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add debugging and make the final write more robust (#822)
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* add debugging and make the final write more robust

* add test based on bug report

* logging: update old loggers

* rename instrument to avoid error in test suite

* save even in case of keyboardinterrupt

* insert argument in all places
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@WilliamHPNielsen @jenshnielsen
WilliamHPNielsen authored and jenshnielsen committed Oct 27, 2017
1 parent e741fbd commit 0cd61ac
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Showing 6 changed files with 106 additions and 33 deletions.
29 changes: 20 additions & 9 deletions qcodes/data/data_set.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@
from .location import FormatLocation
from qcodes.utils.helpers import DelegateAttributes, full_class, deep_update

log = logging.getLogger(__name__)


def new_data(location=None, loc_record=None, name=None, overwrite=False,
io=None, **kwargs):
Expand Down Expand Up @@ -246,14 +248,14 @@ def complete(self, delay=1.5):
Args:
delay (float): seconds between iterations. Default 1.5
"""
logging.info(
log.info(
'waiting for DataSet <{}> to complete'.format(self.location))

failing = {key: False for key in self.background_functions}

completed = False
while True:
logging.info('DataSet: {:.0f}% complete'.format(
log.info('DataSet: {:.0f}% complete'.format(
self.fraction_complete() * 100))

# first check if we're done
Expand All @@ -264,13 +266,13 @@ def complete(self, delay=1.5):
# because we want things like live plotting to get the final data
for key, fn in list(self.background_functions.items()):
try:
logging.debug('calling {}: {}'.format(key, repr(fn)))
log.debug('calling {}: {}'.format(key, repr(fn)))
fn()
failing[key] = False
except Exception:
logging.info(format_exc())
log.info(format_exc())
if failing[key]:
logging.warning(
log.warning(
'background function {} failed twice in a row, '
'removing it'.format(key))
del self.background_functions[key]
Expand All @@ -282,7 +284,7 @@ def complete(self, delay=1.5):
# but only sleep if we're not already finished
time.sleep(delay)

logging.info('DataSet <{}> is complete'.format(self.location))
log.info('DataSet <{}> is complete'.format(self.location))

def get_changes(self, synced_indices):
"""
Expand Down Expand Up @@ -387,8 +389,11 @@ def store(self, loop_indices, ids_values):
self.last_store = time.time()
if (self.write_period is not None and
time.time() > self.last_write + self.write_period):
log.debug('Attempting to write')
self.write()
self.last_write = time.time()
else:
log.debug('.store method: This is not the right time to write')

def default_parameter_name(self, paramname='amplitude'):
""" Return name of default parameter for plotting
Expand Down Expand Up @@ -464,22 +469,26 @@ def read_metadata(self):
return
self.formatter.read_metadata(self)

def write(self, write_metadata=False):
def write(self, write_metadata=False, only_complete=True):
"""
Writes updates to the DataSet to storage.
N.B. it is recommended to call data_set.finalize() when a DataSet is
no longer expected to change to ensure files get closed
Args:
write_metadata (bool): write the metadata to disk
only_complete (bool): passed on to the match_save_range inside
self.formatter.write. Used to ensure that all new data gets
saved even when some columns are strange.
"""
if self.location is False:
return

self.formatter.write(self,
self.io,
self.location,
write_metadata=write_metadata)
write_metadata=write_metadata,
only_complete=only_complete)

def write_copy(self, path=None, io_manager=None, location=None):
"""
Expand Down Expand Up @@ -560,7 +569,9 @@ def finalize(self):
Also closes the data file(s), if the ``Formatter`` we're using
supports that.
"""
self.write()
log.debug('Finalising the DataSet. Writing.')
# write all new data, not only (to?) complete columns
self.write(only_complete=False)

if hasattr(self.formatter, 'close_file'):
self.formatter.close_file(self)
Expand Down
8 changes: 6 additions & 2 deletions qcodes/data/format.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ class Formatter:
ArrayGroup = namedtuple('ArrayGroup', 'shape set_arrays data name')

def write(self, data_set, io_manager, location, write_metadata=True,
force_write=False):
force_write=False, only_complete=True):
"""
Write the DataSet to storage.
Expand All @@ -63,6 +63,8 @@ def write(self, data_set, io_manager, location, write_metadata=True,
location (str): the file location within the io_manager.
write_metadata (bool): if True, then the metadata is written to disk
force_write (bool): if True, then the data is written to disk
only_complete (bool): Used only by the gnuplot formatter's
overridden version of this method
"""
raise NotImplementedError

