forked from fcollman/MosaicPlannerLive
/
Transform.py
449 lines (381 loc) · 19.2 KB
/
Transform.py
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#===============================================================================
#
# License: GPL
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License 2
# as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#
#===============================================================================
import numpy as np
from numpy import sin, pi, cos, arctan, sin, tan, sqrt
from Point import Point
import wx.lib.intctrl
import wx.lib.agw.floatspin
import csv
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas
from matplotlib.figure import Figure
import PositionList
from matplotlib.lines import Line2D
import matplotlib.ticker as mticker
import matplotlib.transforms as mtransforms
class LooseMaxNLocator(mticker.MaxNLocator):
"""
Select no more than N intervals at nice locations with view
limits loosely fitted to the data. Unlike MaxNLocator, the
view limits do not necessarily coincide with tick locations.
"""
def __init__(self, margin = 0.0, **kwargs):
"""
Keyword arguments:
*margin*
Specifies the minimum size of both the lower and upper
margins (between the view limits and the data limits) as
a fraction of the data range. Must be non-negative.
Remaining keyword arguments are passed to MaxNLocator.
"""
mticker.MaxNLocator.__init__(self, **kwargs)
if margin < 0:
raise ValueError('The margin must be non-negative.')
self._margin = margin
def view_limits(self, dmin, dmax):
# begin partial duplication of MaxNLocator.view_limits
if self._symmetric:
maxabs = max(abs(dmin), abs(dmax))
dmin = -maxabs
dmax = maxabs
dmin, dmax = mtransforms.nonsingular(dmin, dmax, expander=0.05)
# end duplication
margin = self._margin * (dmax - dmin) # fraction of data range
vmin = dmin - margin # expand the view
vmax = dmax + margin
bin_boundaries = self.bin_boundaries(vmin, vmax)
# locate ticks with MaxNLocator
# Note: If the lines below change vmin or vmax, the bin boundaries
# later calculated by MaxNLocator.__call__ may differ from those
# calculated here.
vmin = min(vmin, max(bin_boundaries[bin_boundaries <= dmin]))
# expand view to the highest tick below or touching the data
vmax = max(vmax, min(bin_boundaries[bin_boundaries >= dmax]))
# expand view to the lowest tick above or touching the data
return np.array([vmin, vmax])
class Transform():
"""class for storing, applying and fitting linear transformations of 2d points"""
def __init__(self,matrix=None,disp_vector=None,flipVert=False,flipHoriz=False):
if not matrix == None:
self.T=matrix
else:
self.T=np.array([[1,0],[0,1]])
if not disp_vector == None:
self.D=disp_vector
else:
self.D=np.array([0,0])
self.flipVert=flipVert;
self.flipHoriz=flipHoriz;
def transform(self,x,y):
if self.flipVert:
y=-y
if self.flipHoriz:
x=-x
vec=np.array([x,y])
vec_t=np.dot(self.T,vec);
vec_t=vec_t+self.D;
# print "point from:"
# print (x,y)
# print "point to:"
# print (vec_t[0],vec_t[1])
return (vec_t[0],vec_t[1])
def save_settings(self,cfg):
print "saving_transformation"
print self.T
print self.D
cfg.WriteFloat('trans_M00',self.T[0][0])
cfg.WriteFloat('trans_M01',self.T[0][1])
cfg.WriteFloat('trans_M10',self.T[1][0])
cfg.WriteFloat('trans_M11',self.T[1][1])
cfg.WriteFloat('trans_D0',self.D[0])
cfg.WriteFloat('trans_D1',self.D[1])
cfg.WriteBool('trans_flipvert',self.flipVert)
cfg.WriteBool('trans_fliphoriz',self.flipHoriz)
def load_settings(self,cfg):
print "loading transform"
print self.T
print self.D
self.T[0,0]=cfg.ReadFloat('trans_M00',1.0)
self.T[0,1]=cfg.ReadFloat('trans_M01',0.0)
self.T[1,0]=cfg.ReadFloat('trans_M10',0.0)
self.T[1,1]=cfg.ReadFloat('trans_M11',1.0)
self.D[0]=cfg.ReadFloat('trans_D0',0.0)
