def run(self):
try:
outfile, outstring = self.RD.write_reg_file(outdir, refs=self.refs)
counts = self.RD.cloudset().count
if np.std(counts) > 15:
outstr = "\n".join(
[
"wave: {}, beads: {}".format(channel, counts[i])
for i, channel in enumerate(self.RD.waves)
]
)
self.warning.emit(
"Suspicious Registration Result",
"Warning: there was a large variation in the number "
"of beads per channel. Auto-detection may have failed. "
"Try changing 'Min number of beads'...\n\n" + outstr,
)
except RegistrationError as e:
raise err.RegistrationError("Fiducial registration failed:", str(e))
# also write to appdir ... may use it later
if not os.path.isdir(REG_DIR):
os.mkdir(REG_DIR)
outfile2 = os.path.join(REG_DIR, os.path.basename(outfile))
with open(outfile2, "w") as file:
file.write(outstring)
logger.debug("registration file output: {}".format(outfile))
logger.debug("registration file output: {}".format(outfile2))
self.finished.emit(outfile)
def setRegCalibPath(self):
path = QtWidgets.QFileDialog.getExistingDirectory(
self,
"Set Registration Calibration Directory",
"",
QtWidgets.QFileDialog.ShowDirsOnly,
)
if path is None or path == "":
return
RD = llsdir.RegDir(path)
if not RD.isValid:
raise err.RegistrationError(
"Registration Calibration dir not valid: {}".format(RD.path)
)
self.RegCalibPathLineEdit.setText(path)
layout = self.RegCalibRefGroupLayout
group = self.RegCalibRefChannelsGroup
for cb in group.findChildren(QtWidgets.QCheckBox):
layout.removeWidget(cb)
cb.setParent(None)
for wave in RD.parameters.channels.values():
box = QtWidgets.QCheckBox(str(wave), group)
layout.addWidget(box)
box.setChecked(True)
def loadRegistrationFile(self, file=None):
if not file:
file = QtWidgets.QFileDialog.getOpenFileName(
self,
"Choose registration file ",
os.path.expanduser("~"),
"Text Files (*.reg *.txt *.json)",
)[0]
if file is None or file == "":
return
try:
with open(file) as json_data:
regdict = json.load(json_data)
refs = sorted(list(set([t["reference"] for t in regdict["tforms"]])))
# mov = set([t['moving'] for t in regdict['tforms']])
modes = ["None"]
modes.extend(
sorted(
list(
set(
[
t["mode"].title().replace("Cpd", "CPD")
for t in regdict["tforms"]
]
)
)
)
)
self.RegCalib_channelRefCombo.clear()
self.RegCalib_channelRefCombo.addItems([str(r) for r in refs])
self.RegCalib_channelRefModeCombo.clear()
self.RegCalib_channelRefModeCombo.addItems(modes)
self.RegFilePath.setText(file)
except json.decoder.JSONDecodeError as e:
raise err.RegistrationError("Failed to parse registration file", str(e))
except Exception as e:
raise err.RegistrationError("Failed to load registration file", str(e))
def generateCalibrationFile(self):
group = self.RegCalibRefChannelsGroup
refs = [
int(cb.text())
for cb in group.findChildren(QtWidgets.QCheckBox)
if cb.isChecked()
]
path = self.RegCalibPathLineEdit.text()
if not path or path == "":
raise err.InvalidSettingsError("Please load a fiducial dataset path first")
if not len(refs):
raise err.InvalidSettingsError("Select at least one reference channel")
autoThresh = self.RegAutoThreshCheckbox.isChecked()
if autoThresh:
minbeads = int(self.RegMinBeadsSpin.value())
RD = llsdir.RegDir(path, usejson=False, threshold="auto", mincount=minbeads)
else:
threshold = int(self.RegBeadThreshSpin.value())
RD = llsdir.RegDir(path, threshold=threshold, usejson=False)
if not RD.isValid:
raise err.RegistrationError(
"Registration Calibration dir not valid: {}".format(RD.path)
)
outdir = QtWidgets.QFileDialog.getExistingDirectory(
self,
"Chose destination for registration file",
"",
QtWidgets.QFileDialog.ShowDirsOnly,
)
if outdir is None or outdir == "":
return
class RegThread(QtCore.QThread):
finished = QtCore.Signal(str)
warning = QtCore.Signal(str, str)
def __init__(self, RD, outdir, refs):
QtCore.QThread.__init__(self)
self.RD = RD
self.outdir = outdir
self.refs = refs
def run(self):
try:
outfile, outstring = self.RD.write_reg_file(outdir, refs=self.refs)
counts = self.RD.cloudset().count
if np.std(counts) > 15:
outstr = "\n".join(
[
"wave: {}, beads: {}".format(channel, counts[i])
for i, channel in enumerate(self.RD.waves)
]
)
self.warning.emit(
"Suspicious Registration Result",
"Warning: there was a large variation in the number "
"of beads per channel. Auto-detection may have failed. "
"Try changing 'Min number of beads'...\n\n" + outstr,
)
except RegistrationError as e:
raise err.RegistrationError("Fiducial registration failed:", str(e))
# also write to appdir ... may use it later
if not os.path.isdir(REG_DIR):
os.mkdir(REG_DIR)
outfile2 = os.path.join(REG_DIR, os.path.basename(outfile))
with open(outfile2, "w") as file:
file.write(outstring)
logger.debug("registration file output: {}".format(outfile))
logger.debug("registration file output: {}".format(outfile2))
self.finished.emit(outfile)
def finishup(outfile):
self.statusBar.showMessage(
"Registration file written: {}".format(outfile), 5000
)
self.loadRegistrationFile(outfile)
def notifyuser(title, msg):
QtWidgets.QMessageBox.warning(self, title, msg, QtWidgets.QMessageBox.Ok)
self.regthreads = []
regthread = RegThread(RD, outdir, refs)
regthread.finished.connect(finishup)
regthread.warning.connect(notifyuser)
self.regthreads.append(regthread)
self.statusBar.showMessage(
"Calculating registrations for ref channels: {}...".format(refs)
)
regthread.start()
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)