def test_Datasets(self, session):
template = {
'entry:NXentry': {
'name': DeviceDataset('Exp', 'title'),
'def': ConstDataset('NXmonopd', 'string'),
'sry': DeviceDataset('sry',
units=NXAttribute('deg', 'string')),
},
}
session.experiment.update(title='GurkenTitle')
maw(session.getDevice('sry'), 23.7)
session.experiment.setDetectors(['det', ])
setTemplate(template)
self.setScanCounter(session, 46)
count(t=.1)
fin = h5py.File(path.join(session.experiment.datapath,
'test%sn000047.hdf' % year), 'r')
ds = fin['entry/name']
assert (ds[0] == b'GurkenTitle')
ds = fin['entry/def']
assert (ds[0] == b'NXmonopd')
ds = fin['entry/sry']
assert (ds[0] == 23.7)
assert (ds.attrs['units'] == b'deg')
fin.close()
def test_Scan(self, session):
template = {
'entry:NXentry': {
'time': DetectorDataset('timer', 'float32'),
'mon': DetectorDataset('mon1', 'uint32'),
'counts': ImageDataset(0, 0,
signal=NXAttribute(1, 'int32')),
'sry': DeviceDataset('sry'),
},
'data:NXdata': {'None': NXScanLink(), }
}
setTemplate(template)
self.setScanCounter(session, 48)
session.experiment.setDetectors(['det', ])
sry = session.getDevice('sry')
scan(sry, 0, 1, 5, t=0.001)
fin = h5py.File(path.join(session.experiment.datapath,
'test%sn000049.hdf' % year), 'r')
ds = fin['entry/sry']
assert (len(ds) == 5)
ds = fin['entry/time']
assert (len(ds) == 5)
ds = fin['entry/mon']
assert (len(ds) == 5)
ds = fin['entry/counts']
assert (len(ds) == 5)
ds = fin['data/sry']
assert (len(ds) == 5)
assert (ds[0] == 0)
assert (ds[1] == 1)
assert (ds[2] == 2)
assert (ds[3] == 3)
assert (ds.attrs['target'] == b'/entry/sry')
fin.close()
def makeTable(self, table_name):
table = session.getDevice(table_name)
det = self.containsDetector(table)
if det:
self._detector = det
table.removeSetup(det)
devices = table.getTableDevices()
content = dict()
for d in devices:
try:
dev = session.getDevice(d)
content[dev.name] = DeviceDataset(dev.name,
dtype='float32',
units=NXAttribute(
dev.unit, 'string'))
except Exception as e:
session.log.info('Failed to write device %s, Exception: %s', d,
e)
equipment = ','.join(table.setups)
content['equipment'] = ConstDataset(equipment, 'string')
if det:
table.addSetup(det)
content['detector'] = ConstDataset(det, 'string')
return content
def test_Link(self, session):
template = {
'entry:NXentry': {'sry': DeviceDataset('sry'), },
'data:NXdata': {'srlink': NXLink('/entry/sry'), }
}
maw(session.getDevice('sry'), 77.7)
session.experiment.setDetectors(['det', ])
setTemplate(template)
self.setScanCounter(session, 50)
count(t=.1)
fin = h5py.File(path.join(session.experiment.datapath,
'test%sn000051.hdf' % year), 'r')
ds = fin['entry/sry']
assert (ds[0] == 77.7)
ds = fin['data/srlink']
assert (ds[0] == 77.7)
assert (ds.attrs['target'] == b'/entry/sry')
fin.close()
class BOATemplateProvider(NexusTemplateProvider):
"""
NeXus template generation for BOA at SINQ
"""
_boa_default = {
"NeXus_Version": "4.3.0",
"instrument": "BOA",
"owner": DeviceAttribute('BOA', 'responsible'),
"entry:NXentry": {
"title": DeviceDataset('Exp', 'title'),
"proposal_title": DeviceDataset('Exp', 'title'),
"proposal_id": DeviceDataset('Exp', 'proposal'),
"start_time": NXTime(),
"end_time": NXTime(),
"user:NXuser": {
"name": DeviceDataset('Exp', 'users'),
"email": DeviceDataset('Exp', 'localcontact')
},
"sample:NXsample": {
"sample_name": DeviceDataset('Sample', 'samplename'),
"hugo": NexusSampleEnv(),
},
"control:NXmonitor": {
"mode":
DetectorDataset('mode', "string"),
"Monitor":
DetectorDataset('monitorval',
'float32',
units=NXAttribute('counts', 'string')),