self.D[1]=cfg.ReadFloat('trans_D1',0.0)
self.flipVert=cfg.ReadBool('trans_flipvert',False)
self.flipHoriz=cfg.ReadBool('trans_fliphoriz',False)
print self.T
print self.D
def set_transform_by_fit(self,from_pts,to_pts,mode='similarity',flipVert=False,flipHoriz=False):
"""set_transform_by_fit(x1,y1,x2,y2,mode='similarity')
keywords:
from_pts) a list of Point objects from the original space that correspond in a 1-1 way with the Points in to_pts
to_pts) a list of Point objects from the new space that correspond in a 1-1 way with the Points in from_pts
mode) whether these corresponding points should be fit using a 'translation','rigid','similarity' or 'affine' transformation
'translation' only shifts them in x and y
'rigid' does translation plus rotation
'similarity' does rigid plus a scaling factor which is equal in x and y
'affine' does a fully linear transformation
default is similarity
"""
self.flipVert=flipVert
self.flipHoriz=flipHoriz
if mode=='similarity':
# Fill the matrices
A_data = []
for pt in from_pts:
if flipVert:
y=-pt.y
else:
y=pt.y
if flipHoriz:
x=-pt.x
else:
x=pt.x
A_data.append( [-y, x, 1, 0] )
A_data.append( [ x, y, 0, 1] )
b_data = []
for pt in to_pts:
b_data.append(pt.x)
b_data.append(pt.y)
# Solve
A = np.matrix( A_data )
b = np.matrix( b_data ).T
c = np.linalg.lstsq(A, b)[0].T
c = np.array(c)[0]
print("Solved coefficients:")
print(c)
self.T=[[c[1],-c[0]],[c[0],c[1]]]
self.D=[c[2],c[3]]
if mode=='translation':
A_data = []
for pt in from_pts:
if flipVert:
y=-pt.y
else:
y=pt.y
if flipHoriz:
x=-pt.x
else:
x=pt.x
A_data.append( [1, 0] )
A_data.append( [0, 1] )
b_data = []
for index,pt in enumerate(to_pts):
if flipVert:
y=-from_pts[index].y
else:
y=from_pts[index].y
if flipHoriz:
x=-from_pts[index].x
else:
x=from_pts[index].x
b_data.append(pt.x-x)
b_data.append(pt.y-y)
A = np.matrix( A_data )
b = np.matrix( b_data ).T
c = np.linalg.lstsq(A, b)[0].T
c = np.array(c)[0]
self.T=[[1,0],[0,1]]
self.D=[c[0],c[1]]
class TransformCanvasPanel(FigureCanvas):
"""A panel that extends the matplotlib class FigureCanvas for plotting the corresponding points from the two coordinate systems, and their transforms"""
def __init__(self, parent, **kwargs):
"""keyword the same as standard init function for a FigureCanvas"""
self.figure = Figure(figsize=(6,4))
FigureCanvas.__init__(self, parent, -1, self.figure, **kwargs)
self.canvas = self.figure.canvas
#format the appearance
self.figure.set_facecolor((1,1,1))
self.figure.set_edgecolor((1,1,1))
self.canvas.SetBackgroundColour('black')
#add subplots for various things
self.fromplot = self.figure.add_axes([.05,.05,.45,.92])
self.toplot = self.figure.add_axes([.55,.05,.45,.92])
self.fromplot.set_axis_bgcolor('black')
self.toplot.set_axis_bgcolor('black')
self.fromplot.yaxis.set_major_locator(LooseMaxNLocator(nbins=5,margin=.125))
self.fromplot.xaxis.set_major_locator(LooseMaxNLocator(nbins=5,margin=.125))
#self.toplot.yaxis.set_major_locator(LooseMaxNLocator(nbins=5,margin=.0125))
#self.toplot.xaxis.set_major_locator(LooseMaxNLocator(nbins=5,margin=.0125))
def plot_points_in_from(self,xx,yy,color='black'):
self.from_points=Line2D(xx,yy,marker='x',markersize=7,markeredgewidth=1.5,markeredgecolor=color)
self.fromplot.add_line(self.pointLine2D)
def plot_trans_points(self,xx,yy,color='black'):
self.trans_points=Line2D(xx,yy,marker='x',markersize=7,markeredgewidth=1.5,markeredgecolor=color)
self.toplot.add_line(self.trans_points)
for i in range(len(xx)):
numTxt = self.toplot.text(xx[i],yy[i],str(i)+" ",color='g',weight='bold')
numTxt.set_visible(True)
numTxt.set_horizontalalignment('left')
self.toplot.relim()
self.toplot.autoscale_view()
self.draw()
class ChangeTransform(wx.Dialog):
"""simple dialog for changing the camera settings"""
