[Chimera-users] import binary format .raw file

Tom Goddard goddard at sonic.net
Mon Dec 16 10:24:49 PST 2013


Hi Carol,

  I think your best approach is to convert your raw EM map data to another file format that contains a header with the size of the map, value type, byte order, grid plane spacing.  The problem with the raw data is that it cannot be interpreted without specifying additional parameters like the grid size.  Chimera currently doesn't have a method to ask the user for extra information about how to interpret data in a file.  So it isn't a simple matter to add a file format.  Data in raw format is likely to become worthless very quickly when no one remembers the extra parameters, so I strongly encourage avoiding raw format.  I don't know of a program to recommend to convert raw data, but since you generated the data somehow, maybe the program you used can export a more usable file format.

	Tom


On Dec 14, 2013, at 3:47 PM, Carol J Hirschmugl wrote:

> Hello, 
> 
> I am new to chimera, but have seen its capabilities for rendering 3D images of complex data sets, 
> and  think that this will be an appropriate program for excellent image analysis for my 3D tomography data sets. 
> 
> My data sets are in general binary format, (.raw file), 32 float, big endian, x fastest order for an x,y,z 
> data set of 128 x 128 x 128 voxels of grey scale information.   I am using AVIZO and FIJI at present.  Avizo 
> is expensive, and fiji is slow and reduces the data to 8 bit before rendering it, which I find unacceptable. 
> 
> TO move to Chimera - I found the web page in the Users Manual that suggested  
> ADDING A FILE TYPE
> 
> But I am lost by the description of how to proceed since I do not have prior knowledge of python and how to do the mapping to CHIMERA (x,y,z) that is suggested.   
> I gather  I need to write a python code - or numpy code maybe. Can you help or provide more context or a self-tutorial link so I can fill in the details?  
> 
> Thank you, 
> Carol
> 
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