def on_show_imagej(self):
"""Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
"""
logger.debug("Starting ImageJ UI")
ui_service = ij2.get_ui_service(get_context())
if ui_service is not None and not ui_service.isVisible():
if cpprefs.get_headless():
# Silence the auto-updater in the headless preferences
#
ij2.update_never_remind()
ui_service.createUI()
elif ui_service is not None:
ui = ui_service.getDefaultUI()
J.execute_runnable_in_main_thread(
J.run_script(
"""new java.lang.Runnable() {
run: function() {
ui.getApplicationFrame().setVisible(true); }}""",
dict(ui=ui),
),
True,
)
def do_imagej(self, ijb, workspace, when=None):
if when == D_FIRST_IMAGE_SET:
choice = self.prepare_group_choice.value
command = self.prepare_group_command
macro = self.prepare_group_macro.value
options = self.prepare_group_options.value
d = self.pre_command_settings_dictionary
elif when == D_LAST_IMAGE_SET:
choice = self.post_group_choice.value
command = self.post_group_command
macro = self.post_group_macro.value
options = self.post_group_options.value
d = self.pre_command_settings_dictionary
else:
choice = self.command_or_macro.value
command = self.command
macro = self.macro.value
options = self.options.value
d = self.command_settings_dictionary
if choice == CM_COMMAND:
if self.is_advanced(command, d):
self.execute_advanced_command(workspace, command, d)
else:
ijb.execute_command(command.value, options)
elif choice == CM_MACRO:
macro = workspace.measurements.apply_metadata(macro)
ijb.execute_macro(macro)
if (choice != CM_NOTHING and (not cpprefs.get_headless())
and self.pause_before_proceeding):
import wx
wx.MessageBox(
"Please edit the image in ImageJ and hit OK to proceed",
"Waiting for ImageJ")
def interaction_request(self, module, *args, **kwargs):
'''make a request for GUI interaction via a pipeline event
module - target module for interaction request
headless_ok - True if the interaction request can be made in
a headless context. An example is synchronized access to
a shared resource which must be coordinated among all
workers.
'''
# See also:
# main().interaction_handler() in analysis_worker.py
# PipelineController.module_interaction_request() in pipelinecontroller.py
import cellprofiler.preferences as cpprefs
if "headless_ok" in kwargs:
tmp = kwargs.copy()
del tmp["headless_ok"]
headless_ok = kwargs["headless_ok"]
kwargs = tmp
else:
headless_ok = False
if self.interaction_handler is None:
if cpprefs.get_headless() and not headless_ok:
raise self.NoInteractionException()
else:
return module.handle_interaction(*args, **kwargs)
else:
return self.interaction_handler(module, *args, **kwargs)
def prepare_run(self, workspace):
'''Invoke the image_set_list pickling mechanism and save the pipeline'''
pipeline = workspace.pipeline
image_set_list = workspace.image_set_list
if pipeline.test_mode or self.from_old_matlab:
return True
if self.batch_mode.value:
self.enter_batch_mode(workspace)
return True
else:
path = self.save_pipeline(workspace)
if not cpprefs.get_headless():
import wx
wx.MessageBox(
"CreateBatchFiles saved pipeline to %s" % path,
caption="CreateBatchFiles: Batch file saved",
style=wx.OK | wx.ICON_INFORMATION)
if self.go_to_website:
try:
import webbrowser
import urllib
server_path = self.alter_path(os.path.dirname(path))
query = urllib.urlencode(dict(data_dir=server_path))
url = cpprefs.get_batchprofiler_url() + \
"/NewBatch.py?" + query
webbrowser.open_new(url)
except:
import traceback
traceback.print_exc()
return False
def do_imagej(self, workspace, when=None):
if when == D_FIRST_IMAGE_SET:
choice = self.prepare_group_choice.value
command = self.prepare_group_command
macro = self.prepare_group_macro.value
d = self.pre_command_settings_dictionary
elif when == D_LAST_IMAGE_SET:
choice = self.post_group_choice.value
command = self.post_group_command
macro = self.post_group_macro.value
d = self.pre_command_settings_dictionary
else:
choice = self.command_or_macro.value
command = self.command
macro = self.macro.value
d = self.command_settings_dictionary
if choice == CM_COMMAND:
self.execute_advanced_command(workspace, command, d)
elif choice == CM_MACRO:
macro = workspace.measurements.apply_metadata(macro)
script_service = ij2.get_script_service(get_context())
factory = script_service.getByName(self.macro_language.value)
engine = factory.getScriptEngine()
engine.put("ImageJ", get_context())
result = engine.evalS(macro)
if (choice != CM_NOTHING and (not cpprefs.get_headless())
and self.pause_before_proceeding):
import wx
wx.MessageBox(
"Please edit the image in ImageJ and hit OK to proceed",
"Waiting for ImageJ")
def do_imagej(self, ijb, workspace, when=None):
if when == D_FIRST_IMAGE_SET:
choice = self.prepare_group_choice.value
command = self.prepare_group_command
macro = self.prepare_group_macro.value
options = self.prepare_group_options.value
d = self.pre_command_settings_dictionary
elif when == D_LAST_IMAGE_SET:
choice = self.post_group_choice.value
command = self.post_group_command
macro = self.post_group_macro.value
options = self.post_group_options.value
d = self.pre_command_settings_dictionary
else:
choice = self.command_or_macro.value
command = self.command
macro = self.macro.value
options = self.options.value
d = self.command_settings_dictionary
if choice == CM_COMMAND:
if self.is_advanced(command, d):
self.execute_advanced_command(workspace, command, d)
else:
ijb.execute_command(command.value, options)
elif choice == CM_MACRO:
macro = workspace.measurements.apply_metadata(macro)
ijb.execute_macro(macro)
if (choice != CM_NOTHING and
(not cpprefs.get_headless()) and
self.pause_before_proceeding):
import wx
wx.MessageBox("Please edit the image in ImageJ and hit OK to proceed",
"Waiting for ImageJ")
def prepare_run(self, workspace):
'''Invoke the image_set_list pickling mechanism and save the pipeline'''
pipeline = workspace.pipeline
image_set_list = workspace.image_set_list
if pipeline.test_mode or self.from_old_matlab:
return True
if self.batch_mode.value:
self.enter_batch_mode(workspace)
return True
else:
path = self.save_pipeline(workspace)
if not cpprefs.get_headless():
import wx
wx.MessageBox(
"CreateBatchFiles saved pipeline to %s" % path,
caption="CreateBatchFiles: Batch file saved",
style=wx.OK | wx.ICON_INFORMATION)
if self.go_to_website:
try:
import webbrowser
import urllib
server_path = self.alter_path(os.path.dirname(path))
query = urllib.urlencode(dict(data_dir=server_path))
url = cpprefs.get_batchprofiler_url() + \
"/NewBatch.py?" + query
webbrowser.open_new(url)
except:
import traceback
traceback.print_exc()
return False
def do_imagej(self, workspace, when=None):
if when == D_FIRST_IMAGE_SET:
choice = self.prepare_group_choice.value
