def select_model(self, e):
"""
Only one
"""
file_chooser = wx.FileDialog(self,
message="Choose a file",
wildcard="*.biopepa",
style=wx.OPEN | wx.CHANGE_DIR)
if file_chooser.ShowModal() == wx.ID_OK:
path = file_chooser.GetPaths()[0]
self.model_list.Append(path.split('/')[-1])
self.model_parser = Biopepa_Model_Parser()
self.model_parser.parse(path)
self.tree = self.model_parser.build_graph()
file_chooser.Destroy()
else:
file_chooser.Destroy()
def select_model(self, e):
"""
Only one
"""
file_chooser = wx.FileDialog(
self,
message="Choose a file",
wildcard="*.biopepa",
style=wx.OPEN | wx.CHANGE_DIR)
if file_chooser.ShowModal() == wx.ID_OK:
path = file_chooser.GetPaths()[0]
self.model_list.Append(path.split('/')[-1])
self.model_parser = Biopepa_Model_Parser()
self.model_parser.parse(path)
self.tree = self.model_parser.build_graph()
file_chooser.Destroy()
else:
file_chooser.Destroy()
class SessionWizard(wx.wizard.Wizard):
"""
Using a wizard to guide the user through the process of starting a new
session easier. Also looks better than a long scrolling list of things.
"""
def __init__(self, title, img_filename=""):
wx.wizard.Wizard.__init__(self, None, -1, title)
self._STARTED = 0
self._FINISHED = 1
self._CANCELLED = 2
self.pages = []
self.state = self._STARTED
self.tree = None
self.Bind(wizmod.EVT_WIZARD_CANCEL, self.cancel_wizard)
self.Bind(wizmod.EVT_WIZARD_FINISHED, self.finish_wizard)
self.chosen_paths = []
self.species_dict = {}
#WorldState.Instance() = WorldState.Instance()
height, width = self.GetSize()
#PAGE 1
page1 = wizard_page(self, 'Enter Title') # Create a first page
title_label = wx.StaticText(page1, wx.ID_ANY, '', style=wx.ALIGN_LEFT)
self.title_text = wx.TextCtrl(page1, -1, size=(300, -1), validator = TextNotEmptyValidator(title_label))
page1.add_widget(self.title_text)
page1.add_widget(title_label)
line1 = wx.StaticLine(page1)
page1.add_widget(line1)
p1_help_text = "This will be used as the title of your graph, and will appear on any pictures of the graph that are saved."
page1_help = wx.StaticText(page1, wx.ID_ANY, p1_help_text, style=wx.ALIGN_LEFT)
page1_help.Wrap(width)
page1.add_widget(page1_help)
self.add_page(page1)
#PAGE 2
page2 = wizard_page(self, 'Select Results Files')
results_label = wx.StaticText(page2, wx.ID_ANY, '', style=wx.ALIGN_LEFT)
self.file_list = wx.ListBox(page2, -1, size=(300, -1), style=wx.LB_MULTIPLE, validator=ResultsListNotEmptyValidator(results_label))
page2.add_widget(self.file_list)
file_toolbar = wx.BoxSizer(wx.HORIZONTAL)
btn_add_file = wx.Button(page2, -1, "Add")
btn_add_file.Bind(wx.EVT_BUTTON, self.add_files)
btn_rem_file = wx.Button(page2, -1, "Remove")
btn_rem_file.Bind(wx.EVT_BUTTON, self.remove_files)
file_toolbar.Add(btn_add_file, 0, wx.ALL, 5)
file_toolbar.Add(btn_rem_file, 0, wx.ALL, 5)
page2.add_widget(file_toolbar, expand=False)
page2.add_widget(results_label)
line2 = wx.StaticLine(page2)
page2.add_widget(line2)
p2_help_text = "Results files are the CSVs output from BioPEPA.\nMultiple files can be selected."
page2_help = wx.StaticText(page2, wx.ID_ANY, p2_help_text, style=wx.ALIGN_LEFT)
page2_help.Wrap(width)
page2.add_widget(page2_help)
self.add_page(page2)
#PAGE 3
page3 = wizard_page(self, 'Select Model File')
self.model_list = wx.ListBox(page3, -1, size=(300, -1), style=wx.LB_SINGLE)
model_button = wx.Button(page3, -1, "Select")
model_button.Bind(wx.EVT_BUTTON, self.select_model)
page3.add_widget(self.model_list)
page3.add_widget(model_button, expand=False)
line3 = wx.StaticLine(page3)
page3.add_widget(line3)
p3_help_text = "Model files are the .biopepa files. They are used for visualising species moving through the cell.\n\nModel files are not required."
