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 aw_parse_args():
'''Parse the application arguments into setup parameters'''
from cellprofiler.preferences import set_headless, set_plugin_directory
from cellprofiler.preferences import set_ij_plugin_directory
import optparse
global work_announce_address
set_headless()
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option(
"--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=os.environ.get(AW_LOG_LEVEL, logging.INFO))
parser.add_option(
"--plugins-directory",
dest="plugins_directory",
help=
"Folder containing the CellProfiler plugin modules needed by client pipelines",
default=None)
parser.add_option(
"--ij-plugins-directory",
dest="ij_plugins_directory",
help=
"Folder containing the ImageJ plugin .jar and .class files needed bby client pipelines",
default=None)
parser.add_option(
"--jvm-heap-size",
dest="jvm_heap_size",
default="512m",
help=("This is the amount of memory reserved for the "
"Java Virtual Machine (similar to the java -Xmx switch)."
"Example formats: 512000k, 512m, 1g"))
options, args = parser.parse_args()
logging.root.setLevel(options.log_level)
if len(logging.root.handlers) == 0:
logging.root.addHandler(logging.StreamHandler())
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
work_announce_address = options.work_announce_address
#
# Set up the headless plugins and ij plugins directories before doing
# anything so loading will get them
#
if options.plugins_directory is not None:
set_plugin_directory(options.plugins_directory)
else:
logger.warning("Plugins directory not set")
if options.ij_plugins_directory is not None:
logger.debug("Using %s as IJ plugins directory" %
options.ij_plugins_directory)
set_ij_plugin_directory(options.ij_plugins_directory)
else:
logger.debug("IJ plugins directory not set")
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 aw_parse_args():
'''Parse the application arguments into setup parameters'''
from cellprofiler.preferences import \
set_headless, set_awt_headless, \
set_plugin_directory, set_ij_plugin_directory
import optparse
global work_announce_address
set_headless()
set_awt_headless(False)
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option("--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=os.environ.get(AW_LOG_LEVEL, logging.INFO))
parser.add_option("--plugins-directory",
dest="plugins_directory",
help="Folder containing the CellProfiler plugin modules needed by client pipelines",
default=None)
parser.add_option("--ij-plugins-directory",
dest="ij_plugins_directory",
help="Folder containing the ImageJ plugin .jar and .class files needed bby client pipelines",
default=None)
parser.add_option("--jvm-heap-size",
dest="jvm_heap_size",
default=None,
help=("This is the amount of memory reserved for the "
"Java Virtual Machine (similar to the java -Xmx switch)."
"Example formats: 512000k, 512m, 1g"))
options, args = parser.parse_args()
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)
logging.root.setLevel(options.log_level)
if len(logging.root.handlers) == 0:
logging.root.addHandler(logging.StreamHandler())
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
work_announce_address = options.work_announce_address
#
# Set up the headless plugins and ij plugins directories before doing
# anything so loading will get them
#
if options.plugins_directory is not None:
set_plugin_directory(options.plugins_directory)
else:
logger.warning("Plugins directory not set")
if options.ij_plugins_directory is not None:
logger.debug("Using %s as IJ plugins directory" % options.ij_plugins_directory)
set_ij_plugin_directory(options.ij_plugins_directory)
else:
logger.debug("IJ plugins directory not set")
def setUp(self):
#
# Make a temporary directory structure
#
cpprefs.set_headless()
directory = self.directory = tempfile.mkdtemp()
for i in range(3):
os.mkdir(os.path.join(directory, str(i)))
for j in range(3):
os.mkdir(os.path.join(directory, str(i), str(j)))
for k in range(3):
os.mkdir(os.path.join(directory, str(i), str(j), str(k)))
cpprefs.set_default_image_directory(os.path.join(self.directory, "1"))
def setUp(self):
#
# Make a temporary directory structure
#
cpprefs.set_headless()
directory = self.directory = tempfile.mkdtemp()
for i in range(3):
os.mkdir(os.path.join(directory, str(i)))
for j in range(3):
os.mkdir(os.path.join(directory, str(i), str(j)))
for k in range(3):
os.mkdir(os.path.join(directory, str(i), str(j), str(k)))
cpprefs.set_default_image_directory(os.path.join(self.directory, "1"))
def aw_parse_args():
'''Parse the application arguments into setup parameters'''
from cellprofiler.preferences import set_headless, set_plugin_directory
from cellprofiler.preferences import set_ij_plugin_directory
import optparse
global work_announce_address
set_headless()
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option(
"--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=os.environ.get(AW_LOG_LEVEL, logging.INFO))
parser.add_option(
"--plugins-directory",
dest="plugins_directory",
help=
"Folder containing the CellProfiler plugin modules needed by client pipelines",
default=None)
parser.add_option(
"--ij-plugins-directory",
dest="ij_plugins_directory",
help=
"Folder containing the ImageJ plugin .jar and .class files needed bby client pipelines",
default=None)
options, args = parser.parse_args()
logging.root.setLevel(options.log_level)
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
work_announce_address = options.work_announce_address
#
# Set up the headless plugins and ij plugins directories before doing
# anything so loading will get them
#
if options.plugins_directory is not None:
set_plugin_directory(options.plugins_directory)
else:
logger.warning("Plugins directory not set")
if options.ij_plugins_directory is not None:
logger.debug("Using %s as IJ plugins directory" %
options.ij_plugins_directory)
set_ij_plugin_directory(options.ij_plugins_directory)
else:
logger.debug("IJ plugins directory not set")
def setUp(self):
#
# Make three temporary directory structures
#
cpprefs.set_headless()
self.directories = [tempfile.mkdtemp() for i in range(3)]
for directory in self.directories:
for i in range(3):
os.mkdir(os.path.join(directory, str(i)))
for j in range(3):
os.mkdir(os.path.join(directory, str(i), str(j)))
for k in range(3):
os.mkdir(os.path.join(directory, str(i), str(j), str(k)))
cpprefs.set_default_image_directory(os.path.join(self.directories[0], "1"))
cpprefs.set_default_output_directory(os.path.join(self.directories[1], "1"))
self.root_directory = os.path.join(self.directories[2], "1")
def aw_parse_args():
'''Parse the application arguments into setup parameters'''
from cellprofiler.preferences import set_headless, set_plugin_directory
from cellprofiler.preferences import set_ij_plugin_directory
import optparse
global work_announce_address
set_headless()
parser = optparse.OptionParser()
parser.add_option("--work-announce",
dest="work_announce_address",
help="ZMQ port where work announcements are published",
default=None)
parser.add_option("--log-level",
dest="log_level",
help="Logging level for logger: DEBUG, INFO, WARNING, ERROR",
default=os.environ.get(AW_LOG_LEVEL, logging.INFO))
parser.add_option("--plugins-directory",
dest="plugins_directory",
help="Folder containing the CellProfiler plugin modules needed by client pipelines",
default=None)
