GC Image Users' Guide

File Input and Output

• A GCI file with .gci extension stores ancillary data about the image (e.g., its size, color mapping, etc.) in plain text format tagged using an eXtensible Markup Language (XML) schema for GCxGC images.
• A binary file with .bin extension stores the binary image data in time order with each value stored as number, with support for representations up to IEEE double-precision, floating-point (with big-endian byte order).

The File menu in the Image Viewer provides access to utilities for image input and output, including:

• opening and saving images in the GC Image file formats,
• importing and exporting images in other file formats,
• exporting and importing image models and,
• printing images.

As illustrated in Figure 1, there are several File menu options for input and output.

Figure 1: The File menu of the Image Viewer, with the Import Image option selected.

Specifically, the image input and output options are:

• File->Open Image launches a file-system browser to open an image file in GC Image format. The user specifies the folder and GCI filename (with .gci extension). GC Image also expects a binary file (with .bin extension) in the same folder and with the same root filename. If there is a currently open image, another GC Image process is initiated.
• File->Save Image saves the current open image to the GCI file (with .gci extension) and binary file (with .bin extension) from which it was opened or to which it was last saved (whichever is more recent). The image remains open. This menu option is not available if no image is open.
• File->Save As launches a file-system browser to save the current image to a file specified by the user. The user specifies the folder and GCI filename (with .gci extension) and GC Image also saves a binary file (with .bin extension) in the same folder and with the same root filename. The current open image remains open, but the associated file location and name is changed (e.g., for subsequent Save operations). This menu option is not available if no image is open.
• File->Close Image closes the image without saving. If the image has been altered since the last Save or Save As operation, the user is prompted whether or not to save the image before closing. It is best to save the image, if that is desired, before requesting the image be closed. This menu option is not available if no image is open.
• File->Recent Images provides a sub-menu list of the most recently opened images. An image file in the list can be opened by simply selecting the file name from the list. If there is a currently open image, another GC Image process is initiated.
• File->Import Image provides a file-system browser to specify the source location of the foreign-format file. The determination as to the source image file format is made on the basis of the file name extension, so files to be imported should be named with the proper extension. When imported, the image is converted from the foreign file format. GC Image also creates a binary file (with .bin extension or with a .cdf extension for MS files) in the same folder and with the same root filename. If there is a currently open image, another GC Image process is initiated for importing the image. A destination file name is automatically generated for the file from the source name (e.g. example.CVS_img02.gci).

GC Image can import images in a variety of file formats. The import source file browser offers an "All Supported Files" format filter, as well as individual format filters. The import source file format filter defaults to the "All Supported Files" format.

Extension	Format
.asc	ASC - Thermo ASCII XY text format. Metadata values are read for "Sampling Rate" and "Y Axis Multiplier".
.bin	Binary - big-endian, IEEE, single-precision, floating-point; optional byte-swapping supports little-endian format.
.bmp	Bitmap - common Microsoft Windows format.
.cdf	NetCDF - Analytical Data Interchange (ANDI) Protocol for Chromatographic and Mass Spectrometric Data, based on the Unidata/UCAR network Common Data Format.
.ch	CH - Agilent Chemstation IQ Data File Format. Currently, all data values are imported, but not all metadata values are read.
.csv	CSV - Comma-Separated-Values in text format; each line is "<time>, <value>" or each line has "<value>" only, without time or comma.
.gctm	Text format - GC Image Text Mass Spectrometry Format.
.gif	GIF - Graphics Interchange Format.
.jpg	JPEG - Joint Photographic Experts Group format.
.ms	MS - Agilent Mass Spectral Data File Format. Currently, all data values are imported, but not all metadata values are read.
.png	PNG - Portable Network Graphics format.
.qgd	QGD- Shimadzu GCMSsolution Data File Format.
.sed	SED - SAI Experiment Description File Format for High-Precision Mass Spectral Data.
.tif	TIFF - Tagged Image File Format.
.txt	Text format; each line ends with a value, possibly preceded by other text separated by a tab, colon, semi-colon, comma, or space.
.uv	UV - Agilent ultraviolet liquid chromatography Data File Format.

Most of these formats do not provide double-precision floating point numbers for scientific work. Color images may yield unexpected results when the values are extracted. Common import formats for GCxGC data are ASC, CH, CSV, and binary. Common import formats for GCxGC-MS data are CDF or MS. Contact GC Image to request support for additional binary and plain-text formats.