page3_help = wx.StaticText(page3, wx.ID_ANY, p3_help_text, style=wx.ALIGN_LEFT)
page3_help.Wrap(width)
page3.add_widget(page3_help)
self.add_page(page3)
#PAGE 4
page4 = wizard_page(self, 'Species Locations')
self.file_dd = wx.ComboBox(page4, -1, style=wx.CB_READONLY)
self.file_dd.Bind(wx.EVT_COMBOBOX, self.change_file)
self.species_dd = wx.ComboBox(page4, -1, style=wx.CB_READONLY)
self.species_dd.Bind(wx.EVT_COMBOBOX, self.change_species)
self.location_panel = wx.Panel(page4, -1, size=(1000000, 1000000))
page4.add_widget(self.file_dd)
page4.add_widget(self.species_dd)
p4_help_text = "Green: Present at location\nWhite: Absent at location"
page4_help = wx.StaticText(page4, wx.ID_ANY, p4_help_text, style=wx.ALIGN_LEFT)
page4_help.Wrap(width)
page4.add_widget(page4_help)
page4.add_widget(self.location_panel)
page4.Bind(wizmod.EVT_WIZARD_PAGE_SHOWN, self.page4_location_panel_size)
self.add_page(page4)
def page4_location_panel_size(self, e):
(width, height) = self.location_panel.GetSize()
if self.tree:
self.cell = CellSegments2(self.tree, (width, height))
self.location_panel.Bind(wx.EVT_PAINT, self.draw_cell)
self.location_panel.Refresh()
def draw_cell(self, e):
dc = wx.PaintDC(self.location_panel)
self.cell.paint(dc, self.get_current_species_locations())
def get_current_species_locations(self):
return self.species_dict[self.file_dd.GetValue()][self.species_dd.GetValue()]
def add_page(self, page):
'''Add a wizard page to the list.'''
if self.pages:
previous_page = self.pages[-1]
page.SetPrev(previous_page)
previous_page.SetNext(page)
self.pages.append(page)
def run(self):
self.RunWizard(self.pages[0])
def add_files(self, e):
"""
Results files. There can be many, they can be added in multiple goes
"""
open_results_file(self)
for key in WorldState.Instance().session_dict['results'].keys():
self.species_dict[key] = {}
for species in WorldState.Instance().session_dict['results'][key].keys():
if species != 'Time':
try:
(name, location) = species.split("@")
except:
(name, location) = (species, "whole_cell")
if name in self.species_dict[key]:
self.species_dict[key][name].append(location)
else:
self.species_dict[key][name] = [location]
self.populate_file_dd_list()
self.chosen_paths.append(key)
self.file_list.Append(key)
def remove_files(self, e):
"""
Again results files, because there can be many and they can be removed
in multiple goes
"""
old_paths = [path for i, path in enumerate(self.chosen_paths) if i in self.file_list.GetSelections()]
self.chosen_paths = [path for i, path in enumerate(self.chosen_paths) if i not in self.file_list.GetSelections()]
for path in old_paths:
del self.species_dict[path.split('/')[-1]]
self.file_list.Clear()
for path in self.chosen_paths:
self.file_list.Append(path.split('/')[-1])
self.populate_file_dd_list()
def populate_file_dd_list(self):
"""
Get a list of all species, it is called whenever results files are
added or removed
"""
self.file_dd.Clear()
for key in self.species_dict.keys():
self.file_dd.Append(key)
self.file_dd.SetSelection(0)
self.populate_species_dd_list()
def populate_species_dd_list(self):
self.species_dd.Clear()
for species in self.species_dict[self.file_dd.GetValue()]:
self.species_dd.Append(species)
self.species_dd.SetSelection(0)
def change_file(self, e):
self.populate_species_dd_list()
self.location_panel.Refresh()
def change_species(self, e):
self.location_panel.Refresh()
def select_model(self, e):
"""
Only one
"""
file_chooser = wx.FileDialog(
self,
message="Choose a file",
wildcard="*.biopepa",
style=wx.OPEN | wx.CHANGE_DIR)
if file_chooser.ShowModal() == wx.ID_OK:
path = file_chooser.GetPaths()[0]
self.model_list.Append(path.split('/')[-1])
self.model_parser = Biopepa_Model_Parser()
self.model_parser.parse(path)
self.tree = self.model_parser.build_graph()
file_chooser.Destroy()
else:
file_chooser.Destroy()
def Destroy(self):
self.Close()
def cancel_wizard(self, e):
"""
For some reason, finishing normally also comes in here
"""
if self.state != self._FINISHED:
self.state = self._CANCELLED
self.Destroy()
def finish_wizard(self, e):
self.state = self._FINISHED
self.Destroy()
def parse_species(self):
WorldState.Instance().session_dict['species_dict'] = self.species_dict
#Create a line for each result
for result in WorldState.Instance().session_dict['results']:
results_dict = WorldState.Instance().session_dict['results'][result]
WorldState.Instance().session_dict['lines'][result] = {}
for key in results_dict:
if (not key == 'Time'):
WorldState.Instance().session_dict['lines'][result][key] = Line(
results_dict[key],
results_dict['Time'],
result, key,
WorldState.Instance().choose_colour(),
WorldState.Instance().graph_width,
WorldState.Instance().graph_height,
WorldState.Instance().session_dict['xmin'],
WorldState.Instance().session_dict['xmax'],
WorldState.Instance().session_dict['ymin'],
WorldState.Instance().session_dict['ymax'])
class SessionWizard(wx.wizard.Wizard):
"""
Using a wizard to guide the user through the process of starting a new
session easier. Also looks better than a long scrolling list of things.
