📖 Read Chromatographic Data
The chromatopy library provides a set of reader functions designed to read and process chromatographic data from various file formats. These functions typically read data from a specified directory and return a ChromAnalyzer object, which is the central object used in chromatopy to manipulate and analyze chromatographic measurements.
General Syntax
Each of the supported file formats has a corresponding reader function, namely read_asm, read_agilent, read_chromeleon, and read_shimadzu. Following arguments are common to all reader functions:
Required Parameters:
path: The path to the directory containing the chromatographic files.ph: The pH value of the measurement.temperature: The temperature of the measurement.mode: The mode of the measurement, eithercalibrationortimecourse.
Optional Parameters:
id: A unique identifier for theChromAnalyzerobject. If not provided, thepathis used as the ID.name: The name of the measurement. Defaults to "Chromatographic measurement".values: A list of reaction times corresponding to each file in the directory for timecourse measurements or concentrations for calibration measurements. If not provided, the reaction times are extracted from the file names if possible.time_unit: The unit of the time valuessecond,minute, andhour, which can directly be imported fromchromatopy. This is also optional if the unit is embedded in the file names.temperature_unit: The unit of the temperature. The default is Celsius (C).
Returns:
The function returns a ChromAnalyzer object, which can be used to further analyze and manipulate the chromatographic data within the chromatopy framework.
Automatic extraction of reaction time and unit from file names
chromatopy can automatically extract the reaction time and time unit or cocentration values and concentration unit directly from the file names. This is particularly useful when files are named in a way that includes this information (e.g., sample_10min.txt, a11 3.45 hours.json, or B02_35_sec.json). However, this requires the file names to follow a specific format that chromatopy can recognize: It is assumed that the reaction time is the first numerical value which might have a decimal separator, followed by the name of the unit sec, second, min, minute, or hour. For concentration values, the first numerical value is assumed to be the concentration, followed by the name of the unit mM, uM, nM. If the file names do not follow this format, values and units need to be provided manually.
Specification of Reaction Times and Time Unit / Concentrations and Concentration Unit
If the reader function cannot automatically extract this information, you will need to provide it manually:
values: Provide a list of reaction times or concentrations corresponding to each file in the directory. Make sure that the file names are sorted alphabetically, so the order of values in the list matches the file order.unit: Specify the unit of the time values (e.g.,sec,minute,hour,nM,uM,mM,M).
Allotrope Simple Model (ASM) Format
The Allotrope Simple Model (ASM) format is the preferred format to be used with chromatopy. If not already done, you can batch process your chromatographic data with OpenChrom as described to convert your data to the ASM format.
ASM data is read in with the read_asm function. This function reads chromatographic data from a directory containing Allotrope Simple Model (ASM) files. The measurements are assumed to be named alphabetically, allowing sorting by file name.
from chromatopy import ChromAnalyzer
data_dir = "data/asm"
analyzer = ChromAnalyzer.read_asm(
path=data_dir, ph=7.4, temperature=25, mode="timecourse"
)
Other Supported Formats
Agilent ChemStation
Agilent ChemStation files can be read in with the read_agilent function. Please note that this function relies on the existence of either a RESULTS.CSV or a *.TXT file in the *.D directory, which can be generated by the Agilent ChemStation software. Thus, it is recommended to use OpenChrom to convert your data to the ASM format.
Please note, that automatic reaction time and unit detection does not work for RESULTS.CSV files. The reaction time and unit must be provided manually.
from chromatopy import ChromAnalyzer
from chromatopy.units import minute
data_dir = "data/agilent_txt"
reaction_times = [0, 10, 20, 40]
analyzer = ChromAnalyzer.read_agilent(
path=data_dir,
ph=7.4,
temperature=25,
values=reaction_times,
unit=minute,
mode="timecourse",
)
The read_agilent method also reads rdl formatted *.txt files.
from chromatopy import ChromAnalyzer, minute
data_dir = "data/agilent_rdl"
analyzer = ChromAnalyzer.read_agilent(
path=data_dir,
ph=7.4,
temperature=25,
mode="timecourse",
)
Chromeleon
Chromeleon files can be read in with the read_chromeleon function. Please note that this function relies on the existence of a *.txt file in the directory. If applicable use OpenChrom to preproces and convert your files from Thermo Fisher Scientific to the ASM format.
from chromatopy import ChromAnalyzer, minute
data_dir = "data/chromeleon"
analyzer = ChromAnalyzer.read_chromeleon(
path=data_dir,
ph=7.4,
temperature=25,
mode="calibration",
)
Shimadzu
Shimadzu *.txt files can be read in with the read_shimadzu function. This function reads chromatographic data as the previously described functions.
In this dataset, the corresponding reaction times for each measurement are manually specified and the respective time_unit is imported.
from chromatopy import ChromAnalyzer, minute
data_dir = "data/shimadzu"
analyzer = ChromAnalyzer.read_shimadzu(
path=data_dir,
ph=7.4,
temperature=25,
values=[0, 5, 10, 15, 20, 25, 30, 35, 40],
unit=minute,
mode="timecourse",
)
Saving the ChromAnalyzer Object
It is possible to save the current state of the ChromAnalyzer object to a file using the to_json method. This method saves the object as a JSON file, which can be loaded back into the chromatopy framework using the from_json function.