def compressItem(self, item):
def has_tiff(path):
for f in os.listdir(path):
if f.endswith(".tif"):
return True
return False
# figure out what type of folder this is
if not has_tiff(item):
self.statusBar.showMessage(
"No tiffs to compress in " + shortname(item), 4000)
return
worker, thread = newWorkerThread(
workers.CompressionWorker,
item,
"compress",
self.compressTypeCombo.currentText(),
workerConnect={
"status_update":
self.statusBar.showMessage,
"finished":
lambda: self.statusBar.showMessage("Compression finished", 4000
),
},
start=True,
)
self.compressionThreads.append((worker, thread))
def startCUDAWorkers(self):
# initialize the workers and threads
for gpu in self.GPU_SET:
# create new CUDAworker for every thread
# each CUDAworker will control one cudaDeconv process (which only gets
# one wavelength at a time)
# grab the next arguments from the queue
# THIS BREAKS the relationship between num_cuda_threads
# and self.__CUDAworkers_done...
# if len(self.__argQueue)== 0:
# return
if not len(self.__argQueue):
return
args = self.__argQueue.pop(0)
CUDAworker, thread = newWorkerThread(
CudaDeconvWorker,
args,
{"CUDA_VISIBLE_DEVICES": gpu},
wid=gpu,
workerConnect={
# get progress messages from CUDAworker and pass to parent
"file_finished": self.on_file_finished,
"finished": self.on_CUDAworker_done,
# any messages go straight to the log window
# 'error': self.errorstring # implement error signal?
},
)
# need to store worker too otherwise will be garbage collected
self.__CUDAthreads[gpu] = (thread, CUDAworker)
# connect mainGUI abort CUDAworker signal to the new CUDAworker
self.sig_abort.connect(CUDAworker.abort)
# start the thread
thread.start()
def decompressSelected(self):
for item in self.listbox.selectedPaths():
if not util.find_filepattern(item, "*.tar*"):
self.statusBar.showMessage(
"No .tar file found in " + shortname(item), 4000)
continue
def onfinish():
self.listbox.llsObjects[item]._register_tiffs()
self.statusBar.showMessage("Decompression finished", 4000)
worker, thread = newWorkerThread(
workers.CompressionWorker,
item,
"decompress",
self.compressTypeCombo.currentText(),
workerConnect={
"status_update": self.statusBar.showMessage,
"finished": onfinish,
},
start=True,
)
self.compressionThreads.append((worker, thread))
def previewRegistration(self):
RD = llsdir.RegDir(self.RegCalibPathLineEdit.text())
if not RD.isValid:
raise err.RegistrationError(
"Registration Calibration dir not valid. Please check Fiducial Data path above."
)
if not self.RegFilePath.text():
QtWidgets.QMessageBox.warning(
self,
"Must load registration file!",
"No registration file!\n\nPlease click load, "
"and load a registration file. Or use the "
"generate button to generate and load a new one.",
QtWidgets.QMessageBox.Ok,
QtWidgets.QMessageBox.NoButton,
)
return
@QtCore.Slot(np.ndarray, float, float, dict)
def displayRegPreview(array, dx=None, dz=None, params=None):
win = ImgDialog(
array,
info=params,
title="Registration Mode: {} -- RefWave: {}".format(
opts["regMode"], opts["regRefWave"]
),
)
win.overlayButton.click()
win.maxProjButton.click()
self.spimwins.append(win)
self.previewButton.setDisabled(True)
self.previewButton.setText("Working...")
try:
opts = self.getValidatedOptions()
except Exception:
self.previewButton.setEnabled(True)
self.previewButton.setText("Preview")
raise
opts["regMode"] = self.RegCalib_channelRefModeCombo.currentText()
if opts["regMode"].lower() == "none":
opts["doReg"] = False
else:
opts["doReg"] = True
opts["regRefWave"] = int(self.RegCalib_channelRefCombo.currentText())
opts["regCalibPath"] = self.RegFilePath.text()
opts["correctFlash"] = False
opts["medianFilter"] = False
opts["trimZ"] = (0, 0)
opts["trimY"] = (0, 0)
opts["trimX"] = (0, 0)
opts["nIters"] = 0
w, thread = newWorkerThread(
workers.TimePointWorker,
RD,
[0],
None,
opts,
workerConnect={"previewReady": displayRegPreview},
start=True,
)
w.finished.connect(lambda: self.previewButton.setEnabled(True))
w.finished.connect(lambda: self.previewButton.setText("Preview"))
self.previewthreads = (w, thread)
def processFolder(self):
folder = self.camCalibFolderLineEdit.text()
darkavg = None
if os.path.isfile(self.darkAVGLineEdit.text()):
darkavg = tf.imread(self.darkAVGLineEdit.text())
elif os.path.isfile(os.path.join(folder, "dark_AVG.tif")):
darkavg = tf.imread(os.path.join(folder, "dark_AVG.tif"))
darkstd = None
if os.path.isfile(self.darkSTDLineEdit.text()):
darkstd = tf.imread(self.darkSTDLineEdit.text())
elif os.path.isfile(os.path.join(folder, "dark_STD.tif")):
darkstd = tf.imread(os.path.join(folder, "dark_STD.tif"))
if not all([isinstance(a, np.ndarray) for a in (darkavg, darkstd)]):
if not pathHasPattern(folder, "*dark*.tif*"):
QtW.QMessageBox.warning(
self,
"No dark images!",
"Camera calibration requires dark images, but none were provided"
" and none were detected in the specified folder."
" Read documentation on camera calibration for more info.",
QtW.QMessageBox.Ok,
QtW.QMessageBox.NoButton,
)
return
if sum([isinstance(a, np.ndarray) for a in (darkavg, darkstd)]) == 1:
if not pathHasPattern(folder, "*dark*.tif*"):
QtW.QMessageBox.warning(
self,
"No dark images!",
"Camera calibration requires both a dark image average projection, "
" and a standard deviation projection, but only one of the"
" two was provided, and no *dark*.tif images "
" were detected in the specified folder."
" Read documentation on camera calibration for more info.",
QtW.QMessageBox.Ok,
QtW.QMessageBox.NoButton,
)
return
else:
reply = QtW.QMessageBox.question(
self,
"No dark images!",
"Camera calibration requires both a dark image average projection, "
" and a standard deviation projection, but only one of the"
" two was provided. *dark*.tif images "
" were detected in the specified folder, and will still be "
" used to calculate the projection images. Continue?",
QtW.QMessageBox.Yes | QtW.QMessageBox.No,
QtW.QMessageBox.No,
)
if reply != QtW.QMessageBox.Yes:
return
self.worker, self.thread = newWorkerThread(
CamCalibWorker,
folder,
darkavg,
darkstd,
workerConnect={
"progress": self.incrementProgress,
"setProgMax": self.resetWithMax,
"setStatus": self.statusLabel.setText,
"finished": self.abortButton.hide,
},
start=True,
)