def test_04_04_abspath(self):
# Specify an absolute path for the images.
def alter_fn(module):
self.assertTrue(isinstance(module, C.CreateWebPage))
module.directory_choice.dir_choice = C.ABSOLUTE_FOLDER_NAME
module.directory_choice.custom_path = self.alt_directory
filenames = [(None, 'A%02d.png' % i) for i in range(1, 3)]
self.run_create_webpage(filenames, alter_fn=alter_fn)
dom = self.read_html(os.path.join(self.alt_directory, DEFAULT_HTML_FILE))
imgs = dom.getElementsByTagName("img")
self.assertEqual(len(imgs), 2)
for img in imgs:
self.assertTrue(img.hasAttribute("src"))
image_name = str(img.getAttribute("src"))
path = url2pathname(image_name)
self.assertTrue(os.path.exists(path))
def test_04_04_abspath(self):
# Specify an absolute path for the images.
def alter_fn(module):
self.assertTrue(isinstance(module, C.CreateWebPage))
module.directory_choice.dir_choice = C.ABSOLUTE_FOLDER_NAME
module.directory_choice.custom_path = self.alt_directory
filenames = [(None, 'A%02d.png' % i) for i in range(1, 3)]
self.run_create_webpage(filenames, alter_fn=alter_fn)
dom = self.read_html(os.path.join(self.alt_directory, DEFAULT_HTML_FILE))
imgs = dom.getElementsByTagName("img")
self.assertEqual(len(imgs), 2)
for img in imgs:
self.assertTrue(img.hasAttribute("src"))
image_name = str(img.getAttribute("src"))
path = url2pathname(image_name)
self.assertTrue(os.path.exists(path))
def do_update_metadata(self, group):
filelist = self.workspace.file_list
urls = set([
ipd.url for ipd in self.pipeline.get_filtered_image_plane_details(
self.workspace)
])
if len(urls) == 0:
return
def msg(url):
return "Processing %s" % url
import wx
from bioformats.formatreader import get_omexml_metadata
from bioformats.omexml import OMEXML
from cellprofiler.modules.loadimages import url2pathname
with wx.ProgressDialog("Updating metadata",
msg(list(urls)[0]),
len(urls),
style=wx.PD_CAN_ABORT
| wx.PD_APP_MODAL
| wx.PD_ELAPSED_TIME
| wx.PD_REMAINING_TIME) as dlg:
for i, url in enumerate(urls):
if i > 0:
keep_going, _ = dlg.Update(i, msg(url))
if not keep_going:
break
if group.filter_choice == F_FILTERED_IMAGES:
match = group.filter.evaluate(
(cps.FileCollectionDisplay.NODE_IMAGE_PLANE,
Images.url_to_modpath(url), self))
if not match:
continue
metadata = filelist.get_metadata(url)
if metadata is None:
metadata = get_omexml_metadata(url2pathname(url))
filelist.add_metadata(url, metadata)
metadata = OMEXML(metadata)
exemplar = cpp.ImagePlaneDetails(url, None, None, None)
if not self.pipeline.find_image_plane_details(exemplar):
self.pipeline.add_image_plane_details([exemplar])
self.pipeline.add_image_metadata(url, metadata)
self.ipds = self.pipeline.get_filtered_image_plane_details(
self.workspace)
self.update_metadata_keys()
def do_update_metadata(self, group):
filelist = self.workspace.file_list
urls = set([ipd.url for ipd in self.pipeline.get_filtered_image_plane_details(self.workspace)])
if len(urls) == 0:
return
def msg(url):
return "Processing %s" % url
import wx
from bioformats.formatreader import get_omexml_metadata
from bioformats.omexml import OMEXML
from cellprofiler.modules.loadimages import url2pathname
with wx.ProgressDialog(
"Updating metadata",
msg(list(urls)[0]),
len(urls),
style=wx.PD_CAN_ABORT | wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME | wx.PD_REMAINING_TIME,
) as dlg:
for i, url in enumerate(urls):
if i > 0:
keep_going, _ = dlg.Update(i, msg(url))
if not keep_going:
break
if group.filter_choice == F_FILTERED_IMAGES:
match = group.filter.evaluate(
(cps.FileCollectionDisplay.NODE_IMAGE_PLANE, Images.url_to_modpath(url), self)
)
if not match:
continue
metadata = filelist.get_metadata(url)
if metadata is None:
metadata = get_omexml_metadata(url2pathname(url))
filelist.add_metadata(url, metadata)
metadata = OMEXML(metadata)
exemplar = cpp.ImagePlaneDetails(url, None, None, None)
if not self.pipeline.find_image_plane_details(exemplar):
self.pipeline.add_image_plane_details([exemplar])
self.pipeline.add_image_metadata(url, metadata)
self.ipds = self.pipeline.get_filtered_image_plane_details(self.workspace)
self.update_metadata_keys()
def fn():
from bioformats import load_image_url
import javabridge
from scipy.io.matlab.mio import loadmat
from cellprofiler.modules.loadimages import url2pathname
javabridge.attach()
with self.image_dict_lock:
generation = self.image_dict_generation
for k, v in well.iteritems():
sd = {}
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
self.image_dict[k] = sd
for c, fd in enumerate(v):
if PlateData.D_CHANNEL in fd:
channel = fd[PlateData.D_CHANNEL]
else:
channel = str(c+1)
url = fd[PlateData.D_FILENAME]
try:
if url.lower().endswith(".mat"):
img = loadmat(
url2pathname(url),
struct_as_record=True)["Image"]
else:
img = load_image_url(url)
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
sd[channel] = img
except:
traceback.print_exc()
pass
wx.CallAfter(self.update_figure)
javabridge.static_call(
"java/lang/System", "gc", "()V")
javabridge.detach()
def fn():
from bioformats import load_image_url
import javabridge
from scipy.io.matlab.mio import loadmat
from cellprofiler.modules.loadimages import url2pathname
javabridge.attach()
with self.image_dict_lock:
generation = self.image_dict_generation
for k, v in well.iteritems():
sd = {}
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
self.image_dict[k] = sd
for c, fd in enumerate(v):
if PlateData.D_CHANNEL in fd:
channel = fd[PlateData.D_CHANNEL]
else:
channel = str(c + 1)
url = fd[PlateData.D_FILENAME]
try:
if url.lower().endswith(".mat"):
img = loadmat(
url2pathname(url),
struct_as_record=True)["Image"]
else:
img = load_image_url(url)
with self.image_dict_lock:
if self.image_dict_generation > generation:
return
sd[channel] = img
except:
traceback.print_exc()
pass
wx.CallAfter(self.update_figure)
javabridge.static_call(
"java/lang/System", "gc", "()V")
javabridge.detach()
