napary_slider.py

import zarr
import numpy as np
from pathlib import Path
import dask.array as da

%gui qt5
# Note that this Magics command needs to be run in a cell
# before any of the Napari objects are instantiated to
# ensure it has time to finish executing before they are
# called

import napari

# counts example
# adjust the path depending on where the data are stored

tmp_counts = 'EXP-19-CX9100_Excitatory_Hybridization01_Cy5_pos_4.zarr'
st_tmp = zarr.DirectoryStore(tmp_counts)
root_tmp = zarr.group(store=st_tmp, overwrite=False)

# collect the thr
thrs = np.unique(root_tmp['graph_raw_counts']['counting_thr'])

# ------------------------------------------------
# working approach using int as label in the slider
# ------------------------------------------------

points_nd = []
all_counting_thr = root_tmp['graph_raw_counts']['counting_thr'][...]
all_coords = root_tmp['graph_raw_counts']['coords_original'][...]
for idx, thr in enumerate(thrs):
    selected_counts = all_coords[:,all_counting_thr==thr].T
    points = np.concatenate((np.full((selected_counts.shape[0], 1), idx), selected_counts), axis=1)
    points_nd.append(points)
points_nd = np.concatenate(points_nd,axis=0)

viewer = napari.Viewer()
pts_layer = viewer.add_points(points_nd,symbol='+',edge_color='red', face_color='red',size=2, name='counts at different thr')

# ---------------------------------
# not working solution using the thr value (float) as label for the slider
# conversion to int create only the 0 label
# ---------------------------------

points_nd = []
all_counting_thr = root_tmp['graph_raw_counts']['counting_thr'][...]
all_coords = root_tmp['graph_raw_counts']['coords_original'][...]
for idx, thr in enumerate(thrs):
    selected_counts = all_coords[:,all_counting_thr==thr]
    thr_val = all_counting_thr[all_counting_thr==thr]
    points = np.vstack((thr_val, selected_counts))
    points = points.T
    points_nd.append(points)

points_nd = np.concatenate(points_nd,axis=0)

viewer = napari.Viewer()
pts_layer = viewer.add_points(points_nd,symbol='+',edge_color='red', face_color='red',size=2, name='counts at different thr')