def test_deregister():
test_reg = fsa._FS_SINGLETON.handler_reg
test_spec_name = str(uuid.uuid4())
fsa.register_handler(test_spec_name, SynHandlerMod)
assert test_reg[test_spec_name] is SynHandlerMod
fsa.deregister_handler(test_spec_name)
assert test_spec_name not in test_reg
def test_register_fail():
with fsa.handler_context({'syn-mod': SynHandlerMod}):
# shouldn't raise, it is a no-op as it is regiristering
# the same class with the same name
fsa.register_handler('syn-mod', SynHandlerMod)
# should raise as it is trying to change the registered class
with pytest.raises(RuntimeError):
fsa.register_handler('syn-mod', SynHandlerEcho)
def register_builtin_handlers():
"Register all the handlers built in to filestore."
# TODO This will blow up if any non-leaves in the class heirarchy
# have non-empty specs. Make this smart later.
for cls in vars(handlers).values():
if isinstance(cls, type) and issubclass(cls, HandlerBase):
logger.debug("Found Handler %r for specs %r", cls, cls.specs)
for spec in cls.specs:
logger.debug("Registering Handler %r for spec %r", cls, spec)
register_handler(spec, cls)
def setup_module(module):
fs_setup()
register_handler('AD_HDF5', AreaDetectorHDF5Handler)
register_handler('AD_HDF5_SWMR', AreaDetectorHDF5SWMRHandler)
register_handler('AD_HDF5_TS', AreaDetectorHDF5TimestampHandler)
register_handler('AD_HDF5_SWMR_TS', AreaDetectorHDF5SWMRTimestampHandler)
def test_overwrite_global():
h_cache = fsa._FS_SINGLETON._handler_cache
mock_base = dict(spec='syn-mod',
resource_path='',
resource_kwargs={'shape': (5, 7)})
res = fsa.insert_resource(**mock_base)
cache_key = (str(res['id']), SynHandlerMod.__name__)
with fsa.handler_context({'syn-mod': SynHandlerMod}):
fsa.get_spec_handler(res['id'])
assert cache_key in h_cache
fsa.register_handler('syn-mod', SynHandlerEcho, overwrite=True)
assert cache_key not in h_cache
self.filename = str(filename)
def __call__(self, **kwargs):
return load_gr_file(self.filename, **kwargs)[1]
class GeneratedPDFHandler(HandlerBase):
specs = {'genpdf'} | HandlerBase.specs
def __init__(self, filename):
self.filename = str(filename)
def __call__(self, **kwargs):
return np.load(self.filename)
class FileLocation(HandlerBase):
specs = {'fileloc'} | HandlerBase.specs
def __init__(self, filename):
self.filename = filename
def __call__(self, **kwargs):
return self.filename
handlers = [ASEAtomsHandler, PDFGetX3Handler, GeneratedPDFHandler]
for handler in handlers:
for spec in handler.specs:
register_handler(spec, handler)
# 4 -- under-responsive
# 8 -- over-responsive
# 16 -- noisy
pixel_mask = md['pixel_mask']
pixel_mask[pixel_mask > 0] = 1
pixel_mask[pixel_mask == 0] = 2
pixel_mask[pixel_mask == 1] = 0
pixel_mask[pixel_mask == 2] = 1
md['framerate'] = 1. / md['frame_time']
# TODO Return a multi-dimensional PIMS seq
return FixedEigerImages(master_path, md)
deregister_handler('AD_EIGER')
_HANDLER_CACHE.clear()
register_handler('AD_EIGER', LazyEigerHandler)
def print_attrs(name, obj):
print(name)
for key, val in obj.attrs.items():
print(" %s: %s" % (key, val))
###################################################
##for image process
###################################################
class Reverse_Coordinate(object):
def __init__(self, indexable, mask):
from bluesky.examples import *
from bluesky.broker_examples import *
from bluesky.broker_callbacks import LiveImage
from bluesky.tests.utils import setup_test_run_engine
from matplotlib import pyplot as plt
from xray_vision.backend.mpl.cross_section_2d import CrossSection
import numpy as np
import filestore.api as fsapi
import time as ttime
from filestore.handlers import NpyHandler
fsapi.register_handler('npy', NpyHandler)
def stepscan(det, motor):
for i in np.linspace(-5, 5, 75):
yield Msg('open_run')
yield Msg('create')
yield Msg('set', motor, i)
yield Msg('trigger', det)
yield Msg('read', motor)
yield Msg('read', det)
yield Msg('save')
yield Msg('close_run')
ic = LiveImage('det_2d')
table_callback = LiveTable(fields=[motor.name, det_2d._name])
RE = setup_test_run_engine()
RE(stepscan(det_2d, motor), subs={'event': ic, 'all': table_callback}, beamline_id='c08i')
def setup():
fs_setup()
# register the dummy handler to use
register_handler('syn-mod', SynHandlerMod)
class FixedAreaDetectorTiffHandler(HandlerBase):
specs = {'AD_TIFF'} | HandlerBase.specs
def __init__(self, fpath, template, filename, frame_per_point=1):
self._path = fpath
self._fpp = frame_per_point
self._template = template.replace('_%6.6d', '*')
self._filename = self._template % (self._path,
filename)
self._image_sequence = pims.ImageSequence(self._filename)
def __call__(self, point_number):
start = int(point_number * self._fpp)
stop = int((point_number + 1) * self._fpp)
if stop > len(self._image_sequence):
# if asking for an image past the end, make sure we have an up
# to
# date list of the existing files
self._image_sequence = pims.ImageSequence(self._filename)
if stop > len(self._image_sequence):
# if we _still_ don't have enough files, raise
raise IntegrityError("Seeking Frame {0} out of {1} "
" frames.".format(stop, len(self._image_sequence)))
return np.asarray(list(self._image_sequence[start:stop])).squeeze()
import databroker # so that built-in handlers are registered
from filestore.api import deregister_handler, register_handler
deregister_handler('AD_TIFF')
register_handler('AD_TIFF', FixedAreaDetectorTiffHandler)
from dataportal.examples.sample_data import common
import six
import h5py
import os.path as op
import numpy as np
import datetime
import uuid
import logging
logger = logging.getLogger(__name__)
noisy = common.noisy
register_handler('hdf_maps', HDFM)
def save_syn_data(eid, data, base_path=None):
"""
Save a array as hdf format to disk.