parser.add_option("--ij-plugins-directory",
dest="ij_plugins_directory",
help="Folder containing the ImageJ plugin .jar and .class files needed bby client pipelines",
default=None)
options, args = parser.parse_args()
logging.root.setLevel(options.log_level)
if len(logging.root.handlers) == 0:
logging.root.addHandler(logging.StreamHandler())
if not options.work_announce_address:
parser.print_help()
sys.exit(1)
work_announce_address = options.work_announce_address
#
# Set up the headless plugins and ij plugins directories before doing
# anything so loading will get them
#
if options.plugins_directory is not None:
set_plugin_directory(options.plugins_directory)
else:
logger.warning("Plugins directory not set")
if options.ij_plugins_directory is not None:
logger.debug("Using %s as IJ plugins directory" % options.ij_plugins_directory)
set_ij_plugin_directory(options.ij_plugins_directory)
else:
logger.debug("IJ plugins directory not set")
def test_02_01_compare_to_matlab(self):
expected = {
'EC50_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':3.982812,
'EC50_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':4.139827,
'EC50_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':4.178600,
'EC50_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':4.059770,
'EC50_DistCytoplasm_Intensity_MinIntensity_CorrGreen':4.066357,
'EC50_DistCytoplasm_Math_Ratio1':4.491367,
'EC50_DistCytoplasm_Math_Ratio2':3.848722,
'EC50_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':4.948056,
'EC50_DistCytoplasm_Texture_Entropy_CorrGreen_1':4.687104,
'EC50_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':5.0285,
'EC50_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':4.319017,
'EC50_DistCytoplasm_Texture_SumAverage_CorrGreen_1':4.548876,
'EC50_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':4.779139,
'EC50_DistCytoplasm_Texture_Variance_CorrGreen_1':4.218379,
'EC50_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':3.708711,
'EC50_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':4.135146,
'EC50_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':4.5372,
'EC50_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':4.1371,
'EC50_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':4.033999,
'EC50_DistanceCells_Intensity_MinIntensity_CorrGreen':4.079470,
'EC50_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':5.118689,
'EC50_DistanceCells_Texture_Correlation_CorrGreen_1':4.002074,
'EC50_DistanceCells_Texture_Entropy_CorrGreen_1':5.008000,
'EC50_DistanceCells_Texture_InfoMeas1_CorrGreen_1':3.883586,
'EC50_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':3.977216,
'EC50_DistanceCells_Texture_SumAverage_CorrGreen_1':4.9741,
'EC50_DistanceCells_Texture_SumEntropy_CorrGreen_1':5.1455,
'EC50_DistanceCells_Texture_SumVariance_CorrGreen_1':4.593041,
'EC50_DistanceCells_Texture_Variance_CorrGreen_1':4.619517,
'EC50_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':3.751133,
'EC50_Nuclei_Math_Ratio1':4.491367,
'EC50_Nuclei_Math_Ratio2':3.848722,
'EC50_Nuclei_Texture_SumAverage_CorrGreen_1':3.765297,
'EC50_PropCells_AreaShape_Area':4.740853,
'EC50_PropCells_AreaShape_MajorAxisLength':5.064460,
'EC50_PropCells_AreaShape_MinorAxisLength':4.751471,
'EC50_PropCells_AreaShape_Perimeter':4.949292,
'EC50_PropCells_Correlation_Correlation_CorrGreenCorrBlue':3.772565,
'EC50_PropCells_Texture_GaborX_CorrGreen_1':5.007167,
'EC50_PropCells_Texture_InfoMeas2_CorrBlue_1':4.341353,
'EC50_PropCells_Texture_SumVariance_CorrBlue_1':4.298359,
'EC50_PropCells_Texture_SumVariance_CorrGreen_1':4.610826,
'EC50_PropCells_Texture_Variance_CorrBlue_1':4.396352,
'EC50_PropCells_Texture_Variance_CorrGreen_1':4.632468,
'EC50_PropCytoplasm_AreaShape_Area':4.669679,
'EC50_PropCytoplasm_AreaShape_MinorAxisLength':4.754476,
'EC50_PropCytoplasm_AreaShape_Perimeter':4.949292,
'EC50_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':4.072830,
'EC50_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':4.0934,
'EC50_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':3.925800,
'EC50_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':3.9252,
'EC50_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':4.777481,
'EC50_PropCytoplasm_Texture_Entropy_CorrGreen_1':4.4432,
'EC50_PropCytoplasm_Texture_GaborX_CorrGreen_1':5.163371,
'EC50_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':4.701046,
'EC50_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':4.510543,
'EC50_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':4.560315,
'EC50_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':4.966674,
'EC50_ThresholdedCells_Texture_Entropy_CorrBlue_1':4.457866,
'EC50_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':4.624049,
'EC50_ThresholdedCells_Texture_SumAverage_CorrBlue_1':4.686706,
'EC50_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':4.537378,
'EC50_ThresholdedCells_Texture_SumVariance_CorrBlue_1':4.322820,
'EC50_ThresholdedCells_Texture_SumVariance_CorrGreen_1':4.742158,
'EC50_ThresholdedCells_Texture_Variance_CorrBlue_1':4.265549,
'EC50_ThresholdedCells_Texture_Variance_CorrGreen_1':4.860020,
'OneTailedZfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':-4.322503,
'OneTailedZfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':-4.322503,
'OneTailedZfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':-4.322503,
'OneTailedZfactor_DistCytoplasm_Math_Ratio1':0.622059,
'OneTailedZfactor_DistCytoplasm_Math_Ratio2':-4.508284,
'OneTailedZfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':-4.645887,
'OneTailedZfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':-4.279118,
'OneTailedZfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':-4.765570,
'OneTailedZfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':-4.682335,
'OneTailedZfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':-4.415607,
'OneTailedZfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':-4.200105,
'OneTailedZfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':-4.316452,
'OneTailedZfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':-4.316452,
'OneTailedZfactor_DistanceCells_Texture_Correlation_CorrGreen_1':0.202500,
'OneTailedZfactor_DistanceCells_Texture_Entropy_CorrGreen_1':-4.404815,
'OneTailedZfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':-4.508513,
'OneTailedZfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':-4.225356,
'OneTailedZfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':-4.382768,
'OneTailedZfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':0.492125,
'OneTailedZfactor_DistanceCells_Texture_Variance_CorrGreen_1':0.477360,
'OneTailedZfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':0.563780,
'OneTailedZfactor_Nuclei_Math_Ratio1':0.622059,
'OneTailedZfactor_Nuclei_Math_Ratio2':-4.508284,
'OneTailedZfactor_Nuclei_Texture_SumAverage_CorrGreen_1':0.426178,
'OneTailedZfactor_PropCells_AreaShape_Area':-4.216674,
'OneTailedZfactor_PropCells_AreaShape_MajorAxisLength':-4.119131,
'OneTailedZfactor_PropCells_AreaShape_MinorAxisLength':-4.109793,
'OneTailedZfactor_PropCells_AreaShape_Perimeter':-4.068050,
'OneTailedZfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':0.765440,
'OneTailedZfactor_PropCells_Texture_GaborX_CorrGreen_1':0.114982,
'OneTailedZfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':0.108409,
