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2dgui_logic.py
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2dgui_logic.py
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from PyQt4 import QtCore,QtGui
import sys, os, time
import the2dgui
import numpy as np
from util_2d import *
from util_misc import *
import matplotlib.cm as cm
from matplotlib.patches import Rectangle
class the2dlogic(QtGui.QMainWindow,the2dgui.Ui_MainWindow):
def __init__(self,parent=None,app=None):
"""
Initialization of the class. Call the __init__ for the super classes
"""
super(the2dlogic,self).__init__(parent)
self.setupUi(self)
self.connectActions()
self.spefiles = []
self.m = None
self.pwd = os.path.dirname(os.path.abspath(__file__))
self.optical_element = 'Polarizer'
self.which_setup = self.whichSetupComboBox.currentIndex()
self.setup_list = ['old setup','new setup','cool new setup']
self.phase_offset = self.phaseOffsetLineEdit.text().toDouble()[0]
self.current_spot = None
self.app = app
def keyPressEvent(self, event):
if event.key()==QtCore.Qt.Key_Up:
self.move_crosshairs('up')
if event.key()==QtCore.Qt.Key_Down:
self.move_crosshairs('down')
if event.key()==QtCore.Qt.Key_Left:
self.move_crosshairs('left')
if event.key()==QtCore.Qt.Key_Right:
self.move_crosshairs('right')
def move_crosshairs( self, direction ):
x = self.imageview.crosshairs_x
y = self.imageview.crosshairs_y
if not self.current_spot==None:
if direction=='up' or direction=='down':
delta = self.m.spots[self.current_spot].height
elif direction=='left' or direction=='right':
delta = self.m.spots[self.current_spot].width
else:
print 'whoa?'
else:
delta = 1
if direction=='up':
y -= delta
elif direction=='down':
y += delta
elif direction=='left':
x -= delta
elif direction=='right':
x += delta
x = np.clip(x,0,self.m.camera_data.datasize[1])
y = np.clip(y,0,self.m.camera_data.datasize[2])
self.imageview.crosshairs_x = x
self.imageview.crosshairs_y = y
self.crosshair_pick()
def crosshair_pick(self):
x = self.imageview.crosshairs_x
y = self.imageview.crosshairs_y
print 'x0=%f\ty0=%f' % (x,y)
sys.stdout.flush()
self.current_spot = None
if (not self.m==None) and hasattr(self.m,'spots'):
# find the spot which covers these coordinates
for si,s in enumerate(self.m.spots):
if (s.coords[0] <= x) and (s.coords[0]+s.width > x):
if (s.coords[1] <= y) and (s.coords[1]+s.height > y):
self.current_spot = si
x = s.coords[0]+.5*s.width
y = s.coords[1]+.5*s.height
print 'picked spot #%d' % si
sys.stdout.flush()
break
self.imageview.crosshairs_x = x
self.imageview.crosshairs_y = y
self.imageview.hline.set_ydata( np.array([y,y]) )
self.imageview.vline.set_xdata( np.array([x,x]) )
self.imageview.figure.canvas.restore_region(self.imageview.blitbackground)
# self.imageview.figure.canvas.draw()
self.imageview.axes.draw_artist(self.imageview.hline)
self.imageview.axes.draw_artist(self.imageview.vline)
self.imageview.figure.canvas.blit(self.imageview.axes.bbox)
self.dataview_updater()
self.spotInfo_updater()
def main(self):
self.show()
def connectActions(self):
"""Connect the user interface controls to the logic """
self.selectDataDirPushButton.clicked.connect( self.selectDataDir )
self.phaseOffsetLineEdit.editingFinished.connect( self.setPhaseOffset )
self.whichSetupComboBox.activated.connect( self.setWhichSetup )
self.selectSPEComboBox.activated.connect( self.selectSPE )
self.setBGSpotPushButton.clicked.connect( self.setBGSpot )
self.addSignalSpotPushButton.clicked.connect( self.addSignalSpot )
self.createSpotArrayPushButton.clicked.connect( self.createSpotArray )
