def readImage(self, filename):
imagedata = None
if filename:
imagedata = self.getImageFromDB(filename)
if imagedata is None:
if filename == '':
if self.name in ['Hole Targeting','Subsquare Targeting']:
filename = os.path.join(version.getInstalledLocation(),'sq_example.jpg')
elif self.name in ['Square Targeting']:
filename = os.path.join(version.getInstalledLocation(),'gr_example.jpg')
else:
filename = os.path.join(version.getInstalledLocation(),'hl_example.jpg')
try:
orig = mrc.read(filename)
except Exception, e:
try:
orig = numpil.read(filename)
except:
self.logger.exception('Read image failed: %s' % e[-1])
return
self.currentimagedata = {'image':orig}
def readImage(self, filename):
imagedata = None
if filename:
imagedata = self.getImageFromDB(filename)
if imagedata is None:
if filename == '':
if self.name in ['Hole Targeting','Subsquare Targeting']:
filename = os.path.join(version.getInstalledLocation(),'sq_example.jpg')
elif self.name in ['Square Targeting']:
filename = os.path.join(version.getInstalledLocation(),'gr_example.jpg')
else:
filename = os.path.join(version.getInstalledLocation(),'hl_example.jpg')
try:
orig = mrc.read(filename)
except Exception, e:
try:
orig = numpil.read(filename)
except:
self.logger.exception('Read image failed: %s' % e[-1])
return
self.currentimagedata = {'image':orig}
from optparse import OptionParser
import sys
parser = OptionParser()
parser.add_option('-v', '--version', action='store_true', dest='version',
help="get version information")
parser.add_option('-s', '--session', action='store', dest='session',
help="name of existing session to continue")
parser.add_option('-c', '--clients', action='store', dest='clients',
help="comma separated list of clients")
parser.add_option('-p', '--prevapp', action='store_true', dest='prevapp',
help="restart previous application")
(options, args) = parser.parse_args()
if options.version:
import version
print 'Leginon version: %s' % (version.getVersion(),)
print ' Installed in: %s' % (version.getInstalledLocation(),)
sys.exit()
# For terms of the license agreement
# see http://ami.scripps.edu/software/leginon-license
#
from leginon import leginondata
import targetfinder
from pyami import ordereddict
import threading
import os.path
import math
import gui.wx.NewTargetFinder
import version
import targetingsteps
invsqrt2 = math.sqrt(2.0)/2.0
default_template = os.path.join(version.getInstalledLocation(),'holetemplate.mrc')
newworkflow = targetingsteps.templatefinder
newsettingsclass = targetingsteps.makeSettingsClass('NewTargetFinderSettingsData', newworkflow)
newdefaultsettings = targetingsteps.makeDefaultSettings(newworkflow)
class NewTargetFinder(targetfinder.TargetFinder):
panelclass = gui.wx.NewTargetFinder.Panel
settingsclass = newsettingsclass
defaultsettings = dict(targetfinder.TargetFinder.defaultsettings)
defaultsettings.update(newdefaultsettings)
#targetnames = targetfinder.TargetFinder.targetnames + ['Blobs']
workflow = newworkflow
def __init__(self, id, session, managerlocation, **kwargs):
targetfinder.TargetFinder.__init__(self, id, session, managerlocation, **kwargs)
import threading
import time
import manualacquisition
import gui.wx.ManualImageLoader
import player
import instrument
import os
import re
import calibrationclient
import copy
from pyami import arraystats, imagefun, mrc
import numpy
import version
import cameraclient
default_batch = os.path.join(version.getInstalledLocation(),'upload_example.txt')
class AcquireError(Exception):
pass
class ManualImageLoader(manualacquisition.ManualAcquisition):
panelclass = gui.wx.ManualImageLoader.Panel
settingsclass = leginondata.ManualImageLoaderSettingsData
eventoutputs = node.Node.eventoutputs + [event.AcquisitionImagePublishEvent]
defaultsettings = {
'instruments': {'tem': None, 'ccdcamera': None},
'save image': False,
'batch script': default_batch,
'tilt group': 1,
'camera settings': cameraclient.default_settings,
}
# For terms of the license agreement
# see http://ami.scripps.edu/software/leginon-license
#
from leginon import leginondata
import targetfinder
from pyami import ordereddict
import threading
import os.path
import math
import gui.wx.NewTargetFinder
import version
import targetingsteps
invsqrt2 = math.sqrt(2.0) / 2.0
default_template = os.path.join(version.getInstalledLocation(),
'holetemplate.mrc')
newworkflow = targetingsteps.templatefinder
newsettingsclass = targetingsteps.makeSettingsClass(
'NewTargetFinderSettingsData', newworkflow)
newdefaultsettings = targetingsteps.makeDefaultSettings(newworkflow)
class NewTargetFinder(targetfinder.TargetFinder):
panelclass = gui.wx.NewTargetFinder.Panel
settingsclass = newsettingsclass
defaultsettings = dict(targetfinder.TargetFinder.defaultsettings)
defaultsettings.update(newdefaultsettings)
#targetnames = targetfinder.TargetFinder.targetnames + ['Blobs']
workflow = newworkflow
import threading
import time
import manualacquisition
import gui.wx.ManualImageLoader
import player
import instrument
import os
import re
import calibrationclient
import copy
from pyami import arraystats, imagefun, mrc
import numpy
import version
import cameraclient
default_batch = os.path.join(version.getInstalledLocation(),
'upload_example.txt')
class AcquireError(Exception):
pass
class ManualImageLoader(manualacquisition.ManualAcquisition):
panelclass = gui.wx.ManualImageLoader.Panel
settingsclass = leginondata.ManualImageLoaderSettingsData
eventoutputs = node.Node.eventoutputs + [
event.AcquisitionImagePublishEvent
]
defaultsettings = {
'instruments': {
parser = OptionParser()
parser.add_option('-v',
'--version',
action='store_true',
dest='version',
help="get version information")
parser.add_option('-s',
'--session',
action='store',
dest='session',
help="name of existing session to continue")
parser.add_option('-c',
'--clients',
action='store',
dest='clients',
help="comma separated list of clients")
parser.add_option('-p',
'--prevapp',
action='store_true',
dest='prevapp',
help="restart previous application")
(options, args) = parser.parse_args()
if options.version:
import version
print 'Leginon version: %s' % (version.getVersion(), )
print ' Installed in: %s' % (version.getInstalledLocation(), )
sys.exit()
