def load_center_evaluate(idx_row,
df_annot,
path_annot,
path_visu=None,
col_prefix=''):
""" complete pipeline fon input image and seg_pipe, such that load them,
generate points, compute features and using given classifier predict labels
:param (int, DF:row) idx_row:
:param df_annot:
:param str path_annot:
:param str path_visu:
:param str col_prefix:
:return {str: float}:
"""
idx, row = idx_row
dict_row = dict(row)
dict_row['image'] = os.path.splitext(
os.path.basename(dict_row['path_image']))[0]
if idx not in df_annot.index:
logging.debug(
'particular image/slice "%s" does not contain eggs '
'of selected stage %s', idx, col_prefix)
return dict_row
name, img, segm, centres = run_train.load_image_segm_center((None, row))
if centres is None:
logging.debug('center missing "%s"', idx)
return dict_row
assert all(c in df_annot.columns for c in tl_visu.COLUMNS_POSITION_EGG_ANNOT), \
'some required columns %s are missing for %s' % \
(tl_visu.COLUMNS_POSITION_EGG_ANNOT, df_annot.columns)
mask_eggs = estimate_eggs_from_info(df_annot.loc[idx], img.shape[:2])
try:
if EXPORT_ANNOT_EGGS:
path_img = os.path.join(path_annot, idx + '.png')
tl_data.io_imsave(path_img, mask_eggs.astype(np.uint8))
if VISUAL_ANNOT_EGGS:
fig = tl_visu.figure_image_segm_results(img, mask_eggs)
fig.savefig(os.path.join(path_visu, idx + '_eggs.png'))
plt.close(fig)
if VISUAL_SEGM_CENTRES:
run_clust.export_draw_image_centers_clusters(path_visu,
name,
img,
centres,
segm=segm)
labels = np.array([1] * len(centres))
dict_stat = compute_statistic_eggs_centres(dict_row, centres, labels,
mask_eggs, img, segm,
path_visu, col_prefix)
except Exception:
logging.exception('load_center_evaluate')
dict_stat = dict_row
return dict_stat
def perform_img_convert(path_img, path_out, dict_colors):
""" perform the quantization together with loading and exporting
:param str path_img:
:param str path_out:
:param {} dict_colors:
"""
img = tl_data.io.imread(path_img)
if img.ndim == 2:
if len(dict_colors) == 0:
dict_colors = seg_annot.DICT_COLOURS
img_new = convert_labels_2_colors(img, dict_colors, path_out)
elif img.ndim == 3:
if img.shape[2] > 3:
# for some 4 chanel images remove the last one (alpha)
img = img[:, :, :3]
img_new = convert_colors_2_labels(img, dict_colors, path_out)
else:
logging.warning('not supported image format %s', repr(img.shape))
img_new = None
if img_new is not None:
img_new = img_new.astype(np.uint8)
path_img_out = os.path.join(path_out, os.path.basename(path_img))
logging.debug('export "%s"', path_img_out)
tl_data.io_imsave(path_img_out, img_new)
def export_cut_objects(df_row,
path_out,
padding,
use_mask=True,
bg_color=None):
""" cut and expert objects in image according given segmentation
:param df_row:
:param str path_out: path for exporting image
:param int padding: set padding around segmented object
"""
annot, _ = tl_data.load_image_2d(df_row['path_1'])
img, name = tl_data.load_image_2d(df_row['path_2'])
if annot.shape[:2] != img.shape[:2]:
raise ImageDimensionError('image sizes not match %r vs %r' %
(annot.shape, img.shape))
uq_objects = np.unique(annot)
if len(uq_objects) == 1:
return
for idx in uq_objects[1:]:
img_new = tl_data.cut_object(img, annot == idx, padding, use_mask,
bg_color)
path_img = os.path.join(path_out, '%s_%i.png' % (name, idx))
logging.debug('saving image "%s"', path_img)
tl_data.io_imsave(path_img, img_new)
def segm_set_center_levels(name, seg_labels, path_out, levels=DISTANCE_LEVELS):
""" set segmentation levels according distance inside object imsegm
:param str name: image name
:param ndarray seg_labels:
:param str path_out: path for output
:param [float] levels: distance levels fro segmentation levels
"""
seg = np.zeros_like(seg_labels)
