Merge pull request #51 from SystemsGenetics/functional-testing

Add functional tests for QR detector, metadata parsing, and tray summary

Author: AdenAthar

tests/test_Analyses/test_Analysis.py

@@ -0,0 +1,76 @@
+from Granny.Analyses.StarchArea import StarchArea
+from Granny.Models.Images.RGBImage import RGBImage
+
+
+def _get_analysis():
+    """Use StarchArea as a concrete implementation of Analysis."""
+    return StarchArea()
+
+
+def test_parse_qr_from_filename_valid():
+    analysis = _get_analysis()
+    result = analysis._parse_qr_from_filename(
+        "APPLE2025_LOT001_2025-12-02_BB-Late_fruit_01.png"
+    )
+    assert result["project"] == "APPLE2025"
+    assert result["lot"] == "LOT001"
+    assert result["date"] == "2025-12-02"
+    assert result["variety"] == "BB-Late"
+
+
+def test_parse_qr_from_filename_with_path():
+    analysis = _get_analysis()
+    result = analysis._parse_qr_from_filename(
+        "/some/path/to/APPLE2025_LOT001_2025-12-02_BB-Late_fruit_05.png"
+    )
+    assert result["project"] == "APPLE2025"
+    assert result["variety"] == "BB-Late"
+
+
+def test_parse_qr_from_filename_jpg():
+    analysis = _get_analysis()
+    result = analysis._parse_qr_from_filename(
+        "PROJ_LOT_DATE_VAR_fruit_01.jpg"
+    )
+    assert result["project"] == "PROJ"
+    assert result["variety"] == "VAR"
+
+
+def test_parse_qr_from_filename_legacy():
+    """Legacy filenames without QR data should return empty strings."""
+    analysis = _get_analysis()
+    result = analysis._parse_qr_from_filename("apple_fruit_01.png")
+    assert result["project"] == ""
+    assert result["lot"] == ""
+    assert result["date"] == ""
+    assert result["variety"] == ""
+
+
+def test_parse_qr_from_filename_no_match():
+    analysis = _get_analysis()
+    result = analysis._parse_qr_from_filename("random_image.png")
+    assert result["project"] == ""
+
+
+def test_add_qr_metadata_valid():
+    analysis = _get_analysis()
+    img = RGBImage("APPLE2025_LOT001_2025-12-02_BB-Late_fruit_01.png")
+    analysis._add_qr_metadata(img, "APPLE2025_LOT001_2025-12-02_BB-Late_fruit_01.png")
+
+    metadata = img.getMetaData()
+    assert "project" in metadata
+    assert metadata["project"].getValue() == "APPLE2025"
+    assert metadata["lot"].getValue() == "LOT001"
+    assert metadata["date"].getValue() == "2025-12-02"
+    assert metadata["variety"].getValue() == "BB-Late"
+
+
+def test_add_qr_metadata_legacy():
+    """Legacy filenames should not add QR metadata."""
+    analysis = _get_analysis()
+    img = RGBImage("apple_fruit_01.png")
+    analysis._add_qr_metadata(img, "apple_fruit_01.png")
+
+    metadata = img.getMetaData()
+    assert "project" not in metadata
+    assert "lot" not in metadata

tests/test_Models/test_Utils/__init__.py

@@ -0,0 +1,97 @@
+import cv2
+import numpy as np
+from Granny.Utils.QRCodeDetector import QRCodeDetector
+
+
+def test_instantiation():
+    detector = QRCodeDetector()
+    assert detector.detector is not None
+    assert isinstance(detector.barcode_enabled, bool)
+
+
+def test_detect_returns_none_for_blank_image():
+    detector = QRCodeDetector()
+    blank = np.zeros((100, 100, 3), dtype=np.uint8)
+    data, points = detector.detect(blank)
+    assert data is None
+    assert points is None
+
+
+def test_detect_barcode_rotation_invariant():
+    """Barcode detection should work regardless of image rotation."""
+    detector = QRCodeDetector()
+    if not detector.barcode_enabled:
+        return
+
+    # Create a test image with a Code128 barcode using pyzbar's expected input
+    # We'll use a real barcode image if available, otherwise test the rotation logic
+    # by generating a simple barcode-like pattern
+    from pyzbar import pyzbar
+
+    # Create a synthetic barcode image using python-barcode if available
+    try:
+        import barcode
+        from barcode.writer import ImageWriter
+        import tempfile
+        import os
+
+        code = barcode.get("code128", "TEST123", writer=ImageWriter())
+        tmp = tempfile.NamedTemporaryFile(suffix=".png", delete=False)
+        code.save(tmp.name.replace(".png", ""))
+        barcode_path = tmp.name.replace(".png", "") + ".png"
+
+        img = cv2.imread(barcode_path)
+        if img is None:
+            return
+
+        # Test original orientation
+        data, points = detector._detect_barcode(img)
+        assert data == "TEST123"
+
+        # Test 90 degree rotation
+        rotated = cv2.rotate(img, cv2.ROTATE_90_CLOCKWISE)
+        data, points = detector._detect_barcode(rotated)
+        assert data == "TEST123"
+
+        # Test 180 degree rotation
+        rotated = cv2.rotate(img, cv2.ROTATE_180)
+        data, points = detector._detect_barcode(rotated)
+        assert data == "TEST123"
+
+        # Test 270 degree rotation
+        rotated = cv2.rotate(img, cv2.ROTATE_90_COUNTERCLOCKWISE)
+        data, points = detector._detect_barcode(rotated)
+        assert data == "TEST123"
+
+        os.unlink(barcode_path)
+    except ImportError:
+        # python-barcode not installed, skip
+        pass
+
+
+def test_extract_variety_info_pipe_format():
+    detector = QRCodeDetector()
+    info = detector.extract_variety_info("APPLE2026|LOT002|2026-01-23|BB-Early")
+    assert info["project"] == "APPLE2026"
+    assert info["lot"] == "LOT002"
+    assert info["date"] == "2026-01-23"
+    assert info["full"] == "BB-Early"
+    assert info["variety"] == "BB"
+    assert info["timing"] == "Early"
+
+
+def test_extract_variety_info_legacy_format():
+    detector = QRCodeDetector()
+    info = detector.extract_variety_info("BB-Late")
+    assert info["project"] == "UNKNOWN"
+    assert info["lot"] == "UNKNOWN"
+    assert info["full"] == "BB-Late"
+    assert info["variety"] == "BB"
+    assert info["timing"] == "Late"
+
+
+def test_extract_variety_info_malformed_pipe():
+    detector = QRCodeDetector()
+    info = detector.extract_variety_info("only|two")
+    assert info["project"] == "UNKNOWN"
+    assert info["full"] == "only|two"

