def add_channelfn(self, can_remove=True):
'''Add another image channel
can_remove - true if we are allowed to remove this channel
'''
group = cps.SettingsGroup()
self.channels.append(group)
#Check which cellprofiler image we are in the group
#(each channel translates to a single cellprofiler image)
cpimg_index = 0
for channel in self.channels:
if id(channel) == id(group):
break
cpimg_index += 1
group.append("divider", cps.Divider(line=True))
group.append("cpimage_name", cps.ImageNameProvider(
'Image name', default_cpimage_name(cpimg_index)))
channel_numbers = [
str(x) for x in range(0, max(10, len(self.channels)+2)) ]
group.append("channel_number", cps.Choice(
"Channel number:", channel_numbers, channel_numbers[len(self.channels)-1],
doc = """(Used only for multichannel images)
The channels of a multichannel image are numbered starting from 0 (zero).
Each channel is a greyscale image, acquired using different
illumination sources and/or optics. Use this setting to pick
the channel to associate with the image or images you load from
OMERO."""))
group.can_remove = can_remove
if can_remove:
group.append("remover", cps.RemoveSettingButton(
"Remove this channel", "Remove channel", self.channels, group))
def add_channelfn(self, can_remove=True):
'''Add another image channel
can_remove - true if we are allowed to remove this channel
'''
group = cps.SettingsGroup()
self.channels.append(group)
# Check which cellprofiler image we are in the group
# (each channel translates to a single cellprofiler image)
cpimg_index = 0
for channel in self.channels:
if id(channel) == id(group):
break
cpimg_index += 1
group.append("divider", cps.Divider(line=True))
group.append("cpimage_name", cps.ImageNameProvider(
'Image name', default_cpimage_name(cpimg_index)))
channel_numbers = [
str(x) for x in range(0, max(10, len(self.channels) + 2))]
group.append("channel_number", cps.Choice(
"Channel number:", channel_numbers, channel_numbers[len(self.channels) - 1],
doc="""(Used only for multichannel images)
The channels of a multichannel image are numbered starting from 0 (zero).
Each channel is a greyscale image, acquired using different
illumination sources and/or optics. Use this setting to pick
the channel to associate with the image or images you load from
OMERO."""))
group.can_remove = can_remove
if can_remove:
group.append("remover", cps.RemoveSettingButton(
"Remove this channel", "Remove channel", self.channels, group))
def load_channels(self):
'''Add and set channels based on an image from omero '''
try:
self.create_omero_gateway()
id = int(self.omero_object_id.value)
if self.omero_object == MS_IMAGE:
omero_image = self.omero_gateway.getImage(id)
elif self.omero_object == MS_DATASET:
images_from_dataset = self.get_images_from_dataset(id, 1)
if len(images_from_dataset) == 0:
omero_image = None
else:
omero_image = images_from_dataset[0]
elif self.omero_object == MS_PLATE:
wells_from_plate = self.get_wells_from_plate(id, 1)
if len(wells_from_plate) == 0:
omero_image = None
else:
omero_well = wells_from_plate[0]
omero_image = omero_well.getWellSample(0).getImage()
if omero_image is None:
# Don't say plate or dataset not found as they might still exist but do not have
# images attached to them. Another reason for not being able to find images is
# because the omero account used does not have permissions to retrieve the image
# or images.
raise RuntimeError("No image found for %s with id %d" %
(self.omero_object, id))
omero_image_id = omero_image.getId().getValue()
pixels = self.omero_gateway.getPixelsFromImage(omero_image_id)[0]
#The pixels doesn't have all the (logical) channels
#because of lazy loading. So the pixels is requested
#again, but in a way to get the channels as well.
pixels = self.omero_gateway.getPixels(pixels.getId().getValue())
#repopulate channels based on the retrieved pixels.
#note: cannot say self.channels=[] because the channel_count
#is associated with the object self.channels refers to.
for channel in self.channels[:]:
self.channels.remove(channel)
omero_channels = [channel for channel in pixels.iterateChannels()]
number_of_channels = pixels.getSizeC().getValue()
for channel_number in range(0, number_of_channels):
omero_channel = omero_channels[
channel_number].getLogicalChannel()
#load default cpimage name in case the logical channel name
# cannot be retrieved. e.g. when the logical channel name is null
try:
omero_channel_name = omero_channel.getName().getValue(
).strip()
except:
omero_channel_name = default_cpimage_name(channel_number)
self.add_channelfn(channel_number != 0)
self.channels[-1].cpimage_name.set_value(omero_channel_name)
self.channels[-1].channel_number.set_value(str(channel_number))
#Close the session just in case the user decides not to run
#the pipeline.
self.omero_client.closeSession()
self.omero_client = None
wx.MessageBox(
"Retrieved %d channel(s) from OMERO" % number_of_channels, "",
wx.ICON_INFORMATION)
except:
wx.MessageBox(traceback.format_exc(limit=0), "Exception",
wx.ICON_ERROR)
def load_channels(self):
'''Add and set channels based on an image from omero '''
try:
self.create_omero_gateway()
id = int(self.omero_object_id.value)
if self.omero_object == MS_IMAGE:
omero_image = self.omero_gateway.getImage(id)
elif self.omero_object == MS_DATASET:
images_from_dataset = self.get_images_from_dataset(id, 1)
if len(images_from_dataset) == 0:
omero_image = None
else:
omero_image = images_from_dataset[0]
elif self.omero_object == MS_PLATE:
wells_from_plate = self.get_wells_from_plate(id, 1)
if len(wells_from_plate) == 0:
omero_image = None
else:
omero_well = wells_from_plate[0]
omero_image = omero_well.getWellSample(0).getImage()
if omero_image is None:
# Don't say plate or dataset not found as they might still exist but do not have
# images attached to them. Another reason for not being able to find images is
# because the omero account used does not have permissions to retrieve the image
# or images.
raise RuntimeError("No image found for %s with id %d"%(self.omero_object,id))
omero_image_id = omero_image.getId().getValue()
pixels = self.omero_gateway.getPixelsFromImage(omero_image_id)[0]
#The pixels doesn't have all the (logical) channels
#because of lazy loading. So the pixels is requested
#again, but in a way to get the channels as well.
pixels = self.omero_gateway.getPixels(pixels.getId().getValue())
#repopulate channels based on the retrieved pixels.
#note: cannot say self.channels=[] because the channel_count
#is associated with the object self.channels refers to.
for channel in self.channels[:]:
self.channels.remove(channel)
omero_channels = [channel for channel in pixels.iterateChannels()]
number_of_channels = pixels.getSizeC().getValue()
for channel_number in range(0, number_of_channels):
omero_channel = omero_channels[channel_number].getLogicalChannel()
#load default cpimage name in case the logical channel name
# cannot be retrieved. e.g. when the logical channel name is null
try:
omero_channel_name = omero_channel.getName().getValue().strip()
except:
omero_channel_name = default_cpimage_name(channel_number)
self.add_channelfn(channel_number != 0)
self.channels[-1].cpimage_name.set_value(omero_channel_name)
self.channels[-1].channel_number.set_value(str(channel_number))
#Close the session just in case the user decides not to run
#the pipeline.
self.omero_client.closeSession()
self.omero_client = None
wx.MessageBox("Retrieved %d channel(s) from OMERO"%number_of_channels, "", wx.ICON_INFORMATION)
except:
wx.MessageBox(traceback.format_exc(limit=0), "Exception", wx.ICON_ERROR);
