Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cleanup app tests #78

Merged
merged 5 commits into from
Mar 26, 2024
Merged

Cleanup app tests #78

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
1689f1a
line up app test arguments
mgeplf Mar 25, 2024
c558465
use a function to write json files
mgeplf Mar 25, 2024
3132810
`Test_mtype_densities_from_probability_map` doesn't need to be a class
mgeplf Mar 25, 2024
090f17a
last of the json.dump
mgeplf Mar 25, 2024
3d76a5a
use simple assert for shapes
mgeplf Mar 26, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
214 changes: 83 additions & 131 deletions tests/app/test_cell_densities.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,28 +33,13 @@
from tests.densities.test_measurement_to_density import (
get_input_data as get_measurement_to_density_input_data,
)
from tests.utils import write_json

TEST_PATH = Path(__file__).parent.parent
DATA_PATH = TEST_PATH.parent / "atlas_densities" / "app" / "data"
MEASUREMENTS_PATH = DATA_PATH / "measurements"


def _get_cell_density_result(runner):
args = [
"cell-density",
"--hierarchy-path",
str(Path(TEST_PATH, "1.json")),
"--annotation-path",
"annotation.nrrd",
"--nissl-path",
"nissl.nrrd",
"--output-path",
"overall_cell_density.nrrd",
]

return runner.invoke(tested.app, args)


def test_cell_density():
input_ = {
"annotation": np.array(
Expand All @@ -77,45 +62,46 @@ def test_cell_density():
with runner.isolated_filesystem():
for name, array in input_.items():
VoxelData(array, voxel_dimensions=voxel_dimensions).save_nrrd(f"{name}.nrrd")
result = _get_cell_density_result(runner)

args = [
# fmt: off
"cell-density",
"--hierarchy-path", TEST_PATH / "1.json",
"--annotation-path", "annotation.nrrd",
"--nissl-path", "nissl.nrrd",
"--output-path", "overall_cell_density.nrrd",
# fmt: on
]

result = runner.invoke(tested.app, args)

assert result.exit_code == 0

voxel_data = VoxelData.load_nrrd("overall_cell_density.nrrd")
assert voxel_data.raw.dtype == float

# An error should be raised if annotation and nissl don't use the same voxel dimensions
VoxelData(np.ones((3, 1, 3)), voxel_dimensions=[10] * 3).save_nrrd("nissl.nrrd")
result = _get_cell_density_result(runner)
result = runner.invoke(tested.app, args)
assert "voxel_dimensions" in str(result.exception)


def _get_glia_cell_densities_result(runner):
def test_glia_cell_densities():
args = [
# fmt: off
"glia-cell-densities",
"--annotation-path",
"annotation.nrrd",
"--hierarchy-path",
str(Path(TEST_PATH, "1.json")),
"--cell-density-path",
"cell_density.nrrd",
"--glia-density-path",
"glia_density.nrrd",
"--astrocyte-density-path",
"astrocyte_density.nrrd",
"--oligodendrocyte-density-path",
"oligodendrocyte_density.nrrd",
"--microglia-density-path",
"microglia_density.nrrd",
"--glia-proportions-path",
"glia_proportions.json",
"--output-dir",
"densities",
"--annotation-path", "annotation.nrrd",
"--hierarchy-path", TEST_PATH / "1.json",
"--cell-density-path", "cell_density.nrrd",
"--glia-density-path", "glia_density.nrrd",
"--astrocyte-density-path", "astrocyte_density.nrrd",
"--oligodendrocyte-density-path", "oligodendrocyte_density.nrrd",
"--microglia-density-path", "microglia_density.nrrd",
"--glia-proportions-path", "glia_proportions.json",
"--output-dir", "densities",
# fmt: on
]

return runner.invoke(tested.app, args)


def test_glia_cell_densities():
glia_cell_count = sum(glia_cell_counts().values())
input_ = get_glia_input_data(glia_cell_count)
runner = CliRunner()
Expand All @@ -131,57 +117,50 @@ def test_glia_cell_densities():
VoxelData(unconstrained_density, voxel_dimensions=voxel_dimensions).save_nrrd(
glia_type + "_density.nrrd"
)
with open("glia_proportions.json", "w", encoding="utf-8") as out:
json.dump(input_["glia_proportions"], out)
result = _get_glia_cell_densities_result(runner)

write_json("glia_proportions.json", input_["glia_proportions"])

result = runner.invoke(tested.app, args)
assert result.exit_code == 0

neuron_density = VoxelData.load_nrrd("densities/neuron_density.nrrd")
assert neuron_density.raw.dtype == np.float64
npt.assert_array_equal(neuron_density.shape, input_["annotation"].shape)
assert neuron_density.shape == input_["annotation"].shape
assert np.all(neuron_density.raw >= 0.0)

oligodendrocyte_density = VoxelData.load_nrrd("densities/oligodendrocyte_density.nrrd")
assert oligodendrocyte_density.raw.dtype == np.float64
npt.assert_array_equal(neuron_density.shape, input_["annotation"].shape)
assert neuron_density.shape == input_["annotation"].shape