command = self.prepare_group_command
macro = self.prepare_group_macro.value
d = self.pre_command_settings_dictionary
elif when == D_LAST_IMAGE_SET:
choice = self.post_group_choice.value
command = self.post_group_command
macro = self.post_group_macro.value
d = self.pre_command_settings_dictionary
else:
choice = self.command_or_macro.value
command = self.command
macro = self.macro.value
d = self.command_settings_dictionary
if choice == CM_COMMAND:
self.execute_advanced_command(workspace, command, d)
elif choice == CM_MACRO:
macro = workspace.measurements.apply_metadata(macro)
script_service = ij2.get_script_service(get_context())
factory = script_service.getByName(self.macro_language.value)
engine = factory.getScriptEngine()
engine.put("ImageJ", get_context())
result = engine.evalS(macro)
if (choice != CM_NOTHING and
(not cpprefs.get_headless()) and
self.pause_before_proceeding):
import wx
wx.MessageBox("Please edit the image in ImageJ and hit OK to proceed",
"Waiting for ImageJ")
def check_overwrite(self, workspace):
"""Make sure it's ok to overwrite any existing files before starting run
workspace - workspace with all image sets already populated
returns True if ok to proceed, False if user cancels
"""
if self.wants_overwrite_without_warning:
return True
files_to_check = []
metadata_groups = self.get_metadata_groups(workspace)
for metadata_group in metadata_groups:
image_number = metadata_group.image_numbers[0]
files_to_check.append(
self.make_image_file_name(workspace, image_number))
files_to_overwrite = filter(os.path.isfile, files_to_check)
if len(files_to_overwrite) > 0:
if get_headless():
logger.error(
"ExportToACC is configured to refrain from overwriting files and the following file(s) already exist: %s"
% ", ".join(files_to_overwrite))
return False
msg = "Overwrite the following file(s)?\n" +\
"\n".join(files_to_overwrite)
import wx
result = wx.MessageBox(
msg,
caption="ExportToACC: Overwrite existing files",
style=wx.YES_NO | wx.NO_DEFAULT | wx.ICON_QUESTION)
if result != wx.YES:
return False
return True
def interaction_request(self, module, *args, **kwargs):
'''make a request for GUI interaction via a pipeline event
module - target module for interaction request
headless_ok - True if the interaction request can be made in
a headless context. An example is synchronized access to
a shared resource which must be coordinated among all
workers.
'''
# See also:
# main().interaction_handler() in analysis_worker.py
# PipelineController.module_interaction_request() in pipelinecontroller.py
import cellprofiler.preferences as cpprefs
if "headless_ok" in kwargs:
tmp = kwargs.copy()
del tmp["headless_ok"]
headless_ok = kwargs["headless_ok"]
kwargs = tmp
else:
headless_ok = False
if self.interaction_handler is None:
if cpprefs.get_headless() and not headless_ok:
raise self.NoInteractionException()
else:
return module.handle_interaction(*args, **kwargs)
else:
return self.interaction_handler(module, *args, **kwargs)
def show_warning(title, message, get_preference, set_preference):
"""Show a silenceable warning message to the user
title - title for the dialog box
message - message to be displayed
get_preference - function that gets a user preference: do you want to
show this warning?
set_preference - function that sets the user preference if they choose
not to see the warning again.
The message is printed to the console if headless.
"""
from cellprofiler.preferences import get_headless
if get_headless():
print(message)
return
if not get_preference():
return
import wx
if wx.GetApp() is None:
print(message)
return
with wx.Dialog(None, title=title) as dlg:
dlg.Sizer = sizer = wx.BoxSizer(wx.VERTICAL)
subsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(subsizer, 0, wx.EXPAND | wx.ALL, 5)
subsizer.Add(
wx.StaticBitmap(
dlg,
wx.ID_ANY,
wx.ArtProvider.GetBitmap(wx.ART_INFORMATION,
wx.ART_CMN_DIALOG),
),
0,
wx.ALIGN_LEFT | wx.ALIGN_TOP | wx.RIGHT,
5,
)
text = wx.StaticText(dlg, wx.ID_ANY, message)
subsizer.Add(text, 0, wx.ALIGN_LEFT | wx.ALIGN_TOP | wx.ALL, 5)
dont_show = wx.CheckBox(dlg, label="Don't show this message again.")
sizer.Add(dont_show, 0, wx.ALIGN_LEFT | wx.ALL, 5)
buttons_sizer = wx.StdDialogButtonSizer()
buttons_sizer.AddButton(wx.Button(dlg, wx.ID_OK))
buttons_sizer.Realize()
sizer.Add(buttons_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 5)
dlg.Fit()
dlg.ShowModal()
if dont_show.GetValue():
set_preference(False)
def prepare_run(self, workspace): '''Set up omero image providers inside the image_set_list''' pipeline = workspace.pipeline image_set_list = workspace.image_set_list if pipeline.in_batch_mode(): #TODO: Rewrite the OmeroImageProvider such that it can be used in batch mode #e.g. omero session keys could be used to attach to existing sessions to #keep OmeroImageProviders from creating a new session every time an image should be loaded return False if cpp.get_headless(): print 'OmeroLoadImages running in headless mode: image directory parameter will be used as omero object id' self.omero_object_id.set_value(int(cpp.get_default_image_directory())) print 'omero object id = %d'%self.omero_object_id.value print 'omero object type = %s'%self.omero_object.value self.create_omero_gateway() if self.omero_object == MS_IMAGE: omero_image_list = [self.omero_gateway.getImage(self.omero_object_id.value)] elif self.omero_object == MS_DATASET: #Get dataset without leaves(=images&pixels) dataset = self.omero_gateway.getDataset(self.omero_object_id.value, False) self.dataset_name = dataset.getName().getValue() omero_image_list = self.get_images_from_dataset(self.omero_object_id.value) elif self.omero_object == MS_PLATE: self.wells = self.get_wells_from_plate(self.omero_object_id.value) self.plate_name = self.wells[0].getPlate().getName().getValue() omero_image_list = [] for well in self.wells: for wellsample in well.iterateWellSamples(): omero_image_list.append(wellsample.getImage()) #get names and pixels from omero images pixels_list = [] for omero_image in omero_image_list: image_id = omero_image.getId().getValue() pixels_list += self.omero_gateway.getPixelsFromImage(image_id) #add images to image sets image_set_count = len(pixels_list) for i in range(0, image_set_count): image_set = image_set_list.get_image_set(i) pixels = pixels_list[i] pixels_id = pixels.getId().getValue() sizeZ = pixels.getSizeZ().getValue() sizeC = pixels.getSizeC().getValue() sizeT = pixels.getSizeT().getValue() for channel in self.channels: for z in range(0, sizeZ): for t in range(0, sizeT): c = int(channel.channel_number.value) self.save_image_set_info(image_set, channel.cpimage_name.value, P_OMERO, V_OMERO, self.omero_gateway, pixels_id, z, c, t) return True
