Phase Maps | Qacd Quack

TUTORIAL:

Phase Map Creation and Manipulation

k-means clustering

To perform k-means clustering, select Action | k-means Clustering from the menu.
A small dialog box is displayed containing clustering options. You can specify the minimum and maximum number of phases (k), and whether to include all of the elements in the project or just those of the commonest 5 elements (Al, Ca, Fe, Mg, Si) that are present.
Click on the OK button to perform clustering. If you have already done this before, a warning will be displayed informing you that this will delete the results of the previous clustering.
A progress bar is displayed whilst the clustering is performed. For large datasets (number of pixels and number of elements) this can take quite a while, but is very fast for this small test data set.
For each of the k-values, an item is added to the list in the Clusters tab on the left.
Select an item in the list on the left, as usual, to display it on the right. The order of clusters that are returned from the k-means clustering algorithm are re-organised in a repeatable way so that the colours used for particular regions of the cluster map should be fairly constant as you change k.

Create phase maps from cluster map

Select one of the items in the list on the Clusters tab, and click on the New phase(s) button at the bottom to create phase maps from the chosen cluster map.
A new dialog box is displayed showing the cluster map at the top and information about each of the phases below that. Initially the phases are given default names such as <phase 3>; these can be changed by double-clicking on them in the usual manner.
It is possible to select multiple phases in the list control. If one or more phases are selected, they can be deleted by clicking on the Delete selected phases button. When this is done, the corresponding pixels are set invalid and are displayed as white, and the statistics under the cluster map are updated to reflect this.
If two or more phases are selected at the same time, they can be merged into one by clicking on the Merge selected phases button. The selected phases are then merged together and displayed as a single colour.
The fifth column in the list control shows the Original values that comprise a particular phase. Using this information and the value of k, it is possible to reconstruct the phase maps again from scratch at a future date.
When you have finished deleting, merging and renaming phases, click on the OK button to create new phase maps.
The new phase maps are added to the list in the Phases tab. Select one in the usual manner to display it on the right. A phase map is always displayed as black pixels and without a histogram, regardless of the current Plot type.

Create phase map by thresholding filtered element maps

It is also possible to create a phase map by applying thresholds to one or more filtered element maps.
In the Phases tab, click on the New phase button at the bottom.
A large dialog is displayed containing a filtered element map at the top, a list of elements and thresholds in the middle, and the corresponding phase map, which is initially empty, at the bottom. On the right are sliders to change the thresholds, buttons to update and clear thresholds for the current element, and a text box to enter the phase name.
Select an element of interest, such as Na, in the list control in the middle. The filtered Na element map is displayed at the top.
The initial values of the sliders are set to reflect the minimum and maximum values in the filtered element map. Hence the initial thresholds are at the extremes of the values shown and no pixels are removed by this thresholding.
Move the slider for the Lower threshold upwards until it is about 100. Now pixels with values less than 100 are removed from the filtered element map plot at the top of the screen.
Similarly, move the slider for the Upper threshold downwards until it is about 600. Pixels above this threshold are removed from the plot.
Whenever either threshold is moved, the colourmap limits are updated to reflect the change so that the whole colourmap is used to display the remaining pixels.
Click on the Update button to update the thresholds for this element in the list in the middle of the dialog. The phase map at the bottom will be updated.
Thresholds can be applied to more than one element, and the phase map comprises those pixels that are within the thresholds of all elements of interest.
Enter a name for this phase map and click on the OK button.
The new phase map is added to the list in the Phases tab and it is automatically selected so that it is displayed on the right.

Display element map using a phase map

Select, for example, the Normalised tab and click on an element, and select Map and histogram in the Plot type dropdown box.
The element map and its histogram are displayed on the right, and the statistics at the bottom of the application window refer to the entire element map.
In the Phase dropdown box at the top, select one of the newly created phase maps.
The element map and its histogram on the right and the statistics at the bottom of the application window are updated to refer to only those pixels that are in the selected phase map.