def testEditSingleC(self, targetName, greyscale, tmpdir):
sizec = 1
# 1 channel so should default to greyscale model
expected_greyscale = ((greyscale is None) or greyscale)
self.create_image(sizec=sizec)
rd = self.get_render_def(sizec=sizec, greyscale=greyscale)
rdfile = tmpdir.join('render-test-editsinglec.json')
# Should work with json and yaml, but yaml is an optional dependency
rdfile.write(json.dumps(rd))
target = getattr(self, targetName)
self.args += ["edit", target, str(rdfile)]
self.cli.invoke(self.args, strict=True)
iids = self.get_target_imageids(target)
print 'Got %d images' % len(iids)
gw = BlitzGateway(client_obj=self.client)
for iid in iids:
# Get the updated object
img = gw.getObject('Image', iid)
# Note: calling _prepareRE below does NOT suffice!
img._prepareRenderingEngine() # Call *before* getChannels
# Passing noRE to getChannels below also prevents leaking
# the RenderingEngine but then Nones are returned later.
channels = img.getChannels()
assert len(channels) == sizec
for c in xrange(len(channels)):
self.assert_channel_rdef(channels[c], rd['channels'][c + 1])
self.assert_image_rmodel(img, expected_greyscale)
img._closeRE()
assert not gw._assert_unregistered("testEditSingleC")
def testEdit(self, targetName, tmpdir):
sizec = 4
greyscale = None
# 4 channels so should default to colour model
expected_greyscale = False
self.create_image(sizec=sizec)
rd = self.get_render_def(sizec=sizec, greyscale=greyscale)
rdfile = tmpdir.join('render-test-edit.json')
# Should work with json and yaml, but yaml is an optional dependency
rdfile.write(json.dumps(rd))
target = getattr(self, targetName)
self.args += ["edit", target, str(rdfile)]
self.cli.invoke(self.args, strict=True)
iids = self.get_target_imageids(target)
print 'Got %d images' % len(iids)
gw = BlitzGateway(client_obj=self.client)
for iid in iids:
# Get the updated object
img = gw.getObject('Image', iid)
channels = img.getChannels()
assert len(channels) == sizec
for c in xrange(len(channels)):
self.assert_channel_rdef(channels[c], rd['channels'][c + 1])
self.assert_image_rmodel(img, expected_greyscale)
img._closeRE()
assert not gw._assert_unregistered("testEdit")
def info(self, args):
client = self.ctx.conn(args)
gateway = BlitzGateway(client_obj=client)
first = True
for img in self.render_images(gateway, args.object, batch=1):
ro = RenderObject(img)
try:
if args.style == 'plain':
self.ctx.out(ro)
else:
if not first:
self.ctx.die(
103,
"Output styles not supported for multiple images")
self.ctx.out(pydict_text_io.dump(ro.to_dict(), args.style))
first = False
finally:
ro.close()
gateway._assert_unregistered("info")
def edit(self, args):
client = self.ctx.conn(args)
gateway = BlitzGateway(client_obj=client)
newchannels = {}
data = pydict_text_io.load(
args.channels, session=client.getSession())
if 'channels' not in data:
self.ctx.die(104, "ERROR: No channels found in %s" % args.channels)
for chindex, chdict in data['channels'].iteritems():
try:
cindex = int(chindex)
except Exception as e:
self.ctx.err('ERROR: %s' % e)
self.ctx.die(
105, "Invalid channel index: %s" % chindex)
try:
cobj = ChannelObject(chdict)
if (cobj.min is None) != (cobj.max is None):
raise Exception('Both or neither of min and max required')
newchannels[cindex] = cobj
print '%d:%s' % (cindex, cobj)
except Exception as e:
self.ctx.err('ERROR: %s' % e)
self.ctx.die(
105, "Invalid channel description: %s" % chdict)
try:
greyscale = data['greyscale']
except KeyError:
greyscale = None
namedict = {}
cindices = []
rangelist = []
colourlist = []
for (i, c) in newchannels.iteritems():
if c.label:
namedict[i] = c.label
if not c.active:
continue
cindices.append(i)
rangelist.append([c.min, c.max])
colourlist.append(c.color)
iids = []
for img in self.render_images(gateway, args.object, batch=1):
iids.append(img.id)
try:
img.setActiveChannels(
cindices, windows=rangelist, colors=colourlist, noRE=True)
if greyscale is not None:
if greyscale:
img.setGreyscaleRenderingModel()
else:
img.setColorRenderingModel()
img.saveDefaults()
self.ctx.dbg(
"Updated rendering settings for Image:%s" % img.id)
if not args.skipthumbs:
self._generate_thumbs([img])
if args.copy:
