class CalibrationObject(HasTraits):
tweak_dict = Dict
cx = Float
cy = Float
rx = Float
ry = Float
rotation = Property(depends_on='rx,ry,_rotation')
_rotation = Float
center = Property(depends_on='cx,cy')
scale = Float(1)
def _set_rotation(self, rot):
self._rotation = rot
def _get_rotation(self):
# if not (self.rx and self.rx):
# return self._rotation
rot = self._rotation
if not rot:
rot = self.calculate_rotation(self.rx, self.ry)
return rot
def _get_center(self):
return self.cx, self.cy
def set_right(self, x, y):
self.rx = x
self.ry = y
self._rotation = 0
def set_center(self, x, y):
self.cx = x
self.cy = y
def calculate_rotation(self, x, y, sense='east'):
def rotation(a, b):
return calc_rotation(self.cx, self.cy, a, b)
if sense == 'west':
print('x={}, y={}, cx={}, cy={}'.format(x, y, self.cx, self.cy))
if y > self.cy:
rot = calc_rotation(self.cx, self.cy, x, y) - 180
else:
rot = calc_rotation(self.cx, self.cy, x, y) + 180
elif sense == 'north':
if x > self.cx:
rot = rotation(x, -y)
else:
rot = rotation(y, -x)
elif sense == 'south':
rot = rotation(-y, x)
else:
rot = rotation(x, y)
return rot
class PadEntry(HasTraits):
pad = Float
olow_post = Date
ohigh_post = Date
low_post = Property(depends_on='low_post_data, low_post_time')
low_post_date = Date
low_post_time = Time
high_post = Property(depends_on='high_post_data, high_post_time')
high_post_date = Date
high_post_time = Time
def update_pad(self):
self._pad_changed(self.pad)
def _pad_changed(self, pad):
if self.olow_post and self.ohigh_post:
td = timedelta(hours=pad)
lp, hp = self.olow_post, self.ohigh_post
lp -= td
hp += td
self.low_post, self.high_post = lp, hp
def _set_high_post(self, v):
self.high_post_date = v.date()
self.high_post_time = v.time()
def _set_low_post(self, v):
self.low_post_date = v.date()
self.low_post_time = v.time()
def _get_high_post(self):
return datetime.combine(self.high_post_date, self.high_post_time)
def _get_low_post(self):
return datetime.combine(self.low_post_date, self.low_post_time)
def traits_view(self):
l = VGroup(UItem('low_post_time'),
UItem('low_post_date', style='custom'))
h = VGroup(UItem('high_post_time'),
UItem('high_post_date', style='custom'))
v = View(UItem('pad'),
HGroup(l, h),
kind='livemodal',
width=500,
resizable=True,
buttons=['OK', 'Cancel'])
return v
class PadEntry(HasTraits):
pad = Float
olow_post = Date
ohigh_post = Date
low_post = Property(depends_on='low_post_data, low_post_time')
low_post_date = Date
low_post_time = Time
high_post = Property(depends_on='high_post_data, high_post_time')
high_post_date = Date
high_post_time = Time
def update_pad(self):
self._pad_changed(self.pad)
def _pad_changed(self, pad):
if self.olow_post and self.ohigh_post:
td = timedelta(hours=pad)
lp, hp = self.olow_post, self.ohigh_post
lp -= td
hp += td
self.low_post, self.high_post = lp, hp
def _set_high_post(self, v):
self.high_post_date = v.date()
self.high_post_time = v.time()
def _set_low_post(self, v):
self.low_post_date = v.date()
self.low_post_time = v.time()
def _get_high_post(self):
return datetime.combine(self.high_post_date, self.high_post_time)
def _get_low_post(self):
return datetime.combine(self.low_post_date, self.low_post_time)
def traits_view(self):
l = VGroup(UItem('low_post_time'),
UItem('low_post_date', style='custom'))
h = VGroup(UItem('high_post_time'),
UItem('high_post_date', style='custom'))
v = okcancel_view(Item('pad', label='Pad (hrs)'),
HGroup(l, h),
width=500)
return v
class MandelbrotParameters(HasTraits):
""" Stores the parameters needed to visualize the Mandelbrot set.
