def run(self, workspace):
'''Run on an image set'''
image_name = self.image_name.value
m = workspace.measurements
#
# Get the path and file names from the measurements
#
path = m.get_current_image_measurement('PathName_%s' % image_name)
file_name = m.get_current_image_measurement('FileName_%s' % image_name)
#
# Pull out the prefix, middle and suffix from the file name
#
prefix = file_name[:self.number_characters_prefix.value]
if self.number_characters_suffix.value == 0:
suffix = ""
middle = file_name[self.number_characters_prefix.value:]
else:
suffix = file_name[-self.number_characters_suffix.value:]
middle = file_name[self.number_characters_prefix.value:
-self.number_characters_suffix.value]
#
# Possibly apply the renumbering rule
#
if self.action == A_RENUMBER:
if not middle.isdigit():
raise ValueError(
('The middle of the filename, "%s", is "%s".\n'
"It has non-numeric characters and can't be "
"converted to a number") %
( file_name, middle ))
format = '%0'+str(self.number_digits.value)+'d'
middle = format % int(middle)
elif self.action == A_DELETE:
middle = ""
else:
raise NotImplementedError("Unknown action: %s" % self.action.value)
#
# Possibly apply the added text
#
if self.wants_text:
middle += self.text_to_add.value
new_file_name = prefix + middle + suffix
if self.wants_to_replace_spaces:
new_file_name = new_file_name.replace(
" ", self.space_replacement.value)
if self.show_window:
workspace.display_data.old_file_name = file_name
workspace.display_data.new_file_name = new_file_name
if workspace.pipeline.test_mode:
return
#
# Perform the actual renaming
#
# Most likely, we have a handle on the file open in BioFormats
from bioformats.formatreader import clear_image_reader_cache
clear_image_reader_cache()
os.rename(os.path.join(path, file_name),
os.path.join(path, new_file_name))
def exit_thread(self):
from bioformats.formatreader import clear_image_reader_cache
self.notify_socket.close()
clear_image_reader_cache()
J.detach()
if self.with_stop_run_loop:
stop_run_loop()
def exit_thread(self):
from bioformats.formatreader import clear_image_reader_cache
self.notify_socket.close()
clear_image_reader_cache()
J.detach()
if self.with_stop_run_loop:
stop_run_loop()
def OnClose(self, event):
if event.CanVeto() and not self.pipeline_controller.check_close():
event.Veto()
return
try:
self.__workspace.measurements.flush()
except:
logging.warning(
"Failed to flush temporary measurements file during close",
exc_info=True,
)
try:
from bioformats.formatreader import clear_image_reader_cache
clear_image_reader_cache()
except:
logging.warning(
"Failed to clear bioformats reader cache during close", exc_info=True,
)
try:
self.__preferences_view.close()
except:
logging.warning("Failed during close", exc_info=True)
try:
self.pipeline_controller.on_close()
except:
logging.warning("Failed to close the pipeline controller", exc_info=True)
try:
stop_validation_queue_thread()
except:
logging.warning("Failed to stop pipeline validation thread", exc_info=True)
wx.GetApp().ExitMainLoop()
def run(self, workspace):
'''Run on an image set'''
image_name = self.image_name.value
m = workspace.measurements
#
# Get the path and file names from the measurements
#
path = m.get_current_image_measurement('PathName_%s' % image_name)
file_name = m.get_current_image_measurement('FileName_%s' % image_name)
#
# Pull out the prefix, middle and suffix from the file name
#
prefix = file_name[:self.number_characters_prefix.value]
if self.number_characters_suffix.value == 0:
suffix = ""
middle = file_name[self.number_characters_prefix.value:]
else:
suffix = file_name[-self.number_characters_suffix.value:]
middle = file_name[self.number_characters_prefix.
