def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
self.scandb = ScanDB()
self.instdb = InstrumentDB(self.scandb)
print("Connect ScanDB ", self.scandb.engine, self.instname)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def make_uscope_rotation(scandb,
offline_inst='IDE_Microscope',
offline_xyz=('13IDE:m1.VAL', '13IDE:m2.VAL',
'13IDE:m3.VAL'),
online_inst='IDE_SampleStage',
online_xyz=('13XRM:m4.VAL', '13XRM:m6.VAL',
'13XRM:m5.VAL')):
"""
Calculate and store the rotation maxtrix needed to convert
positions from the GSECARS offline microscope (OSCAR)
to the SampleStage in the microprobe station.
This calculates the rotation matrix based on all position
names that occur in the Position List for both instruments.
Note:
The result is saved as a json dictionary to the config table
"""
instdb = InstrumentDB(scandb)
pos_us = read_xyz(instdb, offline_inst, offline_xyz)
pos_ss = read_xyz(instdb, online_inst, online_xyz)
# calculate the rotation matrix
mat_us2ss, v1, v2 = calc_rotmatrix(pos_us, pos_ss)
if mat_us2ss is None:
return
#endif
uscope = instdb.get_instrument(offline_inst)
sample = instdb.get_instrument(online_inst)
uname = uscope.name.replace(' ', '_')
sname = sample.name.replace(' ', '_')
conf_us2ss = "CoordTrans:%s:%s" % (uname, sname)
us2ss = dict(source=offline_xyz,
dest=online_xyz,
rotmat=mat_us2ss.tolist())
scandb.set_config(conf_us2ss, json.dumps(us2ss))
# calculate the rotation matrix going the other way
mat_ss2us, v1, v2 = calc_rotmatrix(pos_ss, pos_us)
conf_ss2us = "CoordTrans:%s:%s" % (sname, uname)
ss2us = dict(source=online_xyz,
dest=offline_xyz,
rotmat=mat_ss2us.tolist())
print("Saving Calibration %s" % conf_ss2us)
scandb.set_config(conf_ss2us, json.dumps(ss2us))
scandb.commit()
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
dbconn_dir = dbconn.get('dbconn_dir', '')
dbconn_file = dbconn.get('dbconn_file', '')
if os.path.exists(dbconn_dir) and len(dbconn_file) > 0:
sys.path.insert(0, dbconn_dir)
mod = __import__(dbconn_file)
conn = mod.conn
scandb = ScanDB(**mod.conn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def make_uscope_rotation(scandb,
offline_inst='IDE_Microscope',
offline_xyz=('13IDE:m1.VAL', '13IDE:m2.VAL', '13IDE:m3.VAL'),
online_inst='IDE_SampleStage',
online_xyz=('13XRM:m4.VAL', '13XRM:m6.VAL', '13XRM:m5.VAL')):
"""
Calculate and store the rotation maxtrix needed to convert
positions from the GSECARS offline microscope (OSCAR)
to the SampleStage in the microprobe station.
This calculates the rotation matrix based on all position
names that occur in the Position List for both instruments.
Note:
The result is saved as a json dictionary to the config table
"""
instdb = InstrumentDB(scandb)
pos_us = read_xyz(instdb, offline_inst, offline_xyz)
pos_ss = read_xyz(instdb, online_inst, online_xyz)
# calculate the rotation matrix
mat_us2ss, v1, v2 = calc_rotmatrix(pos_us, pos_ss)
if mat_us2ss is None:
return
#endif
uscope = instdb.get_instrument(offline_inst)
sample = instdb.get_instrument(online_inst)
uname = uscope.name.replace(' ', '_')
sname = sample.name.replace(' ', '_')
conf_us2ss = "CoordTrans:%s:%s" % (uname, sname)
us2ss = dict(source=offline_xyz, dest=online_xyz,
rotmat=mat_us2ss.tolist())
scandb.set_config(conf_us2ss, json.dumps(us2ss))
# calculate the rotation matrix going the other way
mat_ss2us, v1, v2 = calc_rotmatrix(pos_ss, pos_us)
conf_ss2us = "CoordTrans:%s:%s" % (sname, uname)
ss2us = dict(source=online_xyz, dest=offline_xyz,
rotmat=mat_ss2us.tolist())
print("Saving Calibration %s" % conf_ss2us)
scandb.set_config(conf_ss2us, json.dumps(ss2us))
scandb.commit()
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
if dbconn['port'] in ('', 'None', None):
dbconn.pop('port')
scandb = ScanDB(**dbconn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get("instrument", "microscope_stages")
if dbconn["port"] in ("", "None", None):
dbconn.pop("port")
scandb = ScanDB(**dbconn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.parent.config["stages"].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def connect_scandb(dbname=None, server='postgresql', _larch=None, **kwargs):
if (_larch.symtable.has_symbol(SCANDB_NAME)
and _larch.symtable.get_symbol(SCANDB_NAME) is not None):
scandb = _larch.symtable.get_symbol(SCANDB_NAME)
else:
scandb = ScanDB(dbname=dbname, server=server, **kwargs)