self.clearAllSpotsPushButton.clicked.connect( self.clearAllSpots )
self.initAnalysisPushButton.clicked.connect( self.initAnalysis )
self.checkSpotValidityPushButton.clicked.connect( self.checkSpotValidity )
self.centralwidget.keyPressEvent = self.keyPressEvent
self.cosineFitPushButton.clicked.connect( self.cosineFit )
self.findModDepthsPushButton.clicked.connect( self.findModDepths )
self.showStuffComboBox.activated.connect( self.showStuff )
self.ETrulerPushButton.clicked.connect( self.ETruler )
self.showWhatComboBox.activated.connect( self.dataview_updater )
self.saveContrastImagesPushButton.clicked.connect( self.saveContrastImages )
self.toolButton1.clicked.connect( self.tool1 )
self.toolButton2.clicked.connect( self.tool2 )
self.toolButton3.clicked.connect( self.tool3 )
def tool3(self):
self.tool2()
self.findModDepths()
time.sleep(.1)
def tool2(self):
self.tool1()
self.cosineFit()
time.sleep(.1)
def tool1(self):
self.initAnalysis()
time.sleep(.1)
self.checkSpotValidity()
time.sleep(.1)
def tryToUpdateFile( self, basefilename, what ):
filename = basefilename+'_'+what+'_image.txt'
# if the file exists, try loading and updating it
if os.path.isfile(filename):
try:
sc = np.loadtxt(filename)
except IOError:
sc = getattr(self.m, what+'_image')
# where the current image is not nan, update the old image
new_value_indices = ~np.isnan( getattr(self.m, what+'_image') )
sc[new_value_indices] = getattr(self.m, what+'_image')[new_value_indices]
np.savetxt( filename, sc )
else:
np.savetxt( filename, getattr(self.m, what+'_image') )
def saveContrastImages( self ):
basefilename = self.data_directory + '/' + self.spefiles[self.selectSPEComboBox.currentIndex()][:-4]
self.tryToUpdateFile( basefilename, 'spot_coverage' )
self.tryToUpdateFile( basefilename, 'M_ex' )
self.tryToUpdateFile( basefilename, 'M_em' )
self.tryToUpdateFile( basefilename, 'phase_ex' )
self.tryToUpdateFile( basefilename, 'phase_em' )
self.tryToUpdateFile( basefilename, 'LS' )
self.tryToUpdateFile( basefilename, 'ET_ruler' )
self.tryToUpdateFile( basefilename, 'ET_model_md_fu' )
self.tryToUpdateFile( basefilename, 'ET_model_th_fu' )
self.tryToUpdateFile( basefilename, 'ET_model_gr' )
self.tryToUpdateFile( basefilename, 'ET_model_et' )
# np.savetxt( basefilename+'_M_em_image.txt', self.m.M_em_image )
# np.savetxt( basefilename+'_phase_ex_image.txt', self.m.phase_ex_image )
# np.savetxt( basefilename+'_phase_em_image.txt', self.m.phase_em_image )
# np.savetxt( basefilename+'_LS_image.txt', self.m.LS_image )
# np.savetxt( basefilename+'_ET_ruler_image.txt', self.m.ET_ruler_image )
# np.savetxt( basefilename+'_ET_model_md_fu_image.txt', self.m.ET_model_md_fu_image )
# np.savetxt( basefilename+'_ET_model_th_fu_image.txt', self.m.ET_model_th_fu_image )
# np.savetxt( basefilename+'_ET_model_gr_image.txt', self.m.ET_model_gr_image )
# np.savetxt( basefilename+'_ET_model_et_image.txt', self.m.ET_model_et_image )
self.saveContrastImagesPushButton.setChecked(False)
def ETruler(self):
oldtext = self.setButtonWait( self.ETrulerPushButton )
self.imageview.ET_ruler_rects = []
self.m.ETrulerFFT()
# ruler = []
# for s in self.m.validspots:
# ruler.append(s.ET_ruler)
for s in self.m.validspots:
color = cm.jet(s.ET_ruler)
r = Rectangle( (s.coords[0],s.coords[1]), s.width, s.height, \
facecolor=color, edgecolor=color, alpha=1, zorder=7 )
self.imageview.ET_ruler_rects.append( r )
self.setButtonWait( self.ETrulerPushButton, oldtext )
def showStuff(self):
what = self.showStuffComboBox.currentIndex()
if what==0: # spots
self.imageview.show_stuff( what='spots' )
elif what==1: # M_ex
self.imageview.show_stuff( what='M_ex' )
