import os
import os.path
import glob
from subprocess import call
# fix from
# http://mail.python.org/pipermail/pythonmac-sig/2008-June/020111.html
import pytz
pytz.zoneinfo = pytz.tzinfo
pytz.zoneinfo.UTC = pytz.UTC
from libtiff.libtiff_ctypes import tiff_h_name
# make sure external dependencies match requirements
import external_dependencies
external_dependencies.fetch_external_dependencies('fail')
if sys.platform == "darwin":
import cellprofiler.utilities.version
f = open("cellprofiler/frozen_version.py", "w")
f.write("# MACHINE_GENERATED\nversion_string = '%s'" %
cellprofiler.utilities.version.version_string)
f.close()
APPNAME = 'CellProfiler2.0'
APP = ['CellProfiler.py']
DATA_FILES = [('cellprofiler/icons',
glob.glob(os.path.join('.', 'cellprofiler', 'icons', '*.png')))]
OPTIONS = {
'argv_emulation':
True,
import distutils.errors
import py2exe
import sys
import glob
import subprocess
import re
import os
import _winreg
import matplotlib
import pyreadline
import tempfile
import xml.dom.minidom
# make sure external dependencies match requirements
import external_dependencies
external_dependencies.fetch_external_dependencies('fail')
from cellprofiler.utilities.version import version_number, dotted_version, version_string
f = open("cellprofiler/frozen_version.py", "w")
f.write("# MACHINE_GENERATED\nversion_string = '%s'" % version_string)
f.close()
is_win64 = (os.environ["PROCESSOR_ARCHITECTURE"] == "AMD64")
is_2_6 = sys.version_info[0] >= 2 and sys.version_info[1] >= 6
vcredist = os.path.join("windows",
"vcredist_x64.exe" if is_win64
else "vcredist_x86.exe")
do_modify = is_2_6 and not os.path.exists(vcredist)
class CellProfilerMSI(distutils.core.Command):
description = "Make CellProfiler.msi using the CellProfiler.iss InnoSetup compiler"
__all__ = (start_subimager, get_image, get_metadata, post_image,
stop_subimager, HTTPError)
if __name__ == "__main__":
import wx
import matplotlib
matplotlib.use("WX")
from matplotlib.figure import Figure
from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg, FigureManager
sys.path.append(__root_path)
from external_dependencies import fetch_external_dependencies
if len(sys.argv) > 1:
port = int(sys.argv[1])
else:
fetch_external_dependencies(overwrite=True)
start_subimager()
app = wx.PySimpleApp()
frame = wx.Frame(None,size=(1024,768))
menu = wx.Menu()
metadata_item_id = wx.NewId()
menu.Append(wx.ID_OPEN, "Open")
menu.Append(metadata_item_id, "Open metadata")
menu.Append(wx.ID_SAVEAS, "Save as")
menu.Append(wx.ID_EXIT, "Exit")
menubar = wx.MenuBar()
menubar.Append(menu, "File")
frame.SetMenuBar(menubar)
frame.Sizer = wx.BoxSizer()
figure = Figure()
canvas = FigureCanvasWxAgg(frame, -1, figure)
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
import ilastik
import imp
sys.argv.remove("--ilastik")
il_path = ilastik.__path__
il_file, il_path, il_description = imp.find_module('ilastikMain', il_path)
imp.load_module('__main__', il_file, il_path, il_description)
sys.exit()
# 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:
import subprocess
import cellprofiler.cpmath.setup
import cellprofiler.utilities.setup
from distutils.dep_util import newer_group
#
# Check for dependencies and compile if necessary
#
compile_scripts = [(os.path.join('cellprofiler', 'cpmath', 'setup.py'),
cellprofiler.cpmath.setup),
(os.path.join('cellprofiler', 'utilities', 'setup.py'),
cellprofiler.utilities.setup)]
current_directory = os.path.abspath(os.curdir)
old_pythonpath = os.getenv('PYTHONPATH', None)
import ilastik
import imp
sys.argv.remove("--ilastik")
il_path = ilastik.__path__
il_file, il_path, il_description = imp.find_module('ilastikMain', il_path)
imp.load_module('__main__', il_file, il_path, il_description)
sys.exit()
# 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:
import subprocess
import cellprofiler.cpmath.setup
import cellprofiler.utilities.setup
from distutils.dep_util import newer_group
#
# Check for dependencies and compile if necessary
#
compile_scripts = [(os.path.join('cellprofiler', 'cpmath',
'setup.py'), cellprofiler.cpmath.setup),
(os.path.join('cellprofiler', 'utilities', 'setup.py'),
cellprofiler.utilities.setup)]
current_directory = os.path.abspath(os.curdir)
old_pythonpath = os.getenv('PYTHONPATH', None)
import distutils.errors
import py2exe
import sys
import glob
import subprocess
import re
import os
import _winreg
import matplotlib
import tempfile
import xml.dom.minidom
# make sure external dependencies match requirements
import external_dependencies
external_dependencies.fetch_external_dependencies("fail")
from cellprofiler.utilities.version import version_number, dotted_version, version_string
f = open("cellprofiler/frozen_version.py", "w")
f.write("# MACHINE_GENERATED\nversion_string = '%s'" % version_string)
f.close()
is_win64 = os.environ["PROCESSOR_ARCHITECTURE"] == "AMD64"
is_2_6 = sys.version_info[0] >= 2 and sys.version_info[1] >= 6
vcredist = os.path.join("windows", "vcredist_x64.exe" if is_win64 else "vcredist_x86.exe")
do_modify = is_2_6 and not os.path.exists(vcredist)
class CellProfilerMSI(distutils.core.Command):
description = "Make CellProfiler.msi using the CellProfiler.iss InnoSetup compiler"
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