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dbbs-lab / bsb-core

The Brain Scaffold Builder
https://bsb.readthedocs.io
GNU General Public License v3.0
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FileNotFoundError with file in store #700

Closed Helveg closed 1 year ago

Helveg commented 1 year ago

Opening a network file yields: 

robin@TNG2019:/mnt/c/Users/Robin/Downloads$ pyenv local bsb
(bsb) robin@TNG2019:/mnt/c/Users/Robin/Downloads$ python
Python 3.9.1 (default, Feb 18 2021, 16:03:49)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from bsb.core import from_storage
>>> net = from_storage("network.hdf5")
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'orientation_path' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'depth_from_top' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'depth_from_bottom' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'labels_config' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'orientation_path' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'depth_from_top' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'depth_from_bottom' in {root}.placement.general_placement.distribute.morphologies
/mnt/d/GIT/bsb/bsb/config/_make.py:210: ConfigurationWarning: Unknown attribute: 'labels_config' in {root}.placement.general_placement.distribute.morphologies
Traceback (most recent call last):
  File "/mnt/d/GIT/bsb/bsb/storage/_files.py", line 101, in provide_locally
    raise FileNotFoundError()
FileNotFoundError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/mnt/d/GIT/bsb/bsb/profiling.py", line 157, in decorated
    return f(*args, **kwargs)
  File "/mnt/d/GIT/bsb/bsb/core.py", line 47, in from_storage
    return open_storage(root).load()
  File "/mnt/d/GIT/bsb/bsb/storage/__init__.py", line 257, in load
    return Scaffold(storage=self)
  File "/mnt/d/GIT/bsb/bsb/core.py", line 130, in __init__
    self._bootstrap(config, storage, clear=clear)
  File "/mnt/d/GIT/bsb/bsb/core.py", line 176, in _bootstrap
    self._configuration._bootstrap(self)
  File "/mnt/d/GIT/bsb/bsb/config/_config.py", line 87, in _bootstrap
    scaffold.topology = topology = create_topology(regions, start, end)
  File "/mnt/d/GIT/bsb/bsb/topology/__init__.py", line 30, in create_topology
    topology.do_layout(hint)
  File "/mnt/d/GIT/bsb/bsb/topology/region.py", line 43, in do_layout
    layout = self.get_layout(hint)
  File "/mnt/d/GIT/bsb/bsb/topology/region.py", line 39, in get_layout
    layouts = [dep.get_layout(hint) for dep in self.get_dependencies()]
  File "/mnt/d/GIT/bsb/bsb/topology/region.py", line 39, in <listcomp>
    layouts = [dep.get_layout(hint) for dep in self.get_dependencies()]
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 313, in get_layout
    return Layout(RhomboidData(*self.voxelset.bounds), owner=self)
  File "/home/robin/.pyenv/versions/3.9.1/lib/python3.9/functools.py", line 969, in __get__
    val = self.func(instance)
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 295, in voxelset
    return self.get_voxelset()
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 411, in get_voxelset
    mask = self.get_mask()
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 384, in get_mask
    mask_shape = self._validate()
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 427, in _validate
    shape = self._validate_source_compat()
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 442, in _validate_source_compat
    mask_headers = {s: s.get_header() for s in self._mask_src}
  File "/mnt/d/GIT/bsb/bsb/topology/partition.py", line 442, in <dictcomp>
    mask_headers = {s: s.get_header() for s in self._mask_src}
  File "/mnt/d/GIT/bsb/bsb/storage/_files.py", line 420, in get_header
    with self.file.provide_locally() as (path, encoding):
  File "/home/robin/.pyenv/versions/3.9.1/lib/python3.9/contextlib.py", line 117, in __enter__
    return next(self.gen)
  File "/mnt/d/GIT/bsb/bsb/storage/_files.py", line 104, in provide_locally
    raise FileNotFoundError(f"Can't find {self}")
FileNotFoundError: Can't find <bsb.storage._files.FileDependency object 'file:///home/toromis/Workspace/dbbs/cereb-builder/data/corrections_cereb/annotations_pu.nrrd' at 0x7f14e125ffa0>

but the file should be coming from the store