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):