class TestPointGeneratorMeta(unittest.TestCase):
def setUp(self):
self.PGM = PointGeneratorMeta("test_description")
def test_init(self):
self.assertEqual("test_description", self.PGM.description)
self.assertEqual(self.PGM.label, "")
def test_validate(self):
g = CompoundGenerator([MagicMock()], [], [])
self.PGM.validate(g)
@patch('malcolm.core.vmetas.pointgeneratormeta.CompoundGenerator.from_dict')
def test_validate_dict_then_create_and_return(self, from_dict_mock):
gen_mock = MagicMock()
from_dict_mock.return_value = gen_mock
d = dict()
response = self.PGM.validate(d)
from_dict_mock.assert_called_once_with(d)
self.assertEqual(gen_mock, response)
def test_validate_raises(self):
with self.assertRaises(TypeError):
self.PGM.validate(7)
class ScanTickerPart(ChildPart):
# Generator instance
generator = None
# Where to start
completed_steps = None
# How many steps to do
steps_to_do = None
# When to blow up
exception_step = None
@RunnableController.Configure
@RunnableController.PostRunReady
@RunnableController.Seek
@method_takes(
"generator", PointGeneratorMeta("Generator instance"), REQUIRED,
"axesToMove",
StringArrayMeta(
"List of axes in inner dimension of generator that should be moved"
), REQUIRED, "exceptionStep",
NumberMeta("int32",
"If >0, raise an exception at the end of this step"), 0)
def configure(self, task, completed_steps, steps_to_do, part_info, params):
# If we are being asked to move
if self.name in params.axesToMove:
# Just store the generator and place we need to start
self.generator = params.generator
self.completed_steps = completed_steps
self.steps_to_do = steps_to_do
self.exception_step = params.exceptionStep
else:
# Flag nothing to do
self.generator = None
@RunnableController.Run
@RunnableController.Resume
def run(self, task, update_completed_steps):
# Start time so everything is relative
point_time = time.time()
if self.generator:
for i in range(self.completed_steps,
self.completed_steps + self.steps_to_do):
# Get the point we are meant to be scanning
point = self.generator.get_point(i)
# Update the child counter to be the demand position
position = point.positions[self.name]
task.put(self.child["counter"], position)
# Wait until the next point is due
point_time += point.duration
wait_time = point_time - time.time()
task.sleep(wait_time)
# Update the point as being complete
update_completed_steps(i + 1, self)
# If this is the exception step then blow up
assert i +1 != self.exception_step, \
"Raising exception at step %s" % self.exception_step
Info, AbortedError, BadValueError
from malcolm.core.vmetas import PointGeneratorMeta, NumberMeta, StringArrayMeta
class ParameterTweakInfo(Info):
"""Tweaks"""
def __init__(self, parameter, value):
self.parameter = parameter
self.value = value
sm = RunnableStateMachine
configure_args = [
"generator",
PointGeneratorMeta("Generator instance"), REQUIRED, "axesToMove",
StringArrayMeta(
"List of axes in inner dimension of generator that should be moved"),
[]
]
@method_also_takes("axesToMove",
StringArrayMeta("Default value for configure() axesToMove"),
[])
class RunnableController(ManagerController):
"""RunnableDevice implementer that also exposes GUI for child parts"""
# The stateMachine that this controller implements
stateMachine = sm()
Validate = Hook()
# user programs
NO_PROGRAM = 0 # Do nothing
TRIG_CAPTURE = 4 # Capture 1, Frame 0, Detector 0
TRIG_DEAD_FRAME = 2 # Capture 0, Frame 1, Detector 0
TRIG_LIVE_FRAME = 3 # Capture 0, Frame 1, Detector 1
TRIG_ZERO = 8 # Capture 0, Frame 0, Detector 0
# How many generator points to load each time
POINTS_PER_BUILD = 4000
# All possible PMAC CS axis assignment
cs_axis_names = list("ABCUVWXYZ")
# Args for configure and validate
configure_args = [
"generator", PointGeneratorMeta("Generator instance"), REQUIRED,
"axesToMove", StringArrayMeta(
"List of axes in inner dimension of generator that should be moved"),
[]]
# Class for these motor variables
class MotorInfo(Info):
def __init__(self, cs_axis, cs_port, acceleration, resolution, offset,
max_velocity, current_position, scannable, velocity_settle):
self.cs_axis = cs_axis