"""
# The number of points on each dimension of the grid.
grid_size = Int(500)
# Left limit for the x coordinates.
xmin = Float(-2.0)
# Right limit for the x coordinates.
xmax = Float(1.0, auto_set=False)
# Bottom limit for the y coordinates.
ymin = Float(-1.5, auto_set=False)
# Upper limit for the y coordinates.
ymax = Float(1.5, auto_set=False)
# Convenience property that returns a tuple with the bounds on the x axis.
x_bounds = Property
def _get_x_bounds(self):
return (self.xmin, self.xmax)
# 1D array with the x coordinates of the boundaries of the grid element.
x_coords = Property
def _get_x_coords(self):
# The coordinates have 1 more element than the number of points in
# the grid, because they represent the locations of pixel boundaries.
return numpy.linspace(self.xmin, self.xmax, self.grid_size+1)
# Convenience property that returns a tuple with the bounds on the y axis.
y_bounds = Property(depends_on='ymin,ymax')
def _get_y_bounds(self):
return (self.ymin, self.ymax)
# 1D array with the y coordinates of the boundaries of the grid element.
y_coords = Property(depends_on='ymin,ymax')
def _get_y_coords(self):
# The coordinates have 1 more element than the number of points in
# the grid, because they represent the locations of pixel boundaries.
return numpy.linspace(self.ymin, self.ymax, self.grid_size+1)
class FluxTool(HasTraits):
calculate_button = Button('Calculate')
monitor_age = Property(depends_on='monitor')
color_map_name = Str('jet')
levels = Int(10, auto_set=False, enter_set=True)
model_kind = Str('Plane')
data_source = Str('database')
# plot_kind = Str('Contour')
plot_kind=Enum('Contour','Hole vs J')
# def _plot_kind_default(self,):
monitor=Any
monitors=List
group_positions=Bool(False)
def _monitor_default(self):
return DummyFluxMonitor()
def _get_monitor_age(self):
ma = 28.02e6
if self.monitor:
ma=self.monitor.age
return ma
def traits_view(self):
contour_grp = VGroup(Item('color_map_name',
label='Color Map',
editor=EnumEditor(values=sorted(color_map_name_dict.keys()))),
Item('levels'),
visible_when='plot_kind=="Contour"')
monitor_grp=Item('monitor', editor=EnumEditor(name='monitors'))
v = View(
VGroup(HGroup(UItem('calculate_button'),
UItem('data_source', editor=EnumEditor(values=['database', 'file'])),
monitor_grp),
HGroup(Item('group_positions'), Item('object.monitor.sample', style='readonly',label='Sample')),
HGroup(UItem('plot_kind'),
Item('model_kind', label='Fit Model',
editor=EnumEditor(values=['Bowl', 'Plane']))),
# UItem('plot_kind', editor=EnumEditor(values=['Contour', 'Hole vs J']))),
contour_grp))
return v
class NewBranchView(HasTraits):
name = Property(depends_on='_name')
branches = Any
_name = Str
def traits_view(self):
v = okcancel_view(UItem('name'), width=200, title='New Branch')
return v
def _get_name(self):
return self._name
def _set_name(self, v):
self._name = v
def _validate_name(self, v):
if v not in self.branches:
if ' ' not in v:
return v
class FitSelector(HasTraits):
fits = List(Fit)
update_needed = Event
suppress_refresh_unknowns = Bool
save_event = Event
fit_klass = Fit
command_key = Bool
auto_update = Bool(True)
plot_button = Button('Plot')
default_error_type = 'SD'
show_all_button = Event
show_state = Bool
show_all_label = Property(depends_on='show_state')
use_all_button = Button('Toggle Save')
use_state = Bool
global_fit = Str('Fit')
global_error_type = Str('Error')
fit_types = List(['Fit', ''] + FIT_TYPES)
error_types = List(['Error', ''] + FIT_ERROR_TYPES)
selected = Any
def _get_show_all_label(self):
return 'Hide All' if self.show_state else 'Show All'
def _plot_button_fired(self):
self.update_needed = True
def _auto_update_changed(self):
self.update_needed = True
def _get_fits(self):
fs = self.selected
if not fs:
fs = self.fits
return fs
def _show_all_button_fired(self):
self.show_state = not self.show_state
fs = self._get_fits()
for fi in fs:
fi.show = self.show_state
def _use_all_button_fired(self):
self.use_state = not self.use_state
fs = self._get_fits()
for fi in fs:
fi.use = self.use_state
def _global_fit_changed(self):
if self.global_fit in self.fit_types:
fs = self._get_fits()