# set bourders to 0
# seg_labels = set_boundary_values(seg_labels)
for obj_id in range(1, seg_labels.max() + 1):
im_bin = (seg_labels == obj_id)
if np.sum(im_bin) == 0:
continue
distance = ndimage.distance_transform_edt(im_bin)
probab = distance / np.max(distance)
pos_center = ndimage.measurements.center_of_mass(im_bin)
# logging.debug('object %i with levels: %s', obj_id, repr(levels))
for i, level in enumerate(levels):
mask = probab > level
if i > 0:
radius = int(np.sqrt(np.sum(mask) / np.pi))
im_level = draw_circle(pos_center, radius, mask.shape)
mask = np.logical_and(mask, im_level)
sel = morphology.disk(int(radius * 0.15))
mask = morphology.binary_opening(mask, sel)
seg[mask] = i + 1
path_seg = os.path.join(path_out, name)
tl_data.io_imsave(path_seg, seg.astype(np.uint8))
def segment_image_model(imgs_idx_path,
params,
model,
path_out=None,
path_visu=None,
show_debug_imgs=SHOW_DEBUG_IMAGES):
""" segment image with already estimated model
:param (int, str) imgs_idx_path:
:param dict params: segmentation parameters
:param obj scaler:
:param obj pca:
:param obj model:
:param str path_out: path to dir with segmentation
:param str path_visu: path to dir with debug images
:param bool show_debug_imgs: whether show debug images
:return (str, ndarray):
"""
idx, path_img = parse_imgs_idx_path(imgs_idx_path)
logging.debug('segmenting image: "%s"', path_img)
idx_name = get_idx_name(idx, path_img)
img = load_image(path_img, params['img_type'])
path_img = os.path.join(params['path_exp'], FOLDER_IMAGE,
idx_name + '.png')
tl_data.io_imsave(path_img, img.astype(np.uint8))
debug_visual = dict() if show_debug_imgs else None
try:
segm, segm_soft = seg_pipe.segment_color2d_slic_features_model_graphcut(
img,
model,
sp_size=params['slic_size'],
sp_regul=params['slic_regul'],
dict_features=params['features'],
gc_regul=params['gc_regul'],
gc_edge_type=params['gc_edge_type'],
debug_visual=debug_visual)
path_npz = os.path.join(path_out, idx_name + '.npz')
np.savez_compressed(path_npz, segm_soft)
except Exception:
logging.exception('segment_color2d_slic_features_model_graphcut(...)')
segm = np.zeros(img.shape[:2])
boundary_size = int(np.sqrt(np.prod(segm.shape)) * 0.01)
segm = seg_lbs.assume_bg_on_boundary(segm,
bg_label=0,
boundary_size=boundary_size)
export_visual(idx_name, img, segm, debug_visual, path_out, path_visu)
# gc.collect(), time.sleep(1)
return idx_name, segm
def segment_image_independent(img_idx_path,
params,
path_out,
path_visu=None,
show_debug_imgs=SHOW_DEBUG_IMAGES):
""" segment image indecently (estimate model just for this model)
:param (int, str) img_idx_path:
:param dict params: segmentation parameters
:param str path_out: path to dir with segmentation
:param str path_visu: path to dir with debug images
:return (str, ndarray):
"""
idx, path_img = parse_imgs_idx_path(img_idx_path)
logging.debug('segmenting image: "%s"', path_img)
idx_name = get_idx_name(idx, path_img)
img = load_image(path_img, params['img_type'])
path_img = os.path.join(params['path_exp'], FOLDER_IMAGE,
idx_name + '.png')
tl_data.io_imsave(path_img, img.astype(np.uint8))
debug_visual = dict() if show_debug_imgs else None
try:
segm, segm_soft = seg_pipe.pipe_color2d_slic_features_model_graphcut(
img,
nb_classes=params['nb_classes'],
sp_size=params['slic_size'],
sp_regul=params['slic_regul'],
dict_features=params['features'],
estim_model=params['estim_model'],
pca_coef=params['pca_coef'],
gc_regul=params['gc_regul'],
gc_edge_type=params['gc_edge_type'],
debug_visual=debug_visual)
path_npz = os.path.join(path_out, idx_name + '.npz')
np.savez_compressed(path_npz, segm_soft)
except Exception:
logging.exception('pipe_color2d_slic_features_model_graphcut(...)')
