Hello,
I'm a beginner with Pyable.
I wanted to store a database in a HDF5 file using PyTable. The DB is
made by a CSV file (which contains the subject information) and a lot of
images (I work on MRI so the images are 3 dimensional float32 arrays of
shape (121, 145, 121)). The relation is very simple: there are a 3
images per subject.
My first idea was to create a class Subject like this:
class Subject(tables.IsDescription):
# Subject information
Id = tables.UInt16Col()
...
Image = tables.Float32Col(shape=IMAGE_SIZE)
And the proceed like in the tutorial (open a file, create a group and a
table associated to the Subject class and then append data to this table).
Unfortunately I got an error when creating the table (even before
inserting data):
HDF5-DIAG: Error detected in HDF5 (1.8.4-patch1) thread 140612945950464:
#000: ../../../src/H5Ddeprec.c line 170 in H5Dcreate1(): unable to
create dataset
major: Dataset
minor: Unable to initialize object
#001: ../../../src/H5Dint.c line 428 in H5D_create_named(): unable to
create and link to dataset
major: Dataset
minor: Unable to initialize object
#002: ../../../src/H5L.c line 1639 in H5L_link_object(): unable to
create new link to object
major: Links
minor: Unable to initialize object
#003: ../../../src/H5L.c line 1862 in H5L_create_real(): can't insert
link
major: Symbol table
minor: Unable to insert object
#004: ../../../src/H5Gtraverse.c line 877 in H5G_traverse(): internal
path traversal failed
major: Symbol table
minor: Object not found
#005: ../../../src/H5Gtraverse.c line 703 in H5G_traverse_real():
traversal operator failed
major: Symbol table
minor: Callback failed
#006: ../../../src/H5L.c line 1685 in H5L_link_cb(): unable to create
object
major: Object header
minor: Unable to initialize object
#007: ../../../src/H5O.c line 2677 in H5O_obj_create(): unable to
open object
major: Object header
minor: Can't open object
#008: ../../../src/H5Doh.c line 296 in H5O_dset_create(): unable to
create dataset
major: Dataset
minor: Unable to initialize object
#009: ../../../src/H5Dint.c line 1034 in H5D_create(): can't update
the metadata cache
major: Dataset
minor: Unable to initialize object
#010: ../../../src/H5Dint.c line 799 in H5D_update_oh_info(): unable
to update new fill value header message
major: Dataset
minor: Unable to initialize object
#011: ../../../src/H5Omessage.c line 188 in H5O_msg_append_oh():
unable to create new message in header
major: Attribute
minor: Unable to insert object
#012: ../../../src/H5Omessage.c line 228 in H5O_msg_append_real():
unable to create new message
major: Object header
minor: No space available for allocation
#013: ../../../src/H5Omessage.c line 1940 in H5O_msg_alloc(): unable
to allocate space for message
major: Object header
minor: Unable to initialize object
#014: ../../../src/H5Oalloc.c line 1032 in H5O_alloc(): object header
message is too large
major: Object header
minor: Unable to initialize object
Traceback (most recent call last):
File "00_build_dataset.tmp.py", line 52, in <module>
dump_in_hdf5(**vars(args))
File "00_build_dataset.tmp.py", line 32, in dump_in_hdf5
data_api.Subject)
File "/usr/lib/python2.7/dist-packages/tables/file.py", line 770, in
createTable
chunkshape=chunkshape, byteorder=byteorder)
File "/usr/lib/python2.7/dist-packages/tables/table.py", line 832, in
__init__
byteorder, _log)
File "/usr/lib/python2.7/dist-packages/tables/leaf.py", line 291, in
__init__
super(Leaf, self).__init__(parentNode, name, _log)
File "/usr/lib/python2.7/dist-packages/tables/node.py", line 296, in
__init__
self._v_objectID = self._g_create()
File "/usr/lib/python2.7/dist-packages/tables/table.py", line 983, in
_g_create
self._v_new_title, self.filters.complib or '', obversion )
File "tableExtension.pyx", line 195, in
tables.tableExtension.Table._createTable (tables/tableExtension.c:2181)
tables.exceptions.HDF5ExtError: Problems creating the table
I think that the size of the column is too large (if I remove the Image
field, everything works perfectly).
Therefore what is the best way to store the images (while keeping the
relation)? I have read various post about this subject on the web but
could not find a definitive answer (the more helpful was
http://stackoverflow.com/questions/8843062/python-how-to-store-a-numpy-multidimensional-array-in-pytables).
I was thinking to create an extensible array and store each image in the
same order than the subject. However, I would feel more comfortable if
the subject Id could be inserted too (to join the tables).
Any help?
Mathieu
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