self.cs_port = cs_port
self.acceleration = acceleration
self.resolution = resolution
self.offset = offset
self.max_velocity = max_velocity
class PositionLabellerPart(ChildPart):
# Stored generator for positions
generator = None
# The last index we have loaded
end_index = 0
# Where we should stop loading points
steps_up_to = 0
# Future for plugin run
start_future = None
# If we are currently loading then block loading more points
loading = False
def _make_xml(self, start_index):
# Make xml root
root_el = ET.Element("pos_layout")
dimensions_el = ET.SubElement(root_el, "dimensions")
# Make an index for every hdf index
for i in range(len(self.generator.dimensions)):
ET.SubElement(dimensions_el, "dimension", name="d%d" % i)
# Add the a file close command for the HDF writer
ET.SubElement(dimensions_el, "dimension", name="FilePluginClose")
# Add the actual positions
positions_el = ET.SubElement(root_el, "positions")
end_index = start_index + POSITIONS_PER_XML
if end_index > self.steps_up_to:
end_index = self.steps_up_to
for i in range(start_index, end_index):
point = self.generator.get_point(i)
if i == self.generator.size - 1:
do_close = True
else:
do_close = False
positions = dict(FilePluginClose="%d" % do_close)
for j, value in enumerate(point.indexes):
positions["d%d" % j] = str(value)
position_el = ET.Element("position", **positions)
positions_el.append(position_el)
xml = et_to_string(root_el)
xml_length = len(xml)
assert xml_length < XML_MAX_SIZE, "XML size %d too big" % xml_length
return xml, end_index
@RunnableController.Reset
def reset(self, task):
super(PositionLabellerPart, self).reset(task)
self.abort(task)
@RunnableController.Configure
@RunnableController.PostRunReady
@RunnableController.Seek
@method_takes("generator", PointGeneratorMeta("Generator instance"),
REQUIRED)
def configure(self, task, completed_steps, steps_to_do, part_info, params):
# clear out old subscriptions
task.unsubscribe_all()
self.generator = params.generator
# Delete any remaining old positions
futures = task.post_async(self.child["delete"])
futures += task.put_many_async(
self.child, dict(enableCallbacks=True,
idStart=completed_steps + 1))
self.steps_up_to = completed_steps + steps_to_do
xml, self.end_index = self._make_xml(completed_steps)
# Wait for the previous puts to finish
task.wait_all(futures)
# Put the xml
task.put(self.child["xml"], xml)
# Start the plugin
self.start_future = task.post_async(self.child["start"])
@RunnableController.Run
@RunnableController.Resume
def run(self, task, update_completed_steps):
self.loading = False
task.subscribe(self.child["qty"], self.load_more_positions, task)
task.wait_all(self.start_future)
def load_more_positions(self, number_left, task):
if not self.loading and self.end_index < self.steps_up_to and \
number_left < POSITIONS_PER_XML * N_LOAD_AHEAD:
self.loading = True
xml, self.end_index = self._make_xml(self.end_index)
task.put(self.child["xml"], xml)
self.loading = False
@RunnableController.Abort
@RunnableController.Pause
def abort(self, task):
task.post(self.child["stop"])
def setUp(self):
self.PGM = PointGeneratorMeta("test_description")
class HDFWriterPart(ChildPart):
# Attributes
datasets = None
# Future for the start action
start_future = None
array_future = None
done_when_reaches = 0
def _create_dataset_infos(self, part_info, generator, filename):
# Update the dataset table
uniqueid = "/entry/NDAttributes/NDArrayUniqueId"
generator_rank = len(generator.dimensions)
# Get the detector name from the primary source
ndarray_infos = NDArrayDatasetInfo.filter_values(part_info)
assert len(ndarray_infos) in (0, 1), \
"More than one NDArrayDatasetInfo defined %s" % ndarray_infos
# Add the primary datasource
if ndarray_infos:
ndarray_info = ndarray_infos[0]
yield DatasetProducedInfo(name="%s.data" % ndarray_info.name,
filename=filename,
type="primary",
rank=ndarray_info.rank + generator_rank,
path="/entry/detector/detector",
uniqueid=uniqueid)
# Add any secondary datasources
for calculated_info in \
CalculatedNDAttributeDatasetInfo.filter_values(part_info):
yield DatasetProducedInfo(