for fi in fs:
fi.fit = self.global_fit
def _global_error_type_changed(self):
if self.global_error_type in FIT_ERROR_TYPES:
fs = self._get_fits()
for fi in fs:
fi.error_type = self.global_error_type
def _get_auto_group(self):
return VGroup(
HGroup(
icon_button_editor(
'plot_button',
'refresh',
tooltip='Replot the isotope evolutions. '
'This may take awhile if many analyses are selected'),
icon_button_editor('save_event',
'database_save',
tooltip='Save fits to database'),
Item(
'auto_update',
label='Auto Plot',
tooltip=
'Should the plot refresh after each change ie. "fit" or "show". '
'It is not advisable to use this option with many analyses'
)),
HGroup(
UItem('global_fit', editor=EnumEditor(name='fit_types')),
UItem('global_error_type',
editor=EnumEditor(name='error_types'))))
def traits_view(self):
v = View(
VGroup(self._get_auto_group(), self._get_toggle_group(),
self._get_fit_group()))
return v
def _get_toggle_group(self):
g = HGroup(
# UItem('global_fit',editor=EnumEditor(name='fit_types')),
# UItem('global_error_type', editor=EnumEditor(name='error_types')),
UItem('show_all_button',
editor=ButtonEditor(label_value='show_all_label')),
UItem('use_all_button'))
return g
def _get_columns(self):
cols = [
ObjectColumn(name='name', editable=False),
CheckboxColumn(name='show'),
CheckboxColumn(name='use', label='Save'),
ObjectColumn(name='fit',
editor=EnumEditor(name='fit_types'),
width=150),
ObjectColumn(name='error_type',
editor=EnumEditor(name='error_types'),
width=50)
]
return cols
def _get_fit_group(self):
cols = self._get_columns()
editor = myTableEditor(columns=cols,
selected='selected',
selection_mode='rows',
sortable=False,
edit_on_first_click=False,
clear_selection_on_dclicked=True,
on_command_key=self._update_command_key,
cell_bg_color='red',
cell_font='modern 10')
grp = UItem('fits', style='custom', editor=editor)
return grp
@on_trait_change('fits:[show, fit, use]')
def _fit_changed(self, obj, name, old, new):
if self.command_key:
for fi in self.fits:
fi.trait_set(**{name: new})
self.command_key = False
if self.auto_update:
if name in ('show', 'fit'):
self.update_needed = True
def load_fits(self, keys, fits):
nfs = []
for ki, fi in zip(keys, fits):
pf = next((fa for fa in self.fits if fa.name == ki), None)
fit, et, fod = fi
if pf is None:
pf = self.fit_klass(name=ki)
pf.fit = fit
pf.filter_outliers = fod.get('filter_outliers', False)
pf.filter_iterations = fod.get('iterations', 0)
pf.filter_std_devs = fod.get('std_devs', 0)
pf.error_type = et
nfs.append(pf)
self.fits = nfs
# def load_baseline_fits(self, keys):
# fits = self.fits
# if not fits:
# fits = []
#
# fs = [
# self.fit_klass(name='{}bs'.format(ki), fit='average')
# for ki in keys]
#
# fits.extend(fs)
# self.fits = fits
# def add_peak_center_fit(self):
# fits = self.fits
# if not fits:
# fits = []
#
# fs = self.fit_klass(name='PC', fit='average')
#
# fits.append(fs)
# self.fits = fits
#
# def add_derivated_fits(self, keys):
# fits = self.fits
# if not fits:
# fits = []
#
# fs = [
# self.fit_klass(name='{}E'.format(ki), fit='average')
# for ki in keys
# ]
#
# fits.extend(fs)
# self.fits = fits
def _update_command_key(self, new):
self.command_key = new
class MarkerLabel(Label):
rotate_angle = 0
zero_y = 0
xoffset = 10
indicator_width = 4
indicator_height = 10
visible = Bool(True)
component_height = 100
x = Float
y = Float
data_y = Float
vertical = False
horizontal_line_visible = False
label_with_intensity = False
text = Property(depends_on='_text, label_with_intensity')
_text = Str
def _set_text(self, text):
self._text = text
def _get_text(self):
if self.label_with_intensity:
return '{:0.4f}'.format(self.data_y)
else:
return self._text
def draw(self, gc, component_height):
if not self.text:
self.text = ''
if self.bgcolor != "transparent":
gc.set_fill_color(self.bgcolor_)
#draw tag border
with gc:
if self.vertical:
self.rotate_angle = 90
width, height = self.get_bounding_box(gc)
gc.translate_ctm(self.x, self.zero_y_vert - 35 - height)
else:
if self.horizontal_line_visible:
self._draw_horizontal_line(gc)
gc.translate_ctm(self.x + self.xoffset, self.y)
self._draw_tag_border(gc)
