def load_json_file_array(root, array_name):
# Load the datashape
dsfile = root + ".datashape"
if not path.isfile(dsfile):
dsfile = path.dirname(root) + ".datashape"
if not path.isfile(dsfile):
raise Exception("No datashape file found for array %s" % array_name)
with open(dsfile) as f:
dt = ndt.type(f.read())
# Load the JSON
# TODO: Add stream support to parse_json for compressed JSON, etc.
arr = nd.parse_json(dt, nd.memmap(root + ".json"))
return array(arr)
def load_json_directory_array(root, array_name):
# Load the datashape
dsfile = root + ".datashape"
if not path.isfile(dsfile):
raise Exception("No datashape file found for array %s" % array_name)
with open(dsfile) as f:
dt = ndt.type(f.read())
# Scan for JSON files, assuming they're just #.json
# Sort them numerically
files = sorted([(int(path.splitext(path.basename(x))[0]), x) for x in glob.glob(path.join(root, "*.json"))])
files = [x[1] for x in files]
# Make an array with an extra fixed dimension, then
# read a JSON file into each element of that array
dt = ndt.make_fixed_dim(len(files), dt)
arr = nd.empty(dt)
for i, fname in enumerate(files):
nd.parse_json(arr[i], nd.memmap(fname))
arr.flag_as_immutable()
return array(arr)
def load_blaze_array(conf, dir):
"""Loads a blaze array from the catalog configuration and catalog path"""
# This is a temporary hack, need to transition to using the
# deferred data descriptors for various formats.
fsdir = conf.get_fsdir(dir)
if not path.isfile(fsdir + '.array'):
raise RuntimeError('Could not find blaze array description file %r'
% (fsdir + '.array'))
with open(fsdir + '.array') as f:
arrmeta = yaml.load(f)
tp = arrmeta['type']
imp = arrmeta['import']
ds_str = arrmeta.get('datashape') # optional. HDF5 does not need that.
if tp == 'csv':
with open(fsdir + '.csv', 'r') as f:
rd = csv.reader(f)
if imp.get('headers', False):
# Skip the header line
next(rd)
dat = list(rd)
arr = nd.array(dat, ndt.type(ds_str))[:]
return blaze.array(arr)
elif tp == 'json':
arr = nd.parse_json(ds_str, nd.memmap(fsdir + '.json'))
return blaze.array(arr)
elif tp == 'hdf5':
import tables as tb
from blaze.datadescriptor import HDF5_DDesc
fname = fsdir + '.h5' # XXX .h5 assumed for HDF5
with tb.open_file(fname, 'r') as f:
dp = imp.get('datapath') # specifies a path in HDF5
try:
dparr = f.get_node(f.root, dp, 'Leaf')
except tb.NoSuchNodeError:
raise RuntimeError(
'HDF5 file does not have a dataset in %r' % dp)
dd = HDF5_DDesc(fname, dp)
return blaze.array(dd)
elif tp == 'npy':
import numpy as np
use_memmap = imp.get('memmap', False)
if use_memmap:
arr = np.load(fsdir + '.npy', 'r')
else:
arr = np.load(fsdir + '.npy')
arr = nd.array(arr)
arr = blaze.array(arr)
ds = datashape.dshape(ds_str)
if not matches_datashape_pattern(arr.dshape, ds):
raise RuntimeError(('NPY file for blaze catalog path %r ' +
'has the wrong datashape (%r instead of ' +
'%r)') % (arr.dshape, ds))
return arr
elif tp == 'py':
ds = datashape.dshape(ds_str)