def initold(self, parent, id, title, transform=None):
wx.Dialog.__init__(self, parent, id, title, size=(600, 120))
panel = wx.Panel(self, -1)
vbox = wx.BoxSizer(wx.VERTICAL)
self.corresp_label=wx.StaticText(self,id=wx.ID_ANY,label="Correspondance file")
self.corresp_filepicker=wx.FilePickerCtrl(self,message='Select file with corresponding points list (xf0,yf0,xt0,yt0 \\n xf1,yf1,xt1,yt1\n ...)',\
path="",name='correspondancePicker',\
style=wx.FLP_USE_TEXTCTRL, size=wx.Size(200,20),wildcard='*.csv')
self.corresp_load_button=wx.Button(self,id=wx.ID_ANY,label="Load",name="load correspondance files")
hbox = wx.BoxSizer(wx.HORIZONTAL)
hbox.Add(self.corresp_label,1)
hbox.Add(self.corresp_filepicker,4, wx.EXPAND)
hbox.Add(self.corresp_load_button, 1, wx.EXPAND)
self.transtypeBox=wx.ComboBox(self,id=wx.ID_ANY,value='similarity', size=wx.DefaultSize,
choices=['similarity','rigid','translation','affine'], name='Transformation Type Name')
self.transtypeBox.SetEditable(False)
self.flipHoriz = wx.CheckBox(self)
self.flipVert = wx.CheckBox(self)
self.flipHoriz.SetValue(False)
self.flipVert.SetValue(False)
hbox2 = wx.BoxSizer(wx.HORIZONTAL)
hbox2.Add(wx.StaticText(self,id=wx.ID_ANY,label="Transformation Type:"))
hbox2.Add(self.transtypeBox,border=5);
hbox2.Add(wx.StaticText(self,id=wx.ID_ANY,label="Vertical flip:"))
hbox2.Add(self.flipVert)
hbox2.Add(wx.StaticText(self,id=wx.ID_ANY,label="Horizontal flip:"))
hbox2.Add(self.flipHoriz)
#vbox.Add(hbox,1,wx.EXPAND)
vbox.Add(hbox, 1, wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, 10)
vbox.Add(hbox2,1, wx.ALIGN_RIGHT,5)
self.SetSizer(vbox)
self.Bind(wx.EVT_BUTTON, self.OnCorrespLoad,self.corresp_load_button)
def __init__(self, parent, id, title, transform=None):
wx.Dialog.__init__(self, parent, id, title, size=(640, 490))
panel = wx.Panel(self, -1)
vbox = wx.BoxSizer(wx.VERTICAL)
#define the array picker components for the from array
self.fromarray_label=wx.StaticText(self,id=wx.ID_ANY,label="posList from:")
self.fromarray_filepicker=wx.FilePickerCtrl(self,message='Select an position list containing points in the original coordinate space',\
path="",name='arrayFilePickerCtrl1',\
style=wx.FLP_USE_TEXTCTRL, size=wx.Size(300,100),wildcard='*.*')
self.fromarray_load_button=wx.Button(self,id=wx.ID_ANY,label="Load",name="load button")
self.fromarray_formatBox=wx.ComboBox(self,id=wx.ID_ANY,value='AxioVision',\
size=wx.DefaultSize,choices=['AxioVision','SmartSEM','OMX'], name='File Format For Position List')
self.fromarray_formatBox.SetEditable(False)
#define a horizontal sizer for them and place the file picker components in there
self.hbox1=wx.BoxSizer(wx.HORIZONTAL)
self.hbox1.Add(self.fromarray_label,0)
self.hbox1.Add(self.fromarray_filepicker,1)
self.hbox1.Add(wx.StaticText(self,id=wx.ID_ANY,label="Format:"))
self.hbox1.Add(self.fromarray_formatBox,0)
self.hbox1.Add(self.fromarray_load_button,0)
#define the array picker components for the to array
self.toarray_label=wx.StaticText(self,id=wx.ID_ANY,label="posList to:")
self.toarray_filepicker=wx.FilePickerCtrl(self,message='Select an position list containing points in the new coordinate space',\
path="",name='arrayFilePickerCtrl1',\
style=wx.FLP_USE_TEXTCTRL, size=wx.Size(300,100),wildcard='*.*')
self.toarray_load_button=wx.Button(self,id=wx.ID_ANY,label="Load",name="load button")
self.toarray_formatBox=wx.ComboBox(self,id=wx.ID_ANY,value='AxioVision',\
size=wx.DefaultSize,choices=['AxioVision','SmartSEM','OMX'], name='File Format For Position List')
self.toarray_formatBox.SetEditable(False)
#define a horizontal sizer for them and place the file picker components in there
self.hbox2=wx.BoxSizer(wx.HORIZONTAL)
self.hbox2.Add(self.toarray_label,0)