Defaults to saving files in :path:`~/.fs_cache/YYYY-MM-DD.h5`
Parameters
----------
eid : unicode
id for file name
data : ndarray
The data to be saved
base_path : str, optional
The base-path to use for saving files. If not given
# 4 -- under-responsive
# 8 -- over-responsive
# 16 -- noisy
pixel_mask = md["pixel_mask"]
pixel_mask[pixel_mask > 0] = 1
pixel_mask[pixel_mask == 0] = 2
pixel_mask[pixel_mask == 1] = 0
pixel_mask[pixel_mask == 2] = 1
md["framerate"] = 1.0 / md["frame_time"]
# TODO Return a multi-dimensional PIMS seq
return FixedEigerImages(master_path, md)
deregister_handler("AD_EIGER")
_HANDLER_CACHE.clear()
register_handler("AD_EIGER", LazyEigerHandler)
def print_attrs(name, obj):
print(name)
for key, val in obj.attrs.items():
print(" %s: %s" % (key, val))
###################################################
##for image process
###################################################
class Reverse_Coordinate(object):
def __init__(self, indexable, mask):
def __call__(self, frame=None, channel=None):
# Don't read out the dataset until it is requested for the first time.
self._get_dataset()
return self._dataset[frame, channel - 1, :].squeeze()
def get_roi(self, roi_info, frame=None, max_points=None):
self._get_dataset()
chan = roi_info.chan
bin_low = roi_info.bin_low
bin_high = roi_info.bin_high
roi = np.sum(self._dataset[:, chan - 1, bin_low:bin_high], axis=1)
if max_points is not None:
roi = roi[:max_points]
if len(roi) < max_points:
roi = np.pad(roi, ((0, max_points - len(roi)), ), 'constant')
if frame is not None:
roi = roi[frame, :]
return roi
def __repr__(self):
return '{0.__class__.__name__}(filename={0._filename!r})'.format(self)
fs_api.register_handler(Xspress3HDF5Handler.HANDLER_NAME,
Xspress3HDF5Handler)
def setup():
global conn
db_disconnect()
db_connect(db_name, 'localhost', 27017)
register_handler('AD_HDF5', AreaDetectorHDF5Handler)
def dtype(self):
return self.pixel_type
@property
def shape(self):
return self.frame_shape
class LazyEigerHandler(HandlerBase):
specs = {'AD_EIGER'} | HandlerBase.specs
def __init__(self, fpath, frame_per_point, mapping=None):
# create pims handler
self.vals_dict = EIGER_MD_DICT.copy()
if mapping is not None:
self.vals_dict.update(mapping)
self._base_path = fpath
self.fpp = frame_per_point
def __call__(self, seq_id):
import h5py
master_path = '{}_{}_master.h5'.format(self._base_path, seq_id)
md = {}
print('hdf5 path = %s' % master_path)
with h5py.File(master_path, 'r') as f:
md = {k: f[v].value for k, v in self.vals_dict.items()}
# TODO Return a multi-dimensional PIMS seq.
return FixedEigerImages(master_path, md)
deregister_handler('AD_EIGER')
register_handler('AD_EIGER', LazyEigerHandler)
def register():
import filestore.api as fs_api
fs_api.register_handler(Xspress3HDF5Handler.HANDLER_NAME,
Xspress3HDF5Handler)
from bluesky.examples import *
from bluesky.broker_examples import *
from bluesky.broker_callbacks import LiveImage
from bluesky.tests.utils import setup_test_run_engine
from matplotlib import pyplot as plt
from xray_vision.backend.mpl.cross_section_2d import CrossSection
import numpy as np
import filestore.api as fsapi
import time as ttime
from filestore.handlers import NpyHandler
fsapi.register_handler('npy', NpyHandler)
def stepscan(det, motor):
for i in np.linspace(-5, 5, 75):
yield Msg('open_run')
yield Msg('create')
yield Msg('set', motor, i)
yield Msg('trigger', det)
yield Msg('read', motor)
yield Msg('read', det)
yield Msg('save')
yield Msg('close_run')
ic = LiveImage('det_2d')
table_callback = LiveTable(fields=[motor._name, det_2d._name])
RE = setup_test_run_engine()
RE(stepscan(det_2d, motor),
subs={
def register():
import filestore.api as fs_api
fs_api.register_handler(TimepixHDF5Handler._handler_name,
TimepixHDF5Handler, overwrite=True)