예제 #1
0
파일: tests.py 프로젝트: stiphyMT/plantcv
def test_plantcv_dilate():
    img = cv2.imread(os.path.join(TEST_DATA, TEST_INPUT_BINARY), -1)
    device, dilate_img = pcv.dilate(img=img, kernel=5, i=1, device=0, debug=None)
    # Assert that the output image has the dimensions of the input image
    if all([i == j] for i, j in zip(np.shape(dilate_img), TEST_BINARY_DIM)):
        # Assert that the image is binary
        if all([i == j] for i, j in zip(np.unique(dilate_img), [0, 255])):
            assert 1
        else:
            assert 0
    else:
        assert 0
예제 #2
0
파일: tests.py 프로젝트: migerman1/plantcv
def test_plantcv_dilate():
    img = cv2.imread(os.path.join(TEST_DATA, TEST_INPUT_BINARY), -1)
    device, dilate_img = pcv.dilate(img=img,
                                    kernel=5,
                                    i=1,
                                    device=0,
                                    debug=None)
    # Assert that the output image has the dimensions of the input image
    if all([i == j] for i, j in zip(np.shape(dilate_img), TEST_BINARY_DIM)):
        # Assert that the image is binary
        if all([i == j] for i, j in zip(np.unique(dilate_img), [0, 255])):
            assert 1
        else:
            assert 0
    else:
        assert 0
예제 #3
0
def main():
  # Get options
  args = options()
  
  # Read image
  img, path, filename = pcv.readimage(args.image)
    
  # Pipeline step
  device = 0

  # Convert RGB to HSV and extract the Saturation channel
  device, s = pcv.rgb2gray_hsv(img, 's', device, args.debug)
  
  # Threshold the Saturation image
  device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, args.debug)
  
  # Median Filter
  device, s_mblur = pcv.median_blur(s_thresh, 0, device, args.debug)
  device, s_cnt = pcv.median_blur(s_thresh, 0, device, args.debug)
  
  # Fill small objects
  #device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)
  
  # Convert RGB to LAB and extract the Blue channel
  device, b = pcv.rgb2gray_lab(img, 'b', device, args.debug)
  
  # Threshold the blue image
  device, b_thresh = pcv.binary_threshold(b, 137, 255, 'light', device, args.debug)
  device, b_cnt = pcv.binary_threshold(b, 137, 255, 'light', device, args.debug)
  
  # Fill small objects
  #device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)
  
  # Join the thresholded saturation and blue-yellow images
  device, bs = pcv.logical_and(s_mblur, b_cnt, device, args.debug)
  
  # Apply Mask (for vis images, mask_color=white)
  device, masked = pcv.apply_mask(img, bs, 'white', device, args.debug)
  
  # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
  device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, args.debug)
  device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, args.debug)
  
  # Threshold the green-magenta and blue images
  device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, 'dark', device, args.debug)
  device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, 'light', device, args.debug)
  
  # Join the thresholded saturation and blue-yellow images (OR)
  device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)
  device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)
  
  # Fill small noise
  device, ab_fill1 = pcv.fill(ab, ab_cnt, 2, device, args.debug)
  
  # Dilate to join small objects with larger ones
  device, ab_cnt1=pcv.dilate(ab_fill1, 3, 2, device, args.debug)
  device, ab_cnt2=pcv.dilate(ab_fill1, 3, 2, device, args.debug)
  
  # Fill dilated image mask
  device, ab_cnt3=pcv.fill(ab_cnt2,ab_cnt1,150,device,args.debug)
  device, masked2 = pcv.apply_mask(masked, ab_cnt3, 'white', device, args.debug)
  
  # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
  device, masked2_a = pcv.rgb2gray_lab(masked2, 'a', device, args.debug)
  device, masked2_b = pcv.rgb2gray_lab(masked2, 'b', device, args.debug)
  
  # Threshold the green-magenta and blue images
  device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, 'dark', device, args.debug)
  device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255, 'light', device, args.debug)
  device, ab_fill = pcv.logical_or(masked2a_thresh, masked2b_thresh, device, args.debug)
  
  # Identify objects
  device, id_objects,obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, args.debug)
  
  # Define ROI
  device, roi1, roi_hierarchy= pcv.define_roi(masked2,'rectangle', device, None, 'default', args.debug,True, 525, 0,-490,-150)
  
  # Decide which objects to keep
  device,roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(img,'partial',roi1,roi_hierarchy,id_objects,obj_hierarchy,device, args.debug)
  
  # Object combine kept objects
  device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, args.debug)
  
  ############## VIS Analysis ################
  
  outfile=False
  if args.writeimg==True:
    outfile=args.outdir+"/"+filename
  
  # Find shape properties, output shape image (optional)
  device, shape_header,shape_data,shape_img = pcv.analyze_object(img, args.image, obj, mask, device,args.debug,outfile)
  
  # Shape properties relative to user boundary line (optional)
  device, boundary_header,boundary_data, boundary_img1= pcv.analyze_bound(img, args.image,obj, mask, 325, device,args.debug,outfile)
  
  # Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
  device, color_header,color_data,color_img= pcv.analyze_color(img, args.image, mask, 256, device, args.debug,None,'v','img',300,outfile)
  
  # Output shape and color data

  result=open(args.result,"a")
  result.write('\t'.join(map(str,shape_header)))
  result.write("\n")
  result.write('\t'.join(map(str,shape_data)))
  result.write("\n")
  for row in shape_img:
    result.write('\t'.join(map(str,row)))
    result.write("\n")
  result.write('\t'.join(map(str,color_header)))
  result.write("\n")
  result.write('\t'.join(map(str,color_data)))
  result.write("\n")
  result.write('\t'.join(map(str,boundary_header)))
  result.write("\n")
  result.write('\t'.join(map(str,boundary_data)))
  result.write("\n")
  result.write('\t'.join(map(str,boundary_img1)))
  result.write("\n")
  for row in color_img:
    result.write('\t'.join(map(str,row)))
    result.write("\n")
  result.close()
예제 #4
0
def main():
    # Get options
    args = options()

    # Read image
    img, path, filename = pcv.readimage(args.image)

    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(img, 's', device, args.debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device,
                                            args.debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 0, device, args.debug)
    device, s_cnt = pcv.median_blur(s_thresh, 0, device, args.debug)

    # Fill small objects
    #device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(img, 'b', device, args.debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, 'light', device,
                                            args.debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, 'light', device,
                                         args.debug)

    # Fill small objects
    #device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, args.debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(img, bs, 'white', device, args.debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, args.debug)
    device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, args.debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, 'dark',
                                                  device, args.debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, 'light',
                                                  device, args.debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device,
                                args.debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device,
                                    args.debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 2, device, args.debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, args.debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, args.debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, args.debug)
    img2 = np.copy(img)
    device, masked2 = pcv.apply_mask(img2, ab_cnt3, 'white', device,
                                     args.debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, 'a', device, args.debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, 'b', device, args.debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, 'dark',
                                                   device, args.debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255,
                                                   'light', device, args.debug)
    device, ab_fill = pcv.logical_or(masked2a_thresh, masked2b_thresh, device,
                                     args.debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(
        masked2, ab_fill, device, args.debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(masked2, 'rectangle', device,
                                                 None, 'default', args.debug,
                                                 True, 550, 10, -600, -907)

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
        img, 'partial', roi1, roi_hierarchy, id_objects, obj_hierarchy, device,
        args.debug)

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3,
                                               device, args.debug)

    ############## Landmarks    ################

    device, points = pcv.acute_vertex(obj, 40, 40, 40, img, device, args.debug)
    boundary_line = 900
    # Use acute fxn to estimate tips
    device, points_r, centroid_r, bline_r = pcv.scale_features(
        obj, mask, points, boundary_line, device, args.debug)
    # Get number of points
    tips = len(points_r)
    # Use turgor_proxy fxn to get distances
    device, vert_ave_c, hori_ave_c, euc_ave_c, ang_ave_c, vert_ave_b, hori_ave_b, euc_ave_b, ang_ave_b = pcv.turgor_proxy(
        points_r, centroid_r, bline_r, device, args.debug)
    # Get pseudomarkers along the y-axis
    device, left, right, center_h = pcv.y_axis_pseudolandmarks(
        obj, mask, img, device, args.debug)
    # Re-scale the points
    device, left_r, left_cr, left_br = pcv.scale_features(
        obj, mask, left, boundary_line, device, args.debug)
    device, right_r, right_cr, right_br = pcv.scale_features(
        obj, mask, right, boundary_line, device, args.debug)
    device, center_hr, center_hcr, center_hbr = pcv.scale_features(
        obj, mask, center_h, boundary_line, device, args.debug)

    # Get pseudomarkers along the x-axis
    device, top, bottom, center_v = pcv.x_axis_pseudolandmarks(
        obj, mask, img, device, args.debug)

    # Re-scale the points
    device, top_r, top_cr, top_br = pcv.scale_features(obj, mask, top,
                                                       boundary_line, device,
                                                       args.debug)
    device, bottom_r, bottom_cr, bottom_br = pcv.scale_features(
        obj, mask, bottom, boundary_line, device, args.debug)
    device, center_vr, center_vcr, center_vbr = pcv.scale_features(
        obj, mask, center_v, boundary_line, device, args.debug)

