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fixed bug in tiff export
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@dwaithe
dwaithe committed Nov 21, 2017
1 parent 64eaca3 commit ca33607
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Showing 2 changed files with 70 additions and 29 deletions.
95 changes: 68 additions & 27 deletions focuspoint/correlation_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -319,7 +319,7 @@ def generateWindow(self):
self.replot_btn.clicked.connect(self.plotDataQueueFn)
self.replot_btn2 = QtGui.QPushButton('Replot Data')
self.replot_btn2.clicked.connect(self.plotDataQueueFn)
self.saveAll_btn = QtGui.QPushButton('Save All')
self.saveAll_btn = QtGui.QPushButton('Save all as corr. files (.csv)')
self.saveAll_btn.clicked.connect(self.saveDataQueue)

self.normPlot = QtGui.QCheckBox('Normalise')
Expand Down Expand Up @@ -411,14 +411,14 @@ def generateWindow(self):
self.modelTab2.setColumnWidth(0,80);
self.modelTab2.setColumnWidth(1,140);
self.modelTab2.setColumnWidth(2,30);
self.modelTab2.setColumnWidth(3,100);
self.modelTab2.setColumnWidth(3,150);
self.modelTab2.setColumnWidth(4,100);
self.modelTab2.setColumnWidth(5,100);
self.modelTab2.horizontalHeader().setStretchLastSection(True)
self.modelTab2.resize(800,400)


self.modelTab2.setHorizontalHeaderLabels(QtCore.QString(",data name,plot,,file name").split(","))
self.modelTab2.setHorizontalHeaderLabels(QtCore.QString(",data name,plot,save,file name").split(","))

tableAndBtns = QtGui.QVBoxLayout()
correlationBtns = QtGui.QHBoxLayout()
Expand Down Expand Up @@ -449,19 +449,29 @@ def generateWindow(self):

self.left_panel_second_row_btns = QtGui.QHBoxLayout()

self.photonCountText =QtGui.QLabel()
self.photonCountText = QtGui.QLabel()
self.photonCountText.setText('Bin Duration (ms): ')
self.photonCountEdit = lineEditSp('25',self)
self.photonCountEdit.type ='int_bin'
self.photonCountEdit.setMaxLength(5)
self.photonCountEdit.setFixedWidth(40)
self.photonCountEdit.parObj = self
self.photonCountEdit.resize(40,50)
self.photonCountExport_label = QtGui.QLabel("Export Intensity Timeseries as: ")
self.photonCountExport_label = QtGui.QLabel("Export Individual Timeseries as: ")
self.photonIntensityTraceExportCSV = QtGui.QPushButton('.csv')
self.photonIntensityTraceExportTIF = QtGui.QPushButton('.tiff')

self.left_panel_third_row_btns = QtGui.QHBoxLayout()
self.save_int_timeSeries_csv = QtGui.QPushButton('Export all Timeseries as .csv')
self.save_int_timeSeries_tif = QtGui.QPushButton('Export all Timeseries as .tiff')


self.left_panel_third_row_btns.addWidget(self.save_int_timeSeries_csv)
self.left_panel_third_row_btns.addWidget(self.save_int_timeSeries_tif)
self.left_panel_third_row_btns.addStretch()

self.save_int_timeSeries_csv.clicked.connect(self.save_all_PhotonBinFnCSV)
self.save_int_timeSeries_tif.clicked.connect(self.save_all_PhotonBinFnTIF)


self.cbx = comboBoxSp(self)
Expand All @@ -471,7 +481,7 @@ def generateWindow(self):
self.left_panel_top_btns.addWidget(self.cbx)
self.left_panel_top_btns.addStretch()

self.left_panel_export_fns = QtGui.QGroupBox('Export settings')
self.left_panel_export_fns = QtGui.QGroupBox('Export Binned Intensities')
self.left_panel_second_row_btns.addWidget(self.photonCountText)
self.left_panel_second_row_btns.addWidget(self.photonCountEdit)
self.left_panel_second_row_btns.addWidget(self.photonCountExport_label)
Expand All @@ -483,9 +493,16 @@ def generateWindow(self):
self.photonIntensityTraceExportTIF.clicked.connect(self.reprocessPhotonBinFnTIF)

self.left_panel.addLayout(self.left_panel_top_btns)
self.left_panel_export_fns.setLayout(self.left_panel_second_row_btns)

self.left_panel_vertical_export = QtGui.QVBoxLayout()

self.left_panel_export_fns.setLayout(self.left_panel_vertical_export)
self.left_panel_vertical_export.addLayout(self.left_panel_second_row_btns)
self.left_panel_vertical_export.addLayout(self.left_panel_third_row_btns)




self.left_panel.addWidget(self.left_panel_export_fns)


Expand Down Expand Up @@ -620,28 +637,44 @@ def plotDataQueueFn(self):
self.plot(self.par_obj.subObjectRef[y])
self.plt5.ax = plt.gca()
self.plt5.a.freshDraw()
def save_all_PhotonBinFnCSV(self):
"""Reprocess all images and export .csv images."""
for x in range(0, self.par_obj.numOfLoaded):
self.reprocessPhotonBinFn('CSV',x)
for y in range(0, self.par_obj.subNum):
self.reprocessPhotonBinFn('CSV',x+y+1)

def save_all_PhotonBinFnTIF(self):
"""Reprocess all images and export .tiff images."""
for x in range(0, self.par_obj.numOfLoaded):
self.reprocessPhotonBinFn('TIFF',x)
for y in range(0, self.par_obj.subNum):
self.reprocessPhotonBinFn('TIFF',x+y+1)

def reprocessPhotonBinFnCSV(self):
self.reprocessPhotonBinFn('CSV')
self.reprocessPhotonBinFn('CSV',index)
def reprocessPhotonBinFnTIF(self):
self.reprocessPhotonBinFn('TIFF')
self.reprocessPhotonBinFn('TIFF',index)

def reprocessPhotonBinFn(self,type_ex):
def reprocessPhotonBinFn(self,type_ex,index):
#Time series of photon counts. For visualisation.
print self.par_obj.photonCountBin, 'self.par_obj.photonCountBin'


objId = None
for i in range(0, self.par_obj.numOfLoaded):
if(self.label.objCheck[i].isChecked() == True):
objId = self.par_obj.objectRef[i]
objId.timeSeries1,objId.timeSeriesScale1 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[0],self.par_obj.photonCountBin)
if self.par_obj.objectRef[i].numOfCH == 2:
objId.timeSeries2,objId.timeSeriesScale2 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[1],self.par_obj.photonCountBin)


if index < self.par_obj.numOfLoaded:
objId = self.par_obj.objectRef[index]
objId.timeSeries1,objId.timeSeriesScale1 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[0],self.par_obj.photonCountBin)
if objId.numOfCH == 2:
objId.timeSeries2,objId.timeSeriesScale2 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[1],self.par_obj.photonCountBin)
else:
objId = self.par_obj.subObjectRef[index-self.par_obj.numOfLoaded]
objId.timeSeries1,objId.timeSeriesScale1 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[0],self.par_obj.photonCountBin)
if objId.numOfCH == 2:
objId.timeSeries2,objId.timeSeriesScale2 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[1],self.par_obj.photonCountBin)


for i in range(0, self.par_obj.subNum):
if(self.label.objCheck[i].isChecked() == True):
objId = self.par_obj.subObjectRef[i]
objId.timeSeries1,objId.timeSeriesScale1 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[0],self.par_obj.photonCountBin)
if self.par_obj.subObjectRef[i].numOfCH == 2:
objId.timeSeries2,objId.timeSeriesScale2 = delayTime2bin(np.array(objId.trueTimeArr)/1000000,np.array(objId.subChanArr),objId.ch_present[1],self.par_obj.photonCountBin)

if type_ex == 'CSV':
f = open(self.folderOutput.filepath+'/'+objId.name+'_intensity.csv', 'w')
Expand Down Expand Up @@ -703,15 +736,22 @@ def reprocessDataFn(self):

self.plotDataQueueFn();
self.plot_PhotonCount(self.par_obj.numOfLoaded-1)
self.updateCombo()
def updateCombo(self):
"""Updates photon counting combox box"""
self.cbx.clear()
#Populates comboBox with datafiles to which to apply the time-gating.
for b in range(0,self.par_obj.numOfLoaded):
self.cbx.addItem("Data: "+str(b), b)
for i in range(0, self.par_obj.subNum):
self.cbx.addItem("subData: "+str(b+i+1), b+i+1)
def plot_PhotonCount(self,index):
"""Plots the photon counting"""
object = self.par_obj.objectRef[index]

if index < self.par_obj.numOfLoaded:
object = self.par_obj.objectRef[index]
else:
object = self.par_obj.subObjectRef[index-self.par_obj.numOfLoaded]
self.plt4.clear()
self.canvas4.draw()

Expand Down Expand Up @@ -1007,6 +1047,7 @@ def __activated(self):
self.par_obj.subNum = self.par_obj.subNum+1
self.win_obj.label.generateList()
self.win_obj.plotDataQueueFn()
self.win_obj.updateCombo()
class pushButtonSp2(QtGui.QPushButton):
"""Save button"""
def __init__(self, txt, win_obj, par_obj):
Expand Down Expand Up @@ -1085,7 +1126,7 @@ def generateList(self):


#Adds save button to the file.
sb = pushButtonSp2('save file', self.win_obj, self.par_obj)
sb = pushButtonSp2('save corr. file (.csv)', self.win_obj, self.par_obj)
sb.corr_obj = self.par_obj.objectRef[i]
self.win_obj.modelTab2.setCellWidget(i, 3, sb)

Expand All @@ -1094,7 +1135,7 @@ def generateList(self):
self.win_obj.modelTab2.setCellWidget(i, 4, b)


self.win_obj.label.objCheck.append(cb)
self.objCheck.append(cb)
j = i+1
for i in range(0,self.par_obj.subNum):
self.win_obj.modelTab2.setRowCount(j+i+1)
Expand Down Expand Up @@ -1122,7 +1163,7 @@ def generateList(self):


#Adds save button to the file.
sb = pushButtonSp2('save file', self.win_obj, self.par_obj)
sb = pushButtonSp2('save corr. file (.csv)', self.win_obj, self.par_obj)
sb.corr_obj = self.par_obj.subObjectRef[i]

self.win_obj.modelTab2.setCellWidget(i+j, 3, sb)
Expand Down
4 changes: 2 additions & 2 deletions focuspoint/correlation_objects.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -488,8 +488,8 @@ def processData(self):


self.fit_obj.fill_series_list()
del self.subChanArr
del self.trueTimeArr
#del self.subChanArr
#self.trueTimeArr
del self.dTimeArr


Expand Down

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