class BaseAnnotationItem(ResizableGraphicsItem):
handler_cache = {}
styles = ['font-family', 'font-size', 'text-bold', 'text-italic', 'text-underline', 'text-color', 'color-border', 'color-background']
minSize = ANNOTATION_MINIMUM_QSIZE
def __init__(self, position=None, *args, **kwargs):
super(BaseAnnotationItem, self).__init__(*args, **kwargs)
# Config for each annotation item, holding the settings (styles, etc)
# update-control via the toolbar using add_handler linking
self.config = ConfigManager()
self.config.updated.connect(self.applyStyleConfig)
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setFlag(QGraphicsItem.ItemIsFocusable)
if position:
self.setPos(position)
self.setZValue(-1)
def delete(self):
self.prepareGeometryChange()
self.scene().annotations.remove(self)
self.scene().removeItem(self)
self.removeHandlers()
def keyPressEvent(self, e):
if e.key() == Qt.Key_Backspace and e.modifiers() == Qt.ControlModifier:
self.delete()
else:
return super(BaseAnnotationItem, self).keyPressEvent(e)
def importStyleConfig(self, config):
for k in self.styles:
self.config.set(k, config.get(k))
def addHandlers(self):
m = self.scene().views()[0].m # Hack; need to switch to importing this
for k in self.styles:
self.config.add_handler(k, m.styletoolbarwidgets[k])
def removeHandlers(self):
for k in self.styles:
self.config.remove_handler(k)
def itemChange(self, change, value):
if change == QGraphicsItem.ItemSelectedChange:
if not value:
self.removeHandlers()
elif change == QGraphicsItem.ItemSelectedHasChanged:
if value:
self.addHandlers()
return super(BaseAnnotationItem, self).itemChange(change, value)
class MainWindow(QMainWindow):
def __init__(self):
super(MainWindow, self).__init__()
self.setWindowTitle('PyQtConfig Demo')
self.config = ConfigManager()
CHOICE_A = 1
CHOICE_B = 2
CHOICE_C = 3
CHOICE_D = 4
map_dict = {
'Choice A': CHOICE_A,
'Choice B': CHOICE_B,
'Choice C': CHOICE_C,
'Choice D': CHOICE_D,
}
self.config.set_defaults({
'number': 13,
'text': 'hello',
'active': True,
'combo': CHOICE_C,
})
gd = QGridLayout()
sb = QSpinBox()
gd.addWidget(sb, 0, 1)
self.config.add_handler('number', sb)
te = QLineEdit()
gd.addWidget(te, 1, 1)
self.config.add_handler('text', te)
cb = QCheckBox()
gd.addWidget(cb, 2, 1)
self.config.add_handler('active', cb)
cmb = QComboBox()
cmb.addItems(map_dict.keys())
gd.addWidget(cmb, 3, 1)
self.config.add_handler('combo', cmb, mapper=map_dict)
self.current_config_output = QTextEdit()
gd.addWidget(self.current_config_output, 0, 3, 3, 1)
self.config.updated.connect(self.show_config)
self.show_config()
self.window = QWidget()
self.window.setLayout(gd)
self.setCentralWidget(self.window)
def show_config(self):
self.current_config_output.setText(str(self.config.as_dict()))
class MainWindow(QMainWindow):
def __init__(self):
super(MainWindow, self).__init__()
self.setWindowTitle('PyQtConfig Demo')
self.config = ConfigManager()
CHOICE_A = 1
CHOICE_B = 2
CHOICE_C = 3
CHOICE_D = 4
map_dict = {
'Choice A': CHOICE_A,
'Choice B': CHOICE_B,
'Choice C': CHOICE_C,
'Choice D': CHOICE_D,
}
self.config.set_defaults({
'number': 13,
'text': 'hello',
'active': True,
'combo': CHOICE_C,
})
gd = QGridLayout()
sb = QSpinBox()
gd.addWidget(sb, 0, 1)
self.config.add_handler('number', sb)
te = QLineEdit()
gd.addWidget(te, 1, 1)
self.config.add_handler('text', te)
cb = QCheckBox()
gd.addWidget(cb, 2, 1)
self.config.add_handler('active', cb)
cmb = QComboBox()
cmb.addItems(map_dict.keys())
gd.addWidget(cmb, 3, 1)
self.config.add_handler('combo', cmb, mapper=map_dict)
self.current_config_output = QTextEdit()
gd.addWidget(self.current_config_output, 0, 3, 3, 1)
self.config.updated.connect(self.show_config)
self.show_config()
self.window = QWidget()
self.window.setLayout(gd)
self.setCentralWidget(self.window)
def show_config(self):
self.current_config_output.setText(str(self.config.as_dict()))
class LisaConfigWindow(QDialog):
# class LisaConfigWindow(QMainWindow):
def __init__(self, config_in, ncols=2):
super(LisaConfigWindow, self).__init__()
self.setWindowTitle('Lisa Config')
self.config = ConfigManager()
self.ncols = ncols
# used with other module. If it is set, lisa config is deleted
self.reset_config = False
CHOICE_A = "{pairwise_alpha_per_mm2: 45, return_only_object_with_seeds: true}"
# CHOICE_A = 23
CHOICE_B = 2
CHOICE_C = 3
CHOICE_D = 4
map_dict = {
'Graph-Cut': CHOICE_A,
'Choice B': CHOICE_B,
'Choice C': CHOICE_C,
'Choice D': CHOICE_D,
}
config_def = {
'working_voxelsize_mm': 2.0,
'save_filetype': 'pklz',
# 'manualroi': True,
'segparams': CHOICE_A,
}
config_def.update(config_in)
self.config.set_defaults(config_def)
gd = QGridLayout()
gd_max_i = 0
for key, value in config_in.iteritems():
if type(value) is int:
sb = QSpinBox()
sb.setRange(-100000, 100000)
elif type(value) is float:
sb = QDoubleSpinBox()
elif type(value) is str:
sb = QLineEdit()
elif type(value) is bool:
sb = QCheckBox()
else:
logger.error("Unexpected type in config dictionary")
row = gd_max_i / self.ncols
col = (gd_max_i % self.ncols) * 2
gd.addWidget(QLabel(key),row, col +1)
gd.addWidget(sb, row, col + 2)
self.config.add_handler(key, sb)
gd_max_i += 1
# gd.addWidget(QLabel("save filetype"), 1, 1)
# te = QLineEdit()
# gd.addWidget(te, 1, 2)
# self.config.add_handler('save_filetype', te)
#
# gd.addWidget(QLabel("segmentation parameters"), 2, 1)
# te = QLineEdit()
# gd.addWidget(te, 2, 2)
# self.config.add_handler('segparams', te)
# cb = QCheckBox()
# gd.addWidget(cb, 2, 2)
# self.config.add_handler('active', cb)
# gd.addWidget(QLabel("segmentation parameters"), 3, 1)
# cmb = QComboBox()
# cmb.addItems(map_dict.keys())
# gd.addWidget(cmb, 3, 2)
# self.config.add_handler('segparams', cmb, mapper=map_dict)
self.current_config_output = QTextEdit()
# rid.setColumnMinimumWidth(3, logo.width()/2)
text_col = (self.ncols * 2) + 3
gd.setColumnMinimumWidth(text_col, 500)
gd.addWidget(self.current_config_output, 1, text_col, (gd_max_i/2)-1, 1)
btn_reset_config = QPushButton("Reset and quit", self)
btn_reset_config.clicked.connect(self.btnResetConfig)
gd.addWidget(btn_reset_config, 0, text_col)
btn_save_config = QPushButton("Save and quit", self)
btn_save_config.clicked.connect(self.btnSaveConfig)
gd.addWidget(btn_save_config, (gd_max_i / 2), text_col)
self.config.updated.connect(self.show_config)
self.show_config()
# my line
self.setLayout(gd)
# self.window = QWidget()
# self.window.setLayout(gd)
# self.setCentralWidget(self.window)
def add_grid_line(self, key, value):
pass
def get_config_as_dict(self):
dictionary = self.config.as_dict()
for key, value in dictionary.iteritems():
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
if type(value) == PyQt4.QtCore.QString:
value = str(value)
dictionary[key] = value
return dictionary
def btnResetConfig(self, event=None):
self.reset_config = True
self.close()
def btnSaveConfig(self, event=None):
self.reset_config = False
self.close()
def show_config(self):
text = str(self.get_config_as_dict())
self.current_config_output.setText(text)
class dialogPluginManagement(ui.GenericDialog):
def populate_plugin_list(self):
disabled_plugins = self.config.get('Plugins/Disabled')
while self.plugins_lw.count() > 0: # Empty list
self.plugins_lw.takeItem(0)
for id, plugin in plugin_metadata.items():
item = QListWidgetItem()
item.plugin_metadata = plugin
item.plugin_shortname = id
if 'image' in plugin:
item.setData(Qt.DecorationRole, plugin['image'])
item.setData(Qt.DisplayRole, "%s (v%s)" % (plugin['name'], plugin['version']))
item.setData(Qt.UserRole, plugin['description'])
item.setData(Qt.UserRole + 1, plugin['author'])
if plugin['path'] not in disabled_plugins:
item.setData(Qt.UserRole + 2, "Active")
self.plugins_lw.addItem(item)
def onActivate(self):
items = self.plugins_lw.selectedItems()
disabled_plugins = self.config.get('Plugins/Disabled')
for i in items:
plugin_path = plugin_metadata[i.plugin_shortname]['path']
if plugin_path in disabled_plugins:
disabled_plugins.remove(plugin_path)
self.config.set('Plugins/Disabled', disabled_plugins)
self.populate_plugin_list()
def onDeactivate(self):
items = self.plugins_lw.selectedItems()
disabled_plugins = self.config.get('Plugins/Disabled')
for i in items:
plugin_path = plugin_metadata[i.plugin_shortname]['path']
if plugin_path not in disabled_plugins:
disabled_plugins.append(plugin_path)
self.config.set('Plugins/Disabled', disabled_plugins)
self.populate_plugin_list()
def onRefresh(self):
get_available_plugins(self.config.get('Plugins/Paths')[:], include_deactivated=True)