# self.imageview.cbar.
elif what==2: # M_em
self.imageview.show_stuff( what='M_em' )
elif what==3: # phase_ex
self.imageview.show_stuff( what='phase_ex' )
elif what==4: # phase_ex
self.imageview.show_stuff( what='phase_em' )
elif what==5: # ET_ruler
self.imageview.show_stuff( what='ET_ruler' )
def findModDepths(self):
oldtext = self.setButtonWait( self.findModDepthsPushButton )
self.imageview.M_ex_rects = []
self.imageview.M_em_rects = []
self.imageview.phase_ex_rects = []
self.imageview.phase_em_rects = []
self.m.find_modulation_depths_and_phases()
for s in self.m.validspots:
color = cm.jet(s.M_ex)
r = Rectangle( (s.coords[0],s.coords[1]), s.width, s.height, \
facecolor=color, edgecolor=color, alpha=1, zorder=7 )
self.imageview.M_ex_rects.append( r )
color = cm.jet(s.M_em)
r = Rectangle( (s.coords[0],s.coords[1]), s.width, s.height, \
facecolor=color, edgecolor=color, alpha=1, zorder=7 )
self.imageview.M_em_rects.append( r )
color = cm.jet(s.phase_ex/np.pi+.5)
r = Rectangle( (s.coords[0],s.coords[1]), s.width, s.height, \
facecolor=color, edgecolor=color, alpha=1, zorder=7 )
self.imageview.phase_ex_rects.append( r )
color = cm.jet(s.phase_em/np.pi+.5)
r = Rectangle( (s.coords[0],s.coords[1]), s.width, s.height, \
facecolor=color, edgecolor=color, alpha=1, zorder=7 )
self.imageview.phase_em_rects.append( r )
# self.imageview.axes.add_patch( self.imageview.spot_rects[-1] )
# self.imageview.show_stuff( what='M_ex' )
self.imageview.show_stuff(what='M_ex')
self.showStuffComboBox.setCurrentIndex(1)
self.unsetButtonWait( self.findModDepthsPushButton, oldtext)
def setButtonWait( self, button ):
oldtext = button.text()
button.setText('wait')
button.setStyleSheet('QPushButton {color: red}')
self.app.processEvents()
return oldtext
def unsetButtonWait( self, button, oldtext ):
button.setText( oldtext )
button.setStyleSheet('')
self.app.processEvents()
def cosineFit(self):
oldtext = self.setButtonWait( self.cosineFitPushButton )
self.m.excitation_angles_grid = np.linspace( 0, np.pi, self.NanglesSpinBox.value() )
self.m.emission_angles_grid = np.linspace( 0, np.pi, self.NanglesSpinBox.value() )
self.m.fit_all_portraits_spot_parallel()
self.unsetButtonWait( self.cosineFitPushButton, oldtext )
def checkSpotValidity(self):
oldtext = self.setButtonWait( self.checkSpotValidityPushButton )
self.m.are_spots_valid( SNR=self.SNRSpinBox.value() )
# reset color back to red
for r in self.imageview.spot_rects:
r.set_facecolor('red')
# turn valid spots back on green
for vsi in self.m.validspotindices:
self.imageview.spot_rects[vsi].set_facecolor('green')
self.imageview.spot_rects[vsi].set_edgecolor('green')
# self.imageview.figure.canvas.draw()
self.imageview.show_stuff(what='spots')
self.unsetButtonWait( self.checkSpotValidityPushButton, oldtext )
def initAnalysis(self):
oldtext = self.setButtonWait( self.initAnalysisPushButton )
self.m.collect_data()
self.m.startstop()
self.m.assign_portrait_data()
self.initAnalysisPushButton.setChecked(False)
self.unsetButtonWait( self.initAnalysisPushButton, oldtext )
def createSpotArray(self):
oldtext = self.setButtonWait( self.createSpotArrayPushButton )
res = self.spotEdgeLengthSpinBox.value()
coords = np.round( np.array( [self.imageview.x0, self.imageview.y0, \
self.imageview.x1, self.imageview.y1] ) ).astype(np.int)
if coords[0]>coords[2]:
coords[0],coords[2]=coords[2],coords[0]
if coords[1]>coords[3]:
coords[1],coords[3]=coords[3],coords[1]
