def run_as_data_tool(self):
from cellprofiler.gui.editobjectsdlg import EditObjectsDialog
import wx
from wx.lib.filebrowsebutton import FileBrowseButton
from cellprofiler.modules.namesandtypes import ObjectsImageProvider
from bioformats import load_image
with wx.Dialog(None) as dlg:
dlg.Title = "Choose files for editing"
dlg.Sizer = wx.BoxSizer(wx.VERTICAL)
sub_sizer = wx.BoxSizer(wx.HORIZONTAL)
dlg.Sizer.Add(sub_sizer, 0, wx.EXPAND | wx.ALL, 5)
new_or_existing_rb = wx.RadioBox(dlg,
style=wx.RA_VERTICAL,
choices=("New", "Existing"))
sub_sizer.Add(new_or_existing_rb, 0, wx.EXPAND)
objects_file_fbb = FileBrowseButton(
dlg,
size=(300, -1),
fileMask=
"Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg",
dialogTitle="Select objects file",
labelText="Objects file:",
)
objects_file_fbb.Enable(False)
sub_sizer.AddSpacer(5)
sub_sizer.Add(objects_file_fbb, 0, wx.ALIGN_TOP | wx.ALIGN_RIGHT)
def on_radiobox(event):
objects_file_fbb.Enable(new_or_existing_rb.GetSelection() == 1)
new_or_existing_rb.Bind(wx.EVT_RADIOBOX, on_radiobox)
image_file_fbb = FileBrowseButton(
dlg,
size=(300, -1),
fileMask=
"Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg",
dialogTitle="Select guide image file",
labelText="Guide image:",
)
dlg.Sizer.Add(image_file_fbb, 0, wx.EXPAND | wx.ALL, 5)
allow_overlap_checkbox = wx.CheckBox(dlg, -1,
"Allow objects to overlap")
allow_overlap_checkbox.Value = True
dlg.Sizer.Add(allow_overlap_checkbox, 0, wx.EXPAND | wx.ALL, 5)
buttons = wx.StdDialogButtonSizer()
dlg.Sizer.Add(buttons, 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL,
5)
buttons.Add(wx.Button(dlg, wx.ID_OK))
buttons.Add(wx.Button(dlg, wx.ID_CANCEL))
buttons.Realize()
dlg.Fit()
result = dlg.ShowModal()
if result != wx.ID_OK:
return
self.allow_overlap.value = allow_overlap_checkbox.Value
fullname = objects_file_fbb.GetValue()
guidename = image_file_fbb.GetValue()
if new_or_existing_rb.GetSelection() == 1:
provider = ObjectsImageProvider("InputObjects",
pathname2url(fullname), None, None)
image = provider.provide_image(None)
pixel_data = image.pixel_data
shape = pixel_data.shape[:2]
labels = [pixel_data[:, :, i] for i in range(pixel_data.shape[2])]
else:
labels = None
#
# Load the guide image
#
guide_image = load_image(guidename)
if np.min(guide_image) != np.max(guide_image):
guide_image = (guide_image - np.min(guide_image)) / (
np.max(guide_image) - np.min(guide_image))
if labels is None:
shape = guide_image.shape[:2]
labels = [np.zeros(shape, int)]
with EditObjectsDialog(guide_image, labels, self.allow_overlap,
self.object_name.value) as dialog_box:
result = dialog_box.ShowModal()
if result != wx.OK:
return
labels = dialog_box.labels
n_frames = len(labels)
with wx.FileDialog(None,
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg:
dlg.Path = fullname
dlg.Wildcard = ("Object image file (*.tif,*.tiff)|*.tif;*.tiff|"
"Ilastik project file (*.ilp)|*.ilp")
result = dlg.ShowModal()
fullname = dlg.Path
if result == wx.ID_OK:
if fullname.endswith(".ilp"):
self.save_into_ilp(fullname, labels, guidename)
else:
from bioformats.formatwriter import write_image
from bioformats.omexml import PT_UINT16
