def run(self):
"""The run() function defines the frame and starts the main loop.
self._init_lock is released only when all initialisation is done.
Whatever thread is the current one when wxWindows is initialised
is what it will consider the "main thread." For wxPython 2.4 that
happens when wxPython.wx is imported the first time. For 2.5 it
will be when the wx.App object is created.
"""
import wx
from wxtbx import bitmaps
app = wx.App(0)
self._bitmap_pause = bitmaps.fetch_icon_bitmap('actions', 'stop')
self._bitmap_run = bitmaps.fetch_icon_bitmap('actions', 'runit')
self._frame = XrayFrame(None, -1, "X-ray image display", size=(800, 720))
self._frame.Bind(wx.EVT_IDLE, self.OnIdle)
self.setup_toolbar(self._frame.toolbar)
self._frame.Show()
self._init_lock.release()
app.MainLoop()
# Avoid deadlock where the send_data() function is waiting for the
# semaphore after the frame has closed.
self._next_semaphore.release()
def run(self):
"""The run() function defines the frame and starts the main loop.
self._init_lock is released only when all initialisation is done.
Whatever thread is the current one when wxWindows is initialised
is what it will consider the "main thread." For wxPython 2.4 that
happens when wxPython.wx is imported the first time. For 2.5 it
will be when the wx.App object is created.
"""
import wx
from wxtbx import bitmaps
app = wx.App(0)
self._bitmap_pause = bitmaps.fetch_icon_bitmap('actions', 'stop')
self._bitmap_run = bitmaps.fetch_icon_bitmap('actions', 'runit')
self._frame = XrayFrame(None,
-1,
"X-ray image display",
size=(800, 720))
self._frame.Bind(wx.EVT_IDLE, self.OnIdle)
self.setup_toolbar(self._frame.toolbar)
self._frame.Show()
self._init_lock.release()
app.MainLoop()
# Avoid deadlock where the send_data() function is waiting for the
# semaphore after the frame has closed.
self._next_semaphore.release()
def __init__(self, parent):
wx.Panel.__init__(self, parent=parent, id=wx.ID_ANY)
self.index = None
self.btn_box = wx.BoxSizer(wx.HORIZONTAL)
viewmag_bmp = bitmaps.fetch_icon_bitmap('actions', 'viewmag', size=16)
# self.btn_mag = btn.GenBitmapButton(self, bitmap=viewmag_bmp)
self.btn_mag =GradButton(self, bmp=viewmag_bmp, size=(31, 30),
gradient_percent=0)
del_bmp = bitmaps.fetch_icon_bitmap('actions', 'editdelete', size=16)
# self.btn_delete = btn.GenBitmapButton(self, bitmap=del_bmp)
self.btn_delete = GradButton(self, bmp=del_bmp, size=(31, 30),
gradient_percent=0)
info_bmp = bitmaps.fetch_icon_bitmap('actions', 'info', size=16)
# self.btn_info = btn.GenBitmapButton(self, bitmap=info_bmp)
self.btn_info = GradButton(self, bmp=info_bmp, size=(31, 30),
gradient_percent=0)
self.btn_box.Add(self.btn_mag)
self.btn_box.Add(self.btn_delete, flag=wx.LEFT, border=5)
self.btn_box.Add(self.btn_info, flag=wx.LEFT, border=5)
self.SetSizer(self.btn_box)
self.SetBackgroundColour('white')
self.Fit()
def __init__(self, nb):
Tab.__init__(self, nb)
self.project_list = wx.ListCtrl(self, -1, style=wx.LC_REPORT, size=(700, 400))
self.project_list.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self._load_project)
self._il = wx.ImageList(16,16)
self._il.Add(bitmaps.fetch_icon_bitmap("actions", "agt_action_success", scale=(16,16)))
self.project_list.SetImageList(self._il, wx.IMAGE_LIST_SMALL)
titles = ['', 'Title', '# Jobs', 'Last Action']
sizes = [20,400, 100,140]
for i,t in enumerate(titles):
self.project_list.InsertColumn(i, t)
self.project_list.SetColumnWidth(i, sizes[i])
self.sidebar = wx.BoxSizer(wx.VERTICAL)
new = metallicbutton.MetallicButton(self, -1, 'New', '', bitmaps.fetch_icon_bitmap("actions", "folder_new"), size=(120,40))
delete = metallicbutton.MetallicButton(self, -1, 'Delete', '', bitmaps.fetch_icon_bitmap("actions", "fileclose"), size=(120,40))
load = metallicbutton.MetallicButton(self, -1, 'Load', '', bitmaps.fetch_icon_bitmap("actions", "folder"), size=(120,40))
self.Bind(wx.EVT_BUTTON, self._new_project, new)
self.Bind(wx.EVT_BUTTON, self._load_project, load)
self.Bind(wx.EVT_BUTTON, self._delete_project, delete)
self.sidebar.Add(new, 0, wx.EXPAND|wx.ALL, 5)
self.sidebar.Add(load, 0, wx.EXPAND|wx.ALL, 5)
self.sidebar.Add(delete, 0, wx.EXPAND|wx.ALL, 5)
self.sizer = wx.BoxSizer(wx.HORIZONTAL)
self.sizer.Add(self.project_list, 0, wx.EXPAND | wx.ALL, 5)
self.sizer.Add(self.sidebar, 0, wx.EXPAND | wx.ALL, 5)
self.SetSizer(self.sizer)
def __init__ (self, *args, **kwds) :
from wxtbx import bitmaps
super(ScoreSettingsPanel, self).__init__(*args, **kwds)
# Needed for communication with the root frame.
self._root_frame = self.GetParent().GetParent()
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
self._id_text = wx.NewId()
text = wx.StaticText(self, id= self._id_text, label="")
sizer.Add(text, flag=wx.ALIGN_CENTER)
# The score buttons. XXX Would really like this to be stars or
# some such. Could then zap the static text above.
box = wx.BoxSizer(wx.HORIZONTAL)
self._id_buttons = []
for i in range(6):
btn = wx.Button(self, label="%d" % i)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnScore, btn)
self._id_buttons.append(btn.GetId())
sizer.Add(box)
# XXX Would like to have label and short help for the buttons.
# Buttons in wxWidgets version 2.9.1 and later support text and
# bitmap, see SetBitmap, SetBitmapLabel, SetBitmapDisabled, etc.
box = wx.BoxSizer(wx.HORIZONTAL)
self._id_previous = wx.NewId()
btn = wx.BitmapButton(
self,
id=self._id_previous,
bitmap=bitmaps.fetch_icon_bitmap('actions', '1leftarrow'),
style=wx.BORDER_NONE)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnPrevious, btn)
btn = wx.Button(self, label="Save scores")
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnSave, btn)
self._id_next = wx.NewId()
btn = wx.BitmapButton(
self,
id=self._id_next,
bitmap=bitmaps.fetch_icon_bitmap('actions', '1rightarrow'),
style=wx.BORDER_NONE)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnNext, btn)
sizer.Add(box, flag=wx.ALIGN_CENTER)
