From 7d1e113768a206feeb0b8a6603184b2e73a468ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 7 Jan 2022 19:35:28 +0000
Subject: [PATCH] add deps for testing cv2 and test bugfixes
---
.gitlab-ci.yml | 3 +-
tests/aliby/test_baby_client.py | 54 +++++++++++++++++----------------
tests/aliby/test_local_expt.py | 33 +++++++++-----------
3 files changed, 45 insertions(+), 45 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index da929011..0753cd75 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -34,6 +34,7 @@ Unit test:
stage: test
# allow_failure: true
script:
+ - apt-get install ffmpeg libsm6 libxext6 -y
- poetry run pytest ./tests/
Python Code Lint:
@@ -48,7 +49,7 @@ Static Type:
- poetry run mypy . --exclude 'setup\.py$'
# We can remove the flag once this is resolved https://github.com/pypa/setuptools/issues/2345
-Bump version and release:
+Bump_release:
stage: release
script:
- poetry version ${BUMP_RULE}
diff --git a/tests/aliby/test_baby_client.py b/tests/aliby/test_baby_client.py
index 12fe5089..3c93a5be 100644
--- a/tests/aliby/test_baby_client.py
+++ b/tests/aliby/test_baby_client.py
@@ -2,51 +2,53 @@ import json
import time
import numpy as np
-from core.experiment import ExperimentLocal
-from core.segment import Tiler
-from core.baby_client import BabyClient
+from aliby.experiment import ExperimentLocal
+from aliby.baby_client import BabyClient
+from tile.tiler import Tiler
-root_dir = '/Users/s1893247/PhD/pipeline-core/data/glclvl_0' \
- '.1_mig1_msn2_maf1_sfp1_dot6_03'
+root_dir = (
+ "/Users/s1893247/PhD/pipeline-core/data/glclvl_0" ".1_mig1_msn2_maf1_sfp1_dot6_03"
+)
expt = ExperimentLocal(root_dir, finished=True)
seg_expt = Tiler(expt, finished=True)
print(seg_expt.positions)
-seg_expt.current_position = 'pos007'
+seg_expt.current_position = "pos007"
-config = {"camera": "evolve",
- "channel": "brightfield",
- "zoom": "60x",
- "n_stacks": "5z"}
+config = {"camera": "evolve", "channel": "brightfield", "zoom": "60x", "n_stacks": "5z"}
baby_client = BabyClient(expt, **config)
-print("The session is {}".format(baby_client.sessions['default']))
+print("The session is {}".format(baby_client.sessions["default"]))
# Channel 0, 0, X,Y,Z all
num_timepoints = 5
-traps_tps = [seg_expt.get_traps_timepoint(tp, tile_size=81, channels=[0],
- z=[0, 1, 2, 3, 4]).squeeze()
- for tp in range(num_timepoints)]
+traps_tps = [
+ seg_expt.get_traps_timepoint(
+ tp, tile_size=81, channels=[0], z=[0, 1, 2, 3, 4]
+ ).squeeze()
+ for tp in range(num_timepoints)
+]
segmentations = []
try:
for i, timpoint in enumerate(traps_tps):
print("Sending timepoint {};".format(i))
- status = baby_client.queue_image(timpoint,
- baby_client.sessions['default'],
- assign_mothers=True,
- return_baprobs=True,
- with_edgemasks=True)
+ status = baby_client.queue_image(
+ timpoint,
+ baby_client.sessions["default"],
+ assign_mothers=True,
+ return_baprobs=True,
+ with_edgemasks=True,
+ )
while True:
try:
- print('Loading.', end='')
- result = baby_client.get_segmentation(baby_client.sessions[
- 'default'])
+ print("Loading.", end="")
+ result = baby_client.get_segmentation(baby_client.sessions["default"])
except:
- print('.', end='')
+ print(".", end="")
time.sleep(1)
continue
break
@@ -56,10 +58,10 @@ except Exception as e:
print(segmentations)
raise e
-with open('segmentations.json', 'w') as fd:
+with open("segmentations.json", "w") as fd:
json.dump(segmentations, fd)
-print('Done.')
+print("Done.")
# print(len(segmentations[0]))
# for i in range(5):
# print("trap {}".format(i))
@@ -68,4 +70,4 @@ print('Done.')
#
# import matplotlib.pyplot as plt
# plt.imshow(np.squeeze(batches[0][0, ..., 0]))
-# plt.savefig('test_baby.pdf')
\ No newline at end of file
+# plt.savefig('test_baby.pdf')
diff --git a/tests/aliby/test_local_expt.py b/tests/aliby/test_local_expt.py
index 9b245ae4..026b54bb 100644
--- a/tests/aliby/test_local_expt.py
+++ b/tests/aliby/test_local_expt.py
@@ -3,33 +3,33 @@ from logging.handlers import RotatingFileHandler
import unittest
from pathlib import Path
-from core.experiment import Experiment
+from aliby.experiment import Experiment
## LOGGING
-logger = logging.getLogger('core')
+logger = logging.getLogger("core")
logger.handlers = []
logger.setLevel(logging.DEBUG)
console = logging.StreamHandler()
console.setLevel(logging.WARNING)
-formatter = logging.Formatter('%(name)-12s: %(levelname)-8s %(message)s')
+formatter = logging.Formatter("%(name)-12s: %(levelname)-8s %(message)s")
console.setFormatter(formatter)
logger.addHandler(console)
-file_handler = RotatingFileHandler(filename='test.log',
- maxBytes=1e5,
- backupCount=1)
+file_handler = RotatingFileHandler(filename="test.log", maxBytes=1e5, backupCount=1)
file_handler.setLevel(logging.DEBUG)
-file_formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s '
- '- %(message)s')
+file_formatter = logging.Formatter(
+ "%(asctime)s - %(name)s - %(levelname)s " "- %(message)s"
+)
file_handler.setFormatter(file_formatter)
logger.addHandler(file_handler)
-logger.debug('Set up the loggers as test.')
+logger.debug("Set up the loggers as test.")
+
+data_directory = Path(__file__).parent.parent / "data/"
+root_directory = data_directory / "glclvl_0.1_mig1_msn2_maf1_sfp1_dot6_03"
-data_directory = Path(__file__).parent.parent / 'data/'
-root_directory = data_directory / 'glclvl_0.1_mig1_msn2_maf1_sfp1_dot6_03'
class TestCase(unittest.TestCase):
def setUp(self):
@@ -44,14 +44,11 @@ class TestCase(unittest.TestCase):
self.assertTupleEqual(test_slice.shape, (2, 3, 100, 100, 3))
def test_experiment_metadata(self):
- self.assertTrue('positions' in self.expt.metadata.keys())
- self.assertTrue('channels' in self.expt.metadata.keys())
- self.assertTrue('time_settings' in self.expt.metadata.keys())
- self.assertTrue('zsectioning' in self.expt.metadata.keys())
-
+ self.assertTrue("positions" in self.expt.metadata.keys())
+ self.assertTrue("channels" in self.expt.metadata.keys())
+ self.assertTrue("time_settings" in self.expt.metadata.keys())
+ self.assertTrue("zsectioning" in self.expt.metadata.keys())
if __name__ == "__main__":
unittest.main()
-
-
--
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