self.populate_plugin_list()
def __init__(self, parent, **kwargs):
super(dialogPluginManagement, self).__init__(parent, **kwargs)
self.setWindowTitle(tr("Manage Plugins"))
self.config = ConfigManager()
self.config.defaults = {
'Plugins/Paths': settings.get('Plugins/Paths'),
'Plugins/Disabled': settings.get('Plugins/Disabled'),
}
self.m = parent
self.setFixedSize(self.sizeHint())
self.plugins_lw = QListWidget()
self.plugins_lw.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.plugins_lw.setItemDelegate(pluginListDelegate(self.plugins_lw))
self.plugins_lw.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
page = QWidget()
box = QGridLayout()
paths = QHBoxLayout()
self.pathlist = QLineEdit()
self.config.add_handler('Plugins/Paths', self.pathlist, (lambda x: x.split(';'), lambda x: ';'.join(x)))
paths.addWidget(QLabel('Search Paths:'))
paths.addWidget(self.pathlist)
box.addLayout(paths, 0, 0)
box.addWidget(self.plugins_lw, 1, 0)
buttons = QVBoxLayout()
refresh_btn = QPushButton('Refresh')
refresh_btn.clicked.connect(self.onRefresh)
buttons.addWidget(refresh_btn)
activate_btn = QPushButton('Activate')
activate_btn.clicked.connect(self.onActivate)
buttons.addWidget(activate_btn)
deactivate_btn = QPushButton('Dectivate')
deactivate_btn.clicked.connect(self.onDeactivate)
buttons.addWidget(deactivate_btn)
buttons.addStretch()
box.addLayout(buttons, 1, 1)
page.setLayout(box)
self.layout.addWidget(page)
# Stack it all up, with extra buttons
self.dialogFinalise()
# Refresh the list of available plugins
self._init_timer = QTimer.singleShot(0, self.onRefresh)
def sizeHint(self):
return QSize(600, 300)
class DictWidget(QtGui.QWidget):
def __init__(self, config_in, ncols=2, captions=None, hide_keys=None,
horizontal=False, show_captions=True, accept_button=False,
config_manager=None, radiobuttons=None, dropdownboxes=None):
"""
:param config_in: dictionary
:param ncols:
:param captions:
:param radiobuttons: {"name_of_radiobutton": [
["orig_caption_1", orig_caption_2],
default_value]
]
}
"""
super(DictWidget, self).__init__()
if captions is None:
captions = {}
if hide_keys is None:
hide_keys = []
self.config_in = config_in
self.ncols = ncols
self.captions = captions
self.accept_button = accept_button
self.hide_keys = copy.copy(hide_keys)
self.horizontal = horizontal
self.show_captions = show_captions
if radiobuttons is None:
radiobuttons = {}
self.radiobuttons = radiobuttons
if dropdownboxes is None:
dropdownboxes = {}
self.dropdownboxes = dropdownboxes
# hide also temp keys for lists and ndarrays
# due to load default params
self._get_tmp_composed_keys(config_in)
self.hide_keys.extend(self._tmp_composed_keys_list)
if config_manager is None:
self.config = ConfigManager()
self.config.set_defaults(config_in)
else:
self.config = config_manager
self.mainLayout = QGridLayout(self)
self.setLayout(self.mainLayout)
self.widgets = {}
self.grid_i = 0
self.init_ui()
def _get_tmp_composed_keys(self, cfg):
"""
Get list of temporary keys for lists and ndarrays. This keys are used for reconstruction.
vytvoří to seznam pomocných klíčů pro seznamy a ndarray
:param cfg:
:return:
"""
self._tmp_composed_keys_dict = {}
self._tmp_composed_keys_list = []
toappend = {}
for key, value in cfg.iteritems():
if key in self.dropdownboxes.keys():
continue
if key in self.radiobuttons.keys():
continue
if type(value) in (list, np.ndarray):
self._tmp_composed_keys_dict[key] = []
array = np.asarray(value)
key_array_i = 0
for val in array.tolist():
# key_i = (key, key_array_i)
key_i = ComposedDictMetadata((key, key_array_i))
self._tmp_composed_keys_dict[key].append(key_i)
self._tmp_composed_keys_list.append(key_i)
key_array_i += 1
toappend[key_i] = val
cfg.update(toappend)
def _create_dropdownbox(self, key, value):
# atomic_widget = QWidget()
row, col = self.__calculate_new_grid_position()
# layout = QBoxLayout(self.horizontal)
atomic_widget = QComboBox()
# atomic_widget.addItem("C")
# atomic_widget.addItem("C++")
values = self.dropdownboxes[key]
# values = self.dropdownboxes[key][0]
if value is not None and value in values:
# vali = atomic_widget.findText(value)
atomic_widget.findText(value)
atomic_widget.addItems(values)
# this does not work. I used findText()
# atomic_widget.setCurrentIndex(vali)
# layout.addWidget(cb)
# atomic_widget.setLayout(layout)
return atomic_widget
def _create_radiobutton(self, key, value):
atomic_widget = QWidget()
layout = QBoxLayout(self.horizontal)
for i, rbkey in enumerate(self.radiobuttons[key][0]):
b1 = QRadioButton("Button1")
if i == self.radiobuttons[key][1]:
b1.setChecked(True)
# b1.toggled.connect(lambda:self.btnstate(self.b1))
layout.addWidget(b1)
atomic_widget.setLayout(layout)
return atomic_widget
def init_ui(self):
# self.widgets = {}
# self.grid_i = 0
grid = self.mainLayout
for key, value in self.config_in.iteritems():
if key in self.hide_keys:
continue
if key in self.captions.keys():
caption = self.captions[key]
else:
caption = key
atomic_widget = self.__get_widget_for_primitive_types(key, value)
if atomic_widget is None:
if type(value) in (list, np.ndarray):
array = np.asarray(value)
atomic_widget = self._create_sub_grid_from_ndarray(key, array)
row, col = self.__calculate_new_grid_position()
grid.addWidget(QLabel(caption), row, col + 1)
grid.addLayout(atomic_widget, row, col + 2)
continue
else:
logger.error("Unexpected type in config dictionary")
continue
# import ipdb; ipdb.set_trace()
row, col = self.__calculate_new_grid_position()
grid.addWidget(QLabel(caption), row, col + 1)
grid.addWidget(atomic_widget, row, col + 2)
# gd.setColumnMinimumWidth(text_col, 500)
if self.accept_button:
btn_accept = QPushButton("Accept", self)
btn_accept.clicked.connect(self.btn_accept)
text_col = (self.ncols * 2) + 3
grid.addWidget(btn_accept, (self.grid_i / 2), text_col)
self.config.updated.connect(self.on_config_update)
# def __add_line
def __get_widget_for_primitive_types(self, key, value):
"""
return right widget and connect the value with config_manager
:param key:
:param value:
:return:
"""
if key in self.dropdownboxes.keys():
atomic_widget = self._create_dropdownbox(key,value)
self.config.add_handler(key, atomic_widget)
elif key in self.radiobuttons.keys():
atomic_widget = self._create_radiobutton(key,value)
self.config.add_handler(key, atomic_widget)
elif type(value) is int:
atomic_widget = QSpinBox()
atomic_widget.setRange(-100000, 100000)
self.config.add_handler(key, atomic_widget)
elif type(value) is float:
atomic_widget = QDoubleSpinBox()
atomic_widget.setDecimals(6)
atomic_widget.setMaximum(1000000000)
self.config.add_handler(key, atomic_widget)
elif type(value) is str:
atomic_widget = QLineEdit()
self.config.add_handler(key, atomic_widget)
elif type(value) is bool:
atomic_widget = QCheckBox()
self.config.add_handler(key, atomic_widget)
else:
return None
return atomic_widget
def _create_sub_grid_from_ndarray(self, key, ndarray):
hgrid = QGridLayout(self)
hgrid_i = 0
for val in ndarray.tolist():
# key_i = key + str(hgrid_i)
key_i = (key, hgrid_i)
atomic_widget = self.__get_widget_for_primitive_types(key_i, val)
hgrid.addWidget(atomic_widget, 0, hgrid_i)
hgrid_i += 1
return hgrid
def __calculate_new_grid_position(self):
row = self.grid_i / self.ncols
col = (self.grid_i % self.ncols) * 2
self.grid_i += 1
if self.horizontal:
return col, row
return row, col
def btn_accept(self):
print ("btn_accept: " + str(self.config_as_dict()))
def on_config_update(self):
pass
def config_as_dict(self):
def _primitive_type(value):
if type(value) == PyQt4.QtCore.QString:
value = str(value)
return value
dictionary = self.config.as_dict()
dictionary = copy.copy(dictionary)
for key, value in dictionary.iteritems():
from PyQt4.QtCore import pyqtRemoveInputHook
#pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
# if type(key) == tuple:
if type(key) == ComposedDictMetadata:
dict_key, value_index = key
dict_key = (dict_key)
# if dict_key not in dictionary.keys():
# dictionary[dict_key] = {}
dictionary[dict_key][value_index] = _primitive_type(value)
else:
dictionary[key] = _primitive_type(value)
for key in dictionary.keys():
# if type(key) == tuple:
if type(key) == ComposedDictMetadata:
dictionary.pop(key)
# for key, value in dictionary.iteritems():
# if type(key) == tuple:
# dictionary
return dictionary
class ToolBase(QObject):
'''
Base tool definition for inclusion in the UI. Define specific config settings;
attach a panel widget for configuration.
