def to_rgb_uint8(image, autoscale=True, force_color=None):
ndim = image.ndim
shape = image.shape
try:
colors = image.metadata['colors']
if len(colors) != shape[0]:
colors = None
except (AttributeError, KeyError):
colors = None
# 2D, grayscale
if ndim == 2:
force_color = [force_color] if force_color is not None else None
image = to_rgb(image, force_color)
# 2D non-interleaved RGB
elif ndim == 3 and shape[0] in [3, 4]:
image = image.transpose([1, 2, 0])
autoscale = False
# 2D, has colors attribute
elif ndim == 3 and colors is not None:
image = to_rgb(image, colors, True)
# 2D, RGB
elif ndim == 3 and shape[2] in [3, 4]:
pass
# 2D, is multichannel
elif ndim == 3 and shape[0] < 5: # guessing; could be small z-stack
image = to_rgb(image, None, True)
# 3D, grayscale
elif ndim == 3:
grayscale = True
# 3D, has colors attribute
elif ndim == 4 and colors is not None:
image = to_rgb(image, colors, True)
# 3D, RGB
elif ndim == 4 and shape[3] in [3, 4]:
pass
# 3D, is multichannel
elif ndim == 4 and shape[0] < 5:
image = to_rgb(image, None, True)
else:
raise ValueError(
"No display possible for frames of shape {0}".format(shape))
if autoscale:
image = (normalize(image) * 255).astype(np.uint8)
elif not np.issubdtype(image.dtype, np.uint8):
if np.issubdtype(image.dtype, np.integer):
max_value = np.iinfo(image.dtype).max
# sometimes 12-bit images are stored as unsigned 16-bit
if max_value == 2**16 - 1 and image.max() < 2**12:
max_value = 2**12 - 1
image = (image / max_value * 255).astype(np.uint8)
else:
if image.max() > 1: # unnormalized floats! normalize anyway
image = normalize(image)
image = (image * 255).astype(np.uint8)
return image
def make_input_image(img, save_file_name, message = None, time_stamp = None, x_start = 440, y_start = 70, lamda = 1.33, uml=50, width = 6, fontsize = 18, y_time_stamp = 20):
"""mark the input image, img, at position needletip with a 50µm white scale bar.
time_stamp and message are passed as content to plt.text.
marked image saved to save_file_name.
DONE: checked that the output still has 512x512 pixels.
x_start and y_start are for the scale bar position and have units of pixels.
time stamp might be '+{} min '.format(str(int(np.around(tmax,0))))', for instance.
lamda is lengthscale in microns per pixel.
uml is the length of the scale bar in microns
width is the width of the scalebar"""
#parse inputs
# lamda = 1.33 #microns per pixel for 10X magnification
ycoord = y_start#pixel
xstart = x_start#pixel
# dt = 1 #minutes per frame
# self.lamda = 1.33 #microns per pixel
# self.dt = 1 #minutes per frame
# self.frm = -1
# lamda = self.lamda#1.33
#send grayscale/1_channel images to rgb
if len(img.shape)==2:
img = pims.to_rgb(img.copy())
mydpi=128#64
mult = 1.32642487
#calculate scale bar length
s = 3
# uml = 50#um
pxl = uml/lamda#pxl
#plot image and mark
fig = plt.figure(num=None, frameon=False, figsize=(mult*img.shape[0]/mydpi, mult*img.shape[1]/mydpi), dpi=mydpi, facecolor='w', edgecolor='k')
#alternative initialization #fig = plt.figure(num=None, figsize=(8, 8), dpi=64, facecolor='w', edgecolor='k')
ax = fig.add_subplot(111)
ax.imshow(img)
ax.axis('off')
## add scale lines
l1 = lines.Line2D([xstart, xstart+pxl], [ycoord, ycoord], color='white', linewidth=width, solid_capstyle='butt')
fig.lines.extend([l1])
## add text boxes
if message is not None:
ax.text(x=15, y=50, c='white', s=message, weight='bold', fontsize=fontsize, horizontalalignment='left', verticalalignment='center')
if time_stamp is not None:
ax.text(x=15, y=y_time_stamp, c='white', s=time_stamp, weight='bold', fontsize=fontsize, horizontalalignment='left', verticalalignment='center')
plt.savefig(save_file_name, bbox_inches='tight', pad_inches=0.)
