def __init__(self, fn, number):
self.number = number
# get the components
self.light = model.getComponent(role="light")
self.ccd = model.getComponent(role="ccd")
# TODO: only support TIFF
# prepare the data export
self.exporter = dataio.find_fittest_converter(fn)
# Make the name "fn" -> "~/Pictures/fn-XXXXXX.ext"
path, base = os.path.split(fn)
bn, ext = os.path.splitext(base)
tmpl = os.path.join(path, bn + "-%06d" + ext)
if path.startswith("/"):
# if fn starts with / => don't add ~/Pictures
self.fntmpl = tmpl
else:
self.fntmpl = os.path.join(get_picture_folder(), tmpl)
self._acq_done = threading.Event()
self._n = 0
self._startt = 0 # starting time of acquisition
self._q = queue.Queue() # queue of tuples (str, DataArray) for saving data
# TODO: find the right number of threads, based on CPU numbers (but with
# python threading that might be a bit overkill)
for i in range(4):
t = threading.Thread(target=self._saving_thread, args=(i,))
t.daemon = True
t.start()
def __init__(self, fn, number):
self.number = number
# get the components
self.light = model.getComponent(role="light")
self.ccd = model.getComponent(role="ccd")
# TODO: only support TIFF
# prepare the data export
self.exporter = dataio.find_fittest_converter(fn)
# Make the name "fn" -> "~/Pictures/fn-XXXXXX.ext"
path, base = os.path.split(fn)
bn, ext = os.path.splitext(base)
tmpl = os.path.join(path, bn + "-%06d" + ext)
if path.startswith("/"):
# if fn starts with / => don't add ~/Pictures
self.fntmpl = tmpl
else:
self.fntmpl = os.path.join(get_picture_folder(), tmpl)
self._acq_done = threading.Event()
self._n = 0
self._startt = 0 # starting time of acquisition
self._q = Queue.Queue() # queue of tuples (str, DataArray) for saving data
# TODO: find the right number of threads, based on CPU numbers (but with
# python threading that might be a bit overkill)
for i in range(4):
t = threading.Thread(target=self._saving_thread, args=(i,))
t.daemon = True
t.start()
def on_acquisition_done(self, future, num):
"""
Callback called when the one overview image acquisition is finished.
"""
try:
da = future.result()
except CancelledError:
self._reset_acquisition_gui()
return
except Exception:
# leave the gauge, to give a hint on what went wrong.
logging.exception("Acquisition failed")
self._reset_acquisition_gui("Acquisition failed (see log panel).", level=logging.WARNING)
return
# Store DataArray as TIFF in pyramidal format and reopen as static stream (to be memory-efficient)
# TODO: pick a different name from previous acquisition?
fn = os.path.join(get_picture_folder(), "fastem_overview_%s.ome.tiff" % num)
dataio.tiff.export(fn, da, pyramid=True)
da = open_acquisition(fn)
s = data_to_static_streams(da)[0]
s = FastEMOverviewStream(s.name.value, s.raw[0])
# Dict VA needs to be explicitly copied, otherwise it doesn't detect the change
ovv_ss = self._main_data_model.overview_streams.value.copy()
ovv_ss[num] = s
self._main_data_model.overview_streams.value = ovv_ss
def __init__(self, tab_panel, tab_data):
super(StreakCamAlignSettingsController, self).__init__(tab_data)
self.panel = tab_panel
main_data = tab_data.main
self.streak_ccd = main_data.streak_ccd
self.streak_delay = main_data.streak_delay
self.streak_unit = main_data.streak_unit
self.streak_lens = main_data.streak_lens
self._calib_path = get_picture_folder() # path to the trigger delay calibration folder
self.panel_streak = SettingsPanel(self.panel.pnl_streak)
self.panel_streak.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.panel.pnl_streak.GetSizer().Add(self.panel_streak, 1, border=5,
flag=wx.BOTTOM | wx.EXPAND | wx.ALIGN_CENTER_VERTICAL)
entry_timeRange = create_setting_entry(self.panel_streak, "Time range",
self.streak_unit.timeRange,
self.streak_unit,
conf={"control_type": odemis.gui.CONTROL_COMBO,
"label": "Time range",
"tooltip": "Time needed by the streak unit for one sweep "
