def _save_as_fired(self):
# create raw
try:
raw = self.model.get_raw()
except Exception as err:
error(None, str(err), "Error Creating KIT Raw")
raise
# find default path
stem, _ = os.path.splitext(self.sqd_file)
if not stem.endswith('raw'):
stem += '-raw'
default_path = stem + '.fif'
# save as dialog
dlg = FileDialog(action="save as",
wildcard="fiff raw file (*.fif)|*.fif",
default_path=default_path)
dlg.open()
if dlg.return_code != OK:
return
fname = dlg.path
if not fname.endswith('.fif'):
fname += '.fif'
if os.path.exists(fname):
answer = confirm(None, "The file %r already exists. Should it "
"be replaced?", "Overwrite File?")
if answer != YES:
return
self.queue.put((raw, fname))
self.queue_len += 1
def load_config_file(self, ui_info):
dialog = FileDialog(action="open", wildcard="*.ini")
dialog.open()
if dialog.return_code == OK:
if dialog.path != ui_info.ui.context["object"].project_info.config_file:
shutil.copy(dialog.path, ui_info.ui.context["object"].project_info.config_file)
load_config(self.pipeline, ui_info.ui.context["object"].project_info.config_file)
def OpenFileDialog(action, wildcard, self):
from pyface.api import FileDialog, OK
doaction = action
if action == "new":
doaction = "save as"
dialog = FileDialog(action=doaction, wildcard=wildcard)
dialog.open()
if dialog.return_code == OK:
self.filedir = dialog.directory
self.filename = dialog.filename
self.Configuration_File = os.path.join(dialog.directory, dialog.filename)
if action == "open":
self._config = load_config(dialog.path, self.config_class)
self._config.configure_traits(view=self.config_view())
self.saved = False
self.config_changed = True
if action == "new":
self._config = self.config_class()
self._config.configure_traits(view=self.config_view())
self._save_to_file()
self.saved = False
self.config_changed = True
if action == "save as":
self._save_to_file()
self.saved = True
self.config_changed = False
def _show_open_dialog(self, parent):
"""
Show the dialog to open a project.
"""
# Determine the starting point for browsing. It is likely most
# projects will be stored in the default path used when creating new
# projects.
default_path = self.model_service.get_default_path()
project_class = self.model_service.factory.PROJECT_CLASS
if self.model_service.are_projects_files():
dialog = FileDialog(parent=parent, default_directory=default_path,
title='Open Project')
if dialog.open() == OK:
path = dialog.path
else:
path = None
else:
dialog = DirectoryDialog(parent=parent, default_path=default_path,
message='Open Project')
if dialog.open() == OK:
path = project_class.get_pickle_filename(dialog.path)
if File(path).exists:
path = dialog.path
else:
error(parent, 'Directory does not contain a recognized '
'project')
path = None
else:
path = None
return path
def OpenFileDialog(action, wildcard, self):
from pyface.api import FileDialog, OK
doaction = action
if action == "new":
doaction = "save as"
dialog = FileDialog(action=doaction, wildcard=wildcard)
dialog.open()
if dialog.return_code == OK:
self.filedir = dialog.directory
self.filename = dialog.filename
self.Configuration_File = os.path.join(dialog.directory,
dialog.filename)
if action == "open":
self._config = load_config(dialog.path, self.config_class)
self._config.configure_traits(view=self.config_view())
self.saved = False
self.config_changed = True
if action == "new":
self._config = self.config_class()
self._config.configure_traits(view=self.config_view())
self._save_to_file()
self.saved = False
self.config_changed = True
if action == "save as":
self._save_to_file()
self.saved = True
self.config_changed = False
def action_save(self, info):
# First make a copy of the frame we will save
save_frame = info.object.camera.frame.copy()
# Then find out where to save it
dialog = FileDialog(parent=info.ui.control, action="save as", modal=True, title="Save Image")
try:
dialog.default_directory = info.object._current_folder
except TraitError:
pass # thrown if _current_folder is None
dialog.open()
path = dialog.path
# Store the directory for the next time
info.object._current_folder = dialog.directory
if dialog.return_code != OK:
return
# Default is PNG
if "." not in path:
path += ".png"
# Save it
scipy.misc.imsave(path, save_frame)
def save(self):
extensions = [ '*.bmp', '*.gif', '*.jpg', '*.pdf',
'*.png', '*.svg', '*.tif', '*.xbm' ]
wildcard = FileDialog.create_wildcard('From file name', extensions)
dialog = FileDialog(action = 'save as',
default_directory = self.default_directory,
parent = self.window.control,
wildcard = wildcard)
if dialog.open() == OK:
filename = dialog.path
extension = os.path.splitext(filename)[1]
if not extension:
extension = '.png'
filename += extension
try:
# FIXME: Expose size and background color?
self.editor_area.active_editor.save(filename, bgcolor='white')
except Exception as exc:
msg = 'Failed to save image in %s format' % extension.upper()
dialog = MessageDialog(title = 'Error saving',
message = msg,
detail = str(exc),
parent = self.window.control,
severity = 'error')
dialog.open()
def save_config_file(self, ui_info):
dialog = FileDialog(action="save as", default_filename="config.ini")
dialog.open()
if dialog.return_code == OK:
save_config(self.pipeline, ui_info.ui.context["object"].project_info.config_file)
if dialog.path != ui_info.ui.context["object"].project_info.config_file:
shutil.copy(ui_info.ui.context["object"].project_info.config_file, dialog.path)
def _save_as_fired(self):
# create raw
try:
raw = self.model.get_raw()
except Exception as err:
error(None, str(err), "Error Creating KIT Raw")
raise
# find default path
stem, _ = os.path.splitext(self.sqd_file)
if not stem.endswith('raw'):
stem += '-raw'
default_path = stem + '.fif'
# save as dialog
dlg = FileDialog(action="save as",
wildcard="fiff raw file (*.fif)|*.fif",
default_path=default_path)
dlg.open()
if dlg.return_code != OK:
return
fname = dlg.path
if not fname.endswith('.fif'):
fname += '.fif'
if os.path.exists(fname):
answer = confirm(
None, "The file %r already exists. Should it "
"be replaced?", "Overwrite File?")
if answer != YES:
return
self.queue.put((raw, fname))
self.queue_len += 1
def save_as(self):
dlg = FileDialog( action='save as', wildcard='*.rep')
dlg.open()
if dlg.filename!='':
fi = file(dlg.filename,'w')
dump(self,fi)
fi.close()
def export(self):
dialog = FileDialog(action='save as', title='Export Experiment',
wildcard='csv files (*.csv)|*.csv')
dialog.open()
path = dialog.path
if not path.endswith('.csv'):
path += '.csv'
with open(path, 'w') as f:
fieldnames = [
'well',
'led',
'program',
'program_id',
'total_steps',
'step',
'step_no',
'step_id',
'step_start_time',
'step_duration',
'step_intensity',
'step_pulsed',
'step_pulse_on',
'step_pulse_off',
'step_repeat']
writer = csv.DictWriter(f, fieldnames=fieldnames, restval='None')
writer.writeheader()
for well_group in self.plate.well_groups:
led_row = {'well': well_group.position}
well = well_group.wells[0]
for led in well.leds:
led_row['led'] = led.name
if led.program:
program_row = {}
program_row['program'] = led.program.name
program_row['program_id'] = led.program.ID
program_row['total_steps'] = len(led.program.steps)
prg_does_repeat = led.program._after_end == 'repeat'
program_row.update(led_row)
if len(led.program.steps) == 0:
# Program has no Steps, write now
writer.writerow(program_row)
for step_no, step in enumerate(led.program.steps):
program_row['step'] = step.name
program_row['step_no'] = step_no + 1
program_row['step_id'] = step.ID
step_start = sum(step.duration for step in led.program.steps[:step_no])
program_row['step_start_time'] = step_start
program_row['step_duration'] = step.duration
program_row['step_intensity'] = step.intensity
program_row['step_pulsed'] = ['no', 'yes'][step.is_pulsed]
program_row['step_pulse_on'] = step.pulse_on
program_row['step_pulse_off'] = step.pulse_off
is_last_step = step_no == len(led.program.steps) - 1
step_does_repeat = prg_does_repeat and is_last_step
program_row['step_repeat'] = ['no', 'yes'][step_does_repeat]
writer.writerow(program_row)
else:
writer.writerow(led_row)
def load(self):
dlg = FileDialog( action='open', wildcard='*.rep')
dlg.open()
if dlg.filename!='':
fi = file(dlg.filename,'rb')
s = load(fi)
self.copy_traits(s)
fi.close()
def load(self):
dlg = FileDialog(action='open', wildcard='*.rep')
