def run(self, args, extra_args):
if args.items:
items = []
for path in args.items:
items.append(os.path.realpath(path))
data = SimpleDataInfo.from_paths(items)
else:
data = SimpleDataInfo.from_paths([os.getcwd()])
to_file = None
if args.to_file:
to_file = os.path.realpath(args.to_file)
config = None
if args.config:
filename = os.path.realpath(args.config)
if os.path.exists(filename):
with open(filename, 'r') as f:
config = f.read()
figure_options = {}
if to_file:
if args.width:
figure_options.update({'width': args.width})
if args.height:
figure_options.update({'height': args.height})
if args.dpi:
figure_options.update({'dpi': args.dpi})
view_maps(data,
config,
figure_options=figure_options,
save_filename=to_file)
else:
view_maps(data, config, show_maximized=args.maximize)
def view_mask(self):
data = SimpleDataInfo({'Original mask': load_nifti(self.selectedMaskText.text()).get_data(),
'Slice mask': load_nifti(self.selectedOutputFileText.text()).get_data()})
config = MapPlotConfig()
config.dimension = self.dimensionInput.value()
config.slice_index = self.sliceInput.value()
config.maps_to_show = ['Original mask', 'Slice mask']
start_gui(data=data, config=config, app_exec=False)
def start_gui(data=None,
config=None,
controller=None,
app_exec=True,
show_maximized=False,
window_title=None):
"""Start the GUI with the given data and configuration.
Args:
data (DataInfo): the initial set of data
config (MapPlotConfig): the initial configuration
controller (mdt.gui.maps_visualizer.base.QtController): the controller to use in the application
app_exec (boolean): if true we execute the Qt application, set to false to disable.
show_maximized (true): if we want to show the window in a maximized state
window_title (str): the title of the window
Returns:
MapsVisualizerWindow: the generated window
"""
controller = controller or QtController()
enable_pyqt_exception_hook()
app = QtManager.get_qt_application_instance()
# catches the sigint
timer = QTimer()
timer.start(500)
timer.timeout.connect(lambda: None)
main = MapsVisualizerWindow(controller)
main.set_window_title(window_title)
signal.signal(signal.SIGINT, main.send_sigint)
center_window(main)
if show_maximized:
main.showMaximized()
main.show()
if data is None:
data = SimpleDataInfo({})
controller.apply_action(NewDataAction(data, config=config),
store_in_history=False)
QtManager.add_window(main)
if app_exec:
QtManager.exec_()
return main
def _start_maps_visualizer(self):
folder = self.selectedOutputFolder.text(
) + '/' + self._get_current_model_name()
maps = mdt.load_volume_maps(folder)
a_map = maps[list(maps.keys())[0]]
config = MapPlotConfig()
config.dimension = 2
if len(a_map.shape) > 2:
config.slice_index = a_map.shape[2] // 2
start_gui(data=SimpleDataInfo.from_paths([folder]),
config=config,
app_exec=False)
def view_mask(self):
mask = np.expand_dims(load_brain_mask(self.selectedOutputText.text()),
axis=3)
image_data = load_nifti(self.selectedImageText.text()).get_data()
masked_image = image_data * mask
data = SimpleDataInfo({
'Masked': masked_image,
'DWI': image_data,
'Mask': mask
})
config = MapPlotConfig()
config.dimension = 2
config.slice_index = image_data.shape[2] // 2
config.maps_to_show = ['DWI', 'Masked', 'Mask']
start_gui(data=data, config=config, app_exec=False)
def view_maps(self):
if self._folder is None:
return
maps_to_show = []
for item in [
self.selectMaps.item(index)
for index in range(self.selectMaps.count())
]:
if item.isSelected():
maps_to_show.append(item.text())
data = SimpleDataInfo.from_paths([self._folder])
config = MapPlotConfig()
config.maps_to_show = maps_to_show
config.dimension = self.initialDimensionChooser.value()
config.slice_index = self.initialSliceChooser.value()
start_gui(data=data, config=config, app_exec=False)
def write_view_maps_figure(data,
output_filename,
config=None,
width=None,
height=None,
dpi=None,
figure_options=None,
savefig_settings=None):
"""Saves the view maps figure to a file.