tests/test_Models/test_Utils/test_QRCodeDetector.py

@@ -1,5 +1,88 @@
+import os
+import tempfile
+import pandas as pd
 from Granny.Models.Values.MetaDataValue import MetaDataValue
+from Granny.Models.Values.FloatValue import FloatValue
+from Granny.Models.Values.StringValue import StringValue
+from Granny.Models.Images.RGBImage import RGBImage
+import numpy as np
 
 
+def _make_image(name, rating_val, project=None, lot=None, date=None, variety=None):
+    """Helper to create a test image with metadata."""
+    img = RGBImage(name)
+    img.setImage(np.zeros((10, 10, 3), dtype=np.uint8))
 
-    
+    rating = FloatValue("rating", "rating", "test rating")
+    rating.setMin(0.0)
+    rating.setMax(1.0)
+    rating.setValue(rating_val)
+    img.addValue(rating)
+
+    if project:
+        for key, val in [("project", project), ("lot", lot), ("date", date), ("variety", variety)]:
+            sv = StringValue(key, key, f"test {key}")
+            sv.setValue(val)
+            img.addValue(sv)
+
+    return img
+
+
+def test_write_tray_summary_with_string_columns():
+    """tray_summary.csv should include string metadata columns like project, lot, date, variety."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        mdv = MetaDataValue("results", "results", "test")
+        mdv.setValue(tmpdir)
+
+        images = [
+            _make_image("PROJ_LOT1_2025-01-01_VAR_fruit_01.png", 0.8, "PROJ", "LOT1", "2025-01-01", "VAR"),
+            _make_image("PROJ_LOT1_2025-01-01_VAR_fruit_02.png", 0.6, "PROJ", "LOT1", "2025-01-01", "VAR"),
+        ]
+        mdv.setImageList(images)
+        mdv.writeValue()
+
+        tray_df = pd.read_csv(os.path.join(tmpdir, "tray_summary.csv"))
+        assert "project" in tray_df.columns
+        assert "lot" in tray_df.columns
+        assert "date" in tray_df.columns
+        assert "variety" in tray_df.columns
+        assert tray_df["project"].iloc[0] == "PROJ"
+        assert tray_df["lot"].iloc[0] == "LOT1"
+        assert tray_df["rating"].iloc[0] == 0.7  # average of 0.8 and 0.6
+
+
+def test_write_tray_summary_without_string_columns():
+    """tray_summary.csv should still work without string metadata."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        mdv = MetaDataValue("results", "results", "test")
+        mdv.setValue(tmpdir)
+
+        images = [
+            _make_image("apple_fruit_01.png", 0.9),
+            _make_image("apple_fruit_02.png", 0.7),
+        ]
+        mdv.setImageList(images)
+        mdv.writeValue()
+
+        tray_df = pd.read_csv(os.path.join(tmpdir, "tray_summary.csv"))
+        assert "TrayName" in tray_df.columns
+        assert "rating" in tray_df.columns
+        assert abs(tray_df["rating"].iloc[0] - 0.8) < 0.001
+
+
+def test_results_csv_has_all_rows():
+    """results.csv should have one row per image."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        mdv = MetaDataValue("results", "results", "test")
+        mdv.setValue(tmpdir)
+
+        images = [
+            _make_image("PROJ_LOT1_2025-01-01_VAR_fruit_01.png", 0.5, "PROJ", "LOT1", "2025-01-01", "VAR"),
+            _make_image("PROJ_LOT1_2025-01-01_VAR_fruit_02.png", 0.6, "PROJ", "LOT1", "2025-01-01", "VAR"),
+            _make_image("PROJ_LOT1_2025-01-01_VAR_fruit_03.png", 0.7, "PROJ", "LOT1", "2025-01-01", "VAR"),
+        ]
+        mdv.setImageList(images)
+        mdv.writeValue()
+
+        results_df = pd.read_csv(os.path.join(tmpdir, "results.csv"))
+        assert len(results_df) == 3