value:-self.number_characters_suffix.value]
#
# Possibly apply the renumbering rule
#
if self.action == A_RENUMBER:
if not middle.isdigit():
raise ValueError(
('The middle of the filename, "%s", is "%s".\n'
"It has non-numeric characters and can't be "
"converted to a number") % (file_name, middle))
format = '%0' + str(self.number_digits.value) + 'd'
middle = format % int(middle)
elif self.action == A_DELETE:
middle = ""
else:
raise NotImplementedError("Unknown action: %s" % self.action.value)
#
# Possibly apply the added text
#
if self.wants_text:
middle += self.text_to_add.value
new_file_name = prefix + middle + suffix
if self.wants_to_replace_spaces:
new_file_name = new_file_name.replace(" ",
self.space_replacement.value)
if self.show_window:
workspace.display_data.old_file_name = file_name
workspace.display_data.new_file_name = new_file_name
if workspace.pipeline.test_mode:
return
#
# Perform the actual renaming
#
# Most likely, we have a handle on the file open in BioFormats
from bioformats.formatreader import clear_image_reader_cache
clear_image_reader_cache()
os.rename(os.path.join(path, file_name),
os.path.join(path, new_file_name))
def test_11_01_load_objects(self):
r = np.random.RandomState()
r.seed(1101)
labels = r.randint(0,10, size=(30,20)).astype(np.uint8)
handle, name = tempfile.mkstemp(".png")
fd = os.fdopen(handle, "wb")
img = PIL.Image.fromarray(labels, "L")
img.save(fd, "PNG")
fd.close()
png_path, png_file = os.path.split(name)
sbs_dir = os.path.join(example_images_directory(), "ExampleSBSImages")
csv_text = """%s_%s,%s_%s,%s_DNA,%s_DNA
%s,%s,Channel2-01-A-01.tif,%s
""" % (L.C_OBJECTS_FILE_NAME, OBJECTS_NAME,
L.C_OBJECTS_PATH_NAME, OBJECTS_NAME,
L.C_FILE_NAME, L.C_PATH_NAME,
png_file, png_path, sbs_dir)
pipeline, module, csv_name = self.make_pipeline(csv_text)
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(module, L.LoadData)
module.wants_images.value = True
try:
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(
pipeline, module, None, None, measurements, image_set_list)
pipeline.prepare_run(workspace)
key_names, g = pipeline.get_groupings(workspace)
self.assertEqual(len(g), 1)
module.prepare_group(workspace, g[0][0], g[0][1])
image_set = image_set_list.get_image_set(g[0][1][0]-1)
object_set = cpo.ObjectSet()
workspace = cpw.Workspace(pipeline, module, image_set,
object_set, measurements, image_set_list)
module.run(workspace)
objects = object_set.get_objects(OBJECTS_NAME)
self.assertTrue(np.all(objects.segmented == labels))
self.assertEqual(measurements.get_current_image_measurement(
L.I.FF_COUNT % OBJECTS_NAME), 9)
for feature in (L.I.M_LOCATION_CENTER_X,
L.I.M_LOCATION_CENTER_Y,
L.I.M_NUMBER_OBJECT_NUMBER):
value = measurements.get_current_measurement(
OBJECTS_NAME, feature)
self.assertEqual(len(value), 9)
finally:
clear_image_reader_cache()
os.remove(name)
os.remove(csv_name)
def test_11_01_load_objects(self):
r = np.random.RandomState()
r.seed(1101)
labels = r.randint(0,10, size=(30,20)).astype(np.uint8)
handle, name = tempfile.mkstemp(".png")
fd = os.fdopen(handle, "wb")
img = PIL.Image.fromarray(labels, "L")
img.save(fd, "PNG")
fd.close()
png_path, png_file = os.path.split(name)
sbs_dir = os.path.join(example_images_directory(), "ExampleSBSImages")
csv_text = """%s_%s,%s_%s,%s_DNA,%s_DNA
%s,%s,Channel2-01-A-01.tif,%s
""" % (L.C_OBJECTS_FILE_NAME, OBJECTS_NAME,
L.C_OBJECTS_PATH_NAME, OBJECTS_NAME,
L.C_FILE_NAME, L.C_PATH_NAME,
png_file, png_path, sbs_dir)
pipeline, module, csv_name = self.make_pipeline(csv_text)
assert isinstance(pipeline, cpp.Pipeline)
assert isinstance(module, L.LoadData)
module.wants_images.value = True
try:
image_set_list = cpi.ImageSetList()
measurements = cpmeas.Measurements()
workspace = cpw.Workspace(
pipeline, module, None, None, measurements, image_set_list)
pipeline.prepare_run(workspace)
key_names, g = pipeline.get_groupings(workspace)
self.assertEqual(len(g), 1)
module.prepare_group(workspace, g[0][0], g[0][1])
image_set = image_set_list.get_image_set(g[0][1][0]-1)
object_set = cpo.ObjectSet()
workspace = cpw.Workspace(pipeline, module, image_set,
object_set, measurements, image_set_list)
module.run(workspace)
objects = object_set.get_objects(OBJECTS_NAME)
self.assertTrue(np.all(objects.segmented == labels))
self.assertEqual(measurements.get_current_image_measurement(
L.I.FF_COUNT % OBJECTS_NAME), 9)
for feature in (L.I.M_LOCATION_CENTER_X,
L.I.M_LOCATION_CENTER_Y,
L.I.M_NUMBER_OBJECT_NUMBER):
value = measurements.get_current_measurement(
OBJECTS_NAME, feature)
self.assertEqual(len(value), 9)
finally:
clear_image_reader_cache()
os.remove(name)
os.remove(csv_name)
def exit_thread(self):
from bioformats.formatreader import clear_image_reader_cache
self.notify_socket.close()
clear_image_reader_cache()
J.detach()
def exit_thread(self):
from bioformats.formatreader import clear_image_reader_cache
self.notify_socket.close()
clear_image_reader_cache()
J.detach()