if os.path.exists(fullname):
os.unlink(fullname)
for i, l in enumerate(labels):
write_image(fullname,
l,
PT_UINT16,
t=i,
size_t=len(labels))
class panelConfigure(wx.Panel):
"""
"""
def __init__(self, parent):
"""
"""
wx.Panel.__init__(self,
parent,
wx.ID_ANY,
size=(-1, 300),
style=wx.SUNKEN_BORDER | wx.TAB_TRAVERSAL)
self.parent = parent
self.thumbnail = None
self.mask_file = None
self.source = None
self.sourceType = None
self.track = None
self.trackType = None
lowerSizer = wx.BoxSizer(wx.HORIZONTAL)
#Static box1 (LEFT)
sb_1 = wx.StaticBox(self, -1, "Select Monitor") #, size=(250,-1))
sbSizer_1 = wx.StaticBoxSizer(sb_1, wx.VERTICAL)
n_monitors = options.GetOption("Monitors")
self.MonitorList = [
'Monitor %s' % (int(m) + 1) for m in range(n_monitors)
]
self.thumbnailNumber = wx.ComboBox(self,
-1,
size=(-1, -1),
choices=self.MonitorList,
style=wx.CB_DROPDOWN
| wx.CB_READONLY | wx.CB_SORT)
self.Bind(wx.EVT_COMBOBOX, self.onChangingMonitor,
self.thumbnailNumber)
self.currentSource = wx.TextCtrl(self,
-1,
"No Source Selected",
style=wx.TE_READONLY)
btnSizer_1 = wx.BoxSizer(wx.HORIZONTAL)
self.btnPlay = wx.Button(self, wx.ID_FORWARD, label="Play")
self.btnStop = wx.Button(self, wx.ID_STOP, label="Stop")
self.Bind(wx.EVT_BUTTON, self.onPlay, self.btnPlay)
self.Bind(wx.EVT_BUTTON, self.onStop, self.btnStop)
self.btnPlay.Enable(False)
self.btnStop.Enable(False)
self.applyButton = wx.Button(self, wx.ID_APPLY)
self.applyButton.SetToolTip(wx.ToolTip("Apply and Save to file"))
self.Bind(wx.EVT_BUTTON, self.onApplySource, self.applyButton)
btnSizer_1.Add(self.btnPlay, 0, wx.ALIGN_LEFT | wx.ALL, 5)
btnSizer_1.Add(self.btnStop, 0,
wx.ALIGN_CENTER | wx.LEFT | wx.TOP | wx.DOWN, 5)
btnSizer_1.Add(self.applyButton, 0,
wx.ALIGN_RIGHT | wx.LEFT | wx.RIGHT | wx.TOP, 5)
sbSizer_1.Add(self.thumbnailNumber, 0,
wx.ALIGN_CENTRE | wx.LEFT | wx.RIGHT | wx.TOP, 5)
sbSizer_1.Add(
self.currentSource, 0,
wx.EXPAND | wx.ALIGN_CENTRE | wx.LEFT | wx.RIGHT | wx.TOP, 5)
sbSizer_1.Add(btnSizer_1, 0, wx.EXPAND | wx.ALIGN_BOTTOM | wx.TOP, 5)
lowerSizer.Add(sbSizer_1, 0, wx.EXPAND | wx.ALL, 5)
#Static box2 (CENTER)
sb_2 = wx.StaticBox(self, -1, "Select Video input")
sbSizer_2 = wx.StaticBoxSizer(sb_2, wx.VERTICAL)
grid2 = wx.FlexGridSizer(0, 2, 0, 0)
n_cams = options.GetOption("Webcams")
self.WebcamsList = ['Webcam %s' % (int(w) + 1) for w in range(n_cams)]
rb1 = wx.RadioButton(self, -1, 'Camera', style=wx.RB_GROUP)
source1 = wx.ComboBox(self,
-1,
size=(285, -1),
choices=self.WebcamsList,
style=wx.CB_DROPDOWN | wx.CB_READONLY
| wx.CB_SORT)
self.Bind(wx.EVT_COMBOBOX, self.sourceCallback, source1)
rb2 = wx.RadioButton(self, -1, 'File')
source2 = FileBrowseButton(self,
-1,
labelText='',
size=(300, -1),
changeCallback=self.sourceCallback)
rb3 = wx.RadioButton(self, -1, 'Folder')
source3 = DirBrowseButton(self,
style=wx.DD_DIR_MUST_EXIST,
labelText='',
size=(300, -1),
changeCallback=self.sourceCallback)
self.controls = []
self.controls.append((rb1, source1))
self.controls.append((rb2, source2))
self.controls.append((rb3, source3))
for radio, source in self.controls:
grid2.Add(radio, 0,
wx.ALIGN_LEFT | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 2)
