def ROI_plot(reference,region_names,stretch):
#Define parameters for plot presentation
nobjects = len(region_names) #get number of objects to be drawn
#Make reference image the base image on which to draw
image = hv.Image((np.arange(reference.shape[1]), np.arange(reference.shape[0]), reference))
image.opts(width=int(reference.shape[1]*stretch['width']),
height=int(reference.shape[0]*stretch['height']),
invert_yaxis=True,cmap='gray',
colorbar=True,
toolbar='above',
title="Draw Regions: "+', '.join(region_names))
#Create polygon element on which to draw and connect via stream to PolyDraw drawing tool
poly = hv.Polygons([])
poly_stream = streams.PolyDraw(source=poly, drag=True, num_objects=nobjects, show_vertices=True)
poly.opts(fill_alpha=0.3, active_tools=['poly_draw'])
def centers(data):
try:
x_ls, y_ls = data['xs'], data['ys']
except TypeError:
x_ls, y_ls = [], []
xs = [np.mean(x) for x in x_ls]
ys = [np.mean(y) for y in y_ls]
rois = region_names[:len(xs)]
return hv.Labels((xs, ys, rois))
dmap = hv.DynamicMap(centers, streams=[poly_stream])
return (image * poly * dmap), poly_stream
def ROI_plot(directory, fnames, file, region_names=None):
#Get image
try:
Image_Current_File = os.path.join(os.path.normpath(directory),
fnames[file])
img = cv2.imread(Image_Current_File, cv2.IMREAD_GRAYSCALE)
print(Image_Current_File)
print('file: {}'.format(file))
except IndexError:
print('Max file index exceeded. All images in folder drawn.')
return None, None, None
#get number of objects to be drawn
nobjects = len(region_names) if region_names else 0
#Make reference image the base image on which to draw
image_title = "No Regions to Draw" if nobjects == 0 else "Draw Regions: " + ', '.join(
region_names)
image = hv.Image((np.arange(img.shape[1]), np.arange(img.shape[0]), img))
image.opts(width=int(img.shape[1]),
height=int(img.shape[0]),
invert_yaxis=True,
cmap='gray',
colorbar=True,
toolbar='below',
title=image_title)
#Create polygon element on which to draw and connect via stream to PolyDraw drawing tool
poly = hv.Polygons([])
poly_stream = streams.PolyDraw(source=poly,
drag=True,
num_objects=nobjects,
show_vertices=True)
poly.opts(fill_alpha=0.3, active_tools=['poly_draw'])
def centers(data):
try:
x_ls, y_ls = data['xs'], data['ys']
except TypeError:
x_ls, y_ls = [], []
xs = [np.mean(x) for x in x_ls]
ys = [np.mean(y) for y in y_ls]
rois = region_names[:len(xs)]
return hv.Labels((xs, ys, rois))
if nobjects > 0:
dmap = hv.DynamicMap(centers, streams=[poly_stream])
return (image * poly * dmap), poly_stream, img.shape
else:
return (image), None, img.shape
from random import randint
import holoviews as hv
import panel as pn
from holoviews import opts, streams
LINE = "red"
FILL1 = "green"
FILL2 = "fulvous"
FILL3 = "blue"
hv.extension("bokeh")
path = hv.Path([[(1, 5), (9, 5)]])
poly = hv.Polygons([[(2, 2), (5, 8), (8, 2)]])
path_stream = streams.PolyDraw(source=path, drag=True, show_vertices=True)
poly_stream = streams.PolyDraw(
source=poly,
drag=True,
num_objects=4,
show_vertices=True,
styles={"fill_color": [FILL1, FILL2, FILL3]},
)
def get_plot(path, poly):
return (path * poly).opts(
opts.Polygons(fill_alpha=0.3, active_tools=["poly_draw"]),
opts.Path(color=LINE, height=400, line_width=5, width=400),
)