# Check that an exception is thrown if voxel dimensions aren't consistent
VoxelData(input_["cell_density"], voxel_dimensions=(10, 10, 10)).save_nrrd(
"cell_density.nrrd"
)
result = _get_glia_cell_densities_result(runner)
result = runner.invoke(tested.app, args)
assert "voxel_dimensions" in str(result.exception)

# Check that an exception is thrown if the input cell density has negative values
input_["cell_density"][0, 0, 0] = -1.0
VoxelData(input_["cell_density"], voxel_dimensions=(10, 10, 10)).save_nrrd(
"cell_density.nrrd"
)
result = _get_glia_cell_densities_result(runner)
result = runner.invoke(tested.app, args)
assert "Negative density value" in str(result.exception)


def _get_inh_and_exc_neuron_densities_result(runner):
def test_inhibitory_and_excitatory_neuron_densities():
args = [
# fmt: off
"inhibitory-and-excitatory-neuron-densities",
"--annotation-path",
"annotation.nrrd",
"--hierarchy-path",
str(Path(TEST_PATH, "1.json")),
"--gad1-path",
"gad1.nrrd",
"--nrn1-path",
"nrn1.nrrd",
"--neuron-density-path",
"neuron_density.nrrd",
"--output-dir",
"densities",
"--annotation-path", "annotation.nrrd",
"--hierarchy-path", TEST_PATH / "1.json",
"--gad1-path", "gad1.nrrd",
"--nrn1-path", "nrn1.nrrd",
"--neuron-density-path", "neuron_density.nrrd",
"--output-dir", "densities",
# fmt: on
]

return runner.invoke(tested.app, args)


def test_inhibitory_and_excitatory_neuron_densities():
inhibitory_df = extract_inhibitory_neurons_dataframe(Path(MEASUREMENTS_PATH, "mmc1.xlsx"))
neuron_count = inhibitory_data(inhibitory_df)["neuron_count"]
input_ = get_inhibitory_neuron_input_data(neuron_count)
Expand All @@ -191,52 +170,47 @@ def test_inhibitory_and_excitatory_neuron_densities():
for name in ["annotation", "neuron_density", "gad1", "nrn1"]:
VoxelData(input_[name], voxel_dimensions=voxel_dimensions).save_nrrd(name + ".nrrd")

result = _get_inh_and_exc_neuron_densities_result(runner)
result = runner.invoke(tested.app, args)
assert result.exit_code == 0

inh_neuron_density = VoxelData.load_nrrd("densities/inhibitory_neuron_density.nrrd")
assert inh_neuron_density.raw.dtype == np.float64
npt.assert_array_equal(inh_neuron_density.shape, input_["annotation"].shape)
assert inh_neuron_density.shape == input_["annotation"].shape
assert np.all(inh_neuron_density.raw >= 0.0)

exc_neuron_density = VoxelData.load_nrrd("densities/excitatory_neuron_density.nrrd")
assert exc_neuron_density.raw.dtype == np.float64
npt.assert_array_equal(exc_neuron_density.shape, input_["annotation"].shape)
assert exc_neuron_density.shape == input_["annotation"].shape
assert np.all(exc_neuron_density.raw >= 0.0)

# Check that an exception is thrown if voxel dimensions aren't consistent
VoxelData(input_["neuron_density"], voxel_dimensions=(10, 10, 10)).save_nrrd(
"neuron_density.nrrd"
)
result = _get_inh_and_exc_neuron_densities_result(runner)
result = runner.invoke(tested.app, args)
assert "voxel_dimensions" in str(result.exception)

# Check that an exception is thrown if the input neuron density has negative values
input_["neuron_density"][0, 0, 0] = -1.0
VoxelData(input_["neuron_density"], voxel_dimensions=(25, 25, 25)).save_nrrd(
"neuron_density.nrrd"
)
result = _get_inh_and_exc_neuron_densities_result(runner)
result = runner.invoke(tested.app, args)
assert "Negative density value" in str(result.exception)


def _get_compile_measurements_result(runner):
@pytest.mark.filterwarnings("ignore::atlas_densities.exceptions.AtlasDensitiesWarning")
def test_compile_measurements():
args = [
# fmt: off
"compile-measurements",
"--measurements-output-path",
"measurements.csv",
"--homogenous-regions-output-path",
"homogenous_regions.csv",
"--measurements-output-path", "measurements.csv",
"--homogenous-regions-output-path", "homogenous_regions.csv",
# fmt: on
]

return runner.invoke(tested.app, args)


