def compute_boundary_distance(idx_row, params, path_out=''):
""" compute nearest distance between two segmentation contours
:param (int, str) idx_row:
:param {} params:
:param str path_out:
:return (str, float):
"""
_, row = idx_row
name = os.path.splitext(os.path.basename(row['path_image']))[0]
img = load_image(row['path_image'], params['img_type'])
segm = load_image(row['path_segm'], 'segm')
logging.debug('segment SLIC...')
slic = seg_spx.segment_slic_img2d(img,
params['slic_size'],
params['slic_regul'],
params['slico'])
_, dists = seg_lbs.compute_boundary_distances(segm, slic)
if os.path.isdir(path_out):
logging.debug('visualise results...')
fig = tl_visu.figure_segm_boundary_dist(segm, slic)
fig.savefig(os.path.join(path_out, name + '.jpg'))
return name, np.mean(dists)
def load_image_annot_compute_features_labels(idx_row,
params,
show_debug_imgs=SHOW_DEBUG_IMAGES
):
""" load image and annotation, and compute superpixel features and labels
:param (int, {...}) idx_row: row from table with paths
:param {str: ...} params: segmentation parameters
:param bool show_debug_imgs: whether show debug images
:return (...):
"""
def _path_out_img(params, dir_name, name):
return os.path.join(params['path_exp'], dir_name, name + '.png')
idx, row = idx_row
idx_name = get_idx_name(idx, row['path_image'])
img = load_image(row['path_image'], params['img_type'])
annot = load_image(row['path_annot'], '2d_segm')
logging.debug('.. processing: %s', idx_name)
assert img.shape[:2] == annot.shape[:2], \
'individual size of image %s and seg_pipe %s for "%s" - "%s"' % \
(repr(img.shape), repr(annot.shape), row['path_image'], row['path_annot'])
if show_debug_imgs:
plt.imsave(_path_out_img(params, FOLDER_IMAGE, idx_name),
img,
cmap=plt.cm.gray)
plt.imsave(_path_out_img(params, FOLDER_ANNOT, idx_name), annot)
# duplicate gray band to be as rgb
# if img.ndim == 2:
# img = np.rollaxis(np.tile(img, (3, 1, 1)), 0, 3)
slic = seg_spx.segment_slic_img2d(img,
sp_size=params['slic_size'],
rltv_compact=params['slic_regul'])
img = tl_data.convert_img_color_from_rgb(img,
params.get('clr_space', 'rgb'))
logging.debug('computed SLIC with %i labels', slic.max())
if show_debug_imgs:
img_rgb = use_rgb_image(img)
img_slic = segmentation.mark_boundaries(img_rgb,
slic,
color=(1, 0, 0),
mode='subpixel')
plt.imsave(_path_out_img(params, FOLDER_SLIC, idx_name),
np.clip(img_slic, 0, 1))
slic_label_hist = seg_label.histogram_regions_labels_norm(slic, annot)
labels = np.argmax(slic_label_hist, axis=1)
slic_annot = labels[slic]
if show_debug_imgs:
plt.imsave(_path_out_img(params, FOLDER_SLIC_ANNOT, idx_name),
np.clip(slic_annot, 0, slic_annot.max()))
features, feature_names = seg_fts.compute_selected_features_img2d(
img, slic, params['features'])
return idx_name, img, annot, slic, features, labels, \
slic_label_hist, feature_names
def segment_image(imgs_idx_path,
params,
classif,
path_out,
path_visu=None,
show_debug_imgs=SHOW_DEBUG_IMAGES):
""" perform image segmentation on input image with given paramters
and trained classifier, and save results
:param (int, str) imgs_idx_path:
:param {str: ...} params: segmentation parameters
:param obj classif: trained classifier
:param str path_out: path for output
:param str path_visu: the existing patch means export also visualisation
:param bool show_debug_imgs: whether show debug images
:return (str, ndarray, 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'])
debug_visual = dict() if show_debug_imgs else None
gc_regul = params['gc_regul']
if params['gc_use_trans']:
label_penalty = seg_gc.compute_pairwise_cost_from_transitions(
params['label_transitions'])
gc_regul = (gc_regul * label_penalty)
segm_gc, segm_soft = seg_pipe.segment_color2d_slic_features_model_graphcut(
img,
classif,
sp_size=params['slic_size'],
sp_regul=params['slic_regul'],
dict_features=params['features'],
gc_regul=gc_regul,
gc_edge_type=params['gc_edge_type'],
debug_visual=debug_visual)
segm_map = np.argmax(segm_soft, axis=-1)
for segm, suffix in [(segm_gc, ''), (segm_map, '_MAP')]:
