4.1 Working with a time series of image data sets using bilko.

NetCDF data file

Many satellite data sets are provided in hierarchically structured formats, a bit like complex sets of images. These formats usually include considerable additional metadata data apart from the images themselves. Metadata tags or attributes are used to describe the contents of a data file in such a way that the data is self-describing i.e., no other additional information should be required to unpack and use the data held within the file. NetCDF (network Common Data Form) is a set of interfaces for array-oriented data access and is used widely in the satellite oceanography and ocean modelling community. It is well structured for storing a time series of satellite observations. Data stored in netCDF format is:

• Self-Describing: A netCDF file includes information about the data it contains.
• Portable: A netCDF file can be accessed by computers with different ways of storing integers, characters, and floating-point numbers.
• Direct-access: A small subset of a large dataset may be accessed efficiently, without first reading through all the preceding data.
• Appendable: Data may be appended to a properly structured netCDF file without copying the dataset or redefining its structure.
• Sharable: One writer and multiple readers may simultaneously access the same netCDF file.
• Archivable: Access to all earlier forms of netCDF data will be supported by current and future versions of the netCDF library software.

More information describing netCDF can be obtained at netCDF.

Activity/Question 1

Open the file sst0_ats2_v00a.nc. This netCDF file contains a time series of ATSR global sea surface temperature (skin-temperature) data. Bilko will show the file as a 'tree' of folders, which you can use to investigate the hierarchical structure of the netCDF file. To examine the data you can:

Click on the Scientific Global Attributes tag, in the left frame, to select it and then right click on the same tag in the right frame. Select the option Open Properties. A new window should open which contains the metadata information attached to this netCDF file.

a)	What is the range of SST values reported in the netCDF file metadata?

When you have finished reviewing the Global Scientific Attributes, close this window.

The netCDF data file is a self describing data file that contains 59, 32 bit floating point images that are 720 x 359 pixels in size; you can confirm this by looking in the dimensions section of the file.

Investigate the lat and lon sections of the netCDF file metadata and quickly review the content presented. You should discover that the latitude and longitude resolution of the data within the file is 0.5°.

Activity/Question 2

Select the dimensions tag in the hierarchical file viewer and double click the item to expand the file view. In the right hand window section, select the time attribute and right-click this item. Select the option to Open Properties. Review the contents of the properties window.

a)	What is the temporal resolution and coverage of the data contained in this file (in fractions of a year)?

The data cube

Select the Scientific Data section of the file to reveal the data sets included in the file. There should be one data set called SST; this contains 59 images of 32-bit floating point data, 720 x 360 pixels in size. These images can be opened as a 3-dimensional data cube, which can be analysed as a single data set in Bilko.

Activity

1. Right-click on the SST data set in the right frame of the file view window and select Open connected. Click OK to extract all 59 images connected together as a vertical stack of images, one on top of the other.

2. Review the contents of the Redisplay dialog Make sure that the range of values to display is set from -6.8°C (min) to 37.0°C (max). Click the Apply button to apply these settings to every image in the connected stack. Do not click OK, as you will then have to apply the Redisplay stretch 59 times! (Remember you can always access the Redisplay dialog by right-clicking anywhere in a displayed image when working in Bilko.)

3. Finally, make sure the stack is selected by clicking on the stack window. You are only interested in the data cube stack for the remainder of this lesson and you can close all the other image data sets by selecting the Window » Close All Except menu item. Note that the desktop is now much clearer!

You can visualise the stack as a cube of data that you can explore in three dimensions. Each image can be called to the top of the stack using the Selector that has appeared on your screen. The Selector always be visible when the stack is selected, and will tell you which image is currently displayed on the top of the stack. By default the first image in the series (image 0) is selected when a stach is first opened. Note that if you select an image, the images stay in order so that if you call image 40 to the top of the stack, image 41 will be the next one beneath. You can also scroll through the images one by one using the [TAB] key on your keyboard.

The first image in the data cube is a monthly mean SSTskin map for July 1995, and the last image for May 2000. There are several blank images in the file; these are used as placeholders for the months between January 1996 to July 1996, when the ATSR-2 scan mirror jammed and no data were obtained. Each image represents SSTskin derived from the ATSR-2 sensor for ½ degree latitude x longitude regular grid boxes. Each grid box contains the average of all 1km cloud free SST observations collected by the ATSR-2.

Question 3

a)	Considering the information above, what is the date of the second image data set stored in this stack?

Adding colour

Take a look at the top image of the stack in front of you. It is immediately obvious that all of the image data are upside down in this file!! In terms of data analysis, it doesn`t matter really but it is much easier to work with the data when you are looking at the maps in a conventional manner. You can re-orient the image data cube by reflecting the image data within the stack. Select view » reflect » in y (in the S-N direction) to adjust the orientation of the image data sets. Note that we are working on the top image of the data cube but that the operation is replicated throughout the entire stack of image data so that ALL the image data files have been reflected. This is an important concept when working within the Bilko Stack environment: actions are often replicated across the entire data set using the same limits or settings (such as colour palettes, stretches and filters). This is a great property of stacked data sets when working with a time series of image data sets where you want to compare images using the same settings without having to replicate image processing steps for each individual image.