# The script is run with the following globals,
# and should put the loaded array in a global
# called 'result'.
gbl = {'catconf': conf, # Catalog configuration object
'impdata': imp, # Import data from the .array file
'catpath': dir, # Catalog path
'fspath': fsdir, # Equivalent filesystem path
'dshape': ds # Datashape the result should have
}
if py2help.PY2:
execfile(fsdir + '.py', gbl, gbl)
else:
with open(fsdir + '.py') as f:
code = compile(f.read(), fsdir + '.py', 'exec')
exec(code, gbl, gbl)
arr = gbl.get('result', None)
if arr is None:
raise RuntimeError(('Script for blaze catalog path %r did not ' +
'return anything in "result" variable')
% (dir))
elif not isinstance(arr, blaze.Array):
raise RuntimeError(('Script for blaze catalog path %r returned ' +
'wrong type of object (%r instead of ' +
'blaze.Array)') % (type(arr)))
if not matches_datashape_pattern(arr.dshape, ds):
raise RuntimeError(('Script for blaze catalog path %r returned ' +
'array with wrong datashape (%r instead of ' +
'%r)') % (arr.dshape, ds))
return arr
else:
raise ValueError(('Unsupported array type %r from ' +
'blaze catalog entry %r')
% (tp, dir))
def load_blaze_array(conf, dir):
"""Loads a blaze array from the catalog configuration and catalog path"""
# This is a temporary hack, need to transition to using the
# deferred data descriptors for various formats.
fsdir = conf.get_fsdir(dir)
if not path.isfile(fsdir + '.array'):
raise RuntimeError('Could not find blaze array description file %r' %
(fsdir + '.array'))
with open(fsdir + '.array') as f:
arrmeta = yaml.load(f)
tp = arrmeta['type']
imp = arrmeta['import']
ds_str = arrmeta.get('datashape') # optional. HDF5 does not need that.
if tp == 'csv':
with open(fsdir + '.csv', 'r') as f:
rd = csv.reader(f)
if imp.get('headers', False):
# Skip the header line
next(rd)
dat = list(rd)
arr = nd.array(dat, ndt.type(ds_str))[:]
return blaze.array(arr)
elif tp == 'json':
arr = nd.parse_json(ds_str, nd.memmap(fsdir + '.json'))
return blaze.array(arr)
elif tp == 'hdf5':
import tables as tb
from blaze.datadescriptor import HDF5DataDescriptor
fname = fsdir + '.h5' # XXX .h5 assumed for HDF5
with tb.open_file(fname, 'r') as f:
dp = imp.get('datapath') # specifies a path in HDF5
try:
dparr = f.get_node(f.root, dp, 'Leaf')
except tb.NoSuchNodeError:
raise RuntimeError('HDF5 file does not have a dataset in %r' %
dp)
dd = HDF5DataDescriptor(fname, dp)
return blaze.array(dd)
elif tp == 'npy':
import numpy as np
use_memmap = imp.get('memmap', False)
if use_memmap:
arr = np.load(fsdir + '.npy', 'r')
else:
arr = np.load(fsdir + '.npy')
arr = nd.array(arr)
arr = blaze.array(arr)
ds = datashape.dshape(ds_str)
if not compatible_array_dshape(arr, ds):
raise RuntimeError(
('NPY file for blaze catalog path %r ' +
'has the wrong datashape (%r instead of ' + '%r)') %
(arr.dshape, ds))
return arr
elif tp == 'py':
ds = datashape.dshape(ds_str)
# The script is run with the following globals,
# and should put the loaded array in a global
# called 'result'.
gbl = {
'catconf': conf, # Catalog configuration object
'impdata': imp, # Import data from the .array file
'catpath': dir, # Catalog path
'fspath': fsdir, # Equivalent filesystem path
'dshape': ds # Datashape the result should have
}
if py2help.PY2:
execfile(fsdir + '.py', gbl, gbl)
else:
with open(fsdir + '.py') as f:
code = compile(f.read(), fsdir + '.py', 'exec')
exec(code, gbl, gbl)
arr = gbl.get('result', None)
if arr is None:
raise RuntimeError(
('Script for blaze catalog path %r did not ' +
'return anything in "result" variable') % (dir))
elif not isinstance(arr, blaze.Array):
raise RuntimeError(
('Script for blaze catalog path %r returned ' +
'wrong type of object (%r instead of ' + 'blaze.Array)') %
(type(arr)))
if not compatible_array_dshape(arr, ds):
raise RuntimeError(
('Script for blaze catalog path %r returned ' +
'array with wrong datashape (%r instead of ' + '%r)') %
(arr.dshape, ds))
return arr
else:
raise ValueError(
('Unsupported array type %r from ' + 'blaze catalog entry %r') %
(tp, dir))