# how many spots do we have already?
nspotsbefore = len(self.m.spots)
print nspotsbefore
# now add spots
grid_image_section_into_squares_and_define_spots( self.m, res, coords )
# now populate that list
for s in self.m.spots[nspotsbefore:]:
r = Rectangle( (s.coords[0],s.coords[1]), s.width, s.height, \
facecolor='red', edgecolor='red', alpha=.3, zorder=7 )
self.imageview.spot_rects.append( r )
self.imageview.axes.add_patch( self.imageview.spot_rects[-1] )
# reset selection rectangle
self.imageview.rect.set_xy((0,0))
self.imageview.rect.set_width(0)
self.imageview.rect.set_height(0)
self.imageview.figure.canvas.draw()
self.imageview.show_stuff()
self.unsetButtonWait( self.createSpotArrayPushButton, oldtext )
def setBGSpot(self):
coords = np.round( np.array( [self.imageview.x0, self.imageview.y0, \
self.imageview.x1, self.imageview.y1] ) ).astype(np.int)
if coords[0]>coords[2]:
coords[0],coords[2]=coords[2],coords[0]
if coords[1]>coords[3]:
coords[1],coords[3]=coords[3],coords[1]
# self.bg_region_coords = coords
self.imageview.bg_rect.set_xy((coords[0],coords[1]))
self.imageview.bg_rect.set_width(coords[2]-coords[0])
self.imageview.bg_rect.set_height(coords[3]-coords[1])
# reset selection rectangle
self.imageview.rect.set_xy((0,0))
self.imageview.rect.set_width(0)
self.imageview.rect.set_height(0)
# update canvas
self.imageview.figure.canvas.draw()
self.imageview.show_stuff()
self.m.define_background_spot( coords, intensity_type='mean' )
def addSignalSpot(self):
coords = np.round( np.array( [self.imageview.x0, self.imageview.y0, \
self.imageview.x1, self.imageview.y1] ) ).astype(np.int)
if coords[0]>coords[2]:
coords[0],coords[2]=coords[2],coords[0]
if coords[1]>coords[3]:
coords[1],coords[3]=coords[3],coords[1]
r = Rectangle( (coords[0],coords[1]), coords[2]-coords[0], \
coords[3]-coords[1], facecolor='green', edgecolor='green', alpha=.3, zorder=8 )
self.imageview.spot_rects.append( r )
self.imageview.axes.add_patch( self.imageview.spot_rects[-1] )
# reset selection rectangle
self.imageview.rect.set_xy((0,0))
self.imageview.rect.set_width(0)
self.imageview.rect.set_height(0)
# update canvas
self.imageview.figure.canvas.draw()
self.m.define_spot( coords, intensity_type='mean' )
def clearAllSpots(self):
for r in self.imageview.spot_rects:
r.remove()
self.imageview.spot_rects = []
self.m.spots = []
self.m.initContrastImages()
