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Cleanup app tests (#78)
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* line up app test arguments
* use a function to write json files
* `Test_mtype_densities_from_probability_map` doesn't need to be a class
* use simple assert for shapes
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@mgeplf
mgeplf authored Mar 26, 2024
1 parent 260a25a commit 5b08942
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Showing 5 changed files with 187 additions and 280 deletions.
214 changes: 83 additions & 131 deletions tests/app/test_cell_densities.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,28 +34,13 @@
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 @@ -78,45 +63,46 @@ 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 @@ -132,57 +118,50 @@ 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 @@ -192,52 +171,47 @@ 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 @@ -267,21 +241,16 @@ 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 @@ -295,8 +264,7 @@ 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 @@ -320,32 +288,21 @@ 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 @@ -359,14 +316,9 @@ 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 @@ -386,7 +338,7 @@ 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 @@ -411,7 +363,7 @@ 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)


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