def prepare_run(self, workspace):
'''Set up omero image providers inside the image_set_list'''
pipeline = workspace.pipeline
image_set_list = workspace.image_set_list
if pipeline.in_batch_mode():
# TODO: Rewrite the OmeroImageProvider such that it can be used in batch mode
# e.g., omero session keys could be used to attach to existing sessions to
# keep OmeroImageProviders from creating a new session every time an image should be loaded
return False
if cpp.get_headless():
print 'OmeroLoadImages running in headless mode: image directory parameter will be used as omero object id'
self.omero_object_id.set_value(int(cpp.get_default_image_directory()))
print 'omero object id = %d' % self.omero_object_id.value
print 'omero object type = %s' % self.omero_object.value
self.create_omero_gateway()
if self.omero_object == MS_IMAGE:
omero_image_list = [self.omero_gateway.getImage(self.omero_object_id.value)]
elif self.omero_object == MS_DATASET:
# Get dataset without leaves(=images&pixels)
dataset = self.omero_gateway.getDataset(self.omero_object_id.value, False)
self.dataset_name = dataset.getName().getValue()
omero_image_list = self.get_images_from_dataset(self.omero_object_id.value)
elif self.omero_object == MS_PLATE:
self.wells = self.get_wells_from_plate(self.omero_object_id.value)
self.plate_name = self.wells[0].getPlate().getName().getValue()
omero_image_list = []
for well in self.wells:
for wellsample in well.iterateWellSamples():
omero_image_list.append(wellsample.getImage())
# get names and pixels from omero images
pixels_list = []
for omero_image in omero_image_list:
image_id = omero_image.getId().getValue()
pixels_list += self.omero_gateway.getPixelsFromImage(image_id)
# add images to image sets
image_set_count = len(pixels_list)
for i in range(0, image_set_count):
image_set = image_set_list.get_image_set(i)
pixels = pixels_list[i]
pixels_id = pixels.getId().getValue()
sizeZ = pixels.getSizeZ().getValue()
sizeC = pixels.getSizeC().getValue()
sizeT = pixels.getSizeT().getValue()
for channel in self.channels:
for z in range(0, sizeZ):
for t in range(0, sizeT):
c = int(channel.channel_number.value)
self.save_image_set_info(image_set, channel.cpimage_name.value,
P_OMERO, V_OMERO,
self.omero_gateway, pixels_id, z, c, t)
return True
def show_warning(title, message, get_preference, set_preference):
"""Show a silenceable warning message to the user
title - title for the dialog box
message - message to be displayed
get_preference - function that gets a user preference: do you want to
show this warning?
set_preference - function that sets the user preference if they choose
not to see the warning again.
The message is printed to the console if headless.
"""
from cellprofiler.preferences import get_headless
if get_headless():
print message
return
if not get_preference():
return
import wx
if wx.GetApp() is None:
print message
return
dlg = wx.Dialog(wx.GetApp().GetTopWindow(), title=title)
dlg.Sizer = sizer = wx.BoxSizer(wx.VERTICAL)
subsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(subsizer, 0, wx.EXPAND | wx.ALL, 5)
subsizer.Add(
wx.StaticBitmap(dlg, wx.ID_ANY, wx.ArtProvider.GetBitmap(wx.ART_INFORMATION, wx.ART_CMN_DIALOG)),
0,
wx.ALIGN_LEFT | wx.ALIGN_TOP | wx.RIGHT,
5,
)
text = wx.StaticText(dlg, wx.ID_ANY, message)
subsizer.Add(text, 0, wx.ALIGN_LEFT | wx.ALIGN_TOP | wx.ALL, 5)
dont_show = wx.CheckBox(dlg, label="Don't show this message again.")
sizer.Add(dont_show, 0, wx.ALIGN_LEFT | wx.ALL, 5)
buttons_sizer = wx.StdDialogButtonSizer()
buttons_sizer.AddButton(wx.Button(dlg, wx.ID_OK))
buttons_sizer.Realize()
sizer.Add(buttons_sizer, 0, wx.ALIGN_CENTER_HORIZONTAL | wx.ALL, 5)
dlg.Fit()
dlg.ShowModal()
if dont_show.Value:
set_preference(False)
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
logger.debug("Starting ImageJ UI")
ui_service = ij2.get_ui_service(get_context())
if ui_service is not None and not ui_service.isVisible():
if cpprefs.get_headless():
# Silence the auto-updater in the headless preferences
#
ij2.update_never_remind()
ui_service.createUI()
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
logger.debug("Starting ImageJ UI")
ui_service = ij2.get_ui_service(get_context())
if ui_service is not None and not ui_service.isVisible():
if cpprefs.get_headless():
# Silence the auto-updater in the headless preferences
#
ij2.update_never_remind()
ui_service.createUI()
def prepare_run(self, workspace):
'''Invoke the image_set_list pickling mechanism and save the pipeline'''
pipeline = workspace.pipeline
image_set_list = workspace.image_set_list
if pipeline.test_mode or self.from_old_matlab:
return True
if self.batch_mode.value:
self.enter_batch_mode(workspace)
return True
else:
path = self.save_pipeline(workspace)
if not cpprefs.get_headless():
import wx
wx.MessageBox("CreateBatchFiles saved pipeline to %s" % path,
caption="CreateBatchFiles: Batch file saved",
style=wx.OK | wx.ICON_INFORMATION)
return False
def prepare_run(self, workspace):
'''Invoke the image_set_list pickling mechanism and save the pipeline'''
pipeline = workspace.pipeline
image_set_list = workspace.image_set_list
if pipeline.test_mode or self.from_old_matlab:
return True
if self.batch_mode.value:
self.enter_batch_mode(workspace)
return True
else:
path = self.save_pipeline(workspace)
if not cpprefs.get_headless():
import wx
wx.MessageBox(
"CreateBatchFiles saved pipeline to %s" % path,
caption = "CreateBatchFiles: Batch file saved",
style = wx.OK | wx.ICON_INFORMATION)
return False
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
logger.debug("Starting ImageJ UI")
ui_service = ij2.get_ui_service(get_context())
if ui_service is not None and not ui_service.isVisible():
if cpprefs.get_headless():
# Silence the auto-updater in the headless preferences
#
ij2.update_never_remind()
ui_service.createUI()
elif ui_service is not None:
ui = ui_service.getDefaultUI()
J.execute_runnable_in_main_thread(
J.run_script(
"""new java.lang.Runnable() {
run: function() {
ui.getApplicationFrame().setVisible(true); }}""",
dict(ui=ui)), True)
def prepare_group(self, pipeline, image_set_list, grouping, image_numbers):
'''Handle initialization per-group
pipeline - the pipeline being run
image_set_list - the list of image sets for the whole experiment
grouping - a dictionary that describes the key for the grouping.
For instance, { 'Metadata_Row':'A','Metadata_Column':'01'}
image_numbers - a sequence of the image numbers within the
group (image sets can be retreved as
image_set_list.get_image_set(image_numbers[i]-1)
We use prepare_group to compute the minimum or maximum values
among all images in the group for certain values of
"wants_automatic_[low,high]".
