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en:software:matlab:ta:dev:infodatei

Info file

Idea: Info file (similar to the „Liesmich“ [German for „readme“] files in use in Freiburg for other types of experiments) containing important additional information to a measurement.

Aim: Import in the TA toolbox. The informations get added to the current dataset.

Longterm goal: Import into a laboratory information system.

<note important>Currently (2012-10-22) the following specification of a file format is still very much in development. Therefore, all informations can change at any time without prior notice.
Note: The German version of this document might be more recent.</note>

Recent changes

  • 2012-10-22: v0.2e
    • New Field „Experiment“ in block „GENERAL“
    • New Field „Purpose“ in block „GENERAL“
    • New Field „Buffer“ in block „SAMPLE“
  • 2012-03-31: v0.2d
    • New Field „Shot repetition rate“ in block „GENERAL“
    • Field contents can span over multiple lines1)
  • 2012-01-23: v0.2c
    • Field „Aperture“ in block „SPECTROGRAPH“ divided into „Aperture front“ and „Aperture back“
  • 2012-01-21: v0.2b
    • New field „Aperture“ in block „SPECTROGRAPH“
  • 2012-01-18: v0.2a
    • New field „Software“ in block „GENERAL“
    • New field „Runs“ in block „TIME PROFILES“

Criteria for the file format

  • Machine readable and human readable
  • Pure text (ASCII)
  • Uniquely identifiably
    • Identifier string in the first or second line of the file

General description of the file format

For those who like to see something, rather than reading (dull and) lengthly description: an example can be found further below.

Following a general description of the file format.

  • Format
    • The file format is ASCII (7-bit)
    • Restriction to 7 bit ASCII character table guarantees interoperability between different operating systems.
    • Therefore: No umlauts or other special characters.
  • File name and extension
    • The file extension is „.info“.
    • The filename is identical with the file basename of the corresponding data file.2)
  • The first line of the file consists of an identifier string.
    • Makes it possible to uniquely identify the file format during parsing.
    • Separated by an empty line from the remaining file.
    • Should contain a version number (of the format).
  • Field names
    • Field names may contain spaces, but no special characters and no colons3).
    • Field names must start with a character (no numerical!).
    • Every field name ends with a colon.
    • Field names shall not contain/repeat the block name.4)
  • Values
    • Values always follow a field name
    • Within a block, all values get intended that way that they are left-aligned. Therefore, the longest field name defines the indentation.
    • Values may contain special characters5) and colons.
    • NEW Values may span several lines. In this case, each new line needs to start with a whitespace character (such as space or tab).
  • Use of colons
    • Colons are used to separate field names and values
    • At all other places (e.g., after a block heading) no colon is allowed. Only exception are values.
    • Colons are used internally during parsing to separate field names and values (in Matlab: regexp with option split).
  • The info file is divided into several blocks.
    • Blocks are introduced by block names in capital letters.
  • All field names and descriptions within the file should be in English to guarantee international usability.
  • Blocks and fields may be optional, as long as there are certain fields (acting as „switches“) that can be used while parsing to determine whether these blocks/fields exist in the file.
    • Is no value available for a field, but removing the field seems not reasonable6), the value is „N/A“.
  • About the blocks:
    • Each block starts with a heading (block name) in capital letters.
    • Each block gets separated from the previous part of the file by an empty line.
    • Blocks contain key-value pairs consisting of a field name, followed by its respective value.

Description of each block

In the following, each block of the info file is described. An example of such an info file will follow below.

Besides the identifier string, currently there are the following blocks:

  • GENERAL
  • SAMPLE
  • TRANSIENT
  • SPECTROGRAPH
  • DETECTION
  • RECORDER
  • PUMP
  • PROBE
  • TEMPERATURE
  • MFE
  • TIME PROFILES
  • COMMENT

GENERAL

The block „GENERAL“ contains a bit of general information regarding the measurement.

The fields in detail:

Fieldname Description
Filename Name of the data file
Date Date
Time start Time the measurement was started
Time end Time the measurement was finished
Operator Operator's Name
Label Short, comprehensive, unique (if possible) description/label of the measurement
Used for listing in, e.g., MATLAB®
Experiment Type of experiment
Purpose Reason for performing the experiment
Spectrometer Short, unique (if possible) description/label of the spectrometer used
Software Name of the software/program used for the measurement including its version number (or date)
Runs Number of runs
Shot repetition rate Shot repetition rate of the experiment

Comments

  • Filename
    • If there is one file per time trace (Ox), the file basename; the actual name for each file will be contained in a separate block in this case.
  • Spectrometer
    • For Freiburg: „LP920-K“; for Oxford: „lab-built“ (or something more reasonable)
    • This value is a „switch“ that defines how the info file gets parsed and processed and which (optional) blocks and fields will be looked for.

SAMPLE

The block „SAMPLE“ contains the most important informations regarding the sample.