# Edit first image only, copy to rest
# Don't close source image until outer
# loop is done.
self._copy_single(gateway,
img, args.object,
args.skipthumbs)
break
finally:
img._closeRE()
if namedict:
self._update_channel_names(gateway, iids, namedict)
gateway._assert_unregistered("edit")
def copy(self, args):
client = self.ctx.conn(args)
gateway = BlitzGateway(client_obj=client)
self._copy(gateway, args.object, args.target, args.skipthumbs)
gateway._assert_unregistered("copy")
class TestRender(CLITest):
def setup_method(self, method):
super(TestRender, self).setup_method(method)
self.cli.register("render", RenderControl, "TEST")
self.args += ["render"]
def create_image(self, sizec=4):
self.gw = BlitzGateway(client_obj=self.client)
self.plates = []
for plate in self.import_plates(fields=2, sizeC=sizec, screens=1):
self.plates.append(self.gw.getObject("Plate", plate.id.val))
# Now pick the first Image
self.imgobj = list(self.plates[0].listChildren())[0].getImage(index=0)
self.idonly = "%s" % self.imgobj.id
self.imageid = "Image:%s" % self.imgobj.id
self.plateid = "Plate:%s" % self.plates[0].id
self.screenid = "Screen:%s" % self.plates[0].getParent().id
# And another one as the source for copies
self.source = list(self.plates[0].listChildren())[0].getImage(index=1)
self.source = "Image:%s" % self.source.id
# And for all the images, pre-load a thumbnail
for p in self.plates:
for w in p.listChildren():
for i in range(w.countWellSample()):
img = w.getImage(index=i)
img.getThumbnail(
size=(96,), direct=False)
img._closeRE()
self.imgobj._closeRE()
assert not self.gw._assert_unregistered("create_image")
def get_target_imageids(self, target):
if target in (self.idonly, self.imageid):
return [self.idonly]
if target == self.plateid:
imgs = []
for w in self.plates[0].listChildren():
imgs.extend([w.getImage(0).id, w.getImage(1).id])
return imgs
if target == self.screenid:
imgs = []
for s in self.plates:
for w in self.plates[0].listChildren():
imgs.extend([w.getImage(0).id, w.getImage(1).id])
return imgs
raise Exception('Unknown target: %s' % target)
def get_render_def(self, sizec=4, greyscale=None):
channels = {}
channels[1] = {
'label': self.uuid(),
'color': '123456',
'min': 11,
'max': 22,
}
channels[2] = {
'label': self.uuid(),
'color': '789ABC',
'min': 33,
'max': 44,
}
channels[3] = {
'label': self.uuid(),
'color': 'DEF012',
'min': 55,
'max': 66,
}
channels[4] = {
'label': self.uuid(),
'color': '345678',
'min': 77,
'max': 88,
}
for k in xrange(sizec, 4):
del channels[k + 1]
d = {'channels': channels}
if greyscale is not None:
d['greyscale'] = greyscale
return d
def assert_channel_rdef(self, channel, rdef):
assert channel.getLabel() == rdef['label']
assert channel.getColor().getHtml() == rdef['color']
assert channel.getWindowStart() == rdef['min']
assert channel.getWindowEnd() == rdef['max']
def assert_image_rmodel(self, img, greyscale):
assert img.isGreyscaleRenderingModel() == greyscale
# rendering tests
# ========================================================================
@pytest.mark.parametrize('targetName', sorted(SUPPORTED.keys()))
def testNonExistingImage(self, targetName, tmpdir):
target = SUPPORTED[targetName]
self.args += ["info", target]
with pytest.raises(NonZeroReturnCode):
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('targetName', sorted(SUPPORTED.keys()))