'''
if (self.wants_automatic_high != HIGH_ALL_IMAGES and
self.wants_automatic_low != LOW_ALL_IMAGES):
return True
if not pipeline.in_batch_mode() and not cpprefs.get_headless():
import wx
progress_dialog = wx.ProgressDialog(
"#%d: RescaleIntensity for %s"%(self.module_num, self.image_name.value),
"RescaleIntensity will process %d images while preparing for run" %
(len(image_numbers)),
len(image_numbers),
None,
wx.PD_APP_MODAL |
wx.PD_AUTO_HIDE |
wx.PD_CAN_ABORT)
else:
progress_dialog = None
min_value = None
max_value = None
try:
for i,image_number in enumerate(image_numbers):
image_set = image_set_list.get_image_set(image_number-1)
image = image_set.get_image(self.image_name.value,
must_be_grayscale=True,
cache = False)
if self.wants_automatic_high == HIGH_ALL_IMAGES:
if image.has_mask:
vmax = np.max(image.pixel_data[image.mask])
else:
vmax = np.max(image.pixel_data)
max_value = vmax if max_value is None else max(max_value, vmax)
if self.wants_automatic_low == LOW_ALL_IMAGES:
if image.has_mask:
vmin = np.min(image.pixel_data[image.mask])
else:
vmin = np.min(image.pixel_data)
min_value = vmin if min_value is None else min(min_value, vmin)
if progress_dialog is not None:
should_continue, skip = progress_dialog.Update(i+1)
if not should_continue:
progress_dialog.EndModal(0)
return False
finally:
if progress_dialog is not None:
progress_dialog.Destroy()
if self.wants_automatic_high == HIGH_ALL_IMAGES:
self.set_automatic_maximum(image_set_list, max_value)
if self.wants_automatic_low == LOW_ALL_IMAGES:
self.set_automatic_minimum(image_set_list, min_value)
def merge_files(destination, sources, force_headless=False):
is_headless = force_headless or get_headless()
if not is_headless:
import wx
if len(sources) == 0:
return
if not is_headless:
progress = wx.ProgressDialog("Writing " + destination,
"Loading " + sources[0],
maximum = len(sources) * 4 + 1,
style = wx.PD_CAN_ABORT |
wx.PD_APP_MODAL |
wx.PD_ELAPSED_TIME |
wx.PD_REMAINING_TIME)
count = 0
try:
pipeline = cpp.Pipeline()
has_error = [False]
def callback(caller, event):
if isinstance(event, cpp.LoadExceptionEvent):
has_error = True
wx.MessageBox(
message = "Could not load %s: %s" % (
sources[0], event.error),
caption = "Failed to load %s" % sources[0])
has_error[0] = True
pipeline.add_listener(callback)
if has_error[0]:
return
# distributed processing passes a list of functions, not a
# list of filenames.
pipeline.load(sources[0]() if callable(sources[0]) else sources[0])
mdest = cpmeas.Measurements()
image_set_count = 0
for source in sources:
if not is_headless:
count += 1
keep_going, skip = progress.Update(count, "Loading " + source)
if not keep_going:
return
# distributed processing passes a list of functions
msource = cpmeas.load_measurements(source() if callable(source) else source)
source_image_set_count = 0
for object_name in msource.get_object_names():
if object_name in mdest.get_object_names():
destfeatures = mdest.get_feature_names(object_name)
else:
destfeatures = []
for feature in msource.get_feature_names(object_name):
src_values = msource.get_all_measurements(object_name,
feature)
if np.isscalar(src_values):
# For something like "Experiment", there is a single
# value. Keep the first value seen among all sources.
#
if not feature in destfeatures:
mdest.add_all_measurements(object_name, feature,
[src_values])
else:
source_image_count = max(source_image_set_count,
len(src_values))
if feature in destfeatures:
dest_values = mdest.get_all_measurements(object_name,
feature)
if not isinstance(dest_values, list):
dest_values = dest_values.tolist()
else:
dest_values = [None] * image_set_count
if isinstance(src_values, list):
dest_values += src_values
else:
dest_values += src_values.tolist()
mdest.add_all_measurements(object_name, feature, dest_values)
destset = set(destfeatures)
#
# These are features that are in the destination, but not
# in the source. We have to add Nones to the destination.
#
for feature in destset.difference(
msource.get_feature_names(object_name)):
dest_values = mdest.get_all_measurements(
object_name, feature)
dest_values += [None] * source_image_count
#
# The source may not have all of the objects that are in
# the destination. Add blanks here.
#
destobjects = set(mdest.get_object_names())
for object_name in destobjects.difference(
msource.get_object_names()):
for feature in mdest.get_feature_names(object_name):
dest_values = mdest.get_all_measurements(
object_name, feature)
dest_values += [None] * source_image_count
mdest.add_all_measurements(object_name, feature, dest_values)
image_set_count += source_image_count
mdest.image_set_number = image_set_count
if not is_headless:
keep_going, skip = progress.Update(count+1, "Saving to "+destination)
if not keep_going:
return
pipeline.save_measurements(destination, mdest)
finally:
if not is_headless:
progress.Destroy()
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej','jars')
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
jar_files = sorted(jar_files, cmp = sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej','jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
plugin_directory = get_ij_plugin_directory()
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path += os.pathsep + jarpath
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " + plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib","tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = [x.groups()[0] for x in [
re.match('--jvm-heap-size=([0-9]+[gGkKmM])', y) for y in sys.argv]
if x is not None]
if len(jvm_arg) > 0:
jvm_arg = jvm_arg[0]
else:
jvm_arg = "512m"
args = [r"-Djava.class.path="+class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/"+log4j_properties.replace(os.path.sep, "/")
args += [r"-Dlog4j.configuration="+log4j_properties]
init_logger = False
else:
init_logger = True
if get_headless():
# We're running silently, so don't change the Java preferences
# The following definition uses a process-scope preferences factory
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