_larch.symtable.set_symbol(SCANDB_NAME, scandb)
if (_larch.symtable.has_symbol(INSTDB_NAME)
and _larch.symtable.get_symbol(INSTDB_NAME) is not None):
instdb = _larch.symtable.get_symbol(INSTDB_NAME)
else:
instdb = InstrumentDB(scandb)
_larch.symtable.set_symbol(INSTDB_NAME, instdb)
return scandb
def connect_scandb(scandb=None, dbname=None, _larch=None, **kwargs):
global _scandb, _instdb
if _scandb is not None:
return _scandb
if scandb is None:
scandb = ScanDB(dbname=dbname, **kwargs)
if scandb is not None:
_scandb = scandb
if _larch is not None:
_larch.symtable.set_symbol(SCANDB_NAME, _scandb)
if _instdb is None:
_instdb = InstrumentDB(_scandb)
if _larch is not None:
_larch.symtable.set_symbol(INSTDB_NAME, _instdb)
return _scandb
class PositionPanel(wx.Panel):
"""panel of position lists, with buttons"""
def __init__(self, parent, viewer, config=None, **kws):
wx.Panel.__init__(self, parent, -1, size=(300, 500))
self.size = (300, 600)
self.parent = parent
self.viewer = viewer
self.config = config
self.poslist_query = None
self.image_display = None
self.pos_name = wx.TextCtrl(self, value="", size=(300, 25),
style= wx.TE_PROCESS_ENTER)
self.pos_name.Bind(wx.EVT_TEXT_ENTER, self.onSave1)
tlabel = wx.StaticText(self, label="Save Position: ")
bkws = dict(size=(55, -1))
btn_goto = add_button(self, "Go To", action=self.onGo, **bkws)
btn_erase = add_button(self, "Erase", action=self.onErase, **bkws)
btn_show = add_button(self, "Show", action=self.onShow, **bkws)
# btn_many = add_button(self, "Erase Many", action=self.onEraseMany, **bkws)
brow = wx.BoxSizer(wx.HORIZONTAL)
brow.Add(btn_goto, 0, ALL_EXP|wx.ALIGN_LEFT, 1)
brow.Add(btn_erase, 0, ALL_EXP|wx.ALIGN_LEFT, 1)
brow.Add(btn_show, 0, ALL_EXP|wx.ALIGN_LEFT, 1)
# brow.Add(btn_many, 0, ALL_EXP|wx.ALIGN_LEFT, 1)
self.pos_list = wx.ListBox(self)
self.pos_list.SetBackgroundColour(wx.Colour(253, 253, 250))
self.pos_list.Bind(wx.EVT_LISTBOX, self.onSelect)
self.pos_list.Bind(wx.EVT_RIGHT_DOWN, self.onRightClick)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(tlabel, 0, wx.ALIGN_LEFT|wx.ALL)
sizer.Add(self.pos_name, 0, wx.ALIGN_LEFT|wx.ALL)
sizer.Add(brow, 0, wx.ALIGN_LEFT|wx.ALL)
sizer.Add(self.pos_list, 1, ALL_EXP|wx.ALIGN_CENTER, 3)
pack(self, sizer)
self.init_scandb()
self.last_refresh = 0
self.get_positions_from_db()
self.timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onTimer, self.timer)
self.timer.Start(5000)
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
if dbconn['port'] in ('', 'None', None):
dbconn.pop('port')
scandb = ScanDB(**dbconn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def onSave1(self, event):
"save from text enter"
self.onSave(event.GetString().strip())
def onSave2(self, event):
"save from button push"
self.onSave(self.pos_name.GetValue().strip())
def onSave(self, name):
if len(name) < 1:
return
if name in self.positions and self.viewer.v_replace:
ret = popup(self, "Overwrite Position %s?" % name,
"Veriry Overwrite Position",
style=wx.YES_NO|wx.NO_DEFAULT|wx.ICON_QUESTION)
if ret != wx.ID_YES:
return
imgfile = '%s.jpg' % time.strftime('%b%d_%H%M%S')
imgfile = os.path.join(self.viewer.imgdir, imgfile)
tmp_pos = self.viewer.ctrlpanel.read_position()
imgdata, count = None, 0
if not os.path.exists(self.viewer.imgdir):
os.makedirs(self.viewer.imgdir)
while imgdata is None and count <100:
imgdata = self.viewer.save_image(imgfile)
if imgdata is None:
time.sleep(0.5)
count = count + 1
imgdata['source'] = 'SampleStage'
imgdata['data_format'] = 'file'
imgdata.pop('data')
notes = json.dumps(imgdata)
fullpath = os.path.join(os.getcwd(), imgfile)
self.positions[name] = {'image': fullpath,
'timestamp': time.strftime('%b %d %H:%M:%S'),
'position': tmp_pos,
'notes': notes}
if name not in self.pos_list.GetItems():
self.pos_list.Append(name)
self.instdb.save_position(self.instname, name, tmp_pos,
notes=notes, image=fullpath)
self.pos_list.SetStringSelection(name)
# auto-save file
self.viewer.autosave(positions=self.positions)
self.viewer.write_htmllog(name, self.positions[name])
imgfile_exists = False
t0 = time.time()
if not imgfile_exists and time.time()-t0 < 10:
imgfile_exists = os.path.exists(fullpath)
time.sleep(0.5)
if imgfile_exists:
self.viewer.write_message("Saved Position '%s', image in %s" %
(name, imgfile))
else:
self.viewer.write_message("COULD NOT SAVE IMAGE FILE!!")
