def setUp(self):
from cellprofiler.preferences import set_headless, set_temporary_directory
set_headless()
set_temporary_directory(tempfile.gettempdir())
self.old_import = __builtin__.__import__
__builtin__.__import__ = import_all_but_wx
def setUp(self):
from cellprofiler.preferences import set_headless, set_temporary_directory
set_headless()
set_temporary_directory(tempfile.gettempdir())
self.old_import = builtins.__import__
builtins.__import__ = import_all_but_wx
def main(args=None):
'''Run CellProfiler
args - command-line arguments, e.g. sys.argv
'''
if args is None:
args = sys.argv
import cellprofiler.preferences as cpprefs
cpprefs.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]):
#
# Go headless ASAP
#
cpprefs.set_headless()
for i, arg in enumerate(args):
if arg == "--ij-plugins-directory" and len(args) > i + 1:
cpprefs.set_ij_plugin_directory(args[i + 1])
break
import cellprofiler.worker
cellprofiler.worker.aw_parse_args()
cellprofiler.worker.main()
sys.exit(exit_code)
options, args = parse_args(args)
if options.print_version:
from cellprofiler.utilities.version import \
dotted_version, version_string, git_hash, version_number
print "CellProfiler %s" % dotted_version
print "Git %s" % git_hash
print "Version %s" % version_number
print "Built %s" % version_string.split(" ")[0]
sys.exit(exit_code)
#
# Important to go headless ASAP
#
if (not options.show_gui) or options.write_schema_and_exit:
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
# What's there to do but run if you're running headless?
# Might want to change later if there's some headless setup
options.run_pipeline = True
if options.jvm_heap_size is not None:
from cellprofiler.preferences import set_jvm_heap_mb
set_jvm_heap_mb(options.jvm_heap_size, False)
set_log_level(options)
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
return
if options.batch_commands_file is not None:
get_batch_commands(options.batch_commands_file)
return
if options.add_message_for_user:
if len(args) != 3:
sys.stderr.write("Usage: (for add_message-for-user)\n")
sys.stderr.write(
"CellProfiler --add-message-for-user <caption> <message> <pipeline-or-project>\n"
)
sys.stderr.write("where:\n")
sys.stderr.write(" <caption> - the message box caption\n")
sys.stderr.write(
" <message> - the message displayed inside the message box\n"
)
sys.stderr.write(
" <pipeline-or-project> - the path to the pipeline or project file to modify\n"
)
return
caption = args[0]
message = args[1]
path = args[2]
import h5py
using_hdf5 = h5py.is_hdf5(path)
if using_hdf5:
import cellprofiler.measurement as cpmeas
m = cpmeas.Measurements(filename=path, mode="r+")
pipeline_text = m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"]
else:
with open(path, "r") as fd:
pipeline_text = fd.read()
header, body = pipeline_text.split("\n\n", 1)
pipeline_text = header + \
("\nMessageForUser:%s|%s\n\n" % (caption, message)) + body
if using_hdf5:
m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] = pipeline_text
m.close()
else:
with open(path, "w") as fd:
fd.write(pipeline_text)
print "Message added to %s" % path
return
# necessary to prevent matplotlib trying to use Tkinter as its backend.
# has to be done before CellProfilerApp is imported
from matplotlib import use as mpluse
mpluse('WXAgg')
if options.omero_credentials is not None:
set_omero_credentials_from_string(options.omero_credentials)
if options.plugins_directory is not None:
cpprefs.set_plugin_directory(options.plugins_directory, globally=False)
if options.ij_plugins_directory is not None:
cpprefs.set_ij_plugin_directory(options.ij_plugins_directory,
globally=False)
if options.temp_dir is not None:
if not os.path.exists(options.temp_dir):
os.makedirs(options.temp_dir)
cpprefs.set_temporary_directory(options.temp_dir, globally=False)
if not options.allow_schema_write:
cpprefs.set_allow_schema_write(False)
#
# After the crucial preferences are established, we can start the VM
#
from cellprofiler.utilities.cpjvm import cp_start_vm
cp_start_vm()