super(MarkerLabel, self).draw(gc)
with gc:
gc.translate_ctm(self.x - self.indicator_width / 2.0, self.zero_y)
self._draw_index_indicator(gc, component_height)
def _draw_horizontal_line(self, gc):
with gc:
# print self.x, self.y
gc.set_stroke_color((0, 0, 0, 1))
gc.set_line_width(2)
oy = 7 if self.text else 4
y = self.y + oy
gc.move_to(0, y)
gc.line_to(self.x, y)
gc.stroke_path()
def _draw_index_indicator(self, gc, component_height):
# gc.set_fill_color((1, 0, 0, 1))
w, h = self.indicator_width, self.indicator_height
gc.draw_rect((0, 0, w, h), FILL)
gc.draw_rect((0, component_height, w, h), FILL)
def _draw_tag_border(self, gc):
gc.set_stroke_color((0, 0, 0, 1))
gc.set_line_width(2)
# gc.set_fill_color((1, 1, 1, 1))
bb_width, bb_height = self.get_bounding_box(gc)
offset = 2
xoffset = self.xoffset
gc.lines([(-xoffset, (bb_height + offset) / 2.0),
(0, bb_height + 2 * offset),
(bb_width + offset, bb_height + 2 * offset),
(bb_width + offset, -offset), (0, -offset),
(-xoffset, (bb_height + offset) / 2.0)])
gc.draw_path()
class BaseTemplater(HasTraits):
formatter = Property(depends_on='label')
clear_button = Button
keywords = List
non_keywords = List
label = String
activated = Any
example = Property(depends_on='label')
view_title = Str
predefined_label = Str
predefined_labels = Property(depends_on='user_predefined_labels')
base_predefined_labels = List([''])
user_predefined_labels = List
add_enabled = Property(depends_on='label')
delete_enabled = Property(depends_on='label')
add_label_button = Button
delete_label_button = Button
attribute_keys = Property(depends_on='label')
persistence_name = ''
attributes = List
example_context = Dict
attribute_formats = Dict
def __init__(self, *args, **kw):
super(BaseTemplater, self).__init__(*args, **kw)
self.load()
#persistence
def load(self):
p = os.path.join(paths.hidden_dir, self.persistence_name)
if os.path.isfile(p):
with open(p, 'r') as rfile:
try:
self.user_predefined_labels = pickle.load(rfile)
except BaseException:
pass
def dump(self):
p = os.path.join(paths.hidden_dir, self.persistence_name)
with open(p, 'w') as wfile:
try:
pickle.dump(self.user_predefined_labels, wfile)
except BaseException:
pass
def _get_attribute_keys(self):
ks = []
for k in self.label.split(' '):
if k in self.attributes:
ks.append(k.lower())
return ks
def _get_formatter(self):
ns = []
for k in self.label.split(' '):
if k in self.attributes:
if k == '<SPACE>':
k = ' '
else:
k = k.lower()
try:
f = self.attribute_formats[k]
except KeyError:
f = 's'
k = '{{{}:{}}}'.format(k, f)
ns.append(k)
s = ''.join(ns)
return s
def _get_example(self):
f = self.formatter
return f.format(**self.example_context)
def _get_predefined_labels(self):
return self.base_predefined_labels + self.user_predefined_labels
def _get_add_enabled(self):
return self.label and self.label not in self.predefined_labels
def _get_delete_enabled(self):
return self.label in self.user_predefined_labels
def _delete_label_button_fired(self):
if self.label in self.user_predefined_labels:
self.user_predefined_labels.remove(self.label)
self.dump()
self.load()
self.label = ''
#handlers
def _add_label_button_fired(self):
if self.label not in self.predefined_labels:
self.user_predefined_labels.append(self.label)
self.dump()
self.load()
def _clear_button_fired(self):
self.label = ''
self.predefined_label = ''
def _activated_changed(self, new):
if new:
self.keywords.append(new)
if self.label:
self.label += ' {}'.format(new)
else:
self.label = new
self.activated = None
def _predefined_label_changed(self, new):
self.label = new
class PyannoApplication(HasTraits):
database = Instance(PyannoDatabase)
main_window = Instance(ModelDataView)
database_window = Instance(DatabaseView)
database_ui = Instance(UI)
logging_level = Int(logging.INFO)
pyanno_pathname = Str
db_window_open = Property(Bool)
def _get_db_window_open(self):
return (self.database_ui is not None
and self.database_ui.control is not None)
def open(self):
self._start_logging()
self._open_pyanno_database()
self._open_main_window()
def close(self):
self.database.close()
logger.info('Closing pyAnno -- Goodbye!')
