def fullReconstruction(self):
from .widgets.volumeviewer import VolumeViewer
volumeviewer = VolumeViewer()
self.recontabs.addTab(volumeviewer, '????')
currentitem = self.headermodel.item(self.rawtabview.currentIndex())
if not currentitem:
msg.showMessage(
'Error: You must open files before reconstructing.')
try:
msg.showBusy()
msg.showMessage('Running slice reconstruction...', level=msg.INFO)
currentheader = self.headermodel.item(
self.rawtabview.currentIndex()).header
readprocess = self.workflow.processes[
0] # hopefully! TODO: require a readprocess first
readprocess.path.value = currentheader.startdoc['path']
numofsinograms = currentheader.meta_array('primary').shape[1]
self.workflow.execute_all(None,
readprocess=range(
0, int(numofsinograms),
int(readprocess.chunksize.value)))
except Exception as ex:
msg.logError(ex)
msg.showReady()
msg.clearMessage()
def fullReconstruction(self):
from xicam.Tomography.widgets.volumeviewer import VolumeViewer
volumeviewer = VolumeViewer()
self.recontabs.addTab(volumeviewer, '????')
currentitem = self.headermodel.item(self.rawtabview.currentIndex())
if not currentitem: msg.showMessage('Error: You must open files before reconstructing.')
try:
msg.showBusy()
msg.showMessage('Running slice reconstruction...', level=msg.INFO)
currentheader = self.headermodel.item(self.rawtabview.currentIndex()).header
readprocess = self.workflow.processes[0] # hopefully! TODO: require a readprocess first
readprocess.path.value = currentheader.startdoc['path']
numofsinograms = currentheader.meta_array('primary').shape[1]
executor = DaskExecutor()
client = distributed.Client()
def chunkiterator(workflow):
for i in range(0, int(numofsinograms), int(readprocess.chunksize.value)):
readprocess.sinoindex.value = i
yield executor.execute(workflow)
_reconthread = QThreadFutureIterator(chunkiterator, self.workflow,
callback_slot=partial(self.showReconstruction, mode=self.fullrecon),
except_slot=self.exceptionCallback)
_reconthread.start()
except Exception as ex:
msg.logError(ex)
msg.showReady()
msg.clearMessage()
def showReconstruction(self, result, mode):
print('result:', result)
if mode == self.slice:
sliceviewer = SliceViewer()
sliceviewer.setImage(list(result.values())[0].value.squeeze())
self.recontabs.addTab(sliceviewer, '????')
if mode == self.fullrecon:
self.recontabs.widget(self.recontabs.count() - 1).appendData(
list(result.values())[0].value[::4, ::4, ::4])
msg.showReady()
def sliceReconstruct(self):
currentitem = self.headermodel.item(self.rawtabview.currentIndex())
if not currentitem: msg.showMessage('Error: You must open files before reconstructing.')
try:
msg.showBusy()
msg.showMessage('Running slice reconstruction...', level=msg.INFO)
paths = self.headermodel.item(self.rawtabview.currentIndex()).header.startdoc['paths']
self.workflow.execute(None, paths=paths, threadkey='slicereconstruct',
callback_slot=partial(self.showReconstruction, mode=self.slice),
except_slot=self.exceptionCallback)
except Exception as ex:
msg.logError(ex)
msg.showReady()
msg.clearMessage()
def process_queue(self):
while True:
try:
priority_plan = self.queue.get(
block=True,
timeout=.1) # timeout is arbitrary, we'll come right back
except Empty:
continue
priority, (args,
kwargs) = priority_plan.priority, priority_plan.args
self.sigStart.emit()
msg.showBusy()
try:
self.RE(*args, **kwargs)
except Exception as ex:
msg.showMessage(
"An error occured during a Bluesky plan. See the Xi-CAM log for details."
)
msg.logError(ex)
self.sigException.emit(ex)
finally:
msg.showReady()
self.sigFinish.emit()
def exceptionCallback(self, ex):
msg.notifyMessage("Reconstruction failed;\n see log for error")
msg.showMessage("Reconstruction failed; see log for error")
msg.logError(ex)
msg.showReady()