def list_h5(self, path):
from PYME.IO import h5File
try:
with h5File.openH5(path.rstrip('/').rstrip('\\')) as h5f:
f, length = self._string_to_file(json.dumps(h5f.get_listing()))
self.send_response(200)
encoding = sys.getfilesystemencoding()
self.send_header("Content-type",
"application/json; charset=%s" % encoding)
self.send_header("Content-Length", str(length))
self.end_headers()
return f
except IOError:
self.send_error(404,
"File not found - %s, [%s]" % (self.path, path))
return None
def _aggregate_h5(self):
"""
Support for results aggregation into an HDF5 file, using pytables.
We treat any path components after the .h5r as locations within the file (ie table names).
e.g. /path/to/data.h5r/<tablename>
A few special cases / Table names are accommodated:
MetaData: assumes we have sent PYME metadata in json format and saves to the file using the appropriate metadatahandler
No table name: assumes we have a fitResults object (as returned by remFitBuf and saves to the the appropriate tables (as HDF task queue would)
"""
import numpy as np
from io import BytesIO
#from six.moves import cPickle
from PYME.IO import MetaDataHandler
from PYME.IO import h5File
#path = self.translate_path()
filename, tablename = self.path.lstrip(
'/')[len('__aggregate_h5'):].split('.h5')
filename = self.translate_path(filename + '.h5')
data = self._get_data()
dirname = os.path.dirname(filename)
#if not os.path.exists(dirname):
# os.makedirs(dirname)
makedirs_safe(dirname)
#logging.debug('opening h5r file')
with h5File.openH5(filename, 'a') as h5f:
tablename = tablename.lstrip('/')
h5f.put_file(tablename, data)
#logging.debug('left h5r file')
if USE_DIR_CACHE:
cl.dir_cache.update_cache(filename, int(len(data)))
self.send_response(200)
self.send_header("Content-Length", "0")
self.end_headers()
return
def get_h5_part(self, path):
from PYME.IO import h5File
ctype = self.guess_type(path)
try:
filename, part = path.split('.h5')
part = part.lstrip('/').lstrip('\\')
with h5File.openH5(filename + '.h5') as h5f:
f, length = self._string_to_file(h5f.get_file(part))
self.send_response(200)
self.send_header("Content-type", ctype)
self.send_header("Content-Length", length)
#self.send_header("Last-Modified", self.date_time_string(fs.st_mtime))
self.end_headers()
return f
except IOError:
self.send_error(404,
"File not found - %s, [%s]" % (self.path, path))
return None