    ## Need to convert the points into a list of tuples format to match the scaled points
    points = points.reshape(len(points), 2)
    points = points.tolist()
    temp_out = []
    for p in points:
        p = tuple(p)
        temp_out.append(p)
    points = temp_out
    left = left.reshape(20, 2)
    left = left.tolist()
    temp_out = []
    for l in left:
        l = tuple(l)
        temp_out.append(l)
    left = temp_out
    right = right.reshape(20, 2)
    right = right.tolist()
    temp_out = []
    for r in right:
        r = tuple(r)
        temp_out.append(r)
    right = temp_out
    center_h = center_h.reshape(20, 2)
    center_h = center_h.tolist()
    temp_out = []
    for ch in center_h:
        ch = tuple(ch)
        temp_out.append(ch)
    center_h = temp_out
    ## Need to convert the points into a list of tuples format to match the scaled points
    top = top.reshape(20, 2)
    top = top.tolist()
    temp_out = []
    for t in top:
        t = tuple(t)
        temp_out.append(t)
    top = temp_out
    bottom = bottom.reshape(20, 2)
    bottom = bottom.tolist()
    temp_out = []
    for b in bottom:
        b = tuple(b)
        temp_out.append(b)
    bottom = temp_out
    center_v = center_v.reshape(20, 2)
    center_v = center_v.tolist()
    temp_out = []
    for cvr in center_v:
        cvr = tuple(cvr)
        temp_out.append(cvr)
    center_v = temp_out

    #Store Landmark Data
    landmark_header = ('HEADER_LANDMARK', 'tip_points', 'tip_points_r',
                       'centroid_r', 'baseline_r', 'tip_number', 'vert_ave_c',
                       'hori_ave_c', 'euc_ave_c', 'ang_ave_c', 'vert_ave_b',
                       'hori_ave_b', 'euc_ave_b', 'ang_ave_b', 'left_lmk',
                       'right_lmk', 'center_h_lmk', 'left_lmk_r',
                       'right_lmk_r', 'center_h_lmk_r', 'top_lmk',
                       'bottom_lmk', 'center_v_lmk', 'top_lmk_r',
                       'bottom_lmk_r', 'center_v_lmk_r')

    landmark_data = ('LANDMARK_DATA', points, points_r, centroid_r, bline_r,
                     tips, vert_ave_c, hori_ave_c, euc_ave_c, ang_ave_c,
                     vert_ave_b, hori_ave_b, euc_ave_b, ang_ave_b, left, right,
                     center_h, left_r, right_r, center_hr, top, bottom,
                     center_v, top_r, bottom_r, center_vr)

    ############## VIS Analysis ################

    outfile = False
    #if args.writeimg==True:
    #outfile=args.outdir+"/"+filename

    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(
        img, args.image, obj, mask, device, args.debug, outfile)

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
        img, args.image, obj, mask, 935, device, args.debug, outfile)

    # Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(
        img, args.image, mask, 256, device, args.debug, None, 'v', 'img', 300,
        outfile)

    # Output shape and color data

    result = open(args.result, "a")
    result.write('\t'.join(map(str, shape_header)))
    result.write("\n")
    result.write('\t'.join(map(str, shape_data)))
    result.write("\n")
    for row in shape_img:
        result.write('\t'.join(map(str, row)))
        result.write("\n")
    result.write('\t'.join(map(str, color_header)))
    result.write("\n")
    result.write('\t'.join(map(str, color_data)))
    result.write("\n")
    result.write('\t'.join(map(str, boundary_header)))
    result.write("\n")
    result.write('\t'.join(map(str, boundary_data)))
    result.write("\n")
    result.write('\t'.join(map(str, boundary_img1)))
    result.write("\n")
    for row in color_img:
        result.write('\t'.join(map(str, row)))
        result.write("\n")
    result.write('\t'.join(map(str, landmark_header)))
    result.write("\n")
    result.write('\t'.join(map(str, landmark_data)))
    result.write("\n")
    result.close()
예제 #5
0
def main():
    # Initialize device
    device = 0

    # Parse command-line options
    args = options()

    # Read image
    img, path, filename = pcv.readimage(filename=args.image, debug=args.debug)

    # Convert RGB to LAB and extract the Blue-Yellow channel
    device, blue_channel = pcv.rgb2gray_lab(img=img,
                                            channel="b",
                                            device=device,
                                            debug=args.debug)

    # Threshold the blue image using the triangle autothreshold method
    device, blue_tri = pcv.triangle_auto_threshold(device=device,
                                                   img=blue_channel,
                                                   maxvalue=255,
                                                   object_type="light",
                                                   xstep=1,
                                                   debug=args.debug)

    # Extract core plant region from the image to preserve delicate plant features during filtering
    device += 1
    plant_region = blue_tri[0:1750, 600:2080]
    if args.debug is not None:
        pcv.print_image(filename=str(device) + "_extract_plant_region.png",
                        img=plant_region)

    # Use a Gaussian blur to disrupt the strong edge features in the cabinet
    device, blur_gaussian = pcv.gaussian_blur(device=device,
                                              img=blue_tri,
                                              ksize=(3, 3),
                                              sigmax=0,
                                              sigmay=None,
                                              debug=args.debug)

    # Threshold the blurred image to remove features that were blurred
    device, blur_thresholded = pcv.binary_threshold(img=blur_gaussian,
                                                    threshold=250,
                                                    maxValue=255,
                                                    object_type="light",
                                                    device=device,
                                                    debug=args.debug)

    # Add the plant region back in to the filtered image
    device += 1
    blur_thresholded[0:1750, 600:2080] = plant_region
    if args.debug is not None:
        pcv.print_image(filename=str(device) + "_replace_plant_region.png",
                        img=blur_thresholded)

    # Fill small noise
    device, blue_fill_50 = pcv.fill(img=np.copy(blur_thresholded),
                                    mask=np.copy(blur_thresholded),
                                    size=50,
                                    device=device,
                                    debug=args.debug)

    # Identify objects
    device, contours, contour_hierarchy = pcv.find_objects(img=img,
                                                           mask=blue_fill_50,
                                                           device=device,
                                                           debug=args.debug)

    # Define ROI
    device, roi, roi_hierarchy = pcv.define_roi(img=img,
                                                shape="rectangle",
                                                device=device,
                                                roi=None,
                                                roi_input="default",
                                                debug=args.debug,
                                                adjust=True,
                                                x_adj=565,
                                                y_adj=0,
                                                w_adj=-490,
                                                h_adj=-250)

    # Decide which objects to keep
    device, roi_contours, roi_contour_hierarchy, _, _ = pcv.roi_objects(
        img=img,
        roi_type="partial",
        roi_contour=roi,
        roi_hierarchy=roi_hierarchy,
        object_contour=contours,
        obj_hierarchy=contour_hierarchy,
        device=device,
        debug=args.debug)

    # If there are no contours left we cannot measure anything
    if len(roi_contours) > 0:
        # Object combine kept objects
        device, plant_contour, plant_mask = pcv.object_composition(
            img=img,
            contours=roi_contours,
            hierarchy=roi_contour_hierarchy,
            device=device,
            debug=args.debug)

        outfile = False
        if args.writeimg:
            outfile = args.outdir + "/" + filename

        # Find shape properties, output shape image (optional)
        device, shape_header, shape_data, shape_img = pcv.analyze_object(
            img=img,
            imgname=args.image,
            obj=plant_contour,
            mask=plant_mask,
            device=device,
            debug=args.debug,
            filename=outfile)

        # Shape properties relative to user boundary line (optional)
        device, boundary_header, boundary_data, boundary_img = pcv.analyze_bound(
            img=img,
            imgname=args.image,
            obj=plant_contour,
            mask=plant_mask,
            line_position=440,
            device=device,
            debug=args.debug,
            filename=outfile)

        # Determine color properties: Histograms, Color Slices and Pseudocolored Images,
        # output color analyzed images (optional)
        device, color_header, color_data, color_img = pcv.analyze_color(
            img=img,
            imgname=args.image,
            mask=plant_mask,
            bins=256,
            device=device,
            debug=args.debug,
            hist_plot_type=None,
            pseudo_channel="v",
            pseudo_bkg="img",
            resolution=300,
            filename=outfile)

        # Output shape and color data
        result = open(args.result, "a")
        result.write('\t'.join(map(str, shape_header)) + "\n")
        result.write('\t'.join(map(str, shape_data)) + "\n")
        for row in shape_img:
            result.write('\t'.join(map(str, row)) + "\n")
        result.write('\t'.join(map(str, color_header)) + "\n")
        result.write('\t'.join(map(str, color_data)) + "\n")
        result.write('\t'.join(map(str, boundary_header)) + "\n")
        result.write('\t'.join(map(str, boundary_data)) + "\n")
        result.write('\t'.join(map(str, boundary_img)) + "\n")
        for row in color_img:
            result.write('\t'.join(map(str, row)) + "\n")
        result.close()

