class TestGraphCut(unittest.TestCase):
img = load_sample_image(IMAGE_DROSOPHILA_OVARY_2D)
annot = load_sample_image(ANNOT_DROSOPHILA_OVARY_2D)
def test_count_transitions_segment(self):
img = self.img[:, :, 0]
annot = self.annot.astype(int)
slic = segment_slic_img2d(img, sp_size=15, relative_compact=0.2)
label_hist = histogram_regions_labels_norm(slic, annot)
labels = np.argmax(label_hist, axis=1)
trans = count_label_transitions_connected_segments({'a': slic}, {'a': labels})
path_csv = os.path.join(PATH_OUTPUT, 'labels_transitions.csv')
pd.DataFrame(trans).to_csv(path_csv)
gc_regul = compute_pairwise_cost_from_transitions(trans, 10.)
np.random.seed(0)
features = np.tile(labels, (5, 1)).T.astype(float)
features += np.random.random(features.shape) - 0.5
gmm = estim_class_model_gmm(features, 4)
proba = gmm.predict_proba(features)
segment_graph_cut_general(slic, proba, gc_regul)
class TestPipelinesGMM(unittest.TestCase):
img_obj = load_sample_image(IMAGE_OBJECTS)
img_star = load_sample_image(IMAGE_STAR)
# img_islet = load_sample_image(IMAGE_LANGER_ISLET)
# img_histo = load_sample_image(IMAGE_HISTOL_FLAGSHIP)
# img_disc = load_sample_image(IMAGE_DROSOPHILA_DISC)
# img_ovary = load_sample_image(IMAGE_DROSOPHILA_OVARY_2D)
# img3d = get_image_path(IMAGE_DROSOPHILA_OVARY_3D)
def test_segm_gmm_gc_objects(self):
img = imresize(self.img_obj, (256, 256))
logging.debug('dimension: {}'.format(img.shape))
dict_imgs = dict()
path_dir = os.path.join(PATH_OUTPUT, 'temp_segm-gmm-gc-objects')
if not os.path.isdir(path_dir):
os.mkdir(path_dir)
seg, _ = pipe_color2d_slic_features_model_graphcut(
img, nb_classes=4, dict_features={'color': ['mean']},
sp_size=20, sp_regul=0.2, gc_regul=1., gc_edge_type='model',
debug_visual=dict_imgs)
show_segm_debugs_2d(dict_imgs, path_dir,
'fig_regul-%.2f_edge-%s_debug.png' % (1., 'model'))
show_segm_results_2d(img, seg, path_dir,
'fig_regul-%.2f_edge-%s.png' % (1., 'model'))
def test_segm_gmm_gc_stars(self):
img = self.img_star
logging.debug('dimension: {}'.format(img.shape))
params = copy.deepcopy(DEFAULT_SEGM_PARAMS)
params.update(dict(nb_classes=3, sp_regul=0.2, sp_size=25,
dict_features={'color': ['mean', 'std']}))
run_segm2d_gmm_gc(img, 'temp_segm-gmm-gc-stars', params=params)
class TestPipelinesClassif(unittest.TestCase):
img = load_sample_image(IMAGE_DROSOPHILA_OVARY_2D)[:, :, 0]
annot = load_sample_image(ANNOT_DROSOPHILA_OVARY_2D)
img2 = load_sample_image(IMAGE_DROSOPHILA_OVARY_2D)[:, :, 0]
def test_segm_supervised(self):
img = imresize(self.img, (256, 256))
annot = imresize(self.annot, (256, 256), interp='nearest')
img2 = imresize(self.img2, (256, 256))
path_dir = os.path.join(PATH_OUTPUT, 'temp_segm-supervised_gc')
if not os.path.exists(path_dir):
os.mkdir(path_dir)
sp_size = 10
tp_edge = ['model', 'const']