The fields in detail:

Fieldname Description
Name unique (if possible) and short name of the sample
Description Details of the sample
Buffer Details of the buffer used
Preparation Details of the preparation
Cuvette Cuvette used
Possibly the exact type and manufacturer

TRANSIENT

The fields in detail:

Fieldname Description
Points Number of points of a time trace
Trigger position Position of the Trigger pulse (index)
Length Length of the time trace

SPECTROGRAPH

The fields in detail:

Fieldname Description
Type Type of spectrograph used
Model Model name of spectrograph used
Aperture front Aperture at the front of the spectrograph
Aperture back Aperture at the back of the spectrograph

DETECTION

The fields in detail:

Fieldname Description
Type Type of detector (PMT, CCD)
Model Model name of detector
Power supply Power supply of detector

RECORDER

The block „RECORDER“ contains all parameters of the transient recorder (ideally directly retrieved from the device).

The fields in detail:

Fieldname Description
Averages Number of averages per time trace („shots per point“)
Sensitivity Sensitivity of input
Bandwidth Bandwidth
Time base Time base
Coupling Coupling mode
Impedance Impedance
Model Model name of transient recorder used

PUMP

The fields in detail:

Fieldname Description
Type Type of light source used for pumping (laser, …)
Model Model name of pump light source
Wavelength Wavelength of pump light source
Power Power of pump light beam
Repetition rate Repetition rate of pump light beam
Tunable type Type of tunable light source used (OPO or dye laser)
Tunable model Model name of tunable light source used
Tunable dye In case of dye laser: Name of the laser dye

PROBE

The fields in detail:

Fieldname Description
Type Type of proble light source
Model Model name of proble light source
Wavelength start Start value of wavelength axis
Wavelength stop End value of wavelength axis
Wavelength step Step width of wavelength axis
Wavelength sequence Direction of measurement (up/down/stochastic) or comma-separated list of wavelength regions measured
Power Power of probe light beam
Filter Filter(s) used (comma separated list)
Background Background correction used (none/lamp/fluorescence)

Comments

  • Wavelength start/stop
    • These are the respective start and stop values of the wavelength axie.
    • In case of „down“ measurement the start value is the larger value.
    • MATLAB® should account for the direction and convert the data if necessary.

TEMPERATURE

The fields in detail:

Fieldname Description
Temperature Temperature with unit
Controller Temperature controller used
Cryostat Cryostat used
Cryogen Cryogen used (H2O, LN2, LHe)

MFE

The fields in detail:

Fieldname Description
Field Magnetic field with unit
Coil type Type of coils used
Coil model Model name of coils used
Power supply Power supply used
Gaussmeter verwendetes Gaussmeter

TIME PROFILES

This block is only of interest if - as in Oxford - all time traces are separately (and manually) recorded and saved in separate files. As during a measurement details - such as filters in the probe beam - may change, there are a number of fields with information specific for each time trace.

The fields in detail, each for a single time trace:

Fieldname Description
Filename Filename
Wavelength Wavelength measured at
Averages Number of averages per time profile
Runs Number of independent measurements per time profile
Filter Filter(s) used
comma separated list

Comments

  • Wavelength
    • This is the actual wavelength measured at, even if the filename seems to suggest something different.7)
  • Filter
    • More than one filter may be used at the same time.
    • In case of more than one filter, a comma separated list of filter descriptions.
    • Filters get described by a common scheme:: XX###
      • XX stands for the filter type: LP - long pass; SP - short pass; BP - band pass
      • ### stands for the filter's characteristic/nominal wavelength
      • In case of BP, the scheme is: BP###-###
        (with start and end wavelength of the band)

COMMENT

As long as the comment block is the last block of a file, everything can be added here that seems useful and sensible.

Example

Following an example of an info file for a TA measurement with the full set of (possible) fields and blocks. Depending on where the file gets used, some of these fields/blocks may not be present.

TA Info file - v. 0.2d (2012-03-31)

GENERAL
Filename:               
Date:                   
Time start:             
Time end:               
Operator:               
Label:                  
Spectrometer:           
Software:               
Runs:                   
Shot repetition rate:     

SAMPLE
Name:                   
Description:            
Preparation:            
Cuvette:                

TRANSIENT
Points:                 
Trigger position:       
Length:                 

SPECTROGRAPH
Type:                   
Model:                  
Aperture front:         
Aperture back:          

DETECTION
Type:                   
Model:                  
Power supply:           
Impedance:              
Time constant:          

RECORDER
Model:                  
Averages:               
Sensitivity:            
Bandwidth:              
Time base:              
Coupling:               

PUMP
Type:                   
Model:                  
Wavelength:             
Power:                  
Repetition rate:        
Tunable type:           
Tunable model:          
Tunable dye:            

PROBE
Type:                   
Model:                  
Wavelength start:       
Wavelength stop:        
Wavelength step:        
Wavelength sequence:    
Power:                  
Filter:                 
Background:             

TEMPERATURE
Temperature:            
Controller:             
Cryostat:               
Cryogen:                

MFE
Field:                  
Coil type:              
Coil model:             
Power supply:           
Gaussmeter:             

TIME PROFILES
Scan 1
Filename:               
Wavelength:             
Averages:               
Runs:                   
Filter:                 
Scan 2
Filename:               
Wavelength:             
Averages:               
Runs:                   
Filter:                 