wx.CallAfter(Closure(self.onSelect, event=None, name=name))
def onShow(self, event):
posname = self.pos_list.GetStringSelection()
ipos = self.pos_list.GetSelection()
if posname is None or len(posname) < 1:
return
try:
self.image_display.Show()
self.image_display.Raise()
except:
del self.image_display
self.image_display = None
if self.image_display is None:
self.image_display = ImageDisplayFrame()
self.image_display.Raise()
thispos = self.positions[posname]
try:
notes = json.loads(thispos['notes'])
except:
notes = {'data_format': ''}
if isinstance(notes, basestring):
notes = json.loads(notes)
label = []
stages = self.viewer.config['stages']
posvals = self.positions[posname]['position']
for pvname, value in posvals.items():
value = thispos['position'][pvname]
desc = stages.get(pvname, {}).get('desc', None)
if desc is None:
desc = pvname
label.append("%s=%.4f" % (desc, float(value)))
label = ', '.join(label)
label = '%s: %s' % (posname, label)
data = thispos['image']
if str(notes['data_format']) == 'file':
self.image_display.showfile(data, title=posname,
label=label)
elif str(notes['data_format']) == 'base64':
size = notes.get('image_size', (800, 600))
self.image_display.showb64img(data, size=size,
title=posname, label=label)
else:
print 'Cannot show image for %s' % posname
def onGo(self, event):
posname = self.pos_list.GetStringSelection()
if posname is None or len(posname) < 1:
return
stages = self.viewer.config['stages']
posvals = self.positions[posname]['position']
postext = []
for pvname, value in posvals.items():
label = pvname
desc = stages.get(pvname, {}).get('desc', None)
if desc is not None:
label = '%s (%s)' % (desc, pvname)
postext.append(' %s\t= %.4f' % (label, float(value)))
postext = '\n'.join(postext)
if self.viewer.v_move:
ret = popup(self, "Move to %s?: \n%s" % (posname, postext),
'Verify Move',
style=wx.YES_NO|wx.ICON_QUESTION)
if ret != wx.ID_YES:
return
for pvname, value in posvals.items():
caput(pvname, value)
self.viewer.write_message('moved to %s' % posname)
def onErase(self, event=None, posname=None, query=True):
if posname is None:
posname = self.pos_list.GetStringSelection()
if posname is None or len(posname) < 1:
return
if self.viewer.v_erase and query:
if wx.ID_YES != popup(self, "Erase %s?" % (posname),
'Verify Erase',
style=wx.YES_NO|wx.ICON_QUESTION):
return
pos_names = self.pos_list.GetItems()
ipos = pos_names.index(posname)
self.instdb.remove_position(self.instname, posname)
self.positions.pop(posname)
self.pos_list.Delete(ipos)
self.pos_name.Clear()
self.viewer.write_message('Erased Position %s' % posname)
def onEraseMany(self, event=None):
if self.instdb is not None:
ErasePositionsDialog(self.positions.keys(),
instname=self.instname,
instdb=self.instdb)
def onMicroscopeTransfer(self, event=None):
offline = self.config.get('offline', '')
if self.instdb is not None:
TransferPositionsDialog(offline, instname=self.instname,
instdb=self.instdb, parent=self)
def onMicroscopeCalibrate(self, event=None, **kws):
offline = self.config.get('offline', '')
print 'Calibrate to Offline : ', offline
def onSelect(self, event=None, name=None):
"Event handler for selecting a named position"
if name is None:
name = str(event.GetString().strip())
if name is None or name not in self.positions:
return
self.pos_name.SetValue(name)
def onRightClick(self, event=None):
menu = wx.Menu()
# make basic widgets for popup menu
for item, name in (('popup_up1', 'Move up'),
('popup_dn1', 'Move down'),
('popup_upall', 'Move to top'),
('popup_dnall', 'Move to bottom')):
setattr(self, item, wx.NewId())
wid = getattr(self, item)
self.Bind(wx.EVT_MENU, self.onRightEvent, wid)
menu.Append(wid, name)
self.PopupMenu(menu)
menu.Destroy()
def onRightEvent(self, event=None):
"popup box event handler"
idx = self.pos_list.GetSelection()
if idx < 0: # no item selected
return
wid = event.GetId()
namelist = list(self.positions.keys())[:]
stmp = {}
for name in namelist:
stmp[name] = self.positions[name]
if wid == self.popup_up1 and idx > 0:
namelist.insert(idx-1, namelist.pop(idx))
elif wid == self.popup_dn1 and idx < len(namelist):
namelist.insert(idx+1, namelist.pop(idx))
elif wid == self.popup_upall:
namelist.insert(0, namelist.pop(idx))
elif wid == self.popup_dnall:
namelist.append( namelist.pop(idx))
newpos = {}
for name in namelist:
newpos[name] = stmp[name]
self.init_positions(newpos)
self.viewer.autosave(positions=self.positions)
def set_positions(self, positions):
