def gen_steam_cm_graph(self, graphdata: dict):
"""Make an graph for connection managers"""
mpluse("Agg")
formats = [
"%y", # ticks are mostly years
"%b", # ticks are mostly months
"%d", # ticks are mostly days
"%H:%M", # hrs
"%H:%M", # min
"%S.%f", # secs
]
zero_formats = [""] + formats[:-1]
zero_formats[3] = "%d-%b"
offset_formats = [
"",
"%Y",
"%b %Y",
"%d %b %Y",
"%d %b %Y",
"%d %b %Y %H:%M",
]
munits.registry[datetime] = mdates.ConciseDateConverter(
formats=formats,
zero_formats=zero_formats,
offset_formats=offset_formats)
cur = graphdata["start"]
x = []
for _ in range(len(graphdata["data"])):
cur += graphdata["step"]
x.append(cur)
x = [datetime.utcfromtimestamp(_x / 1000) for _x in x]
y = graphdata["data"]
graphfile = BytesIO()
with pyplot.style.context(
path.join(bundled_data_path(self), "discord.mplstyle")):
fig, ax = pyplot.subplots()
ax.plot(x, y)
ax.set_ylim(bottom=0)
ax.grid()
ax.set(xlabel="Date",
ylabel="%",
title="Steam Connection Managers")
ax.set_yticks(np.arange(0, 100, 5))
fig.savefig(graphfile)
pyplot.close(fig)
graphfile.seek(0)
return graphfile
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
# Script to plot multiple graphs per obsid
# Written by David Gardenier, 2015-2016
import pandas as pd
import numpy as np
from matplotlib import use as mpluse
mpluse('agg') # Prevents errors when running in multiple screens
import matplotlib.pyplot as plt
from matplotlib import gridspec
from scipy.stats import binned_statistic
from plot_power_colours import findbestdataperobsid, findbestdata
class Plots:
'''
Class to determine setup for different plots
'''
def __init__(self, db, obj):
# Set up grid
self.fig = plt.figure(figsize=(15, 10))
self.gs = gridspec.GridSpec(2, 3)
self.db = db
self.df = findbestdataperobsid(db)
self.obj = obj
self.lc = False
self.ps = False
self.sp = False
def lightcurve(self):
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
from __future__ import division # no more "zero" integer division bugs!:P
import sys
import argparse
import os
import numpy as np # array
import ancillary as anc # not so good...but fast
import random
import logging
import warnings
import h5py
from scipy.stats import norm as scipy_norm
import matplotlib.cm as cm
from matplotlib import use as mpluse
mpluse("Agg")
#mpluse("Qt4Agg")
import matplotlib.pyplot as plt
#plt.rc('font',**{'family':'serif','serif':['Computer Modern Roman']})
#plt.rc('text', usetex=True)
plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = 'serif'
import matplotlib.colors as colors
#from matplotlib import rcParams
#rcParams['text.latex.unicode']=True
from matplotlib.ticker import FormatStrFormatter
warnings.simplefilter('ignore', np.RankWarning)
def main():
# ---
if options.run_ilastik:
#
# Fake ilastik into thinking it is __main__
#
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),
# -*- coding: utf-8 -*-
from gi.repository import Gtk
import dinic
import networkx as nx
from matplotlib import use as mpluse
mpluse('GTK3Agg')
from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as FigureCanvas
from matplotlib.backends.backend_gtk3 import NavigationToolbar2GTK3 as NavigationToolbar
import matplotlib.pyplot as plt
import thread
from gi.repository import Gdk
f = plt.figure()
class ConsoleLikeTextBuffer:
def __init__(self):
self.textbuff = Gtk.TextBuffer()
self.end_iter = self.textbuff.get_end_iter()
def get_text_buffer(self):
return self.textbuff
def append_line(self, message):
self.textbuff.insert(self.end_iter, message + "\n")
class ViewableNetworkFlow(dinic.NetworkFlow):
layout = {}
dilayout = {}
def __init__(self):
super(ViewableNetworkFlow, self).__init__()
self.console = ConsoleLikeTextBuffer()
def print_message(self, message):
self.console.append_line(message)
#!/usr/bin/env python -tt
# -*- coding: utf-8 -*-
#STANDARD LIBRARY
import os,sys,time,shutil,subprocess
import logging,platform,ConfigParser,traceback
import numpy as np
from itertools import chain
from math import e
from collections import defaultdict, Counter
#OTHER
from matplotlib import use as mpluse
mpluse('PS')
import matplotlib.pyplot as pyplt
import win32com.client
# #############################################################################
filename = os.path.basename(__file__)
authors = ("David B. H. Barton")
version = "2.7"
LOG=logging.getLogger()
#
#UTILITY LAMBDAS ##############################################################
#flattens a nested list, e.g. flatten([[1,2],[3,4]]) returns [1,2,3,4]
flatten=lambda nested: list(chain.from_iterable(nested))
Reads data from any log files that are present and sorts by composition of cornstarch. Plots a few simple checks and then plots shear stresses v strain rates. Author: Chris Boyle ([email protected] ''' # System from glob import glob from copy import copy import sys # 3rd Party import numpy as np import scipy as sp from matplotlib import use as mpluse mpluse('Agg') # can't remember this is here... fixes a bug perhaps? import matplotlib.pyplot as plt # RPi-R sys.path.append("./../bin") import plothelp as ph from filter import filter as ft import resx ############################################################################################################# ### Setting up. ############################################################################################# # Before the plot can begin, there are a few things to do first: setting up variables, reading the files etc. # Change plotter font to serif, I think it looks nicer than sans fonts. plt.rc('font', family='serif')