dlg.open()
if dlg.filename != '':
fi = file(dlg.filename, 'rb')
s = load(fi)
self.copy_traits(s)
fi.close()
def run_script(self):
dlg = FileDialog(action='open', wildcard='*.py')
dlg.open()
if dlg.filename != '':
#~ try:
rx = self
b = rx.Beamformer
script = dlg.path
execfile(dlg.path)
def _out_to_mat_fired(self):
dialog = FileDialog(default_filename = self.filename+"_MATLAB_Phase"+str(self.plotA["notes"]["start"][2]), action="save as", wildcard=self.file_wildcard3)
dialog.open()
if dialog.return_code == OK:
savefiledir = dialog.directory
savefilename = dialog.filename
path = os.path.join(savefiledir, savefilename)
dataset = {self.plotA, self.plotB, self.plotC, self.plotD}
scio.savemat(path, dataset, True)
def _choose_local_file_fired(self):
dialog = FileDialog(
label='Choose local_file',
action='open')
dialog.open()
if dialog.return_code == OK:
self.local_file_for_fileio = dialog.path
else:
self._write('Error while selecting local file.')
def _logAnalyserSelectButton_fired(self):
"""open a fast file editor for selecting many files """
fileDialog = FileDialog(action="open files")
fileDialog.open()
if fileDialog.return_code == pyface.constant.OK:
self.logAnalysers = fileDialog.paths
logger.info("selected log analysers: %s " % self.logAnalysers)
self.logAnalyserDisplayString = str(
[os.path.split(path)[1] for path in self.logAnalysers])
def _open():
if open_show_dialog:
open_dlg = FileDialog(action='open')
open_dlg.open()
self.editor_area.active_tabwidget = self
if open_dlg.return_code == OK:
open_file_action(open_dlg.path)
else:
open_file_action()
def _open():
if open_show_dialog:
open_dlg = FileDialog(action='open')
open_dlg.open()
self.editor_area.active_tabwidget = self
if open_dlg.return_code == OK:
open_file_action(open_dlg.path)
else:
open_file_action()
def _open_settings(self):
logger.debug("_open_settings call . Opening a settings file")
dialog = FileDialog(action="open",
default_directory=self.default_directory,
wildcard=self.file_wildcard)
dialog.open()
if dialog.return_code == OK:
self.settingsFile = dialog.path
self._load_settings(self.settingsFile)
def _choose_fw_fired(self):
dialog = FileDialog(label='Choose Firmware File',
action='open', wildcard=self.file_wildcard)
dialog.open()
if dialog.return_code == OK:
filepath = os.path.join(dialog.directory, dialog.filename)
self.load_ihx(filepath)
else:
self.set_status('Error while selecting file')
def run_script(self):
dlg = FileDialog( action='open', wildcard='*.py')
dlg.open()
if dlg.filename!='':
#~ try:
rx = self
b = rx.Beamformer
script = dlg.path
execfile(dlg.path)
def ask_user_for_loadfile(title=None):
from pyface.api import FileDialog, OK
dialog = FileDialog(action='open')
if title is not None:
dialog.title = title
dialog.open()
if dialog.return_code != OK:
return
return os.path.join( dialog.directory, dialog.filename )
def _choose_fw_fired(self):
""" Activate file dialog window to choose IntelHex firmware file. """
dialog = FileDialog(label='Choose Firmware File',
action='open', wildcard=self.file_wildcard)
dialog.open()
if dialog.return_code == OK:
filepath = os.path.join(dialog.directory, dialog.filename)
self.load_ihx(filepath)
else:
self.clear('Error while selecting file')
def ask_user_for_loadfile(title=None):
from pyface.api import FileDialog, OK
dialog = FileDialog(action='open')
if title is not None:
dialog.title = title
dialog.open()
if dialog.return_code != OK:
return
return os.path.join(dialog.directory, dialog.filename)
def _save_as_settings(self):
"""Called when user presses save as in Menu bar """
dialog = FileDialog(action="save as",