path_img = os.path.join(path_out, idx_name + suffix + '.png')
logging.debug('export segmentation: %s', path_img)
if np.max(segm) <= 1:
img_seg = Image.fromarray((segm * 255).astype(np.uint8))
else:
img_seg = Image.fromarray(segm.astype(np.uint8))
img_seg.convert('L').save(path_img)
# io.imsave(path_img, segm_gc)
path_npz = os.path.join(path_out, idx_name + '.npz')
np.savez_compressed(path_npz, segm_soft)
# plt.imsave(os.path.join(path_out, idx_name + '_rgb.png'), seg_pipe)
if params.get('visual', False) and path_visu is not None \
and os.path.isdir(path_visu):
export_draw_image_segm_contour(img, segm_gc, path_visu, idx_name,
'_GC')
export_draw_image_segm_contour(img, segm_map, path_visu, idx_name,
'_MAP')
if show_debug_imgs and debug_visual is not None:
path_fig = os.path.join(path_visu, str(idx_name) + '_debug.png')
logging.debug('exporting (debug) visualization: %s', path_fig)
fig = tl_visu.figure_segm_graphcut_debug(debug_visual)
fig.savefig(path_fig, bbox_inches='tight', pad_inches=0.1)
plt.close(fig)
gc.collect()
time.sleep(1)
return idx_name, segm_map, segm_gc
def segment_image(imgs_idx_path, params, classif, path_out, path_visu=None,
show_debug_imgs=SHOW_DEBUG_IMAGES):
""" perform image segmentation on input image with given paramters
and trained classifier, and save results
:param (int, str) imgs_idx_path:
:param {str: ...} params: segmentation parameters
:param obj classif: trained classifier
:param str path_out: path for output
:param str path_visu: the existing patch means export also visualisation
:return (str, ndarray, 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'])
slic = seg_spx.segment_slic_img2d(img, sp_size=params['slic_size'],
rltv_compact=params['slic_regul'])
img = seg_pipe.convert_img_color_space(img, params.get('clr_space', 'rgb'))
features, _ = seg_fts.compute_selected_features_img2d(img, slic,
params['features'])
labels = classif.predict(features)
segm = labels[slic]
path_img = os.path.join(path_out, idx_name + '.png')
logging.debug('export segmentation: %s', path_img)
img_seg = Image.fromarray(segm.astype(np.uint8))
img_seg.convert('L').save(path_img)
# io.imsave(path_img, segm)
# plt.imsave(os.path.join(path_out, idx_name + '_rgb.png'), seg_pipe)
if path_visu is not None and os.path.isdir(path_visu):
export_draw_image_segm_contour(img, segm, path_visu, idx_name)
try: # in case some classiefier do not support predict_proba
proba = classif.predict_proba(features)
segm_soft = proba[slic]
path_npz = os.path.join(path_out, idx_name + '.npz')
np.savez_compressed(path_npz, segm_soft)
except Exception:
logging.warning('classif: %s not support predict_proba(.)',
repr(classif))
proba = None
segm_soft = None
# if probabilities was not estimated of GC regul. is zero
if proba is not None and params['gc_regul'] > 0:
gc_regul = params['gc_regul']
if params['gc_use_trans']:
label_penalty = seg_gc.compute_pairwise_cost_from_transitions(
params['label_transitions'])
gc_regul = (gc_regul * label_penalty)
labels_gc = seg_gc.segment_graph_cut_general(slic, proba, img, features,
gc_regul, edge_type=params['gc_edge_type'])
# labels_gc = seg_gc.segment_graph_cut_simple(slic, proba, gc_regul)
segm_gc = labels_gc[slic]
# relabel according classif classes
segm_gc = classif.classes_[segm_gc]
path_img = os.path.join(path_out, idx_name + '_gc.png')
logging.debug('export segmentation: %s', path_img)
img_seg_gc = Image.fromarray(segm_gc.astype(np.uint8))
img_seg_gc.convert('L').save(path_img)
# io.imsave(path_img, segm_gc)
if path_visu is not None and os.path.isdir(path_visu):
export_draw_image_segm_contour(img, segm_gc, path_visu,
idx_name, '_gc')
if show_debug_imgs:
labels_map = np.argmax(proba, axis=1)
plt.imsave(os.path.join(path_visu, idx_name + '_map.png'),
labels_map[slic])
if not segm_soft is None:
for lb in range(segm_soft.shape[2]):
uc_name = idx_name + '_gc_unary-lb%i.png' % lb
plt.imsave(os.path.join(path_visu, uc_name),
segm_soft[:, :, lb], vmin=0., vmax=1.,
cmap=plt.cm.Greens)
else:
segm_gc = np.zeros(segm.shape)
# gc.collect(), time.sleep(1)
return idx_name, segm, segm_gc
