Automatically Detect a Color Card¶

Automatically detects a Macbeth ColorChecker style color card and creates a labeled mask.

plantcv.transform.detect_color_card(rgb_img, label=None, color_chip_size=None, roi=None, **kwargs)

returns labeled_mask

• Parameters

  • rgb_img - Input RGB image data containing a color card.
  • label - Optional label parameter, modifies the variable name of observations recorded. (default = pcv.params.sample_label)
  • color_chip_size - Type of color card to be detected, ("classic", "passport", "nano", "mini", or "cameratrax", by default None) or a tuple of the (width, height) dimensions of the color card chips in millimeters. If set then size scalings parameters pcv.params.unit, pcv.params.px_width, and pcv.params.px_height are automatically set, and utilized throughout linear and area type measurements stored to Outputs.
  • roi - Optional rectangular ROI as returned by pcv.roi.rectangle within which to look for the color card. (default = None)
  • **kwargs - Other keyword arguments passed to cv2.adaptiveThreshold and cv2.circle.
    • adaptive_method - Adaptive threhold method. 0 (mean) or 1 (Gaussian) (default = 1).
    • block_size - Size of a pixel neighborhood that is used to calculate a threshold value (default = 51). We suggest using 127 if using adaptive_method=0.
    • radius - Radius of circle to make the color card labeled mask (default = 20).
    • min_size - Minimum chip size for filtering objects after edge detection (default = 1000)
    • aspect_ratio - Optional aspect ratio (width / height) below which objects will get removed. Orientation agnogstic since automatically set to the reciprocal if <1 (default = 1.27)
    • solidity - Optional solidity (object area / convex hull area) filter (default = 0.8)

• Returns

  • labeled_mask - Labeled color card mask (useful downstream of this step in pcv.transform.get_color_matrix and pcv.transform.correct_color and pcv.transform.affine_color_correction).

• Context

  • If the goal is to color correct the image colorspace to the standard color card values, consider using pcv.transform.auto_correct_color since this new function is a one-step wrapper of plantcv.transform.detect_color_card, plantcv.transform.std_color_matrix, and plantcv.transform.affine_color_correction.
  • This mask output will be consistent in chip order regardless of orientation, where the white chip is detected and labeled first with index=0.
  • This algorithm uses an adaptive edge detection, and filters objects based on their size, apparent aspect ratio, and solidity.
  • QR codes are often falsely detected by this algorithm, but can be ignored during detection if the optional roi parameter is used.
• Example use:
  • Color Correction Tutorial since this function is called during pcv.transform.auto_correct_color.

from plantcv import plantcv as pcv
rgb_img, path, filename = pcv.readimage("target_img.png")
# Using a supported color card size will automatically set size scaling parameters
cc_mask = pcv.transform.detect_color_card(rgb_img=rgb_img, color_chip_size="passport")
# Or if using another Macbeth ColorChecker you can explicitly set the color chip size (in millimeters)
cc_mask = pcv.transform.detect_color_card(rgb_img=rgb_img, color_chip_size=(12, 12))

avg_chip_size = pcv.outputs.metadata['median_color_chip_size']['value'][0]
avg_chip_w = pcv.outputs.metadata['median_color_chip_width']['value'][0]
avg_chip_h = pcv.outputs.metadata['median_color_chip_height']['value'][0]

# When using detect_color_card, you will always set pos=3
tgt_matrix = pcv.transform.std_color_matrix(pos=3)
headers, card_matrix = pcv.transform.get_color_matrix(rgb_img=rgb_img, mask=cc_mask)
corrected_img = pcv.transform.affine_color_correction(rgb_img=rgb_img,
                                                      source_matrix=card_matrix,
                                                      target_matrix=tgt_matrix)

Image automatically detected and masked

Suppored Color Cards¶

Calibrite ColorChecker Passport

Chip dimensions: 12mm x 12mm

Calibrite ColorChecker Classic

Chip dimensions: 40mm x 40mm

Calibrite ColorChecker Classic Mini

Chip dimensions: 12mm x 12mm

CameraTrax 24ColorCard-2x3

Chip dimensions: 11mm x 11mm

ColorChecker Classic Nano

Chip dimensions: 3mm x 4mm

Source Code: Here