default_directory=self.default_directory,
wildcard=self.file_wildcard)
dialog.open()
if dialog.return_code == OK:
self.settingsFile = dialog.path
if self.settingsFile[-4:] != ".csv":
self.settingsFile += ".csv"
self._save_settings(self.settingsFile)
def add_data(self, info):
fileDialog = FileDialog(action='save as',
title='Save As',
wildcard=self.wildcard,
parent=info.ui.control)
fileDialog.open()
if fileDialog.path == '' or fileDialog.return_code == CANCEL:
return False
else:
info.object.load_from_file(fileDialog.path)
def filedialog():
"""
Open a simple file dialog to pick a file
"""
from pyface.api import FileDialog, OK, confirm, YES
dialog = FileDialog(action="open")
dialog.open()
if dialog.return_code == OK:
return dialog.path
else:
quit()
def _save_LineScans_button_fired(self):
dialog = FileDialog(default_filename = self.filename+"_LineScan_", action="save as", wildcard=self.file_wildcard2)
dialog.open()
if dialog.return_code == OK:
savefiledir = dialog.directory
savefilename = dialog.filename
path = os.path.join(savefiledir, savefilename)
self.LineScans.do_layout(force=True)
plot_gc = PlotGraphicsContext(self.LineScans.outer_bounds)
plot_gc.render_component(self.LineScans)
plot_gc.save(path)
def _choose_fw_fired(self):
""" Activate file dialog window to choose IntelHex firmware file. """
dialog = FileDialog(label='Choose Firmware File',
action='open',
wildcard=self.file_wildcard)
dialog.open()
if dialog.return_code == OK:
filepath = os.path.join(dialog.directory, dialog.filename)
self.load_ihx(filepath)
else:
self.clear('Error while selecting file')
def _on_open(self, info):
""" Menu action to load a script from file. """
file_dialog = FileDialog(action='open',
default_directory=info.object.file_directory,
wildcard='All files (*.*)|*.*')
file_dialog.open()
if file_dialog.path != '':
info.object.load_code_from_file(file_dialog.path)
return
def object_export_dataframe_changed(self, info):
fileDialog = FileDialog(action='save as', title='Save As',
wildcard=self.wildcard,
parent=info.ui.control,
default_filename=info.object.name.replace(' ','_') + '_dataframe')
fileDialog.open()
if fileDialog.path == '' or fileDialog.return_code == CANCEL:
return False
df = info.object.make_db_dataframe()
df.to_csv(fileDialog.path)
def load_config_file(self, ui_info):
dialog = FileDialog(action="open", wildcard="*.ini")
dialog.open()
if dialog.return_code == OK:
if dialog.path != ui_info.ui.context[
"object"].project_info.config_file:
shutil.copy(
dialog.path,
ui_info.ui.context["object"].project_info.config_file)
load_config(self.pipeline,
ui_info.ui.context["object"].project_info.config_file)
def save_config_file(self, ui_info):
dialog = FileDialog(action="save as", default_filename="config.ini")
dialog.open()
if dialog.return_code == OK:
save_config(self.pipeline,
ui_info.ui.context["object"].project_info.config_file)
if dialog.path != ui_info.ui.context[
"object"].project_info.config_file:
shutil.copy(
ui_info.ui.context["object"].project_info.config_file,
dialog.path)
def _on_open(self, info):
""" Menu action to load a script from file. """
file_dialog = FileDialog(action='open',
default_directory=info.object.file_directory,
wildcard='All files (*.*)|*.*')
file_dialog.open()
if file_dialog.path != '':
info.object.load_code_from_file(file_dialog.path)
return
def _load_trans_fired(self):
# find trans file destination
raw_dir = os.path.dirname(self.model.hsp.file)
subject = self.model.mri.subject
trans_file = trans_fname.format(raw_dir=raw_dir, subject=subject)
dlg = FileDialog(action="open", wildcard=trans_wildcard, default_path=trans_file)