'OneTailedZfactor_PropCells_Texture_SumVariance_CorrBlue_1':0.191251,
'OneTailedZfactor_PropCells_Texture_SumVariance_CorrGreen_1':0.559865,
'OneTailedZfactor_PropCells_Texture_Variance_CorrBlue_1':0.254078,
'OneTailedZfactor_PropCells_Texture_Variance_CorrGreen_1':0.556108,
'OneTailedZfactor_PropCytoplasm_AreaShape_Area':-4.223021,
'OneTailedZfactor_PropCytoplasm_AreaShape_MinorAxisLength':-4.095632,
'OneTailedZfactor_PropCytoplasm_AreaShape_Perimeter':-4.068050,
'OneTailedZfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':-4.194663,
'OneTailedZfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':-4.443338,
'OneTailedZfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':0.207265,
'OneTailedZfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':-4.297250,
'OneTailedZfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':-4.525324,
'OneTailedZfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':0.167795,
'OneTailedZfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':0.067560,
'OneTailedZfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':0.478527,
'OneTailedZfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':0.155119,
'OneTailedZfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':0.535907,
'OneTailedZfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':0.572801,
'OneTailedZfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':0.423454,
'OneTailedZfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':0.440500,
'Vfactor_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':0.500429,
'Vfactor_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':0.325675,
'Vfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':0.323524,
'Vfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':0.138487,
'Vfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':0.128157,
'Vfactor_DistCytoplasm_Math_Ratio1':0.503610,
'Vfactor_DistCytoplasm_Math_Ratio2':0.319610,
'Vfactor_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':0.522880,
'Vfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':0.504303,
'Vfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':0.289432,
'Vfactor_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':0.234123,
'Vfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':0.591687,
'Vfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':0.520356,
'Vfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':-0.007649,
'Vfactor_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':0.761198,
'Vfactor_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':0.234655,
'Vfactor_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':0.252240,
'Vfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':0.195125,
'Vfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':0.138299,
'Vfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':0.126784,
'Vfactor_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':0.342691,
'Vfactor_DistanceCells_Texture_Correlation_CorrGreen_1':0.314396,
'Vfactor_DistanceCells_Texture_Entropy_CorrGreen_1':0.311771,
'Vfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':0.410631,
'Vfactor_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':0.170576,
'Vfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':0.223147,
'Vfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':0.269519,
'Vfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':0.571528,
'Vfactor_DistanceCells_Texture_Variance_CorrGreen_1':0.566272,
'Vfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':0.705051,
'Vfactor_Nuclei_Math_Ratio1':0.503610,
'Vfactor_Nuclei_Math_Ratio2':0.319610,
'Vfactor_Nuclei_Texture_SumAverage_CorrGreen_1':0.553708,
'Vfactor_PropCells_AreaShape_Area':0.340093,
'Vfactor_PropCells_AreaShape_MajorAxisLength':0.243838,
'Vfactor_PropCells_AreaShape_MinorAxisLength':0.320691,
'Vfactor_PropCells_AreaShape_Perimeter':0.238915,
'Vfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':0.723520,
'Vfactor_PropCells_Texture_GaborX_CorrGreen_1':0.213161,
'Vfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':0.199791,
'Vfactor_PropCells_Texture_SumVariance_CorrBlue_1':0.078959,
'Vfactor_PropCells_Texture_SumVariance_CorrGreen_1':0.642844,
'Vfactor_PropCells_Texture_Variance_CorrBlue_1':0.199105,
'Vfactor_PropCells_Texture_Variance_CorrGreen_1':0.640818,
'Vfactor_PropCytoplasm_AreaShape_Area':0.325845,
'Vfactor_PropCytoplasm_AreaShape_MinorAxisLength':0.312258,
'Vfactor_PropCytoplasm_AreaShape_Perimeter':0.238915,
'Vfactor_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':0.337565,
'Vfactor_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':0.292900,
'Vfactor_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':0.175528,
'Vfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':0.193308,
'Vfactor_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':0.276152,
'Vfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':0.239567,
'Vfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':0.332380,
'Vfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':0.379141,
'Vfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':0.337740,
'Vfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':0.334520,
'Vfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':0.192882,
'Vfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':0.276245,
'Vfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':0.139166,
'Vfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':0.465237,
'Vfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':0.355399,
'Vfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':0.453937,
'Vfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':0.564371,
'Vfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':0.360566,
'Vfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':0.548770,
'Zfactor_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':0.531914,
'Zfactor_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':0.265558,
'Zfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':0.178586,
'Zfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':0.084566,
'Zfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':0.086476,
'Zfactor_DistCytoplasm_Math_Ratio1':0.623284,
'Zfactor_DistCytoplasm_Math_Ratio2':0.358916,
'Zfactor_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':0.429510,
'Zfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':0.508275,
'Zfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':0.068695,
'Zfactor_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':0.347949,
'Zfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':0.646576,
'Zfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':0.494276,
'Zfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':0.179011,
'Zfactor_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':0.824686,
'Zfactor_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':0.027644,
'Zfactor_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':0.088491,
'Zfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':0.065056,
'Zfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':0.089658,
'Zfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':0.078017,
'Zfactor_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':0.238131,
'Zfactor_DistanceCells_Texture_Correlation_CorrGreen_1':0.301107,
'Zfactor_DistanceCells_Texture_Entropy_CorrGreen_1':0.251143,
'Zfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':0.564957,
