def run_as_data_tool(self): from cellprofiler.gui.editobjectsdlg import EditObjectsDialog import wx from wx.lib.filebrowsebutton import FileBrowseButton from cellprofiler.modules.namesandtypes import ObjectsImageProvider from bioformats import load_image with wx.Dialog(None) as dlg: dlg.Title = "Choose files for editing" dlg.Sizer = wx.BoxSizer(wx.VERTICAL) sub_sizer = wx.BoxSizer(wx.HORIZONTAL) dlg.Sizer.Add(sub_sizer, 0, wx.EXPAND | wx.ALL, 5) new_or_existing_rb = wx.RadioBox(dlg, style=wx.RA_VERTICAL, choices=("New", "Existing")) sub_sizer.Add(new_or_existing_rb, 0, wx.EXPAND) objects_file_fbb = FileBrowseButton( dlg, size=(300, -1), fileMask= "Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg", dialogTitle="Select objects file", labelText="Objects file:", ) objects_file_fbb.Enable(False) sub_sizer.AddSpacer(5) sub_sizer.Add(objects_file_fbb, 0, wx.ALIGN_TOP | wx.ALIGN_RIGHT) def on_radiobox(event): objects_file_fbb.Enable(new_or_existing_rb.GetSelection() == 1) new_or_existing_rb.Bind(wx.EVT_RADIOBOX, on_radiobox) image_file_fbb = FileBrowseButton( dlg, size=(300, -1), fileMask= "Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg", dialogTitle="Select guide image file", labelText="Guide image:", ) dlg.Sizer.Add(image_file_fbb, 0, wx.EXPAND | wx.ALL, 5) allow_overlap_checkbox = wx.CheckBox(dlg, -1, "Allow objects to overlap") allow_overlap_checkbox.Value = True dlg.Sizer.Add(allow_overlap_checkbox, 0, wx.EXPAND | wx.ALL, 5) buttons = wx.StdDialogButtonSizer() dlg.Sizer.Add(buttons, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL, 5) buttons.Add(wx.Button(dlg, wx.ID_OK)) buttons.Add(wx.Button(dlg, wx.ID_CANCEL)) buttons.Realize() dlg.Fit() result = dlg.ShowModal() if result != wx.ID_OK: return self.allow_overlap.value = allow_overlap_checkbox.Value fullname = objects_file_fbb.GetValue() guidename = image_file_fbb.GetValue() if new_or_existing_rb.GetSelection() == 1: provider = ObjectsImageProvider("InputObjects", pathname2url(fullname), None, None) image = provider.provide_image(None) pixel_data = image.pixel_data shape = pixel_data.shape[:2] labels = [pixel_data[:, :, i] for i in range(pixel_data.shape[2])] else: labels = None # # Load the guide image # guide_image = load_image(guidename) if np.min(guide_image) != np.max(guide_image): guide_image = (guide_image - np.min(guide_image)) / ( np.max(guide_image) - np.min(guide_image)) if labels is None: shape = guide_image.shape[:2] labels = [np.zeros(shape, int)] with EditObjectsDialog(guide_image, labels, self.allow_overlap, self.object_name.value) as dialog_box: result = dialog_box.ShowModal() if result != wx.OK: return labels = dialog_box.labels n_frames = len(labels) with wx.FileDialog(None, style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg: dlg.Path = fullname dlg.Wildcard = ("Object image file (*.tif,*.tiff)|*.tif;*.tiff|" "Ilastik project file (*.ilp)|*.ilp") result = dlg.ShowModal() fullname = dlg.Path if result == wx.ID_OK: if fullname.endswith(".ilp"): self.save_into_ilp(fullname, labels, guidename) else: from bioformats.formatwriter import write_image from bioformats.omexml import PT_UINT16 if os.path.exists(fullname): os.unlink(fullname) for i, l in enumerate(labels): write_image(fullname, l, PT_UINT16, t=i, size_t=len(labels))
