def run(self, ips, imgs, para=None):
cmap = ColorManager.get(para['LUT'])
imglut = color_code(imgs[para['Start image'] - 1:para['End image']],
cmap)
self.app.show_img([imglut], 'Color-coded %s' % ips.title)
if para['Creatbar']:
cmapshow = np.ones([32, 256, 3]) * cmap
self.app.show_img([cmapshow.astype('uint8')], 'Color bar')
def on_cmapsel(self, event): key = self.cmapsel.GetValue() lut = ColorManager.get(key) n = self.spn_num.GetValue()+1 idx = np.linspace(0, 255, n).astype(int) self.cs = list(lut[idx]) + [(128,128,128)]*(16-n) for btn, c in zip(self.btns, self.cs): btn.SetBackgroundColour(c) ips = self.app.get_img() if ips is None: return newlut = lut*0 newlut[:n] = lut[idx] ips.lut = newlut ips.update()
def run(self, ips, imgs, para=None):
shp = ips.img.shape[:2]
imgs = [
np.zeros(shp, dtype=np.uint8)
for i in range([1, len(imgs)][para['slice']])
]
newips = ImagePlus(imgs, ips.title + '-mark')
newips.back = ips
idx = [
'None', 'Max', 'Min', 'Mask', '2-8mix', '4-6mix', '5-5mix',
'6-4mix', '8-2mix'
]
modes = ['set', 'max', 'min', 'msk', 0.2, 0.4, 0.5, 0.6, 0.8]
newips.lut = ColorManager.get(para['cm'])
newips.chan_mode = modes[idx.index(para['mode'])]
#newips.range = (0, para['n'])
IPy.show_ips(newips)
def run(self, tps, snap, data, para=None):
rs = data[
para['rs']] * para['s'] if para['rs'] != 'None' else para['s']
cs = data[para[
'cs']] if para['cs'] != 'None' else '#%.2x%.2x%.2x' % para['c']
cm = ColorManager.get(para['cm']) / 255.0
cm = None if para['cs'] == 'None' else colors.ListedColormap(cm, N=256)
plt = self.app.show_plot(para['title'])
data.plot.scatter(x=para['x'],
y=para['y'],
s=rs,
c=cs,
alpha=para['alpha'],
cmap=cm,
grid=para['grid'],
title=para['title'],
ax=plt.add_subplot())
plt.Show()
def run(self, ips, snap, img, para = None):
strc = generate_binary_structure(2, 1 if para['con']=='4-connect' else 2)
lab, n = label(snap, strc, output=np.uint32)
idx = (np.zeros(n+1)).astype(np.uint8)
ls = regionprops(lab)
if para['pro'] == 'area': ps = [i.area for i in ls]
if para['pro'] == 'perimeter': ps = [i.perimeter for i in ls]
if para['pro'] == 'solid': ps = [i.solidity for i in ls]
if para['pro'] == 'eccentricity': ps = [i.major_axis_length/i.minor_axis_length for i in ls]
ps = np.array(ps)
if ps.max() != ps.min():
ps = (ps - ps.min()) / (ps.max() - ps.min())
else: ps = ps / ps.max()
idx[1:] = ps * 245 + 10
img[:] = idx[lab]
ips.lut = ColorManager.get(para['cm'])
def run(self, tps, snap, data, para=None):
pts = np.array(data[[para['x'], para['y'], para['z']]])
rs = data[para['rs']] * para['r'] if para['rs'] != 'None' else [
para['r']
] * len(pts)
cm = ColorManager.get(para['cm']) / 255.0
clip = lambda x: (x - x.min()) / (x.max() - x.min()) * 255
if para['cs'] == 'None': cs = [np.array(para['c']) / 255.0] * len(pts)
else: cs = cm[clip(data[para['cs']]).astype(np.uint8)]
vts, fs, ns, cs = myvi.build_balls(pts.astype(np.float32), list(rs),
cs)
self.frame.viewer.add_surf_asyn('ball', vts, fs, ns, cs)
if para['cube']:
p1 = data[[para['x'], para['y'], para['z']]].min(axis=0)
p2 = data[[para['x'], para['y'], para['z']]].max(axis=0)
vts, fs, ns, cs = myvi.build_cube(p1, p2)
self.frame.viewer.add_surf_asyn('cube',
vts,
fs,
ns,
cs,
mode='grid')
self.frame.Raise()
self.frame = None