        # Find matching NIR image
        device, nirpath = pcv.get_nir(path=path,
                                      filename=filename,
                                      device=device,
                                      debug=args.debug)
        nir_rgb, nir_path, nir_filename = pcv.readimage(nirpath)
        nir_img = cv2.imread(nirpath, 0)

        # Make mask glovelike in proportions via dilation
        device, d_mask = pcv.dilate(plant_mask,
                                    kernel=1,
                                    i=0,
                                    device=device,
                                    debug=args.debug)

        # Resize mask
        prop2, prop1 = conv_ratio()
        device, nmask = pcv.resize(img=d_mask,
                                   resize_x=prop1,
                                   resize_y=prop2,
                                   device=device,
                                   debug=args.debug)

        # Convert the resized mask to a binary mask
        device, bmask = pcv.binary_threshold(img=nmask,
                                             threshold=0,
                                             maxValue=255,
                                             object_type="light",
                                             device=device,
                                             debug=args.debug)

        device, crop_img = crop_sides_equally(mask=bmask,
                                              nir=nir_img,
                                              device=device,
                                              debug=args.debug)

        # position, and crop mask
        device, newmask = pcv.crop_position_mask(img=nir_img,
                                                 mask=crop_img,
                                                 device=device,
                                                 x=34,
                                                 y=9,
                                                 v_pos="top",
                                                 h_pos="right",
                                                 debug=args.debug)

        # Identify objects
        device, nir_objects, nir_hierarchy = pcv.find_objects(img=nir_rgb,
                                                              mask=newmask,
                                                              device=device,
                                                              debug=args.debug)

        # Object combine kept objects
        device, nir_combined, nir_combinedmask = pcv.object_composition(
            img=nir_rgb,
            contours=nir_objects,
            hierarchy=nir_hierarchy,
            device=device,
            debug=args.debug)

        if args.writeimg:
            outfile = args.outdir + "/" + nir_filename

        # Analyze NIR signal data
        device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
            img=nir_img,
            rgbimg=nir_rgb,
            mask=nir_combinedmask,
            bins=256,
            device=device,
            histplot=False,
            debug=args.debug,
            filename=outfile)

        # Analyze the shape of the plant contour from the NIR image
        device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
            img=nir_img,
            imgname=nir_filename,
            obj=nir_combined,
            mask=nir_combinedmask,
            device=device,
            debug=args.debug,
            filename=outfile)

        # Write NIR data to co-results file
        coresult = open(args.coresult, "a")
        coresult.write('\t'.join(map(str, nhist_header)) + "\n")
        coresult.write('\t'.join(map(str, nhist_data)) + "\n")
        for row in nir_imgs:
            coresult.write('\t'.join(map(str, row)) + "\n")
        coresult.write('\t'.join(map(str, nshape_header)) + "\n")
        coresult.write('\t'.join(map(str, nshape_data)) + "\n")
        coresult.write('\t'.join(map(str, nir_shape)) + "\n")
        coresult.close()
예제 #6
0
def main():
    # Initialize device
    device = 0

    # Parse command-line options
    args = options()

    # Read image
    img, path, filename = pcv.readimage(filename=args.image, debug=args.debug)

    # Convert RGB to LAB and extract the Green-Magenta channel
    device, green_channel = pcv.rgb2gray_lab(img=img,
                                             channel="a",
                                             device=device,
                                             debug=args.debug)

    # Invert the Green-Magenta image because the plant is dark green
    device, green_inv = pcv.invert(img=green_channel,
                                   device=device,
                                   debug=args.debug)

    # Threshold the inverted Green-Magenta image to mostly isolate green pixels
    device, green_thresh = pcv.binary_threshold(img=green_inv,
                                                threshold=134,
                                                maxValue=255,
                                                object_type="light",
                                                device=device,
                                                debug=args.debug)

    # Extract core plant region from the image to preserve delicate plant features during filtering
    device += 1
    plant_region = green_thresh[100:2000, 250:2250]
    if args.debug is not None:
        pcv.print_image(filename=str(device) + "_extract_plant_region.png",
                        img=plant_region)

    # Use a Gaussian blur to disrupt the strong edge features in the cabinet
    device, blur_gaussian = pcv.gaussian_blur(device=device,
                                              img=green_thresh,
                                              ksize=(7, 7),
                                              sigmax=0,
                                              sigmay=None,
                                              debug=args.debug)

    # Threshold the blurred image to remove features that were blurred
    device, blur_thresholded = pcv.binary_threshold(img=blur_gaussian,
                                                    threshold=250,
                                                    maxValue=255,
                                                    object_type="light",
                                                    device=device,
                                                    debug=args.debug)

    # Add the plant region back in to the filtered image
    device += 1
    blur_thresholded[100:2000, 250:2250] = plant_region
    if args.debug is not None:
        pcv.print_image(filename=str(device) + "_replace_plant_region.png",
                        img=blur_thresholded)

    # Use a median blur to breakup the horizontal and vertical lines caused by shadows from the track edges
    device, med_blur = pcv.median_blur(img=blur_thresholded,
                                       ksize=5,
                                       device=device,
                                       debug=args.debug)

    # Fill in small contours
    device, green_fill_50 = pcv.fill(img=np.copy(med_blur),
                                     mask=np.copy(med_blur),
                                     size=50,
                                     device=device,
                                     debug=args.debug)

    # Define an ROI for the brass stopper
    device, stopper_roi, stopper_hierarchy = pcv.define_roi(
        img=img,
        shape="rectangle",
        device=device,
        roi=None,
        roi_input="default",
        debug=args.debug,
        adjust=True,
        x_adj=1420,
        y_adj=890,
        w_adj=-920,
        h_adj=-1040)

    # Identify all remaining contours in the binary image
    device, contours, hierarchy = pcv.find_objects(img=img,
                                                   mask=np.copy(green_fill_50),
                                                   device=device,
                                                   debug=args.debug)

    # Remove contours completely contained within the stopper region of interest
    device, remove_stopper_mask = remove_countors_roi(mask=green_fill_50,
                                                      contours=contours,
                                                      hierarchy=hierarchy,
                                                      roi=stopper_roi,
                                                      device=device,
                                                      debug=args.debug)

    # Define an ROI for a screw hole
    device, screw_roi, screw_hierarchy = pcv.define_roi(img=img,
                                                        shape="rectangle",
                                                        device=device,
                                                        roi=None,
                                                        roi_input="default",
                                                        debug=args.debug,
                                                        adjust=True,
                                                        x_adj=1870,
                                                        y_adj=1010,
                                                        w_adj=-485,
                                                        h_adj=-960)

    # Remove contours completely contained within the screw region of interest
    device, remove_screw_mask = remove_countors_roi(mask=remove_stopper_mask,
                                                    contours=contours,
                                                    hierarchy=hierarchy,
                                                    roi=screw_roi,
                                                    device=device,
                                                    debug=args.debug)

    # Identify objects
    device, contours, contour_hierarchy = pcv.find_objects(
        img=img, mask=remove_screw_mask, device=device, debug=args.debug)

    # Define ROI
    device, roi, roi_hierarchy = pcv.define_roi(img=img,
                                                shape="rectangle",
                                                device=device,
                                                roi=None,
                                                roi_input="default",
                                                debug=args.debug,
                                                adjust=True,
                                                x_adj=565,
                                                y_adj=200,
                                                w_adj=-490,
                                                h_adj=-250)

    # Decide which objects to keep
    device, roi_contours, roi_contour_hierarchy, _, _ = pcv.roi_objects(
        img=img,
        roi_type="partial",
        roi_contour=roi,
        roi_hierarchy=roi_hierarchy,
        object_contour=contours,
        obj_hierarchy=contour_hierarchy,
        device=device,
        debug=args.debug)

    # If there are no contours left we cannot measure anything
    if len(roi_contours) > 0:
        # Object combine kept objects
        device, plant_contour, plant_mask = pcv.object_composition(
            img=img,
            contours=roi_contours,
            hierarchy=roi_contour_hierarchy,
            device=device,
            debug=args.debug)

        outfile = False
        if args.writeimg:
            outfile = args.outdir + "/" + filename

        # Find shape properties, output shape image (optional)
        device, shape_header, shape_data, shape_img = pcv.analyze_object(
            img=img,
            imgname=args.image,
            obj=plant_contour,
            mask=plant_mask,
            device=device,
            debug=args.debug,
            filename=outfile)

        # Determine color properties: Histograms, Color Slices and Pseudocolored Images,
        # output color analyzed images (optional)
        device, color_header, color_data, color_img = pcv.analyze_color(
            img=img,
            imgname=args.image,
            mask=plant_mask,
            bins=256,
            device=device,
            debug=args.debug,
            hist_plot_type=None,
            pseudo_channel="v",
            pseudo_bkg="img",
            resolution=300,
            filename=outfile)