COMMENT

Example file for Freiburg

ta-freiburg.info
TA Info file - v. 0.2d (2012-03-31)

GENERAL
Filename:               test
Date:                   20xx-xx-xx
Time start:             00:00:00
Time end:               00:00:00
Operator:               A. Kabelschacht
Label:                  Testprobe
Spectrometer:           LP920-K
Software:               L900, Version 6.9.1
Runs:                   1
Shot repetition rate:   0.0625 Hz

SAMPLE
Name:                   FAD
Description:            FAD in Puffer
Preparation:            
Cuvette:                

TRANSIENT
Points:                 2000
Trigger position:       341
Length:                 10 us

SPECTROGRAPH
Type:                   Czerny-Turner with Triple Grating Turret
Model:                  standard
Aperture front:         
Aperture back:          

DETECTION
Type:                   PMT
Model:                  standard
Power supply:           standard
Impedance:              50 Ohm
Time constant:          

RECORDER
Model:                  
Averages:               10
Sensitivity:            
Bandwidth:              1.0
Time base:              5 ns
Coupling:               

PUMP
Type:                   Laser
Model:                  
Wavelength:             460 nm
Power:                  
Repetition rate:        10 Hz
Tunable type:           OPO
Tunable model:          

PROBE
Type:                   Lamp
Model:                  standard
Wavelength start:       385 nm
Wavelength stop:        655 nm
Wavelength step:        10 nm
Wavelength sequence:    up
Power:                  
Filter:                 
Background:             lamp

TEMPERATURE
Temperature:            285 K
Controller:             
Cryostat:               none
Cryogen:                H2O

COMMENT

Und hier gibt's ein bisschen Freitextkommentar - aber bitte OHNE Umlaute und andere Sonderzeichen!

Example file for Oxford

ta-oxford.info
TA Info file - v. 0.2d (2012-03-31)

GENERAL
Filename:               test
Date:                   20xx-xx-xx
Time start:             00:00:00
Time end:               00:00:00
Operator:               A. Kabelschacht
Label:                  Test sample
Spectrometer:           Oxford CRY Lab
Software:               Slow20111104
Runs:                   1
Shot repetition rate:   1/20 Hz

SAMPLE
Name:                   FAD
Description:            FAD in buffer
Preparation:            
Cuvette:                Hellma QS 10.00

TRANSIENT
Points:                 25000
Trigger position:       2500
Length:                 50 us

SPECTROGRAPH
Type:                   Ebert-Fastie
Model:                  Oriel 77250
Aperture front:         
Aperture back:          

DETECTION
Type:                   PMT
Model:                  Hamamatsu R928
Power supply:           Brandenburg 476R
Impedance:              500 Ohm
Time constant:          50 ns

RECORDER
Model:                  Iwatsu-LeCroy LT342L 500 MHz
Averages:               1
Sensitivity:            5.0 mV
Bandwidth:              500 MHz
Time base:              5.0 us
Coupling:               DC

PUMP
Type:                   Laser
Model:                  Continuum Surelite-1
Wavelength:             450 nm
Power:                  3 mJ
Repetition rate:        1 Hz
Tunable type:           Dye
Tunable model:          Sirah Cobra
Tunable dye:            Coumarin-450

PROBE
Type:                   Lamp
Model:                  Oriel 66021
Wavelength start:       370 nm
Wavelength stop:        650 nm
Wavelength step:        10 nm
Wavelength sequence:    530-650,530-370
Power:                  
Filter:                 LP390,LP500
Background:             

TEMPERATURE
Temperature:            
Controller:             Oxford ITC-503S
Cryostat:               Oxford Instruments
Cryogen:                LN2

MFE
Field:                  22 mT
Coil type:              Helmholtz
Coil model:             
Power supply:           
Gaussmeter:             

TIME PROFILES
Scan 1
Filename:               
Wavelength:             
Averages:               
Runs:                   
Filter:                 
Scan 2
Filename:               
Wavelength:             
Averages:               
Runs:                   
Filter:                 

COMMENT
1)
There is only one requirement: The second and any following line of a multiline entry must start with a whitespace character.
2)
This is a rather ideal case. Therefore, in reality it is not meant to be a strict rule, but rather a recommendation.
3)
The only exception are currently (round) brackets. If there is need for further special characters, parsing of those could be implemented as well. Reason for the restriction is the (direct) conversion of the field names in MATLAB® structs.
4)
Example: „Preparation“ rather than „Sample preparation“ in block „SAMPLE“. On the one hand, field names are much shorter this way, on the other hand, the file becomes easier to read.
5)
In general, whenever possible one should avoid using special characters, as they normally don't survive different file encodings. Until very recently, Matlab used different encodings with different operating systems.
6)
E.g., a field that might be relevant depending on the type of experiment, and only for certain experiments contains no value. In such case it is highly recommended to keep the field, as otherwise one forgets about it.
7)
This problem exists in case of „overlapping“ measurements used to be able to scale the different parts of the spectrum together.
en/software/matlab/ta/dev/infodatei.txt · Last modified: 2020/09/30 21:35 by 127.0.0.1