list_regul = [0, 1, 10]
dict_imgs = dict()
name = 'fig-img%i_regul-%.2f_edge-%s.png'
classif, _, _, _ = train_classif_color2d_slic_features(
[img], [annot], sp_size=sp_size, dict_features=FEATURES_TEXTURE)
segment_color2d_slic_features_model_graphcut(
img,
classif,
sp_size=sp_size,
gc_regul=0.,
dict_features=FEATURES_TEXTURE,
debug_visual=dict_imgs)
show_segm_debugs_2d(dict_imgs, path_dir, name % (1, 0, '_debug'))
for edge in tp_edge:
dict_imgs = dict()
for regul in list_regul:
seg, _ = segment_color2d_slic_features_model_graphcut(
img,
classif,
dict_features=FEATURES_TEXTURE,
sp_size=sp_size,
gc_regul=regul,
gc_edge_type=edge)
show_segm_results_2d(img, seg, path_dir,
name % (1, regul, edge))
seg, _ = segment_color2d_slic_features_model_graphcut(
img2,
classif,
dict_features=FEATURES_TEXTURE,
sp_size=sp_size,
gc_regul=regul,
gc_edge_type=edge,
debug_visual=dict_imgs)
show_segm_results_2d(img2, seg, path_dir,
name % (2, regul, edge))
show_segm_debugs_2d(dict_imgs, path_dir,
name % (2, regul, edge))
dict_imgs = None
class TestSuperpixels(unittest.TestCase):
img = d_spl.load_sample_image(d_spl.IMAGE_LENNA)
seg2d = d_spl.sample_segment_vertical_2d()
seg3d = d_spl.sample_segment_vertical_3d()
def test_segm_connect(self):
logging.debug(self.seg2d)
vertices, edges = seg_spx.make_graph_segm_connect_grid2d_conn4(self.seg2d)
logging.debug('vertices: {} -> edges: {}'.format(vertices, edges))
logging.debug(self.seg3d)
vertices, edges = seg_spx.make_graph_segm_connect_grid3d_conn6(self.seg3d)
logging.debug('vertices: {} -> edges: {}'.format(vertices, edges))
def test_general(self):
slic = seg_spx.segment_slic_img2d(self.img, sp_size=15, rltv_compact=0.2)
logging.debug(np.max(slic))
vertices, edges = seg_spx.make_graph_segm_connect_grid2d_conn4(slic)
logging.debug(repr(vertices))
logging.debug(len(edges))
logging.debug(repr(edges))
fig, axarr = plt.subplots(ncols=2)
axarr[0].imshow(self.img)
axarr[1].imshow(slic, cmap=plt.cm.jet)
fig.savefig(os.path.join(PATH_OUTPUT, 'temp_superpixels.png'))
if logging.getLogger().getEffectiveLevel() == logging.DEBUG:
plt.show()
plt.close(fig)
def test_show_image_features_clr2d(self):
img = load_sample_image(IMAGE_LENNA)
img = transform.resize(img, (128, 128))
slic = segment_slic_img2d(img, sp_size=10, relative_compact=0.2)
features, names = compute_selected_features_color2d(
img, slic, FEATURES_SET_ALL)
path_dir = os.path.join(PATH_OUTPUT, 'temp_image-rgb2d-features')
if not os.path.isdir(path_dir):
os.mkdir(path_dir)
for i in range(features.shape[1]):
fts = features[:, i]
im_fts = fts[slic]
p_fig = os.path.join(path_dir, names[i] + '.png')
plt.imsave(p_fig, im_fts)
self.assertTrue(os.path.isfile(p_fig))
class TestPipelinesGMM(unittest.TestCase):
img_obj = d_spl.load_sample_image(d_spl.IMAGE_OBJECTS)