Args:
data (str, dict, :class:`~mdt.visualization.maps.base.DataInfo`, list, tuple): the data we are showing,
either a dictionary with result maps, a string with a path name, a DataInfo object or a list
with filenames and or directories.
config (str, dict, :class:`~mdt.visualization.maps.base import MapPlotConfig`): either a Yaml string or a
dictionary with configuration settings or a ValidatedMapPlotConfig object to use directly
output_filename (str): the output filename
width (int): the width of the figure, if set it takes precedence over the value in figure_options
height (int): the height of the figure, if set it takes precedence over the value in figure_options
dpi (int): the dpi of the figure, if set it takes precedence over the value in figure_options
figure_options (dict): additional figure options for the matplotlib Figure, supports the
same settings as :func:`view_maps`, that is, if the arguments 'width' and 'height' are not set directly
in this function we can also use those in the figure_options
savefig_settings (dict): extra output options for the savefig command from matplotlib, if dpi is not given, we
use the dpi from the figure_options.
"""
from mdt.gui.maps_visualizer.main import start_gui
from mdt.visualization.maps.base import MapPlotConfig
from mdt.visualization.maps.matplotlib_renderer import MapsVisualizer
import matplotlib.pyplot as plt
from mdt.visualization.maps.base import SimpleDataInfo
if isinstance(data, string_types):
data = SimpleDataInfo.from_paths([data])
elif isinstance(data, dict):
data = SimpleDataInfo(data)
elif isinstance(data, collections.Sequence):
data = SimpleDataInfo.from_paths(data)
elif data is None:
data = SimpleDataInfo({})
if config is None:
config = MapPlotConfig()
elif isinstance(config, string_types):
if config.strip():
config = MapPlotConfig.from_yaml(config)
else:
config = MapPlotConfig()
elif isinstance(config, dict):
config = MapPlotConfig.from_dict(config)
figure_options = figure_options or {}
if dpi is not None:
figure_options['dpi'] = dpi
else:
figure_options['dpi'] = figure_options.get('dpi', 80)
if height is not None and width is not None:
figure_options['figsize'] = (width / figure_options['dpi'],
height / figure_options['dpi'])
elif height is not None and width is None:
width = figure_options.get('width', 800)
figure_options['figsize'] = (width / figure_options['dpi'],
height / figure_options['dpi'])
elif width is not None and height is None:
height = figure_options.get('height', 640)
figure_options['figsize'] = (width / figure_options['dpi'],
height / figure_options['dpi'])
elif 'figsize' in figure_options:
pass
else:
width = figure_options.get('width', 800)
height = figure_options.get('height', 640)
figure_options['figsize'] = (width / figure_options['dpi'],
height / figure_options['dpi'])
if 'width' in figure_options:
del figure_options['width']
if 'height' in figure_options:
del figure_options['height']
figure = plt.figure(**figure_options)
viz = MapsVisualizer(data, figure)
savefig_settings = savefig_settings or {}
savefig_settings['dpi'] = savefig_settings.get('dpi',
figure_options['dpi'])
viz.to_file(output_filename, config, **savefig_settings)
def view_maps(data,
config=None,
figure_options=None,
block=True,
show_maximized=False,
use_qt=True,
window_title=None):
"""View a number of maps using the MDT Maps Visualizer.
