def enscansw(seconds,
enstart,
enstop,
steps,
samplename='enscan',
sampleid=''):
# TODO: do it more generally
# yield from bps.mv(sw_det.setexp, seconds)
yield from bps.mv(sw_det.waxs.cam.acquire_time, seconds)
yield from bps.mv(sw_det.saxs.cam.acquire_time, seconds)
md = RE.md
md['sample'] = samplename
md['sampleid'] = sampleid
first_scan_id = None
dt = datetime.now()
formatted_date = dt.strftime('%Y-%m-%d')
for i, pos in enumerate(np.linspace(enstart, enstop, steps)):
yield from bps.mv(en, pos)
uid = (yield from bp.count([sw_det], md=md))
hdr = db[uid]
quick_view(hdr)
if i == 0:
first_scan_id = hdr.start['scan_id']
dt = datetime.fromtimestamp(hdr.start['time'])
formatted_date = dt.strftime('%Y-%m-%d')
tiff_series.export(hdr.documents(fill=True),
file_prefix=('{start[institution]}/'
'{start[user]}/'
'{start[project]}/'
f'{formatted_date}/'
f'{first_scan_id}-'
'-{start[scan_id]}-'
'-{start[sample]}-'
f'{pos:.2f}eV-'),
directory='Z:/images/users/')
csv.export(hdr.documents(stream_name='baseline'),
file_prefix=('{institution}/'
'{user}/'
'{project}/'
f'{formatted_date}/'
f'{first_scan_id}-'
'{scan_id}-'
'{sample}-'
f'{pos:.2f}eV-'),
directory='Z:/images/users/')
csv.export(
hdr.documents(stream_name='Izero Mesh Drain Current_monitor'),
file_prefix=('{institution}/'
'{user}/'
'{project}/'
f'{formatted_date}/'
f'{first_scan_id}-'
'{scan_id}-'
'{sample}-'
f'{pos:.2f}eV-'),
directory='Z:/images/users/')
def snapsw(seconds, samplename='', sampleid='', num_images=1, dark=0):
# TODO: do it more generally
# yield from bps.mv(sw_det.setexp, seconds)
yield from bps.mv(sw_det.waxs.cam.acquire_time, seconds)
yield from bps.mv(sw_det.saxs.cam.acquire_time, seconds)
yield from bps.mv(sw_det.waxs.cam.shutter_close_delay, 200)
yield from bps.mv(sw_det.saxs.cam.shutter_close_delay, 200)
yield from bps.mv(sw_det.waxs.cam.shutter_open_delay, 200)
yield from bps.mv(sw_det.saxs.cam.shutter_open_delay, 200)
if (dark):
yield from bps.mv(sw_det.saxs.cam.shutter_mode, 0)
if samplename is "":
samplename = "dark"
else:
yield from bps.mv(sw_det.saxs.cam.shutter_mode, 2)
if samplename is "":
samplename = "snap"
md = RE.md
md['sample'] = samplename
md['sampleid'] = sampleid
md['exptime'] = seconds
uid = (yield from bp.count([sw_det], num=num_images, md=md))
hdr = db[uid]
quick_view(hdr)
dt = datetime.fromtimestamp(hdr.start['time'])
formatted_date = dt.strftime('%Y-%m-%d')
energy = hdr.table(stream_name='baseline')['Beamline Energy_energy'][1]
tiff_series.export(hdr.documents(fill=True),
file_prefix=('{start[institution]}/'
'{start[user]}/'
'{start[project]}/'
f'{formatted_date}/'
'{start[scan_id]}-'
'{start[sample]}-'
f'{energy:.2f}eV-'),
directory='Z:/images/users/')
csv.export(hdr.documents(stream_name='baseline'),
file_prefix=('{institution}/'
'{user}/'
'{project}/'
f'{formatted_date}/'
'{scan_id}-'
'{sample}-'
f'{energy:.2f}eV-'),
directory='Z:/images/users/')
csv.export(hdr.documents(stream_name='Izero Mesh Drain Current_monitor'),
file_prefix=('{institution}/'
'{user}/'
'{project}/'
f'{formatted_date}/'
'{scan_id}-'
'{sample}-'
f'{energy:.2f}eV-'),
directory='Z:/images/users/')
def test_export(tmp_path, example_data):
''' runs a test using the `example_data` pytest.fixture.
