class BobGui(JFrame):
def __init__(self):
super(BobGui, self).__init__('BobPy')
# IJ.log('okay?')
# print('okay??')
self.setLayout(BorderLayout())
self.main_panel = JPanel()
# self.main_panel.setLayout(MigLayout('insets 1 10 1 1'))
self.main_panel.setLayout(MigLayout())
dir_panel = JPanel()
dir_panel.setLayout(BoxLayout(dir_panel, BoxLayout.X_AXIS))
dir_label = JLabel('Experiment Folder:')
dir_panel.add(dir_label)
self.dir_text_field = JTextField(10)
self.dir_text_field.addActionListener(
ActionListenerFactory(self, self.text_field_al))
dir_panel.add(self.dir_text_field)
dir_button = JButton('open')
dir_button.addActionListener(
ActionListenerFactory(self, self.choose_dir_al))
dir_panel.add(dir_button)
self.main_panel.add(dir_panel, 'wrap, growx, spanx, pushx')
add_key_args(self.main_panel, 'close_w',
ActionListenerFactory(self, self.close_al), KeyEvent.VK_W,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask())
self.add(self.main_panel, BorderLayout.CENTER)
self.setPreferredSize(Dimension(650, 600))
self.pack()
self.setLocationRelativeTo(None)
self.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.setVisible(True)
def show_exper_info(self):
chf_panel = self.make_chf_panel()
hseg_tree_panel = self.make_hseg_tree_panel()
self.split_pane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self.split_pane.setOneTouchExpandable(True)
self.split_pane.setContinuousLayout(True)
self.split_pane.setResizeWeight(0.5)
self.split_pane.add(chf_panel)
self.split_pane.add(hseg_tree_panel)
self.main_panel.add(self.split_pane, 'grow, wrap')
# self.log_text = JTextArea()
self.main_panel.add(self.log_text, 'grow, wrap')
self.log_text.setLineWrap(True)
self.log_text.setWrapStyleWord(True)
self.revalidate()
def make_chf_panel(self):
""" chf --> common hseg files """
chf_panel = JPanel()
chf_panel.setLayout(MigLayout('insets 0'))
chf_files_label = JLabel('Hemisegment cells')
chf_files_text = JTextArea(
BobGui.archetype_to_str(
self.exper.hseg_cell_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Hemisegment binary image files')
chf_files_text = JTextArea(
BobGui.archetype_to_str(self.exper.hseg_bin_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Intensity Image Files')
# chf_files_text = JTextArea(BobGui.archetype_to_str(self.exper.hseg_intens_im_files_cab().archetype))
# print(self.exper.hseg_intens_im_files_cab().archetype)
# chf_panel.add(chf_files_label, 'growx, wrap')
# chf_panel.add(chf_files_text, 'grow, wrap')
self.intens_im_boxes = []
intens_im_panel = JPanel()
intens_im_panel.setLayout(MigLayout('insets 0'))
for poss_im_file in self.exper.hseg_intens_im_files_cab().archetype:
self.intens_im_boxes.append(JCheckBox(poss_im_file))
intens_im_panel.add(self.intens_im_boxes[-1], 'wrap')
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(intens_im_panel, 'grow, wrap')
mdf_create_button = JButton(
'Create meta_data file from default outline')
# mdf_create_button = JButton('<html>Create meta_data file<br>from default outline</html>')
mdf_create_button.addActionListener(
ActionListenerFactory(self, self.mdf_create_al))
mdf_open_button = JButton('Open existing meta_data file')
mdf_open_button.addActionListener(
ActionListenerFactory(self, self.mdf_open_al))
# meta_data_file_buttton = JButton('Open/Create meta_data file')
# meta_data_file_buttton.addActionListener(ActionListenerFactory(self, self.meta_data_al))
# chf_panel.add(meta_data_file_buttton)
chf_panel.add(mdf_create_button, 'wrap')
chf_panel.add(mdf_open_button, 'wrap')
chf_scroll_pane = JScrollPane()
chf_scroll_pane.getViewport().setView(chf_panel)
return chf_scroll_pane
@staticmethod
def archetype_to_str(archetype):
at_str = ''
for val in archetype:
at_str += str(val) + '\n'
return at_str
def make_hseg_tree_panel(self):
root = DefaultMutableTreeNode(self.exper.name)
for hseg in self.exper.hsegs():
hseg_node = DefaultMutableTreeNode(hseg.name)
root.add(hseg_node)
hseg_at_deviations = self.exper.hseg_files_cab(
).archetype_deviations
if len(hseg_at_deviations[hseg.name]) > 0:
for definer, file_names in hseg_at_deviations[
hseg.name].items():
for file_name in file_names:
node_str = definer + ': ' + file_name
temp = DefaultMutableTreeNode(node_str)
hseg_node.add(temp)