dlg.open()
if dlg.return_code != OK:
return
trans_file = dlg.path
self.model.load_trans(trans_file)
def ask_user_for_savefile(title=None):
#from traitsui.file_dialog import save_file
from pyface.api import FileDialog, OK
dialog = FileDialog(action='save as')
if title is not None:
dialog.title = title
dialog.open()
if dialog.return_code != OK:
return
return os.path.join(dialog.directory, dialog.filename)
def ask_user_for_savefile(title=None):
#from traitsui.file_dialog import save_file
from pyface.api import FileDialog, OK
dialog = FileDialog(action='save as')
if title is not None:
dialog.title = title
dialog.open()
if dialog.return_code != OK:
return
return os.path.join( dialog.directory, dialog.filename )
def _save_fired(self):
if self.n_scale_params:
subjects_dir = self.model.mri.subjects_dir
subject_from = self.model.mri.subject
subject_to = self.model.raw_subject or self.model.mri.subject
else:
subject_to = self.model.mri.subject
# ask for target subject
if self.n_scale_params:
mridlg = NewMriDialog(subjects_dir=subjects_dir, subject_from=subject_from, subject_to=subject_to)
ui = mridlg.edit_traits(kind="modal")
if ui.result != True:
return
subject_to = mridlg.subject_to
# find bem file to run mne_prepare_bem_model
if self.can_prepare_bem_model and self.prepare_bem_model:
bem_job = self.model.get_prepare_bem_model_job(subject_to)
else:
bem_job = None
# find trans file destination
raw_dir = os.path.dirname(self.model.hsp.file)
trans_file = trans_fname.format(raw_dir=raw_dir, subject=subject_to)
dlg = FileDialog(action="save as", wildcard=trans_wildcard, default_path=trans_file)
dlg.open()
if dlg.return_code != OK:
return
trans_file = dlg.path
if not trans_file.endswith(".fif"):
trans_file = trans_file + ".fif"
if os.path.exists(trans_file):
answer = confirm(None, "The file %r already exists. Should it " "be replaced?", "Overwrite File?")
if answer != YES:
return
# save the trans file
try:
self.model.save_trans(trans_file)
except Exception as e:
error(None, str(e), "Error Saving Trans File")
return
# save the scaled MRI
if self.n_scale_params:
job = self.model.get_scaling_job(subject_to)
self.queue.put(job)
self.queue_len += 1
if bem_job is not None:
self.queue.put(bem_job)
self.queue_len += 1
def _on_run_custom_ui(self, info):
""" Run a custom UI on top of the context.
"""
wildcard = FileDialog.WILDCARD_PY.rstrip('|')
file_dialog = FileDialog(action='open',
default_directory=info.object.file_directory,
wildcard=wildcard)
file_dialog.open()
if file_dialog.path != '':
info.object.run_custom_ui(file_dialog.path, live=False)
return
def _on_save_as(self, info):
""" Menu action to save script to file of different name """
file_dialog = FileDialog(action='save as',
default_path=info.object.file_path,
wildcard='All files (*.*)|*.*')
file_dialog.open()
if file_dialog.path != '':
info.object.save_code_to_file(file_dialog.path)
msg = 'Saving script at ', file_dialog.path
logger.debug(msg)
return
def _on_save_as(self, info):
""" Menu action to save script to file of different name """
file_dialog = FileDialog(action='save as',
default_path=info.object.file_directory,
wildcard='All files (*.*)|*.*')
file_dialog.open()
if file_dialog.path != '':
info.object.save_code_to_file(file_dialog.path)
msg = 'Saving script at ', file_dialog.path
logger.debug(msg)
return
def _on_import_data_file(self, info):
""" Loading data files to import data for data contexts.
File formats supported are ASCII, LAS, CSV, pickled files.
ASCII files can be tab- or whitespace- delimited.
If geo cannot be imported, only the pickled files can be
used.
