambient temperature at start,Ambient temperature at end,Group,Label,ScanX,ScanY,Measinfo,Kinetics,Measurement date,
+2,1,="",14.35,22.05,22.08,41.6,41.5,22.6,22.7,1,A450(1),0,0,De=1st Ex=Btm Em=N/A Wdw=N/A (8),0,1/15/2024 10:31:35 AM,
+
+Background information
+Plate,Label,Result,Signal,Flashes/Time,Meastime,MeasInfo,
+2,A450,0,295100,300,00:00:00.000,De=1st Ex=Btm Em=N/A Wdw=N/A (8),
+
+Results for A450(1) - channel 1 (A)
+,01,02,03,04,05,06,07,08,09,10,11,12,
+A,0.3000,0.2700,0.3200,2.0000,1.9500,2.0500,1.5000,2.2000,1.7500,1.2000,0.8500,0.8800,
+B,0.1800,0.1300,0.2700,1.4500,1.8000,2.2000,1.0000,1.0500,1.2000,0.4500,0.6000,0.4000,
+C,0.0900,0.0880,0.1400,1.0000,1.0500,2.1000,0.5000,0.4200,0.4500,0.7800,0.1700,0.2200,
+D,0.1500,0.0870,0.1400,0.4500,0.3800,0.4000,0.2200,0.2200,0.1800,0.1600,0.1200,0.2100,
+E,0.1000,0.0720,0.1050,0.2100,0.1100,0.1750,0.1550,0.1200,0.1300,0.1400,0.5000,0.1150,
+F,0.0950,0.0680,0.0850,0.1050,0.8000,0.1200,0.0950,0.1100,0.1000,0.1200,0.1100,0.4700,
+G,0.0800,0.0580,0.0750,0.0900,0.0850,0.0950,0.1050,0.1850,0.1200,0.1080,0.2700,0.1080,
+H,0.1600,0.0880,0.1080,0.0850,0.1020,0.0800,0.1450,0.0720,0.0880,0.1450,0.1150,0.1300,
+
+
+Basic assay information
+Assay ID: ,,,,101
+Assay Started: ,,,,1/15/2024 10:28:00 AM
+Assay Finished: ,,,,N/A
+Assay Exported: ,,,,1/15/2024 10:35:00 AM
+Protocol ID: ,,,,100250
+Protocol Name: ,,,,Absorbance Test Protocol
+Serial#: ,,,,="1050242"
+
+
+
+Protocol information
+Protocol:
+Protocol name,,,,Absorbance Test Protocol
+Number of assay repeats,,,,1
+Start assay repeat each,,,,N/A
+Number of plate repeats,,,,1
+Start plate repeat each,,,,N/A
+Is label meas. height used,,,,Yes
+Height of measurement,,,,Defined in label
+Is gripper height used,,,,No
+Mode of measurement,,,,By Rows  bi-directional
+Rotated plate,,,,No
+Soft move,,,,No
+Protocol notes,,,,
+
+Plate type:
+Name of the plate type,,,,96 General
+Number of rows,,,,8
+Number of columns,,,,12
+Number of the wells in the plate,,,,96
+Height of the plate,,,,14.35 mm
+
+Coordinates of corners:
+96 General + A450
+14.2 mm x------------------------------------------------------- x 113.29 mm
+10.61 mm                                                           10.7 mm
+
+14.11 mm x------------------------------------------------------ x 113.11 mm
+73.7 mm                                                            73.79 mm
+
+Platemap:
+Plate,,,,1
+Group,,,,1
+
+,01,02,03,04,05,06,07,08,09,10,11,12,
+A,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+B,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+C,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+D,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+E,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+F,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+G,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+H,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+
+ - - Undefined
+
+Plate,,,,2
+Group,,,,1
+
+,01,02,03,04,05,06,07,08,09,10,11,12,
+A,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+B,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+C,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+D,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+E,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+F,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+G,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+H,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,- ,-
+
+ - - Undefined
+
+Calculations:
+No calculations.
+
+Auto export parameters:
+Export format,,,,Plate2
+Include basic assay information,,,,Yes
+Place assay information at,,,,End of file
+Include basic plate information,,,,Yes
+Place plate information at,,,,Beginning of plate
+Include protocol information,,,,Yes
+Protocol info level,,,,Large
+Include error and warning information,,,,Yes
+Include background information,,,,Yes
+Add plate number to the file name,,,,Yes
+Each plate to separate file,,,,No
+Field separator to use,,,,System
+File name format,,,,<DefaultDataFolder>\<Date>\<ProtocolName>_<AssayID>.csv
+
+Operations:
+Plate 1
+  Group 1
+    Measurement
+      Label,,,,A450(1)
+Plate 2
+  Group 1
+    Measurement
+      Label,,,,A450(1)
+
+Labels:
+A450,,,,2000014
+Exc. filter,,,,BFP 450
+Measurement height,,,,13 mm
+Number of flashes,,,,300
+Number of flashes integrated,,,,1
+Excitation light,,,,100%
+Reference excitation light,,,,100%
+Reference AD gain,,,,1
+Reference signal,,,,350888
+Last edited,,,,1/15/2024 10:00:00 AM
+Last edited by,,,,EnVision
+Factory preset,,,,No
+
+Filters:
+BFP 450,,,,216
+Filter type,,,,Emission
+Description,,,,M450 CWL=450nm BW=10nm Tmin=60%
+Used with,,,,Luminescence Absorbance DELFIA - Time-resolved Fluorescence Fluorescence Intensity Fluorescence Polarization LANCE - Time-resolved Fluorescence
+Last edited,,,,1/15/2024 9:50:00 AM
+Last edited by,,,,EnVision
+Factory preset,,,,Yes
+
+Instrument:
+Serial number,,,,1050242
+Nickname,,,,EnVision#Alpha_680nm
+
+
+
+
+Exported with EnVision Workstation version 1.14.3049.1642