def _start_logging(self):
logging.basicConfig(level=self.logging_level)
logger.info('Starting pyAnno')
def _create_pyanno_directory(self):
"""Create a pyanno directort in the user's home if it is missing."""
home_dir = os.getenv('HOME') or os.getenv('HOMEPATH')
logger.debug('Found home directory at ' + str(home_dir))
self.pyanno_pathname = os.path.join(home_dir, PYANNO_PATH_NAME)
try:
logger.debug('Creating pyAnno directory at ' +
self.pyanno_pathname)
os.makedirs(self.pyanno_pathname)
except OSError as e:
logger.debug('pyAnno directory already existing')
if e.errno != errno.EEXIST:
raise
def _open_pyanno_database(self):
# database filename
self._create_pyanno_directory()
db_filename = os.path.join(self.pyanno_pathname, DATABASE_FILENAME)
self.database = PyannoDatabase(db_filename)
def _open_main_window(self):
self.main_window = ModelDataView(application=self)
model = ModelBt.create_initial_state(5, 8)
self.main_window.set_model(model=model)
self.main_window.configure_traits()
def open_database_window(self):
if self.db_window_open:
# windows exists, raise
self.database_ui.control.Raise()
else:
# window was closed or not existent
logger.debug('Open database window')
database_window = DatabaseView(database=self.database,
application=self)
database_ui = database_window.edit_traits(kind='live')
self.database_window = database_window
self.database_ui = database_ui
def close_database_window(self):
# wx specific
self.database_ui.control.Close()
def update_window_from_database_record(self, record):
"""Update main window from pyanno database record.
"""
self.main_window.set_from_database_record(record)
def add_current_state_to_database(self):
mdv = self.main_window
# file name may contain unicode characters
data_id = mdv.annotations_view.annotations_container.name
if data_id is '':
data_id = 'anonymous_annotations'
elif type(data_id) is unicode:
u_data_id = unicodedata.normalize('NFKD', data_id)
data_id = u_data_id.encode('ascii', 'ignore')
try:
self.database.store_result(
data_id, mdv.annotations_view.annotations_container, mdv.model,
mdv.log_likelihood)
except PyannoValueError as e:
logger.info(e)
errmsg = e.args[0]
error('Error: ' + errmsg)
if self.db_window_open:
self.database_window.db_updated = True
def _create_debug_database(self):
"""Create and populate a test database in a temporary file.
"""
from tempfile import mktemp
from pyanno.modelA import ModelA
from pyanno.modelB import ModelB
from pyanno.annotations import AnnotationsContainer
# database filename
tmp_filename = mktemp(prefix='tmp_pyanno_db_')
db = PyannoDatabase(tmp_filename)
def _create_new_entry(model, annotations, id):
value = model.log_likelihood(annotations)
ac = AnnotationsContainer.from_array(annotations, name=id)
db.store_result(id, ac, model, value)
# populate database
model = ModelA.create_initial_state(5)
annotations = model.generate_annotations(100)
_create_new_entry(model, annotations, 'test_id')
modelb = ModelB.create_initial_state(5, 8)
_create_new_entry(modelb, annotations, 'test_id')
annotations = model.generate_annotations(100)
_create_new_entry(modelb, annotations, 'test_id2')
self.database = db
class AnnotationsContainer(HasStrictTraits):
"""Translate from general annotations files and arrays to pyAnno's format.
