def __on_getting_started(self,event):
helpframe = wx.Frame(self,-1,'Add modules: Getting Started',size=(640,480))
sizer = wx.BoxSizer()
helpframe.SetSizer(sizer)
window = wx.html.HtmlWindow(helpframe)
sizer.Add(window,1,wx.EXPAND)
window.AppendToPage(BUILDING_A_PIPELINE_HELP)
helpframe.SetIcon(get_cp_icon())
helpframe.Layout()
helpframe.Show()
def display_helpframe(self, help, title):
helpframe = wx.Frame(self, -1, title, size=(640, 480))
sizer = wx.BoxSizer()
helpframe.SetSizer(sizer)
window = wx.html.HtmlWindow(helpframe)
sizer.Add(window, 1, wx.EXPAND)
window.AppendToPage(help)
helpframe.SetIcon(get_cp_icon())
helpframe.Layout()
helpframe.Show()
def display_helpframe(self, help, title):
helpframe = wx.Frame(self, -1,title, size=(640,480))
sizer = wx.BoxSizer()
helpframe.SetSizer(sizer)
window = wx.html.HtmlWindow(helpframe)
sizer.Add(window,1,wx.EXPAND)
window.AppendToPage(help)
helpframe.SetIcon(get_cp_icon())
helpframe.Layout()
helpframe.Show()
def display_helpframe(self, help, title):
from cellprofiler.gui.html.htmlwindow import HtmlClickableWindow
helpframe = wx.Frame(self, -1, title, size=(640, 480))
sizer = wx.BoxSizer()
helpframe.SetSizer(sizer)
window = HtmlClickableWindow(helpframe)
sizer.Add(window, 1, wx.EXPAND)
window.AppendToPage(help)
helpframe.SetIcon(get_cp_icon())
helpframe.Layout()
helpframe.Show()
def display_helpframe(self, help, title):
from cellprofiler.gui.html.htmlwindow import HtmlClickableWindow
helpframe = wx.Frame(self, -1,title, size=(640,480))
sizer = wx.BoxSizer()
helpframe.SetSizer(sizer)
window = HtmlClickableWindow(helpframe)
sizer.Add(window,1,wx.EXPAND)
window.AppendToPage(help)
helpframe.SetIcon(get_cp_icon())
helpframe.Layout()
helpframe.Show()
def __on_getting_started(self, event):
helpframe = wx.Frame(self,
-1,
'Add modules: Getting Started',
size=(640, 480))
sizer = wx.BoxSizer()
helpframe.SetSizer(sizer)
window = wx.html.HtmlWindow(helpframe)
sizer.Add(window, 1, wx.EXPAND)
window.AppendToPage(BUILDING_A_PIPELINE_HELP)
helpframe.SetIcon(get_cp_icon())
helpframe.Layout()
helpframe.Show()
def run_as_data_tool(self, workspace):
m = workspace.measurements
assert isinstance(m, cpmeas.Measurements)
m.is_first_image = True
image_set_count = m.image_set_count
for i in range(image_set_count):
self.run(workspace)
img_stats = workspace.display_data.statistics
if i == 0:
header = ["Image set"]
for flag_name, object_name, feature, value, pf in img_stats:
header.append(flag_name)
header.append("Pass/Fail")
statistics = [header]
row = [str(i+1)]
ok = True
for flag_name, object_name, feature, value, pf in img_stats:
ok = ok and (pf == "Pass")
row.append(str(value))
row.append("Pass" if ok else "Fail")
statistics.append(row)
if i < image_set_count - 1:
m.next_image_set()
self.show_window = False
if image_set_count > 0:
import wx
from wx.grid import Grid, PyGridTableBase, EVT_GRID_LABEL_LEFT_CLICK
from cellprofiler.gui import get_cp_icon
frame = wx.Frame(workspace.frame, -1, "Flag image results")
sizer = wx.BoxSizer(wx.VERTICAL)
frame.SetSizer(sizer)
grid = Grid(frame, -1)
