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Import Control File Syntax

Some of the import filters require a control file which has to be built by the user before being able to import a particular data set. These control files consist of a simple collection of statements defining the information to be combined into the Epina ImageLab dataset. Each statement requires to be stored in an individual line starting with a hash character (#) followed by a control command. All text after a semicolon is treated as a comment. Empty lines are allowed.

Command Explanation
#author The name of the dataset's author.
#date The date of measurement formatted according to the format YYYY-MM-DD hh:mm:ss. The time of the day (hh:mm:ss) may be omitted.
#element A CSV file containing the image data of a particular element (in EDX images). The control command is followed by the single-word layer identifier (usually an elemental symbol) and the filename of the CSV file containing the data.
#filemask A filemask enabling the user to extract the encoded pixel coordinates from the corresponding filenames. The filemask may contain path information and wildcards. Subdirectories in the file mask are considered to be relative to the location of the control file. The actual filename mask may contain one or more of the following numeric wildcards which can be extended by an additional format definition (separated by a colon) which specifies how many digits are used to generate the corresponding value (including leading zeros). If the format specifier is omitted the generated value has no leading zeros.
<X>, <X:n>the index of the pixels along the x-axis
<Y>, <Y:n>the index of the pixels along the y-axis
<T>, <T:n>the index of the time slot
<R>, <R:n>the index of repeated measurements
#filetype The filetype statement specifies the type of the data; it always has to be the first line in the control file. Currently the following file types are specified: ILAB_CF_SEMEDX (SEM/EDX data), ILAB_CF_THZRCDT (THz spectrometer of Recendt GmbH) and ILAB_RD_TUWSTORAMAN (TUW stand-off Raman data). Apart from specifying the type of data, the filetype statement is also used to check if the control file is a valid control file and appropriate for the import filter. Consequently the filetype statement is mandatory. Without a valid filetype statement the import filter will issue a warning message.
#length_x The width of the image in real coordinates (in mm). Please note that length_x is deprecated and should be replaced by pixsize_x.
#length_y The height of the image in real coordinates (in mm). Please note that length_y is deprecated and should be replaced by pixsize_y.
#npixel_x The width of the image in pixels (i.e. the number of pixels along the x axis).
#npixel_y The height of the image in pixels (i.e. the number of pixels along the y axis).
#nrepeat The number of repeated spectral measurements. If the spectrum of each pixel of an image has been measured repeatedly, the number of repetitions has to specified by this keyword. Leaving it undefined sets a default of 1.
#ntslots The number of time slots. If ntslots is undefined, it is assumed, by default, that the data contains only a single time slot.
#photo A high resolution background photo which can be used for the image stack. Please note that in most cases the calibration of the photo has to be performed manually after the import of the data.
#pixsize_x The distance between two pixels along the x axis (in mm).
#pixsize_y The distance between two pixels along the y axis (in mm).
#sample The sample name. This name is shown in the "sample ID" field of Epina ImageLab.
#tinterval The time interval between images (in seconds).

Examples

SEM/EDX

The following control file assembles 7 EDX images and a SEM photo into an Epina ImageLab dataset. The images are 512 by 400 pixels in size, covering an area of 51.2 by 40 µm. 
#filetype ILAB_CF_SEMEDX  ; SEM/EDX File Structure
#author John Doe
#date 2014-01-22
#sample PAC - Spot 1

; SEM
#photo A15x2600.Jpg    ; SEM photo covering the EDX images

; EDX
#npixel_x 512
#npixel_y 400
#pixsize_x 100   ; distance between pixels in horizontal direction (in nm)
#pixsize_y 1000  ; distance between pixels in horizontal direction (in nm)

#element Al Al-alu-spot1.csv
#element Ca Ca-alu-spot1.csv
#element Cr Cr-alu-spot1.csv
#element Cu Cu-alu-spot1.csv
#element Fe Fe-alu-spot1.csv
#element K K-alu-spot1.csv
#element Mg Mg-alu-spot1.csv

THz Recendt

The following control file specifies the files of a series of THz images taken over time. Each image has an extent of 20 by 20 pixels, the images have been acquired over 194 time slots. The files are stored in subdirectories "mydir001" to "mydir194" (according to the time slots), the data files of the first time slot are named from "spec_1_001_001_01.txt" (lower left pixel) to "spec_1_020_020_01.txt" (upper right pixel), the lower left pixel of the last time slot is named "spec_194_001_001_01.txt": 
#filetype ILAB_CF_THZRCDT       ; THz File Structure
#npixel_x 20
#npixel_y 20
#nrepeat 1
#ntslots 194
#filemask mydir<T:3>\spec_<T>_<X:3>_<Y:3>_<R:2>.txt
#author Jim Doe
#date 2014-12-03 12:32:51