From be4adac9fdc6baf95fb19897c4fc860a22dbbe1b Mon Sep 17 00:00:00 2001
From: Alan Munoz <alan.munoz@ed.ac.uk>
Date: Sun, 9 Jan 2022 20:58:23 +0000
Subject: [PATCH] test skips, bugfixes and postproc update
---
aliby/io/omero.py | 2 +-
aliby/tests/__init__.py | 0
aliby/tests/test_integration.py | 28 -------
aliby/tests/test_units.py | 99 -------------------------
aliby/tile/traps.py | 3 +-
poetry.lock | 14 ++--
pyproject.toml | 2 +-
tests/aliby/test_baby_client.py | 127 ++++++++++++++++++--------------
tests/aliby/test_local_expt.py | 3 +
tests/aliby/test_pipeline.py | 28 +++++--
tests/aliby/test_segment.py | 2 +-
11 files changed, 108 insertions(+), 200 deletions(-)
delete mode 100644 aliby/tests/__init__.py
delete mode 100644 aliby/tests/test_integration.py
delete mode 100644 aliby/tests/test_units.py
diff --git a/aliby/io/omero.py b/aliby/io/omero.py
index 914b68ba..124f562f 100644
--- a/aliby/io/omero.py
+++ b/aliby/io/omero.py
@@ -2,7 +2,7 @@ import h5py
import omero
from omero.gateway import BlitzGateway
from aliby.experiment import get_data_lazy
-from aliby.cells import CellsHDF
+from agora.io.cells import CellsHDF
class Argo:
diff --git a/aliby/tests/__init__.py b/aliby/tests/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/aliby/tests/test_integration.py b/aliby/tests/test_integration.py
deleted file mode 100644
index 10e45f8a..00000000
--- a/aliby/tests/test_integration.py
+++ /dev/null
@@ -1,28 +0,0 @@
-"""
-Testing the "run" functions in the pipeline elements.
-"""
-import pytest
-pytest.mark.skip(reason='All tests still WIP')
-
-# Todo: data needed: an experiment object
-# Todo: data needed: an sqlite database
-# Todo: data needed: a Shelf storage
-class TestPipeline:
- def test_experiment(self):
- pass
-
- def test_omero_experiment(self):
- pass
-
- def test_tiler(self):
- pass
-
- def test_baby_client(self):
- pass
-
- def test_baby_runner(self):
- pass
-
- def test_pipeline(self):
- pass
-
diff --git a/aliby/tests/test_units.py b/aliby/tests/test_units.py
deleted file mode 100644
index 447ab601..00000000
--- a/aliby/tests/test_units.py
+++ /dev/null
@@ -1,99 +0,0 @@
-import pytest
-pytest.mark.skip("all tests still WIP")
-
-
-from core.core import PersistentDict
-
-# Todo: temporary file needed
-class TestPersistentDict:
- @pytest.fixture(autouse=True, scope='class')
- def _get_json_file(self, tmp_path):
- self._filename = tmp_path / 'persistent_dict.json'
-
- def test_persistent_dict(self):
- p = PersistentDict(self._filename)
- p['hello/from/the/other/side'] = "adele"
- p['hello/how/you/doing'] = 'lionel'
- # Todo: run checks
-
-
-# Todo: data needed - small experiment
-class TestExperiment:
- def test_shape(self):
- pass
- def test_positions(self):
- pass
- def test_channels(self):
- pass
- def test_hypercube(self):
- pass
-
-# Todo: data needed - a dummy OMERO server
-class TestConnection:
- def test_dataset(self):
- pass
- def test_image(self):
- pass
-
-# Todo data needed - a position
-class TestTimelapse:
- def test_id(self):
- pass
- def test_name(self):
- pass
- def test_size_z(self):
- pass
- def test_size_c(self):
- pass
- def test_size_t(self):
- pass
- def test_size_x(self):
- pass
- def test_size_y(self):
- pass
- def test_channels(self):
- pass
- def test_channel_index(self):
- pass
-
-# Todo: data needed image and template
-class TestTrapUtils:
- def test_trap_locations(self):
- pass
- def test_tile_shape(self):
- pass
- def test_get_tile(self):
- pass
- def test_centre(self):
- pass
-
-# Todo: data needed - a functional experiment object
-class TestTiler:
- def test_n_timepoints(self):
- pass
- def test_n_traps(self):
- pass
- def test_get_trap_timelapse(self):
- pass
- def test_get_trap_timepoints(self):
- pass
-
-# Todo: data needed - a functional tiler object
-# Todo: running server needed
-class TestBabyClient:
- def test_get_new_session(self):
- pass
- def test_queue_image(self):
- pass
- def test_get_segmentation(self):
- pass
-
-# Todo: data needed - a functional tiler object
-class TestBabyRunner:
- def test_model_choice(self):
- pass
- def test_properties(self):
- pass
- def test_segment(self):
- pass
-
diff --git a/aliby/tile/traps.py b/aliby/tile/traps.py
index e37eb925..b3563d6d 100644
--- a/aliby/tile/traps.py
+++ b/aliby/tile/traps.py
@@ -11,6 +11,7 @@ from skimage.filters import threshold_otsu
from skimage.segmentation import clear_border
from skimage.measure import label, regionprops
from skimage.morphology import disk, closing, square
+from skimage.registration import phase_cross_correlation
def stretch_image(image):
@@ -462,7 +463,7 @@ def align_timelapse_images(
for i in range(1, size_t):
img = centre(np.squeeze(raw_data[channel, i, :, :, 0]))
- shifts, _, _ = feature.register_translation(ref, img)
+ shifts, _, _ = phase_cross_correlation(ref, img)
