Merge branch 'develop'

.readthedocs.yaml

@@ -1,7 +1,11 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 python:
-  version: "3"
   install:
     - requirements: docs/requirements.txt
     - method: pip

flowkit/_models/gating_strategy.py

@@ -589,7 +589,7 @@ def _compensate_sample(self, dim_comp_refs, sample):
         if comp_ref == 'FCS':
             meta = sample.get_metadata()
 
-            if 'spill' not in meta or 'spillover' not in meta:
+            if 'spill' not in meta and 'spillover' not in meta:
                 # GML 2.0 spec states if 'FCS' is specified but no spill is present, treat as uncompensated
                 events = sample.get_events(source='raw')
                 return events.copy()
@@ -601,7 +601,7 @@ def _compensate_sample(self, dim_comp_refs, sample):
 
             detectors = [sample.pnn_labels[i] for i in sample.fluoro_indices]
             fluorochromes = [sample.pns_labels[i] for i in sample.fluoro_indices]
-            matrix = Matrix('fcs', spill, detectors, fluorochromes, null_channels=sample.null_channels)
+            matrix = Matrix('tmp_spill', spill, detectors, fluorochromes, null_channels=sample.null_channels)
         else:
             # lookup specified comp-ref in gating strategy
             matrix = self.comp_matrices[comp_ref]

flowkit/_models/transforms/_matrix.py

@@ -32,9 +32,10 @@ def __init__(
             fluorochromes=None,
             null_channels=None
     ):
-        if matrix_id == 'uncompensated' or matrix_id == 'fcs':
+        # Technically, the GML 2.0 spec states 'FCS' (note uppercase) is reserved, but we'll cover that case-insensitive
+        if matrix_id == 'uncompensated' or matrix_id.lower() == 'fcs':
             raise ValueError(
-                "Matrix IDs 'uncompensated' and 'fcs' are reserved compensation references " +
+                "Matrix IDs 'uncompensated' and 'FCS' are reserved compensation references " +
                 "used in Dimension instances to specify that channel data should either be " +
                 "uncompensated or compensated using the spill value from a Sample's metadata"
             )

flowkit/tests/gating_strategy_tests.py

@@ -4,6 +4,7 @@
 import unittest
 import numpy as np
 import flowkit as fk
+from .session_tests import test_samples_8c_full_set_dict
 
 
 data1_fcs_path = 'data/gate_ref/data1.fcs'
@@ -46,6 +47,9 @@
 )
 comp_matrix_01 = fk.Matrix('MySpill', spill01_data, spill01_detectors, spill01_fluoros)
 
+sample_id_with_spill = '101_DEN084Y5_15_E01_008_clean.fcs'
+sample_with_spill = test_samples_8c_full_set_dict[sample_id_with_spill]
+
 
 class GatingStrategyTestCase(unittest.TestCase):
     def test_add_gate_non_gate_class(self):
@@ -92,6 +96,27 @@ def test_add_duplicate_matrix_id(self):
 
         self.assertRaises(KeyError, gs.add_comp_matrix, comp_matrix_01)
 
+    def test_fcs_defined_spill(self):
+        gs = fk.GatingStrategy()
+
+        asinh_xform = fk.transforms.AsinhTransform('asinh', param_t=262144, param_m=4.0, param_a=0.0)
+        gs.add_transform(asinh_xform)
+
+        dim_cd3 = fk.Dimension(
+            'CD3 APC-H7 FLR-A',
+            range_max=-0.4,
+            transformation_ref='asinh',
+            compensation_ref='FCS'
+        )
+
+        cd3_rect_gate = fk.gates.RectangleGate('cd3_low', dimensions=[dim_cd3])
+        gs.add_gate(cd3_rect_gate, gate_path=('root',))
+
+        gating_result = gs.gate_sample(sample_with_spill)
+        cd3_low_count = gating_result.get_gate_count('cd3_low')
+
+        self.assertEqual(cd3_low_count, 71)
+
     def test_get_max_depth(self):
         gml_path = 'data/gate_ref/gml/gml_all_gates.xml'
         gs = fk.parse_gating_xml(gml_path)