self.imageview.figure.canvas.draw()
def dataview_updater(self):
if not self.current_spot==None:
showWhat = self.showWhatComboBox.currentIndex()
if showWhat==0: # intensity trace
if hasattr(self.m.spots[self.current_spot], 'intensity'):
# print 'showing intensity trace'
self.dataview.clear()
self.dataview.figure.canvas.draw()
self.dataview.axes.plot( self.m.spots[self.current_spot].intensity, 'bx-' )
self.dataview.figure.canvas.draw()
elif showWhat==1: # portrait data
if hasattr(self.m.spots[self.current_spot], 'portraits'):
# print 'showing portrait data'
self.dataview.clear()
self.dataview.figure.canvas.draw()
# collect all intensities
Nemangles = np.unique(self.m.spots[self.current_spot].portraits[0].emangles).size
print self.m.spots[self.current_spot].portraits[0].emangles
allints = np.array([])
for l in self.m.spots[self.current_spot].portraits[0].lines:
allints = np.hstack( (allints,l.intensities) )
maxint = np.max(allints)
scaler = 180.0/Nemangles/2/maxint
for p in self.m.spots[self.current_spot].portraits:
for l in p.lines:
self.dataview.axes.plot( l.exangles, 180/np.pi*l.emangle + scaler*l.intensities, 'bx:' )
self.dataview.axes.fill_between( l.exangles, \
180/np.pi*l.emangle + scaler*l.intensities, \
180/np.pi*l.emangle*np.ones_like(l.intensities), \
facecolor='b', alpha=.4 )
print np.min(l.intensities),' --- ',np.max(l.intensities)
self.dataview.figure.canvas.draw()
elif showWhat==2: # portrait fit
print 'yup'
self.dataview.clear()
self.dataview.figure.canvas.draw()
i=self.dataview.axes.imshow( self.m.spots[self.current_spot].recover_average_portrait_matrix(),\
origin='lower', interpolation='nearest' )
self.dataview.axes.set_position( [.25,.1,.62,.62] )
axis_proj_em = self.dataview.fig.add_axes([.05,.1,.2,.62])
axis_proj_ex = self.dataview.fig.add_axes([.25,.1+.62,.62,.2])
axis_proj_em.plot( self.m.spots[self.current_spot].proj_em, self.m.emission_angles_grid )
axis_proj_em.set_xlim( xmin=np.max(axis_proj_em.get_xlim()), xmax=0 )
[ label.set_rotation(90) for label in axis_proj_em.get_xticklabels() ]
axis_proj_ex.plot( self.m.excitation_angles_grid, self.m.spots[self.current_spot].proj_ex )
axis_proj_ex.set_ylim( ymin=0, ymax=np.max(axis_proj_ex.get_ylim()) )
self.dataview.figure.canvas.draw()
# print dir(self.m.spots[self.current_spot])
else:
self.dataview.clear()
self.dataview.figure.canvas.draw()
def spotInfo_updater(self):