return True
def highlight(position, flow_in, flow_out, background_frame, r_c_mat=None,
hue_scale=80, hue_scale_red=70, hue_scale_blue=90,
r_thresh = 0,
**kwargs):
'''visualize overlay of outward optical flow over the background channel.
for masking the highlight to not consider r_thresh pixels from the center,
the center must also be provided by r_c_mat as returned by get_r_hat_mat
Example Usage:
img = highlight(position=(x_coord, y_coord), flow_in=flow_in, flow_out=flow_out, background_frame=frame_2)
'''
#TODO: use more sophisticated/correct kwargs parsing as done elsewhere
#TODO: add r_thresh set method to argument of highlight
mfo = flow_out
mfi = flow_in
width=background_frame.shape[0]
height=background_frame.shape[1]
filt = np.zeros([width,height,3]) #3 channels for rgb
img = pims.to_rgb(background_frame)
if r_c_mat == None:
r_filter = 1
elif r_c_mat.shape == (width, height):
r_filter = (r_c_mat>r_thresh)
else:
r_filter = 1
#TODO(better): use colormap such as # im_color = cv2.applyColorMap(im_gray, cv2.COLORMAP_COOL)
#subtract nonblue for outward flow
filt[:,:,0] = hue_scale_blue*mfo*r_filter
filt[:,:,1] = hue_scale_blue*mfo*r_filter
#subtract nonred for inward flow
filt[:,:,1] = hue_scale_red*mfi*r_filter
filt[:,:,2] = hue_scale_red*mfi*r_filter
# filt[:,:,2] = filt[:,:,2]/np.max(filt[:,:,2])+1
flowing = np.add(img, -filt)
#clip to 0 to 255
# if np.isnan(np.sum(out_vec)):
# out_vec = out_vec[~np.isnan(out_vec)] # just remove nan elements from out_vec
flowing[flowing<0] = 0
flowing[flowing>255] = 255
#highlight needletip with a yellow x
#TODO: make marker parameters accessable through **kwargs
return drawMarker(flowing, position = position,
color = (255,255,0), markerType = 1 , markerSize = 15, thickness = 2)
def imshow(image, ax=None, mpp=1., origin=(0, 0), ax_labels=False, **kwargs):
"""Show an image. Origin is in pixels."""
_imshow_style = dict(origin='lower',
interpolation='nearest',
cmap=plt.cm.gray,
aspect='equal')
_imshow_style.update(kwargs)
if not is_rgb(image, ndim=2):
try:
from pims import to_rgb
except ImportError:
raise ImportError(
"Imshow requires PIMS to display a non-RGB image")
image = to_rgb(image, kwargs.pop('colors', None), normed=False) / 255.
shape = image.shape[:2]
mpp = validate_tuple(mpp, ndim=2)
origin = validate_tuple(origin, ndim=2)
# extent is defined on the outer edges of the pixels
# we want the center of the topleft to intersect with the origin
extent = [
(origin[1] - 0.5) * mpp[1], (origin[1] + shape[1] - 0.5) * mpp[1],
(origin[0] - 0.5) * mpp[0], (origin[0] + shape[0] - 0.5) * mpp[0]
]
ax.imshow(image, extent=extent, **_imshow_style)
ax.set_xlim(extent[0], extent[1])
ax.set_ylim(extent[3], extent[2])
if ax_labels:
if mpp == 1.:
fmt = '{} [px]'
elif mpl.rcParams['text.usetex']:
fmt = r'{} [\textmu m]'
else:
fmt = r'{} [\xb5m]'
ax.set_xlabel(fmt.format('x'))
ax.set_ylabel(fmt.format('y'))
return ax
def imshow(image, ax=None, mpp=1., origin=(0, 0), ax_labels=False, **kwargs):
"""Show an image. Origin is in pixels."""