"""
def __init__(self, title, img_filename=""):
wx.wizard.Wizard.__init__(self, None, -1, title)
self._STARTED = 0
self._FINISHED = 1
self._CANCELLED = 2
self.pages = []
self.state = self._STARTED
self.tree = None
self.Bind(wizmod.EVT_WIZARD_CANCEL, self.cancel_wizard)
self.Bind(wizmod.EVT_WIZARD_FINISHED, self.finish_wizard)
self.chosen_paths = []
self.species_dict = {}
#WorldState.Instance() = WorldState.Instance()
height, width = self.GetSize()
#PAGE 1
page1 = wizard_page(self, 'Enter Title') # Create a first page
title_label = wx.StaticText(page1, wx.ID_ANY, '', style=wx.ALIGN_LEFT)
self.title_text = wx.TextCtrl(
page1,
-1,
size=(300, -1),
validator=TextNotEmptyValidator(title_label))
page1.add_widget(self.title_text)
page1.add_widget(title_label)
line1 = wx.StaticLine(page1)
page1.add_widget(line1)
p1_help_text = "This will be used as the title of your graph, and will appear on any pictures of the graph that are saved."
page1_help = wx.StaticText(page1,
wx.ID_ANY,
p1_help_text,
style=wx.ALIGN_LEFT)
page1_help.Wrap(width)
page1.add_widget(page1_help)
self.add_page(page1)
#PAGE 2
page2 = wizard_page(self, 'Select Results Files')
results_label = wx.StaticText(page2,
wx.ID_ANY,
'',
style=wx.ALIGN_LEFT)
self.file_list = wx.ListBox(
page2,
-1,
size=(300, -1),
style=wx.LB_MULTIPLE,
validator=ResultsListNotEmptyValidator(results_label))
page2.add_widget(self.file_list)
file_toolbar = wx.BoxSizer(wx.HORIZONTAL)
btn_add_file = wx.Button(page2, -1, "Add")
btn_add_file.Bind(wx.EVT_BUTTON, self.add_files)
btn_rem_file = wx.Button(page2, -1, "Remove")
btn_rem_file.Bind(wx.EVT_BUTTON, self.remove_files)
file_toolbar.Add(btn_add_file, 0, wx.ALL, 5)
file_toolbar.Add(btn_rem_file, 0, wx.ALL, 5)
page2.add_widget(file_toolbar, expand=False)
page2.add_widget(results_label)
line2 = wx.StaticLine(page2)
page2.add_widget(line2)
p2_help_text = "Results files are the CSVs output from BioPEPA.\nMultiple files can be selected."
page2_help = wx.StaticText(page2,
wx.ID_ANY,
p2_help_text,
style=wx.ALIGN_LEFT)
page2_help.Wrap(width)
page2.add_widget(page2_help)
self.add_page(page2)
#PAGE 3
page3 = wizard_page(self, 'Select Model File')
self.model_list = wx.ListBox(page3,
-1,
size=(300, -1),
style=wx.LB_SINGLE)
model_button = wx.Button(page3, -1, "Select")
model_button.Bind(wx.EVT_BUTTON, self.select_model)
page3.add_widget(self.model_list)
page3.add_widget(model_button, expand=False)
line3 = wx.StaticLine(page3)
page3.add_widget(line3)
p3_help_text = "Model files are the .biopepa files. They are used for visualising species moving through the cell.\n\nModel files are not required."