#
# Not so crucial preferences...
#
if options.image_set_file is not None:
cpprefs.set_image_set_file(options.image_set_file)
try:
# ---------------------------------------
#
# Handle command-line tasks that that need to load the modules to run
#
if options.output_html:
from cellprofiler.gui.html.manual import generate_html
webpage_path = options.output_directory if options.output_directory else None
generate_html(webpage_path)
return
if options.print_measurements:
print_measurements(options)
return
if not hasattr(sys, "frozen") and options.code_statistics:
print_code_statistics()
return
if options.write_schema_and_exit:
write_schema(options.pipeline_filename)
return
#
# ------------------------------------------
if options.show_gui:
import wx
wx.Log.EnableLogging(False)
from cellprofiler.gui.app import App
from cellprofiler.workspace import is_workspace_file
if options.pipeline_filename:
if 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
elif options.new_project:
workspace_path = False
pipeline_path = None
else:
workspace_path = None
pipeline_path = None
app = App(0,
workspace_path=workspace_path,
pipeline_path=pipeline_path)
if options.data_file is not None:
cpprefs.set_data_file(os.path.abspath(options.data_file))
from cellprofiler.utilities.version import version_string, version_number
logging.root.info("Version: %s / %d" %
(version_string, version_number))
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.output_directory:
if not os.path.exists(options.output_directory):
os.makedirs(options.output_directory)
cpprefs.set_default_output_directory(options.output_directory)
if options.image_directory:
cpprefs.set_default_image_directory(options.image_directory)
if options.show_gui:
if options.run_pipeline:
app.frame.pipeline_controller.do_analyze_images()
app.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py",
exc_info=True)
exit_code = -1
def main(args):
'''Run CellProfiler
args - command-line arguments, e.g. sys.argv
'''
if any([arg.startswith('--work-announce') for arg in args]):
#
# Go headless ASAP
#
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
for i, arg in enumerate(args):
if arg == "--ij-plugins-directory" and len(args) > i+1:
cpprefs.set_ij_plugin_directory(args[i+1])
break
import cellprofiler.analysis_worker
cellprofiler.analysis_worker.aw_parse_args()
cellprofiler.analysis_worker.main()
sys.exit(0)
options, args = parse_args(args)
if options.jvm_heap_size != None:
from cellprofiler.preferences import set_jvm_heap_mb
set_jvm_heap_mb(options.jvm_heap_size, False)
set_log_level(options)
if not hasattr(sys, "frozen") and options.code_statistics:
print_code_statistics()
return
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
return
if options.batch_commands_file is not None:
get_batch_commands(options.batch_commands_file)
return
if options.run_ilastik:
run_ilastik()
return
if options.add_message_for_user:
if len(args) != 3:
sys.stderr.write("Usage: (for add_message-for-user)\n")
sys.stderr.write("CellProfiler --add-message-for-user <caption> <message> <pipeline-or-project>\n")
sys.stderr.write("where:\n")
sys.stderr.write(" <caption> - the message box caption\n")
sys.stderr.write(" <message> - the message displayed inside the message box\n")
sys.stderr.write(" <pipeline-or-project> - the path to the pipeline or project file to modify\n")
return
caption = args[0]
message = args[1]
path = args[2]
import h5py
using_hdf5 = h5py.is_hdf5(path)
if using_hdf5:
import cellprofiler.measurements as cpmeas
m = cpmeas.Measurements(
filename = path, mode="r+")
pipeline_text = m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"]
else:
with open(path, "r") as fd:
pipeline_text = fd.read()
header, body = pipeline_text.split("\n\n", 1)
pipeline_text = header + \
("\nMessageForUser:%s|%s\n\n" % (caption, message)) + body
if using_hdf5:
m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] = pipeline_text
m.close()
else:
with open(path, "w") as fd:
fd.write(pipeline_text)
print "Message added to %s" % path
return
# necessary to prevent matplotlib trying to use Tkinter as its backend.
# has to be done before CellProfilerApp is imported
from matplotlib import use as mpluse
mpluse('WXAgg')
if (not hasattr(sys, 'frozen')) and options.fetch_external_dependencies:
import external_dependencies
external_dependencies.fetch_external_dependencies(options.overwrite_external_dependencies)
if (not hasattr(sys, 'frozen')) and options.build_extensions:
build_extensions()
if options.build_and_exit:
return
if options.output_html:
from cellprofiler.gui.html.manual import generate_html
webpage_path = options.output_directory if options.output_directory else None
generate_html(webpage_path)
return
if options.print_measurements:
print_measurements(options)
return
if options.omero_credentials is not None:
set_omero_credentials_from_string(options.omero_credentials)
try:
if options.show_gui:
import wx
wx.Log.EnableLogging(False)
from cellprofiler.cellprofilerapp import CellProfilerApp
from cellprofiler.workspace import is_workspace_file
show_splashbox = (options.pipeline_filename is None and
(not options.new_project) and
options.show_splashbox)
if options.pipeline_filename:
if 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
elif options.new_project:
workspace_path = False
pipeline_path = None
else:
workspace_path = None
pipeline_path = None
App = CellProfilerApp(
0,
check_for_new_version = (options.pipeline_filename is None),
show_splashbox = show_splashbox,
workspace_path = workspace_path,
pipeline_path = pipeline_path)
#
# Important to go headless ASAP
#
# cellprofiler.preferences can't be imported before we have a chance
# to initialize the wx app.
#
import cellprofiler.preferences as cpprefs
if not options.show_gui:
cpprefs.set_headless()