This class exposes a few methods to import data from files and arrays, and
converts them to pyAnno's format:
* annotations are 2D integer arrays; rows index items, and columns
annotators
* label classes are numbered 0 to :attr:`nclasses`-1 . The attribute
:attr:`labels` defines a mapping from label tokens to label classes
* missing values are defined as :attr:`pyanno.util.MISSING_VALUE`. The
attribute :attr:`missing_values` contains the missing values tokens
found in the original, raw data
The converted data can be accessed through the :attr:`annotations` property.
The `AnnotationsContainer` is also used as the format to store annotations
in :class:`~pyanno.database.PyannoDatabase` objects.
"""
DEFAULT_MISSING_VALUES_STR = ['-1', 'NA', 'None', '*']
DEFAULT_MISSING_VALUES_NUM = [-1, np.nan, None]
DEFAULT_MISSING_VALUES_ALL = (DEFAULT_MISSING_VALUES_STR +
DEFAULT_MISSING_VALUES_NUM)
#: raw annotations, as they are imported from file or array
raw_annotations = List(List)
#: name of file or array from which the annotations were imported
name = Str
#: list of all labels found in file/array
labels = List
#: labels corresponding to a missing value
missing_values = List
#: number of classes found in the annotations
nclasses = Property(Int, depends_on='labels')
def _get_nclasses(self):
return len(self.labels)
#: number of annotators
nannotators = Property(Int, depends_on='raw_annotations')
def _get_nannotators(self):
return len(self.raw_annotations[0])
#: number of annotations
nitems = Property(Int, depends_on='raw_annotations')
def _get_nitems(self):
return len(self.raw_annotations)
#: annotations in pyAnno format
annotations = Property(Array, depends_on='raw_annotations')
@cached_property
def _get_annotations(self):
nitems, nannotators = len(self.raw_annotations), self.nannotators
anno = np.empty((nitems, nannotators), dtype=int)
# build map from labels and missing values to annotation values
raw2val = dict(list(zip(self.labels, list(range(self.nclasses)))))
raw2val.update([(mv, MISSING_VALUE) for mv in self.missing_values])
# translate
nan_in_missing_values = _is_nan_in_list(self.missing_values)
for i, row in enumerate(self.raw_annotations):
for j, lbl in enumerate(row):
if nan_in_missing_values and _robust_isnan(lbl):
# workaround for the fact that np.nan cannot be used as
# the key to a dictionary, since np.nan != np.nan
anno[i, j] = MISSING_VALUE
else:
anno[i, j] = raw2val[lbl]
return anno
@staticmethod
def _from_generator(rows_generator, missing_values, name=''):
missing_set = set(missing_values)
labels_set = set()
raw_annotations = []
nannotators = None
for n, row in enumerate(rows_generator):
# verify that number of lines is consistent in the whole file
if nannotators is None: nannotators = len(row)
else:
if len(row) != nannotators:
raise PyannoValueError(
'File has inconsistent number of entries '
'on separate lines (line {})'.format(n))
raw_annotations.append(row)
labels_set.update(row)
# remove missing values from set of labels
all_labels = sorted(list(labels_set - missing_set))
missing_values = sorted(list(missing_set & labels_set))
# workaround for np.nan != np.nan, so intersection does not work
if _is_nan_in_list(all_labels):
# uses fact that np.nan < x, for every x
all_labels = all_labels[1:]
missing_values.insert(0, np.nan)
# create annotations object
anno = AnnotationsContainer(raw_annotations=raw_annotations,
labels=all_labels,
missing_values=missing_values,
name=name)
return anno
@staticmethod
def _from_file_object(fobj, missing_values=None, name=''):
"""Useful for testing, as it can be called using a StringIO object.
"""
if missing_values is None:
missing_values = AnnotationsContainer.DEFAULT_MISSING_VALUES_STR
# generator for rows of file-like object
def file_row_generator():
for line in fobj.readlines():
# remove commas and split in individual tokens
line = line.strip().replace(',', ' ')
# ignore empty lines
if len(line) == 0: continue
labels = line.split()
yield labels
return AnnotationsContainer._from_generator(file_row_generator(),
missing_values,
name=name)
@staticmethod
def from_file(filename, missing_values=None):
"""Load annotations from a file.
The file is a text file with a columns separated by spaces and/or
commas, and rows on different lines.
Arguments
---------
filename : string
File name
missing_values : list
List of labels that are considered missing values.