hseg_tree = JTree(root)
hseg_tree.setCellRenderer(BobPyTreeCellRenderer())
hseg_scroll_pane = JScrollPane()
hseg_scroll_pane.getViewport().setView((hseg_tree))
hseg_panel = JPanel(MigLayout('insets 0'))
hseg_panel.add(hseg_scroll_pane, 'grow, span, push, wrap')
run_button = JButton('Run')
run_button.addActionListener(ActionListenerFactory(self, self.run_al))
rerun_button = JButton('Rerun')
rerun_button.addActionListener(
ActionListenerFactory(self, self.rerun_al))
hseg_panel.add(run_button)
hseg_panel.add(rerun_button)
return hseg_panel
def log(self, text):
self.log_text.append(str(text) + '\n')
def text_field_al(self, e):
# self.dir_path =
self.got_exper(self.dir_text_field.getText())
def choose_dir_al(self, e):
dc = DirectoryChooser('Choose a bob_py experiment folder')
# self.dir_path = dc.getDirectory()
# self.dir_text_field.setText(self.dir_path)
# self.dir_text_field.setText('blerg')
# IJ.log('blerg')
# print('boop')
self.got_exper(dc.getDirectory())
def close_al(self, e):
self.dispatchEvent(WindowEvent(self, WindowEvent.WINDOW_CLOSING))
def run_al(self, e):
# dt = br.dtic('Processed experiment {}'.format(self.exper.name))
t = br.tic()
self.exper.make_data()
self.exper.output_cell_cols_def()
self.exper.output_nuc_cols_def()
self.exper.output_new_hdings()
self.exper.log('Processed experiment {} in {:.3f} seconds'.format(
self.exper.name, br.toc(t)))
# br.dtoc(dt)
def rerun_al(self, e):
# dt = br.dtic('Processed experiment {}'.format(self.exper.name))
# t = br.tic()
self.exper = None
self.got_exper(self.dir_path)
self.run_al(None)
# self.exper =
# self.exper.make_data()
# self.exper.output_cell_cols_def()
# self.exper.output_nuc_cols_def()
# self.exper.output_new_hdings()
#
# self.exper.log('Created and processed experiment {} in {:.3f} seconds'.format(self.exper.name, br.toc(t)))
# br.dtoc(dt)
# def meta_data_al(self, e) :
# meta_data_path = self.exper.meta_data_path()
# if not os.path.exists(meta_data_path) :
# txt = make_meta_data_str(self.exper)
# with open(meta_data_path, 'w') as f :
# f.write(txt)
#
# IJ.open(meta_data_path)
def mdf_create_al(self, e):
meta_data_path = self.exper.meta_data_path()
# if not os.path.exists(meta_data_path) :
intens_im_list = []
for check_box in self.intens_im_boxes:
if check_box.isSelected():
intens_im_list.append(check_box.getLabel())
txt = make_meta_data_str2(self.exper, intens_im_list)
with open(meta_data_path, 'w') as f:
f.write(txt)
# IJ.open(meta_data_path)
def mdf_open_al(self, e):
meta_data_path = self.exper.meta_data_path()
IJ.open(meta_data_path)
def got_exper(self, dir_path):
# IJ.log('exper')
self.dir_path = dir_path
self.dir_text_field.setText(self.dir_path)
self.log_text = JTextArea()
self.exper = bob_py.Exper(dir_path, gui=self)
self.show_exper_info()
class BobGui(JFrame):
def __init__(self):
super(BobGui, self).__init__('BobPy')
# cls = self.getClass()
# print(cls)
# self.setLayout(MigLayout())
self.setLayout(BorderLayout())
self.main_panel = JPanel()
self.main_panel.setLayout(MigLayout())
dir_panel = JPanel()
dir_panel.setLayout(BoxLayout(dir_panel, BoxLayout.X_AXIS))
dir_label = JLabel('Experiment Folder:')
dir_panel.add(dir_label)
self.dir_text_field = JTextField(10)
self.dir_text_field.addActionListener(
ActionListenerFactory(self, self.text_field_al))
dir_panel.add(self.dir_text_field)
dir_button = JButton('open')
dir_button.addActionListener(
ActionListenerFactory(self, self.choose_dir_al))
dir_panel.add(dir_button)
self.main_panel.add(dir_panel, 'growx, spanx, pushx, wrap')
add_key_args(self.main_panel, 'close_w',
ActionListenerFactory(self, self.close_al), KeyEvent.VK_W,
Toolkit.getDefaultToolkit().getMenuShortcutKeyMask())
self.add(self.main_panel, BorderLayout.CENTER)
self.setPreferredSize(Dimension(500, 400))
self.pack()
self.setLocationRelativeTo(None)
self.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE)
self.setVisible(True)
def show_exper_info_old(self):
# sb = br.SimilarityBuilder()
cab = br.CollectionArchetypeBuilder()
for hseg in self.exper.hsegs():
all_file_dict = hseg.file_dict()
all_file_dict.update(hseg.cell_file_dict())
all_file_dict.update(hseg.bin_file_dict())
cab.add_collection(hseg.name, all_file_dict)
hseg_at, hseg_at_deviations = cab.get_archetype_info()