'Zfactor_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':0.302767,
'Zfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':0.036459,
'Zfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':0.159798,
'Zfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':0.516938,
'Zfactor_DistanceCells_Texture_Variance_CorrGreen_1':0.501186,
'Zfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':0.691408,
'Zfactor_Nuclei_Math_Ratio1':0.623284,
'Zfactor_Nuclei_Math_Ratio2':0.358916,
'Zfactor_Nuclei_Texture_SumAverage_CorrGreen_1':0.587347,
'Zfactor_PropCells_AreaShape_Area':0.132425,
'Zfactor_PropCells_AreaShape_MajorAxisLength':0.034809,
'Zfactor_PropCells_AreaShape_MinorAxisLength':0.113864,
'Zfactor_PropCells_AreaShape_Perimeter':0.005984,
'Zfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':0.717632,
'Zfactor_PropCells_Texture_GaborX_CorrGreen_1':0.251023,
'Zfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':0.149719,
'Zfactor_PropCells_Texture_SumVariance_CorrBlue_1':0.102050,
'Zfactor_PropCells_Texture_SumVariance_CorrGreen_1':0.611960,
'Zfactor_PropCells_Texture_Variance_CorrBlue_1':0.197090,
'Zfactor_PropCells_Texture_Variance_CorrGreen_1':0.614879,
'Zfactor_PropCytoplasm_AreaShape_Area':0.205042,
'Zfactor_PropCytoplasm_AreaShape_MinorAxisLength':0.072682,
'Zfactor_PropCytoplasm_AreaShape_Perimeter':0.005984,
'Zfactor_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':0.272017,
'Zfactor_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':0.115327,
'Zfactor_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':0.141850,
'Zfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':0.105803,
'Zfactor_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':0.107640,
'Zfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':0.067896,
'Zfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':0.136688,
'Zfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':0.334749,
'Zfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':0.208829,
'Zfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':0.263467,
'Zfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':0.124355,
'Zfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':0.236433,
'Zfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':0.125845,
'Zfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':0.449333,
'Zfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':0.323243,
'Zfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':0.507477,
'Zfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':0.599000,
'Zfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':0.361424,
'Zfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':0.481393
}
temp_dir = tempfile.mkdtemp()
m = None
try:
cpprefs.set_headless()
cpprefs.set_default_output_directory(temp_dir)
print "Writing output to %s"%temp_dir
path = os.path.split(__file__)[0]
matfile_path = os.path.join(path,'calculatestatistics.mat')
if not os.path.isfile(matfile_path):
# Download from GIT URL
matfile_path = os.path.join(temp_dir, 'calculatestatistics.mat')
url = github_url + (
"/cellprofiler/modules/tests/"
"calculatestatistics.mat")
urllib.urlretrieve(url, matfile_path)
measurements = loadmat(matfile_path,
struct_as_record = True)
measurements = measurements['m']
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
m = cpmeas.Measurements()
doses = [0 ,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,10,
0 ,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,10,
0 ,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,10,
0 ,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,10,
10,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,0,
10,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,0,
10,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,0,
10,0 ,1 ,2 ,3 ,4 ,5 ,6 ,7 ,8 ,9 ,0]
for i,dose in enumerate(doses):
m.add_image_measurement("Dose",dose)
for object_name in measurements.dtype.fields:
omeasurements = measurements[object_name][0,0]
for feature_name in omeasurements.dtype.fields:
data = omeasurements[feature_name][0,0][0,i].flatten()
m.add_measurement(object_name, feature_name, data)
if i < len(doses)-1:
m.next_image_set()
pipeline = cpp.Pipeline()
module = C.CalculateStatistics()
module.grouping_values.value = "Dose"
module.dose_values[0].log_transform.value = False
module.dose_values[0].measurement.value = "Dose"
module.dose_values[0].wants_save_figure.value = True
module.dose_values[0].figure_name.value = "EC49_"
module.module_num = 1
pipeline.add_module(module)
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
workspace = cpw.Workspace(pipeline, module, image_set,
cpo.ObjectSet(), m,
image_set_list)
module.post_run(workspace)
for feature_name in m.get_feature_names(cpmeas.EXPERIMENT):
if not expected.has_key(feature_name):
print "Missing measurement: %s"%feature_name
continue
value = m.get_experiment_measurement(feature_name)
e_value = expected[feature_name]
diff = abs(value-e_value) *2 /abs(value+e_value)
self.assertTrue(diff < .05, "%s: Matlab: %f, Python: %f diff: %f" %
(feature_name, e_value, value, diff))
if diff > .01:
print ("Warning: > 1%% difference for %s: Matlab: %f, Python: %f diff: %f" %
(feature_name, e_value, value, diff))
if feature_name.startswith("EC50"):
filename = "EC49_"+feature_name[5:]+".pdf"
self.assertTrue(os.path.isfile(os.path.join(temp_dir, filename)))
finally:
try:
if m is not None:
m.close()
except:
pass
for filename in os.listdir(temp_dir):
path = os.path.join(temp_dir, filename)
os.remove(path)
os.rmdir(temp_dir)
def main(*args):
'''Run the CellProfiler nose tests'''
args = list(args)
if '--noguitests' in args:
args.remove('--noguitests')
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
sys.modules['wx'] = MockModule()
sys.modules['wx.html'] = MockModule()
import matplotlib
matplotlib.use('agg')
with_guitests = False
else:
with_guitests = True
def mock_start_vm(*args, **kwargs):
raise SkipTest
if '--nojavatests' in args:
args.remove('--nojavatests')
javabridge.start_vm = mock_start_vm
elif not with_guitests:
javabridge.activate_awt = mock_start_vm
javabridge.execute_future_in_main_thread = mock_start_vm
javabridge.execute_runnable_in_main_thread = mock_start_vm
addplugins = [CPShutdownPlugin()]
if not "--with-cpshutdown" in args:
args.append("--with-cpshutdown")
if '--with-kill-vm' in args:
args[args.index('--with-kill-vm')] = '--with-javabridge'
if '--with-javabridge' in args:
class_path = get_jars()
args.append('--classpath=%s' % os.pathsep.join(class_path))
if hasattr(sys, "frozen"):
from javabridge.noseplugin import JavabridgePlugin
javabridge_plugin_class = JavabridgePlugin
addplugins.append(JavabridgePlugin())
else:
javabridge_plugin_class = load_entry_point(
'javabridge', 'nose.plugins.0.10', 'javabridge')
javabridge_plugin_class.extra_jvm_args += get_patcher_args(class_path)
if "CP_JDWP_PORT" in os.environ:
javabridge_plugin_class.extra_jvm_args.append(
("-agentlib:jdwp=transport=dt_socket,address=127.0.0.1:%s"
",server=y,suspend=n") % os.environ["CP_JDWP_PORT"])
addplugins.append(javabridge_plugin_class())
#
# Run the shutdown plugin before the javabridge plugin when exiting
#
CPShutdownPlugin.score = javabridge_plugin_class.score + 1
addplugins.append(LoadTestsFromXML())
if len(args) == 0:
args = ['--testmatch=(?:^)test_.*']
args += ['--exe']
if hasattr(sys, "frozen"):
