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support install from git / fix package resources for 3brain_channel_map #30

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tbenst opened this issue Apr 21, 2021 · 0 comments
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@tbenst
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tbenst commented Apr 21, 2021

pip install git+https://github.com/tbenst/glia.git should work

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
o:\users\tyler\code\prairie_view\notebooks\2021-04-20_calc_offset.py in 
----> 2 from prairie_view.files import read_reshape_and_copy
      3 from glob import glob
      4 
      5 ref_zseries_dir = r"E:\tyler\2021-04-20_wt-chrmine_6dpf_6f\fish1\TSeries-zstack-motion-correction-etl-052"
      6 

\\oak-smb-deissero.stanford.edu\groups\deissero\users\tyler\code\prairie_view\prairie_view\files.py in <module>
----> 1 import glia
      2 import matplotlib.pyplot as plt, numpy as np
      3 
      4 def read_and_copy(index_path_tuple, k=lambda x: x):
      5     index, path = index_path_tuple

~\Miniconda3\envs\tyler\lib\site-packages\glia\__init__.py in <module>
      1 from .analysis import *
----> 2 from .artificial import *
      3 from .machine_learning import *
      4 from .eyecandy import *
      5 from .files import *

~\Miniconda3\envs\tyler\lib\site-packages\glia\artificial.py in <module>
      6 import matplotlib.pyplot as plt
      7 from typing import List, Any, Union
----> 8 from .functional import f_filter, f_map, f_reduce
      9 from scipy import signal
     10 from glia.types import Unit

~\Miniconda3\envs\tyler\lib\site-packages\glia\functional.py in <module>
      8 from multiprocessing import Pool
      9 from multiprocessing.pool import ThreadPool
---> 10 from .config import processes
     11 import glia.config as config
     12 from tqdm.auto import tqdm

~\Miniconda3\envs\tyler\lib\site-packages\glia\config.py in <module>
     34 resource_path = '/'.join(('..', 'resources', '3brain_channel_map.npy'))  # Do not use os.path.join()
     35 # or for a file-like stream:
---> 36 channel_map_file = pkg_resources.resource_stream(resource_package, resource_path)
     37 
     38 channel_map_3brain = np.load(channel_map_file)

~\Miniconda3\envs\tyler\lib\site-packages\pkg_resources\__init__.py in resource_stream(self, package_or_requirement, resource_name)
   1147     def resource_stream(self, package_or_requirement, resource_name):
   1148         """Return a readable file-like object for specified resource"""
-> 1149         return get_provider(package_or_requirement).get_resource_stream(
   1150             self, resource_name
   1151         )

~\Miniconda3\envs\tyler\lib\site-packages\pkg_resources\__init__.py in get_resource_stream(self, manager, resource_name)
   1621 
   1622     def get_resource_stream(self, manager, resource_name):
-> 1623         return open(self._fn(self.module_path, resource_name), 'rb')
   1624 
   1625     def _get(self, path):

FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\User\\Miniconda3\\envs\\tyler\\lib\\site-packages\\glia\\..\\resources\\3brain_channel_map.npy'
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