# Register update events for the dynamic widgets.
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateNext, id=self._id_next)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdatePrevious, id=self._id_previous)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateText, id=self._id_text)
def __init__(self, parent, id, title):
wx.Frame.__init__(self, parent, id, title)
self.parent = parent
self.simtbx_phil = inp.generate_simtbx_phil()
self.sparams = self.simtbx_phil.extract()
#self.simtbx_phil.show()
# Setup main sizer
self.main_sizer = wx.BoxSizer(wx.VERTICAL)
# Setup toolbar
self.toolbar = self.CreateToolBar(style=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()
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')
self.toolbar.Realize()
#Processing status bar
self.sb = self.CreateStatusBar()
self.sb.SetFieldsCount(2)
self.sb.SetStatusWidths([-1, -2])
# Output gauge in status bar
self.gauge_process = wx.Gauge(self.sb,
-1,
style=wx.GA_HORIZONTAL | wx.GA_SMOOTH)
rect = self.sb.GetFieldRect(0)
self.gauge_process.SetPosition((rect.x + 2, rect.y + 2))
self.gauge_process.SetSize((rect.width - 4, rect.height - 4))
self.gauge_process.Hide()
# Instantiate windows
self.top_window = frm.TopPanel(self)
# Single input window
self.main_sizer.Add(self.top_window,
1,
flag=wx.ALL | wx.EXPAND,
border=10)
self.main_sizer.Add((-1, 20))
# Bindings
self.Bind(wx.EVT_TOOL, self.onQuit, self.tb_btn_quit)
self.Bind(wx.EVT_TOOL, self.onRun, self.tb_btn_run)
self.Bind(wx.EVT_BUTTON, self.onRunPreview,
self.top_window.opt_btn_prev)
def __init__(self,
parent,
label_style='bold',
content_style='normal',
*args,
**kwargs):
dlg_style = wx.CAPTION | wx.CLOSE_BOX | wx.RESIZE_BORDER | wx.STAY_ON_TOP
IOTABaseDialog.__init__(self,
parent,
style=dlg_style,
label_style=label_style,
content_style=content_style,
size=(400, 400),
title='Recover Completed Run',
*args,
**kwargs)
self.pathlist = wx.ListCtrl(self,
style=wx.LC_REPORT | wx.LC_SINGLE_SEL)
self.selected = None
self.recovery_mode = 0
self.pathlist.InsertColumn(0, "")
self.pathlist.InsertColumn(1, "Status")
self.pathlist.InsertColumn(2, "Path")
bmps = wx.ImageList(width=16, height=16)
finished_bmp = bitmaps.fetch_icon_bitmap('actions',
'button_ok',
size=16)
aborted_bmp = bitmaps.fetch_icon_bitmap('actions', 'cancel', size=16)
unknown_bmp = bitmaps.fetch_icon_bitmap('actions',
'status_unknown',
size=16)
bmps.Add(finished_bmp)
bmps.Add(aborted_bmp)
bmps.Add(unknown_bmp)
self.pathlist.AssignImageList(bmps, which=1)
self.envelope.Add(self.pathlist, 1, flag=wx.EXPAND | wx.ALL, border=10)
# Dialog control
self.dlg_ctr = ct.DialogButtonsCtrl(
self,
preset='OK_CANCEL',
choices=['everything', 'settings only'],
choice_label='Recover: ')
self.envelope.Add(self.dlg_ctr,
flag=wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL,
border=10)
self.Bind(wx.EVT_BUTTON, self.onOK, id=wx.ID_OK)
self.Bind(wx.EVT_BUTTON, self.onCancel, self.dlg_ctr.btn_cancel)
self.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self.onItemActivated, id=-1)
self.place_and_size(set_by='parent', set_size='dialog')
def show_buttons(self):
if hasattr(self, 'abortb'):
self.abortb.Hide()
self.logb = metallicbutton.MetallicButton(self, -1, 'View Log', '', bitmaps.fetch_icon_bitmap("mimetypes", "log"), size=(105, 34))
self.cootb = metallicbutton.MetallicButton(self, -1, 'View In Coot', '', bitmaps.fetch_icon_bitmap("custom", "coot"), size=(105, 34))
self.Bind(wx.EVT_BUTTON, self.view_log, self.logb)
self.Bind(wx.EVT_BUTTON, self.load_coot, self.cootb)
self.button_sizer.Add(self.logb, 0, wx.EXPAND|wx.ALL, 2)
self.button_sizer.Add(self.cootb, 0, wx.EXPAND|wx.ALL, 2)
self.Fit()
def __init__(self,
parent,
label_style='bold',
content_style='normal',
*args,
**kwargs):
dlg_style = wx.CAPTION | wx.CLOSE_BOX | wx.RESIZE_BORDER | wx.STAY_ON_TOP
BaseDialog.__init__(self,
parent,
style=dlg_style,
label_style=label_style,
content_style=content_style,
size=(400, 400),
title='Recover Completed Run',
*args,
**kwargs)
self.pathlist = wx.ListCtrl(self,
style=wx.LC_REPORT | wx.LC_SINGLE_SEL)
self.selected = None
self.pathlist.InsertColumn(0, "")
self.pathlist.InsertColumn(1, "Status")
self.pathlist.InsertColumn(2, "Path")
bmps = wx.ImageList(width=16, height=16)
finished_bmp = bitmaps.fetch_icon_bitmap('actions',
'button_ok',
size=16)
aborted_bmp = bitmaps.fetch_icon_bitmap('actions', 'cancel', size=16)
unknown_bmp = bitmaps.fetch_icon_bitmap('actions',
'status_unknown',
size=16)
bmps.Add(finished_bmp)
bmps.Add(aborted_bmp)
bmps.Add(unknown_bmp)
self.pathlist.AssignImageList(bmps, which=1)
self.main_sizer.Add(self.pathlist,
1,
flag=wx.EXPAND | wx.ALL,
border=10)
# Dialog control
self.main_sizer.Add(self.CreateSeparatedButtonSizer(wx.OK | wx.CANCEL),
flag=wx.EXPAND | wx.ALIGN_RIGHT | wx.ALL,
border=10)
self.Bind(wx.EVT_BUTTON, self.onOK, id=wx.ID_OK)
def __init__(self, parent,
label='', label_size=(100, -1),
label_style='normal',
buttons=False, value=''):
CtrlBase.__init__(self, parent=parent, label_style=label_style)
self.value=value
output_box = wx.FlexGridSizer(1, 4, 0, 10)
self.txt = wx.StaticText(self, label=label, size=label_size)
self.txt.SetFont(self.font)
output_box.Add(self.txt)
self.ctr = wx.TextCtrl(self)
self.ctr.SetValue(self.value)
output_box.Add(self.ctr, flag=wx.EXPAND)
self.btn_browse = wx.Button(self, label='Browse...')
viewmag_bmp = bitmaps.fetch_icon_bitmap('actions', 'viewmag', size=16)
self.btn_mag = wx.BitmapButton(self, bitmap=viewmag_bmp)
output_box.Add(self.btn_browse, flag=wx.RESERVE_SPACE_EVEN_IF_HIDDEN)
output_box.Add(self.btn_mag, flag=wx.RESERVE_SPACE_EVEN_IF_HIDDEN)
if not buttons:
self.btn_browse.Hide()
self.btn_mag.Hide()
output_box.AddGrowableCol(1, 1)
self.SetSizer(output_box)
def add_tool(self, id=wx.ID_ANY, label=None, bitmap=None,
kind=wx.ITEM_NORMAL, shortHelp=None, longHelp=None):
if type(bitmap) in (tuple, list):
if len(bitmap) == 3:
bsz = bitmap[2]
bsc = (bitmap[2], bitmap[2])
else:
bsz = bsc = None
if bitmap[0] == 'custom':
bmp = bitmaps.fetch_custom_icon_bitmap(bitmap[1], size=bsz)
else:
bmp = bitmaps.fetch_icon_bitmap(bitmap[0], bitmap[1], scale=bsc)
else:
bmp = bitmap
short_string = shortHelp if shortHelp else ''
long_string = longHelp if longHelp else ''
if wx4:
return self.toolbar.AddTool(toolId=id,
label=label,
kind=kind,
bitmap=bmp,
shortHelp=short_string)
else:
return self.toolbar.AddLabelTool(id=id,
label=label,
kind=kind,
bitmap=bmp,
shortHelp=short_string,
longHelp=long_string)
def add_item(self, path):
# Generate item
inp_choices, inp_sel = self.set_type_choices(path)
type_choice = ct.DataTypeChoice(self.ctr, choices=inp_choices)
item = ct.InputListItem(path=path,
type=type_choice,
buttons=ct.MiniButtonBoxInput(self.ctr))
self.Bind(wx.EVT_CHOICE, self.onTypeChoice, item.type.type)
item.buttons.btn_mag.Bind(wx.EVT_BUTTON, self.onMagButton)
item.buttons.btn_delete.Bind(wx.EVT_BUTTON, self.onDelButton)
item.buttons.btn_info.Bind(wx.EVT_BUTTON, self.onInfoButton)
# Insert list item
idx = self.ctr.InsertStringItem(self.ctr.GetItemCount() + 1, item.path)
self.ctr.SetItemWindow(idx, 1, item.type, expand=True)
self.ctr.SetItemWindow(idx, 2, item.buttons, expand=True)
# Set drop-down selection, check it for data and open other tabs
item.type.type.SetSelection(inp_sel)
if item.type.type.GetString(inp_sel) in [
'processed pickle', 'processed pickle list',
'processed pickle folder'
]:
self.main_window.toolbar.EnableTool(
self.main_window.tb_btn_run.GetId(), True)
elif item.type.type.GetString(inp_sel) == 'reference MTZ':
self.input_window.opt_chk_useref.Enable()
elif item.type.type.GetString(inp_sel) == 'sequence':
pass
else:
warn_bmp = bitmaps.fetch_icon_bitmap('actions',
'status_unknown',
size=16)
item.buttons.btn_info.SetBitmapLabel(warn_bmp)
item.warning = True
# Record index in all relevant places
item.id = idx
item.buttons.index = idx
item.type.index = idx
item.type_selection = inp_sel
# Resize columns to fit content
col1_width = max([
self.ctr.GetItemWindow(s, col=1).type.GetSize()[0]
for s in range(self.ctr.GetItemCount())
]) + 5
col2_width = item.buttons.GetSize()[0] + 15
col0_width = self.ctr.GetSize()[0] - col1_width - col2_width
self.ctr.SetColumnWidth(0, col0_width)
self.ctr.SetColumnWidth(1, col1_width)
self.ctr.SetColumnWidth(2, col2_width)
# Make sure all the choice lists are the same size
if item.type.type.GetSize()[0] < col1_width - 5:
