def __init__(self,
img,
index=None,
termfile=None,
paramfile=None,
output_file=None,
output_dir=None,
backend='dials',
action_code='spotfind',
min_bragg=10,
n_processors=1,
verbose=False
):
self.img = img
self.backend = backend
self.paramfile = paramfile
self.termfile = termfile
self.n_processors = n_processors
self.index = index
self.verbose = verbose
self.min_bragg = min_bragg
if output_file is not None:
if output_dir is not None:
self.output = os.path.join(os.path.abspath(output_dir), output_file)
else:
self.output = os.path.abspath(output_file)
else:
self.output = None
Thread.__init__(self)
# Determine which processes will be included
if action_code == 'spotfind':
self.run_indexing = False
self.run_integration = False
elif action_code == 'index':
self.run_indexing = True
self.run_integration = False
elif action_code == 'integrate':
self.run_indexing = True
self.run_integration = True
# Initialize IOTA DIALS Processor
if self.backend.lower() == 'dials':
if self.paramfile is not None:
with open(self.paramfile, 'r') as phil_file:
phil_string = phil_file.read()
user_phil = ip.parse(phil_string)
self.dials_phil = phil_scope.fetch(source=user_phil)
else:
self.dials_phil = phil_scope
self.params = self.dials_phil.extract()
if self.backend == 'dials':
self.processor = IOTADialsProcessor(params=self.params)
def __init__(self, parent, id, title):
wx.Frame.__init__(self, parent, id, title, size=(1500, 600))
self.parent = parent
self.term_file = os.path.join(os.curdir, '.terminate_image_tracker')
self.spf_backend = 'mosflm'
self.reset_spotfinder()
# Status bar
self.sb = self.CreateStatusBar()
self.sb.SetFieldsCount(2)
self.sb.SetStatusWidths([100, -1])
# Setup main sizer
self.main_sizer = wx.BoxSizer(wx.VERTICAL)
# Setup toolbar
self.toolbar = self.CreateToolBar(style=wx.TB_3DBUTTONS | wx.TB_TEXT)
quit_bmp = bitmaps.fetch_icon_bitmap('actions', 'exit')
self.tb_btn_quit = self.toolbar.AddLabelTool(
wx.ID_EXIT,
label='Quit',
bitmap=quit_bmp,
shortHelp='Quit',
longHelp='Quit image tracker')
self.toolbar.AddSeparator()
pref_bmp = bitmaps.fetch_icon_bitmap('apps', 'advancedsettings')
self.tb_btn_prefs = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Preferences',
bitmap=pref_bmp,
shortHelp='Preferences',
longHelp='IOTA image tracker preferences')
self.toolbar.AddSeparator()
open_bmp = bitmaps.fetch_icon_bitmap('actions', 'open')
self.tb_btn_open = self.toolbar.AddLabelTool(wx.ID_ANY,
label='Open',
bitmap=open_bmp,
shortHelp='Open',
longHelp='Open folder')
run_bmp = bitmaps.fetch_icon_bitmap('actions', 'run')
self.tb_btn_run = self.toolbar.AddLabelTool(wx.ID_ANY,
label='Run',
bitmap=run_bmp,
shortHelp='Run',
longHelp='Run Spotfinding')
stop_bmp = bitmaps.fetch_icon_bitmap('actions', 'stop')
self.tb_btn_stop = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Stop',
bitmap=stop_bmp,
shortHelp='Stop',
longHelp='Stop Spotfinding')
self.toolbar.AddSeparator()
span_view = bitmaps.fetch_custom_icon_bitmap('zoom_list')
self.tb_btn_view = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='View',
bitmap=span_view,
kind=wx.ITEM_RADIO,
shortHelp='Select to View',
longHelp='Select images to view')
span_zoom = bitmaps.fetch_custom_icon_bitmap('zoom_view')
self.tb_btn_zoom = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Zoom In',
bitmap=span_zoom,
kind=wx.ITEM_RADIO,
shortHelp='Zoom In',
longHelp='Zoom in on chart')
self.toolbar.ToggleTool(self.tb_btn_zoom.GetId(), True)
self.toolbar.EnableTool(self.tb_btn_run.GetId(), False)
self.toolbar.EnableTool(self.tb_btn_stop.GetId(), False)