        # Output shape and color data
        result = open(args.result, "a")
        result.write('\t'.join(map(str, shape_header)) + "\n")
        result.write('\t'.join(map(str, shape_data)) + "\n")
        for row in shape_img:
            result.write('\t'.join(map(str, row)) + "\n")
        result.write('\t'.join(map(str, color_header)) + "\n")
        result.write('\t'.join(map(str, color_data)) + "\n")
        for row in color_img:
            result.write('\t'.join(map(str, row)) + "\n")
        result.close()

        # Find matching NIR image
        device, nirpath = pcv.get_nir(path=path,
                                      filename=filename,
                                      device=device,
                                      debug=args.debug)
        nir_rgb, nir_path, nir_filename = pcv.readimage(nirpath)
        nir_img = cv2.imread(nirpath, 0)

        # Make mask glovelike in proportions via dilation
        device, d_mask = pcv.dilate(plant_mask,
                                    kernel=1,
                                    i=0,
                                    device=device,
                                    debug=args.debug)

        # Resize mask
        prop2, prop1 = conv_ratio()
        device, nmask = pcv.resize(img=d_mask,
                                   resize_x=prop1,
                                   resize_y=prop2,
                                   device=device,
                                   debug=args.debug)

        # Convert the resized mask to a binary mask
        device, bmask = pcv.binary_threshold(img=nmask,
                                             threshold=0,
                                             maxValue=255,
                                             object_type="light",
                                             device=device,
                                             debug=args.debug)

        device, crop_img = crop_sides_equally(mask=bmask,
                                              nir=nir_img,
                                              device=device,
                                              debug=args.debug)

        # position, and crop mask
        device, newmask = pcv.crop_position_mask(img=nir_img,
                                                 mask=crop_img,
                                                 device=device,
                                                 x=0,
                                                 y=1,
                                                 v_pos="bottom",
                                                 h_pos="right",
                                                 debug=args.debug)

        # Identify objects
        device, nir_objects, nir_hierarchy = pcv.find_objects(img=nir_rgb,
                                                              mask=newmask,
                                                              device=device,
                                                              debug=args.debug)

        # Object combine kept objects
        device, nir_combined, nir_combinedmask = pcv.object_composition(
            img=nir_rgb,
            contours=nir_objects,
            hierarchy=nir_hierarchy,
            device=device,
            debug=args.debug)

        if args.writeimg:
            outfile = args.outdir + "/" + nir_filename

        # Analyze NIR signal data
        device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
            img=nir_img,
            rgbimg=nir_rgb,
            mask=nir_combinedmask,
            bins=256,
            device=device,
            histplot=False,
            debug=args.debug,
            filename=outfile)

        # Analyze the shape of the plant contour from the NIR image
        device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
            img=nir_img,
            imgname=nir_filename,
            obj=nir_combined,
            mask=nir_combinedmask,
            device=device,
            debug=args.debug,
            filename=outfile)

        # Write NIR data to co-results file
        coresult = open(args.coresult, "a")
        coresult.write('\t'.join(map(str, nhist_header)) + "\n")
        coresult.write('\t'.join(map(str, nhist_data)) + "\n")
        for row in nir_imgs:
            coresult.write('\t'.join(map(str, row)) + "\n")
        coresult.write('\t'.join(map(str, nshape_header)) + "\n")
        coresult.write('\t'.join(map(str, nshape_data)) + "\n")
        coresult.write('\t'.join(map(str, nir_shape)) + "\n")
        coresult.close()
def process_sv_images_core(vis_id, vis_img, nir_id, nir_rgb, nir_cv2, traits, debug=None):
    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(vis_img, 's', device, debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
    device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)

    # Fill small objects
    # device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(vis_img, 'b', device, debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, 'light', device, debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, 'light', device, debug)

    # Fill small objects
    # device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(vis_img, bs, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, debug)
    device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, 'dark', device, debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, 'light', device, debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 200, device, debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, debug)
    device, masked2 = pcv.apply_mask(masked, ab_cnt3, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, 'a', device, debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, 'dark', device, debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255, 'light', device, debug)

    device, masked2a_thresh_blur = pcv.median_blur(masked2a_thresh, 5, device, debug)
    device, masked2b_thresh_blur = pcv.median_blur(masked2b_thresh, 13, device, debug)

    device, ab_fill = pcv.logical_or(masked2a_thresh_blur, masked2b_thresh_blur, device, debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(masked2, 'rectangle', device, None, 'default', debug, True, 700,
                                                 0, -600, -300)

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(vis_img, 'partial', roi1, roi_hierarchy,
                                                                           id_objects, obj_hierarchy, device,
                                                                           debug)

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(vis_img, roi_objects, hierarchy3, device, debug)

    ############## VIS Analysis ################
    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(vis_img, vis_id, obj, mask, device, debug)

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(vis_img, vis_id, obj, mask, 384, device,
                                                                              debug)

    # Determine color properties: Histograms, Color Slices and
    # Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(vis_img, vis_id, mask, 256, device, debug,
                                                                    None, 'v', 'img', 300)

    # Output shape and color data
    vis_traits = {}
    for i in range(1, len(shape_header)):
        vis_traits[shape_header[i]] = shape_data[i]
    for i in range(1, len(boundary_header)):
        vis_traits[boundary_header[i]] = boundary_data[i]
    for i in range(2, len(color_header)):
        vis_traits[color_header[i]] = serialize_color_data(color_data[i])


    ############################# Use VIS image mask for NIR image#########################
    # Flip mask
    device, f_mask = pcv.flip(mask, "vertical", device, debug)

    # Reize mask
    device, nmask = pcv.resize(f_mask, 0.1154905775, 0.1154905775, device, debug)

    # position, and crop mask
    device, newmask = pcv.crop_position_mask(nir_rgb, nmask, device, 30, 4, "top", "right", debug)

    # Identify objects
    device, nir_objects, nir_hierarchy = pcv.find_objects(nir_rgb, newmask, device, debug)

    # Object combine kept objects
    device, nir_combined, nir_combinedmask = pcv.object_composition(nir_rgb, nir_objects, nir_hierarchy, device, debug)

    ####################################### Analysis #############################################
    device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(nir_cv2, nir_id, nir_combinedmask, 256,
                                                                           device, False, debug)
    device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(nir_cv2, nir_id, nir_combined, nir_combinedmask,
                                                                       device, debug)

    nir_traits = {}
    for i in range(1, len(nshape_header)):
        nir_traits[nshape_header[i]] = nshape_data[i]
    for i in range(2, len(nhist_header)):
        nir_traits[nhist_header[i]] = serialize_color_data(nhist_data[i])

    # Add data to traits table
    traits['sv_area'].append(vis_traits['area'])
    traits['hull_area'].append(vis_traits['hull-area'])
    traits['solidity'].append(vis_traits['solidity'])
    traits['height'].append(vis_traits['height_above_bound'])
    traits['perimeter'].append(vis_traits['perimeter'])

    return [vis_traits, nir_traits]
예제 #8
0
def main():
    # Get options
    args = options()

    # Read image
    img, path, filename = pcv.readimage(args.image)
    # roi = cv2.imread(args.roi)

    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(img, "s", device, args.debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, "light", device, args.debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 0, device, args.debug)
    device, s_cnt = pcv.median_blur(s_thresh, 0, device, args.debug)

    # Fill small objects
    # device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(img, "b", device, args.debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, "light", device, args.debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, "light", device, args.debug)

    # Fill small objects
    # device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, args.debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(img, bs, "white", device, args.debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, "a", device, args.debug)
    device, masked_b = pcv.rgb2gray_lab(masked, "b", device, args.debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, "dark", device, args.debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, "light", device, args.debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 2, device, args.debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, args.debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, args.debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, args.debug)
    device, masked2 = pcv.apply_mask(masked, ab_cnt3, "white", device, args.debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, "a", device, args.debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, "b", device, args.debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, "dark", device, args.debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255, "light", device, args.debug)
    device, ab_fill = pcv.logical_or(masked2a_thresh, masked2b_thresh, device, args.debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, args.debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(
        masked2, "rectangle", device, None, "default", args.debug, True, 550, 0, -600, -925
    )

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
        img, "partial", roi1, roi_hierarchy, id_objects, obj_hierarchy, device, args.debug
    )

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, args.debug)

    ############### Analysis ################

    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(
        img, args.image, obj, mask, device, args.debug, args.outdir + "/" + filename
    )

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
        img, args.image, obj, mask, 900, device, args.debug, args.outdir + "/" + filename
    )

    # Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(
        img, args.image, kept_mask, 256, device, args.debug, None, "v", "img", 300, args.outdir + "/" + filename
    )

    # Output shape and color data
    pcv.print_results(args.image, shape_header, shape_data)
    pcv.print_results(args.image, color_header, color_data)
    pcv.print_results(args.image, boundary_header, boundary_data)
def process_sv_images(session, url, vis_id, nir_id, traits, debug=None):
    """Process side-view images from Clowder.