item.type.type.SetSize((col1_width - 5, -1))
# Attach data object to item
self.ctr.SetItemData(item.id, item)
def start_refinement(self, type, root, title, res, resl, cycles, ins, hkl, id, options):
self.abortb = metallicbutton.MetallicButton(self, -1, 'Abort', '', bitmaps.fetch_icon_bitmap("actions", "stop"), size=(105, 34))
self.Bind(wx.EVT_BUTTON, self.abort, self.abortb)
self.button_sizer.Add(self.abortb, 0, wx.EXPAND|wx.ALL, 2)
self.Fit()
self._refinement = Refinement(self, type, root, title, res, resl, cycles, ins, hkl, id, options)
self._refinement.set_callbacks(self._refinement_started, self._refinement_running, self._refinement_cycle, self._refinement_finished, self._error_dialog)
def setup_toolbar(self):
btn = self.toolbar.AddTool(
toolId=-1,
label="Load file",
bitmap=icons.hkl_file.GetBitmap(),
shortHelp="Load file",
kind=wx.ITEM_NORMAL,
)
self.Bind(wx.EVT_MENU, self.OnLoadFile, btn)
btn = self.toolbar.AddTool(
toolId=-1,
label="Settings",
bitmap=icons.advancedsettings.GetBitmap(),
shortHelp="Settings",
kind=wx.ITEM_NORMAL,
)
self.Bind(wx.EVT_MENU, self.OnShowSettings, btn)
btn = self.toolbar.AddTool(
toolId=-1,
label="Zoom",
bitmap=icons.search.GetBitmap(),
shortHelp="Zoom",
kind=wx.ITEM_NORMAL,
)
self.Bind(wx.EVT_MENU, self.OnZoom, btn)
txt = wx.StaticText(self.toolbar, -1, "Image:")
self.toolbar.AddControl(txt)
self.image_chooser = wx.Choice(self.toolbar, -1, size=(300, -1))
self.toolbar.AddControl(self.image_chooser)
self.Bind(wx.EVT_CHOICE, self.OnChooseImage, self.image_chooser)
btn = self.toolbar.AddTool(
toolId=wx.ID_BACKWARD,
label="Previous",
bitmap=bitmaps.fetch_icon_bitmap("actions", "1leftarrow"),
shortHelp="Previous",
kind=wx.ITEM_NORMAL,
)
self.Bind(wx.EVT_MENU, self.OnPrevious, btn)
btn = self.toolbar.AddTool(
toolId=wx.ID_FORWARD,
label="Next",
bitmap=bitmaps.fetch_icon_bitmap("actions", "1rightarrow"),
shortHelp="Next",
kind=wx.ITEM_NORMAL,
)
self.Bind(wx.EVT_MENU, self.OnNext, btn)
def __init__(self, nb):
Tab.__init__(self, nb)
self.job_list = wx.ListCtrl(self, -1, style=wx.LC_REPORT|wx.LC_SINGLE_SEL, size=(700, 400))
self.job_list.Bind(wx.EVT_LIST_ITEM_ACTIVATED, self._load_job)
titles = ['ID', 'Date', 'Title', 'Type', 'Status', 'R']
sizes = [65,135,225,130,80,60]
for i,t in enumerate(titles):
self.job_list.InsertColumn(i, t, width=sizes[i])
new = metallicbutton.MetallicButton(self, -1, 'New', '', bitmaps.fetch_icon_bitmap("actions", "window_new"), size=(120,40))
load = metallicbutton.MetallicButton(self, -1, 'Load', '', bitmaps.fetch_icon_bitmap("actions", "fileopen"), size=(120,40))
delete = metallicbutton.MetallicButton(self, -1, 'Delete', '', bitmaps.fetch_icon_bitmap("actions", "fileclose"), size=(120,40))
sum = metallicbutton.MetallicButton(self, -1, 'Summary', '', bitmaps.fetch_icon_bitmap("actions", "info"), size=(120,40))
self.Bind(wx.EVT_BUTTON, self._new_job, new)
self.Bind(wx.EVT_BUTTON, self._load_job, load)
self.Bind(wx.EVT_BUTTON, self._delete_job, delete)
self.Bind(wx.EVT_BUTTON, self._show_summary, sum)
import_cif = metallicbutton.MetallicButton(self, -1, 'Import HKL', '', icons.hkl_file.GetBitmap(), size=(120,40))
import_pdb = metallicbutton.MetallicButton(self, -1, 'Import PDB', '', icons.pdb_file.GetBitmap(), size=(120,40))
rcsb_dl = metallicbutton.MetallicButton(self, -1, 'RCSB PDB', '', bitmaps.fetch_icon_bitmap("actions", "down"), size=(120,40))
self.Bind(wx.EVT_BUTTON, self._import_pbd, import_pdb)
self.Bind(wx.EVT_BUTTON, self._import_cif, import_cif)
self.Bind(wx.EVT_BUTTON, self._download_files, rcsb_dl)
self.sidebar = wx.BoxSizer(wx.VERTICAL)
self.sidebar.Add(new, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(load, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(sum, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(delete, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.AddSpacer(20)
self.sidebar.Add(import_cif, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.Add(import_pdb, 0, wx.EXPAND | wx.ALL, 5)
self.sidebar.AddSpacer(10)
self.sidebar.Add(rcsb_dl, 0, wx.EXPAND | wx.ALL, 5)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.job_list, 0, wx.EXPAND|wx.ALL, 5)
self.main.Add(self.sidebar, 0, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.main)
def setup_toolbar(self):
XFBaseClass.setup_toolbar(self)
btn = self.toolbar.AddLabelTool(id=wx.ID_SAVEAS,
label="Save As...",
bitmap=bitmaps.fetch_icon_bitmap("actions","save_all", 32),
shortHelp="Save As...",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnSaveAs, btn)
def add_item(self, path):
# Generate item
inputs, inp_choices, inp_sel = self.set_type_choices(path)
type_choice = ct.DataTypeChoice(self.ctr, choices=inp_choices)
item = ct.InputListItem(path=path,
type=type_choice,
buttons=ct.MiniButtonBoxInput(self.ctr))
self.Bind(wx.EVT_CHOICE, self.onTypeChoice, item.type.type)
# item.buttons.btn_mag.Bind(wx.EVT_BUTTON, self.onMagButton)
# item.buttons.btn_delete.Bind(wx.EVT_BUTTON, self.onDelButton)
# item.buttons.btn_info.Bind(wx.EVT_BUTTON, self.onInfoButton)
self.Bind(wx.EVT_BUTTON, self.onMagButton, item.buttons.btn_mag)
self.Bind(wx.EVT_BUTTON, self.onDelButton, item.buttons.btn_delete)
self.Bind(wx.EVT_BUTTON, self.onInfoButton, item.buttons.btn_info)
# Insert list item
idx = self.ctr.InsertStringItem(self.ctr.GetItemCount() + 1, item.path)
self.ctr.SetItemWindow(idx, 1, item.type, expand=True)
self.ctr.SetItemWindow(idx, 2, item.buttons, expand=True)
# Set drop-down selection, check it for data and open other tabs
item.type.type.SetSelection(inp_sel)
if item.type.type.GetString(inp_sel) in ('coordinates',
'structure factors',
'background',
'raw image file'):
if "image" in item.type.type.GetString(inp_sel):
view_bmp = bitmaps.fetch_custom_icon_bitmap('image_viewer16')
item.buttons.btn_mag.SetBitmapLabel(view_bmp)
else:
warn_bmp = bitmaps.fetch_icon_bitmap('actions',
'status_unknown',
size=16)
item.buttons.btn_info.SetBitmapLabel(warn_bmp)
item.warning = True
# Record index in all relevant places
item.id = idx
item.buttons.index = idx
item.type.index = idx
item.type_selection = inp_sel
# Resize columns to fit content
self.ctr.SetColumnWidth(1, width=-1)
self.ctr.SetColumnWidth(2, width=-1)
self.ctr.SetColumnWidth(0, width=-3)
# Make sure all the choice lists are the same size
if item.type.type.GetSize()[0] < self.ctr.GetColumnWidth(2) - 5:
item.type.type.SetSize((self.ctr.GetColumnWidth(2) - 5, -1))
# Attach data object to item
self.ctr.SetItemData(item.id, item)
self.Layout()
def setup_toolbar(self):
tb_buttons = [
("Show/hide controls",
bitmaps.fetch_icon_bitmap("apps", "advancedsettings"),
self.OnToggleControls),
("Save",
bitmaps.fetch_icon_bitmap("actions", "save_all"),
self.OnSave),
#("Print",
# bitmaps.fetch_icon_bitmap("devices", "printer1"),
# self.OnPrint),
]
tb = wx.ToolBar(self, style=wx.TB_3DBUTTONS|wx.TB_TEXT)
tb.SetToolBitmapSize((32,32))
self.SetToolBar(tb)
for (name, bitmap, function) in tb_buttons :
tool_button = tb.AddLabelTool(-1, name, bitmap, kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, function, tool_button)
self.toolbar = tb
def __init__(self, parent):
wx.Panel.__init__(self, parent=parent, id=wx.ID_ANY)
self.index = None
self.btn_box = wx.BoxSizer(wx.HORIZONTAL)
view_bmp = bitmaps.fetch_custom_icon_bitmap('image_viewer16')
self.btn_viewer = btn.GenBitmapButton(self, bitmap=view_bmp)
viewmag_bmp = bitmaps.fetch_icon_bitmap('actions', 'viewmag', size=16)
self.btn_mag = btn.GenBitmapButton(self, bitmap=viewmag_bmp)
star_on_bmp = bitmaps.fetch_icon_bitmap('actions', 'bookmark_gold',
size=16)
star_off_bmp = bitmaps.fetch_icon_bitmap('actions', 'bookmark_silver',
size=16)
self.btn_flag = btn.GenBitmapToggleButton(self, bitmap=star_off_bmp)
self.btn_flag.SetBitmapSelected(star_on_bmp)
self.btn_box.Add(self.btn_mag)
self.btn_box.Add(self.btn_viewer, flag=wx.LEFT, border=5)
self.btn_box.Add(self.btn_flag, flag=wx.LEFT, border=5)
self.SetSizer(self.btn_box)
self.SetBackgroundColour('white')
self.Fit()
def setup_toolbar (self) :
btn = self.toolbar.AddLabelTool(id=-1,
label="Load file",
bitmap=icons.hkl_file.GetBitmap(),
shortHelp="Load file",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnLoadFile, btn)
btn = self.toolbar.AddLabelTool(id=-1,
label="Settings",
bitmap=icons.advancedsettings.GetBitmap(),