# What's there to do but run if you're running headless?
# Might want to change later if there's some headless setup
options.run_pipeline = True
if options.plugins_directory is not None:
cpprefs.set_plugin_directory(options.plugins_directory)
if options.ij_plugins_directory is not None:
cpprefs.set_ij_plugin_directory(options.ij_plugins_directory)
if options.temp_dir is not None:
if not os.path.exists(options.temp_dir):
os.makedirs(options.temp_dir)
cpprefs.set_temporary_directory(options.temp_dir)
if options.data_file is not None:
cpprefs.set_data_file(os.path.abspath(options.data_file))
if options.image_set_file is not None:
cpprefs.set_image_set_file(options.image_set_file, False)
from cellprofiler.utilities.version import version_string, version_number
logging.root.info("Version: %s / %d" % (version_string, version_number))
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.output_directory:
if not os.path.exists(options.output_directory):
os.makedirs(options.output_directory)
cpprefs.set_default_output_directory(options.output_directory)
if options.image_directory:
cpprefs.set_default_image_directory(options.image_directory)
if options.show_gui:
if options.run_pipeline:
App.frame.pipeline_controller.do_analyze_images()
App.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True)
raise
def main(args):
'''Run CellProfiler
args - command-line arguments, e.g. sys.argv
'''
if any([arg.startswith('--work-announce') for arg in args]):
#
# Go headless ASAP
#
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
import cellprofiler.analysis_worker
cellprofiler.analysis_worker.main()
sys.exit(0)
options, args = parse_args(args)
set_log_level(options)
if not hasattr(sys, "frozen") and options.code_statistics:
print_code_statistics()
return
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
return
if options.batch_commands_file is not None:
get_batch_commands(options.batch_commands_file)
return
if options.run_ilastik:
run_ilastik()
return
# necessary to prevent matplotlib trying to use Tkinter as its backend.
# has to be done before CellProfilerApp is imported
from matplotlib import use as mpluse
mpluse('WXAgg')
if (not hasattr(sys, 'frozen')) and options.fetch_external_dependencies:
import external_dependencies
external_dependencies.fetch_external_dependencies(
options.overwrite_external_dependencies)
if (not hasattr(sys, 'frozen')) and options.build_extensions:
build_extensions()
if options.build_and_exit:
return
if options.output_html:
from cellprofiler.gui.html.manual import generate_html
webpage_path = options.output_directory if options.output_directory else None
generate_html(webpage_path)
return
if options.print_measurements:
print_measurements(options)
return
try:
if options.show_gui:
import wx
wx.Log.EnableLogging(False)
from cellprofiler.cellprofilerapp import CellProfilerApp
show_splashbox = (options.pipeline_filename is None
and options.workspace_filename is None
and (not options.new_workspace)
and options.show_splashbox)
if options.workspace_filename:
workspace_path = os.path.expanduser(options.workspace_filename)
elif options.new_workspace:
workspace_path = False
else:
workspace_path = None
App = CellProfilerApp(
0,
check_for_new_version=(options.pipeline_filename is None),
show_splashbox=show_splashbox,
workspace_path=workspace_path)
#
# Important to go headless ASAP
#
# cellprofiler.preferences can't be imported before we have a chance
# to initialize the wx app.
#
import cellprofiler.preferences as cpprefs
if not options.show_gui:
cpprefs.set_headless()
# What's there to do but run if you're running headless?
# Might want to change later if there's some headless setup
options.run_pipeline = True
if options.plugins_directory is not None:
cpprefs.set_plugin_directory(options.plugins_directory)
if options.ij_plugins_directory is not None:
cpprefs.set_ij_plugin_directory(options.ij_plugins_directory)
if options.temp_dir is not None:
cpprefs.set_temporary_directory(options.temp_dir)
if options.data_file is not None:
cpprefs.set_data_file(os.path.abspath(options.data_file))
if options.image_set_file is not None:
cpprefs.set_image_set_file(options.image_set_file, False)
from cellprofiler.utilities.version import version_string, version_number
logging.root.info("Version: %s / %d" %
(version_string, version_number))
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.output_directory:
cpprefs.set_default_output_directory(options.output_directory)
if options.image_directory:
cpprefs.set_default_image_directory(options.image_directory)
if options.show_gui:
import cellprofiler.gui.cpframe as cpgframe
if options.pipeline_filename:
pipeline_path = os.path.expanduser(options.pipeline_filename)
try:
App.frame.pipeline.load(pipeline_path)
if options.run_pipeline:
App.frame.Command(cpgframe.ID_FILE_ANALYZE_IMAGES)
except:
import wx
wx.MessageBox(
'CellProfiler was unable to load the pipeline file, "%s"'
% options.pipeline_filename,
"Error loading pipeline",
style=wx.OK | wx.ICON_ERROR)
logging.root.error("Unable to load pipeline",
exc_info=True)
App.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py",
exc_info=True)
raise
def get_preferences(self):
'''Get the list of preferences.