sizer.Add(grid, 1, wx.EXPAND)
#
# The flag table supplies the statistics to the grid
# using the grid table interface
#
sort_order = np.arange(len(statistics)-1)
sort_col = [None]
sort_ascending = [None]
def on_label_clicked(event):
col = event.GetCol()
if sort_col[0] == col:
sort_ascending[0] = not sort_ascending[0]
else:
sort_ascending[0] = True
sort_col[0] = col
data = [x[col] for x in statistics[1:]]
try:
data = np.array(data,float)
except ValueError:
data = np.array(data)
if sort_ascending[0]:
sort_order[:] = np.lexsort((data,))
else:
sort_order[::-1] = np.lexsort((data,))
grid.ForceRefresh()
grid.Bind(EVT_GRID_LABEL_LEFT_CLICK, on_label_clicked)
class FlagTable(PyGridTableBase):
def __init__(self):
PyGridTableBase.__init__(self)
def GetColLabelValue(self, col):
if col == sort_col[0]:
if sort_ascending[0]:
return statistics[0][col]+" v"
else:
return statistics[0][col]+" ^"
return statistics[0][col]
def GetNumberRows(self):
return len(statistics)-1
def GetNumberCols(self):
return len(statistics[0])
def GetValue(self, row, col):
return statistics[sort_order[row]+1][col]
grid.SetTable(FlagTable())
frame.Fit()
max_size = int(wx.SystemSettings.GetMetric(wx.SYS_SCREEN_Y) * 3 / 4)
if frame.Size[1] > max_size:
frame.SetSize((frame.Size[0], max_size))
frame.SetIcon(get_cp_icon())
frame.Show()
def __init__(self, *args, **kwds):
if sys.platform.startswith("win"):
kwds["style"] = wx.DEFAULT_FRAME_STYLE | wx.STAY_ON_TOP
wx.Frame.__init__(self, *args, **kwds)
self.Show()
if wx.Platform == '__WXMAC__' and hasattr(self, 'MacGetTopLevelWindowRef'):
try:
from AppKit import NSWindow, NSApp, NSFloatingWindowLevel
window_ref = self.MacGetTopLevelWindowRef()
nsw = NSWindow.alloc().initWithWindowRef_(window_ref)
nsw.setLevel_(NSFloatingWindowLevel)
except ImportError:
print "No AppKit module => can't make progress window stay on top."
self.start_time = time.time()
self.end_times = None
self.current_module = None
self.pause_start_time = None
self.previous_pauses_duration = 0.
# GUI stuff
self.BackgroundColour = cellprofiler.preferences.get_background_color()
self.tbicon = wx.TaskBarIcon()
self.tbicon.SetIcon(get_cp_icon(), "CellProfiler2.0")
self.SetTitle("CellProfiler %s"%(version.title_string))
self.SetSize((640, 480))
self.panel = wx.Panel(self, wx.ID_ANY)
sizer = wx.BoxSizer(wx.VERTICAL)
times_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.elapsed_control = wx.StaticText(self.panel, -1,
label=self.elapsed_label(),
style=wx.ALIGN_LEFT)
self.remaining_control = wx.StaticText(self.panel, -1,
label=self.remaining_label(),
style=wx.ALIGN_RIGHT)
times_sizer.Add(self.elapsed_control, 1, wx.ALIGN_LEFT | wx.ALL, 5)
times_sizer.Add(self.remaining_control, 1, wx.ALIGN_RIGHT | wx.ALL, 5)
sizer.Add(times_sizer, 0, wx.EXPAND)
self.gauge = wx.Gauge(self.panel, -1, style=wx.GA_HORIZONTAL)
self.gauge.SetValue(0)
self.gauge.SetRange(100)
sizer.Add(self.gauge, 0, wx.ALL | wx.EXPAND, 5)
self.image_set_control = wx.StaticText(self.panel, -1, label=image_set_label(None, None))
sizer.Add(self.image_set_control, 0, wx.LEFT | wx.RIGHT, 5)