shortHelp="Settings",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnShowSettings, btn)
btn = self.toolbar.AddLabelTool(id=-1,
label="Zoom",
bitmap=icons.search.GetBitmap(),
shortHelp="Zoom",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnZoom, btn)
txt = wx.StaticText(self.toolbar, -1, "Image:")
self.toolbar.AddControl(txt)
self.image_chooser = wx.Choice(self.toolbar, -1, size=(300,-1))
self.toolbar.AddControl(self.image_chooser)
self.Bind(wx.EVT_CHOICE, self.OnChooseImage, self.image_chooser)
btn = self.toolbar.AddLabelTool(id=wx.ID_BACKWARD,
label="Previous",
bitmap=bitmaps.fetch_icon_bitmap("actions","1leftarrow"),
shortHelp="Previous",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnPrevious, btn)
btn = self.toolbar.AddLabelTool(id=wx.ID_FORWARD,
label="Next",
bitmap=bitmaps.fetch_icon_bitmap("actions","1rightarrow"),
shortHelp="Next",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnNext, btn)
def SetupToolbar (self) :
self.toolbar = self.CreateToolBar(style=wx.TB_3DBUTTONS|wx.TB_TEXT)
self.toolbar.SetToolBitmapSize((32,32))
btn = self.toolbar.AddLabelTool(id=-1,
label="Load file",
bitmap=icons.hkl_file.GetBitmap(),
shortHelp="Load file",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnLoadFile, btn)
btn = self.toolbar.AddLabelTool(id=-1,
label="Save image",
bitmap=icons.save_all.GetBitmap(),
shortHelp="Save image",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnSave, btn)
btn = self.toolbar.AddLabelTool(id=-1,
label="Delete reflection",
bitmap=bitmaps.fetch_icon_bitmap("actions","editdelete"), # FIXME
shortHelp="Delete reflection",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnDeleteReflection, btn)
def SetupToolbar (self) :
self.toolbar = self.CreateToolBar(style=wx.TB_3DBUTTONS|wx.TB_TEXT)
self.toolbar.SetToolBitmapSize((32,32))
btn = self.toolbar.AddLabelTool(id=-1,
label="Load file",
bitmap=icons.hkl_file.GetBitmap(),
shortHelp="Load file",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnLoadFile, btn)
btn = self.toolbar.AddLabelTool(id=-1,
label="Save image",
bitmap=icons.save_all.GetBitmap(),
shortHelp="Save image",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnSave, btn)
btn = self.toolbar.AddLabelTool(id=-1,
label="Delete reflection",
bitmap=bitmaps.fetch_icon_bitmap("actions","editdelete"), # FIXME
shortHelp="Delete reflection",
kind=wx.ITEM_NORMAL)
self.Bind(wx.EVT_MENU, self.OnDeleteReflection, btn)
def __init__(self, pdb_file='/Users/vxn01537/Dropbox/Proton8/test/3HLX.pdb', name='', *args, **kwargs):
wx.Frame.__init__(self,None,-1,'Ligand Explorer: ' + name, size=(800,700))
if os.path.exists(pdb_file):
p = pdb.input(pdb_file)
else:
self.Destroy()
cols = {'C': 'black', 'O': 'red', 'N': 'blue', 'S': 'green', 'H': 'white'}
self._refresh = False
self._labs = []
self._alabs = []
self._ligands = {}
for a in p.atoms_with_labels():
if a.resname not in ['ARG', 'HIS', 'LYS', 'ASP', 'GLU', 'SER', 'THR',
'ASN', 'GLN', 'CYS', 'GLY', 'PRO', 'ALA', 'ILE',
'LEU', 'MET', 'PHE', 'TRP', 'TYR', 'VAL', 'HOH', 'DOD']:
key = '%s %s-%s' % (a.chain_id, a.resname, a.resid().strip())
if not key in self._ligands:
self._ligands[key] = {'at': [], 'id': a.resid().strip()}
self._ligands[key]['at'].append(a)
to_del = []
for k,l in self._ligands.iteritems():
l['c'] = np.array([ a.xyz for a in l['at']])
l['col'] = np.array([ cols.get(a.element.strip() if a.element.strip() else a.name.strip()[0], 'black') for a in l['at']])
if len(l['at']) < 3:
to_del.append(k)
l['rex'] = {}
l['stdevs'] = {}
for a in l['at']:
an = a.name.strip()
for b in l['at']:
bn = b.name.strip()
if a is not b:
if a.distance(b) < 1.8:
l['rex'][an+'-'+bn] = [re.compile(an+'_'+l['id']+' '+bn+'_'+l['id']+' (\d+\.?\d+)\((\d+)\)'),
re.compile(bn+'_'+l['id']+' '+an+'_'+l['id']+' (\d+\.?\d+)\((\d+)\)')]
for d in to_del:
del self._ligands[d]
if 'stdevs' in kwargs:
if os.path.exists(kwargs['stdevs']):
stdevs = open(kwargs['stdevs'])
start = False
for l in stdevs:
if '_geom_bond_atom_site_label_1' in l:
start = True
if '_geom_angle_atom_site_label_1' in l:
break
if start:
for k,lig in self._ligands.iteritems():
for id,rs in lig['rex'].iteritems():
for r in rs:
m = r.match(l)
if m:
d = pow(10, len((m.group(1).split('.'))[1]))
lig['stdevs'][id] = float(m.group(2))/d
stdevs.close()
self.toolbar = wx.ToolBar(self, style=wx.TB_3DBUTTONS|wx.TB_TEXT)
self.res_type = wx.ComboBox(self.toolbar, -1, choices=sorted(self._ligands.keys()), style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._load_residue)
close = self.toolbar.AddLabelTool(wx.ID_ANY, 'Close', bitmaps.fetch_icon_bitmap("actions", "no"))
self.toolbar.AddSeparator()
self.toolbar.AddControl(self.res_type)
self.toolbar.AddSeparator()
save = self.toolbar.AddLabelTool(wx.ID_ANY, 'Save Figure', bitmaps.fetch_icon_bitmap("actions", "save_all"))
self.Bind(wx.EVT_TOOL, self._close, close)
self.Bind(wx.EVT_TOOL, self._save_figure, save)
self.SetToolBar(self.toolbar)
self.toolbar.Realize()
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.viewer = LigandViewer(self)
self.sizer.Add(self.viewer, 1, wx.EXPAND)
self.SetSizer(self.sizer)
#self.Fit()
self._load_residue('')
def __init__(self, *args, **kwds):
from wxtbx import bitmaps
super(ScoreSettingsPanel, self).__init__(*args, **kwds)
# Needed for communication with the root frame.
self._root_frame = self.GetParent().GetParent()
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
self._id_text = wx.NewId()
text = wx.StaticText(self, id=self._id_text, label="")
sizer.Add(text, flag=wx.ALIGN_CENTER)
# The score buttons. XXX Would really like this to be stars or
# some such. Could then zap the static text above.
box = wx.BoxSizer(wx.HORIZONTAL)
self._id_buttons = []
self._id_accel = []
accelerators = []
for idx, i in enumerate(choices):
btn = wx.Button(self, label=i)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnScore, btn)
self._id_buttons.append(btn.GetId())
randomId = wx.NewId()
self._id_accel.append(randomId)
self.Bind(wx.EVT_MENU, self.OnKeyCombo, id=randomId)
accelerators.append(
(wx.ACCEL_NORMAL, ord(shortcuts[idx]), randomId))
sizer.Add(box)
accel_tbl = wx.AcceleratorTable(accelerators)
self.SetAcceleratorTable(accel_tbl)
# XXX Would like to have label and short help for the buttons.
# Buttons in wxWidgets version 2.9.1 and later support text and
# bitmap, see SetBitmap, SetBitmapLabel, SetBitmapDisabled, etc.
box = wx.BoxSizer(wx.HORIZONTAL)
self._id_previous = wx.NewId()
btn = wx.BitmapButton(self,
id=self._id_previous,
bitmap=bitmaps.fetch_icon_bitmap(
'actions', '1leftarrow'),
style=wx.BORDER_NONE)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnPrevious, btn)
btn = wx.Button(self, label="Save scores")
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnSave, btn)
self._id_next = wx.NewId()
btn = wx.BitmapButton(self,
id=self._id_next,
bitmap=bitmaps.fetch_icon_bitmap(
'actions', '1rightarrow'),
style=wx.BORDER_NONE)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnNext, btn)
sizer.Add(box, flag=wx.ALIGN_CENTER)
# Register update events for the dynamic widgets.
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateNext, id=self._id_next)
self.Bind(wx.EVT_UPDATE_UI,
self.OnUpdatePrevious,
id=self._id_previous)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateText, id=self._id_text)
for i in xrange(self._root_frame.image_chooser.GetCount()):
_scores[self._root_frame.get_key(
self._root_frame.image_chooser.GetClientData(i))] = None
def __init__(self, parent, id, title, inputs, refls, in_files, ref_files, selected_refls=None, selected_struct=None, resh=None):
wx.Dialog.__init__(self, parent, id, title)
self._in_files = in_files
self._ref_files = ref_files
self._residue_list = []
if not selected_refls in refls:
selected_refls = None
if not selected_struct in inputs:
selected_struct = None
self.input_sizer = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
self.input_sizer.Add(wx.StaticText(self, -1, 'Title'))
self._title = wx.TextCtrl(self, -1, '', (30, 200))
self.input_sizer.Add(self._title, 0, wx.EXPAND)
self.input_sizer.Add(wx.StaticText(self, -1, 'Reflections'))
self._reflections = wx.ComboBox(self, -1, choices=refls, style=wx.CB_READONLY)
self._reflections.Bind(wx.EVT_COMBOBOX, self._set_res)
self._view_refs = metallicbutton.MetallicButton(self, 0, '', '', bitmaps.fetch_icon_bitmap('actions', 'viewmag', scale=(16,16)), size=(22, 20))
