def main(args=None):
import cellprofiler.preferences
"""Run CellProfiler
args - command-line arguments, e.g. sys.argv
"""
if args is None:
args = sys.argv
cellprofiler.preferences.set_awt_headless(True)
exit_code = 0
switches = ('--work-announce', '--knime-bridge-address')
if any(
[any([arg.startswith(switch) for switch in switches])
for arg in args]):
cellprofiler.preferences.set_headless()
cellprofiler.worker.aw_parse_args()
cellprofiler.worker.main()
sys.exit(exit_code)
options, args = parse_args(args)
if options.print_version:
__version__(exit_code)
if (not options.show_gui) or options.write_schema_and_exit:
cellprofiler.preferences.set_headless()
options.run_pipeline = True
set_log_level(options)
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
if options.batch_commands_file is not None:
get_batch_commands(options.batch_commands_file)
if options.omero_credentials is not None:
set_omero_credentials_from_string(options.omero_credentials)
if options.plugins_directory is not None:
cellprofiler.preferences.set_plugin_directory(
options.plugins_directory, globally=False)
if options.temp_dir is not None:
if not os.path.exists(options.temp_dir):
os.makedirs(options.temp_dir)
cellprofiler.preferences.set_temporary_directory(options.temp_dir,
globally=False)
if not options.allow_schema_write:
cellprofiler.preferences.set_allow_schema_write(False)
if options.output_directory:
if not os.path.exists(options.output_directory):
os.makedirs(options.output_directory)
cellprofiler.preferences.set_default_output_directory(
options.output_directory)
if options.image_directory:
cellprofiler.preferences.set_default_image_directory(
options.image_directory)
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.data_file is not None:
cellprofiler.preferences.set_data_file(
os.path.abspath(options.data_file))
cellprofiler.utilities.cpjvm.cp_start_vm()
if options.image_set_file is not None:
cellprofiler.preferences.set_image_set_file(options.image_set_file)
#
# Handle command-line tasks that that need to load the modules to run
#
if options.print_measurements:
print_measurements(options)
if options.write_schema_and_exit:
write_schema(options.pipeline_filename)
if options.show_gui:
matplotlib.use('WXAgg')
import cellprofiler.gui.app
if options.pipeline_filename:
if cellprofiler.workspace.is_workspace_file(
options.pipeline_filename):
workspace_path = os.path.expanduser(options.pipeline_filename)
pipeline_path = None
else:
pipeline_path = os.path.expanduser(options.pipeline_filename)
workspace_path = None
else:
workspace_path = None
pipeline_path = None
app = cellprofiler.gui.app.App(0,
workspace_path=workspace_path,
pipeline_path=pipeline_path)
if options.run_pipeline:
app.frame.pipeline_controller.do_analyze_images()
app.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
stop_cellprofiler()
def main(args=None):
import cellprofiler.preferences
"""Run CellProfiler
args - command-line arguments, e.g., sys.argv
"""
if args is None:
args = sys.argv
cellprofiler.preferences.set_awt_headless(True)
exit_code = 0
switches = ("--work-announce", "--knime-bridge-address")
if any(
[any([arg.startswith(switch) for switch in switches])
for arg in args]):
cellprofiler.preferences.set_headless()
cellprofiler.worker.aw_parse_args()
cellprofiler.worker.main()
return exit_code
options, args = parse_args(args)
if options.temp_dir is not None:
if not os.path.exists(options.temp_dir):
os.makedirs(options.temp_dir)
cellprofiler.preferences.set_temporary_directory(options.temp_dir,
globally=False)
to_clean = []
if options.pipeline_filename:
o = urlparse(options.pipeline_filename)
if o[0] in ("ftp", "http", "https"):
import urllib2
temp_pipe_file = tempfile.NamedTemporaryFile(mode='w+b',
suffix='.cppipe',
dir=temp_dir,
delete=False)
downloaded_pipeline = urllib2.urlopen(options.pipeline_filename)