"""
try:
import geo
wildcard = 'All files (*.*)|*.*|' + \
'ASCII files (*.asc)|*.asc|' + \
'Text files (*.txt)|*.txt|' + \
'CSV files (*.csv)|*.csv|' + \
'LAS files (*.las)|*.las|' + \
'Pickled files (*.pickle)|*.pickle|'+ \
'Segy files (*.segy)|*.segy'
except ImportError:
wildcard = 'Pickled files (*.pickle)|*.pickle'
app = info.object
file_dialog = FileDialog(
action='open',
default_directory=app.data_directory,
wildcard=wildcard,
)
file_dialog.open()
data_context, filename = None, file_dialog.path
if file_dialog.path != '':
filesplit = os.path.splitext(filename)
if filesplit[1] != '':
configurable_import = ConfigurableImportUI(filename=filename,
wildcard=wildcard)
ui = configurable_import.edit_traits(kind='livemodal')
if ui.result and isinstance(configurable_import.context,
DataContext):
data_context = configurable_import.context
app.load_context(data_context,
mode=configurable_import.save_choice_)
filename = configurable_import.filename
if isinstance(data_context, DataContext):
logger.debug('Loading data from %s' % filename)
else:
logger.error('Unidentified file format for data import: %s' %
filename)
return
def _on_import(self):
"""
Import format: CSV, first column is filename, path relative to CSV.
others are conditions, type is autodetected. first row is header
with names.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "CSV files (*.csv)|*.csv|"
file_dialog.action = 'open'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
csv = pandas.read_csv(file_dialog.path)
csv_folder = Path(file_dialog.path).parent
if self.model.tubes or self.model.tube_traits:
if confirm(
parent=None,
message="This will clear the current conditions and tubes! "
"Are you sure you want to continue?",
title="Clear tubes and conditions?") != YES:
return
for col in csv.columns[1:]:
self.model.tube_traits.append(
TubeTrait(model=self.model,
name=util.sanitize_identifier(col),
type='category'))
for _, row in csv.iterrows():
filename = csv_folder / row[0]
try:
metadata, _ = parse_tube(str(filename), metadata_only=True)
except Exception as e:
warning(
None,
"Had trouble loading file {}: {}".format(filename, str(e)))
continue
metadata['CF_File'] = Path(filename).stem
new_tube = Tube(file=str(filename),
parent=self.model,
metadata=sanitize_metadata(metadata))
self.model.tubes.append(new_tube)
for col in csv.columns[1:]:
new_tube.trait_set(**{util.sanitize_identifier(col): row[col]})
def object_export_data_changed(self, info):
fileDialog = FileDialog(action='save as',
title='Save As',
wildcard=self.wildcard,
parent=info.ui.control,
default_filename=info.object.name)
if info.object.export_format == 'Clipboard':
info.object.save_pandas()
else:
fileDialog.open()
if fileDialog.path == '' or fileDialog.return_code == CANCEL:
return False
else:
info.object.save_pandas(fileDialog.path)
def _on_import_data_file(self, info):
""" Loading data files to import data for data contexts.
File formats supported are ASCII, LAS, CSV, pickled files.
ASCII files can be tab- or whitespace- delimited.
If geo cannot be imported, only the pickled files can be
used.
"""
try:
import geo
wildcard = 'All files (*.*)|*.*|' + \
'ASCII files (*.asc)|*.asc|' + \
'Text files (*.txt)|*.txt|' + \
'CSV files (*.csv)|*.csv|' + \
'LAS files (*.las)|*.las|' + \
'Pickled files (*.pickle)|*.pickle|'+ \
'Segy files (*.segy)|*.segy'
except ImportError:
wildcard = 'Pickled files (*.pickle)|*.pickle'
app = info.object
file_dialog = FileDialog(action = 'open',
default_directory = app.data_directory,
wildcard = wildcard,
)
file_dialog.open()
data_context, filename = None, file_dialog.path
if file_dialog.path != '':
filesplit = os.path.splitext(filename)
if filesplit[1] != '':
configurable_import = ConfigurableImportUI(filename = filename,
wildcard = wildcard)
ui = configurable_import.edit_traits(kind='livemodal')
if ui.result and configurable_import.context:
data_context = configurable_import.context
app.load_context(
data_context, mode=configurable_import.save_choice_)
filename = configurable_import.filename
if data_context:
logger.debug('Loading data from %s' % filename)
else:
logger.error('Unidentified file format for data import: %s' %
filename)
return
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
# TODO - adding a set of files, then a condition, then another
# set doesn't work.
file_dialog = FileDialog()
file_dialog.wildcard = "Flow cytometry files (*.fcs)|*.fcs|"
file_dialog.action = 'open files'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
for path in file_dialog.paths:
try:
tube_meta = fcsparser.parse(path,
meta_data_only = True,
reformat_meta = True)
tube_channels = tube_meta["_channels_"].set_index("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