#
# Patch nose.core.TestProgram.usage
# it will attempt to get usage.txt and it's not worth
# the effort to make that work.
#
from nose.core import TestProgram
TestProgram.usage = lambda cls: ""
nose.main(argv=args, addplugins=addplugins)
def main(*args):
'''Run the CellProfiler nose tests'''
args = list(args)
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
cpprefs.set_awt_headless(True)
if '--noguitests' in args:
args.remove('--noguitests')
sys.modules['wx'] = MockModule()
sys.modules['wx.html'] = MockModule()
import matplotlib
matplotlib.use('agg')
with_guitests = False
wxapp = None
else:
with_guitests = True
import wx
wxapp = wx.App(False)
def mock_start_vm(*args, **kwargs):
raise SkipTest
if '--nojavatests' in args:
args.remove('--nojavatests')
javabridge.start_vm = mock_start_vm
addplugins = [CPShutdownPlugin()]
if not "--with-cpshutdown" in args:
args.append("--with-cpshutdown")
if '--with-kill-vm' in args:
args[args.index('--with-kill-vm')] = '--with-javabridge'
if '--with-javabridge' in args:
class_path = get_jars()
args.append('--classpath=%s' % os.pathsep.join(class_path))
if hasattr(sys, "frozen"):
from javabridge.noseplugin import JavabridgePlugin
javabridge_plugin_class = JavabridgePlugin
addplugins.append(JavabridgePlugin())
else:
javabridge_plugin_class = load_entry_point('javabridge',
'nose.plugins.0.10',
'javabridge')
javabridge_plugin_class.extra_jvm_args += get_patcher_args(class_path)
if "CP_JDWP_PORT" in os.environ:
javabridge_plugin_class.extra_jvm_args.append(
("-agentlib:jdwp=transport=dt_socket,address=127.0.0.1:%s"
",server=y,suspend=n") % os.environ["CP_JDWP_PORT"])
addplugins.append(javabridge_plugin_class())
#
# Run the shutdown plugin before the javabridge plugin when exiting
#
CPShutdownPlugin.score = javabridge_plugin_class.score + 1
addplugins.append(LoadTestsFromXML())
if len(args) == 0:
args = ['--testmatch=(?:^)test_.*']
args += ['--exe']
if hasattr(sys, "frozen"):
#
# Patch nose.core.TestProgram.usage
# it will attempt to get usage.txt and it's not worth
# the effort to make that work.
#
from nose.core import TestProgram
TestProgram.usage = lambda cls: ""
nose.main(argv=args, addplugins=addplugins)
import logging
import logging.config
logging.root.setLevel(logging.INFO)
if len(logging.root.handlers) == 0:
logging.root.addHandler(logging.StreamHandler())
import os
import uuid
import csv
import matplotlib
matplotlib.use('Agg')
import Image
import cellprofiler.preferences as cpprefs
cpprefs.set_headless() # ASAP
cpprefs.set_allow_schema_write(False)
from cellprofiler.pipeline import Pipeline
from cellprofiler.utilities.cpjvm import cp_start_vm, cp_stop_vm
import pydoop.mapreduce.api as api
import pydoop.mapreduce.pipes as pp
from pydoop.avrolib import AvroContext
from pyfeatures.bioimg import BioImgPlane
# basename of the pipeline file, to be uploaded via distributed cache
PIPELINE_BN = 'it.crs4.features.cppipe'
# --- FIXME: the following info should be extracted from the pipeline file
CHANNEL_TAGS = ['D.TIF', 'F.TIF', 'R.TIF']
Website: http://www.cellprofiler.org ''' import base64 from matplotlib.image import pil_to_array import numpy as np import os import PIL.Image as PILImage import scipy.ndimage from StringIO import StringIO import unittest import zlib from cellprofiler.preferences import set_headless set_headless() import cellprofiler.pipeline as cpp import cellprofiler.cpmodule as cpm import cellprofiler.cpimage as cpi import cellprofiler.measurements as cpmeas import cellprofiler.objects as cpo import cellprofiler.workspace as cpw import cellprofiler.cpmath.cpmorphology as morph from cellprofiler.cpmath.outline import outline import cellprofiler.modules.expandorshrinkobjects as E INPUT_NAME = "input" OUTPUT_NAME = "output"
from getpass import getpass
# Import OMERO Python BlitzGateway
from omero.gateway import BlitzGateway
from omero.grid import DoubleColumn, ImageColumn, LongColumn, WellColumn
from omero.constants.namespaces import NSBULKANNOTATIONS
from omero.gateway import FileAnnotationWrapper
from omero.model import OriginalFileI
# Import Cell Profiler Dependencies
import cellprofiler.preferences as cpprefs
import cellprofiler.pipeline as cpp
# Important to set when running headless
cpprefs.set_headless() # noqa
# module used to inject OMERO image planes into Cell Profiler Pipeline
from cellprofiler.modules.injectimage import InjectImage
# Connect to the server
def connect(hostname, username, password):
conn = BlitzGateway(username, password,
host=hostname, secure=True)
conn.connect()
return conn
# Load-plate
def load_plate(conn, plate_id):
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 logging
import logging.config
logging.root.setLevel(logging.INFO)
if len(logging.root.handlers) == 0:
logging.root.addHandler(logging.StreamHandler())
import os
import uuid
import csv
import matplotlib
matplotlib.use('Agg')
import Image
import cellprofiler.preferences as cpprefs
cpprefs.set_headless() # ASAP
cpprefs.set_allow_schema_write(False)
from cellprofiler.pipeline import Pipeline
from cellprofiler.utilities.cpjvm import cp_start_vm, cp_stop_vm
import pydoop.mapreduce.api as api
import pydoop.mapreduce.pipes as pp
from pydoop.avrolib import AvroContext
from pyfeatures.bioimg import BioImgPlane
# basename of the pipeline file, to be uploaded via distributed cache
PIPELINE_BN = 'it.crs4.features.cppipe'
# --- FIXME: the following info should be extracted from the pipeline file
CHANNEL_TAGS = ['D.TIF', 'F.TIF', 'R.TIF']
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 setUp(self):
from cellprofiler.preferences import set_headless
set_headless()
self.old_import = __builtin__.__import__
__builtin__.__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.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
Please see the AUTHORS file for credits.
