def addProgJob(self, job_desc, generator, args, kwargs, finish_slot=None):
job_entry = self.addJob(job_desc)
bg_generator = threads.iterator(
callback_slot=job_entry.progress,
finished_slot=finish_slot,
interrupt_signal=job_entry.sigCancel)(generator)
bg_generator(*args, **kwargs)
def loadFullReconstruction(self):
"""
Sets up a full reconstruction for the current dataset based on the current workflow pipeline and configuration
parameters. Does not run reconstruction if there is one already running. Called when the corresponding toolbar
button is clicked.
"""
if not self.checkPipeline():
return
value = QtGui.QMessageBox.question(None, 'Run Full Reconstruction',
'You are about to run a full reconstruction. '
'This step can take some minutes. Do you want to continue?',
(QtGui.QMessageBox.Yes | QtGui.QMessageBox.Cancel))
if value is QtGui.QMessageBox.Cancel:
return
currentWidget = self.centerwidget.widget(self.currentWidget())
self.manager.updateParameters()
run_state = self.manager.saveState(currentWidget)
recon_iter = threads.iterator(callback_slot=self.bottomwidget.log2local,
interrupt_signal=self.bottomwidget.local_cancelButton.clicked,
finished_slot=self.reconstructionFinished)(self.manager.reconGenerator)
# pstart = self.ui.config_params.child('Start Projection').value()
# pend = self.ui.config_params.child('End Projection').value()
# pstep = self.ui.config_params.child('Step Projection').value()
# sstart = self.ui.config_params.child('Start Sinogram').value()
# send = self.ui.config_params.child('End Sinogram').value()
# sstep = self.ui.config_params.child('Step Sinogram').value()
proj = None
sino = None
chunk = None
for f in self.manager.features:
if 'Reader' in f.name:
proj = f.projections
sino = f.sinograms
chunk = f.chunk
if (not proj and not sino and not chunk) or (not proj[1] and not sino[1] and not chunk):
sino = (0, currentWidget.data.shape[2], 1)
proj = (0, currentWidget.data.shape[0], 1)
chunk = cpu_count()*5
args = (currentWidget, run_state, proj, sino, chunk, cpu_count())
self.manager.recon_queue.put([recon_iter, args])
if self.recon_running:
name = self.centerwidget.tabText(self.centerwidget.currentIndex())
msg.showMessage('Queued reconstruction for {}.'.format(name), timeout=0)
self.runReconstruction()
def loadFullReconstruction(self):
"""
Sets up a full reconstruction for the current dataset based on the current workflow pipeline and configuration
parameters. Does not run reconstruction if there is one already running. Called when the corresponding toolbar
button is clicked.
"""
if not self.checkPipeline():
return
value = QtGui.QMessageBox.question(
None, 'Run Full Reconstruction',
'You are about to run a full reconstruction. '
'This step can take some minutes. Do you want to continue?',
(QtGui.QMessageBox.Yes | QtGui.QMessageBox.Cancel))
if value is QtGui.QMessageBox.Cancel:
return
currentWidget = self.centerwidget.currentWidget()
self.manager.updateParameters()
func_dict, theta, center, pipeline_dict, run_dict = self.manager.saveState(
currentWidget)
recon_iter = threads.iterator(
callback_slot=self.bottom.log2local,
except_slot=self.reconstructionFinished,
interrupt_signal=self.bottom.local_cancelButton.clicked,
finished_slot=self.reconstructionFinished)(
self.manager.reconGenerator)
# set up information for reconstruction
proj, sino, width, proj_chunk, sino_chunk = self.get_reader_dims()
dims = (proj, sino, width, sino_chunk, proj_chunk, cpu_count())
args = (currentWidget, func_dict, theta, center, pipeline_dict,
run_dict, dims)
self.queue_widget.recon_queue.append([recon_iter, args])
self.queue_widget.addRecon(args)
if self.recon_running:
name = self.centerwidget.tabText(self.centerwidget.currentIndex())
msg.showMessage('Queued reconstruction for {}.'.format(name),
timeout=0)
self.runReconstruction()