"from top to bottom of the readout camera chip."}
)
entry_timeRange.value_ctrl.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.ctrl_timeRange = entry_timeRange.value_ctrl
entry_triggerDelay = create_setting_entry(self.panel_streak, "Trigger delay",
self.streak_delay.triggerDelay,
self.streak_delay,
conf={"control_type": odemis.gui.CONTROL_FLT,
"label": "Trigger delay",
"tooltip": "Change the trigger delay value to "
"center the image."},
change_callback=self._onUpdateTriggerDelayMD)
entry_triggerDelay.value_ctrl.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.ctrl_triggerDelay = entry_triggerDelay.value_ctrl
entry_magnification = create_setting_entry(self.panel_streak, "Magnification",
self.streak_lens.magnification,
self.streak_lens,
conf={"control_type": odemis.gui.CONTROL_COMBO,
"label": "Magnification",
"tooltip": "Change the magnification of the input"
"optics for the streak camera system. \n"
"Values < 1: De-magnifying \n"
"Values > 1: Magnifying"})
entry_magnification.value_ctrl.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.combo_magnification = entry_magnification.value_ctrl
# remove border
self.panel_streak.GetSizer().GetItem(0).SetBorder(0)
self.panel_streak.Layout()
self.panel.btn_open_streak_calib_file.Bind(wx.EVT_BUTTON, self._onOpenCalibFile)
self.panel.btn_save_streak_calib_file.Bind(wx.EVT_BUTTON, self._onSaveCalibFile)
def __init__(self, tab_panel, tab_data):
super(StreakCamAlignSettingsController, self).__init__(tab_data)
self.panel = tab_panel
main_data = tab_data.main
self.streak_ccd = main_data.streak_ccd
self.streak_delay = main_data.streak_delay
self.streak_unit = main_data.streak_unit
self.streak_lens = main_data.streak_lens
self._calib_path = get_picture_folder() # path to the trigger delay calibration folder
self.panel_streak = SettingsPanel(self.panel.pnl_streak)
self.panel_streak.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.panel.pnl_streak.GetSizer().Add(self.panel_streak, 1, border=5,
flag=wx.BOTTOM | wx.EXPAND | wx.ALIGN_CENTER_VERTICAL)
entry_timeRange = create_setting_entry(self.panel_streak, "Time range",
self.streak_unit.timeRange,
self.streak_unit,
conf={"control_type": odemis.gui.CONTROL_COMBO,
"label": "Time range",
"tooltip": "Time needed by the streak unit for one sweep "
"from top to bottom of the readout camera chip."}
)
entry_timeRange.value_ctrl.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.ctrl_timeRange = entry_timeRange.value_ctrl
entry_triggerDelay = create_setting_entry(self.panel_streak, "Trigger delay",
self.streak_delay.triggerDelay,
self.streak_delay,
conf={"control_type": odemis.gui.CONTROL_FLT,
"label": "Trigger delay",
"tooltip": "Change the trigger delay value to "
"center the image."},
change_callback=self._onUpdateTriggerDelayMD)
entry_triggerDelay.value_ctrl.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.ctrl_triggerDelay = entry_triggerDelay.value_ctrl
entry_magnification = create_setting_entry(self.panel_streak, "Magnification",
self.streak_lens.magnification,
self.streak_lens,
conf={"control_type": odemis.gui.CONTROL_COMBO,
"label": "Magnification",
"tooltip": "Change the magnification of the input"
"optics for the streak camera system. \n"
"Values < 1: De-magnifying \n"
"Values > 1: Magnifying"})
entry_magnification.value_ctrl.SetBackgroundColour(odemis.gui.BG_COLOUR_PANEL)
self.combo_magnification = entry_magnification.value_ctrl
# remove border
self.panel_streak.GetSizer().GetItem(0).SetBorder(0)
self.panel_streak.Layout()
self.panel.btn_open_streak_calib_file.Bind(wx.EVT_BUTTON, self._onOpenCalibFile)
self.panel.btn_save_streak_calib_file.Bind(wx.EVT_BUTTON, self._onSaveCalibFile)
def _get_snapshot_info(self, dialog=False):
config = conf.get_acqui_conf()
tab, filepath, exporter = self._main_data_model.tab.value, None, None
if dialog:
format_info = get_available_formats()
wildcards, formats = formats_to_wildcards(format_info)