self.Bind(wx.EVT_BUTTON, self._view_file, self._view_refs)
self._refs_sizer = wx.BoxSizer(wx.HORIZONTAL)
self._refs_sizer.Add(self._view_refs, 0, wx.EXPAND|wx.RIGHT, 5)
self._refs_sizer.Add(self._reflections, 1, wx.EXPAND)
self.input_sizer.Add(self._refs_sizer, 0, wx.EXPAND)
self.input_sizer.Add(wx.StaticText(self, -1, 'Structure'))
self._structure = wx.ComboBox(self, -1, choices=inputs, style=wx.CB_READONLY)
self._structure.Bind(wx.EVT_COMBOBOX, self._set_res)
self._view_struct = metallicbutton.MetallicButton(self, 1, '', '', bitmaps.fetch_icon_bitmap('actions', 'viewmag', scale=(16,16)), size=(22, 20))
self.Bind(wx.EVT_BUTTON, self._view_file, self._view_struct)
self._struct_sizer = wx.BoxSizer(wx.HORIZONTAL)
self._struct_sizer.Add(self._view_struct, 0, wx.EXPAND|wx.RIGHT, 5)
self._struct_sizer.Add(self._structure, 1, wx.EXPAND)
self.input_sizer.Add(self._struct_sizer, 0, wx.EXPAND)
self.input_sizer.Add(wx.StaticText(self, -1, 'Type'))
self._refinement_type = wx.ComboBox(self, -1, REFINEMENT_TYPES[0], choices=REFINEMENT_TYPES, style=wx.CB_READONLY)
self._refinement_type.Bind(wx.EVT_COMBOBOX, self._set_type)
self.input_sizer.Add(self._refinement_type, 0, wx.EXPAND)
self.input_sizer.Add(wx.StaticText(self, -1, 'Target'))
self._target = wx.ComboBox(self, -1, REFINEMENT_TARGETS[0], choices=REFINEMENT_TARGETS, style=wx.CB_READONLY)
self._target.Bind(wx.EVT_COMBOBOX, self._set_target)
self.input_sizer.Add(self._target, 0, wx.EXPAND)
self.input_sizer.Add(wx.StaticText(self, -1, 'Cycles'))
self._cycles = wx.SpinCtrl(self, -1, value='10')
self.input_sizer.Add(self._cycles, 0)
self.input_sizer.Add(wx.StaticText(self, -1, 'Resolution'))
self._res_sizer = wx.BoxSizer(wx.HORIZONTAL)
self._res_high = wx.TextCtrl(self, -1, '')
self._res_low = wx.TextCtrl(self, -1, '')
self._res_sizer.Add(self._res_high)
self._res_sizer.Add(self._res_low)
self.input_sizer.Add(self._res_sizer, 0)
self.input_sizer.Add(wx.StaticText(self, -1, 'Options'))
self._opt_sizer = wx.BoxSizer(wx.VERTICAL)
self._auto = wx.CheckBox(self, -1, 'Auto Refinement', (10, 10))
self._opt_sizer.Add(self._auto)
self._auto.Bind(wx.EVT_CHECKBOX, self._set_auto)
self._hydrogens = wx.CheckBox(self, -1, 'Add Hydrogens', (10, 10))
self._opt_sizer.Add(self._hydrogens)
self._anis = wx.CheckBox(self, -1, 'Anisotropic', (10, 10))
self._opt_sizer.Add(self._anis)
self._bloc = wx.CheckBox(self, -1, 'BLOC Refinement', (10, 10))
self._opt_sizer.Add(self._bloc)
self._rfree = wx.CheckBox(self, -1, 'Include Rfree Set', (10, 10))
self._opt_sizer.Add(self._rfree, 0)
self.input_sizer.Add(self._opt_sizer, 0, wx.EXPAND)
self._residues_title = wx.StaticText(self, -1, 'Unrestrained Residues')
self._residues_title.Wrap(100)
self.input_sizer.Add(self._residues_title)
self._residues = wx.ListBox(self, 26, wx.DefaultPosition, (40, 100), [], wx.LB_MULTIPLE)
self.input_sizer.Add(self._residues, 0, wx.EXPAND)
self._ur_title = wx.StaticText(self, -1, 'Un-/Restrained Cycles')
self._ur_title.Wrap(100)
self._ur_cycles = wx.SpinCtrl(self, -1, value='5')
self.input_sizer.Add(self._ur_title, 0, wx.EXPAND)
self.input_sizer.Add(self._ur_cycles, 0)
self._total_title = wx.StaticText(self, -1, 'Total Cycles')
self._total_cycles = wx.SpinCtrl(self, -1, value='1')
self.input_sizer.Add(self._total_title, 0, wx.EXPAND)
self.input_sizer.Add(self._total_cycles, 0)
self._custom_file = FileBrowser(self, 'Text File (*.txt)|*.txt', 'Select a text file containing custom shelx commands')
self._custom_text = wx.TextCtrl(self, -1, '', style=wx.TE_MULTILINE, size=(-1, 100))
self.input_sizer.Add(wx.StaticText(self, -1, 'Custom Commands'), 0, wx.EXPAND)
self.custom_sizer = wx.BoxSizer(wx.VERTICAL)
self.custom_sizer.Add(self._custom_file.sizer(), 0, wx.EXPAND)
self.custom_sizer.Add(self._custom_text, 0, wx.EXPAND)
self.input_sizer.Add(self.custom_sizer, 0, wx.EXPAND)
self._button_sizer = wx.BoxSizer(wx.HORIZONTAL)
self._startb = wx.Button(self, 0, 'Start')
self._startb.Bind(wx.EVT_BUTTON, self._start)
self._button_sizer.Add(self._startb, 1, wx.EXPAND|wx.ALL, 5)
self._cancel = wx.Button(self, 1, 'Cancel')
self._cancel.Bind(wx.EVT_BUTTON, self._close)
self._button_sizer.Add(self._cancel, 1, wx.EXPAND|wx.ALL, 5)
self.input_sizer.Add((10,10))
self.input_sizer.Add(self._button_sizer, 0, wx.EXPAND)
self.main_sizer = wx.BoxSizer(wx.VERTICAL)
self.main_sizer.Add(self.input_sizer, 0, wx.EXPAND|wx.ALL, 5)
#self.main_sizer.Add(self._button_sizer, 0, wx.EXPAND|wx.CENTER, 10)
self.SetSizer(self.main_sizer)
for c in [self._residues, self._residues_title, self._rfree, self._bloc, self._ur_title, self._ur_cycles, self._total_title, self._total_cycles]:
c.Hide()
self.Fit()
if selected_refls in refls or selected_struct in inputs:
if selected_refls in refls:
self._reflections.SetStringSelection(selected_refls)
if selected_struct in inputs:
self._structure.SetStringSelection(selected_struct)
else:
self._hydrogens.SetValue(0)
self._set_res('')
if resh is not None:
self._res_high.SetValue(str(resh))
def __init__(self, nb):
Tab.__init__(self, nb)
self._pdbt = PDBTools()
self._res_size = (200,170)
self._to_save = []
self.fig = Figure((5.0, 4.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.res = wx.StaticBitmap(self, size=self._res_size)
self.res.SetBitmap(wx.EmptyImage(self._res_size[0], self._res_size[1]).ConvertToBitmap())
self._rtypes = ['Aspartate', 'Glutamate', 'Histidine', 'Arginine']
self._rtypess = ['Asp', 'Glu', 'His', 'Arg']
self.ax1 = self.fig.add_subplot(111)
self.ax1.set_position([0.10,0.153,0.80,0.81])
#self.ax1.set_frame_on(False)
[i.set_linewidth(0.5) for i in self.ax1.spines.itervalues()]
self.ax2 = self.ax1.twinx()
self.ax2.set_position([0.10,0.153,0.80,0.81])
self.ax1.tick_params(labelsize=8)
self.ax2.tick_params(labelsize=8)
self._highlight = -2
self._bond_lengths = ''
self._std_devs = ''
self._residue_selection = []
self._chain_lookup = {}
self._residue_type = 0
self._residues = {'asp': {}, 'glu': {}, 'his': {}, 'arg': {}}
self._omitted = {'asp': [], 'glu': [], 'his': [], 'arg': []}
self.omitted_title = wx.StaticBox( self, -1, "Omitted" )
self.omitted_sizer = wx.StaticBoxSizer( self.omitted_title, wx.HORIZONTAL)
self.selected_title = wx.StaticBox( self, -1, "Displayed" )
self.selected_sizer = wx.StaticBoxSizer( self.selected_title, wx.HORIZONTAL)
self.residue_info_title = wx.StaticBox( self, -1, "Residue Info: " )
self.residue_info_sizer = wx.StaticBoxSizer( self.residue_info_title, wx.VERTICAL)
#self.residue_info = wx.FlexGridSizer(rows=0, cols=2, vgap=5, hgap=5)
#self.residue_info.Add(wx.StaticText(self, -1, 'D(C-O)'))
#self._dco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._dco)
#self.residue_info.Add(wx.StaticText(self, -1, 'S(D(C-O))'))
#self._sdco = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._sdco)
#self.residue_info.Add(wx.StaticText(self, -1, 'Level'))
#self._lev = wx.StaticText(self, -1, '')
#self.residue_info.Add(self._lev)
#self.residue_info_sizer.Add(self.residue_info, 0)
self.residue_info_sizer.Add(self.res, 0)
self.residue_sel = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_MULTIPLE)
self.residue_sel.Bind(wx.EVT_LISTBOX, self._update_sel)
self.omitted_res = wx.ListBox(self, 26, wx.DefaultPosition, (70, 80), [], wx.LB_SINGLE)
self.omitted_res.Bind(wx.EVT_LISTBOX, self._goto_omitted)
self.data_box = wx.BoxSizer(wx.HORIZONTAL)
self.data_box.Add(wx.StaticText(self, -1, 'Residue Type'), 0, wx.EXPAND|wx.ALL, 5)
self.res_type = wx.ComboBox(self, -1, choices=[], style=wx.CB_READONLY)
self.res_type.Bind(wx.EVT_COMBOBOX, self._set_residue_type)
self.data_box.Add(self.res_type, 0, wx.EXPAND|wx.ALL, 5)
self.omitted_sizer.Add(self.omitted_res, 1, wx.EXPAND|wx.ALL, 0)
self.selected_sizer.Add(self.residue_sel, 1, wx.EXPAND|wx.ALL, 0)
self.ressel_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.ressel_sizer.Add(self.omitted_sizer, 1, wx.EXPAND|wx.ALL, 5)
self.ressel_sizer.Add(self.selected_sizer, 1, wx.EXPAND|wx.ALL, 5)
lig = metallicbutton.MetallicButton(self, -1, 'Ligands', '', bitmaps.fetch_icon_bitmap('actions', 'viewmag', scale=(16,16)), size=(75, 25))
save = metallicbutton.MetallicButton(self, -1, 'Figure', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
tab = metallicbutton.MetallicButton(self, -1, 'Data', '', bitmaps.fetch_icon_bitmap('actions', 'save_all', scale=(16,16)), size=(65, 25))
