Access tiff images on Linux

[mrakitin]

The tiff images are saved on a Windows machine xf07id1-ws17 (10.7.0.217):

profile_collection/startup/30-detectors.py

Lines 27 to 31 in cb4b7cb

	tiff = C(TIFFPluginWithFileStore, 'TIFF1:',
	write_path_template='/mnt/zdrive/data/%Y/%m/%d/',
	read_path_template='Z:\\images\\data\\%Y\\%m\\%d\\',
	read_attrs=[],
	root='Z:\\images\\data\\')

Even if the volume is mounted on a Linux machine with the following command:

profile_collection/startup/30-detectors.py

Line 91 in cb4b7cb

# sudo mount -t cifs //10.7.0.217/data/ /mnt/zdrive -o user=linuxuser,pass=greateyes

it's still not possible to retrieve the data:

In [15]: imgs = list(db['0372d961'].data('Synced_saxs_image'))  # scan_id=2460
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-15-4c2934cf7df9> in <module>
----> 1 imgs = list(db['0372d961'].data('Synced_saxs_image'))  # scan_id=2460

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/_core.py in data(self, field, stream_name, fill)
    490         for event in self.events(stream_name=stream_name,
    491                                  fields=[field],
--> 492                                  fill=fill):
    493             yield event['data'][field]
    494

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/_core.py in events(self, stream_name, fields, fill)
    380         ev_gen = self.db.get_events([self], stream_name=stream_name,
    381                                     fields=fields, fill=fill)
--> 382         for ev in ev_gen:
    383             yield ev
    384

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/_core.py in get_events(self, headers, stream_name, fields, fill, handler_registry)
   1509                                             stream_name=stream_name,
   1510                                             fill=fill,
-> 1511                                             handler_registry=handler_registry):
   1512             if name == 'event':
   1513                 yield doc

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/_core.py in get_documents(self, headers, stream_name, fields, fill, handler_registry)
   1603                                                                      datum)
   1604
-> 1605                             doc = proc_gen.send(doc)
   1606
   1607                         yield name, self.prepare_hook(name, doc)

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/_core.py in _fill_events_coro(self, descriptors, fields, inplace)
   2053                     d_id = data[dk]
   2054                     data[dk] = (registry_map[(desc_id, dk)]
-> 2055                                 .retrieve(d_id))
   2056                     filled[dk] = d_id
   2057

/opt/conda_envs/collection-2019-2.1-rsoxs/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/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/assets/core.py in 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
     68

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/databroker/assets/handlers.py in __call__(self, point_number)
    106         ret = []
    107         for fn in self._fnames_for_point(point_number):
--> 108             with tifffile.TiffFile(fn) as tif:
    109                 ret.append(tif.asarray())
    110         return np.array(ret).squeeze()

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/tifffile/tifffile.py in __init__(self, arg, name, offset, size, multifile, multifile_close, pages, fastij, is_ome)
   1321
   1322         self._fh = FileHandle(arg, mode='rb',
-> 1323                               name=name, offset=offset, size=size)
   1324         self.offset_size = None
   1325         self.pages = []

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/tifffile/tifffile.py in __init__(self, file, mode, name, offset, size)
   3519         self._close = True
   3520         self.is_file = False
-> 3521         self.open()
   3522
   3523     def open(self):

/opt/conda_envs/collection-2019-2.1-rsoxs/lib/python3.6/site-packages/tifffile/tifffile.py in open(self)
   3530             self._file = os.path.realpath(self._file)
   3531             self._dir, self._name = os.path.split(self._file)
-> 3532             self._fh = open(self._file, self._mode)
   3533             self._close = True
   3534             if self._offset is None:

FileNotFoundError: [Errno 2] No such file or directory: '/home/mrakitin/.ipython/profile_collection/startup/Z:\\images\\data/2019\\05\\29/72271a43-61ff-4dc7-9457_000000.tiff'

Need to figure out a way how to access the data either with the root_map as it's done at XPD, or by more sophisticated methods.

[mrakitin]

We will check what we can do when @danielballan will come back from vacation.

[mrakitin]

xf07id1-ca1 needed this to mount successfully:

$ sudo apt install cifs-utils

[EliotGann]

right, you would need to use the write directory (the linux directory equivalent) to read it from a linux machine. the read directory is for windows. Basically it should pick the directory based on if it is running on windows or linux (for writing or reading)

[tacaswell]

Interesting, at every other beamline where we have mixed windows / linux read/write paths it is in the context of a windows IOC and wanting to access from linux. We do not record the write_path in the database as that is "for the camera" where as the read_path is "for the consumer".

As @mrakitin says, the solution here is to use root_map (https://nsls-ii.github.io/databroker/configuration.html#coping-with-moved-files-or-different-mount-points ) or db.reg.set_root_map({...}), however I am not 100% sure that having a windows-style rpath and a linux-style root is going to work out of the box...