I have exactly the same problem on Ubuntu 10.10 with hugin 2010.0.0.5045
and enblend 4.0-753b534c819d

I tried the tiff ouput workaround. Yet I still have the black
rectangles.

Here is an extract of my .pto file for detailed configuration:

# hugin project file
#hugin_ptoversion 2
p f2 w15000 h1364 v176  E16.548 R0 S404,14224,76,1277 n"TIFF_m c:LZW r:CROP"
m g1 i0 f0 m2 p0.00784314

%%% skipped image and control points data

#hugin_optimizeReferenceImage 0
#hugin_blender enblend
#hugin_remapper nona
#hugin_enblendOptions 
#hugin_enfuseOptions 
#hugin_hdrmergeOptions -m avg -c
#hugin_outputLDRBlended false
#hugin_outputLDRLayers false
#hugin_outputLDRExposureRemapped false
#hugin_outputLDRExposureLayers false
#hugin_outputLDRExposureBlended false
#hugin_outputLDRExposureLayersFused false
#hugin_outputHDRBlended true
#hugin_outputHDRLayers false
#hugin_outputHDRStacks false
#hugin_outputLayersCompression PACKBITS
#hugin_outputImageType tif
#hugin_outputImageTypeCompression LZW
#hugin_outputJPEGQuality 100
#hugin_outputImageTypeHDR tif
#hugin_outputImageTypeHDRCompression LZW


Maybe there is something wrong with this. Otherwise I can give a light version 
of the full project.

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https://bugs.launchpad.net/bugs/678694

Title:
  EXR files quietly clipped (black rectangles in output)

Status in Hugin - Panorama Tools GUI:
  Confirmed

Bug description:
  The EXR file format has a maximum encoding value of 65504.   The Hugin data 
flow maintains the absolute exposure through use of the Ev field which 
effectively scales pixel values.   When using Hugin/Nona on an HDR series that 
includes very bright elements (such as a very bright sky with a very short 
exposure), some pixels end up with values above 65504.   When these are written 
out by Nona, those pixels are written as NaN's in the EXR output file. 

If enblend is then used, the problem is further exacerbated.   A single NaN 
pixel results in NaN for entire rectangle of enblend's pyramids.   The end 
result are large black rectangles in the output file.

If output is changed to TIFF, then everything works fine.

Nona should warn when clipping occurs and then output the maximum possible 
value rather than a NaN.   I assume this is the OpenEXR library itself and 
probably affects other applications.   In fact, if a TIFF generated as above is 
opened in PhotoShop, it looks fine, but if it is resaved as EXR, the same NaN 
pixels are created.



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