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 test_04_01_read_omexml_metadata(self):
path = os.path.join(os.path.dirname(__file__), "Channel1-01-A-01.tif")
xml = F.get_omexml_metadata(path)
pattern = r'<\s*Image\s+ID\s*=\s*"Image:0"\s+Name\s*=\s*"Channel1-01-A-01.tif"\s*>'
self.assertTrue(re.search(pattern, xml))
def test_04_01_read_omexml_metadata(self):
path = os.path.join(example_images_directory(), 'ExampleSBSImages',
'Channel1-01-A-01.tif')
xml = F.get_omexml_metadata(path)
pattern = r'<\s*Image\s+ID\s*=\s*"Image:0"\s+Name\s*=\s*"Channel1-01-A-01.tif"\s*>'
self.assertTrue(re.search(pattern, xml))
def test_04_01_read_omexml_metadata(self):
path = os.path.join(example_images_directory(), 'ExampleSBSImages',
'Channel1-01-A-01.tif')
xml = F.get_omexml_metadata(path)
pattern = r'<\s*Image\s+ID\s*=\s*"Image:0"\s+Name\s*=\s*"Channel1-01-A-01.tif"\s*>'
self.assertTrue(re.search(pattern, xml))
def test_04_01_read_omexml_metadata(self):
path = os.path.join(os.path.dirname(__file__), 'Channel1-01-A-01.tif')
xml = F.get_omexml_metadata(path)
pattern = r'<\s*Image\s+ID\s*=\s*"Image:0"\s+Name\s*=\s*"Channel1-01-A-01.tif"\s*>'
self.assertTrue(re.search(pattern, xml))