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
from matplotlib import use as mpluse
mpluse("TkAgg")
from Laser import *
import matplotlib.pyplot as plt
import math
from math import exp, sqrt, log as ln
# Math helper functions
i15 = 0
q0 = 0
def flagged_trigo(tFunc):
return (lambda x: (tFunc(x) if i15 else tFunc(math.radians(x))))
def flagged_arctrigo(aFunc):
return lambda x: (aFunc(x) if i15 else math.degrees(aFunc(x)))
atan2 = lambda y: (math.atan2(y, q0)
if i15 else math.degrees(math.atan2(y, q0)))
cos = flagged_trigo(math.cos)
sin = flagged_trigo(math.sin)
tan = flagged_trigo(math.tan)
acos = flagged_arctrigo(math.acos)
asin = flagged_arctrigo(math.asin)
atan = flagged_arctrigo(math.atan)
from collections import defaultdict
import numpy as np
from matplotlib import use as mpluse
mpluse('Agg')
import pylab as plt
from IPython import embed
from pyontutils.hierarchies import in_tree
def discretize(data_matrix):
bins = [0,1,10,100]
vals = [None,1,2,3]
for lower, upper, val in zip(bins[:-1],bins[1:], vals[:-1]):
data_matrix[ (data_matrix >= lower) * (data_matrix < upper) ] = val
data_matrix[data_matrix >= bins[-1]] = vals[-1]
return data_matrix
def sCollapseToSrcName(keys, id_name_dict):
"""
Collapse sources that have the same name.
"""
key_collections_dict = defaultdict(set)
new_id_name_dict = {}
for key in keys:
if key not in id_name_dict:
print(key + " is not in this dict")
continue
for example)
'''
# System
import math
from copy import copy
# 3rd Party
import xml.etree.ElementTree as ET
import numpy as np
from numpy import *
from scipy.optimize import curve_fit
try:
import spidev # will error if not on rpi
from matplotlib import use as mpluse
mpluse(
'Agg') # for plotting from commandline (with no xserver or anything)
except:
pass # not on rpi, don't need to use (!xserver) as gui backend
import matplotlib.pyplot as plt
import pandas as pd
# RPi-R
from filter import filter
######################################################################################################################## XML FUNCTIONS
def writeout(path="./../etc/data.xml"):
'''
writeout(**kwargs)
Writes the contents of a data file.
# Fake ilastik into thinking it is __main__
#
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
#
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division # no more "zero" integer division bugs!:P
import sys
import argparse
import os
import numpy as np # array
import time
#import h5py
#import random
#import constants as cst # local constants module
#from scipy.stats import norm as scipy_norm
import ancillary as anc
from matplotlib import use as mpluse
mpluse("Agg")
#mpluse("Qt4Agg")
import matplotlib.pyplot as plt
#plt.rc('font',**{'family':'serif','serif':['Computer Modern Roman']})
#plt.rc('text', usetex=True)
plt.rcParams['text.usetex'] = True
plt.rcParams['font.family'] = 'serif'
#from matplotlib import rcParams
#rcParams['text.latex.unicode']=True
import logging
import warnings
def main():
# ---
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
from sys import path
from matplotlib import use as mpluse
mpluse('Agg')
import matplotlib.pyplot as plt
path.append("./../bin/")
import motor
import resx
from time import sleep
m = motor.motor()
m.start_poll(name="test.csv", controlled=False)
m.update_setpoint(100)
m.set_dc(25)
print "warming up motor"
sleep(2)
m.start_control()
Ku = 4
m.pidc.tuning = (Ku, 0.0, 0.0)
m.pidc.tuning = (1.8, 2.85, 0.0)
errs_ = list()
times = list()
print "control started\ttuning: {}".format(m.pidc.tuning)
m.update_setpoint(100)
print "waiting"
for i in range(0, 1):
#print "speed {:.3f} gd {:.3f} lav {} err {}".format(m.speed, resx.get_strain((m.speed * 2 * 3.14) / 60.0), m.ldc, m.pidc.lerr)
if options.run_ilastik:
#
# Fake ilastik into thinking it is __main__
#
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',
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
Any live cell with two or three live neighbours lives
on to the next generation.
3.
Any live cell with more than three live neighbours
dies, as if by over-population.
4.
Any dead cell with exactly three live neighbours be-
comes a live cell, as if by reproduction.
'''
import random
import sys
import numpy as np
from matplotlib import use as mpluse
mpluse('TkAgg')
from matplotlib import pyplot as plt
from matplotlib.colors import ListedColormap
usage_doc = 'Usage of script: script_nama <size_of_canvas:int>'
choice = [0] * 100 + [1] * 10
random.shuffle(choice)
def create_canvas(size):
canvas = [[False for i in range(size)] for j in range(size)]
return canvas
def seed(canvas):
