def validate_input_ranges(self):
"""Validates input ranges specified by the input widgets.
This method uses CellProfiler's validate methods on settings to test
whether the ranges specified on the UI are acceptable. When these do
not validate, the user is shown an error message that lists all
violations as well as the error message received back from CellProfiler.
"""
# First, test whether selected parameters are valid
message = ''
for i, checkbox in enumerate(self.__check_box_list):
if checkbox.IsChecked():
setting = self.__module.setting(self.__parameters_list[i][1])
input_size = self.get_parameter_input_size(setting)
if input_size == 1:
widget_idx = self.__parameters_to_widgets_list[i][0]
lower_value = self.__lower_bound_spin_ctrl_list[
widget_idx].GetValue()
upper_value = self.__upper_bound_spin_ctrl_list[
widget_idx].GetValue()
elif input_size == 2:
widget_idx = self.__parameters_to_widgets_list[i][0]
lower_value = (
self.__lower_bound_spin_ctrl_list[widget_idx].GetValue(
), self.__lower_bound_spin_ctrl_list[widget_idx +
1].GetValue())
upper_value = (
self.__upper_bound_spin_ctrl_list[widget_idx].GetValue(
), self.__upper_bound_spin_ctrl_list[widget_idx +
1].GetValue())
old_value = setting.get_value()
try:
setting.set_value(lower_value)
setting.test_valid(self.__pipeline)
except cellprofiler.setting.ValidationError as instance:
message += '\'' + str(setting.get_text()) + \
'\': lower bound invalid, ' + \
'\n\t' + str(instance.message) + '\n'
try:
setting.set_value(upper_value)
setting.test_valid(self.__pipeline)
except cellprofiler.setting.ValidationError as instance:
message += '\'' + str(setting.get_text()) + \
'\': upper bound invalid, ' + \
'\n\t' + str(instance.message) + '\n'
setting.set_value(old_value)
# Second, if there are invalid parameters, tell the user
if len(message) > 0:
message = 'Invalid sample settings:\n\n' + message
dialog = wx.MessageDialog(self,
message,
caption='Sample settings error',
style=wx.ICON_ERROR | wx.OK)
dialog.ShowModal()
raise Exception(message)
def validate_input_ranges(self):
"""Validates input ranges specified by the input widgets.
This method uses CellProfiler's validate methods on settings to test
whether the ranges specified on the UI are acceptable. When these do
not validate, the user is shown an error message that lists all
violations as well as the error message received back from CellProfiler.
"""
# First, test whether selected parameters are valid
message = ''
for i, checkbox in enumerate(self.__check_box_list):
if checkbox.IsChecked():
setting = self.__module.setting(self.__parameters_list[i][1])
input_size = self.get_parameter_input_size(setting)
if input_size == 1:
widget_idx = self.__parameters_to_widgets_list[i][0]
lower_value = self.__lower_bound_spin_ctrl_list[widget_idx].GetValue()
upper_value = self.__upper_bound_spin_ctrl_list[widget_idx].GetValue()
elif input_size == 2:
widget_idx = self.__parameters_to_widgets_list[i][0]
lower_value = (self.__lower_bound_spin_ctrl_list[widget_idx].GetValue(),
self.__lower_bound_spin_ctrl_list[widget_idx + 1].GetValue())
upper_value = (self.__upper_bound_spin_ctrl_list[widget_idx].GetValue(),
self.__upper_bound_spin_ctrl_list[widget_idx + 1].GetValue())
old_value = setting.get_value()
try:
setting.set_value(lower_value)
setting.test_valid(self.__pipeline)
except cellprofiler.setting.ValidationError as instance:
message += '\'' + str(setting.get_text()) + \
'\': lower bound invalid, ' + \
'\n\t' + str(instance.message) + '\n'
try:
setting.set_value(upper_value)
setting.test_valid(self.__pipeline)
except cellprofiler.setting.ValidationError as instance:
message += '\'' + str(setting.get_text()) + \
'\': upper bound invalid, ' + \
'\n\t' + str(instance.message) + '\n'
setting.set_value(old_value)
# Second, if there are invalid parameters, tell the user
if len(message) > 0:
message = 'Invalid sample settings:\n\n' + message
dialog = wx.MessageDialog(
self, message, caption='Sample settings error',
style=wx.ICON_ERROR | wx.OK)
dialog.ShowModal()
raise Exception(message)
def save_run_output(self, sample_num, directory_path, output_file):
"""Save the parameter settings and images for the current run of
'self.__module'."""