Default is :attr:`DEFAULT_MISSING_VALUES_STR`
"""
if missing_values is None:
missing_values = AnnotationsContainer.DEFAULT_MISSING_VALUES_STR
with open(filename) as fh:
anno = AnnotationsContainer._from_file_object(
fh, missing_values=missing_values, name=filename)
return anno
@staticmethod
def from_array(x, missing_values=None, name=''):
"""Create an annotations object from an array or list-of-lists.
Arguments
---------
x : ndarray or list-of-lists
Array or list-of-lists containing numerical or string annotations
missing_values : list
List of values that are considered missing values.
Default is :attr:`DEFAULT_MISSING_VALUES_ALL`
name : string
Name of the annotations (for user interaction and used as key in
databases).
"""
if missing_values is None:
missing_values = AnnotationsContainer.DEFAULT_MISSING_VALUES_ALL
# generator for array objects
def array_rows_generator():
for row in x:
yield list(row)
return AnnotationsContainer._from_generator(array_rows_generator(),
missing_values,
name=name)
def save_to(self, filename, set_name=False):
"""Save raw annotations to file.
Arguments
---------
filename : string
File name
set_name : bool
Set the :attr:`name` of the annotation container to the file name
"""
if set_name:
self.name = filename
with open(filename, 'w') as f:
f.writelines((' '.join(map(str, row)) + '\n'
for row in self.raw_annotations))
def func(fget):
fget.__name__ = '_get_' + fget.__name__
fget = cached_property(fget)
x = Property(depends_on=depends_on, fget=fget, force=True, **kwargs)
return x
class FluxTool(HasTraits):
calculate_button = Button('Calculate')
monitor_age = Property(depends_on='monitor')
color_map_name = Str('jet')
marker_size = Int(5)
levels = Int(50, auto_set=False, enter_set=True)
model_kind = Str('Plane')
data_source = Str('database')
# plot_kind = Str('Contour')
plot_kind = Enum('Contour', 'Hole vs J')
# def _plot_kind_default(self,):
monitor = Any
monitors = List
group_positions = Bool(False)
show_labels = Bool(True)
mean_j_error_type = Enum(*ERROR_TYPES)
predicted_j_error_type = Enum(*ERROR_TYPES)
_prev_predicted_j_error_type = Str
use_weighted_fit = Bool(False)
use_monte_carlo = Bool(False)
monte_carlo_ntrials =Int(10000)
save_mean_j = Bool(False)
auto_clear_cache = Bool(False)
def _monitor_default(self):
return DummyFluxMonitor()
def _get_monitor_age(self):
ma = 28.02e6
if self.monitor:
ma = self.monitor.age
return ma
def _use_weighted_fit_changed(self, new):
if new:
self._prev_predicted_j_error_type = self.predicted_j_error_type
self.predicted_j_error_type = 'SD'
else:
self.predicted_j_error_type = self._prev_predicted_j_error_type
def traits_view(self):
contour_grp = HGroup(Item('color_map_name',
label='Color Map',
editor=EnumEditor(values=sorted(color_map_name_dict.keys()))),
Item('levels'),
Item('marker_size'),
visible_when='plot_kind=="Contour"')
monitor_grp = Item('monitor', editor=EnumEditor(name='monitors'))
v = View(
VGroup(HGroup(UItem('calculate_button'),
UItem('data_source', editor=EnumEditor(values=['database', 'file'])),
monitor_grp),
HGroup(Item('save_mean_j', label='Save Mean J'),
Item('auto_clear_cache', label='Auto Clear Cache')),
Item('mean_j_error_type', label='Mean J Error'),
HGroup(Item('use_weighted_fit'),
Item('use_monte_carlo'),
Item('monte_carlo_ntrials',
enabled_when='object.use_monte_carlo')),
Item('predicted_j_error_type', label='Predicted J Error',
enabled_when='not (object.use_weighted_fit or object.use_monte_carlo)'),
HGroup(Item('group_positions'),
Item('object.monitor.sample',
style='readonly', label='Sample')),
Item('show_labels',
label='Display Labels',
tooltip='Display hole labels on plot'),
HGroup(UItem('plot_kind'),
Item('model_kind', label='Fit Model',
editor=EnumEditor(values=['Bowl', 'Plane']))),
# UItem('plot_kind', editor=EnumEditor(values=['Contour', 'Hole vs J']))),
contour_grp))
return v
class SystemObject(HasStrictTraits):
"""
Baseclass for Programs, Sensor, Actuators
"""
#: Names of attributes that accept Callables. If there are custom callables being used, they must be added here.