"set the list of position on the left-side panel"
cur_sel = self.pos_list.GetStringSelection()
self.pos_list.Clear()
self.positions = positions
for name, val in self.positions.items():
self.pos_list.Append(name)
if cur_sel in self.positions:
self.pos_list.SetStringSelection(cur_sel)
self.last_refresh = 0
def onTimer(self, evt=None):
if self.poslist_query is None:
inst = self.instdb.get_instrument(self.instname)
cls, tab = self.instdb.scandb.get_table('positions')
self.poslist_select = tab.select().where(tab.c.instruments_id==inst.id)
npos = len(self.poslist_select.execute().fetchall())
now = time.time()
if (npos != len(self.posnames) or
(now - self.last_refresh) > 600.0):
# print("Timer ", npos, len(self.posnames), now-self.last_refresh)
self.get_positions_from_db()
self.last_refresh = now
def get_positions_from_db(self):
if self.instdb is None:
return
positions = OrderedDict()
iname = self.instname
posnames = self.instdb.get_positionlist(iname)
self.posnames = posnames
for pname in posnames:
thispos = self.instdb.get_position(iname, pname)
image = ''
notes = {}
if thispos.image is not None:
image = thispos.image
if thispos.notes is not None:
notes = thispos.notes
pdat = OrderedDict()
for pvpos in thispos.pvs:
pdat[pvpos.pv.name] = pvpos.value
positions[pname] = dict(position=pdat, image=image, notes=notes)
self.set_positions(positions)
def SavePositions(self, fname):
"""
save positions to external file
"""
out = [POS_HEADER]
for name, val in self.positions.items():
pos = []
notes = val['notes']
img = val['image']
ts = val.get('timestamp', '')
for pvname, val in val['position'].items():
pos.append((pvname, val))
out.append(json.dumps((name, pos, notes, img, ts)))
out.append('')
out = '\n'.join(out)
fout = open(fname, 'w')
fout.write(out)
fout.close()
def LoadPositions(self, fname):
"""
save positions to external file
"""
try:
fh = open(fname, 'r')
text = fh.readlines()
fh.close()
except IOError:
print 'IO Error'
return -1
header = text[0].replace('\n', '').replace('\r', '')
if header != POS_HEADER:
print 'Bad Header', header
return -2
for line in text[1:]:
name, pos, notes, img, ts = json.loads(line)
tmp_pos = OrderedDict(pos)
try:
self.positions[name] = {'image': img, 'timestamp': ts,
'position': tmp_pos, 'notes': notes}
except:
print 'Cannot set', name, tmp_pos, notes, img
try:
self.instdb.save_position(self.instname, name, tmp_pos,
notes=json.dumps(notes), image=img)
except:
print 'Could save ', name, tmp_pos, notes, img
#print(" Import Pos ", name, img, notes)
self.set_positions(self.positions)
return 0
class PositionPanel(wx.Panel):
"""panel of position lists, with buttons"""
def __init__(self, parent, viewer, config=None, **kws):
wx.Panel.__init__(self, parent, -1, size=(300, 500))
self.size = (300, 600)
self.parent = parent
self.viewer = viewer
self.config = config
self.poslist_select = None
self.image_display = None
self.pos_name = wx.TextCtrl(self,
value="",
size=(300, 25),
style=wx.TE_PROCESS_ENTER)
self.pos_name.Bind(wx.EVT_TEXT_ENTER, self.onSave1)
tlabel = wx.StaticText(self, label="Save Position: ")
bkws = dict(size=(55, -1))
btn_goto = add_button(self, "Go To", action=self.onGo, **bkws)
btn_erase = add_button(self, "Erase", action=self.onErase, **bkws)
btn_show = add_button(self, "Show", action=self.onShow, **bkws)
# btn_many = add_button(self, "Erase Many", action=self.onEraseMany, **bkws)
brow = wx.BoxSizer(wx.HORIZONTAL)
brow.Add(btn_goto, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
brow.Add(btn_erase, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
brow.Add(btn_show, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
# brow.Add(btn_many, 0, ALL_EXP|wx.ALIGN_LEFT, 1)
self.pos_list = wx.ListBox(self)
self.pos_list.SetBackgroundColour(wx.Colour(253, 253, 250))
self.pos_list.Bind(wx.EVT_LISTBOX, self.onSelect)
self.pos_list.Bind(wx.EVT_RIGHT_DOWN, self.onRightClick)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(tlabel, 0, wx.ALIGN_LEFT | wx.ALL)
sizer.Add(self.pos_name, 0, wx.ALIGN_LEFT | wx.ALL)
sizer.Add(brow, 0, wx.ALIGN_LEFT | wx.ALL)
sizer.Add(self.pos_list, 1, ALL_EXP | wx.ALIGN_CENTER, 3)
pack(self, sizer)
self.init_scandb()
self.last_refresh = 0
self.get_positions_from_db()
self.timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onTimer, self.timer)
self.timer.Start(2500)
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get('instrument', 'microscope_stages')
dbconn_dir = dbconn.get('dbconn_dir', '')
dbconn_file = dbconn.get('dbconn_file', '')