img_star = d_spl.load_sample_image(d_spl.IMAGE_STAR)
img_islet = d_spl.load_sample_image(d_spl.IMAGE_LANGER_ISLET)
img_histo = d_spl.load_sample_image(d_spl.IMAGE_HISTOL_FLAGSHIP)
img_disc = d_spl.load_sample_image(d_spl.IMAGE_DROSOPHILA_DISC)
img_ovary = d_spl.load_sample_image(d_spl.IMAGE_DROSOPHILA_OVARY_2D)
img3d = d_spl.get_image_path(d_spl.IMAGE_DROSOPHILA_OVARY_3D)
def test_segm_gmm_gc_objects(self):
img = imresize(self.img_obj, (256, 256))
logging.debug('dimension: {}'.format(img.shape))
dict_imgs = dict()
path_dir = os.path.join(PATH_OUTPUT, 'temp_segm-gmm-gc-objects')
if not os.path.isdir(path_dir):
os.mkdir(path_dir)
seg, _ = pipelines.pipe_color2d_slic_features_model_graphcut(
img,
nb_classes=4,
dict_features={'color': ['mean']},
sp_size=20,
sp_regul=0.2,
gc_regul=1.,
gc_edge_type='model',
debug_visual=dict_imgs)
show_segm_debugs_2d(dict_imgs, path_dir,
'fig_regul-%.2f_edge-%s_debug.png' % (1., 'model'))
show_segm_results_2d(img, seg, path_dir,
'fig_regul-%.2f_edge-%s.png' % (1., 'model'))
def test_segm_gmm_gc_stars(self):
img = self.img_star
logging.debug('dimension: {}'.format(img.shape))
params = copy.deepcopy(DEFAULT_SEGM_PARAMS)
params.update(
dict(nb_classes=3,
sp_regul=0.2,
sp_size=25,
dict_features={'color': ['mean', 'std']}))
run_segm2d_gmm_gc(img, 'temp_segm-gmm-gc-stars', dict_params=params)
def test_segm_gmm_gc_langer(self):
img = imresize(self.img_islet, (512, 512))
params = copy.deepcopy(DEFAULT_SEGM_PARAMS)
params.update(dict(sp_regul=0.15, sp_size=5))
run_segm2d_gmm_gc(img,
'temp_segm-gmm-gc-langer',
types_edge=['model_lT'],
list_regul=[0, 1],
dict_params=params)
def test_segm_gmm_gc_histo(self):
img = imresize(self.img_histo, (512, 512))
params = copy.deepcopy(DEFAULT_SEGM_PARAMS)
params.update(dict(sp_regul=0.15, sp_size=15, pca_coef=0.98))
run_segm2d_gmm_gc(img,
'temp_segm-gmm-gc-histology',
types_edge=['model'],
list_regul=[0, 1, 5],
dict_params=params)
def test_segm_gmm_gc_disc(self):
img = imresize(self.img_disc, (512, 512))
params = copy.deepcopy(DEFAULT_SEGM_PARAMS)
params.update(dict(sp_regul=0.2, sp_size=15, pca_coef=0.98))
run_segm2d_gmm_gc(img,
'temp_segm-gmm-gc-disc',
types_edge=['model_l2'],
list_regul=[0, 1, 5],
dict_params=params)
def test_segm_gmm_gc_ovary_2d(self):
img = imresize(self.img_ovary[:, :, 0], (512, 512))
# img = np.rollaxis(np.tile(img[:, :, 0], (3, 1, 1)), 0, 3)
params = copy.deepcopy(DEFAULT_SEGM_PARAMS)
params.update(
dict(nb_classes=4,
pca_coef=0.95,
sp_regul=0.3,
sp_size=10,
dict_features=seg_fts.FEATURES_SET_TEXTURE_SHORT))
run_segm2d_gmm_gc(img,
'temp_segm-gmm-gc-ovary-2d',
list_regul=[0, 2, 10],
dict_params=params)
def test_segm_gmm_gc_ovary_3d(self):
# _ = self.img3d
# TODO, add extension to 3D
# seg = pipelines.pipe_gray3d_slic_features_model_graphcut(img)
pass