self.current_module_control = wx.StaticText(self.panel, -1, label=module_label(None))
sizer.Add(self.current_module_control, 0, wx.LEFT | wx.RIGHT | wx.BOTTOM, 5)
buttons_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.play_pause_button = wx.BitmapButton(self.panel, -1,
bitmap=wx.BitmapFromImage(get_builtin_image('pause')))
self.play_pause_button.SetToolTipString("Pause")
buttons_sizer.Add(self.play_pause_button, 0, wx.ALL, 5)
self.stop_button = wx.BitmapButton(self.panel, -1, bitmap=wx.BitmapFromImage(get_builtin_image('stop')))
self.stop_button.SetToolTipString("Stop")
buttons_sizer.Add(self.stop_button, 0, wx.ALL, 5)
save_bitmap = wx.ArtProvider.GetBitmap(wx.ART_FILE_SAVE,
wx.ART_CMN_DIALOG,
(16,16))
self.save_button = wx.BitmapButton(self.panel, -1, bitmap = save_bitmap)
self.save_button.SetToolTipString("Save measurements")
buttons_sizer.Add(self.save_button, 0, wx.ALL, 5)
sizer.Add(buttons_sizer, 0, wx.CENTER)
self.panel.SetSizer(sizer)
sizer.Fit(self)
# Timer that updates elapsed
timer_id = wx.NewId()
self.timer = wx.Timer(self.panel, timer_id)
self.timer.Start(500)
wx.EVT_TIMER(self.panel, timer_id, self.on_timer)
def run_as_data_tool(self):
'''Run the module as a data tool'''
import wx
from wx.lib.mixins.listctrl import ListCtrlAutoWidthMixin
from cellprofiler.gui import get_cp_icon
#
# Portions of this were cribbed from the wx listctrl demo code
# which is part of the wx source distribution
#
class AWListCtrl(wx.ListCtrl, ListCtrlAutoWidthMixin):
'''A list control with autosizing of the last column'''
def __init__(self,
parent,
ID=wx.ID_ANY,
pos=wx.DefaultPosition,
size=wx.DefaultSize,
style=0):
wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
ListCtrlAutoWidthMixin.__init__(self)
dlg = wx.Dialog(None,
title="Merge output files",
size=(640, 480),
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER
| wx.THICK_FRAME)
dlg.SetIcon(get_cp_icon())
#
# Layout:
# Dialog box
# sizer (vertical)
# list-control
# sizer (horizontal)
# Add...
# Remove
# Up
# Down
# button sizer
# OK
# Cancel
#
dlg.Sizer = sizer = wx.BoxSizer(wx.VERTICAL)
subsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(subsizer, 0, wx.EXPAND | wx.ALL, 5)
subsizer.Add(wx.StaticText(dlg, -1, "Destination file:"), 0,
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 3)
dest_file_ctrl = wx.TextCtrl(dlg)
subsizer.Add(dest_file_ctrl, 1, wx.EXPAND | wx.LEFT, 3)
browse_button = wx.Button(dlg, -1, "Browse...")
subsizer.Add(browse_button, 0, wx.EXPAND)
list_control = AWListCtrl(dlg, style=wx.LC_REPORT)
if sys.platform == 'darwin':
list_control.InsertColumn(0, "Folder", width=200)
list_control.InsertColumn(1, "File", width=-1)
else:
list_control.InsertColumn(0,
"Folder",
format=wx.LC_ALIGN_LEFT,
width=200)
list_control.InsertColumn(1,
"File",
format=wx.LC_ALIGN_LEFT,
width=-1)
sizer.Add(list_control, 1, wx.EXPAND | wx.ALL, 5)
sizer.Add(wx.StaticLine(dlg), 0, wx.EXPAND)
subsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(subsizer, 0, wx.EXPAND | wx.ALL, 5)
add_button = wx.Button(dlg, -1, "Add...")
