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Phase Tool

Phase Tool Tutorial

This tool is for combining elemental images into phases or components.  The tool shows a list of  phases, or a list of maps for the selected phase, depending on the Showing Phases / Showing Maps button, which changes when you click it.  Selected phase or map is in RED.

Note:  NOT Map capability is now available when editing thresholds.  The dialog presented by the 'Edit Threshold' button has a 'Continue' choice as always, and a new 'Not Map' choice.  If this button is clicked, the thresholds will appear as negative, indicating that the NOT map is to be used, which is whatever is NOT red in the thresholded image, i.e., pixels with levels not between the thresholds.  The Results Button, and the %-area column in the list of maps will reflect the change to using a NOT map.



Summary of Use

Open The Phase Tool

Continue adding phases and maps as desired.  Note that:

You can use Results / Show Combined Phase Maps at any time.  The second image shows overlapping pixels and the third (red arrow), unused pixels.  The second or third images are masks that can be used with the PPP tool to get spectra for these pixels.


Setup / Print Map Usage lists the maps and what phases use them.  This makes it easy to spot elemental images that have not yet been used:


Setup / Print Unused Map % Intensities first asks you to click on the unused pixel mask to put it in front, and then lists the percentage of summed pixel intensities in each elemental image that overlaps the unused pixel mask.  This will work for any mask, but for the unused pixel mask in particular, it in effect lists the percentage of counts that are not yet accounted for, for each elemental image.  For example, the high percentages for Ni and Ca below may indicate as-yet unspecified phases.


Setup / Print Thresholded Map vs Phase Percents again asks you first to click on the unused pixel map, and then prints a table listing the phases, and maps for each phase.  For each map, it gives the map name, thresholds values, a percentage of the thresholded (red - i.e. selected for that particular phase) pixels for the map that overlap the zero use mask, and percentages of the thresholded pixels that overlap each of the phases.

Sometimes, the columns don't line up quite right, but they will if you copy and paste (or save and load) the table into a spreadsheet program.

This table might help spot errors in the thresholds for each phase. 

Note that in this case, none of the maps have any thresholded pixels that are not used, because there is only one map used for each phase, so all of the pixels for the map have to be used.  If two maps were used for a phase, then any pixels that were not thresholded in both maps would not be used in the phase.

Also note the diagonal line of 100%'s (I colored these in Excel* by hand) shows that each map shows up entirely in its own phase.  The Al map, used for Phase-04 also happens to half way overlap Phase-03.  To investigate this, I made a color overlay of Phase-03 (green) and thresholded Aluminum (red & blue) with these steps:

  1. Selected Phase-03 in the tool and made a mask of the phase with Results / Show Mask of Selected Phase
  2. Selected the Al map in Phase-04, clicked Edit Threshold, then made a mask of the thresholded map using Thresholds / Make Mask in the Threshold Slider.
  3. Combined the mask from step 1 - in green, with the mask from step 2 - in red and blue, into an RGB overlay using the 2 & 3 Variable Tool


Phase-03 - green

Thresholded Al - red & blue

Color phase map.

Phase-03 is green.

The thresholded Aluminum pixels are either white or magenta in the left map above.  The magenta pixels are the Al pixels that have not been used in any phase.  Note that 52% of the thresholded Al pixels overlap Phase-03, which means 48% are unused.  From the Percent Summed Intensities table above, 4.72% of the Aluminum counts are not yet used.  The difference of a factor of ten between the 48% and 4.72% is because the 48% is of the thresholded pixels, which are only 14.7% of the map:

while the 4.72% is of the summed intensities for the entire map, which is not insignificant in the non-thresholded pixels - what might be considered "background" pixels.

The white pixels in the left map are those that overlap Phase-03.  Inspection shows that these are part of, and account for most of the white (overlap) pixels in the color phase map on the right.  The white pixels in the right map are pixels of any phase that overlap any other phase.

Setup / Print Tool lists the Phases and the maps for each phase, for documentation.  This is the table within Lispix:

And this is the same table after copying and pasting into a spreadsheet program that imports text tab-delimited files: