def recordFrame(self, frame, iter, depthIndex):
# Handle new frame
dh = self.prot['storageDir']
name = 'image_%03d' % iter
if self.prot['zStack']:
# start or append focus stack
arrayInfo = [
{'name': 'Depth', 'values': [self.prot['zStackValues'][depthIndex]]},
{'name': 'X'},
{'name': 'Y'}
]
data = MetaArray(frame.getImage()[np.newaxis, ...], info=arrayInfo)
if depthIndex == 0:
self.currentDepthStack = dh.writeFile(data, name, info=frame.info(), appendAxis='Depth')
else:
data.write(self.currentDepthStack.name(), appendAxis='Depth')
else:
# record single-frame image
arrayInfo = [
{'name': 'X'},
{'name': 'Y'}
]
data = MetaArray(frame.getImage(), info=arrayInfo)
dh.writeFile(data, name, info=frame.info())
def saveMA(self, fileName=None):
if self.imgData is None:
raise HelpfulException("There is no processed data to save.")
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save image data", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
table = self.dbquery.table()
x = table['xPos'].min()
y = table['yPos'].min()
#print "params:", self.imgData.dtype.names
#print "shape:", self.imgData.shape
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.imgData[p] for p in self.imgData.dtype.names], info=[
{'name':'vals', 'cols':[{'name':p} for p in self.imgData.dtype.names]},
{'name':'xPos', 'units':'m', 'values':np.arange(self.imgData.shape[0])*self.spacing+x},
{'name':'yPos', 'units':'m', 'values':np.arange(self.imgData.shape[1])*self.spacing+y},
{'spacing':self.spacing}
])
arr.write(fileName)
def writeFrames(self, frames, dh):
newRec = self.currentStack is None
if newRec:
self.startFrameTime = frames[0][1]['time']
times = [f[1]['time'] for f in frames]
translations = np.array(
[f[1]['transform'].getTranslation() for f in frames])
arrayInfo = [{
'name': 'Time',
'values': array(times) - self.startFrameTime,
'units': 's',
'translation': translations
}, {
'name': 'X'
}, {
'name': 'Y'
}]
imgs = [f[0][np.newaxis, ...] for f in frames]
data = MetaArray(np.concatenate(imgs, axis=0), info=arrayInfo)
if newRec:
self.currentStack = dh.writeFile(data,
'video',
autoIncrement=True,
info=frames[0][1],
appendAxis='Time',
appendKeys=['translation'])
else:
data.write(self.currentStack.name(),
appendAxis='Time',
appendKeys=['translation'])
def saveMA(self, fileName=None):
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save traces", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([
self.currentData['Rs'], self.currentData['Rm'],
self.currentData['Ih']
],
info=[{
'name':
'vals',
'cols': [{
'name': 'Rs',
'units': 'Ohms'
}, {
'name': 'Rm',
'units': 'Ohms'
}, {
'name': 'Ih',
'units': 'A'
}]
}, {
'name': 'time',
'units': 's',
'values': self.currentData['time']
}])
arr.write(fileName)
def write(cls, data, dirHandle, fileName, **args):
"""Write data to fileName.
Return the file name written (this allows the function to modify the requested file name)
"""
ext = cls.extensions[0]
if fileName[-len(ext):] != ext:
fileName = fileName + ext
if not isinstance(data, MA):
data = MA(data)
data.write(os.path.join(dirHandle.name(), fileName), **args)
return fileName
def write(cls, data, dirHandle, fileName, **args):
"""Write data to fileName.
Return the file name written (this allows the function to modify the requested file name)
"""
ext = cls.extensions[0]
if fileName[-len(ext):] != ext:
fileName = fileName + ext
if not isinstance(data, MA):
data = MA(data)
data.write(os.path.join(dirHandle.name(), fileName), **args)
return fileName
def saveMA(self, fileName=None):
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save traces", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.currentData['Rs'], self.currentData['Rm'], self.currentData['Ih']], info=[
{'name':'vals', 'cols':[
{'name':'Rs', 'units':'Ohms'},
{'name':'Rm', 'units':'Ohms'},
{'name':'Ih', 'units':'A'}]},
{'name':'time', 'units':'s', 'values':self.currentData['time']}])
arr.write(fileName)
def writeFrames(self, frames, newRec):
times = [f[1]['time'] for f in frames]
arrayInfo = [
{'name': 'Time', 'values': array(times) - self.startFrameTime, 'units': 's'},
{'name': 'X'},
{'name': 'Y'}
]
#import random
#if random.random() < 0.01:
#raise Exception("TEST")
imgs = [f[0][np.newaxis,...] for f in frames]
data = MetaArray(np.concatenate(imgs, axis=0), info=arrayInfo)
if newRec:
self.currentRecord = self.m.getCurrentDir().writeFile(data, 'video', autoIncrement=True, info=frames[0][1], appendAxis='Time')
self.currentFrameNum = 0
else:
data.write(self.currentRecord.name(), appendAxis='Time')
s = 1.0/self.currentFrameNum
#self.showMessage("Recording %s - %d" % (self.currentRecord.name(), self.currentFrameNum))
self.currentFrameNum += len(frames)