subsizer.Add(add_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
remove_button = wx.Button(dlg, wx.ID_REMOVE, "Remove selected")
subsizer.Add(remove_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
up_button = wx.Button(dlg, wx.ID_UP, "Up")
subsizer.Add(up_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
down_button = wx.Button(dlg, wx.ID_DOWN, "Down")
subsizer.Add(down_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
button_sizer = wx.StdDialogButtonSizer()
button_sizer.AddButton(wx.Button(dlg, wx.ID_OK))
button_sizer.AddButton(wx.Button(dlg, wx.ID_CANCEL))
help_button = wx.Button(dlg, wx.ID_HELP)
button_sizer.AddButton(help_button)
button_sizer.Realize()
subsizer.Add(button_sizer, 0, wx.ALIGN_RIGHT)
dlg.Layout()
#
# Order is a map of item ID to its position in the list control
#
order = {}
add_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_add(event, list_control, order))
remove_button.Bind(
wx.EVT_BUTTON,
lambda event: self.on_remove(event, list_control, order))
browse_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_browse(event, dest_file_ctrl))
up_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_up(event, list_control, order))
down_button.Bind(
wx.EVT_BUTTON,
lambda event: self.on_down(event, list_control, order))
help_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_help(event, list_control))
if dlg.ShowModal() == wx.ID_OK:
sources = []
for i in range(list_control.ItemCount):
item_id = list_control.GetItemData(i)
path = list_control.GetItem(i, 0).GetText()
filename = list_control.GetItem(i, 1).GetText()
sources.append(os.path.join(path, filename))
self.merge_files(dest_file_ctrl.Value, sources)
dlg.Destroy()
def __set_icon(self):
icon = get_cp_icon()
self.SetIcon(icon)
def run_as_data_tool(self):
'''Run the module as a data tool'''
import wx
from wx.lib.mixins.listctrl import ListCtrlAutoWidthMixin
from cellprofiler.gui import get_cp_icon
#
# Portions of this were cribbed from the wx listctrl demo code
# which is part of the wx source distribution
#
class AWListCtrl(wx.ListCtrl, ListCtrlAutoWidthMixin):
'''A list control with autosizing of the last column'''
def __init__(self, parent, ID=wx.ID_ANY, pos=wx.DefaultPosition,
size=wx.DefaultSize, style=0):
wx.ListCtrl.__init__(self, parent, ID, pos, size, style)
ListCtrlAutoWidthMixin.__init__(self)
dlg = wx.Dialog(None, title = "Merge output files",
size=(640,480),
style = wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER |
wx.THICK_FRAME)
dlg.SetIcon(get_cp_icon())
#
# Layout:
# Dialog box
# sizer (vertical)
# list-control
# sizer (horizontal)
# Add...
# Remove
# Up
# Down
# button sizer
# OK
# Cancel
#
dlg.Sizer = sizer = wx.BoxSizer(wx.VERTICAL)
subsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(subsizer, 0, wx.EXPAND | wx.ALL, 5)
subsizer.Add(wx.StaticText(dlg, -1, "Destination file:"), 0,
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL | wx.LEFT, 3)
dest_file_ctrl = wx.TextCtrl(dlg)
subsizer.Add(dest_file_ctrl, 1, wx.EXPAND | wx.LEFT, 3)
browse_button = wx.Button(dlg, -1, "Browse...")
subsizer.Add(browse_button, 0, wx.EXPAND)
list_control = AWListCtrl(dlg, style=wx.LC_REPORT)
if sys.platform == 'darwin':
list_control.InsertColumn(0, "Folder", width=200)
list_control.InsertColumn(1, "File", width=-1)
else:
list_control.InsertColumn(0, "Folder", format=wx.LC_ALIGN_LEFT, width=200)
list_control.InsertColumn(1, "File", format=wx.LC_ALIGN_LEFT, width=-1)
sizer.Add(list_control, 1, wx.EXPAND | wx.ALL, 5)
sizer.Add(wx.StaticLine(dlg), 0, wx.EXPAND)
subsizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(subsizer, 0, wx.EXPAND | wx.ALL, 5)
add_button = wx.Button(dlg, -1, "Add...")
