def applyTform_posList(from_pL, c):
tform_pL = posList(axis = None)
for index,pos in enumerate(from_pL.slicePositions):
#print index, pos
tform_x = c[1]*pos.x - c[0]*pos.y + c[2]
tform_y = c[1]*pos.y + c[0]*pos.x + c[3]
#print tform_x, tform_y
print "%d (x, y): (%f, %f) --> (%f, %f)" %(index, pos.x, pos.y, tform_x, tform_y)
tform_pL.add_position(tform_x,tform_y)
return tform_pL
def getPoints(file):
# read posList file & get datapoints
# return list of points as [[x1,y1],[x2,y2],...]
pL = posList(axis = None)
pL.add_from_file(file)
pt_list = []
for index,pos in enumerate(pL.slicePositions):
pt_list.append([pos.x,pos.y])
print ('%d\t[%f,%f]' %(index, pos.x, pos.y))
return pt_list
def __init__(self, parent, config, **kwargs):
"""keyword the same as standard init function for a FigureCanvas"""
self.figure = Figure(figsize=(5, 9))
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('white')
#add subplots for various things
self.subplot = self.figure.add_axes([.05,.5,.92,.5])
self.posone_plot = self.figure.add_axes([.1,.05,.2,.4])
self.postwo_plot = self.figure.add_axes([.37,.05,.2,.4])
self.corrplot = self.figure.add_axes([.65,.05,.25,.4])
#initialize the camera settings and mosaic settings
self.cfg=config
camera_settings=CameraSettings()
camera_settings.load_settings(config)
mosaic_settings=MosaicSettings()
mosaic_settings.load_settings(config)
#setup a blank position list
self.posList=posList(self.subplot,mosaic_settings,camera_settings)
#start with no MosaicImage
self.mosaicImage=None
#start with relative_motion on, so that keypress calls shift_selected_curved() of posList
self.relative_motion = True
#start with no toolbar and no lasso tool
self.navtoolbar = None
self.lasso = None
self.lassoLock=False
#make a sin plot just to see that things are working
#self.t = arange(0.0,3.0,0.01)
#s = sin(2*pi*self.t)
#self.subplot.plot(self.t,s)
self.canvas.mpl_connect('button_press_event', self.on_press)
self.canvas.mpl_connect('button_release_event', self.on_release)
self.canvas.mpl_connect('key_press_event', self.on_key)
def savePoints(tform_pt, file):
pL = posList(axis = None)
pL.save_position_list()
#TkFileDialogExample(root).pack()
#root.mainloop()
options = {}
options['defaultextension'] = '' # couldn't figure out how this works
options['filetypes'] = [('csv files', '.csv')]
options['initialdir'] = '/Users/SJSmith/Documents/Nick Local/data/ISI-Barrels/Ct1-ISI/R55/Imaging-Sessions'
options['initialfile'] = 'posList.csv'
#options['parent'] = root
#get input pList (ie. original template to be transformed from)
options['title'] = 'Select template PositionList file'
template_csv = tkFileDialog.askopenfilename(**options)
#template_pt = getPoints(template_csv)
template_pL = posList(axis = None)
template_pL.add_from_file(template_csv)
#get target pList (ie. new points from which to calculate transformation)
options['title'] = 'Select target PositionList file'
options['initialdir'] = os.path.split(template_csv)[0]
target_csv = tkFileDialog.askopenfilename(**options)
#target_pt = getPoints(target_csv)
target_pL = posList(axis = None)
target_pL.add_from_file(target_csv)
print "Calculating transformation of %s to %s" %(template_csv, target_csv)
#calculate coefficients
#c = rstTransform(template_pt, target_pt)