Each row in the list has the following form:
Title - the text that appears to the right of the edit box
get_function - retrieves the persistent preference value
set_function - sets the preference value
display - If this is a list, it represents the valid choices.
If it is "dirbrowse", put a directory browse button
to the right of the edit box.
'''
cmaps = list(matplotlib.cm.datad.keys())
cmaps.sort()
return [["Default Input Folder",
cpprefs.get_default_image_directory,
cpprefs.set_default_image_directory,
DIRBROWSE, cphelp.DEFAULT_IMAGE_FOLDER_HELP],
["Default Output Folder",
cpprefs.get_default_output_directory,
cpprefs.set_default_output_directory,
DIRBROWSE, cphelp.DEFAULT_OUTPUT_FOLDER_HELP],
[ "Title font",
self.get_title_font,
self.set_title_font,
FONT, cphelp.TITLE_FONT_HELP],
["Table font",
self.get_table_font,
self.set_table_font,
FONT, cphelp.TABLE_FONT_HELP],
["Default colormap",
cpprefs.get_default_colormap,
cpprefs.set_default_colormap,
cmaps, cphelp.DEFAULT_COLORMAP_HELP],
["Window background",
cpprefs.get_background_color,
cpprefs.set_background_color,
COLOR, cphelp.WINDOW_BACKGROUND_HELP],
["Error color",
cpprefs.get_error_color,
cpprefs.set_error_color,
COLOR, cphelp.ERROR_COLOR_HELP],
["Primary outline color",
cpprefs.get_primary_outline_color,
cpprefs.set_primary_outline_color,
COLOR, cphelp.PRIMARY_OUTLINE_COLOR_HELP],
["Secondary outline color",
cpprefs.get_secondary_outline_color,
cpprefs.set_secondary_outline_color,
COLOR, cphelp.SECONDARY_OUTLINE_COLOR_HELP],
["Tertiary outline color",
cpprefs.get_tertiary_outline_color,
cpprefs.set_tertiary_outline_color,
COLOR, cphelp.TERTIARY_OUTLINE_COLOR_HELP],
["Interpolation mode",
cpprefs.get_interpolation_mode,
cpprefs.set_interpolation_mode,
[cpprefs.IM_NEAREST, cpprefs.IM_BILINEAR, cpprefs.IM_BICUBIC],
cphelp.INTERPOLATION_MODE_HELP],
["Intensity normalization",
cpprefs.get_intensity_mode,
cpprefs.set_intensity_mode,
[cpprefs.INTENSITY_MODE_RAW, cpprefs.INTENSITY_MODE_NORMAL,
cpprefs.INTENSITY_MODE_LOG],
cphelp.INTENSITY_MODE_HELP],
["CellProfiler plugins directory",
cpprefs.get_plugin_directory,
cpprefs.set_plugin_directory,
DIRBROWSE, cphelp.PLUGINS_DIRECTORY_HELP],
["ImageJ plugins directory",
cpprefs.get_ij_plugin_directory,
cpprefs.set_ij_plugin_directory,
DIRBROWSE, cphelp.IJ_PLUGINS_DIRECTORY_HELP],
["Check for updates",
cpprefs.get_check_new_versions,
cpprefs.set_check_new_versions,
CHOICE, cphelp.CHECK_FOR_UPDATES_HELP],
["Display welcome text on startup",
cpprefs.get_startup_blurb,
cpprefs.set_startup_blurb,
CHOICE, cphelp.SHOW_STARTUP_BLURB_HELP],
["Warn if Java runtime environment not present",
cpprefs.get_report_jvm_error,
cpprefs.set_report_jvm_error,
CHOICE, cphelp.REPORT_JVM_ERROR_HELP],
['Show the "Analysis complete" message at the end of a run',
cpprefs.get_show_analysis_complete_dlg,
cpprefs.set_show_analysis_complete_dlg,
CHOICE, cphelp.SHOW_ANALYSIS_COMPLETE_HELP],
['Show the "Exiting test mode" message',
cpprefs.get_show_exiting_test_mode_dlg,
cpprefs.set_show_exiting_test_mode_dlg,
CHOICE, cphelp.SHOW_EXITING_TEST_MODE_HELP],
['Warn if images are different sizes',
cpprefs.get_show_report_bad_sizes_dlg,
cpprefs.set_show_report_bad_sizes_dlg,
CHOICE, cphelp.SHOW_REPORT_BAD_SIZES_DLG_HELP],
['Show the sampling menu',
cpprefs.get_show_sampling,
cpprefs.set_show_sampling,
CHOICE, """<p>Show the sampling menu </p>
<p><i>Note that CellProfiler must be restarted after setting.</i></p>
<p>The sampling menu is an interplace for Paramorama, a plugin for an interactive visualization
program for exploring the parameter space of image analysis algorithms.