Args:
data (str, dict, :class:`~mdt.visualization.maps.base.DataInfo`, list, tuple): the data we are showing,
either a dictionary with result maps, a string with a path name, a DataInfo object or a list
with filenames and/or directories.
config (str, dict, :class:`~mdt.visualization.maps.base import MapPlotConfig`): either a Yaml string or a
dictionary with configuration settings or a ValidatedMapPlotConfig object to use directly
figure_options (dict): figure options for the matplotlib Figure, if figsizes is not given you can also specify
two ints, width and height, to indicate the pixel size of the resulting figure, together with the dpi they
are used to calculate the figsize. Only used if use_qt=False.
block (boolean): if we block the plots or not
show_maximized (boolean): if we show the window maximized or not
window_title (str): the title for the window
use_qt (boolean): if we want to use the Qt GUI, or show the results directly in matplotlib
"""
from mdt.gui.maps_visualizer.main import start_gui
from mdt.visualization.maps.base import MapPlotConfig
from mdt.visualization.maps.matplotlib_renderer import MapsVisualizer
from mdt.visualization.maps.base import SimpleDataInfo
import matplotlib.pyplot as plt
if isinstance(data, string_types):
data = SimpleDataInfo.from_paths([data])
elif isinstance(data, collections.MutableMapping):
data = SimpleDataInfo(data)
elif isinstance(data, collections.Sequence):
if all(isinstance(el, string_types) for el in data):
data = SimpleDataInfo.from_paths(data)
else:
data = SimpleDataInfo({str(ind): v for ind, v in enumerate(data)})
elif data is None:
data = SimpleDataInfo({})
if config is None:
config = MapPlotConfig()
elif isinstance(config, string_types):
if config.strip():
config = MapPlotConfig.from_yaml(config)
else:
config = MapPlotConfig()
elif isinstance(config, dict):
config = MapPlotConfig.from_dict(config)
if use_qt:
start_gui(data,
config,
app_exec=block,
show_maximized=show_maximized,
window_title=window_title)
else:
figure_options = figure_options or {}
figure_options['dpi'] = figure_options.get('dpi', 100)
if 'figsize' not in figure_options:
figure_options['figsize'] = (figure_options.pop('width', 1800) /
figure_options['dpi'],
figure_options.pop('height', 1600) /
figure_options['dpi'])
figure = plt.figure(**figure_options)
viz = MapsVisualizer(data, figure)
viz.show(config, block=block, maximize=show_maximized)
def _remove_files(self):
data = SimpleDataInfo({})
config = MapPlotConfig()
self._controller.apply_action(NewDataAction(data, config))
def _add_new_maps(self, paths):
"""Add the given set of file paths to the current visualization.
This looks at the current set of file paths (from ``self._controller.get_config().get_data()``)
and the given new set of file paths and creates a new merged dataset with all files.
Since it is possible that adding new maps leads to naming collisions this function can rename both the
old and the new maps to better reflect the map names.
Args:
paths (list of str): the list of file paths to add to the visualization
Returns:
list of str: the display names of the newly added maps
"""
def get_file_paths(data_info):
"""Get the file paths"""
paths = []
for map_name in data_info.get_map_names():
file_path = data_info.get_file_path(map_name)
if file_path:
paths.append(file_path)
else:
paths.append(map_name)
return paths
def get_changes(old_data_info, new_data_info):
additions = {}
removals = []
name_updates = {}
paths = get_file_paths(old_data_info) + get_file_paths(new_data_info)
unique_names = get_shortest_unique_names(paths)
new_map_names = unique_names[len(old_data_info.get_map_names()):]
for old_name, new_name in zip(old_data_info.get_map_names(), unique_names):
if old_name != new_name:
removals.append(old_name)
additions[new_name] = old_data_info.get_single_map_info(old_name)
name_updates[old_name] = new_name
for new_map_name, new_map_rename in zip(new_data_info.get_map_names(), new_map_names):
additions[new_map_rename] = new_data_info.get_single_map_info(new_map_name)
return additions, removals, name_updates, new_map_names
current_model = self._controller.get_model()
current_data = current_model.get_data()
adds, rems, name_updates, new_map_names = get_changes(current_data, SimpleDataInfo.from_paths(paths))
data = current_data.get_updated(adds, removals=rems)
config = copy.deepcopy(current_model.get_config())
new_maps_to_show = []
for map_name in config.maps_to_show:
if map_name in name_updates:
new_maps_to_show.append(name_updates[map_name])
else:
new_maps_to_show.append(map_name)
config.maps_to_show = new_maps_to_show
new_map_plot_options = {}
for map_name, plot_options in config.map_plot_options.items():
if map_name in name_updates:
new_map_plot_options[name_updates[map_name]] = plot_options
else:
new_map_plot_options[map_name] = plot_options
config.map_plot_options = new_map_plot_options
if not len(current_data.get_map_names()):
config.slice_index = data.get_max_slice_index(config.dimension) // 2
self._controller.apply_action(NewDataAction(data, config=config))
return new_map_names
def __init__(self):
super(QtController, self).__init__()
self._current_model = SimpleDataConfigModel(SimpleDataInfo({}),
MapPlotConfig())
self._actions_history = []
self._redoable_actions = []
def view_maps(data,
config=None,
figure_options=None,
block=True,
show_maximized=False,
use_qt=True,
window_title=None,
save_filename=None):
"""View a number of maps using the MDT Maps Visualizer.