'''
is_manual_runnable = True
is_auto_runnable = True
is_auto_rerunnable = True
is_disableable = True
progress = pyqtSignal(float)
status = pyqtSignal(str)
config_panel_size = 250
view_widget = 'SpectraViewer'
def __init__(self, parent, *args, **kwargs):
super(ToolBase, self).__init__(parent, *args, **kwargs)
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'is_active': True,
'auto_run_on_config_change': True
})
self.config.updated.connect(self.auto_run_on_config_change)
self.buttonBar = QWidget()
self.configPanels = QWidget()
self.configLayout = QVBoxLayout()
self.configLayout.setContentsMargins(0, 0, 0, 0)
self.configPanels.setLayout(self.configLayout)
self._previous_config_backup_ = {}
self._worker_thread_ = None
self._worker_thread_lock_ = False
self.data = {
'spc': None,
}
self.current_status = 'ready'
self.current_progress = 0
self.progress.connect(self.progress_callback)
self.status.connect(self.status_callback)
def addConfigPanel(self, panel):
self.configLayout.addWidget(panel(self))
def addButtonBar(self, buttons):
'''
Create a button bar
Supplied with a list of QPushButton objects (already created using helper stubs; see below)
:param buttons:
:return:
'''
btnlayout = QHBoxLayout()
btnlayout.addSpacerItem(
QSpacerItem(250, 1, QSizePolicy.Maximum, QSizePolicy.Maximum))
for btn in buttons:
btnlayout.addWidget(btn)
self.configLayout.addLayout(btnlayout)
btnlayout.addSpacerItem(
QSpacerItem(250, 1, QSizePolicy.Maximum, QSizePolicy.Maximum))
def run_manual(self):
pass
def disable(self):
self.status.emit('inactive')
self.config.set('is_active', False)
self.item.setFlags(Qt.NoItemFlags)
def reset(self):
self.config.set_many(self.config.defaults)
def undo(self):
self.config.set_many(self._config_backup_)
def deftaultButtons(self):
buttons = []
if self.is_disableable:
disable = QPushButton(
QIcon(os.path.join(utils.scriptdir, 'icons', 'cross.png')),
'Disable')
disable.setToolTip('Disable this tool')
disable.pressed.connect(self.disable)
buttons.append(disable)
reset = QPushButton(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'arrow-turn-180-left.png')), 'Reset to defaults')
reset.setToolTip('Reset to defaults')
reset.pressed.connect(self.reset)
buttons.append(reset)
undo = QPushButton(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'arrow-turn-180-left.png')), 'Undo')
undo.setToolTip('Undo recent changes')
undo.pressed.connect(self.undo)
buttons.append(undo)
if self.is_auto_runnable:
auto = QPushButton(
QIcon(os.path.join(utils.scriptdir, 'icons', 'lightning.png')),
'Auto')
auto.setToolTip('Auto-update spectra when settings change')
auto.setCheckable(True)
auto.pressed.connect(self.run_manual)
self.config.add_handler('auto_run_on_config_change', auto)
buttons.append(auto)
if self.is_manual_runnable:
apply = QPushButton(
QIcon(os.path.join(utils.scriptdir, 'icons', 'play.png')),
'Apply')
apply.setToolTip('Apply current settings to spectra')
apply.pressed.connect(self.run_manual)
buttons.append(apply)
return buttons
def enable(self):
if self.current_status == 'inactive':
self.status.emit('ready')
self.item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable)
self.config.set('is_active', True)
def activate(self):
self.parent().current_tool = self
self.enable()
self._config_backup_ = self.config.as_dict()
self._refresh_plot_timer_ = QTimer.singleShot(0, self.plot)
self.parent().viewStack.setCurrentWidget(self.parent().spectraViewer)
self.parent().configstack.setCurrentWidget(self.configPanels)
self.parent().configstack.setMaximumHeight(self.config_panel_size)
def set_active(self, active):
self.config.set('is_active', active)
def get_previous_tool(self):
# Get the previous ACTIVE tool in the tool table
n = self.parent().tools.index(self)
for tool in self.parent().tools[n - 1::-1]:
if tool.current_status != 'inactive':
return tool
else:
return None
def get_previous_spc(self):
t = self.get_previous_tool()
if t:
return t.data['spc']
else:
return None
def plot(self, **kwargs):
if 'spc' in self.data:
self.parent().spectraViewer.plot(self.data['spc'], **kwargs)
def get_plotitem(self):
return self.parent().spectraViewer.spectraViewer.plotItem
def auto_run_on_config_change(self):
pass
#if self.is_auto_runnable and self.config.get('is_active') and self.config.get('auto_run_on_config_change'):
# self.run_manual()
def run(self, fn):
'''
Run the target function, passing in the current spectra, and config settings (as dict)
:param fn:
:return:
'''
if self._worker_thread_lock_:
return False # Can't run
self.progress.emit(0)
self.status.emit('active')
spc = self.get_previous_spc()
self._worker_thread_lock_ = True
print(self.config.as_dict())
self._worker_thread_ = Worker(fn=fn,
**{
'spc': deepcopy(spc),
'config': self.config.as_dict(),
'progress_callback':
self.progress.emit,
})
self._worker_thread_.signals.finished.connect(self.finished)
self._worker_thread_.signals.result.connect(self.result)
self._worker_thread_.signals.error.connect(self.error)
self.parent().threadpool.start(self._worker_thread_)
def error(self, error):
self.progress.emit(1.0)
self.status.emit('error')
logging.error(error)
self._worker_thread_lock_ = False
def result(self, result):
self.progress.emit(1)
self.status.emit('complete')
# Apply post-processing
if 'spc' in result:
result['spc'] = self.post_process_spc(result['spc'])
self.data = result
self.plot()
def finished(self):
# Cleanup
self._worker_thread_lock_ = False
def progress_callback(self, progress):
self.current_progress = progress
self.item.setData(Qt.UserRole + 2, progress)
def status_callback(self, status):
self.current_status = status
self.item.setData(Qt.UserRole + 3, status)
def post_process_spc(self, spc):
'''
Apply post-processing to the spectra before loading into the data store, e.g. for outlier
detection, stats etc.
:param spc:
:return:
'''
# Outliers
def identify_outliers(data, m=2):
return abs(data - np.mean(data, axis=0)) < (m *
np.std(data, axis=0))
# Identify outliers on a point by point basis. Count up 'outliers' and score ratio of points that are
# outliers for each specra > 5% (make this configurable) is an outlier.
spc.outliers = np.sum(~identify_outliers(spc.data), axis=1) / float(
spc.data.shape[1])
return spc
class dialogPluginManagement(ui.GenericDialog):
def populate_plugin_list(self):
disabled_plugins = self.config.get('Plugins/Disabled')
while self.plugins_lw.count() > 0: # Empty list
self.plugins_lw.takeItem(0)
for id, plugin in plugin_metadata.items():
item = QListWidgetItem()
item.plugin_metadata = plugin
item.plugin_shortname = id
if 'image' in plugin:
item.setData(Qt.DecorationRole, plugin['image'])
item.setData(Qt.DisplayRole,
"%s (v%s)" % (plugin['name'], plugin['version']))
item.setData(Qt.UserRole, plugin['description'])
item.setData(Qt.UserRole + 1, plugin['author'])
if plugin['path'] not in disabled_plugins:
item.setData(Qt.UserRole + 2, "Active")
self.plugins_lw.addItem(item)
def onActivate(self):
items = self.plugins_lw.selectedItems()
disabled_plugins = self.config.get('Plugins/Disabled')
for i in items:
plugin_path = plugin_metadata[i.plugin_shortname]['path']
if plugin_path in disabled_plugins:
disabled_plugins.remove(plugin_path)
self.config.set('Plugins/Disabled', disabled_plugins)
self.populate_plugin_list()
def onDeactivate(self):
items = self.plugins_lw.selectedItems()
disabled_plugins = self.config.get('Plugins/Disabled')
for i in items:
plugin_path = plugin_metadata[i.plugin_shortname]['path']
if plugin_path not in disabled_plugins:
disabled_plugins.append(plugin_path)
self.config.set('Plugins/Disabled', disabled_plugins)
self.populate_plugin_list()
def onRefresh(self):
get_available_plugins(self.config.get('Plugins/Paths')[:],
include_deactivated=True)
self.populate_plugin_list()
def __init__(self, parent, **kwargs):
super(dialogPluginManagement, self).__init__(parent, **kwargs)
self.setWindowTitle(tr("Manage Plugins"))
self.config = ConfigManager()
self.config.defaults = {
'Plugins/Paths': settings.get('Plugins/Paths'),
'Plugins/Disabled': settings.get('Plugins/Disabled'),
}
self.m = parent
self.setFixedSize(self.sizeHint())
self.plugins_lw = QListWidget()
self.plugins_lw.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.plugins_lw.setItemDelegate(pluginListDelegate(self.plugins_lw))
self.plugins_lw.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
page = QWidget()
box = QGridLayout()
paths = QHBoxLayout()
self.pathlist = QLineEdit()
self.config.add_handler(
'Plugins/Paths', self.pathlist,
(lambda x: x.split(';'), lambda x: ';'.join(x)))
paths.addWidget(QLabel('Search Paths:'))
paths.addWidget(self.pathlist)
box.addLayout(paths, 0, 0)
box.addWidget(self.plugins_lw, 1, 0)
buttons = QVBoxLayout()
refresh_btn = QPushButton('Refresh')
refresh_btn.clicked.connect(self.onRefresh)
buttons.addWidget(refresh_btn)
activate_btn = QPushButton('Activate')
activate_btn.clicked.connect(self.onActivate)
buttons.addWidget(activate_btn)
deactivate_btn = QPushButton('Dectivate')
deactivate_btn.clicked.connect(self.onDeactivate)
buttons.addWidget(deactivate_btn)
buttons.addStretch()
box.addLayout(buttons, 1, 1)
page.setLayout(box)
self.layout.addWidget(page)
# Stack it all up, with extra buttons
self.dialogFinalise()
# Refresh the list of available plugins
self._init_timer = QTimer.singleShot(0, self.onRefresh)
def sizeHint(self):
return QSize(600, 300)
class AnnotatePeaks(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotatePeaks, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Peaks')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Peaks')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_peaks = QListWidgetAddRemove()
self.lw_peaks.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_peaks)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_start = QDoubleSpinBox()
self.add_start.setRange(-1, 12)
self.add_start.setDecimals(3)
self.add_start.setSuffix('ppm')
self.add_start.setSingleStep(0.001)
self.add_end = QDoubleSpinBox()
self.add_end.setRange(-1, 12)
self.add_end.setDecimals(3)
self.add_end.setSuffix('ppm')
self.add_end.setSingleStep(0.001)
addc = QPushButton('Add')
addc.clicked.connect(self.onPeakAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onPeakAdd)
loadc = QPushButton("Import from file")
loadc.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'folder-open-document.png')))
loadc.clicked.connect(self.onPeakImport)
metabh = QPushButton("Auto match via MetaboHunter")
metabh.setIcon(
QIcon(os.path.join(utils.scriptdir, 'icons', 'metabohunter.png')))
metabh.clicked.connect(self.onPeakImportMetabohunter)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_start)
vboxh.addWidget(self.add_end)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vbox.addWidget(loadc)
vbox.addWidget(metabh)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/peaks', self.lw_peaks,
(self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onPeakAdd(self):
c = self.config.get(
'annotation/peaks'
)[:] # Create new list to force refresh on reassign
c.append((self.add_label.text(), float(self.add_start.value()),
float(self.add_end.value())))
self.config.set('annotation/peaks', c)
def onPeakRemove(self):
i = self.lw_peaks.removeItemAt(self.lw_peaks.currentRow())
# c = self.map_list_fwd(i.text())
def onPeakImport(self):
filename, _ = QFileDialog.getOpenFileName(
self.parent(), 'Load peak annotations from file', '',
"All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)"
)
if filename:
c = self.config.get(
'annotation/peaks'
)[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append(row[0], float(row[1]), float(row[2]))
self.config.set('annotation/peaks', c)
def onPeakImportMetabohunter(self):
c = self.config.get(
'annotation/peaks'
)[:] # Create new list to force refresh on reassign
t = self.parent().current_tool
dlg = MetaboHunter(self)
if dlg.exec_():
if 'spc' in t.data:
# We have a spectra; calcuate mean; reduce size if required
spc = t.data['spc']
n = spc.data.shape[1]
ppm = spc.ppm
spcd = np.mean(spc.data, axis=0)