# is this a valid spot?
isvalid = False
s = self.m.spots[self.current_spot]
if hasattr(self.m, 'validspotindices'):
if self.m.validspotindices.count( self.current_spot )>0:
isvalid = True
# prepare info
infostring = "area=( %d--%d, %d--%d )<br>" % (s.coords[0],s.coords[0]+s.width, \
s.coords[1],s.coords[1]+s.height)
if hasattr(s,'SNR'):
if isvalid:
infostring += 'SNR = <font color="#00ff00">%f</font> <br>' % s.SNR
else:
infostring += 'SNR = <font color="#ff0000">%f</font> <br>' % s.SNR
if hasattr(s,'M_ex'):
infostring += 'M<sub>ex</sub> = %f<br>' % s.M_ex
if hasattr(s,'M_em'):
infostring += 'M<sub>em</sub> = %f<br>' % s.M_em
if hasattr(s,'phase_ex'):
infostring += 'φ<sub>ex</sub> = %f deg<br>' % (s.phase_ex*180/np.pi)
if hasattr(s,'phase_em'):
infostring += 'φ<sub>em</sub> = %f deg<br>' % (s.phase_em*180/np.pi)
if hasattr(s,'ET_ruler'):
infostring += 'ET<sub>ruler</sub> = %f<br>' % s.ET_ruler
if hasattr(s,'ET_model_md_fu'):
infostring += 'ET model: M<sub>funnel</sub> = %f<br>' % s.ET_model_md_fu
infostring += 'ET model: θ<sub>funnel</sub> = %f<br>' % (s.ET_model_th_fu*180/np.pi)
infostring += 'ET model: geom. ratio = %f<br>' % s.ET_model_gr
infostring += 'ET model: ET param. = %f<br>' % s.ET_model_et
self.spotInfoTextBrowser.setHtml(infostring)
def selectSPE(self):
print self.selectSPEComboBox.currentIndex()
self.load_and_display_spe_file(fileindex=self.selectSPEComboBox.currentIndex())
def setWhichSetup(self):
self.which_setup = self.whichSetupComboBox.currentIndex()
def setPhaseOffset(self):
self.phaseOffset = self.phaseOffsetLineEdit.text().toDouble()[0]
print "Phase offset set to %f [deg]" % self.phaseOffset
def selectDataDir(self):
fname = QtGui.QFileDialog.getExistingDirectory(self, 'Show me where the data is', \
directory='' )
print "Selected data directory ", fname
self.data_directory = str(fname)
self.selectDataDirPushButton.setText(self.data_directory)
# go to dir
os.chdir( self.data_directory )
print "Looking for SPE data..."
# get all filenames
for file in os.listdir("."):
# get all that end in spe
if file.endswith(".spe") or file.endswith(".SPE"):
# if we don't have it already
if self.spefiles.count(file)==0:
# add it to the list
self.spefiles.append(file)
print "File %s added to the list." % file
else:
print "File %s is already in the list." % file
self.spefiles.sort()
self.motorfiles = ['']*len(self.spefiles)
print "Looking for corresponding motor data..."
for file in os.listdir("."):
if file.endswith(".txt"):
# do we know of the corresponding spe file?
match = [file[:-4]=='MS-'+spe[:-4] for spe in self.spefiles]
if any( match ):
where = np.nonzero(match)[0][0]
self.motorfiles[where] = file
print "Found motorfile matching spe-file basename: %s" % file
print "Any loose ends?"
for i,file in enumerate(self.motorfiles):
if len(file)==0:
print "SPE file %s doesn't have a motor file... removed from list." % self.spefiles[i]
self.spefiles.pop(i)
self.motorfiles.pop(i) # is an empty string, but necessary to prune the list
print "All good."
self.selectSPEComboBox.clear()
for s in self.spefiles:
self.selectSPEComboBox.addItem(s)
self.selectSPEComboBox.setCurrentIndex(0)
if not len(self.spefiles)==0:
self.load_and_display_spe_file(0)
def load_and_display_spe_file(self,fileindex=0):
del(self.m)
# from guppy import hpy; h=hpy()
# w=h.heap()
# print w
print "loading file %s ... " % (self.spefiles[fileindex]),
sys.stdout.flush()
self.m = Movie( self.data_directory+"/"+self.spefiles[fileindex], \
self.data_directory+"/"+self.motorfiles[fileindex], \
phase_offset_excitation=self.phase_offset*np.pi/180.0, \
use_new_fitter=True, \
which_setup=self.setup_list[self.which_setup], \
excitation_optical_element=self.optical_element)
self.imageview.show_image( self.m.camera_data.rawdata[0,:,:], zorder=1, cmap=cm.gray )
# self.imageview.axes.imshow(
# self.imageview.draw()
print "done"
if __name__=='__main__':
app = QtGui.QApplication(sys.argv)
instance = the2dlogic(app=app)
instance.main()
sys.exit(app.exec_())