Vincent Mouchi, Quentin G. Crowley, Teresa Ubide, 2016

Transcription

1 AERYN: Walkthrough This short report will help you operate AERYN with all its capabilities. You can use the example files available with this report (also available at To open AERYN as a standalone application, simply double-click on its icon. In the case you use the Matlab version of AERYN, execute the program as a script from the Command Window, with your Current Folder including the necessary files ( photo.jpg, Background_Aeryn.jpg and aeryn.m ). Import data When the AERYN main window is visible, click on Open from the Control Panel on the top left part of the window. A dialog box appears to let you select a text file on your computer. Choose the folder within which the file is and double-click on the selected file or select it and click on Open. 1

2 The dialog box closes and after a short time (depending on the size of your data) the map is displayed on the Main Plot Area. The title bar of AERYN window is updated to include the name of your file. 1: Control Panel. 3: Side View Plot Area. 5: Histogram Plot Area. 2

3 2: Main Plot Area. 4: Palette Changes Panel. From this point, you can change the color palette and range by entering a value in the corresponding boxes of the Palette Changes Panel, use the slider by dragging it from one side to the other or click on the or arrow buttons. You can use the Side View Plot Area to help you select the correct range of your data by clicking on the Side View button on top of the Control Pannel and the Histogram Plot Area. You can change the unit of the color palette from multiple choices. By default, the value is µg.g -1. You can also choose to transpose the matrix corresponding to the map to invert lines and columns on the Main Plot Area by clicking on the Transpose button on top of the Control Panel. Filtering If the data distribution is difficult to see on the Histogram Plot Area, you may have outliers to remove. To do this, use the Filter part of the Control Panel. You can firstly try an automatic filtering of your data by clicking on Automatic. If you are satisfied by the updated results on the Main Plot Area, the Histogram Plot Area and the Side View Plot Area, click on Validate on the Filter area of the Control Panel. If you wish to try other extreme values, click on Reset filter and enter more appropriate values and click again on Filter for a new assessment. Reiterate as necessary to see a normal distribution on the Histogram Plot Area that will be clear enough to give you absolute values for the palette range. You can also directly enter a minimum and maximum value and click on Filter for an assessment. When you click on Validate, the palette range is automatically changed to better fit the cropped data. You can manually change it if required. For better results, define the lower and upper limits of the palette as the beginning and the end of the normal distribution in the Histogram Plot Area (in this example, approximately from 5000 to 12000). 3

4 Results at this step after cutting values below 0 and over and updating the color palette: Smoothing If the map presents intensive noise (high-frequency fluctuations) that hampers the precise definition of structures and patterns, so it may be interesting to smooth the data to amplify low-frequency fluctuations. To do this, use the Smoothing area on the Control Panel. The Mask value you need to enter must be a positive integer substantially lower than the smallest dimension of your map in terms of number of points. For instance, if you have a 30 by 80 points map, you should enter a value below 30, and preferably below 10 to avoid generating artefacts. Generally, a mask between 3 and 5 is satisfactory. When you have entered a value, click on Smooth. If you are satisfied by the updated results on the Main Plot Area, click on Validate. Otherwise, click on Reset to go back to the previous state. 4

5 Results at the end of this step, after a 5-points mask smoothing: Detrend If you observe a general trend of your map towards one direction, it may be useful to execute a detrending of your map to expose potential fluctuations following an orthogonal direction relative to the main trend. You can in this case use the Detrending part of the Control Panel. Clicking on the Auto detrend button, AERYN will calculate the best fitting plane to the data and remove that trend. You can either accept the changes or cancel this operation by choosing to click on Undo on the very bottom of the Control Panel. Alternatively, you can select a line or column of your map (by selecting the corresponding dimension and entering the number of that line or column) and click on Display. Two new windows will appear to present the initial and final state of that transect. 5

6 On the first window (named Figure 2: Linear trend ), the transect is displayed in black and the calculated linear trend is in red. The other window ( Figure 3 : Detrended vector ) displays the original transect still in black and the corresponding detrended transect in red. If you think this trend can produce satisfactory results once applied to all other transects (either all lines or all columns, depending on what you selected), you can click on Confirm detrend in the Detrending part of the Control Panel after closing the two windows ( Figure 2: Linear trend and Figure 3 : Detrended vector ). Results at this step: Undo At any stage, even after validating an option, you can cancel any number of operations by successively clicking on Undo at the bottom of the Control Panel. Use the History part of the Control Panel to help you keep track of the operations you performed. 6

7 Save At any stage, you can save the current map by clicking on Save map at the bottom of the Control Panel. A dialog box will open to let you choose the folder and the name of the file to be created. Then click on Validate. Three files will be created, sharing the name you provided: a TIFF image file corresponding to your map (which can be resized by any image-processing software such as Adobe Photoshop or Adobe Illustrator); a text file with all the values for each point on the map (which can subsequently be imported in AERYN or Microsoft Excel); and a text file stating the historic of the operations performed on the initial data using AERYN with the values of the selected options. This last file also gives you the minimum, maximum, mean and standard deviation values of this dataset. 7