def openFile(self):
"""
Open file to load in.
"""
if not self.getConfig(gvars.key_batchLoadingMode):
directory = self.getLastOpenedDir()
filenames, selectedFilter = QFileDialog.getOpenFileNames(
self,
caption="Open File",
filter="Video files (*.tif *fits)",
directory=directory,
)
if len(filenames) > 0:
progressbar = ProgressBar(loop_len=len(filenames), parent=self)
for i, full_filename in enumerate(filenames):
if progressbar.wasCanceled():
break
# Make sure name is unique
uniqueName = lib.utils.generate_unique_name(
full_filename=full_filename,
array=self.data.videos.keys(),
)
self.data.load_video_data(
path=full_filename,
name=uniqueName,
alex=self.getConfig(gvars.key_alexEnabled),
view_setup=self.getConfig(gvars.key_viewSetup),
donor_is_first=self.donor_first,
donor_is_left=self.donor_is_left,
bg_correction=self.bg_correction,
)
item = QStandardItem(uniqueName)
item.setCheckable(False)
self.currName = uniqueName
self.currDir = os.path.dirname(full_filename)
self.listModel.appendRow(item)
# refresh listView
self.listView.repaint()
progressbar.increment()
# Select first video if loading into an empty listView
if self.currRow is None:
self.currRow = 0
self.selectListViewTopRow()
index = self.listModel.index(self.currRow, 0)
name = self.listModel.data(index)
self.currName = name
# Write most recently opened directory to getConfig file,
# but only if a file was selected
if self.currDir is not None:
self.setConfig(gvars.key_lastOpenedDir, self.currDir)
else:
self.batchOpen()
def predict_batch(X, model, batch_size=256, progressbar: ProgressBar = None):
"""
Predicts on batches in a loop
"""
batches = (X.shape[0] // batch_size) + 1
y_pred = []
for i in range(batches):
i1 = i * batch_size
i2 = i1 + batch_size
print(X[i1:i2].shape)
y_pred.append(model.predict_on_batch(X[i1:i2]))
if progressbar is not None:
progressbar.increment()
if progressbar.wasCanceled():
break
return np.row_stack(y_pred)
def batchOpen(self):
"""Loads one video at a time and extracts traces, then clears the
video from memory afterwards"""
directory = self.getLastOpenedDir()
trace_window = self.windows[gvars.TraceWindow] # type: TraceWindow
filenames, selectedFilter = QFileDialog.getOpenFileNames(
self,
caption="Open File",
filter="Video files (*.tif *.fits)",
directory=directory,
)
if len(filenames) > 0:
self.processEvents()
progressbar = ProgressBar(loop_len=len(filenames), parent=self)
for i, full_filename in enumerate(filenames):
if progressbar.wasCanceled():
break
else:
progressbar.increment()
self.currName = os.path.basename(full_filename)
if self.currName in self.data.videos:
continue
self.data.load_video_data(
path=full_filename,
name=os.path.basename(full_filename),
donor_is_first=self.donor_first,
donor_is_left=self.donor_is_left,
bg_correction=self.bg_correction,
)
channels = ("green", "red")
for c in channels:
if self.currentVideo().acc.exists:
self.colocalizeSpotsSingleVideo(channel=c,
find_npairs="auto")
else:
self.colocalizeSpotsSingleVideo(channel=c,
find_npairs="spinbox")
self.getTracesSingleVideo()
self.currentVideo().vid = None
for c in self.currentVideo().channels + (
self.currentVideo().acc, ):
c.raw = None
self.listModel.appendRow(QStandardItem(self.currName))
self.listView.repaint()
self.currDir = os.path.dirname(full_filename)
if self.currDir is not None:
self.setConfig(gvars.key_lastOpenedDir, self.currDir)
if len(self.data.traces) > 0:
currently_loaded = trace_window.returnCurrentListViewNames()
# Iterate over all filenames and add to list
for name in self.data.traces.keys():
# If name is already in list, skip it
if name in currently_loaded:
continue
item = QStandardItem(name)
item.setCheckable(True)
trace_window.listModel.appendRow(item)
trace_window.selectListViewTopRow()
trace_window.getCurrentListObject()
trace_window.show()
self.batchLoaded = True
self.refreshInterface()
self.selectListViewTopRow()
self.refreshPlot()
def openFile(self, *args):
"""
Loads ASCII files directly into the TraceWindow.
"""
directory = self.getLastOpenedDir()
filenames, selectedFilter = QFileDialog.getOpenFileNames(
self,
caption="Open File",
filter="Trace files (*.txt *.dat)",
directory=directory,
)
if len(filenames) != 0:
select_top_row = True if len(self.data.traces) == 0 else False
update_every_n = int(10) if len(filenames) > 10 else int(2)
progressbar = ProgressBar(loop_len=len(filenames) / update_every_n,
parent=self)
rows = []
for n, full_filename in enumerate(filenames):
if progressbar.wasCanceled():
break
self.currDir = os.path.dirname(full_filename)
try:
newTrace = TraceContainer(filename=full_filename,
loaded_from_ascii=True)
except AttributeError: # if a non-trace file was selected
warnings.warn(
f"This file could not be read: \n{full_filename}",
UserWarning,
)
continue
if (n % update_every_n) == 0:
progressbar.increment()
# If file wasn't loaded properly, skip
if newTrace.load_successful is False:
continue
# Don't load duplicates
if newTrace.name in self.data.traces.keys():
continue
self.data.traces[newTrace.name] = newTrace
item = QStandardItem(newTrace.name)
rows.append(item)
# Don't touch the GUI until loading is done
[self.listModel.appendRow(row) for row in rows]
[
self.listModel.item(i).setCheckable(True)
for i in range(self.listModel.rowCount())
]
self.listView.repaint()
progressbar.close()
if select_top_row:
self.selectListViewTopRow()
self.getCurrentListObject()
self.setConfig(gvars.key_lastOpenedDir, self.currDir)