# The default file name should be empty because otherwise the
# dialog will add an extension that won't change when the user
# selects a different file type in the dialog.
dlg = wx.FileDialog(self._main_frame,
"Save Snapshot",
config.last_path,
"",
wildcard=wildcards,
style=wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
# Select the last format used
try:
idx = formats.index(config.last_format)
except ValueError:
idx = 0
dlg.SetFilterIndex(idx)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
fmt = formats[dlg.GetFilterIndex()]
extension = format_info[fmt][0]
# Prevent double extensions when an old file is selected
filepath, _ = os.path.splitext(path)
filepath = filepath + extension
config.last_path = os.path.dirname(path)
config.last_format = fmt
config.last_extension = extension
config.write()
exporter = dataio.get_exporter(config.last_format)
dlg.Destroy()
else:
extension = config.last_extension
dirname = get_picture_folder()
basename = time.strftime("%Y%m%d-%H%M%S", time.localtime())
filepath = os.path.join(dirname, basename + extension)
exporter = dataio.get_exporter(config.last_format)
if os.path.exists(filepath):
msg = "File '%s' already exists, cancelling snapshot"
logging.warning(msg, filepath)
tab, filepath, exporter = None, None, None
return tab, filepath, exporter
def _get_export_info(self):
"""
Return str, str, str: full filename, exporter name, export type
Full filename is None if cancelled by user
"""
# Set default to the first of the list
export_type = self.get_export_type(self._data_model.focussedView.value)
formats = EXPORTERS[export_type]
default_exporter = get_converter(formats[0][0])
extension = default_exporter.EXTENSIONS[0]
# TODO: default to the same path/filename as current file (but different extension)
basename = time.strftime("%Y%m%d-%H%M%S", time.localtime())
filepath = os.path.join(get_picture_folder(), basename + extension)
# filepath will be None if cancelled by user
filepath, export_format, export_type = self.ShowExportFileDialog(filepath, default_exporter)
# get rid of the prefix before you ask for the exporter
if any(prefix in export_format.split(' ') for prefix in (PR_PREFIX, PP_PREFIX)):
export_format = export_format.split(' ', 1)[1]
return filepath, export_format, export_type
def __init__(self, fn, number):
self.number = number
# get the components
self.light = model.getComponent(role="light")
self.ccd = model.getComponent(role="ccd")
# prepare the data export
self.exporter = dataio.find_fittest_converter(fn)
# Make the name "fn" -> "~/Pictures + fn + fn-XXXX.ext"
path, base = os.path.split(fn)
bn, ext = os.path.splitext(base)
tmpl = os.path.join(path, bn, bn + "-%05d." + ext)
if path.startswith("/"):
# if fn starts with / => don't add ~/Pictures
self.fntmpl = tmpl
else:
self.fntmpl = os.path.join(get_picture_folder(), tmpl)
self._n = 0
def _get_snapshot_info(self, dialog=False):
config = conf.get_acqui_conf()
tab, filepath, exporter = self._main_data_model.tab.value, None, None
extension = config.last_extension
basename = time.strftime("%Y%m%d-%H%M%S", time.localtime())
if dialog:
filepath = os.path.join(config.last_path, basename + extension)
# filepath will be None if cancelled by user
filepath = ShowAcquisitionFileDialog(self._main_frame, filepath)
else:
dirname = get_picture_folder()
filepath = os.path.join(dirname, basename + extension)
if os.path.exists(filepath):
msg = "File '%s' already exists, cancelling snapshot"
logging.warning(msg, filepath)
tab, filepath = None, None
exporter = dataio.get_converter(config.last_format)
return tab, filepath, exporter
def _get_snapshot_info(self, dialog=False):
config = conf.get_acqui_conf()
tab, filepath, exporter = self._main_data_model.tab.value, None, None
extension = config.last_extension
basename = time.strftime("%Y%m%d-%H%M%S", time.localtime())
if dialog:
filepath = os.path.join(config.last_path, basename + extension)
# filepath will be None if cancelled by user
filepath = ShowAcquisitionFileDialog(self._main_frame, filepath)
else:
dirname = get_picture_folder()
filepath = os.path.join(dirname, basename + extension)
if os.path.exists(filepath):
msg = "File '%s' already exists, cancelling snapshot"
logging.warning(msg, filepath)
tab, filepath = None, None
exporter = dataio.get_converter(config.last_format)
return tab, filepath, exporter
from ConfigParser import NoOptionError
except ImportError: # Python 3 naming
import configparser as ConfigParser
from configparser import NoOptionError
import logging
import math
import os.path
from odemis.dataio import tiff
from odemis.acq.align import delphi
from odemis.gui.util import get_picture_folder, get_home_folder
import sys
from past.builtins import unicode
CONF_PATH = os.path.join(get_home_folder(), u".config/odemis")
ACQUI_PATH = get_picture_folder()
class Config(with_metaclass(ABCMeta, object)):
""" Abstract configuration super class
Configurations are built around the :py:class:`ConfigParser.SafeConfigParser` class.
The main difference is that the filename is fixed, and changes are automatically saved.
"""
@abstractproperty
def file_name(self):
"""Name of the configuration file"""
pass
try:
import ConfigParser
from ConfigParser import NoOptionError
except ImportError: # Python 3 naming
import configparser as ConfigParser
from configparser import NoOptionError
import logging
import math
import os.path
from odemis.dataio import tiff
from odemis.acq.align import delphi
from odemis.gui.util import get_picture_folder, get_home_folder
CONF_PATH = os.path.join(get_home_folder(), u".config/odemis")
ACQUI_PATH = get_picture_folder()
class Config(object):
""" Abstract configuration super class
Configurations are built around the :py:class:`ConfigParser.SafeConfigParser` class.
The main difference is that the filename is fixed, and changes are automatically saved.
"""
__metaclass__ = ABCMeta
@abstractproperty
def file_name(self):