"preset":
DetectorDataset('preset', 'float32'),
"time":
DetectorDataset('elapsedtime',
'float32',
units=NXAttribute('seconds', 'string')),
},
"proton_beam:NXmonitor": {
"data":
DetectorDataset('protoncurr',
'int32',
units=NXAttribute('counts', 'string'))
},
"white_beam:NXmonitor": {
"data":
DetectorDataset('monitorval',
'int32',
units=NXAttribute('counts', 'string'))
},
},
}
_tables = ['Table2', 'Table3', 'Table4', 'Table5', 'Table6']
_detectors = ['embl', 'andor', 'single_el737']
_detector = None
def containsDetector(self, table):
for det in self._detectors:
if det in table.setups:
return det
return None
def makeTable(self, table_name):
table = session.getDevice(table_name)
det = self.containsDetector(table)
if det:
self._detector = det
table.removeSetup(det)
devices = table.getTableDevices()
content = dict()
for d in devices:
try:
dev = session.getDevice(d)
content[dev.name] = DeviceDataset(dev.name,
dtype='float32',
units=NXAttribute(
dev.unit, 'string'))
except Exception as e:
session.log.info('Failed to write device %s, Exception: %s', d,
e)
equipment = ','.join(table.setups)
content['equipment'] = ConstDataset(equipment, 'string')
if det:
table.addSetup(det)
content['detector'] = ConstDataset(det, 'string')
return content
def makeDetector(self):
name = self._detector
if 'single' in name:
name = 'single'
content = dict()
if name == 'single':
content['data'] = DetectorDataset('countval',
'int32',
units=NXAttribute(
'counts', 'string'))
elif name == 'andor':
content['data'] = ImageDataset(0,
0,
signal=NXAttribute(1, 'int32'))
elif name == 'embl':
content['data'] = ImageDataset(0,
0,
signal=NXAttribute(1, 'int32'))
return name, content
def makeData(self, name):
content = dict()
content['data'] = NXLink('/entry/%s/data' % (name))
content['None'] = NXScanLink()
return content
def getTemplate(self):
boa_template = copy.deepcopy(self._boa_default)
entry = boa_template['entry:NXentry']
for tbl in self._tables:
tblcontent = self.makeTable(tbl)
entry[tbl.lower() + ':NXcollection'] = tblcontent
if self._detector:
name, content = self.makeDetector()
entry[name + ':NXdetector'] = content
entry['data:Nxdata'] = self.makeData(name)
else:
session.log.info('No detector FOUND! May be: check setup???')
return boa_template
from nicos.nexus.elements import ConstDataset, DetectorDataset, \
DeviceAttribute, DeviceDataset, ImageDataset, NexusSampleEnv, \
NXAttribute, NXLink, NXScanLink, NXTime
from nicos.nexus.nexussink import NexusTemplateProvider
from nicos_sinq.nexus.specialelements import TwoThetaArray
# Default template for HRPT including most of the devices
hrpt_default = {
"NeXus_Version": "4.3.0",
"instrument": "HRPT",
"owner": DeviceAttribute('HRPT', 'responsible'),
"entry1:NXentry": {
"title": DeviceDataset('Exp', 'title'),
"proposal_title": DeviceDataset('Exp', 'title'),
"proposal_id": DeviceDataset('Exp', 'proposal'),
"start_time": NXTime(),
"definition": ConstDataset('NXmonopd', 'string'),
"end_time": NXTime(),
"user:NXuser": {
"name": DeviceDataset('Exp', 'users'),
"email": DeviceDataset('Exp', 'localcontact')
},
"proposal_user:NXuser": {
"name": DeviceDataset('Exp', 'users'),
},
"sample:NXsample": {
"sample_name":
DeviceDataset('Sample', 'samplename'),
"name":
NXLink('/entry1/sample/sample_name'),
NXAttribute, NXLink, NXScanLink, NXTime
from nicos.nexus.nexussink import NexusTemplateProvider
from nicos_sinq.nexus.specialelements import FixedArray
sans_detector = {
"count_mode":
DetectorDataset("mode", "string"),
"counting_time":
DetectorDataset("elapsedtime",