Website: http://www.cellprofiler.org
"""
import nose
import sys
import numpy as np
np.seterr(all='ignore')
if '--noguitests' in sys.argv:
sys.argv.remove('--noguitests')
import cellprofiler.preferences as cpprefs
cpprefs.set_headless()
sys.modules['wx'] = None
import matplotlib
matplotlib.use('agg')
if '--nojavatests' in sys.argv:
sys.argv.remove('--nojavatests')
import cellprofiler.utilities.jutil as jutil
jutil.start_vm = None
if len(sys.argv) == 0:
args = ['--testmatch=(?:^)test_.*']
else:
args = sys.argv
nose.main(argv=args + ['-w', 'cpa/tests'])
def test_02_01_compare_to_matlab(self):
expected = {
'EC50_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
3.982812,
'EC50_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
4.139827,
'EC50_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
4.178600,
'EC50_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
4.059770,
'EC50_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
4.066357,
'EC50_DistCytoplasm_Math_Ratio1':
4.491367,
'EC50_DistCytoplasm_Math_Ratio2':
3.848722,
'EC50_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
4.948056,
'EC50_DistCytoplasm_Texture_Entropy_CorrGreen_1':
4.687104,
'EC50_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
5.0285,
'EC50_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':
4.319017,
'EC50_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
4.548876,
'EC50_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
4.779139,
'EC50_DistCytoplasm_Texture_Variance_CorrGreen_1':
4.218379,
'EC50_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':
3.708711,
'EC50_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':
4.135146,
'EC50_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':
4.5372,
'EC50_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
4.1371,
'EC50_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
4.033999,
'EC50_DistanceCells_Intensity_MinIntensity_CorrGreen':
4.079470,
'EC50_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':
5.118689,
'EC50_DistanceCells_Texture_Correlation_CorrGreen_1':
4.002074,
'EC50_DistanceCells_Texture_Entropy_CorrGreen_1':
5.008000,
'EC50_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
3.883586,
'EC50_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':
3.977216,
'EC50_DistanceCells_Texture_SumAverage_CorrGreen_1':
4.9741,
'EC50_DistanceCells_Texture_SumEntropy_CorrGreen_1':
5.1455,
'EC50_DistanceCells_Texture_SumVariance_CorrGreen_1':
4.593041,
'EC50_DistanceCells_Texture_Variance_CorrGreen_1':
4.619517,
'EC50_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
3.751133,
'EC50_Nuclei_Math_Ratio1':
4.491367,
'EC50_Nuclei_Math_Ratio2':
3.848722,
'EC50_Nuclei_Texture_SumAverage_CorrGreen_1':
3.765297,
'EC50_PropCells_AreaShape_Area':
4.740853,
'EC50_PropCells_AreaShape_MajorAxisLength':
5.064460,
'EC50_PropCells_AreaShape_MinorAxisLength':
4.751471,
'EC50_PropCells_AreaShape_Perimeter':
4.949292,
'EC50_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
3.772565,
'EC50_PropCells_Texture_GaborX_CorrGreen_1':
5.007167,
'EC50_PropCells_Texture_InfoMeas2_CorrBlue_1':
4.341353,
'EC50_PropCells_Texture_SumVariance_CorrBlue_1':
4.298359,
'EC50_PropCells_Texture_SumVariance_CorrGreen_1':
4.610826,
'EC50_PropCells_Texture_Variance_CorrBlue_1':
4.396352,
'EC50_PropCells_Texture_Variance_CorrGreen_1':
4.632468,
'EC50_PropCytoplasm_AreaShape_Area':
4.669679,
'EC50_PropCytoplasm_AreaShape_MinorAxisLength':
4.754476,
'EC50_PropCytoplasm_AreaShape_Perimeter':
4.949292,
'EC50_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
4.072830,
'EC50_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':
4.0934,
'EC50_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
3.925800,
'EC50_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
3.9252,
'EC50_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
4.777481,
'EC50_PropCytoplasm_Texture_Entropy_CorrGreen_1':
4.4432,
'EC50_PropCytoplasm_Texture_GaborX_CorrGreen_1':
5.163371,
'EC50_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
4.701046,
'EC50_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
4.510543,
'EC50_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':
4.560315,
'EC50_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':
4.966674,
'EC50_ThresholdedCells_Texture_Entropy_CorrBlue_1':
4.457866,
'EC50_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
4.624049,
'EC50_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
4.686706,
'EC50_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
4.537378,
'EC50_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
4.322820,
'EC50_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
4.742158,
'EC50_ThresholdedCells_Texture_Variance_CorrBlue_1':
4.265549,
'EC50_ThresholdedCells_Texture_Variance_CorrGreen_1':
4.860020,
'OneTailedZfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
-4.322503,
'OneTailedZfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
-4.322503,
'OneTailedZfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
-4.322503,
'OneTailedZfactor_DistCytoplasm_Math_Ratio1':
0.622059,
'OneTailedZfactor_DistCytoplasm_Math_Ratio2':
-4.508284,
'OneTailedZfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':
-4.645887,
'OneTailedZfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
-4.279118,
'OneTailedZfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
-4.765570,
'OneTailedZfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
-4.682335,
'OneTailedZfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':
-4.415607,
'OneTailedZfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
-4.200105,
'OneTailedZfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
-4.316452,
'OneTailedZfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':
-4.316452,
'OneTailedZfactor_DistanceCells_Texture_Correlation_CorrGreen_1':
0.202500,
'OneTailedZfactor_DistanceCells_Texture_Entropy_CorrGreen_1':
-4.404815,
'OneTailedZfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
-4.508513,
'OneTailedZfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':
-4.225356,
'OneTailedZfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':
-4.382768,
'OneTailedZfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':
0.492125,
'OneTailedZfactor_DistanceCells_Texture_Variance_CorrGreen_1':
0.477360,
'OneTailedZfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
0.563780,
'OneTailedZfactor_Nuclei_Math_Ratio1':
0.622059,
'OneTailedZfactor_Nuclei_Math_Ratio2':
-4.508284,
'OneTailedZfactor_Nuclei_Texture_SumAverage_CorrGreen_1':
0.426178,
'OneTailedZfactor_PropCells_AreaShape_Area':
-4.216674,
'OneTailedZfactor_PropCells_AreaShape_MajorAxisLength':
-4.119131,
'OneTailedZfactor_PropCells_AreaShape_MinorAxisLength':
-4.109793,
'OneTailedZfactor_PropCells_AreaShape_Perimeter':
-4.068050,
'OneTailedZfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
0.765440,
'OneTailedZfactor_PropCells_Texture_GaborX_CorrGreen_1':
0.114982,
'OneTailedZfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':
0.108409,
'OneTailedZfactor_PropCells_Texture_SumVariance_CorrBlue_1':
0.191251,
'OneTailedZfactor_PropCells_Texture_SumVariance_CorrGreen_1':
0.559865,
'OneTailedZfactor_PropCells_Texture_Variance_CorrBlue_1':