for i, setting in enumerate(self.__module.visible_settings()):
value_to_write = ''
# Do not write settings without values, ie, buttons etc
if setting.get_text() != '':
value_to_write = str(setting.get_value())
if isinstance(setting, cellprofiler.setting.ImageNameProvider):
# Save image
image = \
self.__measurements.get_image(value_to_write)
path = \
os.path.join(directory_path, value_to_write + '_' + str(sample_num))
self.save_image(image, path)
value_to_write += '_' + str(sample_num) + '.jpg'
# ~*~
# elif isinstance(setting, settings.ObjectNameProvider):
# print 'Bingo! ' + str(value_to_write)
# objects =\
# self.__workspace.get_object_set().get_objects(setting.get_value())
# value_to_write = str(len(objects.indices))
# ~^~
if i < len(self.__module.visible_settings()
) - 1 and value_to_write != '':
value_to_write += '\t'
if i == len(self.__module.visible_settings()) - 1:
value_to_write += '\n'
# Write line to 'open_file'
if value_to_write != '':
output_file.write(value_to_write)
def save_run_output(self, sample_num, directory_path, output_file):
"""Save the parameter settings and images for the current run of
'self.__module'."""
for i, setting in enumerate(self.__module.visible_settings()):
value_to_write = ''
# Do not write settings without values, ie, buttons etc
if setting.get_text() != '':
value_to_write = str(setting.get_value())
if isinstance(setting, cellprofiler.setting.ImageNameProvider):
# Save image
image = \
self.__measurements.get_image(value_to_write)
path = \
os.path.join(directory_path, value_to_write + '_' + str(sample_num))
self.save_image(image, path)
value_to_write += '_' + str(sample_num) + '.jpg'
# ~*~
# elif isinstance(setting, settings.ObjectNameProvider):
# print 'Bingo! ' + str(value_to_write)
# objects =\
# self.__workspace.get_object_set().get_objects(setting.get_value())
# value_to_write = str(len(objects.indices))
# ~^~
if i < len(self.__module.visible_settings()) - 1 and value_to_write != '':
value_to_write += '\t'
if i == len(self.__module.visible_settings()) - 1:
value_to_write += '\n'
# Write line to 'open_file'
if value_to_write != '':
output_file.write(value_to_write)
def get_parameters_list(self):
"""Get and return the list of unbounded parameters.
This method first identifies all unbounded parameters in 'module'.
Next, it updates a list of mappings to tuples:
a parameter's 0-based index -> (its label, its 1-based module index),
eg, 0 -> (Crop, 2); 1 -> (Crop, 3); 2 -> (IdentifyPrimaryObjects, 4).
"""
parameters_list = []
# Get unique keys of visible parameters
visible_settings_keys = []
for setting in self.__module.visible_settings():
visible_settings_keys.append(setting.key())
# Update dictionary of visible, unbounded parameters:
# 0-based index in 'parameters_list' -> (label, 1-based module number)
for i, setting in enumerate(self.__module.settings()):
if (setting.key() in visible_settings_keys and
self.get_parameter_type(setting) == PARAM_CLASS_UNBOUNDED):
parameters_list.append((setting.get_text(), i + 1))
return parameters_list
def get_parameters_list(self):
"""Get and return the list of unbounded parameters.
This method first identifies all unbounded parameters in 'module'.
Next, it updates a list of mappings to tuples:
a parameter's 0-based index -> (its label, its 1-based module index),
eg, 0 -> (Crop, 2); 1 -> (Crop, 3); 2 -> (IdentifyPrimaryObjects, 4).
"""
parameters_list = []
# Get unique keys of visible parameters
visible_settings_keys = []
for setting in self.__module.visible_settings():
visible_settings_keys.append(setting.key())
# Update dictionary of visible, unbounded parameters:
# 0-based index in 'parameters_list' -> (label, 1-based module number)
for i, setting in enumerate(self.__module.settings()):
if (setting.key() in visible_settings_keys and
self.get_parameter_type(setting) == PARAM_CLASS_UNBOUNDED):
parameters_list.append((setting.get_text(), i + 1))
return parameters_list
def on_button(self, event):
if event.GetId() == ID_SAMPLE_BUTTON:
# try:
self.validate_input_ranges()
number = self.calc_number_samples()
sample_dialog = wx.MessageDialog(
self,
'Proceed with calculating ' + str(number) + ' samples?',
caption='Confirm sample size',
style=wx.ICON_QUESTION | wx.OK | wx.CANCEL)
if sample_dialog.ShowModal() == wx.ID_OK:
save_dialog = wx.FileDialog(
event.GetEventObject(),
message='Save sampled output',
wildcard='Tab separated values (*.tsv)|*.tsv',
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if save_dialog.ShowModal() == wx.ID_OK:
# 1. Copy original parameter values
original_values = []
for setting in self.__module.visible_settings():
original_values.append(setting.get_value())
# 2. Sample input parameters
self.__sample_list = self.generate_parameter_samples()
# 3. Open output file and write headers
output_file = \
open(save_dialog.GetPath(), 'w')
headers = ''
for i, setting in enumerate(
self.__module.visible_settings()):
# Do not write settings without values, ie, buttons etc
if setting.get_text() != '':
headers += setting.get_text()
if i < len(self.__module.visible_settings()) - 1:
headers += '\t'
headers += '\n'
output_file.write(headers)
# 4. Run pipeline once for each sample
# ~*~
self.Show(False)
progressDialog = wx.ProgressDialog(
parent=self,
title='Sampling parameters',
message='Run 1',
maximum=len(self.__sample_list))
size = progressDialog.GetSize()
size.SetWidth(2 * size.GetWidth())
progressDialog.SetSize(size)
# ~^~
for i, l in enumerate(self.__sample_list):