Expand Down Expand Up @@ -190,7 +192,9 @@ def match_save_range(self, group, file_exists, only_complete=True):
Returns:
Tuple(int, int): the first and last raveled indices that should
be saved.
be saved. Returns None if:
* no data is present
* no new data can be found
"""
inner_setpoint = group.set_arrays[-1]
full_dim_data = (inner_setpoint, ) + group.data
Expand Down
23 changes: 19 additions & 4 deletions qcodes/data/gnuplot_format.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,16 @@
import re
import math
import json
import logging

from qcodes.utils.helpers import deep_update, NumpyJSONEncoder
from .data_array import DataArray
from .format import Formatter


log = logging.getLogger(__name__)


class GNUPlotFormat(Formatter):
"""
Saves data in one or more gnuplot-format files. We make one file for
Expand Down Expand Up @@ -239,7 +243,8 @@ def _get_labels(self, labelstr):
parts = re.split('"\s+"', labelstr[1:-1])
return [l.replace('\\"', '"').replace('\\\\', '\\') for l in parts]

def write(self, data_set, io_manager, location, force_write=False, write_metadata=True):
def write(self, data_set, io_manager, location, force_write=False,
write_metadata=True, only_complete=True):
"""
Write updates in this DataSet to storage.
Expand All @@ -249,6 +254,11 @@ def write(self, data_set, io_manager, location, force_write=False, write_metadat
data_set (DataSet): the data we're storing
io_manager (io_manager): the base location to write to
location (str): the file location within io_manager
only_complete (bool): passed to match_save_range, answers the
following question: Should we write all available new data,
or only complete rows? Is used to make sure that everything
gets written when the DataSet is finalised, even if some
dataarrays are strange (like, full of nans)
"""
arrays = data_set.arrays

Expand All @@ -257,16 +267,20 @@ def write(self, data_set, io_manager, location, force_write=False, write_metadat
existing_files = set(io_manager.list(location))
written_files = set()

# Every group gets it's own datafile
# Every group gets its own datafile
for group in groups:
log.debug('Attempting to write the following '
'group: {}'.format(group))
fn = io_manager.join(location, group.name + self.extension)

written_files.add(fn)

file_exists = fn in existing_files
save_range = self.match_save_range(group, file_exists)
save_range = self.match_save_range(group, file_exists,
only_complete=only_complete)

if save_range is None:
log.debug('Cannot match save range, skipping this group.')
continue

overwrite = save_range[0] == 0 or force_write
Expand All @@ -276,6 +290,7 @@ def write(self, data_set, io_manager, location, force_write=False, write_metadat
with io_manager.open(fn, open_mode) as f:
if overwrite:
f.write(self._make_header(group))
log.debug('Wrote header to file')

for i in range(save_range[0], save_range[1] + 1):
indices = np.unravel_index(i, shape)
Expand All @@ -291,7 +306,7 @@ def write(self, data_set, io_manager, location, force_write=False, write_metadat

one_point = self._data_point(group, indices)
f.write(self.separator.join(one_point) + self.terminator)

log.debug('Wrote to file')
# now that we've saved the data, mark it as such in the data.
# we mark the data arrays and the inner setpoint array. Outer
# setpoint arrays have different dimension (so would need a
Expand Down
13 changes: 9 additions & 4 deletions qcodes/data/hdf5_format.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,8 @@ def _create_data_object(self, data_set, io_manager=None,
return data_set._h5_base_group