self.Bind(wx.EVT_BUTTON, self._view_ligands, lig)
self.Bind(wx.EVT_BUTTON, self._save_figure, save)
self.Bind(wx.EVT_BUTTON, self._save_data, tab)
self.button_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.button_sizer.Add(save, 0, wx.LEFT, 5)
self.button_sizer.Add(tab, 0, wx.LEFT, 5)
self.button_sizer.Add(lig, 0, wx.LEFT, 5)
self.residue_box = wx.BoxSizer(wx.VERTICAL)
self.residue_box.Add(self.data_box, 0)
self.residue_box.Add(self.residue_info_sizer, 0, wx.EXPAND, 10)
self.residue_box.Add(self.ressel_sizer, 0)
self.residue_box.Add(self.button_sizer, 0)
self.main = wx.BoxSizer(wx.HORIZONTAL)
self.main.Add(self.residue_box, 1, wx.EXPAND|wx.ALL, 5)
self.averages = wx.StaticText(self, -1, '', style=wx.ALIGN_RIGHT|wx.ALIGN_CENTER_VERTICAL)
self.bottom_sizer = wx.BoxSizer(wx.HORIZONTAL)
#self.bottom_sizer.Add(self.button_sizer, 0)
self.bottom_sizer.Add(self.averages, 1, wx.EXPAND)
self.canvas_sizer = wx.BoxSizer(wx.VERTICAL)
self.canvas_sizer.Add(self.canvas, 1, wx.EXPAND|wx.ALL)
self.canvas_sizer.Add(self.bottom_sizer, 0, wx.EXPAND)
self.main.Add(self.canvas_sizer, 3, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.main)
self.main.Fit(self)
self.canvas.mpl_connect('button_press_event', self._on_click)
self.canvas.mpl_connect('pick_event', self._show_series)
btn2.AddSegment("Pan")
btn2.AddSegment("Zoom")
btn2.SetSelection(0)
frame.Bind(wx.EVT_RADIOBUTTON, OnRadio, btn2)
v_sizer.Add(wx.StaticText(panel, -1, "Radio buttons"), 0, wx.ALL, 5)
v_sizer.Add(btn2, 0, wx.ALL, 5)
btn3 = SegmentedToggleControl(panel)
btn3.AddSegment("Maps")
btn3.AddSegment("Models")
btn3.AddSegment("Selection")
btn3.Realize()
frame.Bind(wx.EVT_TOGGLEBUTTON, OnToggle, btn3)
v_sizer.Add(wx.StaticText(panel, -1, "Toggle buttons"), 0, wx.ALL, 5)
v_sizer.Add(btn3, 0, wx.ALL, 5)
if (bitmaps is not None) and (bitmaps.icon_lib is not None):
bmp1 = bitmaps.fetch_icon_bitmap("actions", "1leftarrow", 16)
bmp2 = bitmaps.fetch_icon_bitmap("actions", "gohome", 16)
bmp3 = bitmaps.fetch_icon_bitmap("actions", "viewmag", 16)
bmp4 = bitmaps.fetch_icon_bitmap("actions", "1rightarrow", 16)
btn4 = SegmentedButtonControl(panel)
btn4.AddSegment(bitmap=bmp1)
btn4.AddSegment(bitmap=bmp2)
btn4.AddSegment(bitmap=bmp3)
btn4.AddSegment(bitmap=bmp4)
v_sizer.Add(wx.StaticText(panel, -1, "Bitmap buttons"), 0, wx.ALL,
5)
v_sizer.Add(btn4, 0, wx.ALL, 5)
frame.Bind(wx.EVT_BUTTON, OnButton, btn4)
btn5 = SegmentedButtonControl(panel, style=SEGBTN_ROUNDED_CORNERS)
btn5.AddSegment(label="Back", bitmap=bmp1)
btn5.AddSegment(label="Home", bitmap=bmp2)
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, parent, id, title):
wx.Frame.__init__(self, parent, id, title, size=(800, 500))
# TODO: Allow GUI to be loaded with command line args, parse into PHIL
self.iota_phil = inp.master_phil
self.prefs_phil = None
self.target_phil = None
self.term_file = None
# Create some defaults on startup
# Figure out temp folder
self.gparams = self.iota_phil.extract()
tmp_folder = '/tmp/{}_{}'.format(user, pid)
self.gparams.advanced.temporary_output_folder = tmp_folder
self.iota_phil = self.iota_phil.format(python_object=self.gparams)
# Menu bar
menubar = wx.MenuBar()
# Status bar
self.sb = self.CreateStatusBar()
# Help menu item with the about dialog
m_help = wx.Menu()
m_file = wx.Menu()
self.mb_load_script = m_file.Append(wx.ID_OPEN, '&Load Script...')
self.mb_save_script = m_file.Append(wx.ID_SAVE, '&Save Script...')
m_file.AppendSeparator()
self.mb_reset = m_file.Append(wx.ID_ANY, '&Reset Settings')
self.mb_about = m_help.Append(wx.ID_ANY, '&About')
menubar.Append(m_file, '&File')
menubar.Append(m_help, '&Help')
self.SetMenuBar(menubar)
self.main_sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(self.main_sizer)
# 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 IOTA')
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 Preferences')
self.toolbar.AddSeparator()
load_bmp = bitmaps.fetch_icon_bitmap('actions', 'open')
self.tb_btn_load = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Load Script',
bitmap=load_bmp,
shortHelp='Load Script',
longHelp='Load IOTA Script')
save_bmp = bitmaps.fetch_icon_bitmap('actions', 'save')
self.tb_btn_save = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Save Script',
bitmap=save_bmp,
shortHelp='Save Script',
longHelp='Save IOTA Script')
reset_bmp = bitmaps.fetch_icon_bitmap('actions', 'reload')
self.tb_btn_reset = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Reset',
bitmap=reset_bmp,
shortHelp='Reset Settings',
longHelp='Reset IOTA settings with defaults')
self.toolbar.AddSeparator()
analyze_bmp = bitmaps.fetch_icon_bitmap('mimetypes',
'text-x-generic-2')
self.tb_btn_analysis = self.toolbar.AddLabelTool(
wx.ID_ANY,
label='Recover',
bitmap=analyze_bmp,
shortHelp='Recover',
longHelp='Recover run, show statistics and restart if aborted ')
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 all stages of refinement')
# Test buttons for test windows - comment out when not needed
# self.toolbar.AddSeparator()
test_bmp = bitmaps.fetch_icon_bitmap('actions', 'utilities')
self.tb_btn_test = self.toolbar.AddLabelTool(wx.ID_ANY,
label='Test',
bitmap=test_bmp)
self.Bind(wx.EVT_TOOL, self.onRun, self.tb_btn_test)
self.toolbar.RemoveTool(self.tb_btn_test.GetId())
# These buttons will be disabled until input path is provided
self.toolbar.EnableTool(self.tb_btn_run.GetId(), False)
self.toolbar.Realize()
# Instantiate windows
self.input_window = frm.InputWindow(self, phil=self.iota_phil)
# Single input window
self.main_sizer.Add(self.input_window,
1,
flag=wx.ALL | wx.EXPAND,
border=10)
self.main_sizer.Add((-1, 20))
# button bindings
self.Bind(wx.EVT_TOOL, self.onQuit, self.tb_btn_quit)
self.Bind(wx.EVT_TOOL, self.onPreferences, self.tb_btn_prefs)
self.Bind(wx.EVT_TOOL, self.onRun, self.tb_btn_run)
self.Bind(wx.EVT_TOOL, self.onRecovery, self.tb_btn_analysis)
self.Bind(wx.EVT_TOOL, self.onLoadScript, self.tb_btn_load)
self.Bind(wx.EVT_TOOL, self.onOutputScript, self.tb_btn_save)
self.Bind(wx.EVT_TOOL, self.onReset, self.tb_btn_reset)
# Menubar button bindings
self.Bind(wx.EVT_MENU, self.OnAboutBox, self.mb_about)
self.Bind(wx.EVT_MENU, self.onOutputScript, self.mb_save_script)
self.Bind(wx.EVT_MENU, self.onLoadScript, self.mb_load_script)
self.Bind(wx.EVT_MENU, self.onReset, self.mb_reset)
# Bindings to Input Window
self.Bind(wx.EVT_BUTTON, self.onImportOptions,
self.input_window.opt_btn_import)
self.Bind(wx.EVT_BUTTON, self.onProcessOptions,
self.input_window.opt_btn_process)
self.Bind(wx.EVT_BUTTON, self.onAnalysisOptions,
self.input_window.opt_btn_analysis)
# File list control bindings
self.Bind(ulc.EVT_LIST_INSERT_ITEM, self.onItemInserted,
self.input_window.input)
btn2.AddSegment("Pan")
btn2.AddSegment("Zoom")
btn2.SetSelection(0)
frame.Bind(wx.EVT_RADIOBUTTON, OnRadio, btn2)
v_sizer.Add(wx.StaticText(panel, -1, "Radio buttons"), 0, wx.ALL, 5)
v_sizer.Add(btn2, 0, wx.ALL, 5)
btn3 = SegmentedToggleControl(panel)
btn3.AddSegment("Maps")
btn3.AddSegment("Models")
btn3.AddSegment("Selection")
btn3.Realize()
frame.Bind(wx.EVT_TOGGLEBUTTON, OnToggle, btn3)
v_sizer.Add(wx.StaticText(panel, -1, "Toggle buttons"), 0, wx.ALL, 5)
v_sizer.Add(btn3, 0, wx.ALL, 5)
if (bitmaps is not None) and (bitmaps.icon_lib is not None):
bmp1 = bitmaps.fetch_icon_bitmap("actions", "1leftarrow", 16)
bmp2 = bitmaps.fetch_icon_bitmap("actions", "gohome", 16)
bmp3 = bitmaps.fetch_icon_bitmap("actions", "viewmag", 16)
bmp4 = bitmaps.fetch_icon_bitmap("actions", "1rightarrow", 16)
btn4 = SegmentedButtonControl(panel)
btn4.AddSegment(bitmap=bmp1)
btn4.AddSegment(bitmap=bmp2)
btn4.AddSegment(bitmap=bmp3)
btn4.AddSegment(bitmap=bmp4)
v_sizer.Add(wx.StaticText(panel, -1, "Bitmap buttons"), 0, wx.ALL, 5)
v_sizer.Add(btn4, 0, wx.ALL, 5)
frame.Bind(wx.EVT_BUTTON, OnButton, btn4)
btn5 = SegmentedButtonControl(panel, style=SEGBTN_ROUNDED_CORNERS)
btn5.AddSegment(label="Back", bitmap=bmp1)
btn5.AddSegment(label="Home", bitmap=bmp2)
btn5.AddSegment(label="Search", bitmap=bmp3)
def __init__(self, parent, pparams, info):
wx.Panel.__init__(self, parent)
from prime.postrefine.mod_plotter import Plotter
self.info = info
self.pparams = pparams
self.plot = Plotter(info=self.info,
anomalous_flag=self.pparams.target_anomalous_flag)
self.summary_sizer = wx.BoxSizer(wx.VERTICAL)