# Set a hard limit on the size of data we submit to be nice.
if n > 3000:
# Calculate the division required to be under the limit
d = np.ceil(float(n) / 3000)
# Trim axis to multiple of divisor
trim = (n // d) * d
spcd = spcd[:trim]
ppm = ppm[:trim]
# Mean d shape
spcd = np.mean(spcd.reshape(-1, d), axis=1)
ppm = np.mean(ppm.reshape(-1, d), axis=1)
# Submit with settings
hmdbs = metabohunter.request(
ppm,
spcd,
metabotype=dlg.config.get('Metabotype'),
database=dlg.config.get('Database Source'),
ph=dlg.config.get('Sample pH'),
solvent=dlg.config.get('Solvent'),
frequency=dlg.config.get('Frequency'),
method=dlg.config.get('Method'),
noise=dlg.config.get('Noise Threshold'),
confidence=dlg.config.get('Confidence Threshold'),
tolerance=dlg.config.get('Tolerance'))
ha = np.array(hmdbs)
unique_hmdbs = set(hmdbs)
if None in unique_hmdbs:
unique_hmdbs.remove(None)
# Extract out regions
for hmdb in unique_hmdbs:
hb = np.diff(ha == hmdb)
# These are needed to ensure markers are there for objects starting and ending on array edge
if ha[0] == hmdb:
hb[0] == True
if ha[-1] == hmdb:
hb[-1] == True
idx = np.nonzero(hb)[0]
idx = idx.reshape(-1, 2)
if dlg.config.get(
'convert_hmdb_ids_to_names'
) and hmdb in METABOHUNTER_HMDB_NAME_MAP.keys():
label = METABOHUNTER_HMDB_NAME_MAP[hmdb]
else:
label = hmdb
# Now we have an array of all start, stop positions for this item
for start, stop in idx:
c.append((label, ppm[start], ppm[stop]))
self.config.set('annotation/peaks', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%.2f\t%.2f" % tuple(x)
self.fwd_map_cache[s] = x
return s
class MetaboHunter(GenericDialog):
options = {
'Metabotype': {
'All': 'All',
'Drug': 'Drug',
'Food additive': 'Food additive',
'Mammalian': 'Mammalian',
'Microbial': 'Microbial',
'Plant': 'Plant',
'Synthetic/Industrial chemical': 'Synthetic/Industrial chemical',
},
'Database Source': {
'Human Metabolome Database (HMDB)': 'HMDB',
'Madison Metabolomics Consortium Database (MMCD)': 'MMCD',
},
'Sample pH': {
'10.00 - 10.99': 'ph7',
'7.00 - 9.99': 'ph7',
'6.00 - 6.99': 'ph6',
'5.00 - 5.99': 'ph5',
'4.00 - 4.99': 'ph4',
'3.00 - 3.99': 'ph3',
},
'Solvent': {
'All': 'all',
'Water': 'water',
'CDCl3': 'cdcl3',
'CD3OD': '5d3od',
'5% DMSO': '5dmso',
},
'Frequency': {
'All': 'all',
'600 MHz': '600',
'500 MHz': '500',
'400 MHz': '400',
},
'Method': {
'MH1: Highest number of matched peaks':
'HighestNumber',
'MH2: Highest number of matched peaks with shift tolerance':
'HighestNumberNeighbourhood',
'MH3: Greedy selection of metabolites with disjoint peaks':
'Greedy2',
'MH4: Highest number of matched peaks with intensities':
'HighestNumberHeights',
'MH5: Greedy selection of metabolites with disjoint peaks and heights':
'Greedy2Heights',
},
}
def __init__(self, *args, **kwargs):
super(MetaboHunter, self).__init__(*args, **kwargs)
self.setWindowTitle('MetaboHunter')
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'Metabotype': 'All',
'Database Source': 'HMDB',
'Sample pH': 'ph7',
'Solvent': 'water',
'Frequency': 'all',
'Method': 'HighestNumberNeighbourhood',
'Noise Threshold': 0.0001,
'Confidence Threshold': 0.5,
'Tolerance': 0.1,
'convert_hmdb_ids_to_names': True,
})
self.lw_combos = {}
for o in [
'Metabotype', 'Database Source', 'Sample pH', 'Solvent',
'Frequency', 'Method'
]:
row = QVBoxLayout()
cl = QLabel(o)
cb = QComboBox()
cb.addItems(list(self.options[o].keys()))
row.addWidget(cl)
row.addWidget(cb)
self.config.add_handler(o, cb, self.options[o])
self.layout.addLayout(row)
row = QGridLayout()
self.lw_spin = {}
for n, o in enumerate(
['Noise Threshold', 'Confidence Threshold', 'Tolerance']):
cl = QLabel(o)
cb = QDoubleSpinBox()
cb.setDecimals(4)
cb.setRange(0, 1)
cb.setSingleStep(0.01)
cb.setValue(float(self.config.get(o)))
row.addWidget(cl, 0, n)
row.addWidget(cb, 1, n)
self.config.add_handler(o, cb)
self.layout.addLayout(row)
row = QHBoxLayout()
row.addWidget(QLabel("Convert HMDB IDs to chemical names?"))
