# -*- coding: utf-8 -*- ''' Created on 10 May 2016 @author: Lennard Voortman Gives ability to manually change the overlay-metadata. This is free and unencumbered software released into the public domain. Anyone is free to copy, modify, publish, use, compile, sell, or distribute this software, either in source code form or as a compiled binary, for any purpose, commercial or non-commercial, and by any means. In jurisdictions that recognize copyright laws, the author or authors of this software dedicate any and all copyright interest in the software to the public domain. We make this dedication for the benefit of the public at large and to the detriment of our heirs and successors. We intend this dedication to be an overt act of relinquishment in perpetuity of all present and future rights to this software under copyright law. The software is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and non-infringement. In no event shall the authors be liable for any claim, damages or other liability, whether in an action of contract, tort or otherwise, arising from, out of or in connection with the software or the use or other dealings in the software. ''' from __future__ import division from collections import OrderedDict import functools import logging import math from odemis import model from odemis.acq.stream import DataProjection from odemis.gui.plugin import Plugin, AcquisitionDialog import wx class VAHolder(object): pass class ManualOverlayPlugin(Plugin): name = "Manual Overlay" __version__ = "1.1" __author__ = "Lennard Voortman" __license__ = "Public domain" def __init__(self, microscope, main_app): super(ManualOverlayPlugin, self).__init__(microscope, main_app) self.addMenu("Data correction/Overlay corrections...", self.start) self._dlg = None def start(self): dlg = AcquisitionDialog(self, "Manually change the alignment", text="Change the translation, rotation, and pixel size " "of any stream. The display is immediately updated, " "but you need to save the file (as a snapshot) for " "the changes to be permanent.") self._dlg = dlg vah = VAHolder() vah._subscribers = [] vaconf = OrderedDict() tab_data = self.main_app.main_data.tab.value.tab_data_model if not tab_data.streams.value: box = wx.MessageDialog(self.main_app.main_frame, "No stream is present, so it's not possible to modify the alignment.", "No stream", wx.OK | wx.ICON_STOP) box.ShowModal() box.Destroy() return for i, stream in enumerate(tab_data.streams.value): dlg.addStream(stream) # Add 5 VAs for each stream, to modify the overlay metadata poscor = stream.raw[0].metadata.get(model.MD_POS_COR, (0, 0)) rotation = stream.raw[0].metadata.get(model.MD_ROTATION_COR, 0) scalecor = stream.raw[0].metadata.get(model.MD_PIXEL_SIZE_COR, (1, 1)) shear = stream.raw[0].metadata.get(model.MD_SHEAR_COR, 0) vatransx = model.FloatContinuous(-poscor[0], range=(-10e-6, 10e-6), unit="m") vatransy = model.FloatContinuous(-poscor[1], range=(-10e-6, 10e-6), unit="m") varot = model.FloatContinuous(rotation, range=(-math.pi, math.pi), unit="rad") vascalex = model.FloatContinuous(scalecor[0], range=(0.5, 1.5)) vascaley = model.FloatContinuous(scalecor[1], range=(0.5, 1.5)) vashear = model.FloatContinuous(shear, range=(-1, 1)) # Add the VAs to the holder, and to the vaconf mainly to force the order setattr(vah, "%dTransX" % i, vatransx) setattr(vah, "%dTransY" % i, vatransy) setattr(vah, "%dRotation" % i, varot) setattr(vah, "%dScaleX" % i, vascalex) setattr(vah, "%dScaleY" % i, vascaley) setattr(vah, "%dShear" % i, vashear) vaconf["%dTransX" % i] = {"label": "%s trans X" % stream.name.value} vaconf["%dTransY" % i] = {"label": "%s trans Y" % stream.name.value} vaconf["%dRotation" % i] = {"label": "%s rotation" % stream.name.value} vaconf["%dScaleX" % i] = {"label": "%s scale X" % stream.name.value} vaconf["%dScaleY" % i] = {"label": "%s scale Y" % stream.name.value} vaconf["%dShear" % i] = {"label": "%s shear" % stream.name.value} # Create listeners with information of the stream and dimension va_on_transx = functools.partial(self._on_trans, stream, 0) va_on_transy = functools.partial(self._on_trans, stream, 1) va_on_rotation = functools.partial(self._on_rotation, stream) va_on_scalex = functools.partial(self._on_scale, stream, 0) va_on_scaley = functools.partial(self._on_scale, stream, 1) va_on_shear = functools.partial(self._on_shear, stream) # We hold a reference to the listeners to prevent automatic subscription vah._subscribers.append(va_on_transx) vah._subscribers.append(va_on_transy) vah._subscribers.append(va_on_rotation) vah._subscribers.append(va_on_scalex) vah._subscribers.append(va_on_scaley) vah._subscribers.append(va_on_shear) vatransx.subscribe(va_on_transx) vatransy.subscribe(va_on_transy) varot.subscribe(va_on_rotation) vascalex.subscribe(va_on_scalex) vascaley.subscribe(va_on_scaley) vashear.subscribe(va_on_shear) dlg.addSettings(vah, vaconf) # TODO: add a 'reset' button dlg.addButton("Done", None, face_colour='blue') dlg.ShowModal() # The end dlg.Destroy() vah._subscribers = [] self._dlg = None def _force_update_proj(self, st): """ Force updating the projection of the given stream """ # Update in the view of the window, and also the current tab views = [self._dlg.view] views.extend(self.main_app.main_data.tab.value.tab_data_model.views.value) for v in views: for sp in v.stream_tree.getProjections(): # stream or projection if isinstance(sp, DataProjection): s = sp.stream else: s = sp if s is st: sp._shouldUpdateImage() def _on_trans(self, stream, i, value): logging.debug("New trans = %f on stream %s", value, stream.name.value) poscor = stream.raw[0].metadata.get(model.MD_POS_COR, (0, 0)) if i == 0: poscor = (-value, poscor[1]) else: poscor = (poscor[0], -value) stream.raw[0].metadata[model.MD_POS_COR] = poscor self._force_update_proj(stream) def _on_scale(self, stream, i, value): logging.debug("New scale = %f on stream %s", value, stream.name.value) scalecor = stream.raw[0].metadata.get(model.MD_PIXEL_SIZE_COR, (1, 1)) if i == 0: scalecor = (value, scalecor[1]) else: scalecor = (scalecor[0], value) stream.raw[0].metadata[model.MD_PIXEL_SIZE_COR] = scalecor self._force_update_proj(stream) def _on_rotation(self, stream, value): logging.debug("New rotation = %f on stream %s", value, stream.name.value) stream.raw[0].metadata[model.MD_ROTATION_COR] = value self._force_update_proj(stream) def _on_shear(self, stream, value): logging.debug("New shear = %f on stream %s", value, stream.name.value) stream.raw[0].metadata[model.MD_SHEAR_COR] = value self._force_update_proj(stream)