Runs a test using the `suitcase.utils.tests.conftest` fixture
`example_data`.
..note::
Due to the `example_data` `pytest.fixture` this will run multiple tests
each with a range of detectors and a range of event_types. see
`suitcase.utils.tests.conftest` for more info
'''
collector = example_data(ignore=[])
expected_dict = create_expected(collector)
artifacts = export(collector, tmp_path, file_prefix='')
if 'stream_data' in artifacts.keys():
for filename in artifacts['stream_data']:
streamname = str(filename).split('/')[-1].split('.')[0]
actual = pandas.read_csv(filename)
expected = expected_dict[streamname][list(actual.columns.values)]
pandas.testing.assert_frame_equal(actual, expected)
def test_export_events(RE, hw):
'''Test to see if the suitcase.csv.export works on events.
'''
collector = []
def collect(name, doc):
collector.append((name, doc))
RE.subscribe(collect)
RE(count([hw.det], 5))
with tempfile.NamedTemporaryFile(mode='w') as f:
# We don't actually need f itself, just a filepath to template on.
meta, *csvs = export(collector, f.name)
csv, = csvs
docs = (doc for name, doc in collector)
start, descriptor, *events, stop = docs
expected = {}
expected_dict = {'data': {'det': [], 'seq_num': []}, 'time': []}
for event in events:
expected_dict['data']['det'].append(event['data']['det'])
expected_dict['data']['seq_num'].append(event['seq_num'])
expected_dict['time'].append(event['time'])
expected['events'] = pandas.DataFrame(expected_dict['data'],
index=expected_dict['time'])
expected['events'].index.name = 'time'
with open(meta) as f:
actual = json.load(f)
# This next section is used to convert lists to tuples for the assert below
for dims in actual['start']['hints']['dimensions']:
new_dims = []
for dim in dims:
if type(dim) is list:
new_dims.append(tuple(dim))
else:
new_dims.append(dim)
actual['start']['hints']['dimensions'] = [tuple(new_dims)]
expected.update({
'start': start,
'stop': stop,
'descriptors': {
'primary': [descriptor]
}
})
actual['events'] = pandas.read_csv(csv, index_col=0)
assert actual.keys() == expected.keys()
assert actual['start'] == expected['start']
assert actual['descriptors'] == expected['descriptors']
assert actual['stop'] == expected['stop']
assert_frame_equal(expected['events'], actual['events'])
def test_export(RE, hw):
collector = []
def collect(name, doc):
collector.append((name, doc))
RE.subscribe(collect)
RE(count([hw.det], 5))
with tempfile.NamedTemporaryFile(mode='w') as f:
# We don't actually need f itself, just a filepath to template on.
generate_csv(f)
filepaths = export(collector, f.name)
print(filepaths)
def test_file_prefix_formatting(file_prefix_list, example_data, tmp_path):
'''Runs a test of the ``file_prefix`` formatting.
..note::
Due to the `file_prefix_list` and `example_data` `pytest.fixture`'s
this will run multiple tests each with a range of file_prefixes,
detectors and event_types. See `suitcase.utils.conftest` for more info.
'''
collector = example_data()
file_prefix = file_prefix_list()
artifacts = export(collector, tmp_path, file_prefix=file_prefix)
for name, doc in collector:
if name == 'start':
templated_file_prefix = file_prefix.format(
start=doc).partition('-')[0]
break
if artifacts:
unique_actual = set(str(artifact).split('/')[-1].partition('-')[0]
for artifact in artifacts['stream_data'])
assert unique_actual == set([templated_file_prefix])