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Running on Zero
Running on Zero
| from cellquant.labels import (ALL_LABELS, CELL_LABELS, COUNT_COLUMNS, NOSTRIL_LABELS, TOTAL_NUCLEI, TOTAL_PUNCTA, cell_attributes, | |
| cell_label, count_row, nostril_in_nucleus, nostril_label) | |
| def test_cell_label_roundtrip(): | |
| for lab in CELL_LABELS: | |
| a, n = cell_attributes(lab) | |
| assert cell_label(a, n) == lab | |
| def test_nostril_label_roundtrip(): | |
| for lab in NOSTRIL_LABELS: | |
| assert nostril_label(nostril_in_nucleus(lab)) == lab | |
| def test_label_sets_disjoint(): | |
| assert len(ALL_LABELS) == 6 and set(CELL_LABELS).isdisjoint(NOSTRIL_LABELS) | |
| def test_count_columns_order(): | |
| # each group of labels is followed by its total, nuclei first | |
| assert COUNT_COLUMNS == CELL_LABELS + (TOTAL_NUCLEI,) + NOSTRIL_LABELS + (TOTAL_PUNCTA,) | |
| assert len(COUNT_COLUMNS) == 8 and COUNT_COLUMNS.index(TOTAL_NUCLEI) == 4 and COUNT_COLUMNS.index(TOTAL_PUNCTA) == 7 | |
| assert [c for c in COUNT_COLUMNS if c not in (TOTAL_NUCLEI, TOTAL_PUNCTA)] == list(ALL_LABELS) | |
| def test_count_row_sums_each_group(): | |
| counts = {"Cell, Antibody +": 3, "Cell, Antibody -": 5, "Cell, Nostril, Antibody +": 7, "Cell, Nostril, Antibody -": 11, | |
| "Nostril in Nucleus": 13, "Nostril External of Nucleus": 17} | |
| row = count_row(counts) | |
| assert row == [3, 5, 7, 11, 26, 13, 17, 30] | |
| assert len(row) == len(COUNT_COLUMNS) | |
| assert row[COUNT_COLUMNS.index(TOTAL_NUCLEI)] == sum(counts[lab] for lab in CELL_LABELS) | |
| assert row[COUNT_COLUMNS.index(TOTAL_PUNCTA)] == sum(counts[lab] for lab in NOSTRIL_LABELS) | |
| assert all(isinstance(v, int) for v in row) | |
| def test_count_row_missing_labels_count_as_zero(): | |
| assert count_row({}) == [0] * 8 | |
| row = count_row({"Cell, Antibody -": 2, "Nostril External of Nucleus": 4, "unknown label": 99}) | |
| assert row == [0, 2, 0, 0, 2, 0, 4, 4] | |
| assert count_row({"Cell, Antibody +": 1.0}) == [1, 0, 0, 0, 1, 0, 0, 0] # numpy / float counts become ints | |