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())
class DataToolFrame(wx.Frame):
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 on_load_measurements(self, event):
dlg = wx.FileDialog(self, "Load a measurements file",
wildcard = "Measurements file (*.mat,*.h5)|*.mat;*.h5",
style = wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
self.load_measurements(dlg.GetPath())
def on_save_measurements(self, event):
with wx.FileDialog(self, "Save measurements file", wildcard =
"Matlab measurements file (*.mat)|*.mat",
style = wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg:
if dlg.ShowModal() == wx.ID_OK:
self.pipeline.save_measurements(dlg.GetPath(),
self.measurements)
def on_exit(self, event):
self.Close()
def on_image_choose(self, event):
'''Choose an image from the image set'''
dlg = wx.Dialog(self)
dlg.Title = "Choose an image set"
sizer = wx.BoxSizer(wx.VERTICAL)
dlg.SetSizer(sizer)
choose_sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(choose_sizer, 1, wx.EXPAND | wx.ALL, 5)
choose_sizer.Add(wx.StaticText(dlg, -1, label="Image set:"),
0, wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
metadata_db = {}
metadata_features = [
x for x in self.measurements.get_feature_names(cpmeas.IMAGE)
if x.startswith('Metadata')]
sel = None
for i in self.measurements.get_image_numbers():
metadata_key = ','.join(['%s=%s' % (
feature,
self.measurements.get_measurement(cpmeas.IMAGE, feature, i))
for feature in metadata_features])
metadata_db[i] = metadata_key
if i == self.measurements.image_set_number:
sel = i
choices = ["%d: %s" % (i, metadata_db[i])
for i in self.measurements.get_image_numbers()]
choice_ctl = wx.Choice(dlg, -1, choices=choices)
# Select the current image set
if sel is not None:
choice_ctl.SetSelection(sel)
choose_sizer.Add(choice_ctl, 1, wx.EXPAND | wx.LEFT, 5)
button_sizer = wx.StdDialogButtonSizer()
ok_button = wx.Button(dlg, wx.ID_OK)
ok_button.SetDefault()
ok_button.SetHelpText("Press the OK button to change the current image to the one selected above")
button_sizer.AddButton(ok_button)
cancel_button = wx.Button(dlg, wx.ID_CANCEL)
cancel_button.SetHelpText("Press the cancel button if you do not want to change the current image")
button_sizer.AddButton(cancel_button)
button_sizer.Realize()
sizer.Add(button_sizer, 0, wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT|wx.ALL, 5)
dlg.Fit()
if dlg.ShowModal() == wx.ID_OK:
index = choice_ctl.GetSelection()
self.measurements.image_set_number = index+1
def load_measurements(self, measurements_file_name):
self.measurements = cpmeas.load_measurements(
measurements_file_name, can_overwrite = True)
# Start on the first image
self.measurements.next_image_set(1)
def on_run(self, event):
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
workspace = cpw.Workspace(self.pipeline,
self.module,
image_set,
cpo.ObjectSet(),
self.measurements,
image_set_list,
frame=self)
self.module.show_window = True # to make sure it saves display data
self.module.run_as_data_tool(workspace)
self.measurements.flush()
fig = cpf.create_or_find(parent=self,
title="%s Output" % (self.module.module_name),
name="CellProfiler:DataTool:%s" % (self.module.module_name))
self.module.display(workspace, fig)
fig.Refresh()
class DataToolFrame(wx.Frame):
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 on_load_measurements(self, event):
dlg = wx.FileDialog(
self,
"Load a measurements file",
wildcard="Measurements file (*.mat,*.h5)|*.mat;*.h5",
style=wx.FD_OPEN)
if dlg.ShowModal() == wx.ID_OK:
self.load_measurements(dlg.GetPath())
def on_save_measurements(self, event):
with wx.FileDialog(
self,
"Save measurements file",
wildcard="CellProfiler measurements file (*.h5)|*.h5|"
"Matlab measurements file (*.mat)|*.mat",
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT) as dlg:
assert isinstance(dlg, wx.FileDialog)
if dlg.ShowModal() == wx.ID_OK:
if dlg.GetFilterIndex() == 0:
new_measurements = cpmeas.Measurements(
filename=dlg.Path, copy=self.measurements)
new_measurements.flush()
new_measurements.close()
else:
self.pipeline.save_measurements(dlg.GetPath(),
self.measurements)
def on_exit(self, event):
self.Close()
def on_image_choose(self, event):
'''Choose an image from the image set'''
dlg = wx.Dialog(self)
dlg.Title = "Choose an image set"
sizer = wx.BoxSizer(wx.VERTICAL)
dlg.SetSizer(sizer)
choose_sizer = wx.BoxSizer(wx.HORIZONTAL)
sizer.Add(choose_sizer, 1, wx.EXPAND | wx.ALL, 5)
choose_sizer.Add(wx.StaticText(dlg, -1, label="Image set:"), 0,
wx.ALIGN_RIGHT | wx.ALIGN_CENTER_VERTICAL)
metadata_db = {}
metadata_features = [
x for x in self.measurements.get_feature_names(cpmeas.IMAGE)
if x.startswith('Metadata')
]
sel = None
for i in self.measurements.get_image_numbers():
metadata_key = ','.join([
'%s=%s' %
(feature,
self.measurements.get_measurement(cpmeas.IMAGE, feature, i))
for feature in metadata_features
])
metadata_db[i] = metadata_key
if i == self.measurements.image_set_number:
sel = i
choices = [
"%d: %s" % (i, metadata_db[i])
for i in self.measurements.get_image_numbers()
]
choice_ctl = wx.Choice(dlg, -1, choices=choices)
# Select the current image set
if sel is not None:
choice_ctl.SetSelection(sel)
choose_sizer.Add(choice_ctl, 1, wx.EXPAND | wx.LEFT, 5)
button_sizer = wx.StdDialogButtonSizer()
ok_button = wx.Button(dlg, wx.ID_OK)
ok_button.SetDefault()
ok_button.SetHelpText(
"Press the OK button to change the current image to the one selected above"
)
button_sizer.AddButton(ok_button)
cancel_button = wx.Button(dlg, wx.ID_CANCEL)
cancel_button.SetHelpText(
"Press the cancel button if you do not want to change the current image"
)
button_sizer.AddButton(cancel_button)
button_sizer.Realize()
sizer.Add(button_sizer, 0,
wx.ALIGN_CENTER_VERTICAL | wx.ALIGN_RIGHT | wx.ALL, 5)
dlg.Fit()
if dlg.ShowModal() == wx.ID_OK:
index = choice_ctl.GetSelection()
self.measurements.image_set_number = index + 1
def load_measurements(self, measurements_file_name):
self.measurements = cpmeas.load_measurements(measurements_file_name,
can_overwrite=True)
# Start on the first image
self.measurements.next_image_set(1)
def on_run(self, event):
image_set_list = cpi.ImageSetList()
image_set = image_set_list.get_image_set(0)
workspace = cpw.Workspace(self.pipeline,
self.module,
image_set,
cpo.ObjectSet(),
self.measurements,
image_set_list,
frame=self)
self.module.show_window = True # to make sure it saves display data
self.module.run_as_data_tool(workspace)
self.measurements.flush()
if self.module.show_window:
fig = cpf.create_or_find(
parent=self,
title="%s Output" % (self.module.module_name),
name="CellProfiler:DataTool:%s" % (self.module.module_name))
self.module.display(workspace, fig)
fig.figure.canvas.draw()