if os.path.exists(dbconn_dir) and len(dbconn_file) > 0:
sys.path.insert(0, dbconn_dir)
mod = __import__(dbconn_file)
conn = mod.conn
scandb = ScanDB(**mod.conn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.viewer.config['stages'].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def onSave1(self, event):
"save from text enter"
self.onSave(event.GetString().strip())
def onSave2(self, event):
"save from button push"
self.onSave(self.pos_name.GetValue().strip())
def onSave(self, name):
if len(name) < 1:
return
if name in self.positions and self.viewer.v_replace:
ret = popup(self,
"Overwrite Position %s?" % name,
"Veriry Overwrite Position",
style=wx.YES_NO | wx.NO_DEFAULT | wx.ICON_QUESTION)
if ret != wx.ID_YES:
return
imgfile = '%s.jpg' % time.strftime('%b%d_%H%M%S')
imgfile = os.path.join(self.viewer.imgdir, imgfile)
tmp_pos = self.viewer.ctrlpanel.read_position()
imgdata, count = None, 0
if not os.path.exists(self.viewer.imgdir):
os.makedirs(self.viewer.imgdir)
while imgdata is None and count < 100:
imgdata = self.viewer.save_image(imgfile)
if imgdata is None:
time.sleep(0.5)
count = count + 1
imgdata['source'] = 'SampleStage'
imgdata['data_format'] = 'file'
imgdata.pop('data')
notes = json.dumps(imgdata)
fullpath = os.path.join(os.getcwd(), imgfile)
self.positions[name] = {
'image': fullpath,
'timestamp': time.strftime('%b %d %H:%M:%S'),
'position': tmp_pos,
'notes': notes
}
if name not in self.pos_list.GetItems():
self.pos_list.Append(name)
self.instdb.save_position(self.instname,
name,
tmp_pos,
notes=notes,
image=fullpath)
self.pos_list.SetStringSelection(name)
# auto-save file
self.viewer.autosave(positions=self.positions)
self.viewer.write_htmllog(name, self.positions[name])
imgfile_exists = False
t0 = time.time()
if not imgfile_exists and time.time() - t0 < 10:
imgfile_exists = os.path.exists(fullpath)
time.sleep(0.5)
if imgfile_exists:
self.viewer.write_message("Saved Position '%s', image in %s" %
(name, imgfile))
else:
self.viewer.write_message("COULD NOT SAVE IMAGE FILE!!")
wx.CallAfter(Closure(self.onSelect, event=None, name=name))
def onShow(self, event):
posname = self.pos_list.GetStringSelection()
ipos = self.pos_list.GetSelection()
if posname is None or len(posname) < 1:
return
try:
self.image_display.Show()
self.image_display.Raise()
except:
del self.image_display
self.image_display = None
if self.image_display is None:
self.image_display = ImageDisplayFrame()
self.image_display.Raise()
thispos = self.positions[posname]
try:
notes = json.loads(thispos['notes'])
except:
notes = {'data_format': ''}
if isinstance(notes, basestring):
notes = json.loads(notes)
label = []
stages = self.viewer.config['stages']
posvals = self.positions[posname]['position']
for pvname, value in posvals.items():
value = thispos['position'][pvname]
desc = stages.get(pvname, {}).get('desc', None)
if desc is None:
desc = pvname
label.append("%s=%.4f" % (desc, float(value)))
label = ', '.join(label)
label = '%s: %s' % (posname, label)
data = thispos['image']
if str(notes['data_format']) == 'file':
self.image_display.showfile(data, title=posname, label=label)
elif str(notes['data_format']) == 'base64':
size = notes.get('image_size', (800, 600))
self.image_display.showb64img(data,
size=size,
title=posname,
label=label)
else:
print('Cannot show image for %s' % posname)
def onGo(self, event):
posname = self.pos_list.GetStringSelection()
if posname is None or len(posname) < 1:
return
stages = self.viewer.config['stages']
posvals = self.positions[posname]['position']
postext = []
for pvname, value in posvals.items():
label = pvname
desc = stages.get(pvname, {}).get('desc', None)
if desc is not None:
label = '%s (%s)' % (desc, pvname)
postext.append(' %s\t= %.4f' % (label, float(value)))
postext = '\n'.join(postext)
if self.viewer.v_move:
ret = popup(self,
"Move to %s?: \n%s" % (posname, postext),
'Verify Move',
style=wx.YES_NO | wx.ICON_QUESTION)
if ret != wx.ID_YES:
return
for pvname, value in posvals.items():
caput(pvname, value)
self.viewer.write_message('moved to %s' % posname)
def onErase(self, event=None, posname=None, query=True):
if posname is None:
posname = self.pos_list.GetStringSelection()
if posname is None or len(posname) < 1:
return
if self.viewer.v_erase and query:
if wx.ID_YES != popup(self,
"Erase %s?" % (posname),
'Verify Erase',
style=wx.YES_NO | wx.ICON_QUESTION):
return
pos_names = self.pos_list.GetItems()
ipos = pos_names.index(posname)