    Inputs:
    session = requests session object
    url     = Clowder URL
    vis_id  = The Clowder ID of an RGB image
    nir_img = The Clowder ID of an NIR grayscale image
    traits  = traits table (dictionary)
    debug   = None, print, or plot. Print = save to file, Plot = print to screen

    :param session: requests session object
    :param url: str
    :param vis_id: str
    :param nir_id: str
    :param traits: dict
    :param debug: str
    :return traits: dict
    """
    # Read VIS image from Clowder
    vis_r = session.get(posixpath.join(url, "api/files", vis_id), stream=True)
    img_array = np.asarray(bytearray(vis_r.content), dtype="uint8")
    img = cv2.imdecode(img_array, -1)

    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(img, 's', device, debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
    device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)

    # Fill small objects
    # device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(img, 'b', device, debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, 'light', device, debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, 'light', device, debug)

    # Fill small objects
    # device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(img, bs, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, debug)
    device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, 'dark', device, debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, 'light', device, debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 200, device, debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, debug)
    device, masked2 = pcv.apply_mask(masked, ab_cnt3, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, 'a', device, debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, 'dark', device, debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255, 'light', device, debug)

    device, masked2a_thresh_blur = pcv.median_blur(masked2a_thresh, 5, device, debug)
    device, masked2b_thresh_blur = pcv.median_blur(masked2b_thresh, 13, device, debug)

    device, ab_fill = pcv.logical_or(masked2a_thresh_blur, masked2b_thresh_blur, device, debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(masked2, 'rectangle', device, None, 'default', debug, True, 700,
                                                 0, -600, -300)

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(img, 'partial', roi1, roi_hierarchy,
                                                                           id_objects, obj_hierarchy, device,
                                                                           debug)

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, debug)

    ############## VIS Analysis ################
    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(img, vis_id, obj, mask, device, debug)

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(img, vis_id, obj, mask, 384, device,
                                                                              debug)

    # Determine color properties: Histograms, Color Slices and
    # Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(img, vis_id, mask, 256, device, debug,
                                                                    None, 'v', 'img', 300)

    # Output shape and color data
    vis_traits = {}
    for i in range(1, len(shape_header)):
        vis_traits[shape_header[i]] = shape_data[i]
    for i in range(1, len(boundary_header)):
        vis_traits[boundary_header[i]] = boundary_data[i]
    for i in range(2, len(color_header)):
        vis_traits[color_header[i]] = serialize_color_data(color_data[i])
    #print(vis_traits)
    add_plantcv_metadata(session, url, vis_id, vis_traits)

    ############################# Use VIS image mask for NIR image#########################
    # Read NIR image from Clowder
    nir_r = session.get(posixpath.join(url, "api/files", nir_id), stream=True)
    nir_array = np.asarray(bytearray(nir_r.content), dtype="uint8")
    nir = cv2.imdecode(nir_array, -1)
    nir_rgb = cv2.cvtColor(nir, cv2.COLOR_GRAY2BGR)

    # Flip mask
    device, f_mask = pcv.flip(mask, "vertical", device, debug)

    # Reize mask
    device, nmask = pcv.resize(f_mask, 0.1154905775, 0.1154905775, device, debug)

    # position, and crop mask
    device, newmask = pcv.crop_position_mask(nir_rgb, nmask, device, 30, 4, "top", "right", debug)

    # Identify objects
    device, nir_objects, nir_hierarchy = pcv.find_objects(nir_rgb, newmask, device, debug)

    # Object combine kept objects
    device, nir_combined, nir_combinedmask = pcv.object_composition(nir_rgb, nir_objects, nir_hierarchy, device, debug)

    ####################################### Analysis #############################################
    device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(nir, nir_id, nir_combinedmask, 256,
                                                                           device, False, debug)
    device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(nir, nir_id, nir_combined, nir_combinedmask,
                                                                       device, debug)

    nir_traits = {}
    for i in range(1, len(nshape_header)):
        nir_traits[nshape_header[i]] = nshape_data[i]
    for i in range(2, len(nhist_header)):
        nir_traits[nhist_header[i]] = serialize_color_data(nhist_data[i])
    #print(nir_traits)
    add_plantcv_metadata(session, url, nir_id, nir_traits)

    # Add data to traits table
    traits['sv_area'].append(vis_traits['area'])
    traits['hull_area'].append(vis_traits['hull-area'])
    traits['solidity'].append(vis_traits['solidity'])
    traits['height'].append(vis_traits['height_above_bound'])
    traits['perimeter'].append(vis_traits['perimeter'])

    return traits
def process_sv_images(vis_img, nir_img, debug=None):
    """Process side-view images.

    Inputs:
    vis_img = An RGB image.
    nir_img = An NIR grayscale image.
    debug   = None, print, or plot. Print = save to file, Plot = print to screen.

    :param vis_img: str
    :param nir_img: str
    :param debug: str
    :return:
    """
    # Read VIS image
    img, path, filename = pcv.readimage(vis_img)

    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(img, 's', device, debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
    device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)

    # Fill small objects
    # device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(img, 'b', device, debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, 'light', device, debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, 'light', device, debug)

    # Fill small objects
    # device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(img, bs, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, debug)
    device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, 'dark', device, debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, 'light', device, debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 200, device, debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, debug)
    device, masked2 = pcv.apply_mask(masked, ab_cnt3, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, 'a', device, debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, 'dark', device, debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255, 'light', device, debug)

    device, masked2a_thresh_blur = pcv.median_blur(masked2a_thresh, 5, device, debug)
    device, masked2b_thresh_blur = pcv.median_blur(masked2b_thresh, 13, device, debug)

    device, ab_fill = pcv.logical_or(masked2a_thresh_blur, masked2b_thresh_blur, device, debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(masked2, 'rectangle', device, None, 'default', debug, True, 700,
                                                 0, -600, -300)

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(img, 'partial', roi1, roi_hierarchy,
                                                                           id_objects, obj_hierarchy, device,
                                                                           debug)

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, debug)

    ############## VIS Analysis ################
    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(img, vis_img, obj, mask, device, debug)

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(img, vis_img, obj, mask, 384, device,
                                                                              debug)

    # Determine color properties: Histograms, Color Slices and
    # Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(img, vis_img, mask, 256, device, debug,
                                                                    None, 'v', 'img', 300)

    # Output shape and color data
    print('\t'.join(map(str, shape_header)) + '\n')
    print('\t'.join(map(str, shape_data)) + '\n')
    for row in shape_img:
        print('\t'.join(map(str, row)) + '\n')
    print('\t'.join(map(str, color_header)) + '\n')
    print('\t'.join(map(str, color_data)) + '\n')
    print('\t'.join(map(str, boundary_header)) + '\n')
    print('\t'.join(map(str, boundary_data)) + '\n')
    print('\t'.join(map(str, boundary_img1)) + '\n')
    for row in color_img:
        print('\t'.join(map(str, row)) + '\n')

    ############################# Use VIS image mask for NIR image#########################
    # Read NIR image
    nir, path1, filename1 = pcv.readimage(nir_img)
    nir2 = cv2.imread(nir_img, -1)

    # Flip mask
    device, f_mask = pcv.flip(mask, "vertical", device, debug)

    # Reize mask
    device, nmask = pcv.resize(f_mask, 0.1154905775, 0.1154905775, device, debug)

    # position, and crop mask
    device, newmask = pcv.crop_position_mask(nir, nmask, device, 30, 4, "top", "right", debug)

    # Identify objects
    device, nir_objects, nir_hierarchy = pcv.find_objects(nir, newmask, device, debug)

    # Object combine kept objects
    device, nir_combined, nir_combinedmask = pcv.object_composition(nir, nir_objects, nir_hierarchy, device, debug)

    ####################################### Analysis #############################################
    device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(nir2, filename1, nir_combinedmask, 256,
                                                                           device, False, debug)
    device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(nir2, filename1, nir_combined, nir_combinedmask,
                                                                       device, debug)

    print('\t'.join(map(str, nhist_header)) + '\n')
    print('\t'.join(map(str, nhist_data)) + '\n')
    for row in nir_imgs:
        print('\t'.join(map(str, row)) + '\n')
    print('\t'.join(map(str, nshape_header)) + '\n')
    print('\t'.join(map(str, nshape_data)) + '\n')
    print('\t'.join(map(str, nir_shape)) + '\n')
예제 #11
0
def process_sv_images_core(vis_id,
                           vis_img,
                           nir_id,
                           nir_rgb,
                           nir_cv2,
                           traits,
                           debug=None):
    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(vis_img, 's', device, debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, 'light', device, debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 5, device, debug)
    device, s_cnt = pcv.median_blur(s_thresh, 5, device, debug)

    # Fill small objects
    # device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(vis_img, 'b', device, debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, 'light', device,
                                            debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, 'light', device, debug)

    # Fill small objects
    # device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(vis_img, bs, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, 'a', device, debug)
    device, masked_b = pcv.rgb2gray_lab(masked, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, 'dark',
                                                  device, debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, 'light',
                                                  device, debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device,
                                    debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 200, device, debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, debug)
    device, masked2 = pcv.apply_mask(masked, ab_cnt3, 'white', device, debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, 'a', device, debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, 'b', device, debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, 'dark',
                                                   device, debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255,
                                                   'light', device, debug)

    device, masked2a_thresh_blur = pcv.median_blur(masked2a_thresh, 5, device,
                                                   debug)
    device, masked2b_thresh_blur = pcv.median_blur(masked2b_thresh, 13, device,
                                                   debug)

    device, ab_fill = pcv.logical_or(masked2a_thresh_blur,
                                     masked2b_thresh_blur, device, debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(
        masked2, ab_fill, device, debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(masked2, 'rectangle', device,
                                                 None, 'default', debug, True,
                                                 700, 0, -600, -300)