run_headless = (get_headless() and
not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location",
"cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning("Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level","WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not get_headless():
jutil.activate_awt()
def merge_files(destination, sources, force_headless=False):
is_headless = force_headless or get_headless()
if not is_headless:
import wx
if len(sources) == 0:
return
if not is_headless:
progress = wx.ProgressDialog("Writing " + destination,
"Loading " + sources[0],
maximum=len(sources) * 4 + 1,
style=wx.PD_CAN_ABORT
| wx.PD_APP_MODAL | wx.PD_ELAPSED_TIME
| wx.PD_REMAINING_TIME)
count = 0
try:
pipeline = cpp.Pipeline()
has_error = [False]
def callback(caller, event):
if isinstance(event, cpp.LoadExceptionEvent):
has_error = True
wx.MessageBox(message="Could not load %s: %s" %
(sources[0], event.error),
caption="Failed to load %s" % sources[0])
has_error[0] = True
pipeline.add_listener(callback)
pipeline.load(sources[0])
if has_error[0]:
return
if destination.lower().endswith(".h5"):
mdest = cpmeas.Measurements(filename=destination,
multithread=False)
h5_dest = True
else:
mdest = cpmeas.Measurements(multithread=False)
h5_dest = False
for source in sources:
if not is_headless:
count += 1
keep_going, skip = progress.Update(count,
"Loading " + source)
if not keep_going:
return
if h5py.is_hdf5(source):
msource = cpmeas.Measurements(filename=source,
mode="r",
multithread=False)
else:
msource = cpmeas.load_measurements(source)
dest_image_numbers = mdest.get_image_numbers()
source_image_numbers = msource.get_image_numbers()
if (len(dest_image_numbers) == 0
or len(source_image_numbers) == 0):
offset_source_image_numbers = source_image_numbers
else:
offset_source_image_numbers = (
np.max(dest_image_numbers) -
np.min(source_image_numbers) + source_image_numbers +
1)
for object_name in msource.get_object_names():
if object_name in mdest.get_object_names():
destfeatures = mdest.get_feature_names(object_name)
else:
destfeatures = []
for feature in msource.get_feature_names(object_name):
if object_name == cpmeas.EXPERIMENT:
if not mdest.has_feature(object_name, feature):
src_value = msource.get_experiment_measurement(
feature)
mdest.add_experiment_measurement(
feature, src_value)
continue
src_values = msource.get_measurement(
object_name,
feature,
image_set_number=source_image_numbers)
mdest[object_name, feature,
offset_source_image_numbers] = src_values
destset = set(destfeatures)
if not is_headless:
keep_going, skip = progress.Update(count + 1,
"Saving to " + destination)
if not keep_going:
return
if not h5_dest:
pipeline.save_measurements(destination, mdest)
finally:
if not is_headless:
progress.Destroy()
def merge_files(destination, sources, force_headless=False):
is_headless = force_headless or get_headless()
if not is_headless:
import wx
if len(sources) == 0:
return
if not is_headless:
progress = wx.ProgressDialog("Writing " + destination,
"Loading " + sources[0],
maximum = len(sources) * 4 + 1,
style = wx.PD_CAN_ABORT |
wx.PD_APP_MODAL |
wx.PD_ELAPSED_TIME |
wx.PD_REMAINING_TIME)
count = 0
try:
pipeline = cpp.Pipeline()
has_error = [False]
def callback(caller, event):
if isinstance(event, cpp.LoadExceptionEvent):
has_error = True
wx.MessageBox(
message = "Could not load %s: %s" % (
sources[0], event.error),
caption = "Failed to load %s" % sources[0])
has_error[0] = True
pipeline.add_listener(callback)
pipeline.load(sources[0])
if has_error[0]:
return
if destination.lower().endswith(".h5"):
mdest = cpmeas.Measurements(filename=destination,
multithread=False)
h5_dest = True
else:
mdest = cpmeas.Measurements(multithread=False)
h5_dest = False
for source in sources:
if not is_headless:
count += 1
keep_going, skip = progress.Update(count, "Loading " + source)
if not keep_going:
return
if h5py.is_hdf5(source):
msource = cpmeas.Measurements(filename=source,
mode="r",
multithread=False)
else:
msource = cpmeas.load_measurements(source)
dest_image_numbers = mdest.get_image_numbers()
source_image_numbers = msource.get_image_numbers()
if (len(dest_image_numbers) == 0 or
len(source_image_numbers) == 0):
offset_source_image_numbers = source_image_numbers
else:
offset_source_image_numbers = (
np.max(dest_image_numbers) -
np.min(source_image_numbers) + source_image_numbers + 1)
for object_name in msource.get_object_names():
if object_name in mdest.get_object_names():
destfeatures = mdest.get_feature_names(object_name)
else:
destfeatures = []
for feature in msource.get_feature_names(object_name):
if object_name == cpmeas.EXPERIMENT:
if not mdest.has_feature(object_name, feature):
src_value = msource.get_experiment_measurement(
feature)
mdest.add_experiment_measurement(feature,
src_value)
continue
src_values = msource.get_measurement(
object_name,
feature,
image_set_number = source_image_numbers)
mdest[object_name,
feature,
offset_source_image_numbers] = src_values
destset = set(destfeatures)
if not is_headless:
keep_going, skip = progress.Update(count+1, "Saving to "+destination)
if not keep_going:
return
if not h5_dest:
pipeline.save_measurements(destination, mdest)
finally:
if not is_headless:
progress.Destroy()
def merge_files(destination, sources, force_headless=False):
is_headless = force_headless or get_headless()
if not is_headless:
import wx
if len(sources) == 0:
return
if not is_headless:
progress = wx.ProgressDialog("Writing " + destination,
"Loading " + sources[0],
maximum = len(sources) * 4 + 1,
style = wx.PD_CAN_ABORT |
wx.PD_APP_MODAL |
wx.PD_ELAPSED_TIME |
wx.PD_REMAINING_TIME)
count = 0
try:
pipeline = cpp.Pipeline()
has_error = [False]
def callback(caller, event):
if isinstance(event, cpp.LoadExceptionEvent):
has_error = True
wx.MessageBox(
message = "Could not load %s: %s" % (
sources[0], event.error),
caption = "Failed to load %s" % sources[0])
has_error[0] = True
pipeline.add_listener(callback)