conv = QCheckBox()
self.config.add_handler('convert_hmdb_ids_to_names', conv)
row.addWidget(conv)
self.layout.addLayout(row)
self.dialogFinalise()
class AutomatonDialog(GenericDialog):
mode_options = {
'Manual': MODE_MANUAL,
'Watch files': MODE_WATCH_FILES,
'Watch folder': MODE_WATCH_FOLDER,
'Timer': MODE_TIMER,
}
def __init__(self, parent, **kwargs):
super(AutomatonDialog, self).__init__(parent, **kwargs)
self.setWindowTitle("Edit Automaton")
self.config = ConfigManager()
gb = QGroupBox('IPython notebook(s) (*.ipynb)')
grid = QGridLayout()
notebook_path_le = QLineEdit()
self.config.add_handler('notebook_paths', notebook_path_le, mapper=(lambda x: x.split(";"), lambda x: ";".join(x)))
grid.addWidget(notebook_path_le, 0, 0, 1, 2)
notebook_path_btn = QToolButton()
notebook_path_btn.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'document-attribute-i.png')))
notebook_path_btn.clicked.connect(lambda: self.onNotebookBrowse(notebook_path_le))
grid.addWidget(notebook_path_btn, 0, 2, 1, 1)
gb.setLayout(grid)
self.layout.addWidget(gb)
gb = QGroupBox('Automaton mode')
grid = QGridLayout()
mode_cb = QComboBox()
mode_cb.addItems(self.mode_options.keys())
mode_cb.currentIndexChanged.connect(self.onChangeMode)
self.config.add_handler('mode', mode_cb, mapper=self.mode_options)
grid.addWidget(QLabel('Mode'), 0, 0)
grid.addWidget(mode_cb, 0, 1)
grid.addWidget(QLabel('Hold trigger'), 1, 0)
fwatcher_hold_sb = QSpinBox()
fwatcher_hold_sb.setRange(0, 60)
fwatcher_hold_sb.setSuffix(' secs')
self.config.add_handler('trigger_hold', fwatcher_hold_sb)
grid.addWidget(fwatcher_hold_sb, 1, 1)
gb.setLayout(grid)
self.layout.addWidget(gb)
self.watchfile_gb = QGroupBox('Watch files')
grid = QGridLayout()
watched_path_le = QLineEdit()
grid.addWidget(watched_path_le, 0, 0, 1, 2)
self.config.add_handler('watched_files', watched_path_le, mapper=(lambda x: x.split(";"), lambda x: ";".join(x)))
watched_path_btn = QToolButton()
watched_path_btn.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'document-copy.png')))
watched_path_btn.setStatusTip('Add file(s)')
watched_path_btn.clicked.connect(lambda: self.onFilesBrowse(watched_path_le))
grid.addWidget(watched_path_btn, 0, 2, 1, 1)
grid.addWidget(QLabel('Watch window'), 1, 0)
watch_window_sb = QSpinBox()
watch_window_sb.setRange(0, 60)
watch_window_sb.setSuffix(' secs')
self.config.add_handler('watch_window', watch_window_sb)
grid.addWidget(watch_window_sb, 1, 1)
self.watchfile_gb.setLayout(grid)
self.layout.addWidget(self.watchfile_gb)
self.watchfolder_gb = QGroupBox('Watch folder')
grid = QGridLayout()
watched_path_le = QLineEdit()
grid.addWidget(watched_path_le, 0, 0, 1, 3)
self.config.add_handler('watched_folder', watched_path_le)
watched_path_btn = QToolButton()
watched_path_btn.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'folder-horizontal-open.png')))
watched_path_btn.setStatusTip('Add folder')
watched_path_btn.clicked.connect(lambda: self.onFolderBrowse(watched_path_le))
grid.addWidget(watched_path_btn, 0, 3, 1, 1)
grid.addWidget(QLabel('Iterate files in folder'), 3, 0)
loop_folder_sb = QCheckBox()
self.config.add_handler('iterate_watched_folder', loop_folder_sb)
grid.addWidget(loop_folder_sb, 3, 1)
loop_wildcard_le = QLineEdit()
self.config.add_handler('iterate_wildcard', loop_wildcard_le)
grid.addWidget(loop_wildcard_le, 3, 2)
self.watchfolder_gb.setLayout(grid)
self.layout.addWidget(self.watchfolder_gb)
self.timer_gb = QGroupBox('Timer')
grid = QGridLayout()
grid.addWidget(QLabel('Run every'), 0, 0)
watch_timer_sb = QSpinBox()
watch_timer_sb.setRange(0, 60)
watch_timer_sb.setSuffix(' secs')
self.config.add_handler('timer_seconds', watch_timer_sb)
grid.addWidget(watch_timer_sb, 0, 1)
self.timer_gb.setLayout(grid)
self.layout.addWidget(self.timer_gb)
self.manual_gb = QGroupBox('Manual') # No show
grid = QGridLayout()
grid.addWidget(QLabel('No configuration'), 0, 0)
self.manual_gb.setLayout(grid)
self.layout.addWidget(self.manual_gb)
gb = QGroupBox('Output')
grid = QGridLayout()
output_path_le = QLineEdit()
self.config.add_handler('output_path', output_path_le)
grid.addWidget(output_path_le, 0, 0, 1, 2)
notebook_path_btn = QToolButton()
notebook_path_btn.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'folder-horizontal-open.png')))
notebook_path_btn.clicked.connect(lambda: self.onFolderBrowse(notebook_path_le))
grid.addWidget(notebook_path_btn, 0, 2, 1, 1)
export_cb = QComboBox()
export_cb.addItems(IPyexporter_map.keys())
self.config.add_handler('output_format', export_cb)
grid.addWidget(QLabel('Notebook output format'), 1, 0)
grid.addWidget(export_cb, 1, 1)
gb.setLayout(grid)
self.layout.addWidget(gb)
self.layout.addStretch()
self.finalise()
self.onChangeMode(mode_cb.currentIndex())
def onNotebookBrowse(self, t):
global _w
filenames, _ = QFileDialog.getOpenFileNames(_w, "Load IPython notebook(s)", '', "IPython Notebooks (*.ipynb);;All files (*.*)")
if filenames:
self.config.set('notebook_paths', filenames)
def onFolderBrowse(self, t):
global _w
filename = QFileDialog.getExistingDirectory(_w, "Select folder to watch")
if filename:
self.config.set('watched_folder', filename)
def onFilesBrowse(self, t):
global _w
filenames, _ = QFileDialog.getOpenFileNames(_w, "Select file(s) to watch")
if filenames:
self.config.set('watched_files', filenames)
def onChangeMode(self, i):
for m, gb in {MODE_MANUAL: self.manual_gb, MODE_WATCH_FILES: self.watchfile_gb, MODE_WATCH_FOLDER: self.watchfolder_gb, MODE_TIMER: self.timer_gb}.items():
if m == list(self.mode_options.items())[i][1]:
gb.show()
else:
gb.hide()
def sizeHint(self):
return QSize(400, 200)
class AnnotatePeaks(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotatePeaks, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Peaks')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Peaks')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_peaks = QListWidgetAddRemove()
self.lw_peaks.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_peaks)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_start = QDoubleSpinBox()
self.add_start.setRange(-1, 12)
self.add_start.setDecimals(3)
self.add_start.setSuffix('ppm')
self.add_start.setSingleStep(0.001)
self.add_end = QDoubleSpinBox()
self.add_end.setRange(-1, 12)
self.add_end.setDecimals(3)
self.add_end.setSuffix('ppm')
self.add_end.setSingleStep(0.001)
addc = QPushButton('Add')
addc.clicked.connect(self.onPeakAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onPeakAdd)
loadc = QPushButton("Import from file")
loadc.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'folder-open-document.png')))
loadc.clicked.connect(self.onPeakImport)
metabh = QPushButton("Auto match via MetaboHunter")
metabh.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'metabohunter.png')))
metabh.clicked.connect(self.onPeakImportMetabohunter)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_start)
vboxh.addWidget(self.add_end)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vbox.addWidget(loadc)
vbox.addWidget(metabh)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/peaks', self.lw_peaks, (self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onPeakAdd(self):
c = self.config.get('annotation/peaks')[:] # Create new list to force refresh on reassign
c.append( (self.add_label.text(), float(self.add_start.value()), float(self.add_end.value()) ) )
self.config.set('annotation/peaks', c)
def onPeakRemove(self):
i = self.lw_peaks.removeItemAt(self.lw_peaks.currentRow())
# c = self.map_list_fwd(i.text())
def onPeakImport(self):
filename, _ = QFileDialog.getOpenFileName(self.parent(), 'Load peak annotations from file', '', "All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)")
if filename:
c = self.config.get('annotation/peaks')[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append( row[0], float(row[1]), float(row[2]) )
self.config.set('annotation/peaks', c)
def onPeakImportMetabohunter(self):
c = self.config.get('annotation/peaks')[:] # Create new list to force refresh on reassign
t = self.parent().current_tool
dlg = MetaboHunter(self)
if dlg.exec_():
if 'spc' in t.data:
# We have a spectra; calcuate mean; reduce size if required
spc = t.data['spc']
n = spc.data.shape[1]
ppm = spc.ppm
spcd = np.mean(spc.data, axis=0)