def testInfo(self, targetName, tmpdir):
self.create_image()
target = getattr(self, targetName)
self.args += ["info", target]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('style', ['json', 'yaml'])
def testInfoStyle(self, style):
self.create_image()
target = self.imageid
self.args += ["info", target]
self.args += ['--style', style]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('targetName', sorted(SUPPORTED.keys()))
def testCopy(self, targetName, tmpdir):
self.create_image()
target = getattr(self, targetName)
self.args += ["copy", self.source, target]
self.cli.invoke(self.args, strict=True)
@pytest.mark.parametrize('targetName', sorted(SUPPORTED.keys()))
@pytest.mark.broken(
reason=('https://trello.com/c/lyyGuRow/'
'657-incorrect-logical-channels-in-clitest-importplates'))
@pytest.mark.xfail(
reason=('https://trello.com/c/lyyGuRow/'
'657-incorrect-logical-channels-in-clitest-importplates'))
def testEdit(self, targetName, tmpdir):
sizec = 4
greyscale = None
# 4 channels so should default to colour model
expected_greyscale = False
self.create_image(sizec=sizec)
rd = self.get_render_def(sizec=sizec, greyscale=greyscale)
rdfile = tmpdir.join('render-test-edit.json')
# Should work with json and yaml, but yaml is an optional dependency
rdfile.write(json.dumps(rd))
target = getattr(self, targetName)
self.args += ["edit", target, str(rdfile)]
self.cli.invoke(self.args, strict=True)
iids = self.get_target_imageids(target)
print 'Got %d images' % len(iids)
gw = BlitzGateway(client_obj=self.client)
for iid in iids:
# Get the updated object
img = gw.getObject('Image', iid)
channels = img.getChannels()
assert len(channels) == sizec
for c in xrange(len(channels)):
self.assert_channel_rdef(channels[c], rd['channels'][c + 1])
self.assert_image_rmodel(img, expected_greyscale)
img._closeRE()
assert not gw._assert_unregistered("testEdit")
# Once testEdit is no longer broken testEditSingleC could be merged into
# it with sizec and greyscale parameters
@pytest.mark.parametrize('targetName', sorted(SUPPORTED.keys()))
@pytest.mark.parametrize('greyscale', [None, True, False])
def testEditSingleC(self, targetName, greyscale, tmpdir):
sizec = 1
# 1 channel so should default to greyscale model
expected_greyscale = ((greyscale is None) or greyscale)
self.create_image(sizec=sizec)
rd = self.get_render_def(sizec=sizec, greyscale=greyscale)
rdfile = tmpdir.join('render-test-editsinglec.json')
# Should work with json and yaml, but yaml is an optional dependency
rdfile.write(json.dumps(rd))
target = getattr(self, targetName)
self.args += ["edit", target, str(rdfile)]
self.cli.invoke(self.args, strict=True)
iids = self.get_target_imageids(target)
print 'Got %d images' % len(iids)
gw = BlitzGateway(client_obj=self.client)
for iid in iids:
# Get the updated object
img = gw.getObject('Image', iid)
# Note: calling _prepareRE below does NOT suffice!
img._prepareRenderingEngine() # Call *before* getChannels
# Passing noRE to getChannels below also prevents leaking
# the RenderingEngine but then Nones are returned later.
channels = img.getChannels()
assert len(channels) == sizec
for c in xrange(len(channels)):
self.assert_channel_rdef(channels[c], rd['channels'][c + 1])
self.assert_image_rmodel(img, expected_greyscale)
img._closeRE()
assert not gw._assert_unregistered("testEditSingleC")