_imshow_style = dict(origin='lower', interpolation='nearest',
cmap=plt.cm.gray, aspect='equal')
_imshow_style.update(kwargs)
if not is_rgb(image, ndim=2):
try:
from pims import to_rgb
except ImportError:
raise ImportError("Imshow requires PIMS to display a non-RGB image")
image = to_rgb(image, kwargs.pop('colors', None), normed=False) / 255.
shape = image.shape[:2]
mpp = validate_tuple(mpp, ndim=2)
origin = validate_tuple(origin, ndim=2)
# extent is defined on the outer edges of the pixels
# we want the center of the topleft to intersect with the origin
extent = [(origin[1] - 0.5) * mpp[1],
(origin[1] + shape[1] - 0.5) * mpp[1],
(origin[0] - 0.5) * mpp[0],
(origin[0] + shape[0] - 0.5) * mpp[0]]
ax.imshow(image, extent=extent, **_imshow_style)
ax.set_xlim(extent[0], extent[1])
ax.set_ylim(extent[3], extent[2])
if ax_labels:
if mpp == 1.:
fmt = '{} [px]'
elif mpl.rcParams['text.usetex']:
fmt = r'{} [\textmu m]'
else:
fmt = r'{} [\xb5m]'
ax.set_xlabel(fmt.format('x'))
ax.set_ylabel(fmt.format('y'))
return ax
def imshow3d(image3d,
mode='max',
center=None,
mpp=1.,
origin=(0, 0, 0),
axs=None,
ax_labels=False,
**kwargs):
"""Shows the xy, xz, and yz projections of a 3D image.
Parameters
----------
image3d : ndarray
mode : {'max' | 'slice'}
aspect : number
aspect ratio of pixel size z / xy. Default 1.
center : tuple
in pixels
mpp : tuple
microns per pixel
origin : tuple
coordinate of the (center of the) topleft pixel (in pixels)
spacing : number
spacing between images
axs : t
Returns
-------
fig, (ax_xy, ax_zy, ax_zx, ax_extra)
"""
imshow_style = dict(origin='lower',
interpolation='nearest',
cmap=plt.cm.gray,
aspect='auto')
imshow_style.update(kwargs)
if not is_rgb(image3d, ndim=3):
try:
from pims import to_rgb
except ImportError:
raise ImportError(
"Imshow requires PIMS to display a non-RGB image")
image3d = to_rgb(image3d, kwargs.pop('colors', None),
normed=False) / 255.
shape = image3d.shape[:3]
mpp = validate_tuple(mpp, ndim=3)
origin = validate_tuple(origin, ndim=3)
ax_xy, ax_zy, ax_zx, ax_extra = axs
if mode == 'max':
image_xy = image3d.max(0)
image_zx = image3d.max(1)
image_zy = image3d.max(2)
elif mode == 'slice':
center_i = [int(round(c - o)) for c, o in zip(center, origin)]
center_i = [min(max(c, 0), sh - 1) for c, sh in zip(center_i, shape)]
image_xy = image3d[center_i[0], :, :]
image_zx = image3d[:, center_i[1], :]
image_zy = image3d[:, :, center_i[2]]
else:
raise ValueError('Unknown mode "{}"'.format(mode))
if image_zy.ndim == 3:
image_zy = np.transpose(image_zy, (1, 0, 2))
else:
image_zy = image_zy.T
# extent is defined on the outer edges of the pixels
# we want the center of the topleft to intersect with the origin
extent = [
(origin[2] - 0.5) * mpp[2], (origin[2] + shape[2] - 0.5) * mpp[2],
(origin[1] - 0.5) * mpp[1], (origin[1] + shape[1] - 0.5) * mpp[1],
(origin[0] - 0.5) * mpp[0], (origin[0] + shape[0] - 0.5) * mpp[0]
]
extent_xy = extent[:4]
extent_zx = extent[:2] + extent[4:6]
extent_zy = extent[4:6] + extent[2:4]
ax_xy.imshow(image_xy, extent=extent_xy, **imshow_style)
ax_zx.imshow(image_zx, extent=extent_zx, **imshow_style)
ax_zy.imshow(image_zy, extent=extent_zy, **imshow_style)
ax_xy.set_xlim(extent[0], extent[1], auto=False)
ax_xy.set_ylim(extent[3], extent[2], auto=False)
ax_zy.set_xlim(extent[4], extent[5], auto=False)
ax_zy.set_ylim(extent[3], extent[2], auto=False)
ax_zx.set_xlim(extent[0], extent[1], auto=False)
ax_zx.set_ylim(extent[5], extent[4], auto=False)
if ax_labels:
if mpp == 1.:
fmt = '{} [px]'
elif mpl.rcParams['text.usetex']:
fmt = r'{} [\textmu m]'
else:
fmt = r'{} [\xb5m]'
ax_xy.set_xlabel(fmt.format('x'))
ax_xy.set_ylabel(fmt.format('y'))
ax_zy.set_xlabel(fmt.format('z'))
ax_zx.set_ylabel(fmt.format('z'))
return axs
def imshow3d(image3d, mode='max', center=None, mpp=1.,
origin=(0, 0, 0), axs=None, ax_labels=False, **kwargs):
"""Shows the xy, xz, and yz projections of a 3D image.