"float32",
units=NXAttribute("seconds", "string")),
"preset":
DetectorDataset("preset", "float32"),
"x_position":
DeviceDataset("detx"),
"x_null":
DeviceDataset("detx", "offset"),
"y_position":
DeviceDataset("dety"),
"y_null":
DeviceDataset("dety", "offset"),
"chi_position":
DeviceDataset("detphi"),
"detector_x":
FixedArray(-64, 1, 128),
"detector_y":
FixedArray(-64, 1, 128),
"counts":
ImageDataset(0, 0, signal=NXAttribute(1, "int32")),
"data":
def getTemplate(self):
return {
'NeXus_Version': '4.3.0',
'instrument': 'TOFTOF',
'owner': DeviceAttribute('TOFTOF', 'responsible'),
'Scan:NXentry': {
'wavelength': DeviceDataset('chWL', dtype='float32'),
'title': DeviceDataset('det', 'usercomment'),
'proposal': DeviceDataset('Exp', 'title'),
'proposal_number': DeviceDataset('Exp', 'proposal'),
'experiment_identifier': ExperimentTitle(),
'entry_identifier': EntryIdentifier(),
'start_time': StartTime(),
'end_time': EndTime(),
'duration': Duration(),
'FileName': FileName(),
'instrument:NXinstrument': {
'name': ConstDataset('TOFTOF', 'string'),
'platform': ConstDataset('Linux', 'string'),
'chopper:NXchopper': {
'crc': DeviceDataset('chCRC', dtype='int32'),
'delay': DeviceDataset('chdelay', dtype='int32'),
'num_of_channels': DeviceDataset(
'det', 'timechannels', dtype='int32'),
'num_of_detectors': DeviceDataset('det', 'numinputs',
dtype='int32'),
'ratio': DeviceDataset('chRatio', dtype='int32'),
'rotation_speed': DeviceDataset('ch', dtype='float32'),
'slit_type': DeviceDataset('chST', dtype='int32'),
'tof_ch5_90deg_offset': DeviceDataset(
'ch', 'ch5_90deg_offset', dtype='int32'),
'tof_num_inputs': DeviceDataset('det', 'numinputs',
dtype='int32'),
'tof_time_preselection': DeviceDataset(
'det', 'preset', dtype='int32', units=seconds),
},
'detector:NXdetector': {
'box_chan': DetInfo(15),
'box_nr': DetInfo(14),
'det_plate': DetInfo(2),
'det_pos': DetInfo(3),
'det_rack': DetInfo(1),
'det_rpos': DetInfo(4),
'detector_number': DetInfo(0),
'ele_card': DetInfo(10),
'ele_chan': DetInfo(11),
'ele_total': DetInfo(12),
'pixel_mask': DetInfo(13),
'polar_angle': DetInfo(5),
},
'chopper_vac0': DeviceDataset('vac0', dtype='float32'),
'chopper_vac1': DeviceDataset('vac1', dtype='float32'),
'chopper_vac2': DeviceDataset('vac2', dtype='float32'),
'chopper_vac3': DeviceDataset('vac3', dtype='float32'),
'goniometer_phicxcy': GonioDataset(),
'goniometer_xyz': TableDataset(),
'hv_power_supplies': HVDataset(),
'lv_power_supplies': LVDataset(),
},
'mode': Mode(),
'status': Status(),
'to_go': ToGo(),
# 'slit_hg': DeviceDataset('slit.centerx'),
# 'slit_ho': DeviceDataset('slit.centery'),
# 'slit_vg': DeviceDataset('slit.width'),
# 'slit_vo': DeviceDataset('slit.height'),
'user1:NXuser': {
'name': DeviceDataset('Exp', 'localcontact'),
'role': ConstDataset('local_contact', 'string'),
},
'user2:NXuser': {
'name': DeviceDataset('Exp', 'users'),
'role': ConstDataset('experiment_team', 'string'),
},
'sample:NXsample': {
'description': DeviceDataset('Sample', 'samplename'),
'total_counts': SampleCounts(),
'total_count_rate': SampleCountRate(),
},
'monitor:NXmonitor': {
'tof_monitor_input': DeviceDataset('det',
'monitorchannel'),
'tof_time_interval': DeviceDataset('ch', 'frametime'),
'data': MonitorData(),
'elastic_peak': ElasticPeakGuess(),
'integral': MonitorValue(),
'monitor_count_rate': MonitorRate(),
'time_of_flight': MonitorTof(),
},
'data:NXdata': {
'channel_number': ChannelList(),
'data': TOFTOFImageDataset(
0, 0, signal=signal, units='counts',
axes='2theta:channel_number'),
'polar_angle': DetInfo(5),
},
},
}