# Set a hard limit on the size of data we submit to be nice.
if n > 3000:
# Calculate the division required to be under the limit
d = np.ceil(float(n)/3000)
# Trim axis to multiple of divisor
trim = (n//d)*d
spcd = spcd[:trim]
ppm = ppm[:trim]
# Mean d shape
spcd = np.mean( spcd.reshape(-1,d), axis=1)
ppm = np.mean( ppm.reshape(-1,d), axis=1)
# Submit with settings
hmdbs = metabohunter.request(ppm, spcd,
metabotype=dlg.config.get('Metabotype'),
database=dlg.config.get('Database Source'),
ph=dlg.config.get('Sample pH'),
solvent=dlg.config.get('Solvent'),
frequency=dlg.config.get('Frequency'),
method=dlg.config.get('Method'),
noise=dlg.config.get('Noise Threshold'),
confidence=dlg.config.get('Confidence Threshold'),
tolerance=dlg.config.get('Tolerance')
)
ha = np.array(hmdbs)
unique_hmdbs = set(hmdbs)
if None in unique_hmdbs:
unique_hmdbs.remove(None)
# Extract out regions
for hmdb in unique_hmdbs:
hb = np.diff(ha == hmdb)
# These are needed to ensure markers are there for objects starting and ending on array edge
if ha[0] == hmdb:
hb[0] == True
if ha[-1] == hmdb:
hb[-1] == True
idx = np.nonzero(hb)[0]
idx = idx.reshape(-1,2)
if dlg.config.get('convert_hmdb_ids_to_names') and hmdb in METABOHUNTER_HMDB_NAME_MAP.keys():
label = METABOHUNTER_HMDB_NAME_MAP[hmdb]
else:
label = hmdb
# Now we have an array of all start, stop positions for this item
for start, stop in idx:
c.append( (label, ppm[start], ppm[stop]) )
self.config.set('annotation/peaks', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%.2f\t%.2f" % tuple(x)
self.fwd_map_cache[s] = x
return s
class AnnotateClasses(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotateClasses, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Classes')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Sample classes')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_classes = QListWidgetAddRemove()
self.lw_classes.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_classes)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_class = QLineEdit()
addc = QPushButton('Add')
addc.clicked.connect(self.onClassAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onClassAdd)
loadc = QPushButton('Import from file')
loadc.setIcon(QIcon(os.path.join(utils.scriptdir, 'icons', 'folder-open-document.png')))
loadc.clicked.connect(self.onClassImport)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_class)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vboxh.addWidget(loadc)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/sample_classes', self.lw_classes, (self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onClassAdd(self):
c = self.config.get('annotation/sample_classes')[:] # Create new list to force refresh on reassign
c.append( (self.add_label.text(), self.add_class.text()) )
self.config.set('annotation/sample_classes', c)
def onClassRemove(self):
i = self.lw_classes.removeItemAt(self.lw_classes.currentRow())
# c = self.map_list_fwd(i.text())
def onClassImport(self):
filename, _ = QFileDialog.getOpenFileName(self.parent(), 'Load classifications from file', '', "All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)")
if filename:
c = self.config.get('annotation/sample_classes')[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append(row[:2])
self.config.set('annotation/sample_classes', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%s" % tuple(x)
self.fwd_map_cache[s] = x
return s
class MetaboHunter(GenericDialog):
options = {
'Metabotype': {
'All': 'All',
'Drug': 'Drug',
'Food additive': 'Food additive',
'Mammalian': 'Mammalian',
'Microbial': 'Microbial',
'Plant': 'Plant',
'Synthetic/Industrial chemical': 'Synthetic/Industrial chemical',
},
'Database Source': {
'Human Metabolome Database (HMDB)': 'HMDB',
'Madison Metabolomics Consortium Database (MMCD)': 'MMCD',
},
'Sample pH': {
'10.00 - 10.99': 'ph7',
'7.00 - 9.99': 'ph7',
'6.00 - 6.99': 'ph6',
'5.00 - 5.99': 'ph5',
'4.00 - 4.99': 'ph4',
'3.00 - 3.99': 'ph3',
},
'Solvent': {
'All': 'all',
'Water': 'water',
'CDCl3': 'cdcl3',
'CD3OD': '5d3od',
'5% DMSO': '5dmso',
},
'Frequency': {
'All': 'all',
'600 MHz': '600',
'500 MHz': '500',
'400 MHz': '400',
},
'Method': {
'MH1: Highest number of matched peaks': 'HighestNumber',
'MH2: Highest number of matched peaks with shift tolerance': 'HighestNumberNeighbourhood',
'MH3: Greedy selection of metabolites with disjoint peaks': 'Greedy2',
'MH4: Highest number of matched peaks with intensities': 'HighestNumberHeights',
'MH5: Greedy selection of metabolites with disjoint peaks and heights': 'Greedy2Heights',
},
}
def __init__(self, *args, **kwargs):
super(MetaboHunter, self).__init__(*args, **kwargs)
self.setWindowTitle('MetaboHunter')
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'Metabotype': 'All',
'Database Source': 'HMDB',
'Sample pH': 'ph7',
'Solvent': 'water',
'Frequency': 'all',
'Method': 'HighestNumberNeighbourhood',
'Noise Threshold': 0.0001,
'Confidence Threshold': 0.5,
'Tolerance': 0.1,
'convert_hmdb_ids_to_names': True,
})
self.lw_combos = {}
for o in ['Metabotype', 'Database Source', 'Sample pH', 'Solvent', 'Frequency', 'Method']:
row = QVBoxLayout()
cl = QLabel(o)
cb = QComboBox()
cb.addItems(list(self.options[o].keys()))
row.addWidget(cl)
row.addWidget(cb)
self.config.add_handler(o, cb, self.options[o])
self.layout.addLayout(row)
row = QGridLayout()
self.lw_spin = {}
for n, o in enumerate(['Noise Threshold', 'Confidence Threshold', 'Tolerance']):
cl = QLabel(o)
cb = QDoubleSpinBox()
cb.setDecimals(4)
cb.setRange(0, 1)
cb.setSingleStep(0.01)
cb.setValue(float(self.config.get(o)))
row.addWidget(cl, 0, n)
row.addWidget(cb, 1, n)
self.config.add_handler(o, cb)
self.layout.addLayout(row)
row = QHBoxLayout()
row.addWidget(QLabel("Convert HMDB IDs to chemical names?"))
conv = QCheckBox()
self.config.add_handler('convert_hmdb_ids_to_names', conv)
row.addWidget(conv)
self.layout.addLayout(row)
self.dialogFinalise()
class BaseAnnotationItem(ResizableGraphicsItem):
handler_cache = {}
styles = [
'font-family', 'font-size', 'text-bold', 'text-italic',
'text-underline', 'text-color', 'color-border', 'color-background'
]
minSize = ANNOTATION_MINIMUM_QSIZE
def __init__(self, position=None, *args, **kwargs):
super(BaseAnnotationItem, self).__init__(*args, **kwargs)
# Config for each annotation item, holding the settings (styles, etc)
# update-control via the toolbar using add_handler linking
self.config = ConfigManager()
self.config.updated.connect(self.applyStyleConfig)
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setFlag(QGraphicsItem.ItemIsFocusable)
if position:
self.setPos(position)
self.setZValue(-1)
def delete(self):
self.prepareGeometryChange()
self.scene().annotations.remove(self)
self.scene().removeItem(self)
self.removeHandlers()
def keyPressEvent(self, e):
if e.key() == Qt.Key_Backspace and e.modifiers() == Qt.ControlModifier:
self.delete()
else:
return super(BaseAnnotationItem, self).keyPressEvent(e)
def importStyleConfig(self, config):
for k in self.styles:
self.config.set(k, config.get(k))
def addHandlers(self):
m = self.scene().views()[0].m # Hack; need to switch to importing this
for k in self.styles:
self.config.add_handler(k, m.styletoolbarwidgets[k])
def removeHandlers(self):
for k in self.styles:
self.config.remove_handler(k)
def itemChange(self, change, value):
if change == QGraphicsItem.ItemSelectedChange:
if not value:
self.removeHandlers()
elif change == QGraphicsItem.ItemSelectedHasChanged:
if value:
self.addHandlers()
return super(BaseAnnotationItem, self).itemChange(change, value)
class SerialDialog(QDialog):
def __init__(self, settings, parent=None):
super().__init__(parent)
self.settings = settings
self.serialports = []
# port
self.portLabel = QLabel(self.tr("COM Port:"))
self.portComboBox = QComboBox()
self.portLabel.setBuddy(self.portComboBox)
self.refresh_comports(self.portComboBox)
# baudrate
self.baudrateLabel = QLabel(self.tr("Baudrate:"))
self.baudrateComboBox = QComboBox()
self.baudrateLabel.setBuddy(self.baudrateComboBox)
for br in BAUDRATES:
self.baudrateComboBox.addItem(str(br), br)
# buttons
self.dlgbuttons = QDialogButtonBox(
QDialogButtonBox.Ok | QDialogButtonBox.Cancel, Qt.Horizontal)
self.dlgbuttons.rejected.connect(self.reject)
self.dlgbuttons.accepted.connect(self.accept)
# layout
layout = QGridLayout()
layout.addWidget(self.portLabel, 0, 0)
layout.addWidget(self.portComboBox, 0, 1)
layout.addWidget(self.baudrateLabel, 1, 0)
layout.addWidget(self.baudrateComboBox, 1, 1)
layout.addWidget(self.dlgbuttons, 2, 0, 1, 2)
self.setLayout(layout)
self.setWindowTitle(self.tr("Serial Settings"))
# settings
defaults = {
PORT_SETTING: "",
BAUDRATE_SETTING: "115200"
}
self.tmp_settings = ConfigManager()
self.tmp_settings.set_defaults(defaults)
self.tmp_settings.set_many(
{key: self.settings.get(key) for key in defaults.keys()}
)
self.tmp_settings.add_handler(PORT_SETTING, self.portComboBox)
self.tmp_settings.add_handler(BAUDRATE_SETTING, self.baudrateComboBox)
def accept(self):
d = self.tmp_settings.as_dict()
self.settings.set_many(d)
super().accept()
def refresh_comports(self, combobox):
self.serialports = serial_ports()
for port in self.serialports:
combobox.addItem(port)
@property
def port(self):
return self.portComboBox.currentText()
@port.setter
def port(self, value):
if value in self.serialports:
self.portComboBox.setCurrentIndex(
self.portComboBox.findText(value))
else:
raise ValueError("serial port '%s' not available" % value)