will generate a text file, which specifies: (1) all unique combinations of
the sampled parameter values; (2) the mapping from each combination of parameter values to
one or more output images; and (3) the actual output images.</p>
<p>More information on how to use the plugin can be found
<a href="http://www.comp.leeds.ac.uk/scsajp/applications/paramorama2/">here</a>.</p>
<p><b>References</b>
<ul>
<li>Visualization of parameter space for image analysis. Pretorius AJ, Bray MA, Carpenter AE
and Ruddle RA. (2011) IEEE Transactions on Visualization and Computer Graphics, 17(12), 2402-2411.</li>
</ul>"""],
['Warn if a pipeline was saved in an old version of CellProfiler',
cpprefs.get_warn_about_old_pipeline,
cpprefs.set_warn_about_old_pipeline,
CHOICE,
cphelp.WARN_ABOUT_OLD_PIPELINES_HELP],
['Use more figure space',
cpprefs.get_use_more_figure_space,
cpprefs.set_use_more_figure_space,
CHOICE,
cphelp.USE_MORE_FIGURE_SPACE_HELP
],
['Maximum number of workers',
cpprefs.get_max_workers,
cpprefs.set_max_workers,
IntegerPreference(1, cpprefs.default_max_workers() * 4),
cphelp.MAX_WORKERS_HELP],
['Temporary folder',
cpprefs.get_temporary_directory,
(lambda x:cpprefs.set_temporary_directory(x, globally=True)),
DIRBROWSE,
cphelp.TEMP_DIR_HELP],
['Maximum memory for Java (MB)',
cpprefs.get_jvm_heap_mb,
cpprefs.set_jvm_heap_mb,
IntegerPreference(128, 64000),
cphelp.JVM_HEAP_HELP],
['Save pipeline and/or file list in addition to project',
cpprefs.get_save_pipeline_with_project,
cpprefs.set_save_pipeline_with_project,
cpprefs.SPP_ALL,
cphelp.SAVE_PIPELINE_WITH_PROJECT_HELP],
['Folder name regular expression guesses',
cpprefs.get_pathname_re_guess_file,
cpprefs.set_pathname_re_guess_file,
FILEBROWSE,
cphelp.FOLDER_RE_GUESS_HELP],
['File name regular expression guesses',
cpprefs.get_filename_re_guess_file,
cpprefs.set_filename_re_guess_file,
FILEBROWSE,
cphelp.FILE_RE_GUESS_HELP],
['Batch Profiler URL',
cpprefs.get_batchprofiler_url,
cpprefs.set_batchprofiler_url,
None,
cphelp.BATCHPROFILER_URL_HELP]
]
def main(args=None):
'''Run CellProfiler
args - command-line arguments, e.g. sys.argv
'''
if args is None:
args = sys.argv
import cellprofiler.preferences as cpprefs
cpprefs.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]):
#
# Go headless ASAP
#
cpprefs.set_headless()
for i, arg in enumerate(args):
if arg == "--ij-plugins-directory" and len(args) > i + 1:
cpprefs.set_ij_plugin_directory(args[i + 1])
break
import cellprofiler.analysis_worker
cellprofiler.analysis_worker.aw_parse_args()
cellprofiler.analysis_worker.main()
sys.exit(exit_code)
options, args = parse_args(args)
if options.print_version:
from cellprofiler.utilities.version import \
dotted_version, version_string, git_hash, version_number
print "CellProfiler %s" % dotted_version
print "Git %s" % git_hash
print "Version %s" % version_number
print "Built %s" % version_string.split(" ")[0]
sys.exit(exit_code)
#
# Important to go headless ASAP
#
if (not options.show_gui) or options.write_schema_and_exit:
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
# What's there to do but run if you're running headless?
# Might want to change later if there's some headless setup
options.run_pipeline = True
if options.jvm_heap_size is not None:
from cellprofiler.preferences import set_jvm_heap_mb
set_jvm_heap_mb(options.jvm_heap_size, False)
set_log_level(options)
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
return
if options.batch_commands_file is not None:
get_batch_commands(options.batch_commands_file)
return
if options.run_ilastik:
run_ilastik()
return
if options.add_message_for_user:
if len(args) != 3:
sys.stderr.write("Usage: (for add_message-for-user)\n")
sys.stderr.write("CellProfiler --add-message-for-user <caption> <message> <pipeline-or-project>\n")
sys.stderr.write("where:\n")
sys.stderr.write(" <caption> - the message box caption\n")
sys.stderr.write(" <message> - the message displayed inside the message box\n")
sys.stderr.write(" <pipeline-or-project> - the path to the pipeline or project file to modify\n")
return
caption = args[0]
message = args[1]
path = args[2]
import h5py
using_hdf5 = h5py.is_hdf5(path)
if using_hdf5:
import cellprofiler.measurements as cpmeas
m = cpmeas.Measurements(
filename=path, mode="r+")
pipeline_text = m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"]
else:
with open(path, "r") as fd:
pipeline_text = fd.read()
header, body = pipeline_text.split("\n\n", 1)
pipeline_text = header + \
("\nMessageForUser:%s|%s\n\n" % (caption, message)) + body
if using_hdf5:
m[cpmeas.EXPERIMENT, "Pipeline_Pipeline"] = pipeline_text
m.close()
else:
with open(path, "w") as fd:
fd.write(pipeline_text)