name="%s.%s" % (ndarray_info.name, calculated_info.name),
filename=filename,
type="secondary",
rank=ndarray_info.rank + generator_rank,
path="/entry/%s/%s" %
(calculated_info.name, calculated_info.name),
uniqueid=uniqueid)
# Add all the other datasources
for dataset_info in NDAttributeDatasetInfo.filter_values(part_info):
if dataset_info.type == "detector":
# Something like I0
name = "%s.data" % dataset_info.name
type = "primary"
elif dataset_info.type == "monitor":
# Something like Iref
name = "%s.data" % dataset_info.name
type = "monitor"
elif dataset_info.type == "position":
# Something like x
name = "%s.value" % dataset_info.name
type = "position_value"
else:
raise AttributeError(
"Bad dataset type %r, should be in %s" %
(dataset_info.type, attribute_dataset_types))
yield DatasetProducedInfo(name=name,
filename=filename,
type=type,
rank=dataset_info.rank + generator_rank,
path="/entry/%s/%s" %
(dataset_info.name, dataset_info.name),
uniqueid=uniqueid)
# Add any setpoint dimensions
for dim in generator.axes:
yield DatasetProducedInfo(name="%s.value_set" % dim,
filename=filename,
type="position_set",
rank=1,
path="/entry/detector/%s_set" % dim,
uniqueid="")
@RunnableController.Reset
def reset(self, task):
super(HDFWriterPart, self).reset(task)
self.abort(task)
@RunnableController.Configure
@method_takes("generator", PointGeneratorMeta("Generator instance"),
REQUIRED, "filePath",
StringMeta("File path to write data to"), REQUIRED)
def configure(self, task, completed_steps, steps_to_do, part_info, params):
self.done_when_reaches = completed_steps + steps_to_do
# For first run then open the file
# Enable position mode before setting any position related things
task.put(self.child["positionMode"], True)
# Setup our required settings
# TODO: this should be different for windows detectors
file_path = params.filePath.rstrip(os.sep)
file_dir, filename = file_path.rsplit(os.sep, 1)
assert "." in filename, \
"File extension for %r should be supplied" % filename
futures = task.put_many_async(
self.child,
dict(enableCallbacks=True,
fileWriteMode="Stream",
swmrMode=True,
positionMode=True,
dimAttDatasets=True,
lazyOpen=True,
arrayCounter=0,
filePath=file_dir + os.sep,
fileName=filename,
fileTemplate="%s%s"))
futures += self._set_dimensions(task, params.generator)
xml = self._make_layout_xml(params.generator, part_info)
layout_filename = os.path.join(file_dir,
"%s-layout.xml" % self.params.mri)
open(layout_filename, "w").write(xml)
futures += task.put_async(self.child["xml"], layout_filename)
# Wait for the previous puts to finish
task.wait_all(futures)
# Reset numCapture back to 0
task.put(self.child["numCapture"], 0)
# We want the HDF writer to flush this often:
flush_time = 1 # seconds
# (In particular this means that HDF files can be read cleanly by
# SciSoft at the start of a scan.)
assert params.generator.duration > 0, \
"Duration %s for generator must be >0 to signify constant exposure"\
% params.generator.duration
n_frames_between_flushes = max(
2, round(flush_time / params.generator.duration))
task.put(self.child["flushDataPerNFrames"], n_frames_between_flushes)
task.put(self.child["flushAttrPerNFrames"], n_frames_between_flushes)
# Start the plugin
self.start_future = task.post_async(self.child["start"])
# Start a future waiting for the first array
self.array_future = task.when_matches_async(self.child["arrayCounter"],
1)
# Return the dataset information
dataset_infos = list(
self._create_dataset_infos(part_info, params.generator, filename))
return dataset_infos
@RunnableController.PostRunReady
@RunnableController.Seek
def seek(self, task, completed_steps, steps_to_do, part_info):
self.done_when_reaches = completed_steps + steps_to_do
# Just reset the array counter
task.put(self.child["arrayCounter"], 0)
# Start a future waiting for the first array
self.array_future = task.when_matches_async(self.child["arrayCounter"],
1)
@RunnableController.Run
@RunnableController.Resume
def run(self, task, update_completed_steps):
task.wait_all(self.array_future)
task.unsubscribe_all()
task.subscribe(self.child["uniqueId"], update_completed_steps, self)
