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 load(self, ips):
self.slength = len(ips.imgs)
self.para['End image'] = self.slength
self.view = [(list, 'LUT', ColorManager.names(), str, 'LUT', ''),
(int, 'Start image', (1, self.slength), 0, 'Start image',
'1~%d' % self.slength),
(int, 'End image', (2, self.slength), 0, 'End image',
'start~%d' % self.slength),
(bool, 'Creatbar', 'Creat time color scale bar')]
return True
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
from ..lookuptables_plg import LUT from imagepy.app import ColorManager plgs = [LUT(i, j) for i, j, _ in ColorManager.gets(tag='adv')]
def __init__( self, parent, app=None):
wx.Panel.__init__ ( self, parent, id = wx.ID_ANY, pos = wx.DefaultPosition, size = wx.Size(-1,-1), style = wx.TAB_TRAVERSAL )
outsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer = wx.BoxSizer( wx.VERTICAL )
sizer_color = wx.BoxSizer( wx.HORIZONTAL )
self.app = app
self.btns = []
self.btn_make = wx.Button( self, wx.ID_ANY, 'New Mark', wx.DefaultPosition, wx.DefaultSize, 0 )
sizer_color.Add(self.btn_make, 0, wx.ALL, 2)
for i in range(11):
btn = wx.Button( self, wx.ID_ANY, str(i), wx.DefaultPosition, wx.DefaultSize, 0 )
btn.SetMaxSize( wx.Size( 30,-1 ) )
self.btns.append(btn)
sizer_color.Add( btn, 0, wx.ALL, 2 )
self.spn_num = wx.SpinCtrl( self, wx.ID_ANY, wx.EmptyString, wx.DefaultPosition, wx.DefaultSize, wx.SP_ARROW_KEYS, 2, 15, 0 )
self.spn_num.SetMaxSize(wx.Size(45, -1))
sizer_color.Add( self.spn_num, 0, wx.ALL|wx.EXPAND, 2 )
sizer.Add(sizer_color, 0, wx.ALL|wx.EXPAND, 0)
sizer_other = wx.BoxSizer( wx.HORIZONTAL )
self.btn_update = wx.Button( self, wx.ID_ANY, 'Update', wx.DefaultPosition, wx.DefaultSize, 0 )
sizer_other.Add( self.btn_update, 0, wx.ALL, 2)
self.cmapsel = CMapSelCtrl(self)
self.cmapsel.SetItems(ColorManager.gets(tag='base'))
sizer_other.Add(self.cmapsel, 0, wx.ALL|wx.EXPAND, 2 )
com_backChoices = [ u"No Background" ]
self.com_back = wx.ComboBox( self, wx.ID_ANY, u"No Background", wx.DefaultPosition, wx.DefaultSize, com_backChoices, wx.CB_READONLY)
self.com_back.SetSelection( 0 )
sizer_other.Add( self.com_back, 1, wx.ALL|wx.EXPAND, 2 )
com_modeChoices = [ u"None", u"Max", u"Min", u"Mask", u"2-8mix", u"4-6mix", u"5-5mix", u"6-4mix", u"8-2mix" ]
self.com_mode = wx.ComboBox( self, wx.ID_ANY, u"Min", wx.DefaultPosition, wx.DefaultSize, com_modeChoices, wx.CB_READONLY )
self.com_mode.SetSelection( 0 )
sizer_other.Add( self.com_mode, 0, wx.ALL|wx.EXPAND, 2 )
self.chk_hide = wx.CheckBox( self, wx.ID_ANY, u"Hide", wx.DefaultPosition, wx.DefaultSize, 0 )
sizer_other.Add( self.chk_hide, 0, wx.ALIGN_CENTER|wx.ALL, 0 )
sizer.Add(sizer_other, 0, wx.ALL|wx.EXPAND, 0)
#sizer_tol = wx.GridSizer( 0, 3, 0, 0 )
self.pens = []
name = ['01.gif','03.gif','05.gif','10.gif','fill.gif']
path = osp.abspath(osp.dirname(__file__))
for i in (0,1,2,3,4):
pen = wx.BitmapButton(self, wx.ID_ANY, make_bitmap(wx.Bitmap(osp.join(path, 'imgs', name[i]))),#make_bitmap(wx.Bitmap(data[1])),
wx.DefaultPosition, (30, 30), wx.BU_AUTODRAW|wx.RAISED_BORDER )
#wx.Button( self, wx.ID_ANY, str(i), wx.DefaultPosition, wx.DefaultSize, 0 )
pen.SetMaxSize( wx.Size( 30,-1 ) )
self.pens.append( pen )
sizer_color.Add( pen, 0, wx.ALL, 2 )
outsizer.AddStretchSpacer(prop=1)
#outsizer.Add(sizer_tol, 0, wx.ALL, 0)
outsizer.Add(sizer, 0, wx.ALL, 0)
outsizer.AddStretchSpacer(prop=1)
self.SetSizer( outsizer )
self.Layout()
# Connect Events
self.spn_num.Bind( wx.EVT_SPINCTRL, self.on_cmapsel )
self.com_back.Bind(wx.EVT_COMBOBOX_DROPDOWN, self.on_items )
self.cmapsel.Bind(wx.EVT_COMBOBOX, self.on_cmapsel)
self.com_back.Bind( wx.EVT_COMBOBOX, self.on_setback)
self.com_mode.Bind( wx.EVT_COMBOBOX, self.on_mode)
self.chk_hide.Bind( wx.EVT_CHECKBOX, self.on_mode)
self.pens[-1].Bind( wx.EVT_BUTTON, self.on_fill)
for i in self.btns: i.Bind(wx.EVT_BUTTON, self.on_color)
for i in range(4): self.pens[i].Bind(wx.EVT_BUTTON, \
lambda e, x=(1,3,5,10)[i]: self.on_pen(x))
self.btn_make.Bind( wx.EVT_BUTTON, self.on_make)
def on_color(self, event):
ColorManager.set_front(self.btns.index(event.GetEventObject()))