self.toolbar.Realize()
# Setup timers
self.spf_timer = wx.Timer(self)
self.uc_timer = wx.Timer(self)
self.ff_timer = wx.Timer(self)
self.tracker_panel = TrackerPanel(self)
self.data_dict = self.tracker_panel.image_list.image_list.ctr.data.copy(
)
self.img_list_initialized = False
self.main_sizer.Add(self.tracker_panel, 1, wx.EXPAND)
# Generate default DIALS PHIL file
default_phil = ip.parse(default_target)
self.phil = phil_scope.fetch(source=default_phil)
self.params = self.phil.extract()
self.params.output.strong_filename = None
self.phil = self.phil.format(python_object=self.params)
# Bindings
self.Bind(wx.EVT_TOOL, self.onQuit, self.tb_btn_quit)
self.Bind(wx.EVT_TOOL, self.onGetImages, self.tb_btn_open)
self.Bind(wx.EVT_TOOL, self.onRunSpotfinding, self.tb_btn_run)
self.Bind(wx.EVT_TOOL, self.onStop, self.tb_btn_stop)
self.Bind(wx.EVT_BUTTON, self.onSelView,
self.tracker_panel.btn_view_sel)
self.Bind(wx.EVT_BUTTON, self.onWrtFile,
self.tracker_panel.btn_wrt_file)
self.Bind(wx.EVT_BUTTON, self.onAllView,
self.tracker_panel.btn_view_all)
self.Bind(wx.EVT_TOOL, self.onZoom, self.tb_btn_zoom)
self.Bind(wx.EVT_TOOL, self.onList, self.tb_btn_view)
# Spotfinder / timer bindings
self.Bind(thr.EVT_SPFDONE, self.onSpfOneDone)
self.Bind(thr.EVT_SPFALLDONE, self.onSpfAllDone)
self.Bind(thr.EVT_SPFTERM, self.onSpfTerminated)
self.Bind(wx.EVT_TIMER, self.onSpfTimer, id=self.spf_timer.GetId())
self.Bind(wx.EVT_TIMER, self.onUCTimer, id=self.uc_timer.GetId())
self.Bind(wx.EVT_TIMER, self.onPlotOnlyTimer, id=self.ff_timer.GetId())
# Settings bindings
#self.Bind(wx.EVT_BUTTON, self.onSpfOptions, self.tracker_panel.spf_options)
self.Bind(wx.EVT_SPINCTRL, self.onMinBragg,
self.tracker_panel.min_bragg.ctr)
self.Bind(wx.EVT_SPINCTRL, self.onChartRange,
self.tracker_panel.chart_window.ctr)
# Read arguments if any
self.args, self.phil_args = parse_command_args('').parse_known_args()
self.spf_backend = self.args.backend
self.tracker_panel.min_bragg.ctr.SetValue(self.args.bragg)
if self.args.file is not None:
self.results_file = self.args.file
self.start_spotfinding(from_file=True)
elif self.args.path is not None:
path = os.path.abspath(self.args.path)
self.open_images_and_get_ready(path=path)
if self.args.start:
print 'IMAGE_TRACKER: STARTING FROM FIRST RECORDED IMAGE'
self.start_spotfinding()
elif self.args.proceed:
print 'IMAGE_TRACKER: STARTING FROM IMAGE RECORDED 1 MIN AGO'
self.start_spotfinding(min_back=-1)
elif self.args.time > 0:
min_back = -self.args.time[0]
print 'IMAGE_TRACKER: STARTING FROM IMAGE RECORDED {} MIN AGO' \
''.format(min_back)
self.start_spotfinding(min_back=min_back)
def __init__(self,
img,
index=None,
termfile=None,
paramfile=None,
output_file=None,
output_dir=None,
backend='dials',
action_code='spotfind',
min_bragg=10,
n_processors=1,
verbose=False
):
self.img = img
self.backend = backend
self.paramfile = paramfile
self.termfile = termfile
self.n_processors = n_processors
self.index = index
self.verbose = verbose
self.min_bragg = min_bragg
if output_file is not None:
if output_dir is not None:
self.output = os.path.join(os.path.abspath(output_dir), output_file)
else:
self.output = os.path.abspath(output_file)
else:
self.output = None
Thread.__init__(self)
# Determine which processes will be included
if action_code == 'spotfind':
self.run_indexing = False
self.run_integration = False
elif action_code == 'index':
self.run_indexing = True
self.run_integration = False
elif action_code == 'integrate':
self.run_indexing = True
