Several file formats for reading in data are supported by Glotaran. Two types of files can be distinguished:
Read more about the various file formats and how to convert your data into a format that is readable by Glotaran below. Please note that support for some file format is not enabled by default by means of (optional) plugins which you can find in Glotaran under the menu button Tools - Plugins.
Time-gated spectrum represents measurements taken simultaneously at a great number of wavelengths and at a certain time delay with respect to the exciting pulse t. A time-gated spectrum may be represented as a vector of length n, where n is the number of wavelengths at which measurements were made at time delay t. A set of time-gated spectrum taken at distinct times t1, t3,…, tm, may be collected into a matrix of dimensions n by m. Such a matrix is termed a time-resolved spectrum. The 'time explicit' data format allows input of data in the following form.
The format of the input file is as follows.
Note that each column represents a time-gated spectrum, and each row represents a decay trace. For an example input file in `Time explicit' format, see Example of time explicit data file. All entries above are space delimited. `Heading line 1' and `Heading line 2' are two lines that may be filled as the user likes (e.g., with a data file title). The line containing `Time explicit' indicates the format that the input data is to take. The line containing `Intervalnr' and a scalar m indicates the number of distinct time points m at which measurements were taken, (note that the number of wavelengths n need not be specified). The following line contains the real-valued times t1,…, tm at which measurements were taken. The first value of each of the remaining lines represent the wavelength at which the decay trace contained on that row was taken. The rest of each remaining row represents a (space-delimited) decay trace Ψ(t1,λ),Ψ(t2,λ),…,Ψ(tm,λ). After all datapoints are specified the file can contain line 'Integrated fluorescence' followed by tab or space delimited vector containing total fluorescence for each timestep. Note that for real experiments the number of data points Ψ(t,λ) is on the order of 10,000-100,000.
Decay traces represent measurements taken at a great number of times at some particular wavelength λ. A decay trace may be represented as a vector of length m, where m is the number of time points at which measurements were made. A set of decay traces taken at distinct wavelengths λ1, λ2, …, λn, may be collected into a matrix of dimensions m by n. Such a matrix is again termed a time-resolved spectrum. The `Wavelength explicit' data format allows input of data to TIM in the following format.
The format of the input file is as follows.
Note that each column represents a decay trace, and each row represents a time-gated spectrum. For an example input file in `Wavelength explicit' format, see Example of time explicit data file. All entries above are space delimited. `Heading line 1' and `Heading line 2' are two lines that may be filled as the user likes (e.g., with a data file title). The line containing `Wavelength explicit' indicates the format that the input data is to take. The line containing `Intervalnr' and a scalar n indicates the number of distinct wavelengths n at which measurements were taken, (note that the number of time points m need not be specified). The following line contains the real-valued wavelengths λ1, λ2, …, λn at which measurements were taken. The first value of each of the remaining lines represent the time at which the time-gated spectrum contained on that row was taken. The rest of each remaining row represents a (space-delimited) time-gated spectrum Ψ(t,λ1),Ψ(t,λ2),…,Ψ(t,λm). After all datapoints are specified the file can contain line 'Integrated fluorescence' followed by tab or space delimited vector containing total fluorescence for each timestep. Note that for real experiments the number of data points Ψ(t,λ) is on the order of 10,000-100,000.
RAW format was developed in the Laboratoire d'Optique et Biosciences, Ecole Polytechnique, to store pump-probe data. The header of the file contain following information:
after header all data points (transmition of the sample) saved in the column, starting from first time point. Example of a data file: HB180301.RAW.
The AVG format is commonly used to hold averaged transient spectra data. In this format for every recorded wavelength (in rows) and at every probe delay (columns) two values are specified. The first values is the actual measured (average) value, and the second is the corresponding error (due to fluctuation in the laser light). Currently nothing is done with the error value for each data point but just ignored in order to successfully read in the file. The probe delay used for each data point is included in the header of the file (the lines starting with the “#” symbol).
Typical file structure is as follows:
# Comments # etc. # # Delay: -1000.000 -100.000 1579.06 1.0039832 0.00062804847 1.0049483 0.00060386888 1575.69 1.0044705 0.00064121636 1.0053659 0.00062344205 1572.33 1.0048679 0.0007405209 1.0058121 0.00072175045
which corresponds to:
Wavelength | avg-value | error-value | avg-value | error-value |
---|---|---|---|---|
wavelength1 | avg-val1-at-time1 | error-value1-at-time1 | avg-val1-at-time2 | error-value1-at-time2 |
wavelength2 | avg-val2-at-time1 | error-value2-at-time1 | avg-val2-at-time2 | error-value2-at-time2 |
wavelength3 | avg-val3-at-time1 | error-value3-at-time1 | avg-val3-at-time2 | error-value3-at-time2 |