Le 05/07/2013 00:31, Anthony Scopatz a écrit :
On Thu, Jul 4, 2013 at 4:13 PM, Mathieu Dubois <duboismathieu_g...@yahoo.fr <mailto: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 <http://00_build_dataset.tmp.py>", line 52, in <module> dump_in_hdf5(**vars(args)) File "00_build_dataset.tmp.py <http://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?
IMAGE_SIZE is a tuple containing (121, 145, 121).
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 ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net <mailto:Pytables-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/pytables-users ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
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