0.254078,
'OneTailedZfactor_PropCells_Texture_Variance_CorrGreen_1':
0.556108,
'OneTailedZfactor_PropCytoplasm_AreaShape_Area':
-4.223021,
'OneTailedZfactor_PropCytoplasm_AreaShape_MinorAxisLength':
-4.095632,
'OneTailedZfactor_PropCytoplasm_AreaShape_Perimeter':
-4.068050,
'OneTailedZfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
-4.194663,
'OneTailedZfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':
-4.443338,
'OneTailedZfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':
0.207265,
'OneTailedZfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
-4.297250,
'OneTailedZfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
-4.525324,
'OneTailedZfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':
0.167795,
'OneTailedZfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
0.067560,
'OneTailedZfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
0.478527,
'OneTailedZfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
0.155119,
'OneTailedZfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
0.535907,
'OneTailedZfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
0.572801,
'OneTailedZfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':
0.423454,
'OneTailedZfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':
0.440500,
'Vfactor_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.500429,
'Vfactor_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.325675,
'Vfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.323524,
'Vfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
0.138487,
'Vfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
0.128157,
'Vfactor_DistCytoplasm_Math_Ratio1':
0.503610,
'Vfactor_DistCytoplasm_Math_Ratio2':
0.319610,
'Vfactor_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.522880,
'Vfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':
0.504303,
'Vfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.289432,
'Vfactor_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':
0.234123,
'Vfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
0.591687,
'Vfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.520356,
'Vfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':
-0.007649,
'Vfactor_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':
0.761198,
'Vfactor_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':
0.234655,
'Vfactor_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':
0.252240,
'Vfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
0.195125,
'Vfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
0.138299,
'Vfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':
0.126784,
'Vfactor_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':
0.342691,
'Vfactor_DistanceCells_Texture_Correlation_CorrGreen_1':
0.314396,
'Vfactor_DistanceCells_Texture_Entropy_CorrGreen_1':
0.311771,
'Vfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
0.410631,
'Vfactor_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':
0.170576,
'Vfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':
0.223147,
'Vfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':
0.269519,
'Vfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':
0.571528,
'Vfactor_DistanceCells_Texture_Variance_CorrGreen_1':
0.566272,
'Vfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
0.705051,
'Vfactor_Nuclei_Math_Ratio1':
0.503610,
'Vfactor_Nuclei_Math_Ratio2':
0.319610,
'Vfactor_Nuclei_Texture_SumAverage_CorrGreen_1':
0.553708,
'Vfactor_PropCells_AreaShape_Area':
0.340093,
'Vfactor_PropCells_AreaShape_MajorAxisLength':
0.243838,
'Vfactor_PropCells_AreaShape_MinorAxisLength':
0.320691,
'Vfactor_PropCells_AreaShape_Perimeter':
0.238915,
'Vfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
0.723520,
'Vfactor_PropCells_Texture_GaborX_CorrGreen_1':
0.213161,
'Vfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':
0.199791,
'Vfactor_PropCells_Texture_SumVariance_CorrBlue_1':
0.078959,
'Vfactor_PropCells_Texture_SumVariance_CorrGreen_1':
0.642844,
'Vfactor_PropCells_Texture_Variance_CorrBlue_1':
0.199105,
'Vfactor_PropCells_Texture_Variance_CorrGreen_1':
0.640818,
'Vfactor_PropCytoplasm_AreaShape_Area':
0.325845,
'Vfactor_PropCytoplasm_AreaShape_MinorAxisLength':
0.312258,
'Vfactor_PropCytoplasm_AreaShape_Perimeter':
0.238915,
'Vfactor_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.337565,
'Vfactor_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':
0.292900,
'Vfactor_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.175528,
'Vfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.193308,
'Vfactor_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.276152,
'Vfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':
0.239567,
'Vfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':
0.332380,
'Vfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.379141,
'Vfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.337740,
'Vfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':
0.334520,
'Vfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':
0.192882,
'Vfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':
0.276245,
'Vfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
0.139166,
'Vfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
0.465237,
'Vfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
0.355399,
'Vfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
0.453937,
'Vfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
0.564371,
'Vfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':
0.360566,
'Vfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':
0.548770,
'Zfactor_DistCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.531914,
'Zfactor_DistCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.265558,
'Zfactor_DistCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.178586,
'Zfactor_DistCytoplasm_Intensity_MinIntensityEdge_CorrGreen':
0.084566,
'Zfactor_DistCytoplasm_Intensity_MinIntensity_CorrGreen':
0.086476,
'Zfactor_DistCytoplasm_Math_Ratio1':
0.623284,
'Zfactor_DistCytoplasm_Math_Ratio2':
0.358916,
'Zfactor_DistCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.429510,
'Zfactor_DistCytoplasm_Texture_Entropy_CorrGreen_1':
0.508275,
'Zfactor_DistCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.068695,
'Zfactor_DistCytoplasm_Texture_InverseDifferenceMoment_CorrGreen_1':
0.347949,
'Zfactor_DistCytoplasm_Texture_SumAverage_CorrGreen_1':
0.646576,
'Zfactor_DistCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.494276,
'Zfactor_DistCytoplasm_Texture_Variance_CorrGreen_1':
0.179011,
'Zfactor_DistanceCells_Correlation_Correlation_CorrGreenCorrBlue':
0.824686,
'Zfactor_DistanceCells_Intensity_IntegratedIntensityEdge_CorrGreen':
0.027644,
'Zfactor_DistanceCells_Intensity_LowerQuartileIntensity_CorrGreen':
0.088491,
'Zfactor_DistanceCells_Intensity_MeanIntensityEdge_CorrGreen':
0.065056,
'Zfactor_DistanceCells_Intensity_MinIntensityEdge_CorrGreen':
0.089658,
'Zfactor_DistanceCells_Intensity_MinIntensity_CorrGreen':
0.078017,
'Zfactor_DistanceCells_Texture_AngularSecondMoment_CorrGreen_1':
0.238131,
'Zfactor_DistanceCells_Texture_Correlation_CorrGreen_1':
0.301107,
'Zfactor_DistanceCells_Texture_Entropy_CorrGreen_1':