self.hbox2.Add(self.toarray_filepicker,1)
self.hbox2.Add(wx.StaticText(self,id=wx.ID_ANY,label="Format:"))
self.hbox2.Add(self.toarray_formatBox,0)
self.hbox2.Add(self.toarray_load_button,0)
#options for the transformation
self.fit_transform_button=wx.Button(self,id=wx.ID_ANY,label="FitTransform",name="Fit correspondances to transform")
self.transtypeBox=wx.ComboBox(self,id=wx.ID_ANY,value='similarity', size=wx.DefaultSize, choices=['similarity','rigid','translation','affine'], name='Transformation Type Name')
self.transtypeBox.SetEditable(False)
self.flipHoriz = wx.CheckBox(self)
self.flipVert = wx.CheckBox(self)
self.flipHoriz.SetValue(False)
self.flipVert.SetValue(False)
self.hbox3 = wx.BoxSizer(wx.HORIZONTAL)
self.hbox3.Add(wx.StaticText(self,id=wx.ID_ANY,label="Transformation Type:"))
self.hbox3.Add(self.transtypeBox,border=5);
self.hbox3.Add(wx.StaticText(self,id=wx.ID_ANY,label="Vertical flip:"))
self.hbox3.Add(self.flipVert)
self.hbox3.Add(wx.StaticText(self,id=wx.ID_ANY,label="Horizontal flip:"))
self.hbox3.Add(self.flipHoriz)
self.hbox3.Add(self.fit_transform_button)
#vbox.Add(hbox,1,wx.EXPAND)
self.transformCanvas=TransformCanvasPanel(self)
vbox = wx.BoxSizer(wx.VERTICAL)
vbox.Add(self.hbox1, 0, wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, 5)
vbox.Add(self.hbox2, 0, wx.ALIGN_CENTER | wx.TOP | wx.BOTTOM, 5)
vbox.Add(self.hbox3,0, wx.ALIGN_RIGHT,5)
vbox.Add(self.transformCanvas,1,wx.EXPAND,10)
self.SetSizer(vbox)
self.Bind(wx.EVT_BUTTON, self.OnFitTransform,self.fit_transform_button)
self.Bind(wx.EVT_BUTTON, self.OnFromLoad,self.fromarray_load_button)
self.Bind(wx.EVT_BUTTON, self.OnToLoad,self.toarray_load_button)
self.posListFrom=PositionList.posList(self.transformCanvas.fromplot,shownumbers=True)
self.posListTo=PositionList.posList(self.transformCanvas.toplot,shownumbers=True)
self.transform=Transform()
def OnFitTransform(self,evt):
fromPts=self.posListFrom.getXYpoints()
toPts=self.posListTo.getXYpoints()
transType=self.transtypeBox.GetValue()
flipVert=self.flipVert.GetValue()
flipHoriz=self.flipHoriz.GetValue()
self.transform.set_transform_by_fit(fromPts,toPts,mode=transType,flipVert=flipVert,flipHoriz=flipHoriz)
xxt=[]
yyt=[]
#self.posListTrans=PositionList.posList(self.transformCanvas.toplot,shownumbers=True)
for index,pt in enumerate(fromPts):
(xt,yt)=self.transform.transform(pt.x,pt.y)
xxt.append(xt)
yyt.append(yt)
#self.posListTrans.add_position(xt,yt,edgecolor='g',withpoint=True,selected=True)
print "to points:"
print (toPts[index].x,toPts[index].y)
print "trans points:"
print (xt,yt)
print "from points:"
print (pt.x,pt.y)
self.transformCanvas.plot_trans_points(xxt,yyt,color='g')
# def OnCorrespLoad(self,evt):
# filename=self.corresp_filepicker.GetPath()
# coorespReader = csv.reader(open(filename, 'rb'), delimiter=',', quotechar='#')
# headerline = coorespReader.next()
# pts_from=[]
# pts_to=[]
# for row in coorespReader:
# if len(row)==4:
# (xf,yf,xt,yt)=row
# print row
# pts_from.append(Point(float(xf),float(yf)))
# pts_to.append(Point(float(xt),float(yt)))
# self.pts_from=pts_from
# self.pts_to=pts_to
def OnFromLoad(self,evt):
"""event handler for the array load button"""
format=self.fromarray_formatBox.GetValue()
file=self.fromarray_filepicker.GetPath()
self.posListFrom.LoadFromFile(file,format)
self.transformCanvas.fromplot.relim()
self.transformCanvas.fromplot.autoscale_view()
self.transformCanvas.draw()
def OnToLoad(self,evt):
"""event handler for the array load button"""
format=self.toarray_formatBox.GetValue()
file=self.toarray_filepicker.GetPath()
self.posListTo.LoadFromFile(file,format)
self.transformCanvas.toplot.relim()
self.transformCanvas.toplot.autoscale_view()
self.transformCanvas.draw()
def getTransform(self):
return self.transform