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Imaging.py
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Imaging.py
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import numpy as np
import matplotlib.pyplot as plt
import skimage.transform as sk_t
from skimage.measure import profile_line
class Image:
'''Initialize Image class. Parameters:
1) image - greyscale image represented as numpy array
2) rotation - rotation to be applied to image in degrees
3) pxpermm_x - image scale in pixels per mm of x
4) pxpermm_y - Image scale in pixels per mm of y (if not specified scale x == scale y)
5) mask = list format, e.g. [0,1]
'''
def __init__(self, image, rotate, pxpermm_x, pxpermm_y = None, flipud = False, fliplr = False):
self.im = sk_t.rotate(image, rotate, resize=False)
if flipud:
self.im = np.flipud(self.im)
if fliplr:
self.im = np.fliplr(self.im)
if pxpermm_y:
self.sc_x = pxpermm_x
self.sc_y = pxpermm_y
else:
self.sc_x = pxpermm_x
self.sc_y = pxpermm_x
self.o = np.array([0., 0.])
self.shape = image.shape
self.r = rotate
def px_to_mm(self, p_px):
'''Calculates position of point in mm, given position in px'''
h = self.shape[0]
p = np.array(p_px, dtype=np.float64)
p *= np.array([1., -1.]) #Convert handedness
p += np.array([0., h]) #Translate origin to BL corner
p[0] = p[0]/self.sc_x
p[1] = p[1]/self.sc_y
p -= self.o
return p
def mm_to_px(self, p_mm):
'''Calculates position of point in px, given position in mm'''
h = self.shape[0]
p = np.array(p_mm)
p += self.o
p[0] = p[0]*self.sc_x
p[1] = p[1]*self.sc_y
p *= np.array([1., -1.]) #Convert handedness
p += np.array([0., h]) #Translate origin to TR corner
return np.array(p, dtype=np.int64)
def set_origin(self, p_px):
'''Sets origin of image from value in pixels'''
self.o = np.array([0., 0.])
p_mm = self.px_to_mm(p_px)
self.o = p_mm
self.o_px = p_px
def get_origin(self):
'''Returns the position of the origin in pixels'''
o = np.array([0., 0.])
o_px = self.mm_to_px(o)
return o_px
def plot_mm(self, ax, multiply_by = None, mask = None, extent = None, **kwargs):
'''Plot image with axes in physical units. kwargs are passed
to plt.imshow method.'''
x0 = 0
x1 = self.im.shape[1]
y0 = 0
y1 = self.im.shape[0]
x0, y0 = self.px_to_mm([x0, y0])
x1, y1 = self.px_to_mm([x1, y1])
if extent:
self.extent = extent
else:
self.extent = [x0, x1, y1, y0]
img = self.im
if multiply_by:
if mask:
if len(mask) > 1:
self.masked_im = np.ma.masked_outside(img, mask[0], mask[1])
return ax.imshow(self.masked_im*multiply_by, extent = self.extent, **kwargs)
else:
self.masked_im = np.ma.masked_less_equal(img, mask[0])
return ax.imshow(self.masked_im*multiply_by, extent = self.extent, **kwargs)
else:
return ax.imshow(img*multiply_by, extent = self.extent, **kwargs)
else:
return ax.imshow(img, extent = self.extent, **kwargs)
def plot_px(self, ax, **kwargs):
'''Plot image with axes pixels. kwargs are passed
to plt.imshow method.'''
return ax.imshow(self.im, **kwargs)
def plot_mm_split(self, ax, channel = 'b', multiply_by = None, mask = None, extent = None, **kwargs):
''' Plot image with axes in physical units and split channels. kwargs are passed
to plt.imshow method.'''
x0 = 0
x1 = self.im.shape[1]
y0 = 0
y1 = self.im.shape[0]
x0, y0 = self.px_to_mm([x0, y0])
x1, y1 = self.px_to_mm([x1, y1])
if extent:
self.extent = extent
else:
self.extent = [x0, x1, y1, y0]
b, g, r = self.im[:, :, 0], self.im[:, :, 1], self.im[:, :, 2]
if channel == 'b':
img = b
elif channel == 'g':
img = g
elif channel == 'r':
img = r
if multiply_by:
if mask:
self.masked_im = np.ma.masked_less_equal(img, mask)
return ax.imshow(self.masked_im*multiply_by, extent = self.extent, **kwargs)
else:
return ax.imshow(img*multiply_by, extent = self.extent, **kwargs)
else:
return ax.imshow(img, extent = self.extent, **kwargs)
def profile_mm(self, src_mm, dst_mm, width_mm, **kwargs):
src_px = np.flip( self.mm_to_px(src_mm) )
dst_px = np.flip( self.mm_to_px(dst_mm) )
width_px = int(width_mm*self.sc_x)
p = profile_line(self.im, src_px, dst_px, linewidth=width_px, **kwargs)
r = np.linspace(src_mm, dst_mm, len(p))
return r, p
def create_im(self, im):
out = Image(im, 0., self.sc_x)
out.set_origin(self.o_px)
return out