[NeXus-tech] cbf2nx in contrib

Mon Oct 3 16:40:05 BST 2011

Hi all,

I've just had a play with the cbf2nx tool in contrib. Please fine the file structure it created below.

The initial NXentry is the only recognizable feature. All the rest seems to be a CBF file embedded in HDF5.

Herb Bernstein sees it like that as well: http://scripts.iucr.org/pipermail/imgcif-l/2011-October/000292.html

In the email he makes the point that there is 'no agreed statement of the representation of a PX experiment in NeXus'. The people using CBF here tend to support that view. CBF has more stringent rules and an API that you can query for useful scientific properties of your detectors (like: Where is this detector pixel in hkl space?). That would be very difficult to do in NeXus with the multiple routes you can pursue to define the instrument's geometry.

I'm trying to get our guys to work out a reasonable mapping between CBF and NeXus (and back under certain conditions maybe). But in that exercise cbf2nx is of no help whatsoever.

I'm not too happy with it in the repository, even in contrib, in the current state. Someone might mistake the output as a NeXus file, because is implied by the name and environment it is found in. What's your view?

Regards,

Tobias

$ ./cbf2nx -e 5 example.cbf convertedcbffile.nxs
$ nxdir -p . --path-mode both convertedcbffile.nxs
/image_1:NXentry/
/image_1:NXentry/array_data:category/
/image_1:NXentry/array_data:category/array_id:column/
/image_1:NXentry/array_data:category/array_id:column/data:SDS[7]
/image_1:NXentry/array_data:category/array_id:column/data:SDS#items:ATTR
/image_1:NXentry/array_data:category/binary_id:column/
/image_1:NXentry/array_data:category/binary_id:column/data:SDS[1]
/image_1:NXentry/array_data:category/binary_id:column/data:SDS#items:ATTR
/image_1:NXentry/array_data:category/data:column/
/image_1:NXentry/array_data:category/data:column/data:SDS[3072,3072]
/image_1:NXentry/array_data:category/data:column/data:SDS#NXcifarraybyteorder:ATTR
/image_1:NXentry/array_data:category/data:column/data:SDS#NXcifarrayelementsign:ATTR
/image_1:NXentry/array_data:category/data:column/data:SDS#NXcifarrayelementsize:ATTR
/image_1:NXentry/array_data:category/data:column/data:SDS#NXcifarrayelementtype:ATTR
/image_1:NXentry/array_data:category/data:column/data:SDS#NXciftype:ATTR
/image_1:NXentry/array_data:category/data:column/data:SDS#items:ATTR
/image_1:NXentry/array_element_size:category/
/image_1:NXentry/array_element_size:category/array_id:column/
/image_1:NXentry/array_element_size:category/array_id:column/data:SDS[15]
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/image_1:NXentry/array_element_size:category/index:column/
/image_1:NXentry/array_element_size:category/index:column/data:SDS[3]
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/image_1:NXentry/array_element_size:category/size:column/
/image_1:NXentry/array_element_size:category/size:column/data:SDS[21]
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/image_1:NXentry/array_intensities:category/
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/image_1:NXentry/array_intensities:category/binary_id:column/
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/image_1:NXentry/array_intensities:category/gain:column/
/image_1:NXentry/array_intensities:category/gain:column/data:SDS[4]
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/image_1:NXentry/array_intensities:category/linearity:column/
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/image_1:NXentry/array_intensities:category/pixel_fast_bin_size:column/
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/image_1:NXentry/array_intensities:category/pixel_slow_bin_size:column/data:SDS[1]
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/image_1:NXentry/array_intensities:category/undefined_value:column/
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/image_1:NXentry/array_intensities:category/undefined_value:column/data:SDS#items:ATTR
/image_1:NXentry/array_structure_list:category/
/image_1:NXentry/array_structure_list:category/array_id:column/
/image_1:NXentry/array_structure_list:category/array_id:column/data:SDS[15]
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/image_1:NXentry/array_structure_list:category/axis_set_id:column/
/image_1:NXentry/array_structure_list:category/axis_set_id:column/data:SDS[19]
/image_1:NXentry/array_structure_list:category/axis_set_id:column/data:SDS#items:ATTR
/image_1:NXentry/array_structure_list:category/dimension:column/
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/image_1:NXentry/array_structure_list_axis:category/
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/image_1:NXentry/array_structure_list_axis:category/axis_id:column/data:SDS[19]
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/image_1:NXentry/array_structure_list_axis:category/axis_set_id:column/
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/image_1:NXentry/diffrn_scan_frame_axis:category/
/image_1:NXentry/diffrn_scan_frame_axis:category/angle:column/
/image_1:NXentry/diffrn_scan_frame_axis:category/angle:column/data:SDS[24]
/image_1:NXentry/diffrn_scan_frame_axis:category/angle:column/data:SDS#items:ATTR
/image_1:NXentry/diffrn_scan_frame_axis:category/axis_id:column/
/image_1:NXentry/diffrn_scan_frame_axis:category/axis_id:column/data:SDS[62]
/image_1:NXentry/diffrn_scan_frame_axis:category/axis_id:column/data:SDS#items:ATTR
/image_1:NXentry/diffrn_scan_frame_axis:category/displacement:column/
/image_1:NXentry/diffrn_scan_frame_axis:category/displacement:column/data:SDS[26]
/image_1:NXentry/diffrn_scan_frame_axis:category/displacement:column/data:SDS#items:ATTR
/image_1:NXentry/diffrn_scan_frame_axis:category/frame_id:column/
/image_1:NXentry/diffrn_scan_frame_axis:category/frame_id:column/data:SDS[34]
/image_1:NXentry/diffrn_scan_frame_axis:category/frame_id:column/data:SDS#items:ATTR
/image_1:NXentry/diffrn_source:category/
/image_1:NXentry/diffrn_source:category/diffrn_id:column/
/image_1:NXentry/diffrn_source:category/diffrn_id:column/data:SDS[3]
/image_1:NXentry/diffrn_source:category/diffrn_id:column/data:SDS#items:ATTR
/image_1:NXentry/diffrn_source:category/source:column/
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/image_1:NXentry/diffrn_source:category/source:column/data:SDS#items:ATTR
/image_1:NXentry/diffrn_source:category/type:column/
/image_1:NXentry/diffrn_source:category/type:column/data:SDS[21]
/image_1:NXentry/diffrn_source:category/type:column/data:SDS#items:ATTR

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