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Download NY Head model files automatically if missing #192

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merged 8 commits into from Apr 12, 2023
Merged

Download NY Head model files automatically if missing #192

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7e7834e
Added automatic download of New York Head model, if query can not be …
torbjone Mar 30, 2023
1b345ea
Switch to automatic download of NY Head file, if not given
torbjone Apr 11, 2023
ce1b1b4
flake8 fix
torbjone Apr 11, 2023
4de111c
Flake8 bare except
torbjone Apr 11, 2023
d9058eb
Tested changing COVERALLS_REPO_TOKEN to GITHUB_TOKEN
torbjone Apr 11, 2023
58ffd40
Tested changing COVERALLS_REPO_TOKEN to GITHUB_TOKEN
torbjone Apr 11, 2023
21e3b6e
Updated version and added catching of errors
torbjone Apr 12, 2023
fc5ceb6
Flake8 fix
torbjone Apr 12, 2023
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4 changes: 2 additions & 2 deletions .github/workflows/coveralls.yml
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Expand Up @@ -35,7 +35,7 @@ jobs:
pip install neuron
- name: Test with pytest and coveralls
env:
COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
py.test -v --cov=lfpykit/tests/
coveralls
coveralls --service=github
23 changes: 16 additions & 7 deletions lfpykit/eegmegcalc.py
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Expand Up @@ -1406,22 +1406,31 @@ def _load_head_model(self, nyhead_file):
nyhead_file = os.path.join(os.getcwd(), "sa_nyhead.mat")
self.head_file = os.path.abspath(nyhead_file)
if not os.path.isfile(self.head_file):

print(f"New York head model file not found: {self.head_file}")
print(f"Now downloading as {self.head_file} (710 MB). "
+ "This might take a while ...")
import urllib
from urllib.request import urlopen
import ssl
print("New York head-model file not found: %s" % self.head_file)
yn = input(f"Download as {self.head_file} (710 MB)? [y/n]: ")
if yn == 'y':
print("Now downloading. This might take a while ...")
try:
nyhead_url = 'https://www.parralab.org/nyhead/sa_nyhead.mat'
u = urlopen(nyhead_url,
context=ssl._create_unverified_context())
localFile = open(self.head_file, 'wb')
localFile.write(u.read())
localFile.close()
print("Download done!")
else:
print("Exiting program ...")
sys.exit()
except urllib.error.URLError:
print("URLError: Is the internet connection working?")
raise
except PermissionError:
print("PermissionError: Write access is needed "
+ "for downloading head model.")
raise
except Exception:
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I think this should capture URLError (as in URLError: <urlopen error [Errno -2] Name or service not known> or URLError: <urlopen error [Errno 8] nodename nor servname provided, or not known>), otherwise this looks good!

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I don't think URLError is a built-in error in python though, are you sure we should do this? I considered catching both PermissionError and URLErrors, but originally decided against it, since in the end I did not supply any more information than what was already effectively given in the error name.

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URLError is raised by urllib which is part of the standard distribution. I think it is fine to capture it as well as PermissionError then. Having consecutive excepts should be ok, according to the docs:

import sys
try:
    f = open('myfile.txt')
    s = f.readline()
    i = int(s.strip())
except OSError as err:
    print("OS error:", err)
except ValueError:
    print("Could not convert data to an integer.")
except Exception as err:
    print(f"Unexpected {err=}, {type(err)=}")
    raise

print("Unable to find or download New York head model file")
raise

self.head_data = h5py.File(self.head_file, 'r')["sa"]
self.cortex = np.array(self.head_data["cortex75K"]["vc"])
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2 changes: 1 addition & 1 deletion lfpykit/version.py
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@@ -1 +1 @@
version = "0.5"
version = "0.5.1"