self.instdb.remove_position(self.instname, posname)
self.positions.pop(posname)
self.pos_list.Delete(ipos)
self.pos_name.Clear()
self.viewer.write_message('Erased Position %s' % posname)
def onEraseMany(self, event=None):
if self.instdb is not None:
ErasePositionsDialog(self.positions.keys(),
instname=self.instname,
instdb=self.instdb)
def onMicroscopeTransfer(self, event=None):
offline = self.config.get('offline', '')
if self.instdb is not None:
TransferPositionsDialog(offline,
instname=self.instname,
instdb=self.instdb,
parent=self)
def onMicroscopeCalibrate(self, event=None, **kws):
offline = self.config.get('offline', '')
print('Calibrate to Offline : ', offline)
def onSelect(self, event=None, name=None):
"Event handler for selecting a named position"
if name is None:
name = str(event.GetString().strip())
if name is None or name not in self.positions:
return
self.pos_name.SetValue(name)
def onRightClick(self, event=None):
menu = wx.Menu()
# make basic widgets for popup menu
for item, name in (('popup_up1', 'Move up'), ('popup_dn1',
'Move down'),
('popup_upall', 'Move to top'), ('popup_dnall',
'Move to bottom')):
setattr(self, item, wx.NewId())
wid = getattr(self, item)
self.Bind(wx.EVT_MENU, self.onRightEvent, wid)
menu.Append(wid, name)
self.PopupMenu(menu)
menu.Destroy()
def onRightEvent(self, event=None):
"popup box event handler"
idx = self.pos_list.GetSelection()
if idx < 0: # no item selected
return
wid = event.GetId()
namelist = list(self.positions.keys())[:]
stmp = {}
for name in namelist:
stmp[name] = self.positions[name]
if wid == self.popup_up1 and idx > 0:
namelist.insert(idx - 1, namelist.pop(idx))
elif wid == self.popup_dn1 and idx < len(namelist):
namelist.insert(idx + 1, namelist.pop(idx))
elif wid == self.popup_upall:
namelist.insert(0, namelist.pop(idx))
elif wid == self.popup_dnall:
namelist.append(namelist.pop(idx))
newpos = {}
for name in namelist:
newpos[name] = stmp[name]
self.init_positions(newpos)
self.viewer.autosave(positions=self.positions)
def set_positions(self, positions):
"set the list of position on the left-side panel"
cur_sel = self.pos_list.GetStringSelection()
self.pos_list.Clear()
self.positions = positions
for name, val in self.positions.items():
self.pos_list.Append(name)
if cur_sel in self.positions:
self.pos_list.SetStringSelection(cur_sel)
self.last_refresh = 0
def onTimer(self, evt=None):
if self.poslist_select is None:
inst = self.instdb.get_instrument(self.instname)
cls, tab = self.instdb.scandb.get_table('position')
self.poslist_select = tab.select().where(
tab.c.instrument_id == inst.id)
npos = len(self.poslist_select.execute().fetchall())
now = time.time()
if (npos != len(self.posnames) or (now - self.last_refresh) > 900.0):
# print("Timer ", npos, len(self.posnames), now-self.last_refresh)
self.get_positions_from_db()
self.last_refresh = now
def get_positions_from_db(self):
if self.instdb is None:
return
positions = OrderedDict()
iname = self.instname
posnames = self.instdb.get_positionlist(iname)
self.posnames = posnames
for pname in posnames:
thispos = self.instdb.get_position(iname, pname)
# print(pname, thispos)
image = ''
notes = {}
if thispos.image is not None:
image = thispos.image
if thispos.notes is not None:
notes = thispos.notes
pdat = OrderedDict()
for pvpos in thispos.pv:
pdat[pvpos.pv.name] = pvpos.value
positions[pname] = dict(position=pdat, image=image, notes=notes)
self.set_positions(positions)
def SavePositions(self, fname):
"""
save positions to external file
"""
out = [POS_HEADER]
for name, val in self.positions.items():
pos = []
notes = val['notes']
img = val['image']
ts = val.get('timestamp', '')
for pvname, val in val['position'].items():
pos.append((pvname, val))
out.append(json.dumps((name, pos, notes, img, ts)))
out.append('')
out = '\n'.join(out)
fout = open(fname, 'w')
fout.write(out)
fout.close()
def LoadPositions(self, fname):
"""
save positions to external file
"""
try:
fh = open(fname, 'r')
text = fh.readlines()
fh.close()
except IOError:
print('IO Error')
return -1
header = text[0].replace('\n', '').replace('\r', '')
if header != POS_HEADER:
print('Bad Header', header)
return -2
for line in text[1:]:
name, pos, notes, img, ts = json.loads(line)
tmp_pos = OrderedDict(pos)
try:
self.positions[name] = {
'image': img,
'timestamp': ts,
'position': tmp_pos,
'notes': notes
}
except:
print('Cannot set', name, tmp_pos, notes, img)
try:
self.instdb.save_position(self.instname,
name,
tmp_pos,