print "Message added to %s" % path
return
# necessary to prevent matplotlib trying to use Tkinter as its backend.
# has to be done before CellProfilerApp is imported
from matplotlib import use as mpluse
mpluse('WXAgg')
if options.omero_credentials is not None:
set_omero_credentials_from_string(options.omero_credentials)
if options.plugins_directory is not None:
cpprefs.set_plugin_directory(options.plugins_directory,
globally=False)
if options.ij_plugins_directory is not None:
cpprefs.set_ij_plugin_directory(options.ij_plugins_directory,
globally=False)
if options.temp_dir is not None:
if not os.path.exists(options.temp_dir):
os.makedirs(options.temp_dir)
cpprefs.set_temporary_directory(options.temp_dir, globally=False)
if not options.allow_schema_write:
cpprefs.set_allow_schema_write(False)
#
# After the crucial preferences are established, we can start the VM
#
from cellprofiler.utilities.cpjvm import cp_start_vm
cp_start_vm()
#
# Not so crucial preferences...
#
if options.image_set_file is not None:
cpprefs.set_image_set_file(options.image_set_file)
try:
# ---------------------------------------
#
# Handle command-line tasks that that need to load the modules to run
#
if options.output_html:
from cellprofiler.gui.html.manual import generate_html
webpage_path = options.output_directory if options.output_directory else None
generate_html(webpage_path)
return
if options.print_measurements:
print_measurements(options)
return
if not hasattr(sys, "frozen") and options.code_statistics:
print_code_statistics()
return
if options.write_schema_and_exit:
write_schema(options.pipeline_filename)
return
#
# ------------------------------------------
if options.show_gui:
import wx
wx.Log.EnableLogging(False)
from cellprofiler.gui.app import App
from cellprofiler.workspace import is_workspace_file
if options.pipeline_filename:
if 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
elif options.new_project:
workspace_path = False
pipeline_path = None
else:
workspace_path = None
pipeline_path = None
app = App(0, workspace_path=workspace_path, pipeline_path=pipeline_path)
if options.data_file is not None:
cpprefs.set_data_file(os.path.abspath(options.data_file))
from cellprofiler.utilities.version import version_string, version_number
logging.root.info("Version: %s / %d" % (version_string, version_number))
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.output_directory:
if not os.path.exists(options.output_directory):
os.makedirs(options.output_directory)
cpprefs.set_default_output_directory(options.output_directory)
if options.image_directory:
cpprefs.set_default_image_directory(options.image_directory)
if options.show_gui:
if options.run_pipeline:
app.frame.pipeline_controller.do_analyze_images()
app.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True)
exit_code = -1
def get_preferences(self):
'''Get the list of preferences.
Each row in the list has the following form:
Title - the text that appears to the right of the edit box
get_function - retrieves the persistent preference value
set_function - sets the preference value
display - If this is a list, it represents the valid choices.
If it is "dirbrowse", put a directory browse button
to the right of the edit box.
'''
cmaps = list(matplotlib.cm.datad.keys())
cmaps.sort()
return [
[
"Default Input Folder", cpprefs.get_default_image_directory,
cpprefs.set_default_image_directory, DIRBROWSE,
cphelp.DEFAULT_IMAGE_FOLDER_HELP
],
[
"Default Output Folder", cpprefs.get_default_output_directory,
cpprefs.set_default_output_directory, DIRBROWSE,
cphelp.DEFAULT_OUTPUT_FOLDER_HELP
],
[
"Title font", self.get_title_font, self.set_title_font, FONT,
cphelp.TITLE_FONT_HELP
],
[
"Table font", self.get_table_font, self.set_table_font, FONT,
cphelp.TABLE_FONT_HELP
],
[
"Default colormap", cpprefs.get_default_colormap,
cpprefs.set_default_colormap, cmaps,
cphelp.DEFAULT_COLORMAP_HELP
],
[
"Window background", cpprefs.get_background_color,
cpprefs.set_background_color, COLOR,
cphelp.WINDOW_BACKGROUND_HELP
],
[
"Error color", cpprefs.get_error_color,
cpprefs.set_error_color, COLOR, cphelp.ERROR_COLOR_HELP
],
[
"Primary outline color", cpprefs.get_primary_outline_color,
