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Chlorophyll Data - Printable Version

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Chlorophyll Data - Sandy - 2019-01-11


I was wondering if there is any way to extract numerical data on chlorophyll concentration?


RE: Chlorophyll Data - Sylvain Herlédan - 2019-01-11

Hi Sandy,

Syntool doesn't have access to the geophysical data (it only loads pre-processed images), so extracting the numerical data is quite difficult.

There is a way to get very approximative results, but it is a rather convoluted solution to get hardly usable results. Please note that the values you obtain using this method are not suitable for analysis or any research work:
  1. click on the cholorophyll concentration granule on the map, a side panel will open and show the min and max values we used when we generated the image. Note these values.
  2. open the processing tools menu (either with the cogwheel button in the top bar or with the Shift+T shortcut)
  3. in this menu select the ".npy" tab
  4. draw an area on the map (keep the Shift key pressed while selecting the area with the mouse using drag'n'drop, or enter the coordinates in the form)
  5. click on the "Execute" button, after a few seconds a dialog will open and provide a link to the extracted data
  6. download the extracted file and save it on your computer
  7. open a Python console and execute the code below (replace MIN and MAX by the values you noted at step 1 and the path to the extracted file)
    import numpy
    packed_data = numpy.load('PATH_TO_YOUR_NPY_FILE')
    logmin = numpy.log(MIN)
    logmax = numpy.log(MAX)
    logscale_data = logmin + packed_data * (logmax - logmin) / 254.0
    linscale_data = numpy.exp(logscale_data)

    # linscale_data should contains numerical values in mg.mm-3

It is definitely easier to get the original data from the OceanColour website or from the PODAAC.