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

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Merged
nathan-stender merged 2 commits into from
Mar 16, 2026
Merged

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

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8e32eba
Fix Perkin Elmer Envision parser to recognize A450 and similar labels…
nathan-stender Mar 16, 2026
9f49e25
Fix imports and correct absorbance value parsing to use floats
nathan-stender Mar 16, 2026
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10 changes: 7 additions & 3 deletions src/allotropy/parsers/perkin_elmer_envision/perkin_elmer_envision_structure.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -291,7 +291,7 @@ class Result:
uuid: str
col: str
row: str
value: int
value: float


def create_results(reader: CsvReader) -> list[Result]:
Expand All @@ -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
]
Expand Down Expand Up @@ -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)
Expand Down
170 changes: 170 additions & 0 deletions tests/parsers/perkin_elmer_envision/testdata/PE_Envision_absorbance_A450_example.csv
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Original file line number Diff line number Diff line change
@@ -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
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