self.run_integration = True
# Initialize IOTA DIALS Processor
if self.backend.lower() == 'dials':
if self.paramfile is not None:
with open(self.paramfile, 'r') as phil_file:
phil_string = phil_file.read()
user_phil = ip.parse(phil_string)
self.dials_phil = phil_scope.fetch(source=user_phil)
else:
default_params, _ = write_defaults(method='dials',
write_target_file=False,
write_param_file=False)
default_phil_string = '\n'.join(default_params)
default_phil = ip.parse(default_phil_string)
self.dials_phil = phil_scope.fetch(source=default_phil)
self.params = self.dials_phil.extract()
# Modify default DIALS parameters
# These parameters will be set no matter what
self.params.output.datablock_filename = None
self.params.output.indexed_filename = None
self.params.output.strong_filename = None
self.params.output.refined_experiments_filename = None
self.params.output.integrated_filename = None
self.params.output.integrated_experiments_filename = None
self.params.output.profile_filename = None
self.params.output.integration_pickle = None
# These parameters will be set only if there's no script
if self.paramfile is None:
self.params.indexing.stills.method_list = ['fft3d']
if self.backend == 'dials':
self.processor = IOTADialsProcessor(params=self.params,
write_pickle=False)
def initialize_spotfinder(self):
self.done_list = []
self.data_list = []
self.spotfinding_info = []
self.plot_idx = 0
self.bookmark = 0
self.all_info = []
self.current_min_bragg = 0
self.waiting = False
self.submit_new_images = False
self.terminated = False
# Read arguments if any
self.args, self.phil_args = parse_command_args('').parse_known_args()
# Generate DIALS PHIL file
if self.args.paramfile is None:
default_phil = ip.parse(default_target)
self.phil = phil_scope.fetch(source=default_phil)
else:
with open(self.args.paramfile, 'r') as phil_file:
phil_string = phil_file.read()
user_phil = ip.parse(phil_string)
self.phil = phil_scope.fetch(source=user_phil)
self.params = self.phil.extract()
# Set backend
self.spf_backend = self.args.backend
# Determine how far the DIALS processing will go
if 'index' in self.args.action:
self.run_indexing = True
elif 'int' in self.args.action:
self.run_indexing = True
self.run_integration = True
self.tracker_panel.min_bragg.ctr.SetValue(self.args.bragg)
# Determine how the tracker will track images: from file output by
# iota.single_image, or by turning over actual files. If the latter,
# determine at what point the tracker will start the tracking
auto_start = True
min_back = None
if self.args.file is not None:
self.results_file = self.args.file
elif self.args.path is not None:
path = os.path.abspath(self.args.path)
self.open_images_and_get_ready(path=path)
if self.args.start:
print 'IMAGE_TRACKER: STARTING FROM FIRST RECORDED IMAGE'
elif self.args.proceed:
print 'IMAGE_TRACKER: STARTING FROM IMAGE RECORDED 1 MIN AGO'
min_back = -1
elif self.args.time > 0:
min_back = -self.args.time[0]
print 'IMAGE_TRACKER: STARTING FROM IMAGE RECORDED {} MIN AGO' \
''.format(min_back)
else:
auto_start = False
# Initialize processing thread
if self.args.file is None:
self.proc_thread = thr.InterceptorThread(
self,
data_folder=self.data_folder,
term_file=self.term_file,
proc_params=self.params,
backend=self.args.backend,
n_proc=self.args.nproc,
min_back=min_back,
run_indexing=self.run_indexing,
run_integration=self.run_integration)
else:
self.proc_thread = thr.InterceptorFileThread(
self, results_file=self.args.file, reorder=self.args.reorder)
if auto_start:
self.start_spotfinding()