add tests and test data for SpectralMatrix class

Author: whitews

data/spectral_data/spectral_comp_matrix.npy

@@ -16,7 +16,7 @@
 from tests.session_export_tests import SessionExportTestCase
 from tests.workspace_tests import WorkspaceTestCase
 from tests.gating_results_tests import GatingResultsTestCase
-from tests.matrix_tests import MatrixTestCase
+from tests.matrix_tests import MatrixTestCase, SpectralMatrixTestCase
 from tests.transform_tests import TransformsTestCase
 from tests.gate_tests import GateTestCase
 from tests.string_repr_tests import StringReprTestCase

data/spectral_data/spectral_fluoro_indices.npy

@@ -16,6 +16,13 @@
     detectors_8c,
     fluorochromes_8c,
     csv_8c_comp_null_channel_file_path,
+    spectral_event_data,
+    spectral_fluoro_indices,
+    spectral_comp_matrix,
+    spectral_all_detectors,
+    spectral_true_detectors,
+    spectral_sample,
+    spectral_truth_comp_events
 )
 
 
@@ -109,3 +116,73 @@ def test_null_channels(self):
 
         self.assertIsInstance(comp_events1, np.ndarray)
         self.assertIsInstance(comp_events2, np.ndarray)
+
+class SpectralMatrixTestCase(unittest.TestCase):
+    """
+    Tests related to the SpectralMatrix class
+    """
+    def setUp(self):
+        self.spectral_event_data = spectral_event_data
+        self.spectral_fluoro_indices = spectral_fluoro_indices
+        self.spectral_comp_matrix = spectral_comp_matrix
+        self.spectral_all_detectors = spectral_all_detectors
+        self.spectral_true_detectors = spectral_true_detectors
+
+    def test_spectral_matrix_create(self):
+        spec_matrix = fk.SpectralMatrix(
+            self.spectral_comp_matrix,
+            detectors=self.spectral_all_detectors,
+            true_detectors=self.spectral_true_detectors
+        )
+        self.assertIsInstance(spec_matrix, fk.SpectralMatrix)
+
+    def test_spectral_matrix_equal(self):
+        spec_matrix = fk.SpectralMatrix(
+            self.spectral_comp_matrix,
+            detectors=self.spectral_all_detectors,
+            true_detectors=self.spectral_true_detectors
+        )
+        spec_matrix2 = copy.deepcopy(spec_matrix)
+
+        self.assertEqual(spec_matrix, spec_matrix2)
+
+    def test_spectral_matrix_not_equal(self):
+        spec_matrix = fk.SpectralMatrix(
+            self.spectral_comp_matrix,
+            detectors=self.spectral_all_detectors,
+            true_detectors=self.spectral_true_detectors
+        )
+        spec_matrix2 = copy.deepcopy(spec_matrix)
+        spec_matrix2.matrix += 0.00001
+
+        self.assertNotEqual(spec_matrix, spec_matrix2)
+
+    def test_spectral_matrix_as_dataframe(self):
+        spec_matrix = fk.SpectralMatrix(
+            self.spectral_comp_matrix,
+            detectors=self.spectral_all_detectors,
+            true_detectors=self.spectral_true_detectors
+        )
+        df_spec_matrix = spec_matrix.as_dataframe()
+
+        self.assertIsInstance(df_spec_matrix, pd.DataFrame)
+        self.assertListEqual(list(df_spec_matrix.columns), spec_matrix.detectors)
+        self.assertListEqual(list(df_spec_matrix.index), spec_matrix.true_detectors)
+
+    def test_spectral_matrix_apply(self):
+        spec_matrix = fk.SpectralMatrix(
+            self.spectral_comp_matrix,
+            detectors=self.spectral_all_detectors,
+            true_detectors=self.spectral_true_detectors
+        )
+        comp_events = spec_matrix.apply(spectral_sample)
+
+        # Compare only the fluoro channel events
+        # The spectral Sample was created from a npy array and
+        # went through the FlowIO conversion process so the events
+        # are slightly different.
+        np.testing.assert_array_almost_equal(
+            spectral_truth_comp_events[:, spectral_sample.fluoro_indices],
+            comp_events[:, spectral_sample.fluoro_indices],
+            decimal=8
+        )

data/spectral_data/spectral_raw_events.npy

@@ -2,6 +2,7 @@
 Configuration of test data
 """
 import numpy as np
+import os
 import warnings
 import flowkit as fk
 