# TODO - do we still need to check for transient?
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name : trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(Source = tube_meta['$SRC'],
_file = path,
_parent = self.model)
if 'TUBE NAME' in tube_meta:
tube.Tube = tube_meta['TUBE NAME']
elif '$SMNO' in tube_meta:
tube.Tube = tube_meta['$SMNO']
self.model.tubes.append(tube)
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
# TODO - adding a set of files, then a condition, then another
# set doesn't work.
file_dialog = FileDialog()
file_dialog.wildcard = "Flow cytometry files (*.fcs)|*.fcs|"
file_dialog.action = 'open files'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
for path in file_dialog.paths:
try:
tube_meta = fcsparser.parse(path,
meta_data_only=True,
reformat_meta=True)
#tube_channels = tube_meta["_channels_"].set_index("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
# TODO - do we still need to check for transient?
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name: trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(Source=tube_meta['$SRC'],
_file=path,
_parent=self.model)
if 'TUBE NAME' in tube_meta:
tube.Tube = tube_meta['TUBE NAME']
elif '$SMNO' in tube_meta:
tube.Tube = tube_meta['$SMNO']
self.model.tubes.append(tube)
def perform(self, event):
""" Performs the action. """
extensions = [
'*.png', '*.jpg', '*.jpeg', '*.tiff', '*.bmp', '*.ps', '*.eps',
'*.tex', '*.rib', '*.wrl', '*.oogl', '*.pdf', '*.vrml', '*.obj',
'*.iv', '*.pov', '*x3d'
]
descriptions = [
'PNG', 'JPG', 'JPEG', 'TIFF', 'Bitmap', 'PostScript', 'EPS',
'TeX', 'RIB', 'WRL', 'Geomview', 'PDF', 'VRML', 'Wavefront',
'Povray', 'X3D'
]
wildcard = ''
for description, extension in zip(descriptions, extensions):
wildcard += '{} ({})|{}|'.format(description, extension, extension)
wildcard += 'Determine by extension (*.*)|(*.*)'
dialog = FileDialog(
parent = self.window.control,
title = 'Save scene to image',
action = 'save as',
wildcard = wildcard
)
if dialog.open() == OK:
scene = self.scene_manager.current_scene
if scene is not None:
scene.save(dialog.path)
return
def popup_save(parent=None):
"""Popup a dialog asking for an image name to save the scene to.
This is used mainly to save a scene in full screen mode. Returns a
filename, returns empty string if action was cancelled. `parent` is
the parent widget over which the dialog will be popped up.
"""
from pyface.api import FileDialog, OK
extensions = ['*.png', '*.jpg', '*.tiff', '*.bmp', '*.ps',
'*.eps', '*.pdf', '*.tex', '*.rib', '*.wrl',
'*.oogl', '*.vrml', '*.obj', '*.iv', '*.pov',
'*.x3d']
descriptions = ["PNG", "JPG", "TIFF", "Bitmap", "PostScript",
"EPS", "PDF", "Tex", "RIB", "WRL",
"Geomview", "VRML", "Wavefront", "Open Inventor",
"Povray", "X3D"]
wildcard = ""
for description, extension in zip(descriptions, extensions):
wildcard += "{} ({})|{}|".format(description,
extension,
extension)
wildcard += "Determine by extension (*.*)|(*.*)"
dialog = FileDialog(
parent=parent, title='Save scene to image',
action='save as', default_filename="snapshot.png",
wildcard=wildcard
)
if dialog.open() == OK:
return dialog.path
else:
return ''
def _file_dialog_(self, action, **kw):
'''
'''
# print 'file_dialog', kw
dlg = FileDialog(action=action, **kw)
if dlg.open() == OK:
return dlg.path
def perform(self, event):
plot_component = self.container.component
filter = 'PNG file (*.png)|*.png|\nTIFF file (*.tiff)|*.tiff|'
dialog = FileDialog(action='save as', wildcard=filter)
if dialog.open() != OK:
return
# Remove the toolbar before saving the plot, so the output doesn't
# include the toolbar.
plot_component.remove_toolbar()
filename = dialog.path
width, height = plot_component.outer_bounds
gc = PlotGraphicsContext((width, height), dpi=72)
gc.render_component(plot_component)
try:
gc.save(filename)
except KeyError as e:
errmsg = ("The filename must have an extension that matches "
"a graphics format, such as '.png' or '.tiff'.")