# distributed processing passes a list of functions, not a
# list of filenames.
pipeline.load(sources[0]() if callable(sources[0]) else sources[0])
if has_error[0]:
return
mdest = cpmeas.Measurements()
for source in sources:
if not is_headless:
count += 1
keep_going, skip = progress.Update(count, "Loading " + source)
if not keep_going:
return
# distributed processing passes a list of functions
msource = cpmeas.load_measurements(source() if callable(source) else source)
dest_image_numbers = mdest.get_image_numbers()
source_image_numbers = msource.get_image_numbers()
if len(dest_image_numbers) == 0:
offset_source_image_numbers = source_image_numbers
else:
offset_source_image_numbers = (
np.max(dest_image_numbers) + source_image_numbers)
for object_name in msource.get_object_names():
if object_name in mdest.get_object_names():
destfeatures = mdest.get_feature_names(object_name)
else:
destfeatures = []
for feature in msource.get_feature_names(object_name):
if object_name == cpmeas.EXPERIMENT:
if not mdest.has_feature(object_name, feature):
src_value = msource.get_experiment_measurement(
feature)
mdest.add_experiment_measurement(feature,
src_value)
continue
src_values = msource.get_measurement(
object_name,
feature,
image_set_number = source_image_numbers)
for image_number, value in zip(
offset_source_image_numbers, src_values):
mdest.add_measurement(
object_name, feature, value,
image_set_number = image_number)
destset = set(destfeatures)
if not is_headless:
keep_going, skip = progress.Update(count+1, "Saving to "+destination)
if not keep_going:
return
pipeline.save_measurements(destination, mdest)
finally:
if not is_headless:
progress.Destroy()
def run(self, workspace):
'''Run the module. Add the measurements. '''
statistics_dict = {}
ratio_dict = {}
for channel in self.channels:
provider = workspace.image_set.get_image_provider(channel.cpimage_name.value)
assert isinstance(provider, OmeroImageProvider)
name = provider.get_name()
omero_image_name = provider.get_omero_image_name()
omero_image_id = provider.get_image_id()
pixels_id = provider.get_pixels_id()
z = provider.get_z()
c = provider.get_c()
t = provider.get_t()
header = []
row = []
ratio = []
m = workspace.measurements
measurements = ()
if self.omero_object == MS_DATASET:
measurements += ((M_DATASET_NAME, self.dataset_name, 3.0),
(M_DATASET_ID, self.omero_object_id.value, 1.0))
elif self.omero_object == MS_PLATE:
#CellProfiler starts counting image sets from 1
well = self.wells[workspace.measurements.image_set_number-1]
well_row = well.getRow().getValue()
well_column = well.getColumn().getValue()
well_id = well.getId().getValue()
measurements += ((M_PLATE_NAME, self.plate_name, 3.0),
(M_PLATE_ID, self.omero_object_id.value, 1.0),
(M_WELL_ROW, well_row, 1.0),
(M_WELL_COLUMN, well_column, 1.0),
(M_WELL_ID, well_id, 3.0))
measurements += ((M_IMAGE_NAME, omero_image_name, 3.0),
(M_IMAGE_ID, omero_image_id, 1.0),
(M_PIXELS_ID, pixels_id, 1.0),
(M_Z, z, 0.5),
(M_C, c, 0.5),
(M_T, t, 0.5))
for tag, value, r in measurements:
m.add_image_measurement("_".join((tag, name)), value)
header.append(tag)
row.append(value)
ratio.append(r)
statistics = [header, row]
ratio = [x / sum(ratio) for x in ratio]
statistics_dict[channel.channel_number.value] = statistics
ratio_dict[channel.channel_number.value] = ratio
workspace.display_data.statistics = statistics_dict
workspace.display_data.ratio = ratio_dict
if cpp.get_headless(): #headless mode
for channel in self.channels:
image_name, channel_number = channel.cpimage_name.value, channel.channel_number.value
print "--- image name: %s\tchannel: %s"%(image_name, channel_number)
(header, row) = workspace.display_data.statistics[channel_number]
for i in range(0, len(header)):
print "\t%s: %s"%(header[i], row[i])
path = os.path.split(os.path.abspath(sys.argv[0]))[0]
path = os.path.join(path, 'cellprofiler','utilities')
else:
path = os.path.split(__file__)[0]
p = subprocess.Popen(["java","-cp", path, "findlibjvm"],
stdout=subprocess.PIPE)
stdout, stderr = p.communicate()
jvm_dir = stdout.strip()
ctypes.CDLL(os.path.join(jvm_dir, "libjvm.so"))
if jvm_dir is None:
from cellprofiler.preferences \
import get_report_jvm_error, set_report_jvm_error, get_headless
from cellprofiler.preferences import set_has_reported_jvm_error
if not get_headless():
import wx
app = wx.GetApp()
if app is not None and get_report_jvm_error():
dlg = wx.Dialog(wx.GetApp().GetTopWindow(),
title="Java not installed properly")
sizer = wx.BoxSizer(wx.VERTICAL)
dlg.SetSizer(sizer)
text = wx.StaticText(dlg,-1,
"CellProfiler can't find Java on your computer.")
text.Font = wx.Font(int(dlg.Font.GetPointSize()*5/4),
dlg.Font.GetFamily(),
dlg.Font.GetStyle(),
wx.FONTWEIGHT_BOLD)
sizer.Add(text, 0, wx.ALIGN_LEFT | wx.ALL, 5)
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej', 'jars')
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
jar_files = sorted(jar_files, cmp=sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej', 'jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
if (get_ij_plugin_directory() is not None
and os.path.isdir(get_ij_plugin_directory())):
plugin_directory = get_ij_plugin_directory()
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
#
# Add any .jar files in the directory
#
class_path += os.pathsep + os.pathsep.join([
os.path.join(plugin_directory, jarfile)
for jarfile in os.listdir(plugin_directory)
if jarfile.lower().endswith(".jar")
])
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib", "tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = [
x.groups()[0] for x in
[re.match('--jvm-heap-size=([0-9]+[gGkKmM])', y) for y in sys.argv]
if x is not None
]
if len(jvm_arg) > 0:
jvm_arg = jvm_arg[0]
else:
jvm_arg = "512m"
args = [
r"-Djava.class.path=" + class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg
]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/" + log4j_properties.replace(
os.path.sep, "/")
args += [r"-Dlog4j.configuration=" + log4j_properties]
init_logger = False
else:
init_logger = True
if get_headless():
# We're running silently, so don't change the Java preferences
# The following definition uses a process-scope preferences factory
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"
]
run_headless = (get_headless()
and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location", "cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning(
"Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level",
"WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not get_headless():
jutil.activate_awt()
def run(self, workspace):
'''Run the module. Add the measurements. '''
statistics_dict = {}
ratio_dict = {}
for channel in self.channels:
provider = workspace.image_set.get_image_provider(
channel.cpimage_name.value)
assert isinstance(provider, OmeroImageProvider)
name = provider.get_name()
omero_image_name = provider.get_omero_image_name()
omero_image_id = provider.get_image_id()
pixels_id = provider.get_pixels_id()
z = provider.get_z()
c = provider.get_c()
t = provider.get_t()
header = []
row = []
ratio = []
m = workspace.measurements
measurements = ()
if self.omero_object == MS_DATASET:
measurements += ((M_DATASET_NAME, self.dataset_name, 3.0),
(M_DATASET_ID, self.omero_object_id.value,
1.0))
elif self.omero_object == MS_PLATE:
#CellProfiler starts counting image sets from 1
well = self.wells[workspace.measurements.image_set_number - 1]
well_row = well.getRow().getValue()
well_column = well.getColumn().getValue()
well_id = well.getId().getValue()
measurements += ((M_PLATE_NAME, self.plate_name, 3.0),
(M_PLATE_ID, self.omero_object_id.value,
1.0), (M_WELL_ROW, well_row, 1.0),
(M_WELL_COLUMN, well_column,
1.0), (M_WELL_ID, well_id, 3.0))
measurements += ((M_IMAGE_NAME, omero_image_name,
3.0), (M_IMAGE_ID, omero_image_id,
1.0), (M_PIXELS_ID, pixels_id, 1.0),
(M_Z, z, 0.5), (M_C, c, 0.5), (M_T, t, 0.5))
for tag, value, r in measurements:
m.add_image_measurement("_".join((tag, name)), value)
header.append(tag)
row.append(value)
ratio.append(r)
statistics = [header, row]
ratio = [x / sum(ratio) for x in ratio]
statistics_dict[channel.channel_number.value] = statistics
ratio_dict[channel.channel_number.value] = ratio
workspace.display_data.statistics = statistics_dict
workspace.display_data.ratio = ratio_dict
if cpp.get_headless(): #headless mode
for channel in self.channels:
image_name, channel_number = channel.cpimage_name.value, channel.channel_number.value
print "--- image name: %s\tchannel: %s" % (image_name,
channel_number)
(header,
row) = workspace.display_data.statistics[channel_number]
for i in range(0, len(header)):
print "\t%s: %s" % (header[i], row[i])
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej','jars')
def sort_fn(a, b):
aa,bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename
for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")]
jar_files = sorted(jar_files, cmp = sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej','jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
plugin_directory = get_ij_plugin_directory()
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
if (plugin_directory is not None and
os.path.isdir(plugin_directory)):
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path += os.pathsep + jarpath
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " + plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib","tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = jutil.get_jvm_heap_size_arg()
if jvm_arg is None:
jvm_arg = "512m"
args = [r"-Djava.class.path="+class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/"+log4j_properties.replace(os.path.sep, "/")
args += [r"-Dlog4j.configuration="+log4j_properties]
init_logger = False
else:
init_logger = True
if plugin_directory is not None and os.path.isdir(plugin_directory):
# For IJ1 compatibility
args += [r"-Dplugins.dir=%s" % plugin_directory]
