Satellite Data Visualization

Choose a polygon

(Optional) Enter a name (use only alphanumeric characters, underscores, or periods) and click "Apply".

Choose the method to create your polygon.

Draw polygon on map

Type coordinates

Load shapefile

Draw polygon using the toolbar at the top left corner of the map.

Enter decimal latitudes and longitudes for vertices of polygon, separated by commas, then click "Create polygon". Use lon/lat < 0 for west/south. Lists must be the same length, with >2 values each, in the same order so that each latitude is paired with longitude.

Click "Browse" to find a shapefile. Select the "shp" file and all files with the same name but different extensions (e.g. dbf, prj, sbx...), then "Open". Shapefile must contain a Simple Features (sf) object. If the sf contains multiple polygons, a button will appear below to select the polygon you want to use. WARNING: polygons with a large number of vertices may take several seconds to load.

Browse...

List of latitudes:

List of longitudes:

Minimum % coverage.
Composites with lower coverage in the selected polygon will not be plotted on the density plot or time series, or used in the model fit.

Outlier detection method
SD = standard deviation
IQR = interquartile range

Statistic
Calculate either the mean or median value of each composite, to be used in the time series and model fit.

Range of pixel values
Choose the range of values allowed in the calculation of the statistics and model fit (pixels outside this range will be omitted).
If a limit is left blank, it will be ignored.

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Fit a model to the points on the time series.
Choose fit method, model shape, and point smoothing method.

LOESS span
Controls the degree of smoothing.

Set the range of days to use in the model fit, and the limits of the day of peak amplitude and the first day of the bloom.

t_range

t_max

t_start

Select the method used to calculate t_start :
Either a percentage of the curve amplitude between 0.01 and 90 (peak minus background), or a constant threshold between 0.01 and 5 (difference between the fitted curve and background value, calculated in linear space).

% amplitude

Constant threshold

Set % curve amplitude to mark start of bloom.

Set increase over background to mark start of bloom.

Switch to ON to consider t_{max_fit} a parameter in the regression.
WARNING: This will disable t_start limits.

Switch to ON to allow background values to vary linearly as a function of day.

Switch to ON to weight each point in the time series by percent coverage.

When calculating magnitude (area under the curve between t_start and t_end) and amplitude of the curve, should the background be removed first?

Remove background

Flags
Fits will be flagged if they meet certain criteria that indicate potential problems with the fit (NOTE: this does not affect the fit itself). Combinations of flags will be written as a single number (for example, 13 for flags 1 and 3). Click below for details. Optionally adjust the parameters of some flags.

Flag 1: Amplitude ratio limits

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Flag 2: Magnitude ratio limits

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Threshold coefficient
The start of the phytoplankton bloom is considered to be the point before t_max when [chla] drops below a threshold for > 14 days.
Threshold = chla_median * threshold coefficient

NOTE: If you opted to log the data when loading, chla_median is calculated by taking the median of the logged data and transforming it back to linear space to compute the threshold. The threshold itself is then logged again to determine the bloom initiation.

Time series
Select a series of years and the polygons you would like to process using the current settings, then click "Run time series" to generate the following:

time series plots (.png),

tables of statistics (.csv),

a single .csv file containing the fitted parameters for all selected years and polygons, and

a .csv file containing the settings used for the time series, for reference.

Files will be zipped to a folder following the naming convention satellite_ region_ compositeLength_ years_ cellSizes_ variable_ fitmethod_ timecreated.
Make sure at least one polygon is selected.
When processing is complete and the new filename appears over the download button, click "Download results (.zip)".

Select your polygons

Download results (.zip)

Save settings (.txt)