at_str = ''
for val in hseg_at:
at_str += str(val) + '\n'
chf_panel = self.make_chf_panel(at_str)
hseg_tree_panel = self.make_hseg_tree_panel(hseg_at_deviations)
self.split_pane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self.split_pane.setOneTouchExpandable(True)
self.split_pane.setContinuousLayout(True)
self.split_pane.setResizeWeight(0.5)
self.split_pane.add(chf_panel)
self.split_pane.add(hseg_tree_panel)
self.main_panel.add(self.split_pane, 'grow')
self.revalidate()
def show_exper_info(self):
# sb = br.SimilarityBuilder()
# cab = br.CollectionArchetypeBuilder()
#
# for hseg in self.exper.hsegs() :
# all_file_dict = hseg.file_dict()
# all_file_dict.update(hseg.cell_file_dict())
# all_file_dict.update(hseg.bin_file_dict())
# cab.add_collection(hseg.name, all_file_dict)
#
# hseg_at, hseg_at_deviations = cab.get_archetype_info()
#
# at_str = ''
# for val in hseg_at :
# at_str += str(val) + '\n'
chf_panel = self.make_chf_panel()
hseg_tree_panel = self.make_hseg_tree_panel()
self.split_pane = JSplitPane(JSplitPane.HORIZONTAL_SPLIT)
self.split_pane.setOneTouchExpandable(True)
self.split_pane.setContinuousLayout(True)
self.split_pane.setResizeWeight(0.5)
self.split_pane.add(chf_panel)
self.split_pane.add(hseg_tree_panel)
self.main_panel.add(self.split_pane, 'grow')
self.revalidate()
def make_chf_panel_old(self, at_str):
""" cf --> common hseg files """
chf_panel = JPanel()
# chf_panel.setLayout(BoxLayout(chf_panel, BoxLayout.Y_AXIS))
chf_panel.setLayout(MigLayout('insets 0'))
# chf_panel.setAlignmentX(Component.LEFT_ALIGNMENT)
chf_label = JLabel('Common Hemeisegment Files')
# chf_label.setAlignmentX(Component.LEFT_ALIGNMENT)
chf_panel.add(chf_label, 'grow, wrap')
chf_text_area = JTextArea(at_str)
chf_panel.add(chf_text_area, 'grow, push, span')
return chf_panel
def make_chf_panel(self):
""" chf --> common hseg files """
chf_panel = JPanel()
# chf_panel.setLayout(BoxLayout(chf_panel, BoxLayout.Y_AXIS))
chf_panel.setLayout(MigLayout('insets 0'))
# chf_panel.setAlignmentX(Component.LEFT_ALIGNMENT)
chf_files_label = JLabel('Hemisegment cells')
chf_files_text = JTextArea(
BobGui.archetype_to_str(
self.exper.hseg_cell_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Hemisegment binary image files')
chf_files_text = JTextArea(
BobGui.archetype_to_str(self.exper.hseg_bin_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow, wrap')
chf_files_label = JLabel('Other hemisegment files')
chf_files_text = JTextArea(
BobGui.archetype_to_str(self.exper.hseg_files_cab().archetype))
chf_panel.add(chf_files_label, 'growx, wrap')
chf_panel.add(chf_files_text, 'grow')
# chf_label = JLabel('Common Hemeisegment Files')
# # chf_label.setAlignmentX(Component.LEFT_ALIGNMENT)
#
# chf_panel.add(chf_label, 'grow, wrap')
#
# chf_text_area = JTextArea(at_str)
# chf_panel.add(chf_text_area, 'grow, push, span')
return chf_panel
@staticmethod
def archetype_to_str(archetype):
at_str = ''
for val in archetype:
at_str += str(val) + '\n'
return at_str
# def make_hseg_tree_panel(self, hseg_at_deviations) :
def make_hseg_tree_panel(self):
root = DefaultMutableTreeNode(self.exper.name)
for hseg in self.exper.hsegs():
hseg_node = DefaultMutableTreeNode(hseg.name)
root.add(hseg_node)
hseg_at_deviations = self.exper.hseg_all_files_cab(
).archetype_deviations
if len(hseg_at_deviations[hseg.name]) > 0:
for definer, file_names in hseg_at_deviations[
hseg.name].items():
for file_name in file_names:
node_str = definer + ': ' + file_name
temp = DefaultMutableTreeNode(node_str)
hseg_node.add(temp)
hseg_tree = JTree(root)
hseg_tree.setCellRenderer(BobPyTreeCellRenderer())
hseg_scroll_pane = JScrollPane()
hseg_scroll_pane.getViewport().setView((hseg_tree))
return hseg_scroll_pane
def text_field_al(self, e):
self.dir_path = self.dir_text_field.getText()
self.got_exper(self.dir_path)
def choose_dir_al(self, e):
dc = DirectoryChooser('Choose a bob_py experiment folder')
self.dir_path = dc.getDirectory()
self.dir_text_field.setText(self.dir_path)
self.got_exper(self.dir_path)
def close_al(self, e):
self.dispatchEvent(WindowEvent(self, WindowEvent.WINDOW_CLOSING))
def got_exper(self, dir_path):
self.exper = bob_py.Exper(dir_path)
self.show_exper_info()