sfont = wx.Font(norm_font_size, wx.DEFAULT, wx.NORMAL, wx.NORMAL)
bfont = wx.Font(norm_font_size, wx.DEFAULT, wx.NORMAL, wx.BOLD)
self.SetFont(bfont)
# Run information
run_box = wx.StaticBox(self, label='Run Information')
run_box.SetFont(sfont)
run_box_sizer = wx.StaticBoxSizer(run_box, wx.VERTICAL)
run_box_grid = wx.FlexGridSizer(3, 2, 5, 20)
self.title_txt = wx.StaticText(self, label='')
self.title_txt.SetFont(sfont)
self.folder_txt = wx.StaticText(self, label='')
self.folder_txt.SetFont(sfont)
run_box_grid.AddMany([(wx.StaticText(self, label='Title')),
(self.title_txt, 1, wx.EXPAND),
(wx.StaticText(self, label='Directory')),
(self.folder_txt, 1, wx.EXPAND)])
run_box_grid.AddGrowableCol(1, 1)
run_box_sizer.Add(run_box_grid, flag=wx.EXPAND | wx.ALL, border=10)
self.summary_sizer.Add(run_box_sizer,
flag=wx.EXPAND | wx.ALL,
border=10)
# Table 1
tb1_box = wx.StaticBox(self, label='Merging Statistics')
tb1_box.SetFont(sfont)
tb1_box_sizer = wx.StaticBoxSizer(tb1_box, wx.HORIZONTAL)
self.tb1_labels, self.tb1_data = self.plot.table_one()
self.tb1 = ct.TableCtrl(self,
rlabels=self.tb1_labels,
contents=self.tb1_data,
label_style='bold')
# Buttons (placeholder for now)
btn_box_sizer = wx.BoxSizer(wx.VERTICAL)
line_bmp = bitmaps.fetch_custom_icon_bitmap('line_graph24')
self.btn_stats = ct.GradButton(self,
bmp=line_bmp,
label=' Statistical charts',
size=(250, -1))
txt_bmp = bitmaps.fetch_icon_bitmap('mimetypes', 'txt', scale=(24, 24))
self.btn_table1 = ct.GradButton(self,
bmp=txt_bmp,
label=' Output Table 1',
size=(250, -1))
btn_box_sizer.Add(self.btn_stats)
self.Bind(wx.EVT_BUTTON, self.onPlotStats, self.btn_stats)
btn_box_sizer.Add(self.btn_table1, flag=wx.TOP, border=5)
self.Bind(wx.EVT_BUTTON, self.onWriteTableOne, self.btn_table1)
tb1_box_sizer.Add(self.tb1, flag=wx.EXPAND | wx.ALL, border=10)
tb1_box_sizer.AddStretchSpacer()
tb1_box_sizer.Add(btn_box_sizer,
flag=wx.ALIGN_RIGHT | wx.ALL,
border=10)
self.summary_sizer.Add(tb1_box_sizer,
flag=wx.EXPAND | wx.ALL,
border=10)
self.SetSizer(self.summary_sizer)
def __init__(self, parent, id, title, phil=None, prefix='prime'):
wx.Frame.__init__(self, parent, id, title, size=(800, 500))
self.prime_filename = '{}.phil'.format(prefix)
# Toolbar
self.toolbar = self.CreateToolBar(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='Exit PRIME')
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='PRIME Preferences')
self.toolbar.AddSeparator()
load_bmp = bitmaps.fetch_icon_bitmap('actions', 'open')
self.tb_btn_load = self.toolbar.AddLabelTool(wx.ID_ANY,
label='Load Script',
bitmap=load_bmp,
shortHelp='Load Script',
longHelp='Load PRIME Script')
save_bmp = bitmaps.fetch_icon_bitmap('actions', 'save')
self.tb_btn_save = self.toolbar.AddLabelTool(wx.ID_ANY,
label='Save Script',
bitmap=save_bmp,
shortHelp='Save Script',
longHelp='Save PRIME Script')
reset_bmp = bitmaps.fetch_icon_bitmap('actions', 'reload')
self.tb_btn_reset = self.toolbar.AddLabelTool(wx.ID_ANY,
label='Reset',
bitmap=reset_bmp,
shortHelp='Reset Settings',
longHelp='Reset PRIME settings with defaults')
self.toolbar.AddSeparator()
analyze_bmp = bitmaps.fetch_icon_bitmap('mimetypes', 'text-x-generic-2')
self.tb_btn_analysis = self.toolbar.AddLabelTool(wx.ID_ANY, label='Recover',
bitmap=analyze_bmp,
shortHelp='Recover',
longHelp='Show past results')
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 scaling, merging and post-refinement with PRIME')
# These buttons will be disabled until input path is provided
self.toolbar.EnableTool(self.tb_btn_run.GetId(), False)
self.toolbar.Realize()
# Status bar
self.sb = self.CreateStatusBar()
self.sb.SetFieldsCount(3)
self.sb.SetStatusWidths([320, 200, -2])
# Menu bar
menubar = wx.MenuBar()
m_help = wx.Menu()
m_file = wx.Menu()
self.mb_load_script = m_file.Append(wx.ID_OPEN, '&Load Script...')
self.mb_save_script = m_file.Append(wx.ID_SAVE, '&Save Script...')
self.mb_about = m_help.Append(wx.ID_ANY, '&About')
menubar.Append(m_file, '&File')
menubar.Append(m_help, '&Help')
self.SetMenuBar(menubar)
# Place elements in main PRIME window
main_box = wx.BoxSizer(wx.VERTICAL)
# Instantiate windows
self.input_window = frm.PRIMEInputWindow(self, phil=phil)
# Single input window
main_box.Add(self.input_window, 1, flag=wx.ALL | wx.EXPAND, border=10)
main_box.Add((-1, 20))
# Menubar button bindings
self.Bind(wx.EVT_MENU, self.OnAboutBox, self.mb_about)
self.Bind(wx.EVT_MENU, self.onSaveScript, self.mb_save_script)
self.Bind(wx.EVT_MENU, self.onLoadScript, self.mb_load_script)
# Toolbar button bindings
self.Bind(wx.EVT_TOOL, self.onQuit, self.tb_btn_quit)
self.Bind(wx.EVT_TOOL, self.onPreferences, self.tb_btn_prefs)
self.Bind(wx.EVT_TOOL, self.onRecovery, self.tb_btn_analysis)
self.Bind(wx.EVT_TOOL, self.onRun, self.tb_btn_run)
self.Bind(wx.EVT_TOOL, self.onLoadScript, self.tb_btn_load)
self.Bind(wx.EVT_TOOL, self.onSaveScript, self.tb_btn_save)
self.Bind(wx.EVT_TOOL, self.onReset, self.tb_btn_reset)
# Draw the main window sizer
self.SetSizer(main_box)
def __init__(self,
parent,
id,
title,
params,
prime_file,
mp_method='python',
command=None,
recover=False):
wx.Frame.__init__(self,
parent,
id,
title,
size=(800, 900),
style=wx.SYSTEM_MENU | wx.CAPTION | wx.CLOSE_BOX
| wx.RESIZE_BORDER)
self.logtext = ''
self.pparams = params
self.prime_file = prime_file
self.out_file = os.path.join(self.pparams.run_no, 'log.txt')
self.bookmark = 0
self.prev_pids = []
self.aborted = False
self.command = command
self.mp_method = mp_method
self.current_cycle = -1
self.main_panel = wx.Panel(self)
self.main_sizer = wx.BoxSizer(wx.VERTICAL)
# Toolbar
self.prime_toolbar = self.CreateToolBar(wx.TB_TEXT)
abort_bmp = bitmaps.fetch_icon_bitmap('actions', 'stop')
self.tb_btn_abort = self.prime_toolbar.AddLabelTool(wx.ID_ANY,
label='Abort',
bitmap=abort_bmp,
shortHelp='Abort')
self.prime_toolbar.Realize()
# Status box
self.status_panel = wx.Panel(self.main_panel)
self.status_sizer = wx.BoxSizer(wx.VERTICAL)
self.status_box = wx.StaticBox(self.status_panel, label='Status')
self.status_box_sizer = wx.StaticBoxSizer(self.status_box,
wx.HORIZONTAL)
self.status_txt = wx.StaticText(self.status_panel, label='')
self.status_box_sizer.Add(self.status_txt,
flag=wx.ALL | wx.ALIGN_CENTER,
border=10)
self.status_sizer.Add(self.status_box_sizer,
flag=wx.EXPAND | wx.ALL,
border=3)
self.status_panel.SetSizer(self.status_sizer)
# Tabbed output window(s)
self.prime_panel = wx.Panel(self.main_panel)
self.prime_nb = wx.Notebook(self.prime_panel, style=0)
self.log_tab = LogTab(self.prime_nb)
self.graph_tab = RuntimeTab(self.prime_nb, params=self.pparams)
self.prime_nb.AddPage(self.log_tab, 'Log')
self.prime_nb.AddPage(self.graph_tab, 'Charts')
self.prime_nb.SetSelection(1)
self.prime_sizer = wx.BoxSizer(wx.VERTICAL)
self.prime_sizer.Add(self.prime_nb,
1,
flag=wx.EXPAND | wx.ALL,
border=3)
self.prime_panel.SetSizer(self.prime_sizer)
self.main_sizer.Add(self.status_panel,
flag=wx.EXPAND | wx.ALL,
border=3)
self.main_sizer.Add(self.prime_panel,
1,
flag=wx.EXPAND | wx.ALL,
border=3)
self.main_panel.SetSizer(self.main_sizer)
#Processing status bar
self.sb = self.CreateStatusBar()
self.sb.SetFieldsCount(2)
self.sb.SetStatusWidths([-1, -2])
# Output gauge in status bar
self.gauge_prime = wx.Gauge(self.sb,
-1,
style=wx.GA_HORIZONTAL | wx.GA_SMOOTH)
rect = self.sb.GetFieldRect(0)
self.gauge_prime.SetPosition((rect.x + 2, rect.y + 2))
self.gauge_prime.SetSize((rect.width - 4, rect.height - 4))
self.gauge_prime.Hide()
# Output polling timer
self.timer = wx.Timer(self)
# Event bindings
self.Bind(thr.EVT_ALLDONE, self.onFinishedProcess)
self.sb.Bind(wx.EVT_SIZE, self.onStatusBarResize)
self.Bind(wx.EVT_TIMER, self.onTimer, id=self.timer.GetId())
# Button bindings
self.Bind(wx.EVT_TOOL, self.onAbort, self.tb_btn_abort)
if not recover:
self.run()
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.run_indexing = False
self.run_integration = False
self.running_clustering = False
# 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)
# 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)
# Settings bindings
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)
self.Bind(wx.EVT_CHECKBOX, self.onChartRange,
self.tracker_panel.chart_window.toggle)
# Initialize tracker
self.initialize_spotfinder()
def __init__(self, *args, **kwds):
from wxtbx import bitmaps
super().__init__(*args, **kwds)
