Export 5-band orthomosaic from RedEdge-MX

[mchape]

Hi,

I am using Agisoft Metashape to stitch the MicaSense RedEdge-MX sample data, from the complete flight, which is in link 1.

To do this I follow the MicaSense RedEdge MX processing workflow in Agisoft Metashape(see link 2) . It seems to work find and I obtain the orthomosaic and DEM.

But when I export them as a .tiff to precess them in QGIS, the orthomosaic seems to be corrupted, and what I visualize is something the attached image(somethign like the noise in old TVs). However the DEM seems to be exported correctly.

I wanted to export a 5-band orthomosaic where I have the info of the 5 band bands all together in one archive. Any suggestions on what could be wrong?

Thanks in advance,


Link 1: https://www.micasense.com/rededge-mx-sample-data
Link 2: https://agisoft.freshdesk.com/support/solutions/articles/31000148780-micasense-rededge-mx-processing-workflow-including-reflectance-calibration-in-agisoft-metashape-pro

[Alexey Pasumansky]

Hello mchape,

Which version of Metashape you are using? Can you also provide the export settings used for orthomosaic and a PDF report generated from the corresponding project?

[mchape]

Hi Alexey,

I am using version 1.5.2.

I am using the predefined export settings.  See the attach image and the pdf report.

Best regards,
Miguel

[Paulo]

Miguel.

I processed the same data set with Metashape 1.5.3...generated a OrthoMosaic and exported to tif (5 bands + alpha channel Transparency)...

It shows correctly in Global mapper RGB as Band 3, Band 2, Band 1 same as in Metashape...

Must be a bug displaying multiband imagery (16 bit per band) in QGIS....

In second Screen copy (attached in next message), I used raster calculator to create false color CIR composite with:

•   B1 as NIR B5
•   B2 as RED B3
•   B3 as GREEN B2

In Global mapper same composite CIR was created using Raster Calculator tool...

[Paulo]

CIR screen capture example

[mchape]

Hi Paulo,

Thanks for your answer. You are right, I can also see the orthomosaic correctly in Global Mapper. So the problem must be within QGIS.

Any idea if it is possible to solve this?

Best reagrds,
MIguel

[mchape]

I can see in the histogram that I have a band 6(light blue) which I do not know it comes from, in my exported image. The histogram with the correct values correspond to the 5-band orthomosaic from MicaSense Sample Data.See the images.

I tried by just setting the values of the corrspondent band, but still the image is with a lot of noise.

The question now is, if this sixth band is something that QGIS add, because a bug, or it is something that I add in MetaShape, and how can I remove it.

And since in Global Mapper it does not appear I would bet is something QGIS adds. But I also tried with different QGIS version and this still the same.

[Paulo]

Mchape,

when you export your 5 band orthoMosaic with Write Alpha Channel option on, then Metashape will create a 6 band ortho tif with 5 original bands (B, G, R, RE and NIR) plus alpha band that represents transparency (all values within ortho imagery boundary equal to 65535).

So in QGIS maybe you have to specify this band 6 as transparent .....

[mchape]

Seems that without adding the alpha channel, QGIS handles it correctly. Moreover I normalized the image before, dividing each band by 32768, as they explain in the link: https://agisoft.freshdesk.com/support/solutions/articles/31000148780-micasense-rededge-mx-processing-workflow-including-reflectance-calibration-in-agisoft-metashape-pro

The only thing, is  that I had to set up a brightes value in QGIS in order to see the image correctly. See the images. I don't know if that could mean that calibration was made wrong.

[mchape]

This is the raw image, with bright 0 in QGIS.

[Paulo]

Yes , in my examples I didn't perform reflectance calibration....

But it does affect brightness as when you do calibrate in Metashape, you have to bump up brightness to about 1200 % to see images ....

[mchape]

I had to do the same. Have you work before with RedEdge imagery? Is this a common issue with the RedEdge in Metashape or just with this sample images?

Thanks for all you response, they are very helpful.

[Paulo]

I have not done much work on Micasense apart from demo set....Maybe others can help on this......