GC Image Users' Guide

Image Input and Output

GC Image represents each pixel value with a double-precision, 64-bit, floating-point number that provides much higher precision than most standard digital image formats. For this reason and to support storage of ancillary data, the GC Image software employs special file formats for representing GCxGC images. For each GCxGC image, there are two files:

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 an IEEE double-precision, floating-point number with big-endian byte order.

GC Image uses a different binary format, described in chapter GCxGC-MS Data, for GCxGC-MS data.

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, 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 .gci filename. GC Image also expects a binary .bin file in the same folder and with the same filename root. If there is a currently open image, another GC Image process is initiated.

File->Save saves the current open image to the GCI .gci and binary .bin files 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 .gci filename and GC Image also saves a binary .bin file in the same folder and with the same filename root. The current open image remains open, but the associated file location is changed (e.g., for subsequent Save operations). This menu option is not available if no image is open.

File->Close 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 pop-up dialog box for importing an image in a foreign file format (i.e., not GC Image format) and opening the imported image. If there is a currently open image, another GC Image process is initiated to import the image.

When imported, the image is converted from the foreign file format to the GC Image format and stored in the folder and file location specified by the user. The user can invoke a file-system browser to help specify the source location of the foreign-format file and the destination location of the GC Image format file. The determination as to the source image file type is made on the basis of the file name extension, so files to be imported should be named with the proper extension. For the destination, the user specifies the folder and GCI .gci filename. GC Image also saves a binary .bin file in the same folder and with the same filename root.

GC Image can import images in a variety of file formats.

Extension Format

.asc ASC - Thermo ASCII XY text format. Currently, 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 Mass Spectrometric Data, based on the Unidata/UCAR network Common Data Format. Currently, not all ANDI metadata values are read.

.ch CH - Agilent Chemstation IQ Data File Format. Currently, 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.

.gif GIF - Graphics Interchange Format.

.jpg JPEG - Joint Photographic Experts Group format.

.png PNG - Portable Network Graphics format.

.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.

Extension	Format
.asc	ASC - Thermo ASCII XY text format. Currently, 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 Mass Spectrometric Data, based on the Unidata/UCAR network Common Data Format. Currently, not all ANDI metadata values are read.
.ch	CH - Agilent Chemstation IQ Data File Format. Currently, 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.
.gif	GIF - Graphics Interchange Format.
.jpg	JPEG - Joint Photographic Experts Group format.
.png	PNG - Portable Network Graphics format.
.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.

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. The most common import formats for GCxGC images are ASC, CH, CSV, and binary. The most common import format for GCxGC-MS images is CDF. Additional binary and plain-text formats will be supported in the future.

For file formats, such as CSV, that do not supply the dimensions of the image, enter dimensional parameters (in pixels or time units) and the sampling rate in the pop-up dialog box.

If desired, choose to apply a specified processing configuration file, as described in chapter 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 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.

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->Print Image launches a print dialog to print an image, shown in Figure 2. 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. This interface is still being developed to provide more extensive printing choices. Additionally, individual windows can be copied to a buffer with the <ALT>-<PrtSc> keys and then pasted into presentation software.

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.

Figure 2: 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 Template - save blob peak template as text in XML format.
Import Graphics - import a graphics table.
Export Graphics - export a graphics table.

and an option to exit:

Exit - terminate the program.

The options for saving blob peak tables and templates are described in chapters Detection and Analysis and Pattern Recognition. The options for importing and exporting graphics tables are described in chapter Graphics. When the exit action is selected, the currently open image is discarded. If an image is open and has been altered since the last Save or Save As operation, GC Image prompts the user whether or not the image is to be saved before exiting. It is best to save changed images that are to be retained when they are changed to prevent the loss of unsaved work (e.g., in the event of a system crash or power failure) and before requesting the program to exit.

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