notes=json.dumps(notes),
image=img)
except:
print('Could save ', name, tmp_pos, notes, img)
#print(" Import Pos ", name, img, notes)
self.set_positions(self.positions)
return 0
class PositionPanel(wx.Panel):
"""panel of position lists, with buttons"""
def __init__(self, parent, config=None):
wx.Panel.__init__(self, parent, -1, size=(300, 500))
self.size = (300, 500)
self.parent = parent
self.config = config
self.image_display = None
self.pos_name = wx.TextCtrl(self, value="", size=(285, 25), style=wx.TE_PROCESS_ENTER)
self.pos_name.Bind(wx.EVT_TEXT_ENTER, self.onSave1)
tlabel = wx.StaticText(self, label="Save Position: ")
bkws = dict(size=(55, -1))
btn_save = add_button(self, "Save", action=self.onSave2, **bkws)
btn_goto = add_button(self, "Go To", action=self.onGo, **bkws)
btn_erase = add_button(self, "Erase", action=self.onErase, **bkws)
btn_show = add_button(self, "Show", action=self.onShow, **bkws)
# btn_many = add_button(self, "Erase Many", action=self.onEraseMany, **bkws)
brow = wx.BoxSizer(wx.HORIZONTAL)
brow.Add(btn_save, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
brow.Add(btn_goto, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
brow.Add(btn_erase, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
brow.Add(btn_show, 0, ALL_EXP | wx.ALIGN_LEFT, 1)
# brow.Add(btn_many, 0, ALL_EXP|wx.ALIGN_LEFT, 1)
self.pos_list = wx.ListBox(self)
self.pos_list.SetBackgroundColour(wx.Colour(253, 253, 250))
self.pos_list.Bind(wx.EVT_LISTBOX, self.onSelect)
self.pos_list.Bind(wx.EVT_RIGHT_DOWN, self.onRightClick)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(tlabel, 0, wx.ALIGN_LEFT | wx.ALL)
sizer.Add(self.pos_name, 0, wx.ALIGN_LEFT | wx.ALL)
sizer.Add(brow, 0, wx.ALIGN_LEFT | wx.ALL)
sizer.Add(self.pos_list, 1, ALL_EXP | wx.ALIGN_CENTER, 3)
# print(" Position Panel ", self.GetSize(), self.size)
pack(self, sizer)
self.init_scandb()
self.last_refresh = 0
self.get_positions_from_db()
self.timer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.onTimer, self.timer)
self.timer.Start(3000)
def init_scandb(self):
dbconn = self.config
if dbconn is not None:
self.instname = dbconn.get("instrument", "microscope_stages")
if dbconn["port"] in ("", "None", None):
dbconn.pop("port")
scandb = ScanDB(**dbconn)
self.instdb = InstrumentDB(scandb)
if self.instdb.get_instrument(self.instname) is None:
pvs = self.parent.config["stages"].keys()
self.instdb.add_instrument(self.instname, pvs=pvs)
def onSave1(self, event):
"save from text enter"
self.onSave(event.GetString().strip())
def onSave2(self, event):
"save from button push"
self.onSave(self.pos_name.GetValue().strip())
def onSave(self, name):
if len(name) < 1:
return
if name in self.positions and self.parent.v_replace:
ret = popup(
self,
"Overwrite Position %s?" % name,
"Veriry Overwrite Position",
style=wx.YES_NO | wx.NO_DEFAULT | wx.ICON_QUESTION,
)
if ret != wx.ID_YES:
return
imgfile = "%s.jpg" % time.strftime("%b%d_%H%M%S")
imgfile = os.path.join(self.parent.imgdir, imgfile)
tmp_pos = self.parent.ctrlpanel.read_position()
imgdata, count = None, 0
while imgdata is None and count < 100:
imgdata = self.parent.save_image(imgfile)
if imgdata is None:
time.sleep(0.5)
count = count + 1
imgdata["source"] = "SampleStage"
imgdata["data_format"] = "file"
imgdata.pop("data")
notes = json.dumps(imgdata)
fullpath = os.path.join(os.getcwd(), imgfile)
self.positions[name] = {
"image": fullpath,
"timestamp": time.strftime("%b %d %H:%M:%S"),
"position": tmp_pos,
"notes": notes,
}
if name not in self.pos_list.GetItems():
self.pos_list.Append(name)
self.instdb.save_position(self.instname, name, tmp_pos, notes=notes, image=fullpath)
self.pos_list.SetStringSelection(name)
# auto-save file
self.parent.autosave(positions=self.positions)
self.parent.write_htmllog(name, self.positions[name])
self.parent.write_message("Saved Position '%s', image in %s" % (name, imgfile))
wx.CallAfter(Closure(self.onSelect, event=None, name=name))
def onShow(self, event):
posname = self.pos_list.GetStringSelection()
ipos = self.pos_list.GetSelection()
if posname is None or len(posname) < 1:
return
try:
self.image_display.Show()
self.image_display.Raise()
except:
del self.image_display
self.image_display = None
if self.image_display is None:
self.image_display = ImageDisplayFrame()
self.image_display.Raise()
thispos = self.positions[posname]
try:
notes = json.loads(thispos["notes"])
except:
notes = {"data_format": ""}
label = []
stages = self.parent.config["stages"]