segm = np.zeros(img.shape[:2])
boundary_size = int(params['slic_size'] * 3)
segm = seg_lbs.assume_bg_on_boundary(segm,
bg_label=0,
boundary_size=boundary_size)
export_visual(idx_name, img, segm, debug_visual, path_out, path_visu)
# gc.collect(), time.sleep(1)
return idx_name, segm
def perform_img_inpaint(path_img, labels):
""" perform the quantization together with loading and exporting
:param str path_img: image path
"""
logging.debug('repaint labels %r for image: "%s"', labels, path_img)
img = np.array(tl_data.io.imread(path_img), dtype=np.float)
for label in labels:
img[img == label] = np.nan
# interpolate nearest fo label
valid_mask = ~np.isnan(img)
im_paint = seg_annot.image_inpaint_pixels(img, valid_mask)
tl_data.io_imsave(path_img, im_paint.astype(np.uint8))
def perform_quantize_image(path_image, list_colors, method='color'):
""" perform the quantization together with loading and exporting
:param str path_image:
:param [(int, int, int)] list_colors: list of possible colours
"""
logging.debug('quantize img: "%s"', path_image)
im = tl_data.io_imread(path_image)
if not im.ndim == 3:
logging.warning('not valid color image of dims %r', im.shape)
return
im = im[:, :, :3]
# im = io.imread(path_image)[:, :, :3]
if method == 'color':
im_q = seg_annot.quantize_image_nearest_color(im, list_colors)
elif method == 'position':
im_q = seg_annot.quantize_image_nearest_pixel(im, list_colors)
else:
logging.error('not implemented method "%s"', method)
im_q = np.zeros(im.shape)
path_image = os.path.splitext(path_image)[0] + '.png'
tl_data.io_imsave(path_image, im_q.astype(np.uint8))
def perform_image_relabel(path_img, path_out, labels_old, labels_new):
""" perform the quantization together with loading and exporting
:param str path_img:
:param str path_out:
:param str labels_new:
:param str labels_old:
"""
logging.debug('repaint labels %r -> %r for image: "%s"',
labels_old, labels_new, path_img)
img = np.array(tl_data.io.imread(path_img), dtype=int)
max_label = int(max(img.max(), max(labels_old)))
lut = np.array(range(max_label + 1))
for label_old, label_new in zip(labels_old, labels_new):
lut[label_old] = label_new
img = lut[img]
# for label_old, label_new in zip(labels_old, labels_new):
# img[img == label_old] = label_new
logging.debug('resulting image labels: %r', np.unique(img).tolist())
path_img_out = os.path.join(path_out, os.path.basename(path_img))
tl_data.io_imsave(path_img_out, img)
def image_segmentation(idx_row, params, debug_export=DEBUG_EXPORT):
""" image segmentation which prepare inputs (imsegm, centres)
and perform segmentation of various imsegm methods
:param (int, str) idx_row: input image and centres
:param dict params: segmentation parameters
:return str: image name
"""
_, row_path = idx_row
for k in dict(row_path):
if isinstance(k, str) and k.startswith('path_'):
row_path[k] = tl_data.update_path(row_path[k], absolute=True)
logging.debug('segmenting image: "%s"', row_path['path_image'])
name = os.path.splitext(os.path.basename(row_path['path_image']))[0]
img = load_image(row_path['path_image'])
# make the image like RGB
img_rgb = np.rollaxis(np.tile(img, (3, 1, 1)), 0, 3)
seg = load_image(row_path['path_segm'], 'segm')
assert img_rgb.shape[:2] == seg.shape, \
'image %r and segm %r do not match' % (img_rgb.shape[:2], seg.shape)
if not os.path.isfile(row_path['path_centers']):
logging.warning('no center was detected for "%s"', name)
return name
centers = tl_data.load_landmarks_csv(row_path['path_centers'])
centers = tl_data.swap_coord_x_y(centers)
if not list(centers):
logging.warning('no center was detected for "%s"', name)
return name
# img = seg / float(seg.max())
slic = seg_spx.segment_slic_img2d(img_rgb,
sp_size=params['slic_size'],
relative_compact=params['slic_regul'])
path_segm = os.path.join(params['path_exp'], 'input', name + '.png')
export_draw_image_segm(path_segm, img_rgb, segm_obj=seg, centers=centers)
seg_simple = simplify_segm_3cls(seg)
path_segm = os.path.join(params['path_exp'], 'simple', name + '.png')
export_draw_image_segm(path_segm, seg_simple - 1.)
dict_segment = create_dict_segmentation(params, slic, seg, img, centers)
image_name = name + '.png'
centre_name = name + '.csv'
# iterate over segmentation methods and perform segmentation on this image
for method in dict_segment:
(fn, args) = dict_segment[method]
logging.debug(' -> %s on "%s"', method, name)
path_dir = os.path.join(params['path_exp'], method) # n.split('_')[0]
path_segm = os.path.join(path_dir, image_name)
path_centre = os.path.join(path_dir + DIR_CENTRE_POSIX, centre_name)
path_fig = os.path.join(path_dir + DIR_VISUAL_POSIX, image_name)
path_debug = os.path.join(path_dir + DIR_DEBUG_POSIX, name)
# assuming that segmentation may fail
try:
t = time.time()
if debug_export and 'rg2sp' in method:
os.mkdir(path_debug)
segm_obj, centers, dict_export = fn(*args,
debug_export=path_debug)
else:
segm_obj, centers, dict_export = fn(*args)
# also export ellipse params here or inside the segm fn
if dict_export is not None:
for k in dict_export:
export_partial(k, dict_export[k], path_dir, name)
logging.info('running time of %r on image "%s" is %d s',
fn.__name__, image_name,
time.time() - t)
tl_data.io_imsave(path_segm, segm_obj.astype(np.uint8))
export_draw_image_segm(path_fig, img_rgb, seg, segm_obj, centers)
# export also centers
centers = tl_data.swap_coord_x_y(centers)
tl_data.save_landmarks_csv(path_centre, centers)
except Exception:
logging.exception('segment fail for "%s" via %s', name, method)
return name
