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Fix single field issue in _compute_z_spacing #141

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merged 2 commits into from
Jun 14, 2024
Merged

Fix single field issue in _compute_z_spacing #141

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685e65d
Fix single field issue in _compute_z_spacing
jluethi Jun 14, 2024
eed04f4
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 14, 2024
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4 changes: 3 additions & 1 deletion src/faim_ipa/hcs/imagexpress/StackAcquisition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,9 @@ def _compute_z_spacing(self, files: pd.DataFrame) -> Optional[float]:
channel_with_stack = np.sort(files[files["z"] == "2"]["channel"].unique())[0]
subset = files[files["channel"] == channel_with_stack]
subset = subset[subset["well"] == np.sort(subset["well"].unique())[0]]
subset = subset[subset["field"] == np.sort(subset["field"].unique())[0]]
first_field = np.sort(subset["field"].unique())[0]
if first_field is not None:
subset = subset[subset["field"] == np.sort(subset["field"].unique())[0]]

plane_positions = []

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15 changes: 15 additions & 0 deletions tests/hcs/imagexpress/test_ImageXpress.py
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Expand Up @@ -355,3 +355,18 @@ def test_time_lapse_acquistion(time_lapse_acquisition: PlateAcquisition):
assert tile.position.y in [0, 256]
assert tile.position.x in [0]
assert tile.shape == (256, 256)


def test_single_field_stack_acquistion(stack_acquisition: PlateAcquisition):
# Regular z spacing in dataset
files = stack_acquisition._parse_files()
z_step = stack_acquisition._compute_z_spacing(files)
assert z_step == 5

# Select the subset of only a single field to process
files = files[files["field"] == "s1"]
# When only a single field is available per well, the files dataframe
# has it set to None
files["field"] = None
z_step = stack_acquisition._compute_z_spacing(files)
assert z_step == 5
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