# In headless mode, we have to avoid changing the Java preferences.
#
# Aside from that, we need to prevent ImageJ from exiting and from
# displaying the updater dialog - at least temporarily, we do that
# through preferences. We use the HeadlessPreferencesFactory to
# limit the scope of the changes to this process - otherwise we'd
# turn off updating for the machine.
#
# TODO: ImageJ is implementing a pluggable mechanism to control the
# quit process. We can also contribute a pluggable mechanism
# that gives us more control over the updater.
#
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"]
run_headless = (get_headless() and
not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location",
"cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning("Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level","WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not get_headless():
jutil.activate_awt()
if get_ij_plugin_directory() is not None:
__args.append("-Dplugins.dir="+get_ij_plugin_directory())
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
__log4j_properties = os.path.join(__path, "log4j.properties")
if os.path.exists(__log4j_properties):
__log4j_properties = "file:/"+__log4j_properties.replace(os.path.sep, "/")
__args += [r"-Dlog4j.configuration="+__log4j_properties]
__init_logger = False
else:
__init_logger = True
if ((get_headless() and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
or sys.platform=="darwin"):
__args += [ r"-Djava.awt.headless=true" ]
logger.debug("JVM arguments: " + " ".join(__args))
jutil.start_vm(__args)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location",
"cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning("Bioformats version does not support directory cacheing")
finally:
jutil.detach()
def merge_files(destination, sources, force_headless=False):
is_headless = force_headless or get_headless()
if not is_headless:
import wx
if len(sources) == 0:
return
if not is_headless:
progress = wx.ProgressDialog("Writing " + destination,
"Loading " + sources[0],
maximum = len(sources) * 4 + 1,
style = wx.PD_CAN_ABORT |
wx.PD_APP_MODAL |
wx.PD_ELAPSED_TIME |
wx.PD_REMAINING_TIME)
count = 0
try:
pipeline = cpp.Pipeline()
has_error = [False]
def callback(caller, event):
if isinstance(event, cpp.LoadExceptionEvent):
has_error = True
wx.MessageBox(
message = "Could not load %s: %s" % (
sources[0], event.error),
caption = "Failed to load %s" % sources[0])
has_error[0] = True
pipeline.add_listener(callback)
# distributed processing passes a list of functions, not a
# list of filenames.
pipeline.load(sources[0]() if callable(sources[0]) else sources[0])
if has_error[0]:
return
mdest = cpmeas.Measurements()
for source in sources:
if not is_headless:
count += 1
keep_going, skip = progress.Update(count, "Loading " + source)
if not keep_going:
return
# distributed processing passes a list of functions
msource = cpmeas.load_measurements(source() if callable(source) else source)
dest_image_numbers = mdest.get_image_numbers()
source_image_numbers = msource.get_image_numbers()
if len(dest_image_numbers) == 0:
offset_source_image_numbers = source_image_numbers
else:
offset_source_image_numbers = (
np.max(dest_image_numbers) + source_image_numbers)
for object_name in msource.get_object_names():
if object_name in mdest.get_object_names():
destfeatures = mdest.get_feature_names(object_name)
else:
destfeatures = []
for feature in msource.get_feature_names(object_name):
if object_name == cpmeas.EXPERIMENT:
if not mdest.has_feature(object_name, feature):
src_value = msource.get_experiment_measurement(
feature)
mdest.add_experiment_measurement(feature,
src_value)
continue
src_values = msource.get_measurement(
object_name,
feature,
image_set_number = source_image_numbers)
for image_number, value in zip(
offset_source_image_numbers, src_values):
mdest.add_measurement(
object_name, feature, value,
image_set_number = image_number)
destset = set(destfeatures)
if not is_headless:
keep_going, skip = progress.Update(count+1, "Saving to "+destination)
if not keep_going:
return
pipeline.save_measurements(destination, mdest)
finally:
if not is_headless:
progress.Destroy()
path = os.path.split(os.path.abspath(sys.argv[0]))[0]
path = os.path.join(path, 'cellprofiler', 'utilities')
else:
path = os.path.split(__file__)[0]
p = subprocess.Popen(["java", "-cp", path, "findlibjvm"],
stdout=subprocess.PIPE)
stdout, stderr = p.communicate()
jvm_dir = stdout.strip()
ctypes.CDLL(os.path.join(jvm_dir, "libjvm.so"))
if jvm_dir is None:
from cellprofiler.preferences \
import get_report_jvm_error, set_report_jvm_error, get_headless
from cellprofiler.preferences import set_has_reported_jvm_error
if not get_headless():
import wx
app = wx.GetApp()
if app is not None and get_report_jvm_error():
dlg = wx.Dialog(wx.GetApp().GetTopWindow(),
title="Java not installed properly")
sizer = wx.BoxSizer(wx.VERTICAL)
dlg.SetSizer(sizer)
text = wx.StaticText(
dlg, -1, "CellProfiler can't find Java on your computer.")