@property
def baudrate(self):
return self.baudrateComboBox.currentData()
class AutomatonDialog(GenericDialog):
mode_options = {
'Manual': MODE_MANUAL,
'Watch files': MODE_WATCH_FILES,
'Watch folder': MODE_WATCH_FOLDER,
'Timer': MODE_TIMER,
}
def __init__(self, parent, **kwargs):
super(AutomatonDialog, self).__init__(parent, **kwargs)
self.setWindowTitle("Edit Automaton")
self.config = ConfigManager()
gb = QGroupBox('IPython notebook(s) (*.ipynb)')
grid = QGridLayout()
notebook_path_le = QLineEdit()
self.config.add_handler('notebook_paths',
notebook_path_le,
mapper=(lambda x: x.split(";"),
lambda x: ";".join(x)))
grid.addWidget(notebook_path_le, 0, 0, 1, 2)
notebook_path_btn = QToolButton()
notebook_path_btn.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'document-attribute-i.png')))
notebook_path_btn.clicked.connect(
lambda: self.onNotebookBrowse(notebook_path_le))
grid.addWidget(notebook_path_btn, 0, 2, 1, 1)
gb.setLayout(grid)
self.layout.addWidget(gb)
gb = QGroupBox('Automaton mode')
grid = QGridLayout()
mode_cb = QComboBox()
mode_cb.addItems(self.mode_options.keys())
mode_cb.currentIndexChanged.connect(self.onChangeMode)
self.config.add_handler('mode', mode_cb, mapper=self.mode_options)
grid.addWidget(QLabel('Mode'), 0, 0)
grid.addWidget(mode_cb, 0, 1)
grid.addWidget(QLabel('Hold trigger'), 1, 0)
fwatcher_hold_sb = QSpinBox()
fwatcher_hold_sb.setRange(0, 60)
fwatcher_hold_sb.setSuffix(' secs')
self.config.add_handler('trigger_hold', fwatcher_hold_sb)
grid.addWidget(fwatcher_hold_sb, 1, 1)
gb.setLayout(grid)
self.layout.addWidget(gb)
self.watchfile_gb = QGroupBox('Watch files')
grid = QGridLayout()
watched_path_le = QLineEdit()
grid.addWidget(watched_path_le, 0, 0, 1, 2)
self.config.add_handler('watched_files',
watched_path_le,
mapper=(lambda x: x.split(";"),
lambda x: ";".join(x)))
watched_path_btn = QToolButton()
watched_path_btn.setIcon(
QIcon(os.path.join(utils.scriptdir, 'icons', 'document-copy.png')))
watched_path_btn.setStatusTip('Add file(s)')
watched_path_btn.clicked.connect(
lambda: self.onFilesBrowse(watched_path_le))
grid.addWidget(watched_path_btn, 0, 2, 1, 1)
grid.addWidget(QLabel('Watch window'), 1, 0)
watch_window_sb = QSpinBox()
watch_window_sb.setRange(0, 60)
watch_window_sb.setSuffix(' secs')
self.config.add_handler('watch_window', watch_window_sb)
grid.addWidget(watch_window_sb, 1, 1)
self.watchfile_gb.setLayout(grid)
self.layout.addWidget(self.watchfile_gb)
self.watchfolder_gb = QGroupBox('Watch folder')
grid = QGridLayout()
watched_path_le = QLineEdit()
grid.addWidget(watched_path_le, 0, 0, 1, 3)
self.config.add_handler('watched_folder', watched_path_le)
watched_path_btn = QToolButton()
watched_path_btn.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'folder-horizontal-open.png')))
watched_path_btn.setStatusTip('Add folder')
watched_path_btn.clicked.connect(
lambda: self.onFolderBrowse(watched_path_le))
grid.addWidget(watched_path_btn, 0, 3, 1, 1)
grid.addWidget(QLabel('Iterate files in folder'), 3, 0)
loop_folder_sb = QCheckBox()
self.config.add_handler('iterate_watched_folder', loop_folder_sb)
grid.addWidget(loop_folder_sb, 3, 1)
loop_wildcard_le = QLineEdit()
self.config.add_handler('iterate_wildcard', loop_wildcard_le)
grid.addWidget(loop_wildcard_le, 3, 2)
self.watchfolder_gb.setLayout(grid)
self.layout.addWidget(self.watchfolder_gb)
self.timer_gb = QGroupBox('Timer')
grid = QGridLayout()
grid.addWidget(QLabel('Run every'), 0, 0)
watch_timer_sb = QSpinBox()
watch_timer_sb.setRange(0, 60)
watch_timer_sb.setSuffix(' secs')
self.config.add_handler('timer_seconds', watch_timer_sb)
grid.addWidget(watch_timer_sb, 0, 1)
self.timer_gb.setLayout(grid)
self.layout.addWidget(self.timer_gb)
self.manual_gb = QGroupBox('Manual') # No show
grid = QGridLayout()
grid.addWidget(QLabel('No configuration'), 0, 0)
self.manual_gb.setLayout(grid)
self.layout.addWidget(self.manual_gb)
gb = QGroupBox('Output')
grid = QGridLayout()
output_path_le = QLineEdit()
self.config.add_handler('output_path', output_path_le)
grid.addWidget(output_path_le, 0, 0, 1, 2)
notebook_path_btn = QToolButton()
notebook_path_btn.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'folder-horizontal-open.png')))
notebook_path_btn.clicked.connect(
lambda: self.onFolderBrowse(notebook_path_le))
grid.addWidget(notebook_path_btn, 0, 2, 1, 1)
export_cb = QComboBox()
export_cb.addItems(IPyexporter_map.keys())
self.config.add_handler('output_format', export_cb)
grid.addWidget(QLabel('Notebook output format'), 1, 0)
grid.addWidget(export_cb, 1, 1)
gb.setLayout(grid)
self.layout.addWidget(gb)
self.layout.addStretch()
self.finalise()
self.onChangeMode(mode_cb.currentIndex())
def onNotebookBrowse(self, t):
global _w
filenames, _ = QFileDialog.getOpenFileNames(
_w, "Load IPython notebook(s)", '',
"IPython Notebooks (*.ipynb);;All files (*.*)")
if filenames:
self.config.set('notebook_paths', filenames)
def onFolderBrowse(self, t):
global _w
filename = QFileDialog.getExistingDirectory(_w,
"Select folder to watch")
if filename:
self.config.set('watched_folder', filename)
def onFilesBrowse(self, t):
global _w
filenames, _ = QFileDialog.getOpenFileNames(_w,
"Select file(s) to watch")
if filenames:
self.config.set('watched_files', filenames)
def onChangeMode(self, i):
for m, gb in {
MODE_MANUAL: self.manual_gb,
MODE_WATCH_FILES: self.watchfile_gb,
MODE_WATCH_FOLDER: self.watchfolder_gb,
MODE_TIMER: self.timer_gb
}.items():
if m == list(self.mode_options.items())[i][1]:
gb.show()
else:
gb.hide()
def sizeHint(self):
return QSize(400, 200)
class AnnotateClasses(GenericDialog):
def __init__(self, parent, config=None, *args, **kwargs):
super(AnnotateClasses, self).__init__(parent, *args, **kwargs)
self.setWindowTitle('Annotate Classes')
if config:
# Copy in starting state
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults(config)
self.fwd_map_cache = {}
# Correlation variables
gb = QGroupBox('Sample classes')
vbox = QVBoxLayout()
# Populate the list boxes
self.lw_classes = QListWidgetAddRemove()
self.lw_classes.setSelectionMode(QAbstractItemView.ExtendedSelection)
vbox.addWidget(self.lw_classes)
vboxh = QHBoxLayout()
self.add_label = QLineEdit()
self.add_class = QLineEdit()
addc = QPushButton('Add')
addc.clicked.connect(self.onClassAdd)
remc = QPushButton('Remove selected')
remc.clicked.connect(self.onClassAdd)
loadc = QPushButton('Import from file')
loadc.setIcon(
QIcon(
os.path.join(utils.scriptdir, 'icons',
'folder-open-document.png')))
loadc.clicked.connect(self.onClassImport)
vboxh.addWidget(self.add_label)
vboxh.addWidget(self.add_class)
vboxh.addWidget(addc)
vbox.addWidget(remc)
vbox.addLayout(vboxh)
vboxh.addWidget(loadc)
gb.setLayout(vbox)
self.layout.addWidget(gb)
self.config.add_handler('annotation/sample_classes', self.lw_classes,
(self.map_list_fwd, self.map_list_rev))
self.dialogFinalise()
def onClassAdd(self):
c = self.config.get(
'annotation/sample_classes'
)[:] # Create new list to force refresh on reassign
c.append((self.add_label.text(), self.add_class.text()))
self.config.set('annotation/sample_classes', c)
def onClassRemove(self):
i = self.lw_classes.removeItemAt(self.lw_classes.currentRow())
# c = self.map_list_fwd(i.text())
def onClassImport(self):
filename, _ = QFileDialog.getOpenFileName(
self.parent(), 'Load classifications from file', '',
"All compatible files (*.csv *.txt *.tsv);;Comma Separated Values (*.csv);;Plain Text Files (*.txt);;Tab Separated Values (*.tsv);;All files (*.*)"
)
if filename:
c = self.config.get(
'annotation/sample_classes'
)[:] # Create new list to force refresh on reassign
with open(filename, 'rU') as f:
reader = csv.reader(f, delimiter=b',', dialect='excel')
for row in reader:
if row not in c:
c.append(row[:2])
self.config.set('annotation/sample_classes', c)
def map_list_fwd(self, s):
" Receive text name, return the indexes "
return self.fwd_map_cache[s]
def map_list_rev(self, x):
" Receive the indexes, return the label"
s = "%s\t%s" % tuple(x)
self.fwd_map_cache[s] = x
return s
class MainWindow(QMainWindow):
def __init__(self):
super(MainWindow, self).__init__()
self.setWindowTitle('PyQtConfig Demo')
self.vis = ConfigManager()
#
# CHOICE_A = 1
# CHOICE_B = 2
# CHOICE_C = 3
# CHOICE_D = 4
#
# map_dict = {
# 'Choice A': CHOICE_A,
# 'Choice B': CHOICE_B,
# 'Choice C': CHOICE_C,
# 'Choice D': CHOICE_D,
# }
self.vis.set_defaults({
'text1': 'hello1',
'text2': 'hello2',
'text3': 'hello3',
'text4': 'hello4',
})
# self.vis.set_defaults({
# 'number': 13,
# 'text': 'hello',
# 'active': True,
# 'combo': CHOICE_C,
# })
gd = QGridLayout()
#
# sb = QSpinBox()
# gd.addWidget(sb, 0, 1)
# self.vis.add_handler('number', sb)
#
# te = QLineEdit()
# gd.addWidget(te, 1, 1)
# self.vis.add_handler('text', te)
#
# cb = QCheckBox()
# gd.addWidget(cb, 2, 1)
# self.vis.add_handler('active', cb)
#
# cmb = QComboBox()
# cmb.addItems(map_dict.keys())
# gd.addWidget(cmb, 3, 1)
# self.vis.add_handler('combo', cmb, mapper=map_dict)
#
# self.current_config_output = QTextEdit()
# gd.addWidget(self.current_config_output, 0, 3, 3, 1)
i=0
print self.vis.as_dict()
for item in self.vis.as_dict().keys():
te = QLineEdit()
te.setEnabled(False)
self.vis.add_handler(item,te)
gd.addWidget(te,i,1)
i=i+1
# self.vis.updated.connect(self.show_config)
# self.show_config()
self.window = QWidget()
self.window.setLayout(gd)
self.setCentralWidget(self.window)
class DictGui(QDialog):
