added EUST2, EUSTAPF

amygda/cli.py

@@ -17,6 +17,8 @@
     "GPALL1F",
     "CHNMCMM2",
     "GB1ECSDP",
+    "EUST2",
+    "EUSTAPF",
 }
 
 PINK = (138, 41, 231)
@@ -41,12 +43,16 @@ def build_parser() -> argparse.ArgumentParser:
     _add_common_image_arguments(filter_parser)
     filter_parser.set_defaults(handler=handle_filter)
 
-    segment_parser = subparsers.add_parser("segment", help="Identify wells in an input image.")
+    segment_parser = subparsers.add_parser(
+        "segment", help="Identify wells in an input image."
+    )
     _add_common_image_arguments(segment_parser)
     _add_segment_arguments(segment_parser)
     segment_parser.set_defaults(handler=handle_segment)
 
-    measure_parser = subparsers.add_parser("measure", help="Measure growth from an input image.")
+    measure_parser = subparsers.add_parser(
+        "measure", help="Measure growth from an input image."
+    )
     _add_common_image_arguments(measure_parser)
     _add_plate_design_argument(measure_parser)
     _add_measure_arguments(measure_parser)
@@ -136,7 +142,9 @@ def handle_run(options: argparse.Namespace) -> None:
     plate = _build_plate(raw_info, options.plate_design)
 
     filtered_info = run_filter_stage(plate, raw_info)
-    segmented_info = run_segment_stage(plate, filtered_info, options, reuse_loaded_image=True)
+    segmented_info = run_segment_stage(
+        plate, filtered_info, options, reuse_loaded_image=True
+    )
     run_measure_stage(plate, segmented_info, options, reuse_loaded_state=True)
 
 
@@ -364,7 +372,9 @@ def save_drug_images(
             groups,
             key=lambda group: float(np.min(well_drug_conc[group[:, 0], group[:, 1]])),
         )
-        panels = [_extract_oriented_drug_panel(plate, group) for group in ordered_groups]
+        panels = [
+            _extract_oriented_drug_panel(plate, group) for group in ordered_groups
+        ]
         panel = _concatenate_panels_horizontally(panels)
         if control_panel is not None:
             panel = _stack_panels_vertically_left_aligned([control_panel, panel])
@@ -739,7 +749,9 @@ def _build_positive_control_panel(plate: PlateMeasurement) -> np.ndarray:
 
     control_positions = np.array(plate.well_positive_controls, dtype=int)
     if control_positions.size == 0:
-        raise RuntimeError("No positive control wells were found for this plate design.")
+        raise RuntimeError(
+            "No positive control wells were found for this plate design."
+        )
 
     groups = _group_drug_positions(control_positions)
     ordered_groups = sorted(groups, key=lambda group: int(np.min(group[:, 1])))

amygda/config/EUST2-conc-matrix.txt

@@ -0,0 +1,8 @@
+32,     32,     4,      4,      8,      256,    8,      4,      8,      16,     32,     64
+16,     16,     2,      2,      4,      2,      4,      0.25,   0.5,    1,      2,      4
+8,      8,      1,      1,      2,      1,      2,      0.06,   0.12,   0.25,   0.5,    1
+4,      4,      0.5,    0.5,    1,      0.5,    1,      1,      2,      4,      8,      16
+0.015,  0.03,   0.06,   0.12,   0.25,   0.5,    0.12,   0.25,   0.5,    1,      2,      4
+0.25,   0.5,    1,      2,      4,      8,      0.5,    1,      2,      4,      8,      16
+0.25,   0.5,    1,      2,      4,      8,      0.5,    1,      2,      4,      8,      16
+0.5,    1,      2,      4,      8,      16,     64,     128,    256,    512,    0,      0      

amygda/config/EUST2-dilution-matrix.txt

@@ -0,0 +1,8 @@
+    4,  4,  4,  4,  4,  4,  4,  1,  2,  3,  4,  5
+    3,  3,  3,  3,  3,  3,  3,  1,  2,  3,  4,  5
+    2,  2,  2,  2,  2,  2,  2,  1,  2,  3,  4,  5
+    1,  1,  1,  1,  1,  1,  1,  1,  2,  3,  4,  5
+    1,  2,  3,  4,  5,  6,  1,  2,  3,  4,  5,  6
+    1,  2,  3,  4,  5,  6,  1,  2,  3,  4,  5,  6
+    1,  2,  3,  4,  5,  6,  1,  2,  3,  4,  5,  6
+    1,  2,  3,  4,  5,  6,  1,  2,  3,  4,  0,  0