text.Font = wx.Font(int(dlg.Font.GetPointSize() * 5 / 4),
dlg.Font.GetFamily(), dlg.Font.GetStyle(),
wx.FONTWEIGHT_BOLD)
sizer.Add(text, 0, wx.ALIGN_LEFT | wx.ALL, 5)
if java_home is None or sys.platform == "darwin":
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global USE_IJ2
global logger
if hasattr(sys, 'frozen') and sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
else:
root_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(root_path)[0]
path = os.path.join(root_path, 'bioformats')
imagej_path = os.path.join(root_path, 'imagej')
loci_jar = os.path.join(path, "loci_tools.jar")
ij2_jar = os.path.join(imagej_path, "imagej-2.0-SNAPSHOT-all.jar")
ij_jar = os.path.join(imagej_path, "ij.jar")
imglib_jar = os.path.join(imagej_path, "imglib.jar")
javacl_jar = os.path.join(imagej_path, "javacl-1.0-beta-4-shaded.jar")
USE_IJ2 = get_ij_version() == IJ_2
if os.path.exists(ij2_jar) and USE_IJ2:
class_path = os.pathsep.join((loci_jar, ij2_jar))
USE_IJ2 = True
else:
USE_IJ2 = False
class_path = os.pathsep.join((loci_jar, ij_jar, imglib_jar,
javacl_jar))
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib","tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = [x.groups()[0] for x in [
re.match('--jvm-heap-size=([0-9]+[gGkKmM])', y) for y in sys.argv]
if x is not None]
if len(jvm_arg) > 0:
jvm_arg = jvm_arg[0]
else:
jvm_arg = "512m"
args = [r"-Djava.class.path="+class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg]
if get_ij_plugin_directory() is not None:
args.append("-Dplugins.dir="+get_ij_plugin_directory())
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/"+log4j_properties.replace(os.path.sep, "/")
args += [r"-Dlog4j.configuration="+log4j_properties]
init_logger = False
else:
init_logger = True
run_headless = (get_headless() and
not os.environ.has_key("CELLPROFILER_USE_XVFB"))
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location",
"cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning("Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level","WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not run_headless:
jutil.activate_awt()
__args.append("-Dplugins.dir=" + get_ij_plugin_directory())
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
__log4j_properties = os.path.join(__path, "log4j.properties")
if os.path.exists(__log4j_properties):
__log4j_properties = "file:/" + __log4j_properties.replace(
os.path.sep, "/")
__args += [r"-Dlog4j.configuration=" + __log4j_properties]
__init_logger = False
else:
__init_logger = True
if ((get_headless() and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
or sys.platform == "darwin"):
__args += [r"-Djava.awt.headless=true"]
logger.debug("JVM arguments: " + " ".join(__args))
jutil.start_vm(__args)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location", "cacheDirectoryListings", "(Z)V",
True)
except:
logger.warning("Bioformats version does not support directory cacheing")
finally:
jutil.detach()
def start_cellprofiler_jvm():
'''Start the Java VM with arguments appropriate for CellProfiler'''
global logger
if hasattr(sys, 'frozen'):
if sys.platform != 'darwin':
root_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
bioformats_path = os.path.join(root_path, 'bioformats')
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
imagej_path = os.path.join(root_path, 'imagej', 'jars')
def sort_fn(a, b):
aa, bb = [(0 if x.startswith("cellprofiler-java") else 1, x)
for x in a, b]
return cmp(aa, bb)
jar_files = [
jar_filename for jar_filename in os.listdir(imagej_path)
if jar_filename.lower().endswith(".jar")
]
jar_files = sorted(jar_files, cmp=sort_fn)
else:
bioformats_path = os.path.abspath(os.path.split(__file__)[0])
root_path = os.path.split(bioformats_path)[0]
jar_files = get_cellprofiler_jars()
imagej_path = os.path.join(root_path, 'imagej', 'jars')
class_path = os.pathsep.join(
[os.path.join(imagej_path, jar_file) for jar_file in jar_files])
if os.environ.has_key("CLASSPATH"):
class_path += os.pathsep + os.environ["CLASSPATH"]
plugin_directory = get_ij_plugin_directory()
logger.debug("Using %s as imagej plugin directory" % plugin_directory)
if (plugin_directory is not None and os.path.isdir(plugin_directory)):
#
# Add the plugin directory to pick up .class files in a directory
# hierarchy.
#
class_path += os.pathsep + plugin_directory
logger.debug("Adding %s to class path" % plugin_directory)
#
# Add any .jar files in the directory
#
for jarfile in os.listdir(plugin_directory):
jarpath = os.path.join(plugin_directory, jarfile)
if jarfile.lower().endswith(".jar"):
logger.debug("Adding %s to class path" % jarpath)
class_path += os.pathsep + jarpath
else:
logger.debug("Skipping %s" % jarpath)
else:
logger.info("Plugin directory doesn't point to valid folder: " +
plugin_directory)
if sys.platform.startswith("win") and not hasattr(sys, 'frozen'):
# Have to find tools.jar
from cellprofiler.utilities.setup import find_jdk
jdk_path = find_jdk()
if jdk_path is not None:
tools_jar = os.path.join(jdk_path, "lib", "tools.jar")
class_path += os.pathsep + tools_jar
else:
logger.warning("Failed to find tools.jar")
jvm_arg = jutil.get_jvm_heap_size_arg()
if jvm_arg is None:
jvm_arg = "512m"
args = [
r"-Djava.class.path=" + class_path,
r"-Dloci.bioformats.loaded=true",
#r"-verbose:class",
#r"-verbose:jni",
r"-Xmx%s" % jvm_arg
]
#
# Get the log4j logger setup from a file in the bioformats directory
# if such a file exists.
#
log4j_properties = os.path.join(bioformats_path, "log4j.properties")
if os.path.exists(log4j_properties):
log4j_properties = "file:/" + log4j_properties.replace(
os.path.sep, "/")
args += [r"-Dlog4j.configuration=" + log4j_properties]
init_logger = False
else:
init_logger = True
if plugin_directory is not None and os.path.isdir(plugin_directory):
# For IJ1 compatibility
args += [r"-Dplugins.dir=%s" % plugin_directory]
# In headless mode, we have to avoid changing the Java preferences.
#
# Aside from that, we need to prevent ImageJ from exiting and from
# displaying the updater dialog - at least temporarily, we do that
# through preferences. We use the HeadlessPreferencesFactory to
# limit the scope of the changes to this process - otherwise we'd
# turn off updating for the machine.
#
# TODO: ImageJ is implementing a pluggable mechanism to control the
# quit process. We can also contribute a pluggable mechanism
# that gives us more control over the updater.
#
args += [
"-Djava.util.prefs.PreferencesFactory="
"org.cellprofiler.headlesspreferences.HeadlessPreferencesFactory"
]
run_headless = (get_headless()
and not os.environ.has_key("CELLPROFILER_USE_XVFB"))
run_headless = False
logger.debug("JVM arguments: " + " ".join(args))
jutil.start_vm(args, run_headless)
logger.debug("Java virtual machine started.")
jutil.attach()
try:
jutil.static_call("loci/common/Location", "cacheDirectoryListings",
"(Z)V", True)
except:
logger.warning(
"Bioformats version does not support directory cacheing")
#
# Start the log4j logger to avoid error messages.
#
if init_logger:
try:
jutil.static_call("org/apache/log4j/BasicConfigurator",
"configure", "()V")
log4j_logger = jutil.static_call("org/apache/log4j/Logger",
"getRootLogger",
"()Lorg/apache/log4j/Logger;")
warn_level = jutil.get_static_field("org/apache/log4j/Level",
"WARN",
"Lorg/apache/log4j/Level;")
jutil.call(log4j_logger, "setLevel", "(Lorg/apache/log4j/Level;)V",
warn_level)
del logger
del warn_level
except:
logger.error("Failed to initialize log4j\n", exc_info=True)
if not get_headless():
jutil.activate_awt()