# print '\nStarting run ' + str(i+1) + '...'
for j, value in enumerate(l):
if value is not None:
setting_nr = self.__parameters_list[j][1]
setting = self.__module.setting(setting_nr)
setting.set_value(value)
# print str(setting.get_text()) + ' -> ' + str(setting.get_value())
# ~*~
progressDialog.Update(
i + 1,
newmsg='Executing run ' + str(i + 1) + \
' of ' + str(len(self.__sample_list)))
# ~^~
# It's not very efficient to run the complete pipeline
# when only the last module's parameter values are
# different. However, this is the only way I can get
# the images to update correctly for the last module. Ie,
# when I don't prepare and run the pipeline from scratch
# for every different configuration of the last module,
# I get the images generated by the first run for every
# run.
# 4.1 Prepare to run pipeline
self.prepare_for_run()
# 4.2 Run modules
for module in self.__pipeline.modules():
if module.get_module_num(
) <= self.__module.get_module_num():
self.run_module(module)
# 4.3 Save output
self.save_run_output(i, save_dialog.GetDirectory(),
output_file)
# This is the way to run headless, if only I could get at the images...
# self.stop_now = False
# running_pipeline = self.__pipeline.run_with_yield(
# run_in_background=False,
# status_callback=self.status_callback)
# while not self.stop_now:
# measurements = running_pipeline.next()
# print '...run completed.'
# 5. Close output file
output_file.close()
# ~*~
progressDialog.Destroy()
# ~^~
# 6. Set parameters back to original values and close window
for i, setting in enumerate(
self.__module.visible_settings()):
setting.set_value(original_values[i])
self.Close(True)
def on_button(self, event):
if event.GetId() == ID_SAMPLE_BUTTON:
# try:
self.validate_input_ranges()
number = self.calc_number_samples()
sample_dialog = wx.MessageDialog(
self,
'Proceed with calculating ' + str(number) + ' samples?',
caption='Confirm sample size',
style=wx.ICON_QUESTION | wx.OK | wx.CANCEL)
if sample_dialog.ShowModal() == wx.ID_OK:
save_dialog = wx.FileDialog(
event.GetEventObject(),
message='Save sampled output',
wildcard='Tab separated values (*.tsv)|*.tsv',
style=wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT)
if save_dialog.ShowModal() == wx.ID_OK:
# 1. Copy original parameter values
original_values = []
for setting in self.__module.visible_settings():
original_values.append(setting.get_value())
# 2. Sample input parameters
self.__sample_list = self.generate_parameter_samples()
# 3. Open output file and write headers
output_file = \
open(save_dialog.GetPath(), 'w')
headers = ''
for i, setting in enumerate(self.__module.visible_settings()):
# Do not write settings without values, ie, buttons etc
if setting.get_text() != '':
headers += setting.get_text()
if i < len(self.__module.visible_settings()) - 1:
headers += '\t'
headers += '\n'
output_file.write(headers)
# 4. Run pipeline once for each sample
# ~*~
self.Show(False)
progressDialog = wx.ProgressDialog(
parent=self, title='Sampling parameters',
message='Run 1', maximum=len(self.__sample_list))
size = progressDialog.GetSize()
size.SetWidth(2 * size.GetWidth())
progressDialog.SetSize(size)
# ~^~
for i, l in enumerate(self.__sample_list):
# print '\nStarting run ' + str(i+1) + '...'
for j, value in enumerate(l):
if value is not None:
setting_nr = self.__parameters_list[j][1]
setting = self.__module.setting(setting_nr)
setting.set_value(value)
# print str(setting.get_text()) + ' -> ' + str(setting.get_value())
# ~*~
progressDialog.Update(
i + 1,
newmsg='Executing run ' + str(i + 1) + \
' of ' + str(len(self.__sample_list)))
# ~^~
# It's not very efficient to run the complete pipeline
# when only the last module's parameter values are
# different. However, this is the only way I can get
# the images to update correctly for the last module. Ie,
# when I don't prepare and run the pipeline from scratch
# for every different configuration of the last module,
# I get the images generated by the first run for every
# run.
# 4.1 Prepare to run pipeline
self.prepare_for_run()
# 4.2 Run modules
for module in self.__pipeline.modules():
if module.get_module_num() <= self.__module.get_module_num():
self.run_module(module)
# 4.3 Save output
self.save_run_output(i, save_dialog.GetDirectory(), output_file)
# This is the way to run headless, if only I could get at the images...
# self.stop_now = False
# running_pipeline = self.__pipeline.run_with_yield(
# run_in_background=False,
# status_callback=self.status_callback)
# while not self.stop_now:
# measurements = running_pipeline.next()
# print '...run completed.'
# 5. Close output file
output_file.close()
# ~*~
progressDialog.Destroy()
# ~^~
# 6. Set parameters back to original values and close window
for i, setting in enumerate(self.__module.visible_settings()):
setting.set_value(original_values[i])
self.Close(True)