subsizer.Add(add_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
remove_button = wx.Button(dlg, wx.ID_REMOVE, "Remove selected")
subsizer.Add(remove_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
up_button = wx.Button(dlg, wx.ID_UP, "Up")
subsizer.Add(up_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
down_button = wx.Button(dlg, wx.ID_DOWN, "Down")
subsizer.Add(down_button, 0, wx.ALIGN_CENTER_HORIZONTAL)
button_sizer = wx.StdDialogButtonSizer()
button_sizer.AddButton(wx.Button(dlg, wx.ID_OK))
button_sizer.AddButton(wx.Button(dlg, wx.ID_CANCEL))
help_button = wx.Button(dlg, wx.ID_HELP)
button_sizer.AddButton(help_button)
button_sizer.Realize()
subsizer.Add(button_sizer, 0, wx.ALIGN_RIGHT )
dlg.Layout()
#
# Order is a map of item ID to its position in the list control
#
order = {}
add_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_add(event, list_control, order))
remove_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_remove(event, list_control,
order))
browse_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_browse(event, dest_file_ctrl))
up_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_up(event, list_control, order))
down_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_down(event, list_control, order))
help_button.Bind(wx.EVT_BUTTON,
lambda event: self.on_help(event, list_control))
if dlg.ShowModal() == wx.ID_OK:
sources = []
for i in range(list_control.ItemCount):
item_id = list_control.GetItemData(i)
path = list_control.GetItem(i, 0).GetText()
filename = list_control.GetItem(i, 1).GetText()
sources.append(os.path.join(path, filename))
self.merge_files(dest_file_ctrl.Value, sources)
dlg.Destroy()
def run_as_data_tool(self, workspace):
m = workspace.measurements
assert isinstance(m, cpmeas.Measurements)
m.is_first_image = True
image_set_count = m.image_set_count
for i in range(image_set_count):
self.run(workspace)
img_stats = workspace.display_data.statistics
if i == 0:
header = ["Image set"]
for flag_name, object_name, feature, value, pf in img_stats:
header.append(flag_name)
header.append("Pass/Fail")
statistics = [header]
row = [str(i + 1)]
ok = True
for flag_name, object_name, feature, value, pf in img_stats:
ok = ok and (pf == "Pass")
row.append(str(value))
row.append("Pass" if ok else "Fail")
statistics.append(row)
if i < image_set_count - 1:
m.next_image_set()
self.show_window = False
if image_set_count > 0:
import wx
from wx.grid import Grid, PyGridTableBase, EVT_GRID_LABEL_LEFT_CLICK
from cellprofiler.gui import get_cp_icon
frame = wx.Frame(workspace.frame, -1, "Flag image results")
sizer = wx.BoxSizer(wx.VERTICAL)
frame.SetSizer(sizer)
grid = Grid(frame, -1)
sizer.Add(grid, 1, wx.EXPAND)
#
# The flag table supplies the statistics to the grid
# using the grid table interface
#
sort_order = np.arange(len(statistics) - 1)
sort_col = [None]
sort_ascending = [None]
def on_label_clicked(event):
col = event.GetCol()
if sort_col[0] == col:
sort_ascending[0] = not sort_ascending[0]
else:
sort_ascending[0] = True
sort_col[0] = col
data = [x[col] for x in statistics[1:]]
try:
data = np.array(data, float)
except ValueError:
data = np.array(data)
if sort_ascending[0]:
sort_order[:] = np.lexsort((data, ))
else:
sort_order[::-1] = np.lexsort((data, ))
grid.ForceRefresh()
grid.Bind(EVT_GRID_LABEL_LEFT_CLICK, on_label_clicked)
class FlagTable(PyGridTableBase):
def __init__(self):
PyGridTableBase.__init__(self)
def GetColLabelValue(self, col):
if col == sort_col[0]:
if sort_ascending[0]:
return statistics[0][col] + " v"
else:
return statistics[0][col] + " ^"
return statistics[0][col]
def GetNumberRows(self):
return len(statistics) - 1
def GetNumberCols(self):
return len(statistics[0])
def GetValue(self, row, col):
return statistics[sort_order[row] + 1][col]
grid.SetTable(FlagTable())
