def load_image_segm_center(idx_row, path_out=None, dict_relabel=None):
""" by paths load images and segmentation and weather centers exist,
load them if the path out is given r\draw visualisation of inputs
:param (int, DF:row) idx_row:
:param str path_out: path to output directory
:param {} dict_relabel:
:return (str, ndarray, ndarray, [[int, int]]):
"""
idx, row_path = idx_row
for k in ['path_image', 'path_segm', 'path_centers']:
row_path[k] = tl_data.update_path(row_path[k])
assert os.path.exists(row_path[k]), 'missing %s' % row_path[k]
idx_name = get_idx_name(idx, row_path['path_image'])
img_struc, img_gene = tl_data.load_img_double_band_split(
row_path['path_image'], im_range=None)
# img_rgb = np.array(Image.open(row_path['path_img']))
img_rgb = tl_data.merge_image_channels(img_struc, img_gene)
if np.max(img_rgb) > 1:
img_rgb = img_rgb / float(np.max(img_rgb))
seg_ext = os.path.splitext(os.path.basename(row_path['path_segm']))[-1]
if seg_ext == '.npz':
with np.load(row_path['path_segm']) as npzfile:
segm = npzfile[npzfile.files[0]]
if dict_relabel is not None:
segm = seg_lbs.merge_probab_labeling_2d(segm, dict_relabel)
else:
segm = tl_data.io_imread(row_path['path_segm'])
if dict_relabel is not None:
segm = seg_lbs.relabel_by_dict(segm, dict_relabel)
if row_path['path_centers'] is not None \
and os.path.isfile(row_path['path_centers']):
ext = os.path.splitext(os.path.basename(row_path['path_centers']))[-1]
if ext == '.csv':
centers = tl_data.load_landmarks_csv(row_path['path_centers'])
centers = tl_data.swap_coord_x_y(centers)
elif ext == '.png':
centers = tl_data.io_imread(row_path['path_centers'])
# relabel loaded segm into relevant one
centers = np.array(LUT_ANNOT_CENTER_RELABEL)[centers]
else:
logging.warning('not supported file format %s', ext)
centers = None
else:
centers = None
if is_drawing(path_out):
export_visual_input_image_segm(path_out, idx_name, img_rgb, segm,
centers)
return idx_name, img_rgb, segm, centers
def expert_visual(row, method_name, path_out, max_fig_size=10):
""" export several visualisation segmentation and annotation
:param {str: ...} row:
:param str method_name:
:param str path_out:
:param int max_fig_size:
"""
im_name = os.path.splitext(os.path.basename(row['path_image']))[0]
img, _ = tl_data.load_image_2d(row['path_image'])
# annot = tl_data.load_image(row['path_annot'])
egg_segm, _ = tl_data.load_image_2d(row['path_egg-segm'])
in_segm, _ = tl_data.load_image_2d(row['path_in-segm'])
centers = tl_data.load_landmarks_csv(row['path_centers'])
centers = np.array(tl_data.swap_coord_x_y(centers))
fig_size = max_fig_size * np.array(img.shape[:2]) / float(np.max(
img.shape))
fig_name = '%s_%s.jpg' % (im_name, method_name)
fig, ax = plt.subplots(figsize=fig_size[::-1])
ax.imshow(img[:, :, 0], cmap=plt.cm.gray)
ax.imshow(egg_segm, alpha=0.15)
ax.contour(egg_segm, levels=np.unique(egg_segm), linewidths=(3, ))
ax.plot(centers[:, 1], centers[:, 0], 'ob')
tl_visu.figure_image_adjustment(fig, img.shape)
path_fig = os.path.join(path_out, NAME_DIR_VISUAL_1, fig_name)
fig.savefig(path_fig, bbox_inches='tight', pad_inches=0)
plt.close(fig)
fig, ax = plt.subplots(figsize=fig_size[::-1])
# ax.imshow(np.max(in_segm) - in_segm, cmap=plt.cm.gray)
ax.imshow(LUT_COLOR[in_segm], vmin=0., vmax=1., alpha=0.5)
ax.contour(in_segm, levels=np.unique(in_segm), colors='k')
ax.imshow(egg_segm, alpha=0.3)
ax.contour(egg_segm, levels=np.unique(egg_segm), linewidths=(5, ))
ax.plot(centers[:, 1], centers[:, 0], 'or')
tl_visu.figure_image_adjustment(fig, img.shape)
path_fig = os.path.join(path_out, NAME_DIR_VISUAL_2, fig_name)
fig.savefig(path_fig, bbox_inches='tight', pad_inches=0)
plt.close(fig)
fig, ax = plt.subplots(figsize=fig_size[::-1])
ax.imshow(img[:, :, 0], cmap=plt.cm.gray, alpha=1.)
ax.contour(in_segm, levels=np.unique(in_segm), colors='w')
ax.imshow(egg_segm, alpha=0.3)
ax.contour(egg_segm, levels=np.unique(egg_segm), linewidths=(5, ))
ax.plot(centers[:, 1], centers[:, 0], 'og')
tl_visu.figure_image_adjustment(fig, img.shape)
path_fig = os.path.join(path_out, NAME_DIR_VISUAL_3, fig_name)
fig.savefig(path_fig, bbox_inches='tight', pad_inches=0)
plt.close(fig)
def cluster_points_draw_export(dict_row, params, path_out=None):
""" cluster points into centers and export visualisations
:param {} dict_row:
:param {str: ...} params:
:param str path_out:
:return {}:
"""
assert all(n in dict_row for n in ['path_points', 'path_image', 'path_segm']), \
'missing some required fields: %s' % repr(dict_row)
name = os.path.splitext(os.path.basename(dict_row['path_points']))[0]
points = tl_data.load_landmarks_csv(dict_row['path_points'])
if len(points) == 0:
logging.debug('no points to cluster for "%s"', name)
points = tl_data.swap_coord_x_y(points)
centres, clust_labels = cluster_center_candidates(
points,
max_dist=params['DBSCAN_max_dist'],
min_samples=params['DBSCAN_min_samples'])
path_csv = os.path.join(path_out, FOLDER_CENTER, name + '.csv')
tl_data.save_landmarks_csv(path_csv, tl_data.swap_coord_x_y(centres))
path_visu = os.path.join(path_out, FOLDER_CLUSTER_VISUAL)
img, segm = None, None
if dict_row['path_image'] is not None and os.path.isfile(
dict_row['path_image']):
img = tl_data.io_imread(dict_row['path_image'])
if dict_row['path_segm'] is not None and os.path.isfile(
dict_row['path_segm']):
segm = tl_data.io_imread(dict_row['path_segm'])
export_draw_image_centers_clusters(path_visu, name, img, centres, points,
clust_labels, segm)
dict_row.update({
'image': name,
'path_centers': path_csv,
'nb_centres': len(centres)
})
return dict_row
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 {str: ...} 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 %s and segm %s do not match' \
% (repr(img_rgb.shape[:2]), repr(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 len(centers) == 0:
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'],
rltv_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 %s on image "%s" is %d s',
repr(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.error('segment fail for "%s" via %s with \n %s', name,
method, traceback.format_exc())
return name