cpprefs.set_primary_outline_color, COLOR,
cphelp.PRIMARY_OUTLINE_COLOR_HELP
],
[
"Secondary outline color", cpprefs.get_secondary_outline_color,
cpprefs.set_secondary_outline_color, COLOR,
cphelp.SECONDARY_OUTLINE_COLOR_HELP
],
[
"Tertiary outline color", cpprefs.get_tertiary_outline_color,
cpprefs.set_tertiary_outline_color, COLOR,
cphelp.TERTIARY_OUTLINE_COLOR_HELP
],
[
"Interpolation mode", cpprefs.get_interpolation_mode,
cpprefs.set_interpolation_mode,
[cpprefs.IM_NEAREST, cpprefs.IM_BILINEAR,
cpprefs.IM_BICUBIC], cphelp.INTERPOLATION_MODE_HELP
],
[
"Intensity normalization", cpprefs.get_intensity_mode,
cpprefs.set_intensity_mode,
[
cpprefs.INTENSITY_MODE_RAW, cpprefs.INTENSITY_MODE_NORMAL,
cpprefs.INTENSITY_MODE_LOG
], cphelp.INTENSITY_MODE_HELP
],
[
"CellProfiler plugins directory", cpprefs.get_plugin_directory,
cpprefs.set_plugin_directory, DIRBROWSE,
cphelp.PLUGINS_DIRECTORY_HELP
],
[
"ImageJ plugins directory", cpprefs.get_ij_plugin_directory,
cpprefs.set_ij_plugin_directory, DIRBROWSE,
cphelp.IJ_PLUGINS_DIRECTORY_HELP
],
[
"Check for updates", cpprefs.get_check_new_versions,
cpprefs.set_check_new_versions, CHOICE,
cphelp.CHECK_FOR_UPDATES_HELP
],
[
"Display welcome text on startup", cpprefs.get_startup_blurb,
cpprefs.set_startup_blurb, CHOICE,
cphelp.SHOW_STARTUP_BLURB_HELP
],
[
"Warn if Java runtime environment not present",
cpprefs.get_report_jvm_error, cpprefs.set_report_jvm_error,
CHOICE, cphelp.REPORT_JVM_ERROR_HELP
],
[
'Show the "Analysis complete" message at the end of a run',
cpprefs.get_show_analysis_complete_dlg,
cpprefs.set_show_analysis_complete_dlg, CHOICE,
cphelp.SHOW_ANALYSIS_COMPLETE_HELP
],
[
'Show the "Exiting test mode" message',
cpprefs.get_show_exiting_test_mode_dlg,
cpprefs.set_show_exiting_test_mode_dlg, CHOICE,
cphelp.SHOW_EXITING_TEST_MODE_HELP
],
[
'Warn if images are different sizes',
cpprefs.get_show_report_bad_sizes_dlg,
cpprefs.set_show_report_bad_sizes_dlg, CHOICE,
cphelp.SHOW_REPORT_BAD_SIZES_DLG_HELP
],
[
'Show the sampling menu', cpprefs.get_show_sampling,
cpprefs.set_show_sampling, CHOICE,
"""<p>Show the sampling menu </p>
<p><i>Note that CellProfiler must be restarted after setting.</i></p>
<p>The sampling menu is an interplace for Paramorama, a plugin for an interactive visualization
program for exploring the parameter space of image analysis algorithms.
will generate a text file, which specifies: (1) all unique combinations of
the sampled parameter values; (2) the mapping from each combination of parameter values to
one or more output images; and (3) the actual output images.</p>
<p>More information on how to use the plugin can be found
<a href="http://www.comp.leeds.ac.uk/scsajp/applications/paramorama2/">here</a>.</p>
<p><b>References</b>
<ul>
<li>Visualization of parameter space for image analysis. Pretorius AJ, Bray MA, Carpenter AE
and Ruddle RA. (2011) IEEE Transactions on Visualization and Computer Graphics, 17(12), 2402-2411.</li>
</ul>"""
],
[
'Warn if a pipeline was saved in an old version of CellProfiler',
cpprefs.get_warn_about_old_pipeline,
cpprefs.set_warn_about_old_pipeline, CHOICE,
cphelp.WARN_ABOUT_OLD_PIPELINES_HELP
],
[
'Use more figure space', cpprefs.get_use_more_figure_space,
cpprefs.set_use_more_figure_space, CHOICE,
cphelp.USE_MORE_FIGURE_SPACE_HELP
],
[
'Maximum number of workers', cpprefs.get_max_workers,
cpprefs.set_max_workers,
IntegerPreference(1,
cpprefs.default_max_workers() * 4),
cphelp.MAX_WORKERS_HELP
],
[
'Temporary folder', cpprefs.get_temporary_directory,
(lambda x: cpprefs.set_temporary_directory(x, globally=True)),
DIRBROWSE, cphelp.TEMP_DIR_HELP
],
[
'Maximum memory for Java (MB)', cpprefs.get_jvm_heap_mb,
cpprefs.set_jvm_heap_mb,
IntegerPreference(128, 64000), cphelp.JVM_HEAP_HELP
],
[
'Save pipeline and/or file list in addition to project',
cpprefs.get_save_pipeline_with_project,
cpprefs.set_save_pipeline_with_project, cpprefs.SPP_ALL,
cphelp.SAVE_PIPELINE_WITH_PROJECT_HELP
],
[
'Folder name regular expression guesses',
cpprefs.get_pathname_re_guess_file,
cpprefs.set_pathname_re_guess_file, FILEBROWSE,
cphelp.FOLDER_RE_GUESS_HELP
],
[
'File name regular expression guesses',
cpprefs.get_filename_re_guess_file,
cpprefs.set_filename_re_guess_file, FILEBROWSE,