frame.Fit()
max_size = int(
wx.SystemSettings.GetMetric(wx.SYS_SCREEN_Y) * 3 / 4)
if frame.Size[1] > max_size:
frame.SetSize((frame.Size[0], max_size))
frame.SetIcon(get_cp_icon())
frame.Show()
def __init__(self, *args, **kwds):
'''Instantiate a data tool frame
module_name: name of module to instantiate
measurements_file_name: name of measurements file
'''
assert kwds.has_key("module_name"), "DataToolFrame() needs a module_name argument"
assert kwds.has_key("measurements_file_name"), "DataToolFrame() needs a measurements_file_name argument"
module_name = kwds["module_name"]
measurements_file_name = kwds["measurements_file_name"]
kwds_copy = kwds.copy()
del kwds_copy["module_name"]
del kwds_copy["measurements_file_name"]
kwds_copy["title"]="%s data tool"%module_name
wx.Frame.__init__(self, *args, **kwds_copy)
self.module = instantiate_module(module_name)
self.pipeline = cpp.Pipeline()
if h5py.is_hdf5(measurements_file_name):
self.workspace = cpw.Workspace(self.pipeline, self.module, None, None, None,
None)
self.workspace.load(measurements_file_name, True)
self.measurements = self.workspace.measurements
else:
self.pipeline.load(measurements_file_name)
self.load_measurements(measurements_file_name)
self.workspace = cpw.Workspace(self.pipeline, self.module, None, None,
self.measurements, None)
self.module.module_num = len(self.pipeline.modules())+1
self.pipeline.add_module(self.module)
self.sizer = wx.BoxSizer(wx.VERTICAL)
module_panel = wx.lib.scrolledpanel.ScrolledPanel(self,-1,style=wx.SUNKEN_BORDER)
module_panel.BackgroundColour = cpprefs.get_background_color()
self.BackgroundColour = cpprefs.get_background_color()
self.module_view = ModuleView(module_panel, self.workspace, True)
self.module_view.set_selection(self.module.module_num)
def on_change(caller, event):
setting = event.get_setting()
proposed_value = event.get_proposed_value()
setting.value = proposed_value
self.pipeline.edit_module(event.get_module().module_num, False)
self.module_view.reset_view()
self.module_view.add_listener(on_change)
#
# Add a panel for the "run" button
#
panel = wx.Panel(self)
panel_sizer = wx.BoxSizer(wx.HORIZONTAL)
button = wx.Button(panel, label = "Run")
self.sizer.Add(module_panel, 1, wx.EXPAND)
self.sizer.Add(panel, 0, wx.EXPAND)
panel_sizer.AddStretchSpacer()
panel_sizer.Add(button, 0, wx.RIGHT, button.Size[1])
panel.SetSizer(panel_sizer)
wx.EVT_BUTTON(self, button.Id, self.on_run)
#
# Add a file menu
#
file_menu = wx.Menu()
file_menu.Append(ID_FILE_LOAD_MEASUREMENTS, "&Load measurements")
file_menu.Append(ID_FILE_SAVE_MEASUREMENTS, "&Save measurements")
file_menu.Append(ID_FILE_EXIT, "E&xit")
self.MenuBar = wx.MenuBar()
self.MenuBar.Append(file_menu, "&File")
self.Bind(wx.EVT_MENU, self.on_load_measurements, id=ID_FILE_LOAD_MEASUREMENTS)
self.Bind(wx.EVT_MENU, self.on_save_measurements, id=ID_FILE_SAVE_MEASUREMENTS)
self.Bind(wx.EVT_MENU, self.on_exit, id=ID_FILE_EXIT)
accelerators = wx.AcceleratorTable([
(wx.ACCEL_CMD, ord("W"), ID_FILE_EXIT),
(wx.ACCEL_CMD, ord("O"), ID_FILE_LOAD_MEASUREMENTS),
(wx.ACCEL_CMD, ord("S"), ID_FILE_SAVE_MEASUREMENTS)])
self.SetAcceleratorTable(accelerators)
#
# Add an image menu
#
image_menu = wx.Menu()
image_menu.Append(ID_IMAGE_CHOOSE, "&Choose")
self.MenuBar.Append(image_menu, "&Image")
self.Bind(wx.EVT_MENU, self.on_image_choose, id=ID_IMAGE_CHOOSE)
self.SetSizer(self.sizer)
self.Size = (self.module_view.get_max_width(), self.Size[1])
module_panel.Layout()
self.Show()
self.tbicon = wx.TaskBarIcon()
self.tbicon.SetIcon(get_cp_icon(), "CellProfiler2.0")
self.SetIcon(get_cp_icon())
def __init__(self, *args, **kwds):
'''Instantiate a data tool frame
module_name: name of module to instantiate
measurements_file_name: name of measurements file
'''
assert kwds.has_key(