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
        vis_img, 'partial', roi1, roi_hierarchy, id_objects, obj_hierarchy,
        device, debug)

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(vis_img, roi_objects,
                                               hierarchy3, device, debug)

    ############## VIS Analysis ################
    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(
        vis_img, vis_id, obj, mask, device, debug)

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
        vis_img, vis_id, obj, mask, 384, device, debug)

    # Determine color properties: Histograms, Color Slices and
    # Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(
        vis_img, vis_id, mask, 256, device, debug, None, 'v', 'img', 300)

    # Output shape and color data
    vis_traits = {}
    for i in range(1, len(shape_header)):
        vis_traits[shape_header[i]] = shape_data[i]
    for i in range(1, len(boundary_header)):
        vis_traits[boundary_header[i]] = boundary_data[i]
    for i in range(2, len(color_header)):
        vis_traits[color_header[i]] = serialize_color_data(color_data[i])

    ############################# Use VIS image mask for NIR image#########################
    # Flip mask
    device, f_mask = pcv.flip(mask, "vertical", device, debug)

    # Reize mask
    device, nmask = pcv.resize(f_mask, 0.1154905775, 0.1154905775, device,
                               debug)

    # position, and crop mask
    device, newmask = pcv.crop_position_mask(nir_rgb, nmask, device, 30, 4,
                                             "top", "right", debug)

    # Identify objects
    device, nir_objects, nir_hierarchy = pcv.find_objects(
        nir_rgb, newmask, device, debug)

    # Object combine kept objects
    device, nir_combined, nir_combinedmask = pcv.object_composition(
        nir_rgb, nir_objects, nir_hierarchy, device, debug)

    ####################################### Analysis #############################################
    device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
        nir_cv2, nir_id, nir_combinedmask, 256, device, False, debug)
    device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
        nir_cv2, nir_id, nir_combined, nir_combinedmask, device, debug)

    nir_traits = {}
    for i in range(1, len(nshape_header)):
        nir_traits[nshape_header[i]] = nshape_data[i]
    for i in range(2, len(nhist_header)):
        nir_traits[nhist_header[i]] = serialize_color_data(nhist_data[i])

    # Add data to traits table
    traits['sv_area'].append(vis_traits['area'])
    traits['hull_area'].append(vis_traits['hull-area'])
    traits['solidity'].append(vis_traits['solidity'])
    traits['height'].append(vis_traits['height_above_bound'])
    traits['perimeter'].append(vis_traits['perimeter'])

    return [vis_traits, nir_traits]
def main():
    # Get options
    args = options()

    # Read image
    img, path, filename = pcv.readimage(args.image)

    # Pipeline step
    device = 0

    # Convert RGB to HSV and extract the Saturation channel
    device, s = pcv.rgb2gray_hsv(img, "s", device, args.debug)

    # Threshold the Saturation image
    device, s_thresh = pcv.binary_threshold(s, 36, 255, "light", device, args.debug)

    # Median Filter
    device, s_mblur = pcv.median_blur(s_thresh, 0, device, args.debug)
    device, s_cnt = pcv.median_blur(s_thresh, 0, device, args.debug)

    # Fill small objects
    # device, s_fill = pcv.fill(s_mblur, s_cnt, 0, device, args.debug)

    # Convert RGB to LAB and extract the Blue channel
    device, b = pcv.rgb2gray_lab(img, "b", device, args.debug)

    # Threshold the blue image
    device, b_thresh = pcv.binary_threshold(b, 137, 255, "light", device, args.debug)
    device, b_cnt = pcv.binary_threshold(b, 137, 255, "light", device, args.debug)

    # Fill small objects
    # device, b_fill = pcv.fill(b_thresh, b_cnt, 10, device, args.debug)

    # Join the thresholded saturation and blue-yellow images
    device, bs = pcv.logical_and(s_mblur, b_cnt, device, args.debug)

    # Apply Mask (for vis images, mask_color=white)
    device, masked = pcv.apply_mask(img, bs, "white", device, args.debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked_a = pcv.rgb2gray_lab(masked, "a", device, args.debug)
    device, masked_b = pcv.rgb2gray_lab(masked, "b", device, args.debug)

    # Threshold the green-magenta and blue images
    device, maskeda_thresh = pcv.binary_threshold(masked_a, 127, 255, "dark", device, args.debug)
    device, maskedb_thresh = pcv.binary_threshold(masked_b, 128, 255, "light", device, args.debug)

    # Join the thresholded saturation and blue-yellow images (OR)
    device, ab = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)
    device, ab_cnt = pcv.logical_or(maskeda_thresh, maskedb_thresh, device, args.debug)

    # Fill small noise
    device, ab_fill1 = pcv.fill(ab, ab_cnt, 2, device, args.debug)

    # Dilate to join small objects with larger ones
    device, ab_cnt1 = pcv.dilate(ab_fill1, 3, 2, device, args.debug)
    device, ab_cnt2 = pcv.dilate(ab_fill1, 3, 2, device, args.debug)

    # Fill dilated image mask
    device, ab_cnt3 = pcv.fill(ab_cnt2, ab_cnt1, 150, device, args.debug)
    device, masked2 = pcv.apply_mask(masked, ab_cnt3, "white", device, args.debug)

    # Convert RGB to LAB and extract the Green-Magenta and Blue-Yellow channels
    device, masked2_a = pcv.rgb2gray_lab(masked2, "a", device, args.debug)
    device, masked2_b = pcv.rgb2gray_lab(masked2, "b", device, args.debug)

    # Threshold the green-magenta and blue images
    device, masked2a_thresh = pcv.binary_threshold(masked2_a, 127, 255, "dark", device, args.debug)
    device, masked2b_thresh = pcv.binary_threshold(masked2_b, 128, 255, "light", device, args.debug)
    device, ab_fill = pcv.logical_or(masked2a_thresh, masked2b_thresh, device, args.debug)

    # Identify objects
    device, id_objects, obj_hierarchy = pcv.find_objects(masked2, ab_fill, device, args.debug)

    # Define ROI
    device, roi1, roi_hierarchy = pcv.define_roi(
        masked2, "rectangle", device, None, "default", args.debug, True, 500, 0, -600, -885
    )

    # Decide which objects to keep
    device, roi_objects, hierarchy3, kept_mask, obj_area = pcv.roi_objects(
        img, "partial", roi1, roi_hierarchy, id_objects, obj_hierarchy, device, args.debug
    )

    # Object combine kept objects
    device, obj, mask = pcv.object_composition(img, roi_objects, hierarchy3, device, args.debug)

    ############## VIS Analysis ################

    outfile = False
    if args.writeimg == True:
        outfile = args.outdir + "/" + filename

    # Find shape properties, output shape image (optional)
    device, shape_header, shape_data, shape_img = pcv.analyze_object(
        img, args.image, obj, mask, device, args.debug, outfile
    )

    # Shape properties relative to user boundary line (optional)
    device, boundary_header, boundary_data, boundary_img1 = pcv.analyze_bound(
        img, args.image, obj, mask, 845, device, args.debug, outfile
    )

    # Determine color properties: Histograms, Color Slices and Pseudocolored Images, output color analyzed images (optional)
    device, color_header, color_data, color_img = pcv.analyze_color(
        img, args.image, mask, 256, device, args.debug, None, "v", "img", 300, outfile
    )

    # Output shape and color data

    result = open(args.result, "a")
    result.write("\t".join(map(str, shape_header)))
    result.write("\n")
    result.write("\t".join(map(str, shape_data)))
    result.write("\n")
    for row in shape_img:
        result.write("\t".join(map(str, row)))
        result.write("\n")
    result.write("\t".join(map(str, color_header)))
    result.write("\n")
    result.write("\t".join(map(str, color_data)))
    result.write("\n")
    result.write("\t".join(map(str, boundary_header)))
    result.write("\n")
    result.write("\t".join(map(str, boundary_data)))
    result.write("\n")
    result.write("\t".join(map(str, boundary_img1)))
    result.write("\n")
    for row in color_img:
        result.write("\t".join(map(str, row)))
        result.write("\n")
    result.close()

    ############################# Use VIS image mask for NIR image#########################
    # Find matching NIR image
    device, nirpath = pcv.get_nir(path, filename, device, args.debug)
    nir, path1, filename1 = pcv.readimage(nirpath)
    nir2 = cv2.imread(nirpath, -1)

    # Flip mask
    device, f_mask = pcv.flip(mask, "vertical", device, args.debug)

    # Reize mask
    device, nmask = pcv.resize(f_mask, 0.1304, 0.1304, device, args.debug)

    # position, and crop mask
    device, newmask = pcv.crop_position_mask(nir, nmask, device, 65, 0, "top", "left", args.debug)