posvals = self.positions[posname]["position"]
for pvname, value in posvals.items():
value = thispos["position"][pvname]
desc = stages.get(pvname, {}).get("desc", None)
if desc is None:
desc = pvname
label.append("%s=%.4f" % (desc, float(value)))
label = ", ".join(label)
label = "%s: %s" % (posname, label)
data = thispos["image"]
if str(notes["data_format"]) == "file":
self.image_display.showfile(data, title=posname, label=label)
elif str(notes["data_format"]) == "base64":
size = notes.get("image_size", (800, 600))
self.image_display.showb64img(data, size=size, title=posname, label=label)
else:
print "Cannot show image for %s" % posname
def onGo(self, event):
posname = self.pos_list.GetStringSelection()
if posname is None or len(posname) < 1:
return
stages = self.parent.config["stages"]
posvals = self.positions[posname]["position"]
postext = []
for pvname, value in posvals.items():
label = pvname
desc = stages.get(pvname, {}).get("desc", None)
if desc is not None:
label = "%s (%s)" % (desc, pvname)
postext.append(" %s\t= %.4f" % (label, float(value)))
postext = "\n".join(postext)
if self.parent.v_move:
ret = popup(
self, "Move to %s?: \n%s" % (posname, postext), "Verify Move", style=wx.YES_NO | wx.ICON_QUESTION
)
if ret != wx.ID_YES:
return
for pvname, value in posvals.items():
caput(pvname, value)
self.parent.write_message("moved to %s" % posname)
def onErase(self, event):
posname = self.pos_list.GetStringSelection()
ipos = self.pos_list.GetSelection()
if posname is None or len(posname) < 1:
return
if self.parent.v_erase:
if wx.ID_YES != popup(self, "Erase %s?" % (posname), "Verify Erase", style=wx.YES_NO | wx.ICON_QUESTION):
return
self.instdb.remove_position(self.instname, posname)
self.positions.pop(posname)
self.pos_list.Delete(ipos)
self.pos_name.Clear()
self.parent.write_message("Erased Position %s" % posname)
def onEraseMany(self, event=None):
if self.instdb is not None:
ErasePositionsDialog(self.positions.keys(), instname=self.instname, instdb=self.instdb)
def onSelect(self, event=None, name=None):
"Event handler for selecting a named position"
if name is None:
name = str(event.GetString().strip())
if name is None or name not in self.positions:
return
self.pos_name.SetValue(name)
def onRightClick(self, event=None):
menu = wx.Menu()
# make basic widgets for popup menu
for item, name in (
("popup_up1", "Move up"),
("popup_dn1", "Move down"),
("popup_upall", "Move to top"),
("popup_dnall", "Move to bottom"),
):
setattr(self, item, wx.NewId())
wid = getattr(self, item)
self.Bind(wx.EVT_MENU, self.onRightEvent, wid)
menu.Append(wid, name)
self.PopupMenu(menu)
menu.Destroy()
def onRightEvent(self, event=None):
"popup box event handler"
idx = self.pos_list.GetSelection()
if idx < 0: # no item selected
return
wid = event.GetId()
namelist = list(self.positions.keys())[:]
stmp = {}
for name in namelist:
stmp[name] = self.positions[name]
if wid == self.popup_up1 and idx > 0:
namelist.insert(idx - 1, namelist.pop(idx))
elif wid == self.popup_dn1 and idx < len(namelist):
namelist.insert(idx + 1, namelist.pop(idx))
elif wid == self.popup_upall:
namelist.insert(0, namelist.pop(idx))
elif wid == self.popup_dnall:
namelist.append(namelist.pop(idx))
newpos = {}
for name in namelist:
newpos[name] = stmp[name]
self.init_positions(newpos)
self.parent.autosave(positions=self.positions)
def set_positions(self, positions):
"set the list of position on the left-side panel"
cur_sel = self.pos_list.GetStringSelection()
self.pos_list.Clear()
self.positions = positions
for name, val in self.positions.items():
self.pos_list.Append(name)
if cur_sel in self.positions:
self.pos_list.SetStringSelection(cur_sel)
self.last_refresh = time.time()
def onTimer(self, evt=None):
posnames = self.instdb.get_positionlist(self.instname)
if len(posnames) != len(self.posnames) or (time.time() - self.last_refresh) > 15.0:
self.get_positions_from_db()
def get_positions_from_db(self):
if self.instdb is None:
return
positions = OrderedDict()
iname = self.instname
posnames = self.instdb.get_positionlist(iname)
self.posnames = posnames
for pname in posnames:
thispos = self.instdb.get_position(iname, pname)
image = ""
notes = {}
if thispos.image is not None:
image = thispos.image
if thispos.notes is not None:
notes = thispos.notes
pdat = OrderedDict()
for pvpos in thispos.pvs:
pdat[pvpos.pv.name] = pvpos.value
positions[pname] = dict(position=pdat, image=image, notes=notes)
self.set_positions(positions)