if str(e.message) != '':
errmsg = ("Unknown filename extension: '%s'\n" %
str(e.message)) + errmsg
error(None, errmsg, title="Invalid Filename Extension")
# Restore the toolbar.
plot_component.add_toolbar()
def resize_and_save_matplotlib_figure(figure):
''' To save a matplotlib figure with custom width and height in pixels
requires changing the bounding box while is being rendered! '''
# get figure size
figure_size = MatplotlibFigureSize(figure=figure)
old_dpi = figure_size.dpi
old_width_inches = figure_size.width_inches
old_height_inches = figure_size.height_inches
ui = figure_size.edit_traits(kind='modal')
widget = ui.control
# maybe change figure size
if ui.result:
figure.dpi = figure_size.dpi # set new dpi
figure.bbox_inches.p1 = figure_size.width_inches, figure_size.height_inches # set new width and height in inches
else:
return
# get file name with (correct choice of formats)
fd = FileDialog(
action='save as',
wildcard=FileDialog.create_wildcard('All available formats', ['*.eps', '*.png', '*.pdf', '*.ps', '*.svg']),
)
if fd.open() != OK:
return
file_name = fd.path
# save it
figure.savefig(file_name)
# restore original figure size
figure.dpi = old_dpi # restore old dpi
figure.bbox_inches.p1 = old_width_inches, old_height_inches # restore old width and height in inches
def on_export(self):
"""
Shows a dialog to export a file
"""
dialog = FileDialog(parent=self.window.control, action='save as')
if dialog.open() == OK:
self.view.export(dialog.path)
def _save_(self, type_='pic', path=None):
"""
"""
if path is None:
dlg = FileDialog(action='save as')
if dlg.open() == OK:
path = dlg.path
self.status_text = 'Image Saved: %s' % path
if path is not None:
if type_ == 'pdf':
self._render_to_pdf(filename=path)
else:
# auto add an extension to the filename if not present
# extension is necessary for PIL compression
# set default save type_ DEFAULT_IMAGE_EXT='.png'
# see http://infohost.nmt.edu/tcc/help/pubs/pil/formats.html
saved = False
for ei in IMAGE_EXTENSIONS:
if path.endswith(ei):
self._render_to_pic(path)
saved = True
break
if not saved:
self._render_to_pic(path + DEFAULT_IMAGE_EXT)
def save(self):
""" Save the current file.
If needed, this code prompts for a path.
Returns
-------
saved : bool
Whether or not the file was saved.
"""
editor = self.active_editor
try:
editor.save()
except IOError:
# If you are trying to save to a file that doesn't exist, open up a
# FileDialog with a 'save as' action.
dialog = FileDialog(
parent=self.window.control,
action='save as',
wildcard='*.py',
)
if dialog.open() == OK:
editor.save(dialog.path)
else:
return False
return True
def perform(self, event):
plot_component = self.container.component
filter = 'PNG file (*.png)|*.png|\nTIFF file (*.tiff)|*.tiff|'
dialog = FileDialog(action='save as', wildcard=filter)
if dialog.open() != OK:
return
# Remove the toolbar before saving the plot, so the output doesn't
# include the toolbar.
plot_component.remove_toolbar()
filename = dialog.path
width, height = plot_component.outer_bounds
gc = PlotGraphicsContext((width, height), dpi=72)
gc.render_component(plot_component)
try:
gc.save(filename)
except KeyError as e:
errmsg = ("The filename must have an extension that matches "
"a graphics format, such as '.png' or '.tiff'.")
if str(e.message) != '':
errmsg = ("Unknown filename extension: '%s'\n" %
str(e.message)) + errmsg
error(None, errmsg, title="Invalid Filename Extension")
# Restore the toolbar.
plot_component.add_toolbar()
def save_file():
wildcard='*.txt'
dialog = FileDialog(title='Select the file to save as...',
action='save as', wildcard=wildcard)
if dialog.open() == Pyface_OK:
return dialog.path
return ''
