[Chimera-users] reading in hdf5 files in chimera

[Thomas Goddard]

Hi Josh,

   If you open a file in Chimera with suffix *.hdf or *.h5 then it will 
be interpreted as an EMAN HDF file.  EMAN is a single particle analysis 
package that requires a very specific format for the data.  The "Chimera 
map" file format (suffix *.cmap or *.cmp) is also HDF and it attempts to 
find any 3-d arrays in your hdf file.  You should try using the Chimera 
map format.  Either change the suffix on your file name or use the "all 
(ask type)" file type option in the File Open dialog.

	Tom


Example of HDF format written by Chimera (Chimera map format) follows. 
Chimera map file reader will allow all fields to be missing (except the 
3d data).

#  /image (group, any name allowed)
#    name "centriole" (attribute)
#    step (1.2, 1.2, 1.2) (attribute)
#    origin (-123.4, -522, 34.5) (attribute)
#    cell_angles (90.0, 90.0, 90.0) (attribute)
#    rotation_axis (0.0, 0.0, 1.0) (attribute)
#    rotation_angle 45.0 (attribute, degrees)
#    /data (3d array of uint8 (123,542,82)) (dataset, any name allowed)
#    /data_x (3d array of uint8 (123,542,82), alternate chunk shape) 
(dataset, any name allowed)
#    /data_2 (3d array of uint8 (61,271,41)) (dataset, any name allowed)
#        subsample_spacing (2, 2, 2) (attribute)
#    (more subsampled or alternate chunkshape versions of same data)


Example of HDF format written by EMAN (2d micrograph example):

# Example EMAN micrograph micrograph_616003.hdf file layout.
# Command: h5dump -A micrograph_616003.hdf
#
# /MDF (group)
#  /images (group)
#    image_id_max 0 (attribute)
#    /0
#      EMAN.HostEndian "little" (attribute)
#      EMAN.ImageEndian "big"
#      EMAN.apix_x 1  ("EMAN." is part of attribute name).
#      EMAN.apix_y 1
#      EMAN.apix_z 1
#      EMAN.is_complex 0
#      EMAN.is_complex_ri 1
#      EMAN.is_complex_x 0
#      EMAN.maximum 0.315815
#      EMAN.mean 0.189981
#      EMAN.mean_nonzero 0.189981
#      EMAN.minimum -0.704721
#      EMAN.nx 2916
#      EMAN.ny 4374
#      EMAN.nz 1
#      EMAN.sigma 0.0325618
#      EMAN.sigma_nonzero 0.0325618
#      EMAN.square_sum 473871
#      image (2d array of floats (2916,4374)) (dataset)


Joshua Turner wrote:
> Hi,
> 
> I have created a 3D hdf5 file and am having trouble displaying it in 
> Chimera. Is there something specific chimera looks for that it needs to 
> read in the .h5 file, to be able to display the file? Thanks,
> 
> Josh
>