After the source is specified, GC Image presents a dialog for import parameters, shown in Figure 2

Figure 2: The Import Parameters dialog.

For file formats that do not provide the modulation period, the user must enter the length of the modulation period in seconds. For file formats, such as CSV, that do not supply the dimensions of the image, the user must enter dimensional parameters (in pixels or time units) and the sampling rate in the pop-up dialog. If desired, the start time can be set to a non-zero offset. If the image metadata values are read from the source file, the value fields in the pop-up dialog will have values and be gray. Grayed values may be overridden by double-clicking in the text box and then entering a value. For some formats with time stamps for each data value, the import dialog has an optional flag to indicate that missing data values should be interpolated by nearest-neighbor or linear interpolation, or that the missing values should be filled by zeroes. If the modulation period times the sampling rate is not an integer number of samples, the user may indicate whether or not padding should be performed and if so whether or not the padding details should be shown. If padding is performed, the number of pixels in each secondary chromatogram is rounded up to the next largest integer and one pixel in the background of some secondary chromatograms is duplicated to compensate for the extra, fractional sampling intervals in every secondary chromatogram. The image can be altered by adding or removing data through the CPA (Cropping, Prepending, Appending) interface. GC Image will ignore CPA fields that are left blank. For example, if the first dimension is from time "blank", to five minutes, the regular start time will be used and the imported image will run until it reaches five minutes or end of file. The lower bounds for first and second dimensions are zero.

If desired, the user may choose to apply a specified processing configuration file, as described in Configuration Files . If desired, designate optional phase shift, optional background removal, optional blob detection (if background removal is performed), optional template matching with a specified template file (if blob detection is performed) with a specified template, optional saving of the blob table to a specified file (if blob detection is performed), optional saving of summary report, optional saving of the image to a specified file, and optional exiting. These operations are described in subsequent chapters.

• File->Export Image launches a file-system browser for exporting an image in a foreign file format (i.e. , not GC Image format). When exported, the currently open image is converted from the GC Image format to the external file format and stored in the folder and file location specified by the user. The user may choose to attach or not to attach axes to the exported image. This menu option is not available if no image is open.

  GC Image can export to a variety of image formats:

  Extension	Format
  .bmp	Bitmap - common Windows format.
  .jpg	JPEG - Joint Photographic Experts Group.
  .png	PNG - Portable Network Graphics.
  .pnm	PNM - Portable Anymap File Format.
  .tif	TIFF - Tagged Image File Format.
  .csv	CSV - Comma Separated Value format
  .gctm	Text format - GC Image Text Mass Spectrometry Format.

  Most foreign image file formats do not support the high-precision representation used by GC Image, so exported images may have significantly degraded precision. However, relatively little precision is required for viewing, printing, and other simple purposes. Additional binary and plain-text formats will be supported in the future.
• File->Export Image Model exports an image model to a file in XML-based GC Model (GCM) format. The model format distills essential information from the image in a form that is smaller and easier to communicate than large GCxGC datasets. The model represents peaks by horizontal and vertical profiles computed by directional integration. Multi-channel (e.g., MS) images contain profiles for each channel. Other models will be developed and supported in future versions.
• File->Import Image Model imports an image model from a file in GC Model (GCM) format.
• File->Print Image launches a print dialog to print an image, shown in Figure 3. The user can preview the printed page at varying magnifications; can control margins, orientation, and alignment; can stretch the image to a full page (changing aspect ratio); and can choose to attach or not to attach axes. Also, regions can be copied to the clipboard from the image view or 3D view, with the <F2> key, as described above and individual windows can be copied to the clipboard with the <ALT>-<PrtSc> keys, and then pasted into other applications (e.g., presentation software).

Figure 3: The Print Image popup.

The File menu also provides options for reading and writing image-related data:

• Save Blob Table - save blob peak table as text in comma-separated-file (.csv) format.
• Save Blob Set Table - save blob set table as text in comma-separated-file format.
• Save Summary Report - Save Summary Report.
• Save Template - save blob peak template as text in XML format.
• Import Graphics - import a graphics table.
• Export Graphics - export a graphics table.
• Save Journal - Save viewable journal of actions.
• Save Script - Save runnable script of actions.

and an option to exit:

• Exit - terminate the program.

The options for saving blob peak tables and templates are described in