grid2.Add(source, 0,
wx.ALIGN_CENTRE | wx.ALIGN_CENTER_VERTICAL | wx.ALL, 2)
self.Bind(wx.EVT_RADIOBUTTON, self.onChangeSource, radio)
source.Enable(False)
self.controls[0][1].Enable(True)
#grid2.Add(wx.StaticText(self, -1, ""))
sbSizer_2.Add(grid2)
lowerSizer.Add(sbSizer_2, 0, wx.EXPAND | wx.ALL, 5)
#Static box3 (RIGHT)
sb_3 = wx.StaticBox(self, -1, "Set Tracking Parameters")
sbSizer_3 = wx.StaticBoxSizer(sb_3, wx.VERTICAL)
sbSizer_31 = wx.BoxSizer(wx.HORIZONTAL)
self.activateTracking = wx.CheckBox(self, -1, "Activate Tracking")
self.activateTracking.SetValue(False)
self.activateTracking.Bind(wx.EVT_CHECKBOX, self.onActivateTracking)
self.isSDMonitor = wx.CheckBox(self, -1, "Sleep Deprivation Monitor")
self.isSDMonitor.SetValue(False)
self.isSDMonitor.Bind(wx.EVT_CHECKBOX, self.onSDMonitor)
self.isSDMonitor.Enable(False)
sbSizer_31.Add(self.activateTracking, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 5)
sbSizer_31.Add(self.isSDMonitor, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 5)
self.pickMaskBrowser = FileBrowseButton(self,
-1,
labelText='Mask File')
#sbSizer_3.Add ( self.activateTracking , 0, wx.ALIGN_LEFT|wx.LEFT|wx.RIGHT|wx.TOP, 5 )
sbSizer_3.Add(sbSizer_31, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 5)
sbSizer_3.Add(self.pickMaskBrowser, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP | wx.EXPAND,
5)
#trackingTypeSizer = wx.Sizer(wx.HORIZONTAL)
self.trackDistanceRadio = wx.RadioButton(
self, -1, "Activity as distance traveled", style=wx.RB_GROUP)
self.trackVirtualBM = wx.RadioButton(
self, -1, "Activity as midline crossings count")
self.trackPosition = wx.RadioButton(self, -1, "Only position of flies")
sbSizer_3.Add(wx.StaticText(self, -1, "Calculate fly activity as..."),
0, wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 5)
sbSizer_3.Add(self.trackDistanceRadio, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 2)
sbSizer_3.Add(self.trackVirtualBM, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 2)
sbSizer_3.Add(self.trackPosition, 0,
wx.ALIGN_LEFT | wx.LEFT | wx.RIGHT | wx.TOP, 2)
lowerSizer.Add(sbSizer_3, -1, wx.EXPAND | wx.ALL, 5)
self.SetSizer(lowerSizer)
self.Bind(EVT_THUMBNAIL_CLICKED, self.onThumbnailClicked)
def __getSource(self):
"""
check which source is ticked and what is the associated value
"""
for (r, s), st in zip(self.controls, range(3)):
if r.GetValue():
source = s.GetValue()
sourceType = st
return source, sourceType
def __getTrackingType(self):
"""
return which tracking we are chosing
['DISTANCE','VBS','XY_COORDS']
"""
if self.trackDistanceRadio.GetValue(): trackType = "DISTANCE"
elif self.trackVirtualBM.GetValue(): trackType = "VBS"
elif self.trackPosition.GetValue(): trackType = "XY_COORDS"
return trackType
def onPlay(self, event=None):
"""
"""
if self.thumbnail:
self.thumbnail.Play()
self.btnStop.Enable(True)
def onStop(self, event=None):
"""
"""
if self.thumbnail and self.thumbnail.isPlaying:
self.thumbnail.Stop()
self.btnStop.Enable(False)
def onThumbnailClicked(self, evt):
"""
Picking thumbnail by clicking on it
"""
self.monitor_number = evt.number + 1