@@ -13,10 +14,9 @@
 comp_file_path = "data/comp_complete_example.csv"
 fcs_2d_file_path = "data/test_data_2d_01.fcs"
 fcs_index_sorted_path = "data/index_sorted/index_sorted_example.fcs"
-sample_id_with_spill = "101_DEN084Y5_15_E01_008_clean.fcs"
 csv_8c_comp_file_path = "data/8_color_data_set/den_comp.csv"
 csv_8c_comp_null_channel_file_path = "data/8_color_data_set/den_comp_null_channel.csv"
-
+spectral_data_dir = "data/spectral_data"
 
 fcs_file_paths = ["data/100715.fcs", "data/109567.fcs", "data/113548.fcs"]
 
@@ -28,6 +28,7 @@
 test_samples_base_set = fk.load_samples(fcs_file_paths)
 test_samples_8c_full_set = fk.load_samples("data/8_color_data_set/fcs_files")
 test_samples_8c_full_set_dict = {s.id: s for s in test_samples_8c_full_set}
+sample_id_with_spill = "101_DEN084Y5_15_E01_008_clean.fcs"
 sample_with_spill = test_samples_8c_full_set_dict[sample_id_with_spill]
 
 with warnings.catch_warnings():
@@ -200,6 +201,40 @@
 spill01_data = np.array([[1, 0.02, 0.06], [0.11, 1, 0.07], [0.09, 0.01, 1]])
 comp_matrix_01 = fk.Matrix(spill01_data, spill01_detectors, spill01_fluoros)
 
+#
+# Spectral Matrix
+#
+spectral_event_data = np.load(os.path.join(spectral_data_dir, "spectral_raw_events.npy"))
+spectral_fluoro_indices = np.load(os.path.join(spectral_data_dir, "spectral_fluoro_indices.npy"))
+spectral_all_detectors = [
+    'B510-A', 'B537-A', 'B602-A', 'B660-A', 'B675-A', 'B710-A', 'B750-A', 'B810-A',
+    'R675-A', 'R710-A', 'R780-A', 'UV379-A', 'UV446-A', 'UV515-A', 'UV585-A', 'UV610-A',
+    'UV660-A', 'UV736-A', 'UV809-A', 'V427-A', 'V450-A', 'V510-A', 'V540-A', 'V576-A', 'V595-A',
+    'V660-A', 'V710-A', 'V750-A', 'V785-A', 'YG585-A', 'YG602-A', 'YG730-A', 'YG780-A', 'B576-A',
+    'R660-A', 'R680-A', 'R730-A', 'UV540-A', 'UV695-A', 'V470-A', 'V615-A', 'V680-A',
+    'V845-A', 'YG660-A', 'YG670-A', 'YG695-A', 'YG750-A', 'YG825-A'
+]
+spectral_true_detectors = [
+    'B510-A', 'B537-A', 'B602-A', 'B660-A', 'B675-A', 'B710-A', 'B750-A', 'B810-A',
+    'R675-A', 'R710-A', 'R780-A', 'UV379-A', 'UV446-A', 'UV515-A', 'UV585-A', 'UV610-A',
+    'UV660-A', 'UV736-A', 'UV809-A', 'V427-A', 'V450-A', 'V510-A', 'V540-A', 'V576-A', 'V595-A',
+    'V660-A', 'V710-A', 'V750-A', 'V785-A', 'YG585-A', 'YG602-A', 'YG730-A', 'YG780-A'
+]
+spectral_sample_labels = [
+    'Time', 'FSC-A', 'FSC-W', 'FSC-H','SSC-A', 'SSC-W', 'SSC-H',
+    'UV379-A', 'UV446-A', 'UV515-A', 'UV540-A', 'UV585-A', 'UV610-A', 'UV660-A', 'UV695-A',
+    'UV736-A', 'UV809-A', 'V427-A', 'V450-A', 'V470-A', 'V510-A', 'V540-A', 'V576-A',
+    'V595-A', 'V615-A', 'V660-A', 'V680-A', 'V710-A', 'V750-A', 'V785-A', 'V845-A',
+    'B510-A', 'B537-A', 'B576-A', 'B602-A', 'B660-A', 'B675-A', 'B710-A', 'B750-A',
+    'B810-A', 'YG585-A', 'YG602-A', 'YG660-A', 'YG670-A', 'YG695-A', 'YG730-A', 'YG750-A',
+    'YG780-A', 'YG825-A', 'R660-A', 'R675-A', 'R680-A', 'R710-A', 'R730-A', 'R780-A'
+]
+spectral_sample = fk.Sample(
+    spectral_event_data, sample_id='spectral_sample.fcs', channel_labels=spectral_sample_labels
+)
+spectral_comp_matrix = np.load(os.path.join(spectral_data_dir, "spectral_comp_matrix.npy"))
+spectral_truth_comp_events = np.load(os.path.join(spectral_data_dir, "truth", "spectral_comp_events.npy"))
+
 # pnn, pns lists
 
 detectors_8c = [