# If a huge move is detected at a single time point it is taken
# to be inaccurate and the correction from the previous time point
# is used.
diff --git a/poetry.lock b/poetry.lock
index 68e0e8b1..f93587a0 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -110,17 +110,21 @@ xgboost = "1.4.2"
[[package]]
name = "aliby-post"
-version = "0.1.0"
+version = "0.1.1"
description = "Post-processing tools for aliby pipeline."
category = "main"
optional = false
-python-versions = ">=3.7,<4.0"
+python-versions = ">=3.7.1,<3.11"
[package.dependencies]
+aliby-agora = ">=0.2.0"
catch22 = ">=0.2.0,<0.3.0"
leidenalg = ">=0.8.8,<0.9.0"
more-itertools = ">=8.12.0,<9.0.0"
numpy = ">=1.17.3"
+omni-gaussian = "*"
+pandas = ">=1.3.5,<2.0.0"
+PyYAML = ">=6.0,<7.0"
scipy = ">=1.4.1"
[[package]]
@@ -1909,7 +1913,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[metadata]
lock-version = "1.1"
python-versions = ">=3.7.1,<3.11"
-content-hash = "b6fb40c30458a9245b90757bd4d62d41fc51d9ffa544a8f6812ce5acf0cfc8df"
+content-hash = "e1e7066cb95566d8b8151a3dc7fc74d2dce27c535c55e6acdb708ce6a6b55c19"
[metadata.files]
absl-py = [
@@ -2015,8 +2019,8 @@ aliby-baby = [
{file = "aliby_baby-0.1.2-py3-none-any.whl", hash = "sha256:f8f11b82db89a74ad8cc48059370af889f246a83d4cbc45ce75d9475a15605f7"},
]
aliby-post = [
- {file = "aliby-post-0.1.0.tar.gz", hash = "sha256:aab49a84f17ac03b15ae41becd591716ad93cf35c12619f64794ef2aa86ccaad"},
- {file = "aliby_post-0.1.0-py3-none-any.whl", hash = "sha256:a4bcd6d5df5152f10c0bacd4970b59234df8eaa757ba2c0662d00f70d077949a"},
+ {file = "aliby-post-0.1.1.tar.gz", hash = "sha256:426510854767402adc06ed62b7867866dcad054838432ffe26ebb91861c85828"},
+ {file = "aliby_post-0.1.1-py3-none-any.whl", hash = "sha256:6bd666a37b83ee750c9837ce08a8541d16290811fadcf020378b6122f3b1f8bd"},
]
appdirs = [
{file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
diff --git a/pyproject.toml b/pyproject.toml
index 0d257b76..b46e1308 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,8 +30,8 @@ zeroc-ice = "3.6.5"
tensorflow = ">=1.15,<=2.3"
aliby-agora = ">=0.2.0"
aliby-baby = "*"
-aliby-post = "*"
omni-gaussian = "*"
+aliby-post = "^0.1.1"
[tool.poetry.dev-dependencies]
diff --git a/tests/aliby/test_baby_client.py b/tests/aliby/test_baby_client.py
index 3c93a5be..f8ca071c 100644
--- a/tests/aliby/test_baby_client.py
+++ b/tests/aliby/test_baby_client.py
@@ -1,73 +1,88 @@
+import pytest
+
+pytest.mark.skip
+
import json
import time
import numpy as np
from aliby.experiment import ExperimentLocal
from aliby.baby_client import BabyClient
-from tile.tiler import Tiler
+from aliby.tile.tiler import Tiler
+
-root_dir = (
- "/Users/s1893247/PhD/pipeline-core/data/glclvl_0" ".1_mig1_msn2_maf1_sfp1_dot6_03"
-)
+@pytest.mark.skip(reason="No longer usable, requires local files. Kept until replaced.")