"module_name"), "DataToolFrame() needs a module_name argument"
assert kwds.has_key(
"measurements_file_name"
), "DataToolFrame() needs a measurements_file_name argument"
module_name = kwds["module_name"]
measurements_file_name = kwds["measurements_file_name"]
kwds_copy = kwds.copy()
del kwds_copy["module_name"]
del kwds_copy["measurements_file_name"]
kwds_copy["title"] = "%s data tool" % module_name
wx.Frame.__init__(self, *args, **kwds_copy)
self.module = instantiate_module(module_name)
self.module.use_as_data_tool = True
self.pipeline = cpp.Pipeline()
if h5py.is_hdf5(measurements_file_name):
self.workspace = cpw.Workspace(self.pipeline, self.module, None,
None, None, None)
self.workspace.load(measurements_file_name, True)
self.measurements = self.workspace.measurements
else:
self.pipeline.load(measurements_file_name)
self.load_measurements(measurements_file_name)
self.workspace = cpw.Workspace(self.pipeline, self.module, None,
None, self.measurements, None)
self.module.module_num = len(self.pipeline.modules()) + 1
self.pipeline.add_module(self.module)
self.sizer = wx.BoxSizer(wx.VERTICAL)
module_panel = wx.lib.scrolledpanel.ScrolledPanel(
self, -1, style=wx.SUNKEN_BORDER)
module_panel.BackgroundColour = cpprefs.get_background_color()
self.BackgroundColour = cpprefs.get_background_color()
self.module_view = ModuleView(module_panel, self.workspace, True)
self.module_view.set_selection(self.module.module_num)
def on_change(caller, event):
setting = event.get_setting()
proposed_value = event.get_proposed_value()
setting.value = proposed_value
self.pipeline.edit_module(event.get_module().module_num, False)
self.module_view.reset_view()
self.module_view.request_validation()
self.module_view.add_listener(on_change)
#
# Add a panel for the "run" button
#
panel = wx.Panel(self)
panel_sizer = wx.BoxSizer(wx.HORIZONTAL)
button = wx.Button(panel, label="Run")
self.sizer.Add(module_panel, 1, wx.EXPAND)
self.sizer.Add(panel, 0, wx.EXPAND)
panel_sizer.AddStretchSpacer()
panel_sizer.Add(button, 0, wx.RIGHT, button.Size[1])
panel.SetSizer(panel_sizer)
wx.EVT_BUTTON(self, button.Id, self.on_run)
#
# Add a file menu
#
file_menu = wx.Menu()
file_menu.Append(ID_FILE_LOAD_MEASUREMENTS, "&Load measurements")
file_menu.Append(ID_FILE_SAVE_MEASUREMENTS, "&Save measurements")
file_menu.Append(ID_FILE_EXIT, "E&xit")
self.MenuBar = wx.MenuBar()
self.MenuBar.Append(file_menu, "&File")
self.Bind(wx.EVT_MENU,
self.on_load_measurements,
id=ID_FILE_LOAD_MEASUREMENTS)
self.Bind(wx.EVT_MENU,
self.on_save_measurements,
id=ID_FILE_SAVE_MEASUREMENTS)
self.Bind(wx.EVT_MENU, self.on_exit, id=ID_FILE_EXIT)
accelerators = wx.AcceleratorTable([
(wx.ACCEL_CMD, ord("W"), ID_FILE_EXIT),
(wx.ACCEL_CMD, ord("O"), ID_FILE_LOAD_MEASUREMENTS),
(wx.ACCEL_CMD, ord("S"), ID_FILE_SAVE_MEASUREMENTS)
])
self.SetAcceleratorTable(accelerators)
#
# Add an image menu
#
image_menu = wx.Menu()
image_menu.Append(ID_IMAGE_CHOOSE, "&Choose")
self.MenuBar.Append(image_menu, "&Image")
self.Bind(wx.EVT_MENU, self.on_image_choose, id=ID_IMAGE_CHOOSE)
self.SetSizer(self.sizer)
self.Size = (self.module_view.get_max_width(), self.Size[1])
module_panel.Layout()
self.Show()
self.tbicon = wx.TaskBarIcon()
self.tbicon.SetIcon(get_cp_icon(), "CellProfiler2.0")
self.SetIcon(get_cp_icon())
def __init__(self, *args, **kwds):
if sys.platform.startswith("win"):
kwds["style"] = wx.DEFAULT_FRAME_STYLE | wx.STAY_ON_TOP
wx.Frame.__init__(self, *args, **kwds)
self.Show()
if wx.Platform == '__WXMAC__' and hasattr(self,
'MacGetTopLevelWindowRef'):
try:
from AppKit import NSWindow, NSApp, NSFloatingWindowLevel
window_ref = self.MacGetTopLevelWindowRef()
nsw = NSWindow.alloc().initWithWindowRef_(window_ref)
nsw.setLevel_(NSFloatingWindowLevel)
except ImportError:
print "No AppKit module => can't make progress window stay on top."
