def export_figure(idx_row, df_slices_info, path_out):
""" load image, segmentation and csv with centres
1) draw figure with image, segmentation and csv
2) draw expety annotation
3) expert figure
:param idx_row:
:param df_slices_info:
:param path_out:
"""
_, row = idx_row
img_name = os.path.splitext(os.path.basename(row['path_image']))[0]
try:
if img_name not in df_slices_info.index:
logging.debug('missing image in annotation - "%s"', img_name)
return
img = tl_data.io_imread(row['path_image'])
segm = tl_data.io_imread(row['path_segm'])
df = pd.read_csv(os.path.join(row['path_centers']), index_col=0)
centres = df[['X', 'Y']].values
fig = figure_draw_img_centre_segm(None, img, centres, segm)
row_slice = df_slices_info.loc[img_name]
fig = figure_draw_annot_csv(fig, img, row_slice)
tl_visu.figure_image_adjustment(fig, img.shape)
fig.savefig(os.path.join(path_out, img_name + '.png'))
plt.close(fig)
except Exception:
logging.exception('failed for: %s', img_name)
def cluster_points_draw_export(dict_row, params, path_out=None):
""" cluster points into centers and export visualisations
:param dict dict_row:
:param dict params:
:param str path_out:
:return dict:
"""
assert all(n in dict_row for n in ['path_points', 'path_image', 'path_segm']), \
'missing some required fields: %r' % 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 not list(points):
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 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 redraw visualisation of inputs
:param (int, DF:row) idx_row: tuple of index and row
:param str path_out: path to output directory
:param dict dict_relabel: look-up table for relabeling
:return(str, ndarray, ndarray, [[int, int]]): idx_name, img_rgb, segm, centers
"""
idx, row_path = idx_row
for k in ['path_image', 'path_segm', 'path_centers']:
row_path[k] = tl_data.update_path(row_path[k])
if not os.path.exists(row_path[k]):
raise FileNotFoundError('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'], allow_pickle=True) 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 group_images_frequent_colors(paths_img, ratio_threshold=1e-3):
""" look all images and estimate most frequent colours
:param [str] paths_img: path to images
:param float ratio_threshold: percentage of nb, clr pixels to be assumed as important
:return [int]:
>>> from skimage import data
>>> from imsegm.utilities.data_io import io_imsave
>>> path_img = './sample-image.png'
>>> io_imsave(path_img, data.astronaut())
>>> d_clrs = group_images_frequent_colors([path_img], ratio_threshold=3e-4)
>>> sorted([d_clrs[c] for c in d_clrs], reverse=True) # doctest: +NORMALIZE_WHITESPACE
[27969, 1345, 1237, 822, 450, 324, 313, 244, 229, 213, 163, 160, 158, 157,
150, 137, 120, 119, 117, 114, 98, 92, 92, 91, 81]
>>> os.remove(path_img)
"""
logging.debug('passing %i images', len(paths_img))
dict_colors = dict()
for path_im in paths_img:
img = io_imread(path_im)
local_dict_colors = image_frequent_colors(img, ratio_threshold)
for clr in local_dict_colors:
if clr not in dict_colors:
dict_colors[clr] = 0
dict_colors[clr] += local_dict_colors[clr]
logging.info('img folder colours: %r', dict_colors)
return dict_colors
def extract_activation(path_img, path_out):
name = os.path.splitext(os.path.basename(path_img))[0]
img = io_imread(path_img)
mask = img[:, :, 0] > 5
im_struc = img[:, :, 0]
im_struc_gauss = ndimage.gaussian_filter(im_struc, 1)
im_gene = img[:, :, 1]
im_gene_gauss = ndimage.gaussian_filter(im_gene, 1)
mask_struc = im_struc_gauss > filters.threshold_otsu(im_struc_gauss[mask])
ms = np.median(im_struc_gauss[mask_struc])
mask_gene = im_gene_gauss > filters.threshold_otsu(im_gene_gauss[mask])
mg = np.median(im_gene_gauss[mask_gene])
ration_gene = np.sum(mask_gene) / float(np.sum(mask))
coef = (ms / mg * 2.5) if ration_gene > 0.3 else (ms / mg * 5)
im_mean = np.max(np.array([im_gene_gauss + (im_struc_gauss / coef)]), axis=0)
otsu = filters.threshold_otsu(im_mean[mask])
im_gene = im_mean.copy()
im_gene[im_gene < otsu] = 0
# gmm = GaussianMixture(n_components=3, n_init=10)
# data = np.array([im_gene_gauss[mask].ravel(), im_struc_gauss[mask]]).T
# gmm.fit(data)
# id_max = np.argmax(gmm.means_[:, 0])
# gm_mean = gmm.means_[id_max, 0]
# gm_std = np.sqrt(gmm.covariances_[id_max, 0, 0])
# im_gene[im_gene_gauss < (gm_mean - gm_std)] = 0
# p_out = os.path.join(path_out, name)
export_image(path_out, im_gene, name)
def load_image(path_img, img_type=TYPE_LOAD_IMAGE):
""" load image from given path according specification
:param str path_img:
:param str img_type:
:return ndarray:
"""