    # Identify objects
    device, nir_objects, nir_hierarchy = pcv.find_objects(nir, newmask, device, args.debug)

    # Object combine kept objects
    device, nir_combined, nir_combinedmask = pcv.object_composition(nir, nir_objects, nir_hierarchy, device, args.debug)

    ####################################### Analysis #############################################
    outfile1 = False
    if args.writeimg == True:
        outfile1 = args.outdir + "/" + filename1

    device, nhist_header, nhist_data, nir_imgs = pcv.analyze_NIR_intensity(
        nir2, filename1, nir_combinedmask, 256, device, False, args.debug, outfile1
    )
    device, nshape_header, nshape_data, nir_shape = pcv.analyze_object(
        nir2, filename1, nir_combined, nir_combinedmask, device, args.debug, outfile1
    )

    coresult = open(args.coresult, "a")
    coresult.write("\t".join(map(str, nhist_header)))
    coresult.write("\n")
    coresult.write("\t".join(map(str, nhist_data)))
    coresult.write("\n")
    for row in nir_imgs:
        coresult.write("\t".join(map(str, row)))
        coresult.write("\n")

    coresult.write("\t".join(map(str, nshape_header)))
    coresult.write("\n")
    coresult.write("\t".join(map(str, nshape_data)))
    coresult.write("\n")
    coresult.write("\t".join(map(str, nir_shape)))
    coresult.write("\n")
    coresult.close()
예제 #13
0
def main():
   
    # Get options
    args = options()
    if args.debug:
      print("Analyzing your image dude...")
    # Read image
    img = cv2.imread(args.image, flags=0)
    # if a region of interest is specified read it in
    roi = cv2.imread(args.roi)
    # Pipeline step
    device = 0
    
    # Start by examining the distribution of pixel intensity values
    if args.debug:
      pcv.plot_hist(img, 'hist_img')
      
    # Will intensity transformation enhance your ability to isolate object of interest by thesholding?
    device, he_img = pcv.HistEqualization(img, device, args.debug)
    if args.debug:
      pcv.plot_hist(he_img, 'hist_img_he')
    
    # Laplace filtering (identify edges based on 2nd derivative)
    device, lp_img = pcv.laplace_filter(img, 1, 1, device, args.debug)
    if args.debug:
      pcv.plot_hist(lp_img, 'hist_lp')
    
    # Lapacian image sharpening, this step will enhance the darkness of the edges detected
    device, lp_shrp_img = pcv.image_subtract(img, lp_img, device, args.debug)
    if args.debug:
      pcv.plot_hist(lp_shrp_img, 'hist_lp_shrp')
      
    # Sobel filtering  
    # 1st derivative sobel filtering along horizontal axis, kernel = 1, unscaled)
    device, sbx_img = pcv.sobel_filter(img, 1, 0, 1, 1, device, args.debug)
    if args.debug:
      pcv.plot_hist(sbx_img, 'hist_sbx')
      
    # 1st derivative sobel filtering along vertical axis, kernel = 1, unscaled)
    device, sby_img = pcv.sobel_filter(img, 0, 1, 1, 1, device, args.debug)
    if args.debug:
      pcv.plot_hist(sby_img, 'hist_sby')
      
    # Combine the effects of both x and y filters through matrix addition
    # This will capture edges identified within each plane and emphesize edges found in both images
    device, sb_img = pcv.image_add(sbx_img, sby_img, device, args.debug)
    if args.debug:
      pcv.plot_hist(sb_img, 'hist_sb_comb_img')
    
    # Use a lowpass (blurring) filter to smooth sobel image
    device, mblur_img = pcv.median_blur(sb_img, 1, device, args.debug)
    device, mblur_invert_img = pcv.invert(mblur_img, device, args.debug)
    
    # combine the smoothed sobel image with the laplacian sharpened image
    # combines the best features of both methods as described in "Digital Image Processing" by Gonzalez and Woods pg. 169 
    device, edge_shrp_img = pcv.image_add(mblur_invert_img, lp_shrp_img, device, args.debug)
    if args.debug:
      pcv.plot_hist(edge_shrp_img, 'hist_edge_shrp_img')
      
    # Perform thresholding to generate a binary image
    device, tr_es_img = pcv.binary_threshold(edge_shrp_img, 145, 255, 'dark', device, args.debug)
    
    # Prepare a few small kernels for morphological filtering
    kern = np.zeros((3,3), dtype=np.uint8)
    kern1 = np.copy(kern)
    kern1[1,1:3]=1
    kern2 = np.copy(kern)
    kern2[1,0:2]=1
    kern3 = np.copy(kern)
    kern3[0:2,1]=1
    kern4 = np.copy(kern)
    kern4[1:3,1]=1
    
    # Prepare a larger kernel for dilation
    kern[1,0:3]=1
    kern[0:3,1]=1
    
    # Perform erosion with 4 small kernels
    device, e1_img = pcv.erode(tr_es_img, kern1, 1, device, args.debug)
    device, e2_img = pcv.erode(tr_es_img, kern2, 1, device, args.debug)
    device, e3_img = pcv.erode(tr_es_img, kern3, 1, device, args.debug)
    device, e4_img = pcv.erode(tr_es_img, kern4, 1, device, args.debug)
    
    # Combine eroded images
    device, c12_img = pcv.logical_or(e1_img, e2_img, device, args.debug)
    device, c123_img = pcv.logical_or(c12_img, e3_img, device, args.debug)
    device, c1234_img = pcv.logical_or(c123_img, e4_img, device, args.debug)
    
    # Perform dilation
    device, dil_img = pcv.dilate(c1234_img, kern, 1, device, args.debug)
    
    # Get masked image
    # The dilated image may contain some pixels which are not plant
    device, masked_erd = pcv.apply_mask(img, c1234_img, 'black', device, args.debug)
    device, masked_erd_dil = pcv.apply_mask(img, dil_img, 'black', device, args.debug)
    
    # Need to remove the edges of the image, we did that by generating a set of rectangles to mask the edges
    # img is (254 X 320)
    device, box1_img, rect_contour1, hierarchy1 = pcv.rectangle_mask(img, (1,1), (64,252), device, args.debug)
    device, box2_img, rect_contour2, hierarchy2 = pcv.rectangle_mask(img, (256,1), (318,252), device, args.debug)
    device, box3_img, rect_contour3, hierarchy3 = pcv.rectangle_mask(img, (1,184), (318,252), device, args.debug)
    device, box4_img, rect_contour4, hierarchy4 = pcv.border_mask(img, (1,1), (318,252), device, args.debug)
    
    # combine boxes to filter the edges and car out of the photo
    device, bx12_img = pcv.logical_or(box1_img, box2_img, device, args.debug)
    device, bx123_img = pcv.logical_or(bx12_img, box3_img, device, args.debug)
    device, bx1234_img = pcv.logical_or(bx123_img, box4_img, device, args.debug)
    device, inv_bx1234_img = pcv.invert(bx1234_img, device, args.debug)
    
    # Apply the box mask to the image
    device, masked_img = pcv.apply_mask(masked_erd_dil, inv_bx1234_img, 'black', device, args.debug)
    
    # Generate a binary to send to the analysis function
    device, mask = pcv.binary_threshold(masked_img, 1, 255, 'light', device, args.debug)
    pcv.analyze_NIR_intensity(img, args.image, mask, 256, device, args.debug, 'example')
def main():
    # Parse command-line options
    args = options()

    device = 0

    # Open output file
    out = open(args.outfile, "w")

    # Open the image file
    img, path, fname = pcv.readimage(filename=args.image, debug=args.debug)
    # Classify healthy and unhealthy plant pixels
    device, masks = pcv.naive_bayes_classifier(img=img,
                                               pdf_file=args.pdfs,
                                               device=device)