self.thumbnail = evt.thumbnail
self.thumbnailNumber.SetValue(self.MonitorList[self.monitor_number -
1])
self.updateThumbnail()
def onChangingMonitor(self, evt):
"""
Picking thumbnail by using the dropbox
"""
sel = evt.GetString()
self.monitor_number = self.MonitorList.index(sel) + 1
self.thumbnail = self.parent.scrollThumbnails.previewPanels[
self.monitor_number] #this is not very elegant
self.updateThumbnail()
def updateThumbnail(self):
"""
Refreshing thumbnail data
"""
if options.HasMonitor(self.monitor_number):
sourceType, source, track, mask_file, trackType, isSDMonitor = options.GetMonitor(
self.monitor_number)
else:
sourceType, source, track, mask_file, trackType, isSDMonitor = [
0, '', False, '', 1, False
]
if sourceType == 0 and source != '':
source = self.WebcamsList[source]
self.source = self.thumbnail.source = source
self.sourceType = self.thumbnail.sourceType = sourceType
self.thumbnail.track = track
if self.thumbnail.hasMonitor():
self.thumbnail.mon.isSDMonitor = isSDMonitor
#update first static box
active = self.thumbnail.hasMonitor()
self.applyButton.Enable(active)
self.btnPlay.Enable(active)
self.btnStop.Enable(active and self.thumbnail.isPlaying)
text = os.path.split(str(self.source))[1] or "No Source Selected"
self.currentSource.SetValue(text)
#update second static box
for radio, src in self.controls:
src.Enable(False)
src.SetValue('')
radio, src = self.controls[self.sourceType]
radio.SetValue(True)
src.Enable(True)
src.SetValue(self.source)
#update third static box
self.activateTracking.SetValue(self.thumbnail.track)
self.isSDMonitor.SetValue(isSDMonitor)
self.pickMaskBrowser.SetValue(mask_file or '')
[self.trackDistanceRadio, self.trackVirtualBM,
self.trackPosition][trackType].SetValue(True)
def sourceCallback(self, event):
"""
"""
self.applyButton.Enable(True)
def onChangeSource(self, event):
"""
"""
radio_selected = event.GetEventObject()
for radio, source in self.controls:
if radio is radio_selected:
source.Enable(True)
else:
source.Enable(False)
self.applyButton.Enable(True)
def onApplySource(self, event):
"""
"""
source, sourceType = self.__getSource()
track = self.activateTracking.GetValue()
self.mask_file = self.pickMaskBrowser.GetValue()
self.trackType = self.__getTrackingType()
if self.thumbnail:
if sourceType > 0: camera = source
else: camera = self.WebcamsList.index(source)
self.thumbnail.source = camera
self.thumbnail.sourceType = sourceType
#Change the source text
self.currentSource.SetValue(os.path.split(source)[1])
#Set thumbnail's source
self.thumbnail.setMonitor(camera)
#Enable buttons
self.btnPlay.Enable(True)
self.activateTracking.Enable(True)
self.pickMaskBrowser.Enable(True)
self.saveMonitorConfiguration()
def saveMonitorConfiguration(self):
"""
"""
options.SetMonitor(self.monitor_number, self.thumbnail.sourceType,
self.thumbnail.source + 1, self.thumbnail.track,
self.mask_file, self.trackType,
self.thumbnail.mon.isSDMonitor)
options.Save()
def onActivateTracking(self, event):
"""
"""
if self.thumbnail:
self.thumbnail.track = event.IsChecked()
def onSDMonitor(self, event):
"""
"""
if self.thumbnail:
self.thumbnail.mon.isSDMonitor = event.IsChecked()
