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I downloaded the MODIS level 2 data for precipitable water vapor (MOD05_L2.A2015193.1535.006.2015194020321.hdf) and the corresponding geolocation file (MOD03.A2015193.1535.006.2015193213734.hdf). When viewed in Panopoly the Water_Vapor_Infrared field is of type Geo2D and I can plot it on a map. However, the Water_Vapor_Near_Infrared is labelled as type 2D and can't be projected onto a map. I Downloaded the ModisSwath tool and reprojected the MOD05_L2.A2015193.1535.006.2015194020321.hdf using the geolocation file MOD03.A2015193.1535.006.2015193213734.hdf which seems to have worked. But when I look at the reprojected data in Panoply it is still only 2D!

How do I convert the Water_Vapor_Near_Infrared data so that it can be projected onto a map? Is there a specific setting I need to use in the ModisSwath tool or is there a way to do it straight from Panoply (I've also tried it in a few other programs like SeaDAS with no luck).

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This is not a full answer to the question. It answers specifically how to render Water Vapor Near Infrared retrievals data on a map.

How do I convert the Water_Vapor_Near_Infrared data so that it can be projected onto a map?

If you look at the Metadata included in the MOD05_L2 product you would notice that there is a difference here.

Water Vapor Infrared retrievals are specified on a swath with a 5km reference pixel size. Geolocation is included in the MOD05 product.

    OBJECT=DataField_9
            DataFieldName="Water_Vapor_Infrared"
            DataType=DFNT_INT16
            DimList=("Cell_Along_Swath_5km","Cell_Across_Swath_5km")
    END_OBJECT=DataField_9

Water Vapor Near Infrared are provided on a swath with a 1km reference pixel size. The locations of the 1km pixels are included in the MOD03 product.

    OBJECT=DataField_7
            DataFieldName="Water_Vapor_Near_Infrared"
            DataType=DFNT_INT16
            DimList=("Cell_Along_Swath_1km","Cell_Across_Swath_1km")
    END_OBJECT=DataField_7

Unfortunately there is no way to tell Panoply to use Geolocation fields from a separate file.

Reprojection with MODIS Swath Tool would not help either to convert the data into a format recognizable by Panoply, since it does reproject the data onto a regular grid, but Panoply cannot understand this either. However any GIS tool such as QGIS would be able to read and display the reprojected file.

MOD05 Water Vapor NIR retrievals

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