EM metadata dictionaries for EM software

[wmoore]

Try to identify the metadata attributes used by various EM software, to look for common attributes for OME data model, and how to convert between them.

• EMAN2 ​http://blake.bcm.edu/emanwiki/Eman2Metadata
• SPIDER file format ​http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html Not sure how to actually get the attributes from an image.

When EMAN2 reads a SPIDER image, it reads various Spider attributes but maintains them as clearly coming from SPIDER (same as MRC). Keeps these even if duplicated in EMAN2. E.g. 'SPIDER.nslice' and 'nz':

>>> from EMAN2 import *
>>> d = EMData()
>>> d.read_image("circ001.spi")
>>> display(d)
>>> dic = d.get_attr_dict()
>>> dic
{'changecount': 2, 'SPIDER.time': '05:1162:', 'minimum': 0.0, 'SPIDER.imgnum': 0, 'mean_nonzero': 1.0,
 'SPIDER.date': 'A-212-RP', 'SPIDER.angvalid': 0, 'SPIDER.reclen': 300, 'SPIDER.headrec': 4, 'apix_z': 1.0, 
'apix_y': 1.0, 'apix_x': 1.0, 'HostEndian': 'little', 'nx': 75, 'ny': 75, 'nz': 1, 'SPIDER.irec': 79.0,
 'sigma_nonzero': 0.0, 'is_complex_ri': 1, 'SPIDER.istack': 0, 'is_complex_x': 0, 'SPIDER.nslice': 1,
 'ImageEndian': 'big', 'SPIDER.type': 1, 'SPIDER.title': '1', 'SPIDER.dz': 0.0, 'SPIDER.dx': 0.0, 
'SPIDER.dy': 0.0, 'maximum': 1.0, 'SPIDER.headlen': 1200, 'datatype': 7, 'square_sum': 793.0, 'SPIDER.Kangle': 0,
 'is_complex': 0, 'sigma': 0.34802955389022827,
 'mean': 0.14097778499126434}

Can also use Spider to read SPIDER images and Headers in Python...

>>> from Spider.Spiderarray import * 
>>> dir(Spider.Spiderarray)
['Image', 'SpiderHeaderClass', '_HAS_NUMPY_', '__builtins__', '__doc__', '__file__', '__name__', 'array2image', 'array2spider', 'getSpiderHeader', 'image2array', 'makeSpiderHeader', 'numpy', 'spider2array', 'struct', 'sys']
>>> array = spider2array("circ001.dat")
>>> array
array([[ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       ..., 
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.],
       [ 0.,  0.,  0., ...,  0.,  0.,  0.]], dtype=float32)
>>> h = getSpiderHeader("circ001.dat")
>>> h
[1, 1.0, 75.0, 79.0, 0.0, 1.0, 1.0, 1.0, 0.0, 0.14097778499126434, 0.34802955389022827, 0.0, 75.0, 4.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1200.0, 300.0, 0.0, -1.0, 0.0, 0.0]
>>> for i in range(len(h)):
...     print i, h[i]
... 
#  see http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html
0 1			#
1 1.0		# NSLICE
2 75.0		# NROW
3 79.0		# IREC
4 0.0		# UNUSED
5 1.0
6 1.0
7 1.0		# FMAX
8 0.0		# FMIN
9 0.140977784991		# AV
10 0.34802955389		# SIG
11 0.0
12 75.0
13 4.0
14 0.0
15 0.0
16 0.0
17 0.0
18 0.0
19 0.0
20 0.0
21 0.0
22 1200.0
23 300.0
24 0.0
25 -1.0
26 0.0
27 0.0