+def test_client():
+ 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)
+ expt = ExperimentLocal(root_dir, finished=True)
+ seg_expt = Tiler(expt, finished=True)
-print(seg_expt.positions)
-seg_expt.current_position = "pos007"
+ print(seg_expt.positions)
+ 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)
+ 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
+ # 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,
- )
- while True:
- try:
- print("Loading.", end="")
- result = baby_client.get_segmentation(baby_client.sessions["default"])
- except:
- print(".", end="")
- time.sleep(1)
- continue
- break
- print("Received timepoint {}".format(i))
- segmentations.append(result)
-except Exception as e:
- print(segmentations)
- raise e
+ 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,
+ )
+ while True:
+ try:
+ print("Loading.", end="")
+ result = baby_client.get_segmentation(
+ baby_client.sessions["default"]
+ )
+ except:
+ print(".", end="")
+ time.sleep(1)
+ continue
+ break
+ print("Received timepoint {}".format(i))
+ segmentations.append(result)
+ except Exception as e:
+ print(segmentations)
+ raise e
-with open("segmentations.json", "w") as fd:
- json.dump(segmentations, fd)
+ with open("segmentations.json", "w") as fd:
+ json.dump(segmentations, fd)
-print("Done.")
-# print(len(segmentations[0]))
-# for i in range(5):
-# print("trap {}".format(i))
-# for k, v in segmentations[0][i].items():
-# print(k, v)
-#
-# import matplotlib.pyplot as plt
-# plt.imshow(np.squeeze(batches[0][0, ..., 0]))
-# plt.savefig('test_baby.pdf')
+ print("Done.")
+ # print(len(segmentations[0]))
+ # for i in range(5):
+ # print("trap {}".format(i))
+ # for k, v in segmentations[0][i].items():
+ # print(k, v)
+ #
+ # import matplotlib.pyplot as plt
+ # plt.imshow(np.squeeze(batches[0][0, ..., 0]))
+ # plt.savefig('test_baby.pdf')
diff --git a/tests/aliby/test_local_expt.py b/tests/aliby/test_local_expt.py
index 026b54bb..d9a38b84 100644
--- a/tests/aliby/test_local_expt.py
+++ b/tests/aliby/test_local_expt.py
@@ -1,3 +1,5 @@
+import pytest
+
import logging
from logging.handlers import RotatingFileHandler
import unittest
@@ -31,6 +33,7 @@ data_directory = Path(__file__).parent.parent / "data/"
root_directory = data_directory / "glclvl_0.1_mig1_msn2_maf1_sfp1_dot6_03"
+@pytest.mark.skip(reason="No longer usable, requires local files. Kept until replaced.")
class TestCase(unittest.TestCase):
def setUp(self):
self.expt = Experiment.from_source(root_directory, finished=True)
diff --git a/tests/aliby/test_pipeline.py b/tests/aliby/test_pipeline.py
index 1adb4456..451a0504 100644
--- a/tests/aliby/test_pipeline.py
+++ b/tests/aliby/test_pipeline.py
@@ -1,19 +1,29 @@
-import os
import unittest
+
+import pytest
+import os
+
from pathlib import Path
from aliby.baby_client import BabyRunner
-from aliby.experiment import ExperimentOMERO
-from aliby.pipeline import ExperimentLocal
+from aliby.experiment import ExperimentOMERO, ExperimentLocal
from aliby.tile.tiler import Tiler
+@pytest.fixture
+def server_user():
+ return os.environ.get("SERVER_USER")
+
+
+@pytest.fixture
+def server_password():
+ return os.environ.get("SERVER_PASSWORD")
+
+
+@pytest.mark.skip(reason="Local analysis not yet implemented")
class TestLocal(unittest.TestCase):
def setUp(self) -> None:
- self.root_dir = (
- "/Users/s1893247/PhD/pipeline-core/data/glclvl_0"
- ".1_mig1_msn2_maf1_sfp1_dot6_03"
- )
+ self.root_dir = "./data/" ".1_mig1_msn2_maf1_sfp1_dot6_03"
self.raw_expt = ExperimentLocal(self.root_dir, finished=True)
self.tiler = Tiler(self.raw_expt, finished=False)
@@ -50,9 +60,11 @@ class TestLocal(unittest.TestCase):
p.unlink()
+# FIXME reimplement this being careful with credentials
+@pytest.mark.skip(reason="credentials are not present in current repo")
class TestRemote(unittest.TestCase):
def setUp(self) -> None:
- self.root_dir = "/Users/s1893247/PhD/pipeline-core/data/ome_test"
+ self.root_dir = "./"
self.raw_expt = ExperimentOMERO(
51,
username="root",
diff --git a/tests/aliby/test_segment.py b/tests/aliby/test_segment.py
index 65c2bf6c..10a21d5c 100644
--- a/tests/aliby/test_segment.py
+++ b/tests/aliby/test_segment.py
@@ -1,7 +1,7 @@
import unittest
import numpy as np
-from aliby.tile.tiler import align_timelapse_images
+from aliby.tile.traps import align_timelapse_images
class TestCase(unittest.TestCase):
--
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