def write(self, data_set, io_manager=None, location=None,
force_write=False, flush=True, write_metadata=True):
force_write=False, flush=True, write_metadata=True,
only_complete=False):
"""
Writes a data_set to an hdf5 file.
Expand All @@ -137,12 +138,16 @@ def write(self, data_set, io_manager=None, location=None,
force_write (bool): if True creates a new file to write to
flush (bool) : whether to flush after writing, can be disabled
for testing or performance reasons
only_complete (bool): Not used by this formatter, but must be
included in the call signature to avoid an "unexpected
keyword argument" TypeError.
N.B. It is recommended to close the file after writing, this can be
done by calling ``HDF5Format.close_file(data_set)`` or
``data_set.finalize()`` if the data_set formatter is set to an hdf5 formatter.
Note that this is not required if the dataset is created from a Loop as this
includes a data_set.finalize() statement.
``data_set.finalize()`` if the data_set formatter is set to an
hdf5 formatter. Note that this is not required if the dataset
is created from a Loop as this includes a data_set.finalize()
statement.
The write function consists of two parts, writing DataArrays and
writing metadata.
Expand Down
38 changes: 26 additions & 12 deletions qcodes/loops.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,16 +63,19 @@

log = logging.getLogger(__name__)


def active_loop():
return ActiveLoop.active_loop


def active_data_set():
loop = active_loop()
if loop is not None and loop.data_set is not None:
return loop.data_set
else:
return None


class Loop(Metadatable):
"""
The entry point for creating measurement loops
Expand Down Expand Up @@ -780,16 +783,16 @@ def _compile_one(self, action, new_action_indices):
return action

def _run_wrapper(self, *args, **kwargs):
# try:
self._run_loop(*args, **kwargs)
# finally:
if hasattr(self, 'data_set'):
# TODO (giulioungaretti) WTF?
# somehow this does not show up in the data_set returned by
# run(), but it is saved to the metadata
ts = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
self.data_set.add_metadata({'loop': {'ts_end': ts}})
self.data_set.finalize()
try:
self._run_loop(*args, **kwargs)
finally:
if hasattr(self, 'data_set'):
# TODO (giulioungaretti) WTF?
# somehow this does not show up in the data_set returned by
# run(), but it is saved to the metadata
ts = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
self.data_set.add_metadata({'loop': {'ts_end': ts}})
self.data_set.finalize()

def _run_loop(self, first_delay=0, action_indices=(),
loop_indices=(), current_values=(),
Expand Down Expand Up @@ -835,19 +838,24 @@ def _run_loop(self, first_delay=0, action_indices=(),
new_values = current_values + (value,)
data_to_store = {}

if hasattr(self.sweep_values, "parameters"): # combined parameter
if hasattr(self.sweep_values, "parameters"): # combined parameter
set_name = self.data_set.action_id_map[action_indices]
if hasattr(self.sweep_values, 'aggregate'):
value = self.sweep_values.aggregate(*set_val)
log.debug('Calling .store method of DataSet because '
'sweep_values.parameters exist')
self.data_set.store(new_indices, {set_name: value})
for j, val in enumerate(set_val): # set_val list of values to set [param1_setpoint, param2_setpoint ..]
# set_val list of values to set [param1_setpoint, param2_setpoint ..]
for j, val in enumerate(set_val):
set_index = action_indices + (j+n_callables, )
set_name = (self.data_set.action_id_map[set_index])
data_to_store[set_name] = val
else:
set_name = self.data_set.action_id_map[action_indices]
data_to_store[set_name] = value

log.debug('Calling .store method of DataSet because a sweep step'
' was taken')
self.data_set.store(new_indices, data_to_store)

if not self._nest_first:
Expand All @@ -856,6 +864,8 @@ def _run_loop(self, first_delay=0, action_indices=(),

try:
for f in callables:
log.debug('Going through callables at this sweep step.'
' Calling {}'.format(f))
f(first_delay=delay,
loop_indices=new_indices,
current_values=new_values)
Expand Down Expand Up @@ -889,14 +899,18 @@ def _run_loop(self, first_delay=0, action_indices=(),

# run the background task one last time to catch the last setpoint(s)
if self.bg_task is not None:
log.debug('Running the background task one last time.')
self.bg_task()

# the loop is finished - run the .then actions
log.debug('Finishing loop, running the .then actions...')
for f in self._compile_actions(self.then_actions, ()):
log.debug('...running .then action {}'.format(f))
f()

# run the bg_final_task from the bg_task:
if self.bg_final_task is not None:
log.debug('Running the bg_final_task')
self.bg_final_task()

def _wait(self, delay):
Expand Down
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