On Thu, Jul 4, 2013 at 4:13 PM, Mathieu Dubois
<duboismathieu_g...@yahoo.fr>wrote:
> 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).
>
Hi Mathieu,
This shouldn't be the case. What is the value of IMAGE_SIZE?
Be Well
Anthony
>
> 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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