    # Use the identified blue mesh area to build a mask for the pot area
    # First errode the blue mesh region to remove background
    device, mesh_errode = pcv.erode(img=masks["Background_Blue"],
                                    kernel=9,
                                    i=3,
                                    device=device,
                                    debug=args.debug)
    # Define a region of interest for blue mesh contours
    device, pot_roi, pot_hierarchy = pcv.define_roi(img=img,
                                                    shape='rectangle',
                                                    device=device,
                                                    roi=None,
                                                    roi_input='default',
                                                    debug=args.debug,
                                                    adjust=True,
                                                    x_adj=0,
                                                    y_adj=500,
                                                    w_adj=0,
                                                    h_adj=-650)
    # Find blue mesh contours
    device, mesh_objects, mesh_hierarchy = pcv.find_objects(img=img,
                                                            mask=mesh_errode,
                                                            device=device,
                                                            debug=args.debug)
    # Keep blue mesh contours in the region of interest
    device, kept_mesh_objs, kept_mesh_hierarchy, kept_mask_mesh, _ = pcv.roi_objects(
        img=img,
        roi_type='partial',
        roi_contour=pot_roi,
        roi_hierarchy=pot_hierarchy,
        object_contour=mesh_objects,
        obj_hierarchy=mesh_hierarchy,
        device=device,
        debug=args.debug)
    # Flatten the blue mesh contours into a single object
    device, mesh_flattened, mesh_mask = pcv.object_composition(
        img=img,
        contours=kept_mesh_objs,
        hierarchy=kept_mesh_hierarchy,
        device=device,
        debug=args.debug)
    # Initialize a pot mask
    pot_mask = np.zeros(np.shape(masks["Background_Blue"]), dtype=np.uint8)
    # Find the minimum bounding rectangle for the blue mesh region
    rect = cv2.minAreaRect(mesh_flattened)
    # Create a contour for the minimum bounding box
    box = cv2.boxPoints(rect)
    box = np.int0(box)
    # Create a mask from the bounding box contour
    cv2.drawContours(pot_mask, [box], 0, (255), -1)
    # If the bounding box area is too small then the plant has likely occluded too much of the pot for us to use this
    # as a marker for the pot area
    if np.sum(pot_mask) / 255 < 2900000:
        print(np.sum(pot_mask) / 255)
        # Create a new pot mask
        pot_mask = np.zeros(np.shape(masks["Background_Blue"]), dtype=np.uint8)
        # Set the mask area to the ROI area
        box = np.array([[0, 500], [0, 2806], [2304, 2806], [2304, 500]])
        cv2.drawContours(pot_mask, [box], 0, (255), -1)
    # Dialate the blue mesh area to include the ridge of the pot
    device, pot_mask_dilated = pcv.dilate(img=pot_mask,
                                          kernel=3,
                                          i=60,
                                          device=device,
                                          debug=args.debug)
    # Mask the healthy mask
    device, healthy_masked = pcv.apply_mask(img=cv2.merge(
        [masks["Healthy"], masks["Healthy"], masks["Healthy"]]),
                                            mask=pot_mask_dilated,
                                            mask_color="black",
                                            device=device,
                                            debug=args.debug)
    # Mask the unhealthy mask
    device, unhealthy_masked = pcv.apply_mask(img=cv2.merge(
        [masks["Unhealthy"], masks["Unhealthy"], masks["Unhealthy"]]),
                                              mask=pot_mask_dilated,
                                              mask_color="black",
                                              device=device,
                                              debug=args.debug)
    # Convert the masks back to binary
    healthy_masked, _, _ = cv2.split(healthy_masked)
    unhealthy_masked, _, _ = cv2.split(unhealthy_masked)

    # Fill small objects
    device, fill_image_healthy = pcv.fill(img=np.copy(healthy_masked),
                                          mask=np.copy(healthy_masked),
                                          size=300,
                                          device=device,
                                          debug=args.debug)
    device, fill_image_unhealthy = pcv.fill(img=np.copy(unhealthy_masked),
                                            mask=np.copy(unhealthy_masked),
                                            size=1000,
                                            device=device,
                                            debug=args.debug)
    # Define a region of interest
    device, roi1, roi_hierarchy = pcv.define_roi(img=img,
                                                 shape='rectangle',
                                                 device=device,
                                                 roi=None,
                                                 roi_input='default',
                                                 debug=args.debug,
                                                 adjust=True,
                                                 x_adj=450,
                                                 y_adj=1000,
                                                 w_adj=-400,
                                                 h_adj=-1000)
    # Filter objects that overlap the ROI
    device, id_objects, obj_hierarchy_healthy = pcv.find_objects(
        img=img, mask=fill_image_healthy, device=device, debug=args.debug)
    device, _, _, kept_mask_healthy, _ = pcv.roi_objects(
        img=img,
        roi_type='partial',
        roi_contour=roi1,
        roi_hierarchy=roi_hierarchy,
        object_contour=id_objects,
        obj_hierarchy=obj_hierarchy_healthy,
        device=device,
        debug=args.debug)
    device, id_objects, obj_hierarchy_unhealthy = pcv.find_objects(
        img=img, mask=fill_image_unhealthy, device=device, debug=args.debug)
    device, _, _, kept_mask_unhealthy, _ = pcv.roi_objects(
        img=img,
        roi_type='partial',
        roi_contour=roi1,
        roi_hierarchy=roi_hierarchy,
        object_contour=id_objects,
        obj_hierarchy=obj_hierarchy_unhealthy,
        device=device,
        debug=args.debug)
    # Combine the healthy and unhealthy mask
    device, mask = pcv.logical_or(img1=kept_mask_healthy,
                                  img2=kept_mask_unhealthy,
                                  device=device,
                                  debug=args.debug)

    # Output a healthy/unhealthy image
    classified_img = cv2.merge([
        np.zeros(np.shape(mask), dtype=np.uint8), kept_mask_healthy,
        kept_mask_unhealthy
    ])
    pcv.print_image(img=classified_img,
                    filename=os.path.join(
                        args.outdir,
                        os.path.basename(args.image)[:-4] + ".classified.png"))

    # Output a healthy/unhealthy image overlaid on the original image
    overlayed = cv2.addWeighted(src1=np.copy(classified_img),
                                alpha=0.5,
                                src2=np.copy(img),
                                beta=0.5,
                                gamma=0)
    pcv.print_image(img=overlayed,
                    filename=os.path.join(
                        args.outdir,
                        os.path.basename(args.image)[:-4] + ".overlaid.png"))

    # Extract hue values from the image
    device, h = pcv.rgb2gray_hsv(img=img,
                                 channel="h",
                                 device=device,
                                 debug=args.debug)

    # Extract the plant hue values
    plant_hues = h[np.where(mask == 255)]

    # Initialize hue histogram
    hue_hist = {}
    for i in range(0, 180):
        hue_hist[i] = 0

    # Store all hue values
    hue_values = []

    # Populate histogram
    total_px = len(plant_hues)
    for hue in plant_hues:
        hue_hist[hue] += 1
        hue_values.append(hue)

    # Parse the filename
    genotype, treatment, replicate, timepoint = os.path.basename(
        args.image)[:-4].split("_")
    replicate = replicate.replace("#", "")
    if timepoint[-3:] == "dbi":
        timepoint = -1
    else:
        timepoint = timepoint.replace("dpi", "")

    # Output results
    for i in range(0, 180):
        out.write("\t".join(
            map(str, [
                genotype, treatment, timepoint, replicate, total_px, i,
                hue_hist[i]
            ])) + "\n")
    out.close()

    # Calculate basic statistics
    healthy_sum = int(np.sum(kept_mask_healthy))
    unhealthy_sum = int(np.sum(kept_mask_unhealthy))
    healthy_total_ratio = healthy_sum / float(healthy_sum + unhealthy_sum)
    unhealthy_total_ratio = unhealthy_sum / float(healthy_sum + unhealthy_sum)
    stats = open(args.outfile[:-4] + ".stats.txt", "w")
    stats.write("%s, %f, %f, %f, %f" %
                (os.path.basename(args.image), healthy_sum, unhealthy_sum,
                 healthy_total_ratio, unhealthy_total_ratio) + '\n')
    stats.close()

    # Fit a 3-component Gaussian Mixture Model
    gmm = mixture.GaussianMixture(n_components=3,
                                  covariance_type="full",
                                  tol=0.001)
    gmm.fit(np.expand_dims(hue_values, 1))
    gmm3 = open(args.outfile[:-4] + ".gmm3.txt", "w")
    gmm3.write("%s, %f, %f, %f, %f, %f, %f, %f, %f, %f" %
               (os.path.basename(args.image), gmm.means_.ravel()[0],
                gmm.means_.ravel()[1], gmm.means_.ravel()[2],
                np.sqrt(gmm.covariances_.ravel()[0]),
                np.sqrt(gmm.covariances_.ravel()[1]),
                np.sqrt(gmm.covariances_.ravel()[2]), gmm.weights_.ravel()[0],
                gmm.weights_.ravel()[1], gmm.weights_.ravel()[2]) + '\n')
    gmm3.close()

    # Fit a 2-component Gaussian Mixture Model
    gmm = mixture.GaussianMixture(n_components=2,
                                  covariance_type="full",
                                  tol=0.001)
    gmm.fit(np.expand_dims(hue_values, 1))
    gmm2 = open(args.outfile[:-4] + ".gmm2.txt", "w")
    gmm2.write("%s, %f, %f, %f, %f, %f, %f" %
               (os.path.basename(args.image), gmm.means_.ravel()[0],
                gmm.means_.ravel()[1], np.sqrt(gmm.covariances_.ravel()[0]),
                np.sqrt(gmm.covariances_.ravel()[1]), gmm.weights_.ravel()[0],
                gmm.weights_.ravel()[1]) + '\n')
    gmm2.close()

    # Fit a 1-component Gaussian Mixture Model
    gmm = mixture.GaussianMixture(n_components=1,
                                  covariance_type="full",
                                  tol=0.001)
    gmm.fit(np.expand_dims(hue_values, 1))
    gmm1 = open(args.outfile[:-4] + ".gmm1.txt", "w")
    gmm1.write(
        "%s, %f, %f, %f" %
        (os.path.basename(args.image), gmm.means_.ravel()[0],
         np.sqrt(gmm.covariances_.ravel()[0]), gmm.weights_.ravel()[0]) + '\n')
    gmm1.close()