for line in downloaded_pipeline:
temp_pipe_file.write(line)
options.pipeline_filename = temp_pipe_file.name
to_clean.append(os.path.join(temp_dir, temp_pipe_file.name))
if options.image_set_file:
o = urlparse(options.image_set_file)
if o[0] in ("ftp", "http", "https"):
import urllib2
temp_set_file = tempfile.NamedTemporaryFile(mode='w+b',
suffix='.csv',
dir=temp_dir,
delete=False)
downloaded_set_csv = urllib2.urlopen(options.image_set_file)
for line in downloaded_set_csv:
temp_set_file.write(line)
options.image_set_file = temp_set_file.name
to_clean.append(os.path.join(temp_dir, temp_set_file.name))
if options.data_file:
o = urlparse(options.data_file)
if o[0] in ("ftp", "http", "https"):
import urllib2
temp_data_file = tempfile.NamedTemporaryFile(mode='w+b',
suffix='.csv',
dir=temp_dir,
delete=False)
downloaded_data_csv = urllib2.urlopen(options.data_file)
for line in downloaded_data_csv:
temp_data_file.write(line)
options.data_file = temp_data_file.name
to_clean.append(os.path.join(temp_dir, temp_data_file.name))
if options.print_version:
__version__(exit_code)
if (not options.show_gui) or options.write_schema_and_exit:
cellprofiler.preferences.set_headless()
options.run_pipeline = True
if options.batch_commands_file:
cellprofiler.preferences.set_headless()
options.run_pipeline = False
options.show_gui = False
set_log_level(options)
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
if options.batch_commands_file is not None:
try:
nr_per_batch = int(options.images_per_batch)
except ValueError:
logging.warning(
"non-integer argument to --images-per-batch. Defaulting to 1.")
nr_per_batch = 1
get_batch_commands(options.batch_commands_file, nr_per_batch)
if options.omero_credentials is not None:
set_omero_credentials_from_string(options.omero_credentials)
if options.plugins_directory is not None:
cellprofiler.preferences.set_plugin_directory(
options.plugins_directory, globally=False)
if not options.allow_schema_write:
cellprofiler.preferences.set_allow_schema_write(False)
if options.output_directory:
if not os.path.exists(options.output_directory):
os.makedirs(options.output_directory)
cellprofiler.preferences.set_default_output_directory(
options.output_directory)
if options.image_directory:
cellprofiler.preferences.set_default_image_directory(
options.image_directory)
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.data_file is not None:
cellprofiler.preferences.set_data_file(
os.path.abspath(options.data_file))
try:
if not options.show_gui:
cellprofiler.utilities.cpjvm.cp_start_vm()
if options.image_set_file is not None:
cellprofiler.preferences.set_image_set_file(options.image_set_file)
#
# Handle command-line tasks that that need to load the modules to run
#
if options.print_measurements:
print_measurements(options)
if options.write_schema_and_exit:
write_schema(options.pipeline_filename)
if options.show_gui:
matplotlib.use("WXAgg")
import cellprofiler.gui.app
if options.pipeline_filename:
if cellprofiler.workspace.is_workspace_file(
options.pipeline_filename):
workspace_path = os.path.expanduser(
options.pipeline_filename)
pipeline_path = None
else:
pipeline_path = os.path.expanduser(
options.pipeline_filename)
workspace_path = None
else:
workspace_path = None
pipeline_path = None
app = cellprofiler.gui.app.App(0,
workspace_path=workspace_path,
pipeline_path=pipeline_path)
if options.run_pipeline:
app.frame.pipeline_controller.do_analyze_images()
app.MainLoop()
return
elif options.run_pipeline:
exit_code = run_pipeline_headless(options, args)
finally:
# Cleanup the temp files we made, if any
if len(to_clean) > 0:
for each_temp in to_clean:
os.remove(each_temp)
# If anything goes wrong during the startup sequence headlessly, the JVM needs
# to be explicitly closed
if not options.show_gui:
stop_cellprofiler()
return exit_code