amygda/config/EUST2-drug-matrix.txt

@@ -0,0 +1,8 @@
+KAN,STR,TIA,SYN,LZD,MUP,VAN,CHL,CHL,CHL,CHL,CHL
+KAN,STR,TIA,SYN,LZD,MUP,VAN,FUS,FUS,FUS,FUS,FUS
+KAN,STR,TIA,SYN,LZD,MUP,VAN,PEN,PEN,PEN,PEN,PEN
+KAN,STR,TIA,SYN,LZD,MUP,VAN,TMP,TMP,TMP,TMP,TMP
+RIF,RIF,RIF,RIF,RIF,RIF,CLI,CLI,CLI,CLI,CLI,CLI
+ERY,ERY,ERY,ERY,ERY,ERY,FOX,FOX,FOX,FOX,FOX,FOX
+CIP,CIP,CIP,CIP,CIP,CIP,GEN,GEN,GEN,GEN,GEN,GEN
+TET,TET,TET,TET,TET,TET,SMX,SMX,SMX,SMX,POS,POS

amygda/config/EUSTAPF-conc-matrix.txt

@@ -0,0 +1,8 @@
+0.5,        1,          2,        0.5,          1,      0.25,       0.03,       0.25,       0.25,       0.5,        0.03,       0.5
+1,          2,          4,          1,          2,      0.5,        0.06,       0.5,        0.5,        1,          0.06,       1
+2,          4,          8,          2,          4,      1,          0.12,       1,          1,          2,          0.12,       2 
+4,          8,          16,         4,          8,      2,          0.25,       2,          2,          4,          0.25,       4
+0.5,        0.5,        0.12,       0.5,        16,     4,          0.5,        4,          4,          8,          0.5,        8
+1,          1,          0.25,       1,          4,      0,          1,          8,          8,          16,         1,          256
+2,          2,          0.5,        2,          8,      0,          0.25,       0.5,        1,          2,          0,          0
+4,          4,          1,          4,          16,     1,          2,          4,          8,          6,          0,          0

amygda/config/EUSTAPF-dilution-matrix.txt

@@ -0,0 +1,8 @@
+1,      1,      1,      1,      1,      1,      1,      1,      1,      1,      1,      1 
+2,      2,      2,      2,      2,      2,      2,      2,      2,      2,      2,      2
+3,      3,      3,      3,      3,      3,      3,      3,      3,      3,      3,      3
+4,      4,      4,      4,      4,      4,      4,      4,      4,      4,      4,      4
+1,      1,      1,      1,      5,      5,      5,      5,      5,      5,      5,      5
+2,      2,      2,      2,      1,      0,      6,      6,      6,      6,      6,      6
+3,      3,      3,      3,      2,      0,      1,      2,      3,      4,      0,      0
+4,      4,      4,      4,      3,      1,      2,      3,      4,      1,      0,      0

amygda/config/EUSTAPF-drug-matrix.txt

@@ -0,0 +1,8 @@
+CPT,SXT,LZD,TET,TEI,ERY,TLA,TOB,GEN,VAN,RIF,MUP
+CPT,SXT,LZD,TET,TEI,ERY,TLA,TOB,GEN,VAN,RIF,MUP
+CPT,SXT,LZD,TET,TEI,ERY,TLA,TOB,GEN,VAN,RIF,MUP
+CPT,SXT,LZD,TET,TEI,ERY,TLA,TOB,GEN,VAN,RIF,MUP
+FUS,DAP,CLI,LEVO,TEI,ERY,TLA,TOB,GEN,VAN,RIF,MUP
+FUS,DAP,CLI,LEVO,NOR,DT1,TLA,TOB,GEN,VAN,RIF,MUP
+FUS,DAP,CLI,LEVO,NOR,DT2,MXF,MXF,MXF,MXF,POS,NEG
+FUS,DAP,CLI,LEVO,NOR,FOX,FOX,FOX,FOX,FOX2,POS,POS

tests/test_core.py

@@ -182,6 +182,29 @@ def test_identify_wells_finds_synthetic_grid(tmp_path: Path) -> None:
     assert np.count_nonzero(plate.well_radii) == 6
 
 
+@pytest.mark.parametrize(
+    ("design", "expected_pos_count"),
+    [
+        ("EUST2", 2),
+        ("EUSTAPF", 3),
+    ],
+)
+def test_initialize_plate_layout_for_new_designs(
+    tmp_path: Path, design: str, expected_pos_count: int
+) -> None:
+    plate = PlateMeasurement(
+        tmp_path,
+        categories={"ImageFileName": "plate"},
+        plate_design=design,
+    )
+    plate.initialize_plate_layout()
+
+    assert plate.well_drug_name is not None
+    assert plate.well_drug_name.shape == (8, 12)
+    assert plate.well_positive_controls_number == expected_pos_count
+    assert "POS" in plate.drug_names
+
+
 def test_legacy_arguments_emit_deprecation_warnings(tmp_path: Path) -> None:
     with pytest.deprecated_call():
         PlateMeasurement(