path_img = os.path.abspath(os.path.expanduser(path_img))
assert os.path.isfile(path_img), 'missing: "%s"' % path_img
if img_type == 'segm':
img = tl_data.io_imread(path_img)
elif img_type == '2d_struct':
img, _ = tl_data.load_img_double_band_split(path_img)
assert img.ndim == 2, 'image can be only single color'
else:
logging.error('not supported loading img_type: %s', img_type)
img = tl_data.io_imread(path_img)
logging.debug('image shape: %r, value range %f - %f', img.shape, img.min(),
img.max())
return img
def main(path_annot, path_out, nb_comp=5):
list_paths = sorted(glob.glob(path_annot))
logging.info('nb images: %i SAMPLES: %r', len(list_paths),
[os.path.basename(p) for p in list_paths[:5]])
list_segms = []
for path_seg in list_paths:
seg = tl_data.io_imread(path_seg)
list_segms.append(seg)
list_rays, _ = tl_rg.compute_object_shapes(list_segms,
ray_step=RAY_STEP,
interp_order='spline',
smooth_coef=1)
logging.info('nb eggs: %i, nb rays: %i', len(list_rays), len(list_rays[0]))
x_axis = np.linspace(0, 360, len(list_rays[0]), endpoint=False)
df = pd.DataFrame(np.array(list_rays), columns=x_axis.astype(int))
path_csv = os.path.join(path_out, NAME_CSV_RAY_ALL)
logging.info('exporting all Rays: %s', path_csv)
df.to_csv(path_csv)
# SINGLE MODEL
model, list_cdf = tl_rg.transform_rays_model_cdf_mixture(list_rays, 1)
cdf = np.array(np.array(list_cdf))
# path_model = os.path.join(path_out, NAME_NPZ_MODEL_SINGLE)
# logging.info('exporting model: %s', path_model)
# np.savez(path_model, name='cdf', cdfs=cdf, mix_model=model)
path_model = os.path.join(path_out, NAME_PKL_MODEL_SINGLE)
logging.info('exporting model: %s', path_model)
with open(path_model, 'wb') as fp:
pickle.dump({'name': 'cdf', 'cdfs': cdf, 'mix_model': model}, fp)
# MIXTURE MODEL
model, list_mean_cdf = tl_rg.transform_rays_model_sets_mean_cdf_mixture(
list_rays, nb_comp)
# path_model = os.path.join(path_out, NAME_NPZ_MODEL_MIXTURE)
# logging.info('exporting model: %s', path_model)
# np.savez(path_model, name='set_cdfs', cdfs=list_mean_cdf,
# mix_model=model)
path_model = os.path.join(path_out, NAME_PKL_MODEL_MIXTURE)
logging.info('exporting model: %s', path_model)
with open(path_model, 'wb') as fp:
pickle.dump(
{
'name': 'set_cdfs',
'cdfs': list_mean_cdf,
'mix_model': model
}, fp)
def load_correct_segm(path_img):
""" load segmentation and correct it with simple morphological operations
:param str path_img:
:return (ndarray, ndarray):
"""
assert os.path.isfile(path_img), 'missing: %s' % path_img
logging.debug('loading image: %s', path_img)
img = tl_data.io_imread(path_img)
seg = (img > 0)
seg = morphology.binary_opening(seg, selem=morphology.disk(25))
seg = morphology.remove_small_objects(seg)
seg_lb = measure.label(seg)
seg_lb[seg == 0] = 0
return seg, seg_lb
def load_sample_image(name_img=IMAGE_LENNA):
""" load sample image
:param str name_img:
:return ndarray:
>>> img = load_sample_image(IMAGE_LENNA)
>>> img.shape
(512, 512, 3)
"""
path_img = get_image_path(name_img)
assert os.path.exists(path_img), 'missing: "%s"' % path_img
logging.debug('image (%s): %s', os.path.exists(path_img), path_img)
img = io_imread(path_img)
return img
def load_sample_image(name_img=IMAGE_LENNA):
""" load sample image
:param str name_img:
:return ndarray:
>>> img = load_sample_image(IMAGE_LENNA)
>>> img.shape
(512, 512, 3)
"""
path_img = get_image_path(name_img)
if not os.path.isfile(path_img):
raise FileNotFoundError('missing: "%s"' % path_img)
logging.debug('image (%s): %s', os.path.exists(path_img), path_img)
img = io_imread(path_img)
return img
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 load_experiment(path_expt, name, path_dataset=None, path_images=None,
nb_workers=NB_WORKERS):
path_atlas = os.path.join(path_expt, BASE_NAME_ATLAS + name + '.png')
atlas = io_imread(path_atlas)
if (atlas.max() == 255 or atlas.max() == 1.) and len(np.unique(atlas)) < 128:
# assume it is scratched image
atlas = sk_segm.relabel_sequential(atlas)[0]
path_csv = os.path.join(path_expt, BASE_NAME_ENCODE + name + '.csv')
df_weights = pd.read_csv(path_csv, index_col=None)
path_npz = os.path.join(path_expt, BASE_NAME_DEFORM + name + '.npz')
if os.path.isfile(path_npz):
dict_deforms = dict(np.load(open(path_npz, 'rb')))
assert len(df_weights) == len(dict_deforms), \
'unresistant weights (%i) and (%i)' \
% (len(df_weights), len(dict_deforms))
else:
dict_deforms = None
segms = load_images(path_dataset, df_weights['image'].values, nb_workers)
images = load_images(path_images, df_weights['image'].values, nb_workers)
return atlas, df_weights, dict_deforms, segms, images