# Needed for communication with the root frame.
self._root_frame = self.GetParent().GetParent()
sizer = wx.BoxSizer(wx.VERTICAL)
self.SetSizer(sizer)
self._id_text = wx.NewId()
text = wx.StaticText(self, id=self._id_text, label="")
sizer.Add(text, flag=wx.ALIGN_CENTER)
# The score buttons. XXX Would really like this to be stars or
# some such. Could then zap the static text above.
box = wx.BoxSizer(wx.HORIZONTAL)
self._id_buttons = []
for i in range(6):
btn = wx.Button(self, label="%d" % i)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnScore, btn)
self._id_buttons.append(btn.GetId())
sizer.Add(box)
# XXX Would like to have label and short help for the buttons.
# Buttons in wxWidgets version 2.9.1 and later support text and
# bitmap, see SetBitmap, SetBitmapLabel, SetBitmapDisabled, etc.
box = wx.BoxSizer(wx.HORIZONTAL)
self._id_previous = wx.NewId()
btn = wx.BitmapButton(
self,
id=self._id_previous,
bitmap=bitmaps.fetch_icon_bitmap("actions", "1leftarrow"),
style=wx.BORDER_NONE,
)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnPrevious, btn)
btn = wx.Button(self, label="Save scores")
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnSave, btn)
self._id_next = wx.NewId()
btn = wx.BitmapButton(
self,
id=self._id_next,
bitmap=bitmaps.fetch_icon_bitmap("actions", "1rightarrow"),
style=wx.BORDER_NONE,
)
box.Add(btn, flag=wx.ALIGN_CENTER, border=5)
self.Bind(wx.EVT_BUTTON, self.OnNext, btn)
sizer.Add(box, flag=wx.ALIGN_CENTER)
# Register update events for the dynamic widgets.
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateNext, id=self._id_next)
self.Bind(wx.EVT_UPDATE_UI,
self.OnUpdatePrevious,
id=self._id_previous)
self.Bind(wx.EVT_UPDATE_UI, self.OnUpdateText, id=self._id_text)
for i in range(self._root_frame.image_chooser.GetCount()):
_scores[self._root_frame.get_key(
self._root_frame.image_chooser.GetClientData(i))] = None
def __init__(self, job, title, root):
wx.Frame.__init__(self,None,-1,'Job Summary', size=(500,300))
self.toolbar = wx.ToolBar(self, style=wx.TB_3DBUTTONS|wx.TB_TEXT)
close = self.toolbar.AddLabelTool(wx.ID_ANY, 'Close', bitmaps.fetch_icon_bitmap("actions", "no"))
self.Bind(wx.EVT_TOOL, self._close, close)
self.toolbar.AddSeparator()
self.toolbar.AddControl(wx.StaticText(self.toolbar, -1, title))
self.SetToolBar(self.toolbar)
self.toolbar.Realize()
self.table = wx.FlexGridSizer(cols=2, rows=0, hgap=5, vgap=5)
if os.path.exists(job):
r = pickle.load(open(job, 'rb'))
p = r.parameters()
#self.table.Add(wx.StaticText(self, -1, 'Job:'))
#self.table.Add(wx.StaticText(self, -1, title))
self.table.Add(wx.StaticText(self, -1, 'Title:'))
self.table.Add(wx.StaticText(self, -1, p['title']), 0, wx.EXPAND|wx.BOTTOM, 10)
self.table.Add(wx.StaticText(self, -1, 'Started:'))
self.table.Add(wx.StaticText(self, -1, time.strftime("%H:%M %d-%m-%Y", time.localtime(p['time']))))
self.table.Add(wx.StaticText(self, -1, 'Time Taken:'))
self.table.Add(wx.StaticText(self, -1, str(round((p['timef']-p['time'])/60,1)) + ' mins'), 0, wx.EXPAND|wx.BOTTOM, 10)
self.table.Add(wx.StaticText(self, -1, 'Input HKL:'))
self.table.Add(wx.StaticText(self, -1, p['hkl'].replace(root, '')))
self.table.Add(wx.StaticText(self, -1, 'Input INS:'))
self.table.Add(wx.StaticText(self, -1, p['ins'].replace(root, '')), 0, wx.EXPAND|wx.BOTTOM, 10)
self.table.Add(wx.StaticText(self, -1, 'Status:'))
self.table.Add(wx.StaticText(self, -1, p['status']))
self.table.Add(wx.StaticText(self, -1, 'Type:'))
self.table.Add(wx.StaticText(self, -1, REFINEMENT_TYPES[p['type']]))
self.table.Add(wx.StaticText(self, -1, 'Target:'))
self.table.Add(wx.StaticText(self, -1, REFINEMENT_TARGETS[p['target']] if 'target' in p else 'Unknown'))
if p['type'] == PART_UNRESTRAINED:
self.table.Add(wx.StaticText(self, -1, 'Unrestrained Residues:'))
self.table.Add(wx.StaticText(self, -1, ', '.join(p['options']['residues'])), 0, wx.EXPAND|wx.BOTTOM, 10)
if p['type'] == FULL_MATRIX:
self.table.Add(wx.StaticText(self, -1, 'BLOC 1:'))
self.table.Add(wx.StaticText(self, -1, 'Yes' if p['options']['bloc'] else 'No'))
self.table.Add(wx.StaticText(self, -1, 'Include Rfree:'))
self.table.Add(wx.StaticText(self, -1, 'Yes' if p['options']['rfree'] else 'No'), 0, wx.EXPAND|wx.BOTTOM, 10)
self.table.Add(wx.StaticText(self, -1, 'Cycles:'))
self.table.Add(wx.StaticText(self, -1, str(p['total_cycles'])))
self.table.Add(wx.StaticText(self, -1, 'Resolution'))
self.table.Add(wx.StaticText(self, -1, '%.2f - %.2f' % (p['res'], p['resl'])))
self.table.Add(wx.StaticText(self, -1, 'R:'))
self.table.Add(wx.StaticText(self, -1, '-' if p['r'] == -1 else (p['r'] if type(p['r']) == type(str()) else '%.4f' % p['r'])))
self.table.Add(wx.StaticText(self, -1, 'Rfree:'))
self.table.Add(wx.StaticText(self, -1, '-' if p['rfree'] == -1 else '%.4f' % p['rfree']), 0, wx.EXPAND|wx.BOTTOM, 10)
self.table.Add(wx.StaticText(self, -1, 'Hydrogens:'))
self.table.Add(wx.StaticText(self, -1,'Yes' if p['options']['hydrogens'] else 'No'))
self.table.Add(wx.StaticText(self, -1, 'Anistropic:'))
self.table.Add(wx.StaticText(self, -1,'Yes' if p['options']['anis'] else 'No'))
self.table.Add(wx.StaticText(self, -1, 'Custom Commands:'))
cust = ''
if 'custom' in p['options']:
if p['options']['custom']:
cust = p['options']['custom']
if 'custom_text' in p['options']:
if p['options']['custom_text']:
if cust:
cust += "\n"
cust += p['options']['custom_text']
if not cust:
cust = 'N/A'
self.table.Add(wx.StaticText(self, -1, cust))
self.fig = Figure((3.0, 2.0), dpi=100)
col = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BACKGROUND)
self.fig.patch.set_facecolor((col[0]/255.0, col[1]/255.0, col[2]/255.0))
self.canvas = FigCanvas(self, -1, self.fig)
self.ax1 = self.fig.add_subplot(111)
self.ax2 = self.ax1.twinx()
self.ax1.set_ylabel('wR2', fontsize=9)
self.ax1.tick_params(labelsize=8)
self.ax1.yaxis.set_major_formatter(FormatStrFormatter('%5.3f'))
self.ax2.tick_params(labelsize=8)
self.ax2.yaxis.set_major_formatter(FormatStrFormatter('%4.1f'))
self.ax2.set_ylabel('GooF', fontsize=9)
x = range(len(p['cycles'].keys()))
y = [ p['cycles'][i+1][0] for i in x ]
y2 = [ p['cycles'][i+1][1] for i in x ]
self.ax1.plot(x, y, 'r^-')
self.ax2.plot(x,y2, 'bo-')
self.ax1.set_xticks(x)
self.ax1.set_xticklabels([ str(i+1) for i in x ], rotation='vertical', size=8)
self.sizer = wx.BoxSizer(wx.VERTICAL)
self.sizer.Add(self.table, 0, wx.EXPAND|wx.ALL, 5)
self.sizer.Add(self.canvas, 0, wx.EXPAND|wx.ALL, 5)
self.SetSizer(self.sizer)
self.Fit()