self.start_time = time.time()
self.end_times = None
self.current_module = None
self.pause_start_time = None
self.previous_pauses_duration = 0.
# GUI stuff
self.BackgroundColour = cellprofiler.preferences.get_background_color()
self.tbicon = wx.TaskBarIcon()
self.tbicon.SetIcon(get_cp_icon(), "CellProfiler2.0")
self.SetTitle("CellProfiler %s" % (version.title_string))
self.SetSize((640, 480))
self.panel = wx.Panel(self, wx.ID_ANY)
sizer = wx.BoxSizer(wx.VERTICAL)
times_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.elapsed_control = wx.StaticText(self.panel,
-1,
label=self.elapsed_label(),
style=wx.ALIGN_LEFT)
self.remaining_control = wx.StaticText(self.panel,
-1,
label=self.remaining_label(),
style=wx.ALIGN_RIGHT)
times_sizer.Add(self.elapsed_control, 1, wx.ALIGN_LEFT | wx.ALL, 5)
times_sizer.Add(self.remaining_control, 1, wx.ALIGN_RIGHT | wx.ALL, 5)
sizer.Add(times_sizer, 0, wx.EXPAND)
self.gauge = wx.Gauge(self.panel, -1, style=wx.GA_HORIZONTAL)
self.gauge.SetValue(0)
self.gauge.SetRange(100)
sizer.Add(self.gauge, 0, wx.ALL | wx.EXPAND, 5)
self.image_set_control = wx.StaticText(self.panel,
-1,
label=image_set_label(
None, None))
sizer.Add(self.image_set_control, 0, wx.LEFT | wx.RIGHT, 5)
self.current_module_control = wx.StaticText(self.panel,
-1,
label=module_label(None))
sizer.Add(self.current_module_control, 0,
wx.LEFT | wx.RIGHT | wx.BOTTOM, 5)
buttons_sizer = wx.BoxSizer(wx.HORIZONTAL)
self.play_pause_button = wx.BitmapButton(
self.panel,
-1,
bitmap=wx.BitmapFromImage(get_builtin_image('pause')))
self.play_pause_button.SetToolTipString("Pause")
buttons_sizer.Add(self.play_pause_button, 0, wx.ALL, 5)
self.stop_button = wx.BitmapButton(self.panel,
-1,
bitmap=wx.BitmapFromImage(
get_builtin_image('stop')))
self.stop_button.SetToolTipString("Stop")
buttons_sizer.Add(self.stop_button, 0, wx.ALL, 5)
save_bitmap = wx.ArtProvider.GetBitmap(wx.ART_FILE_SAVE,
wx.ART_CMN_DIALOG, (16, 16))
self.save_button = wx.BitmapButton(self.panel, -1, bitmap=save_bitmap)
self.save_button.SetToolTipString("Save measurements")
buttons_sizer.Add(self.save_button, 0, wx.ALL, 5)
sizer.Add(buttons_sizer, 0, wx.CENTER)
self.panel.SetSizer(sizer)
sizer.Fit(self)
# Timer that updates elapsed
timer_id = wx.NewId()
self.timer = wx.Timer(self.panel, timer_id)
self.timer.Start(500)
wx.EVT_TIMER(self.panel, timer_id, self.on_timer)
def __set_icon(self):
icon = get_cp_icon()
self.SetIcon(icon)