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Overview
References:
List of journal references
Downloads:
Images and tools
Lesson
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Images:
MER_RR_2COLRA 200402~.N1 Description
Useful information:
The Benguela Current System
The MERIS product grid.
MERIS level 2 flags
Bitwise operators and Meris flags
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In this section you will investigate the relationship between the algal_1 pigment index (chlorophyll) and fluorescence line height (FLH).
FLH is an indicator of solar induced chlorophyll fluorescence, an is expected to increase as chlorophyll concentration increases.
However, the relationship is not necessarily straight forward for a number of reasons:
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Fluorescence yield depends not just on the amount of chlorophyll, present, but also on the intensity of the sunlight.
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Fluorescence may vary with species assemblage, nutrient availability and the general state of 'health' of the plankton in a bloom.
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The absorption coefficient of water is high in the red, so if the plankton are found relatively deep in the water, the radiance due to chlorophyll fluorescence may be absorbed by the water before it reaches the surface.
Never-the-less, FLH may be a useful indicator of chlorophyll, and the MERIS channels 7, 8 and 9 were chosen so as to provide a measure
of the chlorophyll fluorescence peak. We may therefore expect FLH and chlorophyll concentration to be correlated in some way.
Before you carry out the calculations, however, it makes sense to create a bit-mask,
which may be used to mask the output of formulae used to calculate FLH and chlorophyll, and may also be used to mask multiple bands in one go.
Creating a bit-mask
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Activity / Question 1
Open the two formulae mer2water_a1b.frm and mer2water_a1b_create_mask.frm;
use Windows > Tile Horizontal to see both at the same time.
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a) |
What is the main difference between the one you used in the previous section, and the one to create the mask?
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b) |
What type of image will the new formula produce? What numerical format would you use to save this mask?
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This type of image, consisting of either 0 or 1, could be saved in one bit, and is therefore known as a bit-mask.
A bit-mask may easily be used to remove invalid data from any type of image, regardless of numerical format,
simply by multiplying the image plane containing the original data by the image plane containing the mask. We can take advantage of
this by calculating FLH and masking the result of the calculations in one go.
Open the bands included in the formula, and connect them into a stack, with a blank to take the new mask.
Activate the formula and select Options! from the menu bar; set the output to 8-bit integer,
and uncheck the special handling of nulls check box.
Copy and paste the formula onto the stack to create the mask, and save the mask as mer_20040201_a1b_mask.dat.
Repeat the procedure with the formula mer2water_create_mask.frm to create a bit-mask to select pixels
classified as water only. Save this mask as mer_20040201_watermask.dat
Calculating FLH
For MERIS fluorescence line height (FLH) is defined by the following relationship:
where λ1, λ3 is the fluorescence spectral range, i.e. the bands immediately outside the fluorescence peak, MERIS bands 7 and 9;
λ2 is the fluorescence emission band (band 8); L2, L3 is the radiance of the baseline, and
L2 is the radiance in the fluorescence band.
By using reflectances instead of radiances, we will to some extent compensate for the relationship between fluorescence and incident light;
thus making it likely that the calculated FLH will correlate more strongly with chlorophyll.
Open the reflectance bands 7, 8 and 9, and connect them into a stack with the bitmask mer_20040201_watermask.dat,
and a blank to the FLH.
Open the formula flh.frm and check that all the image planes are in the order described in the formula.
In Options! set the output to 32-bit float, and uncheck 'Use special handling for nulls';
then copy and paste the formula onto the stack to calculate FLH, and save the new image as mer_20040201_flh_w.dat
Close the stack and reopen the FLH image you just saved, choosing a suitable Redisplay stretch.
It is very important not to try a Redisplay stretch until the stack has been closed.
The reason for this is that the stack contains a mixture of numerical formats, the mask is 8-bit integer, the reflectances
16-bit and the FLH 32-bit float. If you try a Redisplay stretch for the FLOAT image, Bilko will attempt to
apply this also to the other data in the set, fail to achieve this, and crash.
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Question 2
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a) |
How does the bloom appear in the FLH image?
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b) |
Based on this result, would you consider using FLH as a quality control
criterion alongside the flags to mask pixels of doubtful quality?
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Calculating chlorophyll concentrations
The algal_1 data has been saved as 8-bit integer data. The relationship between these numerical values and the chlorophyll concentrations may be found in the 'properties' of this data set, which you can open by right-clicking on the algal_1 folder in right frame of the N1 file structure window. (Note that you cannot have the algal_1 data opened as an image when you do this.)
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