0.251143,
'Zfactor_DistanceCells_Texture_InfoMeas1_CorrGreen_1':
0.564957,
'Zfactor_DistanceCells_Texture_InverseDifferenceMoment_CorrGreen_1':
0.302767,
'Zfactor_DistanceCells_Texture_SumAverage_CorrGreen_1':
0.036459,
'Zfactor_DistanceCells_Texture_SumEntropy_CorrGreen_1':
0.159798,
'Zfactor_DistanceCells_Texture_SumVariance_CorrGreen_1':
0.516938,
'Zfactor_DistanceCells_Texture_Variance_CorrGreen_1':
0.501186,
'Zfactor_Nuclei_Correlation_Correlation_CorrGreenCorrBlue':
0.691408,
'Zfactor_Nuclei_Math_Ratio1':
0.623284,
'Zfactor_Nuclei_Math_Ratio2':
0.358916,
'Zfactor_Nuclei_Texture_SumAverage_CorrGreen_1':
0.587347,
'Zfactor_PropCells_AreaShape_Area':
0.132425,
'Zfactor_PropCells_AreaShape_MajorAxisLength':
0.034809,
'Zfactor_PropCells_AreaShape_MinorAxisLength':
0.113864,
'Zfactor_PropCells_AreaShape_Perimeter':
0.005984,
'Zfactor_PropCells_Correlation_Correlation_CorrGreenCorrBlue':
0.717632,
'Zfactor_PropCells_Texture_GaborX_CorrGreen_1':
0.251023,
'Zfactor_PropCells_Texture_InfoMeas2_CorrBlue_1':
0.149719,
'Zfactor_PropCells_Texture_SumVariance_CorrBlue_1':
0.102050,
'Zfactor_PropCells_Texture_SumVariance_CorrGreen_1':
0.611960,
'Zfactor_PropCells_Texture_Variance_CorrBlue_1':
0.197090,
'Zfactor_PropCells_Texture_Variance_CorrGreen_1':
0.614879,
'Zfactor_PropCytoplasm_AreaShape_Area':
0.205042,
'Zfactor_PropCytoplasm_AreaShape_MinorAxisLength':
0.072682,
'Zfactor_PropCytoplasm_AreaShape_Perimeter':
0.005984,
'Zfactor_PropCytoplasm_Correlation_Correlation_CorrGreenCorrBlue':
0.272017,
'Zfactor_PropCytoplasm_Intensity_IntegratedIntensity_CorrGreen':
0.115327,
'Zfactor_PropCytoplasm_Intensity_LowerQuartileIntensity_CorrGreen':
0.141850,
'Zfactor_PropCytoplasm_Intensity_MedianIntensity_CorrGreen':
0.105803,
'Zfactor_PropCytoplasm_Texture_AngularSecondMoment_CorrGreen_1':
0.107640,
'Zfactor_PropCytoplasm_Texture_Entropy_CorrGreen_1':
0.067896,
'Zfactor_PropCytoplasm_Texture_GaborX_CorrGreen_1':
0.136688,
'Zfactor_PropCytoplasm_Texture_InfoMeas2_CorrGreen_1':
0.334749,
'Zfactor_PropCytoplasm_Texture_SumEntropy_CorrGreen_1':
0.208829,
'Zfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrBlue_1':
0.263467,
'Zfactor_ThresholdedCells_Texture_AngularSecondMoment_CorrGreen_1':
0.124355,
'Zfactor_ThresholdedCells_Texture_Entropy_CorrBlue_1':
0.236433,
'Zfactor_ThresholdedCells_Texture_InfoMeas2_CorrBlue_1':
0.125845,
'Zfactor_ThresholdedCells_Texture_SumAverage_CorrBlue_1':
0.449333,
'Zfactor_ThresholdedCells_Texture_SumEntropy_CorrBlue_1':
0.323243,
'Zfactor_ThresholdedCells_Texture_SumVariance_CorrBlue_1':
0.507477,
'Zfactor_ThresholdedCells_Texture_SumVariance_CorrGreen_1':
0.599000,
'Zfactor_ThresholdedCells_Texture_Variance_CorrBlue_1':
0.361424,
'Zfactor_ThresholdedCells_Texture_Variance_CorrGreen_1':
0.481393
}
temp_dir = tempfile.mkdtemp()
try:
cpprefs.set_headless()
cpprefs.set_default_output_directory(temp_dir)
print "Writing output to %s" % temp_dir
path = os.path.split(__file__)[0]
measurements = loadmat(os.path.join(path,
'calculatestatistics.mat'),
struct_as_record=True)
measurements = measurements['m']
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
m = cpmeas.Measurements()
doses = [
0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 0, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 0, 0, 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, 10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 10,
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 10, 0, 1, 2, 3, 4, 5, 6, 7, 8,
9, 0, 10, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0
]
for i, dose in enumerate(doses):
m.add_image_measurement("Dose", dose)
for object_name in measurements.dtype.fields:
omeasurements = measurements[object_name][0, 0]
for feature_name in omeasurements.dtype.fields:
data = omeasurements[feature_name][0, 0][0, i]
m.add_measurement(object_name, feature_name, data)
if i < len(doses) - 1:
m.next_image_set()
pipeline = cpp.Pipeline()
module = C.CalculateStatistics()
module.grouping_values.value = "Dose"
module.dose_values[0].log_transform.value = False
module.dose_values[0].measurement.value = "Dose"
module.dose_values[0].wants_save_figure.value = True
module.dose_values[0].figure_name.value = "EC49_"
module.module_num = 1
pipeline.add_module(module)
def callback(caller, event):
self.assertFalse(isinstance(event, cpp.RunExceptionEvent))
workspace = cpw.Workspace(pipeline, module, image_set,
cpo.ObjectSet(), m, image_set_list)
module.post_run(workspace)
for feature_name in m.get_feature_names(cpmeas.EXPERIMENT):
if not expected.has_key(feature_name):
print "Missing measurement: %s" % feature_name
continue
value = m.get_experiment_measurement(feature_name)
e_value = expected[feature_name]
diff = abs(value - e_value) * 2 / abs(value + e_value)
self.assertTrue(
diff < .05, "%s: Matlab: %f, Python: %f diff: %f" %
(feature_name, e_value, value, diff))
if diff > .01:
print(
"Warning: > 1%% difference for %s: Matlab: %f, Python: %f diff: %f"
% (feature_name, e_value, value, diff))
if feature_name.startswith("EC50"):
filename = "EC49_" + feature_name[5:] + ".pdf"
self.assertTrue(
os.path.isfile(os.path.join(temp_dir, filename)))
finally:
try:
workspace.measurements.hdf5_dict.hdf5_file.close()
except:
pass
for filename in os.listdir(temp_dir):
path = os.path.join(temp_dir, filename)
os.remove(path)
os.rmdir(temp_dir)
import os from bioformats.formatwriter import write_image from bioformats import PT_UINT8 import shutil from StringIO import StringIO import tempfile import unittest from urllib import URLopener from urllib2 import urlopen import xml.dom.minidom as DOM import zipfile import zlib import cellprofiler.preferences as cpprefs cpprefs.set_headless() import cellprofiler.workspace as cpw import cellprofiler.grid as cpg import cellprofiler.image as cpi import cellprofiler.module as cpm import cellprofiler.object as cpo import cellprofiler.measurement as cpmeas import cellprofiler.pipeline as cpp import cellprofiler.modules.createwebpage as C from cellprofiler.modules.loadimages import C_FILE_NAME, C_PATH_NAME, C_URL from cellprofiler.modules.loadimages import pathname2url, url2pathname IMAGE_NAME = "image" THUMB_NAME = "thumb" DEFAULT_HTML_FILE = "default.html"
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
Website: http://www.cellprofiler.org
'''
__version__ = "$Revision$"
import base64
from matplotlib.image import pil_to_array
import numpy as np
import os
import PIL.Image as PILImage
import scipy.ndimage
from StringIO import StringIO
import unittest
import zlib
from cellprofiler.preferences import set_headless
set_headless()
import cellprofiler.pipeline as cpp
import cellprofiler.cpmodule as cpm
import cellprofiler.cpimage as cpi
import cellprofiler.measurements as cpmeas
import cellprofiler.objects as cpo
import cellprofiler.workspace as cpw
import cellprofiler.modules.calculatemath as C
OUTPUT_MEASUREMENTS = "outputmeasurements"
MATH_OUTPUT_MEASUREMENTS = "_".join(("Math", OUTPUT_MEASUREMENTS))
OBJECT = ["object%d" % i for i in range(2)]
def setUp(self):
from cellprofiler.preferences import set_headless
set_headless()
self.old_import = __builtin__.__import__
__builtin__.__import__ = import_all_but_wx
