def test_hdf5_runtime_error(db_all, RE):
RE.subscribe(db_all.insert)
RE(count([det], 5, delay=0.1), owner="Tom")
hdr = db_all[-1]
fname = tempfile.NamedTemporaryFile()
if hasattr(hdr, 'db'):
hdf5.export(hdr, fname.name, db=None)
else:
with pytest.raises(RuntimeError):
hdf5.export(hdr, fname.name, db=None)
def test_hdf5_export_single():
"""
Test the hdf5 export with a single header and
verify the output is correct
"""
temperature_ramp.run()
hdr = db[-1]
fname = tempfile.NamedTemporaryFile()
hdf5.export(hdr, fname.name)
shallow_header_verify(fname.name, hdr)
def test_hdf5_export_single():
"""
Test the hdf5 export with a single header and
verify the output is correct
"""
temperature_ramp.run()
hdr = db[-1]
fname = tempfile.NamedTemporaryFile()
hdf5.export(hdr, fname.name)
shallow_header_verify(fname.name, hdr)
def test_hdf5_export_single_no_uid(db_all, RE, hw):
"""
Test the hdf5 export with a single header and
verify the output is correct. No uid is used.
"""
RE.subscribe(db_all.insert)
hw.motor.delay = 0.1
RE(scan([hw.det], hw.motor, -1, 1, 10), owner="Tom")
hdr = db_all[-1]
fname = tempfile.NamedTemporaryFile()
hdf5.export(hdr, fname.name, use_uid=False, db=db_all)
shallow_header_verify(fname.name, hdr, db_all, use_uid=False)
def test_hdf5_export_with_fields_single(db_all, RE, hw):
"""
Test the hdf5 export with a single header and
verify the output is correct; fields kwd is used.
"""
RE.subscribe(db_all.insert)
hw.motor.delay = 0.1
RE(scan([hw.det], hw.motor, -1, 1, 10), owner="Tom")
hdr = db_all[-1]
fname = tempfile.NamedTemporaryFile()
hdf5.export(hdr, fname.name, fields=['point_dev']) #, db=db_all)
shallow_header_verify(fname.name, hdr, db_all, fields=['point_dev'])
def test_hdf5_export_single_stream_name(mds_all):
"""
Test the hdf5 export with a single header and
verify the output is correct. No uid is used.
"""
mds = mds_all
temperature_ramp.run(mds)
db = Broker(mds, fs=None)
hdr = db[-1]
fname = tempfile.NamedTemporaryFile()
hdf5.export(hdr, fname.name, mds, stream_name='primary')
shallow_header_verify(fname.name, hdr, mds, stream_name='primary')
def test_hdf5_export_with_fields_single(mds_all):
"""
Test the hdf5 export with a single header and
verify the output is correct; fields kwd is used.
"""
mds = mds_all
temperature_ramp.run(mds)
db = Broker(mds, fs=None)
hdr = db[-1]
fname = tempfile.NamedTemporaryFile()
hdf5.export(hdr, fname.name, mds, fields=['point_dev'])
shallow_header_verify(fname.name, hdr, mds, fields=['point_dev'])
def test_hdf5_export_list():
"""
Test the hdf5 export with a list of headers and
verify the output is correct
"""
temperature_ramp.run()
temperature_ramp.run()
hdrs = db[-2:]
fname = tempfile.NamedTemporaryFile()
# test exporting a list of headers
hdf5.export(hdrs, fname.name)
for hdr in hdrs:
shallow_header_verify(fname.name, hdr)
def test_hdf5_export_list():
"""
Test the hdf5 export with a list of headers and
verify the output is correct
"""
temperature_ramp.run()
temperature_ramp.run()
hdrs = db[-2:]
fname = tempfile.NamedTemporaryFile()
# test exporting a list of headers
hdf5.export(hdrs, fname.name)
for hdr in hdrs:
shallow_header_verify(fname.name, hdr)
def ESM_export(scan_ID, filename):
'''
This routine is used to export a data file to an HDF5 file for transfer to other analysis
software.
PARAMETERS
----------
scan_ID : list.
The scan id numbers (as a list) for the data to export, can be -1, -2 to indicate the last
or second to last scan etc.
filename : str.
The filename to use for the output data file.
filestring : str, output
The file path, and file name, of the file that was created.
'''
#reference the header file for the scan to be saved.
hdr = db[scan_ID]
# check if the filename includes the '.h5' extension and add it if not.
if not filename.endswith('.h5'):
filename += '.h5'
# give the filepath of where to store the h5 file
filepath = '/direct/XF21ID1/hdf5_files/' + datetime.today().strftime(
'%Y_%m')
#check if a current month directory exists, if not create it.
if not os.path.exists(filepath):
os.makedirs(filepath)
#create the file path and file name string
filestring = filepath + '/' + filename
#check if the file already exists, if so ask user if overwrite is necesary.
if os.path.isfile(filestring):
if ask_user_continue(
'The file already exists, continuing will overwrite it') == 0:
raise RuntimeError('user quit save')
else:
os.remove(filestring)
# actually write the new file
hdf5.export(hdr, filestring)
# return the file path and file name so the user can find it.
return filestring
def test_hdf5_export_list(db_all, RE):
"""
Test the hdf5 export with a list of headers and
verify the output is correct
"""
RE.subscribe(db_all.insert)
RE(count([det], 5, delay=0.1), owner="Tom")
RE(count([det], 6, delay=0.1), owner="Ken")
hdrs = db_all[-2:]
fname = tempfile.NamedTemporaryFile()
# test exporting a list of headers
hdf5.export(hdrs, fname.name, db=db_all)
for hdr in hdrs:
shallow_header_verify(fname.name, hdr, db=db_all)
def test_hdf5_export_list(mds_all):
"""
Test the hdf5 export with a list of headers and
verify the output is correct
"""
mds = mds_all
temperature_ramp.run(mds)
temperature_ramp.run(mds)
db = Broker(mds, fs=None)
hdrs = db[-2:]
fname = tempfile.NamedTemporaryFile()
# test exporting a list of headers
hdf5.export(hdrs, fname.name, mds)
for hdr in hdrs:
shallow_header_verify(fname.name, hdr, mds)