def runSlicePreview(self,
datawidget,
func_dict,
theta,
center,
stack_dict,
prange=None,
dims=None):
"""
Callback function that receives the necessary widgets/information required to run a preview and
add it to the viewer.TomoViewer.previewViewer
Parameters
----------
datawidget : viewers.TomoViewer
Widget containing dataset
func_dict: dict
Dictionary of function names and partials with keywords for the reconstruction
theta: list
List of values representing angular location of camera (for reconstruction)
center: float
Center of rotation of dataset
stack_dict : dict
Dictionary describing the workflow pipeline being run. This is displayed to the left of the preview image in
the viewer.TomoViewer.previewViewer
prange: dict, optional
Dictionary containing parameter being tested for TestParamRange, and the function the parameter belongs to
dims : tuple, optional
Tuple containing dimensions of dataset to be reconstructed
"""
callback = partial(self.centerwidget.currentWidget().addSlicePreview,
stack_dict,
slice_no=self.preview_slices,
prange=prange)
err_message = 'Unable to compute slice preview. Check log for details.'
except_slot = lambda: msg.showMessage(err_message)
bg_fold = threads.iterator(callback_slot=callback,
finished_slot=msg.clearMessage,
lock=threads.mutex,
except_slot=except_slot)
bg_fold(self.manager.reconGenerator)(datawidget, func_dict, theta,
center, None, None, dims, None,
'Slice')
def run3DPreview(self,
datawidget,
func_dict,
theta,
center,
stack_dict,
prange=None,
dims=None):
"""
Callback function that receives the partial stack and corresponding dictionary required to run a preview and
add it to the viewer.TomoViewer.preview3DViewer
Parameters
----------
datawidget : viewers.TomoViewer
Widget containing dataset
func_dict: dict
Dictionary of function names and partials with keywords for the reconstruction
theta: list
List of values representing angular location of camera (for reconstruction)
center: float
Center of rotation of dataset
stack_dict : dict
Dictionary describing the workflow pipeline being run. This is displayed to the left of the preview image in
the viewer.TomoViewer.previewViewer
dims : tuple, optional
Tuple containing dimensions of dataset to be reconstructed
"""
self.manager.updateParameters()
callback = partial(
self.centerwidget.widget(self.currentIndex()).add3DPreview,
stack_dict)
err_message = 'Unable to compute 3D preview. Check log for details.'
except_slot = lambda: msg.showMessage(err_message)
bg_fold = threads.iterator(callback_slot=callback,
finished_slot=msg.clearMessage,
lock=threads.mutex,
except_slot=except_slot)
bg_fold(self.manager.reconGenerator)(datawidget, func_dict, theta,
center, None, None, dims, None,
'3D')
def runFullReconstruction(self):
"""
Sets up a full reconstruction to be run in a background thread for the current dataset based on the current
workflow pipeline and configuration parameters. Called when the corresponding toolbar button is clicked.
Made obsolete by loadFullReconstruction and runReconstruction
"""
if not self.checkPipeline():
return
value = QtGui.QMessageBox.question(None, 'Run Full Reconstruction',
'You are about to run a full reconstruction. '
'This step can take some minutes. Do you want to continue?',
(QtGui.QMessageBox.Yes | QtGui.QMessageBox.Cancel))
if value is QtGui.QMessageBox.Cancel:
return
name = self.centerwidget.tabText(self.centerwidget.currentIndex())
msg.showMessage('Computing reconstruction for {}...'.format(name),timeout = 0)
self.bottomwidget.local_console.clear()
self.manager.updateParameters()
recon_iter = threads.iterator(callback_slot=self.bottomwidget.log2local,
interrupt_signal=self.bottomwidget.local_cancelButton.clicked,
finished_slot=self.reconstructionFinished)(self.manager.functionStackGenerator)