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C2R processor
C2R processor
8/7/11 10:57 AM
Hello BEAM team

I am trying to use the Regional Case-2 processor in BEAM 4.9.

I could not understand how to determine the conversion factors and exponents (for TSM & CHL) to be used.

Or, should I use the default values that appear in the boxes? what is the scope of differences in the results?

regarding the Input - should I use a native L1b image? or after radiometry correction? radiance or reflectance?

Thank you for your time and effort

Best Regards,
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RE: C2R processor
8/9/11 3:53 PM as a reply to Tomer Ketter.
Hello Tomer,

The conversion factors for TSM and CHL are dependent on the neural net. You should keep the default values.
We observed that using radiometric correction operator improves the results. Use the Smile effect correction and the Equalisation.
If you want to use a special atmospheric correction algorithm you should start from reflectance. But if you don't have such a special algorithm you should start from radiances.

best wishes
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RE: C2R processor
8/14/11 10:23 AM as a reply to Marco Peters.
Dear Marco,

What is the relation between ALGAL 2 INDEX and C2R processor algorithm?

Whom can I contact for more information regarding the TSM & CHL conversion factors?

How can I regionally calibrate C2R for my study area?

I hope its not too many questions for one message....
Thanks again for your time!

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RE: C2R processor
8/15/11 10:25 AM as a reply to Tomer Ketter.
Hello Tomer,

you should contact Roland Doerffer. He is responsible for the scientific part of the processor.
roland DOT doerffer AT hzg DOT de

best wishes
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RE: C2R processor
8/28/11 9:05 AM as a reply to Marco Peters.
Hi Marco!
I already wrote to Roland and he helped me alot.

now after using the C2R processor i export the chl_conc layer to geo-tiff (see attached file). original values are 0 to 40 approx.

after doing so, i import this product into ArcGis but i get completely different pixel values.

is this a known issue?

after importing into ArcGis, I plan to extract pixel values from the GeoTiff using a n-8 mask based on a point shapefile.
Is there a way to do this in BEAM? maybe i could save all the trouble..

thanks again,
Attachments: MER_FRS_1PNPDE20110822_081739_000001913105_00409_49561_1283.N1.zip (1,895.5k)
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RE: C2R processor
8/31/11 10:46 AM as a reply to Tomer Ketter.
For extracting pixels you can use the gpt command line tool you find in the bin directory of your BEAM installation.

 2  gpt PixEx [options]
 5  Extracts pixels from given locations and source products.
 7Computed Properties:
 8PixExMeasurementReader measurements
11Parameter Options:
12  -PcoordinatesFile=<file>              Path to a file containing geo-coordinates. BEAM's placemark files can be used.
13  -PexportBands=<boolean>               Specifies if bands are to be exported
14                                        Default value is 'true'.
15  -PexportExpressionResult=<boolean>    If true, the expression result is exported per pixel, otherwise the expression
16                                        is used as filter (all pixels in given window must be valid).
17                                        Default value is 'true'.
18  -PexportKmz=<boolean>                 If set to true, a Google KMZ file will be created, which contains the coordinates where pixels are found.
19                                        Default value is 'false'.
20  -PexportMasks=<boolean>               Specifies if masks are to be exported
21                                        Default value is 'true'.
22  -PexportSubScenes=<boolean>           If set to true, sub-scenes of the regions, where pixels are found, are exported.
23                                        Default value is 'false'.
24  -PexportTiePoints=<boolean>           Specifies if tie-points are to be exported
25                                        Default value is 'true'.
26  -Pexpression=<string>                 Band maths expression (optional). Defines valid pixels.
27  -PinputPaths=<file,file,file,...>     The paths to be scanned for input products. May point to a single file or a directory.
28                                        If path ends with '**' the directory is scanned recursively.
29  -PoutputDir=<file>                    The output directory.
30                                        This is a mandatory parameter.
31  -PoutputFilePrefix=<string>           The prefix is used to name the output files.
32                                        Default value is 'pixEx'.
33  -PsubSceneBorderSize=<int>            An additional border around the region where pixels are found.
34                                        Default value is '0'.
35  -PtimeDifference=<string>             The acceptable time difference compared to the time given for a coordinate.
36                                        The format is a number followed by (D)ay, (H)our or (M)inute.
37                                        Default value is '1D'.
38  -PwindowSize=<integer>                Side length of surrounding window (uneven)
39                                        Default value is '1'.
41Graph XML Format:
42  <graph id="someGraphId">
43    <version>1.0</version>
44    <node id="someNodeId">
45      <operator>PixEx</operator>
46      <sources>
47        <sourceProducts>${sourceProducts}</sourceProducts>
48      </sources>
49      <parameters>
50        <inputPaths>file,file,file,...</inputPaths>
51        <exportBands>boolean</exportBands>
52        <exportTiePoints>boolean</exportTiePoints>
53        <exportMasks>boolean</exportMasks>
54        <coordinates>
55          <coordinate>
56            <name>string</name>
57            <latitude>float</latitude>
58            <longitude>float</longitude>
59            <dateTime>date</dateTime>
60          </coordinate>
61          <.../>
62        </coordinates>
63        <timeDifference>string</timeDifference>
64        <coordinatesFile>file</coordinatesFile>
65        <windowSize>integer</windowSize>
66        <outputDir>file</outputDir>
67        <outputFilePrefix>string</outputFilePrefix>
68        <expression>string</expression>
69        <exportExpressionResult>boolean</exportExpressionResult>
70        <exportSubScenes>boolean</exportSubScenes>
71        <subSceneBorderSize>int</subSceneBorderSize>
72        <exportKmz>boolean</exportKmz>
73      </parameters>
74    </node>
75  </graph>
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RE: C2R processor
9/5/11 11:39 AM as a reply to Ralf Quast.
Dear Ralf and Marco,
Thank you for the help so far.
still I couldnt find a way to export a proper geo-tiff with the real values.
please see the attached file from my previous message.
the problem is that in BEAM i can see real CHL-a values when using the C2R processor, but after exporting the band to geo-tiff, I open the product in other software but the pixel values are completely different.

Is there some built-In pixel-value-conversion in BEAM?

How can I replicate this in ArcGis or Global Mapper?

How can I export a 'true' geo-tiff?

Thank you again.

Best Regards,
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RE: C2R processor
Answer Answer (Unmark)
9/5/11 4:20 PM as a reply to Tomer Ketter.
Hello Tomer,

the GeoTiff export always writes the raw data values of band as stated in the help (Export GeoTIFF Product).
This means you need to scale the values before using them in other applications.
To find out how you have to scale the values you select the band and open the information tool view ().
There you can see that the scaling factor is 1.0 and the offset is 0.0 for chl_a, but the data is log10 scaled.

1Scaling factor:                    1.0
2Scaling offset:                    0.0
3Is log 10 scaled:                  true

This means you have to do Math.pow(10.0, value) before using the data.
In general the scaling method within BEAM looks like the following code snippet:
1public final double scale(double v) {
2    v = v * scalingFactor + scalingOffset;
3    if (log10Scaled) {
4        v = Math.pow(10.0, v);
5    }
6    return v;

You can also create a virtual band (via the 'Create Band by Band Maths...' action)
The resulting band will not be log scaled. Raw and geo-physical values will be the same.
By doing this you don't need to scale the values in ArcGis or Global Mapper.

best wishes
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