def run_as_data_tool(self): from cellprofiler.gui.editobjectsdlg import EditObjectsDialog import wx from wx.lib.filebrowsebutton import FileBrowseButton from cellprofiler.modules.namesandtypes import ObjectsImageProvider from bioformats import load_image with wx.Dialog(None) as dlg: dlg.Title = "Choose files for editing" dlg.Sizer = wx.BoxSizer(wx.VERTICAL) box = wx.StaticBox(dlg, -1, "Choose or create new objects file") sub_sizer = wx.StaticBoxSizer(box, wx.HORIZONTAL) dlg.Sizer.Add(sub_sizer, 0, wx.EXPAND | wx.ALL, 5) new_or_existing_rb = wx.RadioBox(dlg, style=wx.RA_VERTICAL, choices = ("New", "Existing")) sub_sizer.Add(new_or_existing_rb, 0, wx.EXPAND) objects_file_fbb = FileBrowseButton( dlg, size=(300, -1), fileMask="Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg", dialogTitle="Select objects file", labelText="Objects file:") objects_file_fbb.Enable(False) sub_sizer.AddSpacer(5) sub_sizer.Add(objects_file_fbb, 0, wx.ALIGN_TOP | wx.ALIGN_RIGHT) def on_radiobox(event): objects_file_fbb.Enable(new_or_existing_rb.GetSelection() == 1) new_or_existing_rb.Bind(wx.EVT_RADIOBOX, on_radiobox) image_file_fbb = FileBrowseButton( dlg, size=(300, -1), fileMask="Objects file (*.tif, *.tiff, *.png, *.bmp, *.jpg)|*.tif;*.tiff;*.png;*.bmp;*.jpg", dialogTitle="Select guide image file", labelText="Guide image:") dlg.Sizer.Add(image_file_fbb, 0, wx.EXPAND | wx.ALL, 5) allow_overlap_checkbox = wx.CheckBox(dlg, -1, "Allow objects to overlap") allow_overlap_checkbox.Value = True dlg.Sizer.Add(allow_overlap_checkbox, 0, wx.EXPAND | wx.ALL, 5) buttons = wx.StdDialogButtonSizer() dlg.Sizer.Add(buttons, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL, 5) buttons.Add(wx.Button(dlg, wx.ID_OK)) buttons.Add(wx.Button(dlg, wx.ID_CANCEL)) buttons.Realize() dlg.Fit() result = dlg.ShowModal() if result != wx.ID_OK: return self.allow_overlap.value = allow_overlap_checkbox.Value fullname = objects_file_fbb.GetValue() guidename = image_file_fbb.GetValue() if new_or_existing_rb.GetSelection() == 1: provider = ObjectsImageProvider( "InputObjects", pathname2url(fullname), None, None) image = provider.provide_image(None) pixel_data = image.pixel_data shape = pixel_data.shape[:2] labels = [pixel_data[:, :, i] for i in range(pixel_data.shape[2])] else: labels = None # # Load the guide image # guide_image = load_image(guidename) if np.min(guide_image) != np.max(guide_image): guide_image = ((guide_image - np.min(guide_image)) / (np.max(guide_image) - np.min(guide_image))) if labels is None: shape = guide_image.shape[:2] labels = [np.zeros(shape, int)] with EditObjectsDialog( guide_image, labels, self.allow_overlap, self.object_name.value) as dialog_box: result = dialog_box.ShowModal() if result != wx.OK: return labels = dialog_box.labels n_frames = len(labels) with wx.FileDialog(None, style = wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg: dlg.Path = fullname dlg.Wildcard = ("Object image file (*.tif,*.tiff)|*.tif;*.tiff|" "Ilastik project file (*.ilp)|*.ilp") result = dlg.ShowModal() fullname = dlg.Path if result == wx.ID_OK: if fullname.endswith(".ilp"): self.save_into_ilp(fullname, labels, guidename) else: from bioformats.formatwriter import write_image from bioformats.omexml import PT_UINT16 if os.path.exists(fullname): os.unlink(fullname) for i, l in enumerate(labels): write_image(fullname, l, PT_UINT16, t = i, size_t = len(labels))