# TODO: what happens if we miss the last frame?
task.when_matches(self.child["uniqueId"], self.done_when_reaches)
@RunnableController.PostRunIdle
def post_run_idle(self, task):
# If this is the last one, wait until the file is closed
task.wait_all(self.start_future)
@RunnableController.Abort
def abort(self, task):
task.post(self.child["stop"])
def _set_dimensions(self, task, generator):
num_dims = len(generator.dimensions)
assert num_dims <= 10, \
"Can only do 10 dims, you gave me %s" % num_dims
attr_dict = dict(numExtraDims=num_dims - 1)
# Fill in dim name and size
# NOTE: HDF writer has these filled with fastest moving first
# while dimensions is slowest moving first
for i in range(10):
suffix = SUFFIXES[i]
if i < num_dims:
forward_i = num_dims - i - 1
index_name = "d%d" % forward_i
index_size = generator.dimensions[forward_i].size
else:
index_name = ""
index_size = 1
attr_dict["posNameDim%s" % suffix] = index_name
attr_dict["extraDimSize%s" % suffix] = index_size
futures = task.put_many_async(self.child, attr_dict)
return futures
def _make_nxdata(self, name, rank, entry_el, generator, link=False):
# Make a dataset for the data
data_el = ET.SubElement(entry_el, "group", name=name)
ET.SubElement(data_el,
"attribute",
name="signal",
source="constant",
value=name,
type="string")
pad_dims = []
for d in generator.dimensions:
if len(d.axes) == 1:
pad_dims.append("%s_set" % d.axes[0])
else:
pad_dims.append(".")
pad_dims += ["."] * rank
ET.SubElement(data_el,
"attribute",
name="axes",
source="constant",
value=",".join(pad_dims),
type="string")
ET.SubElement(data_el,
"attribute",
name="NX_class",
source="constant",
value="NXdata",
type="string")
# Add in the indices into the dimensions array that our axes refer to
for i, d in enumerate(generator.dimensions):
for axis in d.axes:
ET.SubElement(data_el,
"attribute",
name="%s_set_indices" % axis,
source="constant",
value=str(i),
type="string")
if link:
ET.SubElement(data_el,
"hardlink",
name="%s_set" % axis,
target="/entry/detector/%s_set" % axis)
else:
self._make_set_points(d, axis, data_el,
generator.units[axis])
return data_el
def _make_set_points(self, dimension, axis, data_el, units):
axis_vals = ["%.12g" % p for p in dimension.get_positions(axis)]
axis_el = ET.SubElement(data_el,
"dataset",
name="%s_set" % axis,
source="constant",
type="float",
value=",".join(axis_vals))
ET.SubElement(axis_el,
"attribute",
name="units",
source="constant",
value=units,
type="string")
def _make_layout_xml(self, generator, part_info):
# Make a root element with an NXEntry
root_el = ET.Element("hdf5_layout")
entry_el = ET.SubElement(root_el, "group", name="entry")
ET.SubElement(entry_el,
"attribute",
name="NX_class",
source="constant",
value="NXentry",
type="string")
# Check that there is only one primary source of detector data
ndarray_infos = NDArrayDatasetInfo.filter_values(part_info)
if not ndarray_infos:
# Still need to put the data in the file, so manufacture something
primary_rank = 1
else:
primary_rank = ndarray_infos[0].rank
# Make an NXData element with the detector data in it in
# /entry/detector/detector
data_el = self._make_nxdata("detector", primary_rank, entry_el,
generator)
det_el = ET.SubElement(data_el,
"dataset",
name="detector",
source="detector",
det_default="true")
ET.SubElement(det_el,
"attribute",
name="NX_class",
source="constant",
value="SDS",
type="string")
# Now add any calculated sources of data
for dataset_info in \
CalculatedNDAttributeDatasetInfo.filter_values(part_info):
# if we are a secondary source, use the same rank as the det
attr_el = self._make_nxdata(dataset_info.name,
primary_rank,
entry_el,
generator,
link=True)
ET.SubElement(attr_el,
"dataset",
name=dataset_info.name,
source="ndattribute",
ndattribute=dataset_info.attr)
# And then any other attribute sources of data
for dataset_info in NDAttributeDatasetInfo.filter_values(part_info):
# if we are a secondary source, use the same rank as the det
attr_el = self._make_nxdata(dataset_info.name,
dataset_info.rank,
entry_el,
generator,
link=True)
ET.SubElement(attr_el,
"dataset",
name=dataset_info.name,
source="ndattribute",
ndattribute=dataset_info.attr)
# Add a group for attributes
NDAttributes_el = ET.SubElement(entry_el,
"group",
name="NDAttributes",
ndattr_default="true")
ET.SubElement(NDAttributes_el,
"attribute",
name="NX_class",
source="constant",
value="NXcollection",
type="string")
xml = et_to_string(root_el)
return xml