@pytest.mark.filterwarnings("ignore::atlas_densities.exceptions.AtlasDensitiesWarning")
def test_compile_measurements():
runner = CliRunner()
with runner.isolated_filesystem():
result = _get_compile_measurements_result(runner)
result = runner.invoke(tested.app, args)
assert result.exit_code == 0

dataframe = pd.read_csv("measurements.csv")
Expand Down Expand Up @@ -266,21 +240,16 @@ def test_compile_measurements():

def _get_measurements_to_average_densities_result(runner, hierarchy_path, measurements_path):
args = [
# fmt: off
"measurements-to-average-densities",
"--hierarchy-path",
hierarchy_path,
"--annotation-path",
"annotation.nrrd",
"--region-name",
"Basic cell groups and regions",
"--cell-density-path",
"cell_density.nrrd",
"--neuron-density-path",
"neuron_density.nrrd",
"--measurements-path",
measurements_path,
"--output-path",
"average_densities.csv",
"--hierarchy-path", hierarchy_path,
"--annotation-path", "annotation.nrrd",
"--region-name", "Basic cell groups and regions",
"--cell-density-path", "cell_density.nrrd",
"--neuron-density-path", "neuron_density.nrrd",
"--measurements-path", measurements_path,
"--output-path", "average_densities.csv",
# fmt: on
]

return runner.invoke(tested.app, args)
Expand All @@ -294,8 +263,7 @@ def test_measurements_to_average_densities():
for name in ["annotation", "cell_density", "neuron_density"]:
VoxelData(input_[name], voxel_dimensions=voxel_dimensions).save_nrrd(name + ".nrrd")
input_["measurements"].to_csv("measurements.csv", index=False)
with open("hierarchy.json", "w", encoding="utf-8") as out:
json.dump(input_["hierarchy"], out, indent=1, separators=(",", ": "))
write_json("hierarchy.json", input_["hierarchy"])

result = _get_measurements_to_average_densities_result(
runner, hierarchy_path="hierarchy.json", measurements_path="measurements.csv"
Expand All @@ -319,32 +287,21 @@ def test_measurements_to_average_densities():
assert np.all(actual["measurement_unit"] == "number of cells per mm^3")


def _get_fitting_result(runner):
@pytest.mark.filterwarnings("ignore::atlas_densities.exceptions.AtlasDensitiesWarning")
def test_fit_average_densities():
args = [
# fmt: off
"fit-average-densities",
"--hierarchy-path",
"hierarchy.json",
"--annotation-path",
"annotation.nrrd",
"--neuron-density-path",
"neuron_density.nrrd",
"--gene-config-path",
"gene_config.yaml",
"--average-densities-path",
"average_densities.csv",
"--homogenous-regions-path",
"homogenous_regions.csv",
"--fitted-densities-output-path",
"fitted_densities.csv",
"--fitting-maps-output-path",
"fitting_maps.json",
"--hierarchy-path", "hierarchy.json",
"--annotation-path", "annotation.nrrd",
"--neuron-density-path", "neuron_density.nrrd",
"--gene-config-path", "gene_config.yaml",
"--average-densities-path", "average_densities.csv",
"--homogenous-regions-path", "homogenous_regions.csv",
"--fitted-densities-output-path", "fitted_densities.csv",
"--fitting-maps-output-path", "fitting_maps.json",
# fmt: on
]

return runner.invoke(tested.app, args)


@pytest.mark.filterwarnings("ignore::atlas_densities.exceptions.AtlasDensitiesWarning")
def test_fit_average_densities():
runner = CliRunner()
with runner.isolated_filesystem():
input_ = get_fitting_input_data()
Expand All @@ -354,14 +311,9 @@ def test_fit_average_densities():
input_["homogenous_regions"].to_csv("homogenous_regions.csv", index=False)
input_["average_densities"].to_csv("average_densities.csv", index=False)

with open("hierarchy.json", "w", encoding="utf-8") as out:
json.dump(input_["hierarchy"], out, indent=1, separators=(",", ": "))

with open("realigned_slices.json", "w", encoding="utf-8") as out:
json.dump(input_["realigned_slices"], out, indent=1, separators=(",", ": "))

with open("std_cells.json", "w", encoding="utf-8") as out:
json.dump(input_["cell_density_stddevs"], out, indent=1, separators=(",", ": "))
write_json("hierarchy.json", input_["hierarchy"])
write_json("realigned_slices.json", input_["realigned_slices"])
write_json("std_cells.json", input_["cell_density_stddevs"])

with open("gene_config.yaml", "w", encoding="utf-8") as out:
gene_config = {
Expand All @@ -379,7 +331,7 @@ def test_fit_average_densities():

yaml.dump(gene_config, out)

result = _get_fitting_result(runner)
result = runner.invoke(tested.app, args)
assert result.exit_code == 0

densities = pd.read_csv("fitted_densities.csv")
Expand All @@ -404,7 +356,7 @@ def test_fit_average_densities():
VoxelData(input_["neuron_density"], voxel_dimensions=(10, 10, 10)).save_nrrd(
"neuron_density.nrrd"
)
result = _get_fitting_result(runner)
result = runner.invoke(tested.app, args)
assert "Negative density value" in str(result.exception)


Expand Down
Loading
Loading