Parameters
----------
image3d : ndarray
mode : {'max' | 'slice'}
aspect : number
aspect ratio of pixel size z / xy. Default 1.
center : tuple
in pixels
mpp : tuple
microns per pixel
origin : tuple
coordinate of the (center of the) topleft pixel (in pixels)
spacing : number
spacing between images
axs : t
Returns
-------
fig, (ax_xy, ax_zy, ax_zx, ax_extra)
"""
imshow_style = dict(origin='lower', interpolation='nearest',
cmap=plt.cm.gray, aspect='auto')
imshow_style.update(kwargs)
if not is_rgb(image3d, ndim=3):
try:
from pims import to_rgb
except ImportError:
raise ImportError("Imshow requires PIMS to display a non-RGB image")
image3d = to_rgb(image3d, kwargs.pop('colors', None), normed=False) / 255.
shape = image3d.shape[:3]
mpp = validate_tuple(mpp, ndim=3)
origin = validate_tuple(origin, ndim=3)
ax_xy, ax_zy, ax_zx, ax_extra = axs
if mode == 'max':
image_xy = image3d.max(0)
image_zx = image3d.max(1)
image_zy = image3d.max(2)
elif mode == 'slice':
center_i = [int(round(c - o)) for c, o in zip(center, origin)]
center_i = [min(max(c, 0), sh - 1) for c, sh in zip(center_i, shape)]
image_xy = image3d[center_i[0], :, :]
image_zx = image3d[:, center_i[1], :]
image_zy = image3d[:, :, center_i[2]]
else:
raise ValueError('Unknown mode "{}"'.format(mode))
if image_zy.ndim == 3:
image_zy = np.transpose(image_zy, (1, 0, 2))
else:
image_zy = image_zy.T
# extent is defined on the outer edges of the pixels
# we want the center of the topleft to intersect with the origin
extent = [(origin[2] - 0.5) * mpp[2],
(origin[2] + shape[2] - 0.5) * mpp[2],
(origin[1] - 0.5) * mpp[1],
(origin[1] + shape[1] - 0.5) * mpp[1],
(origin[0] - 0.5) * mpp[0],
(origin[0] + shape[0] - 0.5) * mpp[0]]
extent_xy = extent[:4]
extent_zx = extent[:2] + extent[4:6]
extent_zy = extent[4:6] + extent[2:4]
ax_xy.imshow(image_xy, extent=extent_xy, **imshow_style)
ax_zx.imshow(image_zx, extent=extent_zx, **imshow_style)
ax_zy.imshow(image_zy, extent=extent_zy, **imshow_style)
ax_xy.set_xlim(extent[0], extent[1], auto=False)
ax_xy.set_ylim(extent[3], extent[2], auto=False)
ax_zy.set_xlim(extent[4], extent[5], auto=False)
ax_zy.set_ylim(extent[3], extent[2], auto=False)
ax_zx.set_xlim(extent[0], extent[1], auto=False)
ax_zx.set_ylim(extent[5], extent[4], auto=False)
if ax_labels:
if mpp == 1.:
fmt = '{} [px]'
elif mpl.rcParams['text.usetex']:
fmt = r'{} [\textmu m]'
else:
fmt = r'{} [\xb5m]'
ax_xy.set_xlabel(fmt.format('x'))
ax_xy.set_ylabel(fmt.format('y'))
ax_zy.set_xlabel(fmt.format('z'))
ax_zx.set_ylabel(fmt.format('z'))
return axs
def array_to_pixmap(self, array):
array = np.swapaxes(pims.to_rgb(array), 0, 1)
image = pixmap_from_array(array)
return image
