bed3f1ebd41020f9bbd31ba30b78902775eddbc8,plantcv/plantcv/morphology/segment_angle.py,,segment_angle,#Any#Any#,14

Before Change

        // Calculate degrees from slopes
        segment_angles.append(np.arctan(slope[0]) * 180 / np.pi)

    angle_header = ["HEADER_ANGLE"]
    angle_data = ["ANGLE_DATA"]
    for i, cnt in enumerate(objects):
        // Label slope lines
        w = label_coord_x[i]
        h = label_coord_y[i]
        text = "{:.2f}".format(segment_angles[i])
        cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
                    fontScale=.55, color=(150, 150, 150), thickness=2)
        segment_label = "ID" + str(i)
        angle_header.append(segment_label)
    angle_data.extend(segment_angles)

    if "morphology_data" not in outputs.measurements:
        outputs.measurements["morphology_data"] = {}
    outputs.measurements["morphology_data"]["segment_angles"] = segment_angles

    // Auto-increment device
    params.device += 1

    if params.debug == "print":
        print_image(labeled_img, os.path.join(params.debug_outdir, str(params.device) + "_segmented_angles.png"))
    elif params.debug == "plot":
        plot_image(labeled_img)

    return angle_header, angle_data, labeled_img

After Change

    label_coord_x = []
    label_coord_y = []
    segment_angles = []

    labeled_img = segmented_img.copy()

    rand_color = color_palette(len(objects))

    for i, cnt in enumerate(objects):
        // Find bounds for regression lines to get drawn
        rect = cv2.minAreaRect(cnt)
        pts = cv2.boxPoints(rect)
        df = pd.DataFrame(pts, columns=("x", "y"))
        x_max = int(df["x"].max())
        x_min = int(df["x"].min())

        // Find line fit to each segment
        [vx, vy, x, y] = cv2.fitLine(objects[i], cv2.DIST_L2, 0, 0.01, 0.01)
        slope = -vy / vx
        left_list = int(((x - x_min) * slope) + y)
        right_list = int(((x - x_max) * slope) + y)

        if slope > 1000000 or slope < -1000000:
            print("Slope of contour with ID//", i, "is", slope, "and cannot be plotted.")
        else:
            // Draw slope lines
            cv2.line(labeled_img, (x_max - 1, right_list), (x_min, left_list), rand_color[i], 1)

        // Store coordinates for labels
        label_coord_x.append(objects[i][0][0][0])
        label_coord_y.append(objects[i][0][0][1])

        // Calculate degrees from slopes
        segment_angles.append(np.arctan(slope[0]) * 180 / np.pi)

    segment_ids = []
    for i, cnt in enumerate(objects):
        // Label slope lines
        w = label_coord_x[i]
        h = label_coord_y[i]
        text = "{:.2f}".format(segment_angles[i])
        cv2.putText(img=labeled_img, text=text, org=(w, h), fontFace=cv2.FONT_HERSHEY_SIMPLEX,
                    fontScale=.55, color=(150, 150, 150), thickness=2)
        segment_label = "ID" + str(i)
        segment_ids.append(i)

    outputs.add_measurement(variable="segment_angles", trait="segment_angles",
                            method="plantcv.plantcv.morphology.segment_angles", scale="degrees", datatype=list,
                            value=segment_angles, label=segment_ids)

    // Auto-increment device
    params.device += 1

Instances