cphelp.FILE_RE_GUESS_HELP
],
[
'Batch Profiler URL', cpprefs.get_batchprofiler_url,
cpprefs.set_batchprofiler_url, None,
cphelp.BATCHPROFILER_URL_HELP
]
]
def main(args):
'''Run CellProfiler
args - command-line arguments, e.g. sys.argv
'''
if any([arg.startswith('--work-announce') for arg in args]):
#
# Go headless ASAP
#
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
import cellprofiler.analysis_worker
cellprofiler.analysis_worker.main()
sys.exit(0)
options, args = parse_args(args)
set_log_level(options)
if not hasattr(sys, "frozen") and options.code_statistics:
print_code_statistics()
return
if options.print_groups_file is not None:
print_groups(options.print_groups_file)
return
if options.batch_commands_file is not None:
get_batch_commands(options.batch_commands_file)
return
if options.run_ilastik:
run_ilastik()
return
# necessary to prevent matplotlib trying to use Tkinter as its backend.
# has to be done before CellProfilerApp is imported
from matplotlib import use as mpluse
mpluse('WXAgg')
if (not hasattr(sys, 'frozen')) and options.fetch_external_dependencies:
import external_dependencies
external_dependencies.fetch_external_dependencies(options.overwrite_external_dependencies)
if (not hasattr(sys, 'frozen')) and options.build_extensions:
build_extensions()
if options.build_and_exit:
return
if options.output_html:
from cellprofiler.gui.html.manual import generate_html
webpage_path = options.output_directory if options.output_directory else None
generate_html(webpage_path)
return
if options.print_measurements:
print_measurements(options)
return
try:
if options.show_gui:
import wx
wx.Log.EnableLogging(False)
from cellprofiler.cellprofilerapp import CellProfilerApp
show_splashbox = (options.pipeline_filename is None and
options.workspace_filename is None and
(not options.new_workspace) and
options.show_splashbox)
if options.workspace_filename:
workspace_path = os.path.expanduser(options.workspace_filename)
elif options.new_workspace:
workspace_path = False
else:
workspace_path = None
App = CellProfilerApp(
0,
check_for_new_version = (options.pipeline_filename is None),
show_splashbox = show_splashbox,
workspace_path = workspace_path)
#
# Important to go headless ASAP
#
# cellprofiler.preferences can't be imported before we have a chance
# to initialize the wx app.
#
import cellprofiler.preferences as cpprefs
if not options.show_gui:
cpprefs.set_headless()
# What's there to do but run if you're running headless?
# Might want to change later if there's some headless setup
options.run_pipeline = True
if options.plugins_directory is not None:
cpprefs.set_plugin_directory(options.plugins_directory)
if options.ij_plugins_directory is not None:
cpprefs.set_ij_plugin_directory(options.ij_plugins_directory)
if options.temp_dir is not None:
cpprefs.set_temporary_directory(options.temp_dir)
if options.data_file is not None:
cpprefs.set_data_file(os.path.abspath(options.data_file))
if options.image_set_file is not None:
cpprefs.set_image_set_file(options.image_set_file, False)
from cellprofiler.utilities.version import version_string, version_number
logging.root.info("Version: %s / %d" % (version_string, version_number))
if options.run_pipeline and not options.pipeline_filename:
raise ValueError("You must specify a pipeline filename to run")
if options.output_directory:
cpprefs.set_default_output_directory(options.output_directory)
if options.image_directory:
cpprefs.set_default_image_directory(options.image_directory)
if options.show_gui:
import cellprofiler.gui.cpframe as cpgframe
if options.pipeline_filename:
pipeline_path = os.path.expanduser(options.pipeline_filename)
try:
App.frame.pipeline.load(pipeline_path)
if options.run_pipeline:
App.frame.Command(cpgframe.ID_FILE_ANALYZE_IMAGES)
except:
import wx
wx.MessageBox(
'CellProfiler was unable to load the pipeline file, "%s"' %
options.pipeline_filename, "Error loading pipeline",
style = wx.OK | wx.ICON_ERROR)
logging.root.error("Unable to load pipeline", exc_info=True)
App.MainLoop()
return
elif options.run_pipeline:
run_pipeline_headless(options, args)
except Exception, e:
logging.root.fatal("Uncaught exception in CellProfiler.py", exc_info=True)
raise