page3_help = wx.StaticText(page3,
wx.ID_ANY,
p3_help_text,
style=wx.ALIGN_LEFT)
page3_help.Wrap(width)
page3.add_widget(page3_help)
self.add_page(page3)
#PAGE 4
page4 = wizard_page(self, 'Species Locations')
self.file_dd = wx.ComboBox(page4, -1, style=wx.CB_READONLY)
self.file_dd.Bind(wx.EVT_COMBOBOX, self.change_file)
self.species_dd = wx.ComboBox(page4, -1, style=wx.CB_READONLY)
self.species_dd.Bind(wx.EVT_COMBOBOX, self.change_species)
self.location_panel = wx.Panel(page4, -1, size=(1000000, 1000000))
page4.add_widget(self.file_dd)
page4.add_widget(self.species_dd)
p4_help_text = "Green: Present at location\nWhite: Absent at location"
page4_help = wx.StaticText(page4,
wx.ID_ANY,
p4_help_text,
style=wx.ALIGN_LEFT)
page4_help.Wrap(width)
page4.add_widget(page4_help)
page4.add_widget(self.location_panel)
page4.Bind(wizmod.EVT_WIZARD_PAGE_SHOWN,
self.page4_location_panel_size)
self.add_page(page4)
def page4_location_panel_size(self, e):
(width, height) = self.location_panel.GetSize()
if self.tree:
self.cell = CellSegments2(self.tree, (width, height))
self.location_panel.Bind(wx.EVT_PAINT, self.draw_cell)
self.location_panel.Refresh()
def draw_cell(self, e):
dc = wx.PaintDC(self.location_panel)
self.cell.paint(dc, self.get_current_species_locations())
def get_current_species_locations(self):
return self.species_dict[self.file_dd.GetValue()][
self.species_dd.GetValue()]
def add_page(self, page):
'''Add a wizard page to the list.'''
if self.pages:
previous_page = self.pages[-1]
page.SetPrev(previous_page)
previous_page.SetNext(page)
self.pages.append(page)
def run(self):
self.RunWizard(self.pages[0])
def add_files(self, e):
"""
Results files. There can be many, they can be added in multiple goes
"""
open_results_file(self)
for key in WorldState.Instance().session_dict['results'].keys():
self.species_dict[key] = {}
for species in WorldState.Instance(
).session_dict['results'][key].keys():
if species != 'Time':
try:
(name, location) = species.split("@")
except:
(name, location) = (species, "whole_cell")
if name in self.species_dict[key]:
self.species_dict[key][name].append(location)
else:
self.species_dict[key][name] = [location]
self.populate_file_dd_list()
self.chosen_paths.append(key)
self.file_list.Append(key)
def remove_files(self, e):
"""
Again results files, because there can be many and they can be removed
in multiple goes
"""
old_paths = [
path for i, path in enumerate(self.chosen_paths)
if i in self.file_list.GetSelections()
]
self.chosen_paths = [
path for i, path in enumerate(self.chosen_paths)
if i not in self.file_list.GetSelections()
]
for path in old_paths:
del self.species_dict[path.split('/')[-1]]
self.file_list.Clear()
for path in self.chosen_paths:
self.file_list.Append(path.split('/')[-1])
self.populate_file_dd_list()
def populate_file_dd_list(self):
"""
Get a list of all species, it is called whenever results files are
added or removed
"""
self.file_dd.Clear()
for key in self.species_dict.keys():
self.file_dd.Append(key)
self.file_dd.SetSelection(0)
self.populate_species_dd_list()
def populate_species_dd_list(self):
self.species_dd.Clear()
for species in self.species_dict[self.file_dd.GetValue()]:
self.species_dd.Append(species)
self.species_dd.SetSelection(0)
def change_file(self, e):
self.populate_species_dd_list()
self.location_panel.Refresh()
def change_species(self, e):
self.location_panel.Refresh()
def select_model(self, e):
"""
Only one
"""
file_chooser = wx.FileDialog(self,
message="Choose a file",
wildcard="*.biopepa",
style=wx.OPEN | wx.CHANGE_DIR)
if file_chooser.ShowModal() == wx.ID_OK:
path = file_chooser.GetPaths()[0]
self.model_list.Append(path.split('/')[-1])
self.model_parser = Biopepa_Model_Parser()
self.model_parser.parse(path)
self.tree = self.model_parser.build_graph()
file_chooser.Destroy()
else:
file_chooser.Destroy()
def Destroy(self):
self.Close()
def cancel_wizard(self, e):
"""
For some reason, finishing normally also comes in here
"""
if self.state != self._FINISHED:
self.state = self._CANCELLED
self.Destroy()
def finish_wizard(self, e):
self.state = self._FINISHED
self.Destroy()
def parse_species(self):
WorldState.Instance().session_dict['species_dict'] = self.species_dict
#Create a line for each result
for result in WorldState.Instance().session_dict['results']:
results_dict = WorldState.Instance(
).session_dict['results'][result]
WorldState.Instance().session_dict['lines'][result] = {}
for key in results_dict:
if (not key == 'Time'):
WorldState.Instance(
).session_dict['lines'][result][key] = Line(
results_dict[key], results_dict['Time'], result, key,
WorldState.Instance().choose_colour(),
WorldState.Instance().graph_width,
WorldState.Instance().graph_height,
WorldState.Instance().session_dict['xmin'],
WorldState.Instance().session_dict['xmax'],
WorldState.Instance().session_dict['ymin'],
WorldState.Instance().session_dict['ymax'])