Args:
data (str, dict, :class:`~mdt.visualization.maps.base.DataInfo`, list, tuple): the data we are showing,
either a dictionary with result maps, a string with a path name, a DataInfo object or a list
with filenames and/or directories.
config (str, dict, :class:`~mdt.visualization.maps.base import MapPlotConfig`): either a Yaml string or a
dictionary with configuration settings or a ValidatedMapPlotConfig object to use directly
figure_options (dict): Used when ``use_qt`` is False or when ``write_figure`` is used.
Sets the figure options for the matplotlib Figure.
If figsizes is not given you can also specify two ints, width and height, to indicate the pixel size of
the resulting figure, together with the dpi they are used to calculate the figsize.
block (boolean): if we block the plots or not
show_maximized (boolean): if we show the window maximized or not
window_title (str): the title for the window
use_qt (boolean): if we want to use the Qt GUI, or show the results directly in matplotlib
save_filename (str): save the figure to file. If set, we will not display the viewer.
"""
from mdt.gui.maps_visualizer.main import start_gui
from mdt.visualization.maps.base import MapPlotConfig
from mdt.visualization.maps.matplotlib_renderer import MapsVisualizer
from mdt.visualization.maps.base import SimpleDataInfo
import matplotlib.pyplot as plt
from mdt.gui.maps_visualizer.actions import NewDataAction
from mdt.gui.maps_visualizer.base import SimpleDataConfigModel
if isinstance(data, str):
data = SimpleDataInfo.from_paths([data])
elif isinstance(data, collections.MutableMapping):
data = SimpleDataInfo(data)
elif isinstance(data, collections.Sequence):
if all(isinstance(el, str) for el in data):
data = SimpleDataInfo.from_paths(data)
else:
data = SimpleDataInfo({str(ind): v for ind, v in enumerate(data)})
elif data is None:
data = SimpleDataInfo({})
if config is None:
config = MapPlotConfig()
elif isinstance(config, str):
if config.strip():
config = MapPlotConfig.from_yaml(config)
else:
config = MapPlotConfig()
elif isinstance(config, dict):
config = MapPlotConfig.from_dict(config)
config = config.create_valid(data)
if not use_qt or save_filename:
settings = {'dpi': 100, 'width': 1800, 'height': 1600}
if save_filename:
settings = {'dpi': 80, 'width': 800, 'height': 600}
settings.update(figure_options or {})
if 'figsize' not in settings:
settings['figsize'] = (settings['width'] / settings['dpi'],
settings['height'] / settings['dpi'])
del settings['width']
del settings['height']
figure = plt.figure(**settings)
viz = MapsVisualizer(data, figure)
if save_filename:
viz.to_file(save_filename, config, dpi=settings['dpi'])
else:
viz.show(config, block=block, maximize=show_maximized)
else:
start_gui(data,
config,
app_exec=block,
show_maximized=show_maximized,
window_title=window_title)
