def squish_rgb(fname):
'''
take in rgb image and just give us the first channel
'''
return skimage.io.imread(fname)[0,:,:]
# we want to create an roi
# if we pick one it will stay the same for all the frames
# we select vertices of the bottom frame second from the left
verts = [(496.91606404958685, 406.69266528925613),
(499.2249483471075, 249.68853305785117),
(345.68414256198355, 245.64798553719001),
(341.64359504132238, 396.87990702479328)]
# use justin's roi utility
roi, roi_bbox, roi_box = bebi103.verts_to_roi(verts, 480, 640)
# define a function roi
def load_roi(fname, roi_bbox = None):
'''
define a roi area
'''
return squish_rgb(fname)[roi_bbox]
# we can load the stack of images
ic = skimage.io.ImageCollection(im_glob, conserve_memory = True, load_func = load_roi, roi_bbox = roi_bbox)
# when we look at this image we want to constrast the sand from the jelly fish as much as possible
# with sns.axes_style('white'):
# skimage.io.imshow(ic[0])
fname = './data/goehring_FRAP_data/PH_138_A.tif'
vert = (16.435483870967744, 10.274193548387103)
b = (vert[0], vert[1] + 40)
c = (vert[0] + 40, vert[1])
d = (vert[0] + 40, vert[1] + 40)
verts = np.array([vert, b, c, d])
# use justin's roi utility
roi, roi_bbox, roi_box = bebi103.verts_to_roi(verts, 128, 128)
img_num = 149
# define a function roi
def load_roi(fname, img_num=0, roi_bbox = None):
'''
define a roi area
'''
out = np.empty(149)
print ("running function")
# print (out)
# for i in range(img_num):