# class LisaConfigWindow(QMainWindow):
def __init__(self, config_in, ncols=2):
super(DictGui, self).__init__()
self.setWindowTitle('Lisa Config')
self.config = ConfigManager()
self.ncols = ncols
# used with other module. If it is set, lisa config is deleted
self.reset_config = False
CHOICE_A = "{pairwise_alpha_per_mm2: 45, return_only_object_with_seeds: true}"
# CHOICE_A = 23
CHOICE_B = 2
CHOICE_C = 3
CHOICE_D = 4
map_dict = {
'Graph-Cut': CHOICE_A,
'Choice B': CHOICE_B,
'Choice C': CHOICE_C,
'Choice D': CHOICE_D,
}
config_def = {
'working_voxelsize_mm': 2.0,
'save_filetype': 'pklz',
# 'manualroi': True,
'segparams': CHOICE_A,
}
config_def.update(config_in)
self.config.set_defaults(config_def)
gd = QGridLayout()
gd_max_i = 0
for key, value in config_in.items():
if type(value) is int:
sb = QSpinBox()
sb.setRange(-100000, 100000)
elif type(value) is float:
sb = QDoubleSpinBox()
elif type(value) is str:
sb = QLineEdit()
elif type(value) is bool:
sb = QCheckBox()
else:
logger.error("Unexpected type in config dictionary")
row = gd_max_i / self.ncols
col = (gd_max_i % self.ncols) * 2
gd.addWidget(QLabel(key), row, col + 1)
gd.addWidget(sb, row, col + 2)
self.config.add_handler(key, sb)
gd_max_i += 1
# gd.addWidget(QLabel("save filetype"), 1, 1)
# te = QLineEdit()
# gd.addWidget(te, 1, 2)
# self.config.add_handler('save_filetype', te)
#
# gd.addWidget(QLabel("segmentation parameters"), 2, 1)
# te = QLineEdit()
# gd.addWidget(te, 2, 2)
# self.config.add_handler('segparams', te)
# cb = QCheckBox()
# gd.addWidget(cb, 2, 2)
# self.config.add_handler('active', cb)
# gd.addWidget(QLabel("segmentation parameters"), 3, 1)
# cmb = QComboBox()
# cmb.addItems(map_dict.keys())
# gd.addWidget(cmb, 3, 2)
# self.config.add_handler('segparams', cmb, mapper=map_dict)
self.current_config_output = QTextEdit()
# rid.setColumnMinimumWidth(3, logo.width()/2)
text_col = (self.ncols * 2) + 3
gd.setColumnMinimumWidth(text_col, 500)
gd.addWidget(self.current_config_output, 1, text_col,
(gd_max_i / 2) - 1, 1)
btn_reset_config = QPushButton("Default", self)
btn_reset_config.clicked.connect(self.btnResetConfig)
gd.addWidget(btn_reset_config, 0, text_col)
btn_save_config = QPushButton("Ok", self)
btn_save_config.clicked.connect(self.btnSaveConfig)
gd.addWidget(btn_save_config, (gd_max_i / 2), text_col)
self.config.updated.connect(self.show_config)
self.show_config()
# my line
self.setLayout(gd)
# self.window = QWidget()
# self.window.setLayout(gd)
# self.setCentralWidget(self.window)
def add_grid_line(self, key, value):
pass
def get_config_as_dict(self):
dictionary = self.config.as_dict()
for key, value in dictionary.items():
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
# import ipdb; ipdb.set_trace() # noqa BREAKPOINT
if type(value) == QString:
value = str(value)
dictionary[key] = value
return dictionary
def btnResetConfig(self, event=None):
self.reset_config = True
self.close()
def btnSaveConfig(self, event=None):
self.reset_config = False
self.close()
def show_config(self):
text = str(self.get_config_as_dict())
self.current_config_output.setText(text)
class ToolBase(QObject):
'''
Base tool definition for inclusion in the UI. Define specific config settings;
attach a panel widget for configuration.
'''
is_manual_runnable = True
is_auto_runnable = True
is_auto_rerunnable = True
is_disableable = True
progress = pyqtSignal(float)
status = pyqtSignal(str)
config_panel_size = 250
view_widget = 'SpectraViewer'
def __init__(self, parent, *args, **kwargs):
super(ToolBase, self).__init__(parent, *args, **kwargs)
self.config = ConfigManager()
self.config.hooks.update(custom_pyqtconfig_hooks.items())
self.config.set_defaults({
'is_active': True,
'auto_run_on_config_change': True
})
self.config.updated.connect(self.auto_run_on_config_change)
self.buttonBar = QWidget()
self.configPanels = QWidget()
self.configLayout = QVBoxLayout()
self.configLayout.setContentsMargins(0,0,0,0)
self.configPanels.setLayout(self.configLayout)
self._previous_config_backup_ = {}
self._worker_thread_ = None
self._worker_thread_lock_ = False
self.data = {
'spc': None,
}
self.current_status = 'ready'
self.current_progress = 0
self.progress.connect(self.progress_callback)
self.status.connect(self.status_callback)
def addConfigPanel(self, panel):
self.configLayout.addWidget( panel(self) )
def addButtonBar(self, buttons):
'''
Create a button bar
Supplied with a list of QPushButton objects (already created using helper stubs; see below)
:param buttons:
:return:
'''
btnlayout = QHBoxLayout()
btnlayout.addSpacerItem(QSpacerItem(250, 1, QSizePolicy.Maximum, QSizePolicy.Maximum))
for btn in buttons:
btnlayout.addWidget(btn)
self.configLayout.addLayout(btnlayout)
btnlayout.addSpacerItem(QSpacerItem(250, 1, QSizePolicy.Maximum, QSizePolicy.Maximum))
def run_manual(self):
pass
def disable(self):
self.status.emit('inactive')
self.config.set('is_active', False)
self.item.setFlags(Qt.NoItemFlags)
def reset(self):
self.config.set_many( self.config.defaults )
def undo(self):
self.config.set_many(self._config_backup_)
def deftaultButtons(self):
buttons = []
if self.is_disableable:
disable = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'cross.png')), 'Disable')
disable.setToolTip('Disable this tool')
disable.pressed.connect(self.disable)
buttons.append(disable)
reset = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'arrow-turn-180-left.png')), 'Reset to defaults')
reset.setToolTip('Reset to defaults')
reset.pressed.connect(self.reset)
buttons.append(reset)
undo = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'arrow-turn-180-left.png')), 'Undo')
undo.setToolTip('Undo recent changes')
undo.pressed.connect(self.undo)
buttons.append(undo)
if self.is_auto_runnable:
auto = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'lightning.png')), 'Auto')
auto.setToolTip('Auto-update spectra when settings change')
auto.setCheckable(True)
auto.pressed.connect(self.run_manual)
self.config.add_handler('auto_run_on_config_change', auto)
buttons.append(auto)
if self.is_manual_runnable:
apply = QPushButton(QIcon(os.path.join(utils.scriptdir, 'icons', 'play.png')), 'Apply')
apply.setToolTip('Apply current settings to spectra')
apply.pressed.connect(self.run_manual)
buttons.append(apply)
return buttons
def enable(self):
if self.current_status == 'inactive':
self.status.emit('ready')
self.item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable)
self.config.set('is_active', True)
def activate(self):
self.parent().current_tool = self
self.enable()
self._config_backup_ = self.config.as_dict()
self._refresh_plot_timer_ = QTimer.singleShot(0, self.plot)
self.parent().viewStack.setCurrentWidget(self.parent().spectraViewer)
self.parent().configstack.setCurrentWidget(self.configPanels)
self.parent().configstack.setMaximumHeight(self.config_panel_size)
def set_active(self, active):
self.config.set('is_active', active)
def get_previous_tool(self):
# Get the previous ACTIVE tool in the tool table
n = self.parent().tools.index(self)
for tool in self.parent().tools[n-1::-1]:
if tool.current_status != 'inactive':
return tool
else:
return None
def get_previous_spc(self):
t = self.get_previous_tool()
if t:
return t.data['spc']
else:
return None
def plot(self, **kwargs):
if 'spc' in self.data:
self.parent().spectraViewer.plot(self.data['spc'], **kwargs)
def get_plotitem(self):
return self.parent().spectraViewer.spectraViewer.plotItem
def auto_run_on_config_change(self):
pass
#if self.is_auto_runnable and self.config.get('is_active') and self.config.get('auto_run_on_config_change'):
# self.run_manual()
def run(self, fn):
'''
Run the target function, passing in the current spectra, and config settings (as dict)
:param fn:
:return:
'''
if self._worker_thread_lock_:
return False # Can't run
self.progress.emit(0)
self.status.emit('active')
spc = self.get_previous_spc()
self._worker_thread_lock_ = True
print(self.config.as_dict())
self._worker_thread_ = Worker(fn = fn, **{
'spc': deepcopy(spc),
'config': self.config.as_dict(),
'progress_callback': self.progress.emit,
})
self._worker_thread_.signals.finished.connect(self.finished)
self._worker_thread_.signals.result.connect(self.result)
self._worker_thread_.signals.error.connect(self.error)
self.parent().threadpool.start(self._worker_thread_)
def error(self, error):
self.progress.emit(1.0)
self.status.emit('error')
logging.error(error)
self._worker_thread_lock_ = False
def result(self, result):
self.progress.emit(1)
self.status.emit('complete')
# Apply post-processing
if 'spc' in result:
result['spc'] = self.post_process_spc(result['spc'])
self.data = result
self.plot()
def finished(self):
# Cleanup
self._worker_thread_lock_ = False
def progress_callback(self, progress):
self.current_progress = progress
self.item.setData(Qt.UserRole + 2, progress)
def status_callback(self, status):
self.current_status = status
self.item.setData(Qt.UserRole + 3, status)
def post_process_spc(self, spc):
'''
Apply post-processing to the spectra before loading into the data store, e.g. for outlier
detection, stats etc.
:param spc:
:return:
'''
# Outliers
def identify_outliers(data, m=2):
return abs(data - np.mean(data, axis=0)) < (m * np.std(data,axis=0))
# Identify outliers on a point by point basis. Count up 'outliers' and score ratio of points that are
# outliers for each specra > 5% (make this configurable) is an outlier.
spc.outliers = np.sum( ~identify_outliers(spc.data), axis=1 ) / float(spc.data.shape[1])
return spc
