swmr says it is enabled but it doesn't seem to work
ambarb opened this issue · comments
This scan is a step scan, mid-way or more through. Using get_fastccd_images()
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/csxtools/utils.py:181: UserWarning: Images and get_images are deprecated. Use Header.data('fccd_image') instead.
images = header.db.get_images(header, tag)
---------------------------------------------------------------------------
OSError Traceback (most recent call last)
<ipython-input-48-9e807f3dbb64> in <module>()
1 #%%capture
----> 2 images = get_fastccd_images(h, (bgnd8[0], bgnd2, bgnd1), flat=None)
3
4 stack = get_images_to_4D(images)
5
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/csxtools/utils.py in get_fastccd_images(light_header, dark_headers, flat, gain, tag, roi)
119 logger.info("Computed dark images in %.3f seconds", ttime.time() - t)
120
--> 121 events = _get_images(light_header, tag, roi)
122
123 # Ok, so lets return a pims pipeline which does the image conversion
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/csxtools/utils.py in _get_images(header, tag, roi)
179 def _get_images(header, tag, roi=None):
180 t = ttime.time()
--> 181 images = header.db.get_images(header, tag)
182 t = ttime.time() - t
183 logger.info("Took %.3f seconds to read data using get_images", t)
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/_core.py in get_images(self, headers, name, stream_name, handler_registry)
1712 headers=headers,
1713 name=name, stream_name=stream_name,
-> 1714 handler_registry=handler_registry)
1715
1716 def get_resource_uids(self, header):
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/_core.py in __init__(self, mds, reg, es, headers, name, handler_registry, handler_override, stream_name)
606 self.handler_registry = defaultdict(lambda: handler_override)
607 with self.reg.handler_context(self.handler_registry) as reg:
--> 608 example_frame = reg.retrieve(first_uid)
609 # Try to duck-type as a numpy array, but fall back as a general
610 # Python object.
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/assets/base_registry.py in retrieve(self, datum_id)
176 return self._api.retrieve(self._datum_col, datum_id,
177 self._datum_cache, self.get_spec_handler,
--> 178 logger)
179
180 def get_datum(self, datum_id):
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/assets/core.py in retrieve(col, datum_id, datum_cache, get_spec_handler, logger)
63 def retrieve(col, datum_id, datum_cache, get_spec_handler, logger):
64 datum = _get_datum_from_datum_id(col, datum_id, datum_cache, logger)
---> 65 handler = get_spec_handler(datum['resource'])
66 return handler(**datum['datum_kwargs'])
67
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/assets/base_registry.py in get_spec_handler(self, resource)
260 if root:
261 rpath = os.path.join(root, rpath)
--> 262 ret = handler(rpath, **kwargs)
263 h_cache[key] = ret
264 return ret
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/assets/handlers.py in __init__(self, filename, frame_per_point)
201 super(AreaDetectorHDF5Handler, self).__init__(
202 filename=filename, key=hardcoded_key,
--> 203 frame_per_point=frame_per_point)
204
205
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/assets/handlers.py in __init__(self, filename, key, frame_per_point)
151 self._dataset = None
152 self._data_objects = {}
--> 153 self.open()
154
155 def get_file_list(self, datum_kwarg_gen):
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/databroker/assets/handlers.py in open(self)
173 return
174
--> 175 self._file = h5py.File(self._filename, 'r')
176
177 def close(self):
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/h5py/_hl/files.py in __init__(self, name, mode, driver, libver, userblock_size, swmr, **kwds)
310 with phil:
311 fapl = make_fapl(driver, libver, **kwds)
--> 312 fid = make_fid(name, mode, userblock_size, fapl, swmr=swmr)
313
314 if swmr_support:
/opt/conda_envs/analysis-2018-2.1/lib/python3.6/site-packages/h5py/_hl/files.py in make_fid(name, mode, userblock_size, fapl, fcpl, swmr)
140 if swmr and swmr_support:
141 flags |= h5f.ACC_SWMR_READ
--> 142 fid = h5f.open(name, flags, fapl=fapl)
143 elif mode == 'r+':
144 fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/_objects.pyx in h5py._objects.with_phil.wrapper()
h5py/h5f.pyx in h5py.h5f.open()
OSError: Unable to open file (file is already open for write (may use <h5clear file> to clear file consistency flags))This may be some other issue not associated with the profile. I believe there is also a trac issue. If we are changing how we save the data (as per @stuwilkins project for image saving), then perhaps we can close this.