#: The purpose of this list is that these Callables will be initialized properly.
#: :class:`~automate.program.ProgrammableSystemObject` introduces 5 basic callables
#: (see also :ref:`automate-programs`).
callables = []
def get_default_callables(self):
""" Get a dictionary of default callables, in form {name:callable}. Re-defined in subclasses."""
return {}
#: Reference to System object
system = Instance(SystemBase, transient=True)
#: Description of the object (shown in WEB interface)
description = CUnicode
#: Python Logger instance for this object. System creates each object its own logger instance.
logger = Instance(logging.Logger, transient=True)
#: Tags are used for (for example) grouping objects. See :ref:`groups`.
tags = TagSet(trait=CUnicode)
#: Name property is determined by System namespace. Can be read/written.
name = Property(trait=Unicode, depends_on='name_changed_event')
log_level = Int(logging.INFO)
def _log_level_changed(self, new_value):
if self.logger:
self.logger.setLevel(new_value)
@cached_property
def _get_name(self):
try:
return self.system.reverse[self]
except (KeyError, AttributeError):
return 'System not initialized!'
def _set_name(self, new_name):
if not is_valid_variable_name(new_name):
raise NameError('Illegal name %s' % new_name)
try:
if self in list(self.system.namespace.values()):
del self.system.namespace[self.name]
except NameError:
pass
self.system.namespace[new_name] = self
self.logger = self.system.logger.getChild('%s.%s' % (self.__class__.__name__, new_name))
#: If set to *True*, current SystemObject is hidden in the UML diagram of WEB interface.
hide_in_uml = CBool(False)
_order = Int
_count = 0
#: Attributes that can be edited by user in WEB interface
view = ['hide_in_uml']
#: The data type name (as string) of the object. This is written in the initialization, and is used by WEB
#: interface Django templates.
data_type = ''
#: If editable=True, a quick edit widget will appear in the web interface. Define in subclasses.
editable = False
# Namespace triggers this event when object name name is changed
name_changed_event = Event
_passed_arguments = Tuple(transient=True)
_postponed_callables = Dict(transient=True)
@property
def class_name(self):
# For Django templates
return self.__class__.__name__
@property
def object_type(self):
"""
A read-only property that gives the object type as string; sensor, actuator, program, other.
Used by WEB interface templates.
"""
from .statusobject import AbstractSensor, AbstractActuator
from .program import Program
if isinstance(self, AbstractSensor):
return 'sensor'
elif isinstance(self, AbstractActuator):
return 'actuator'
elif isinstance(self, Program):
return 'program'
else:
return 'other'
def __init__(self, name='', **traits):
# Postpone traits initialization to be launched by System
self.logger = logging.getLogger('automate.%s' % self.__class__.__name__)
self._order = SystemObject._count
SystemObject._count += 1
self._passed_arguments = name, traits
if 'system' in traits:
self.setup_system(traits.pop('system'))
self.setup_callables()
def __setstate__(self, state, trait_change_notify=True):
self.logger = logging.getLogger('automate.%s' % self.__class__.__name__)
self._order = state.pop('_order')
self._passed_arguments = None, state
def get_status_display(self, **kwargs):
"""
Redefine this in subclasses if status can be represented in human-readable way (units etc.)
"""
if 'value' in kwargs:
return str(kwargs['value'])
return self.class_name
def get_as_datadict(self):
"""
Get information about this object as a dictionary. Used by WebSocket interface to pass some
relevant information to client applications.
"""
return dict(type=self.__class__.__name__, tags=list(self.tags))
def setup(self, *args, **kwargs):
"""
Initialize necessary services etc. here. Define this in subclasses.
"""
pass
def setup_system(self, system, name_from_system='', **kwargs):
"""
Set system attribute and do some initialization. Used by System.
"""
if not self.system:
self.system = system
name, traits = self._passed_arguments
new_name = self.system.get_unique_name(self, name, name_from_system)
if not self in self.system.reverse:
self.name = new_name
self.logger = self.system.logger.getChild('%s.%s' % (self.__class__.__name__, self.name))
self.logger.setLevel(self.log_level)
if name is None and 'name' in traits: # Only __setstate__ sets name to None. Default is ''.
del traits['name']
for cname in self.callables:
if cname in traits:
c = self._postponed_callables[cname] = traits.pop(cname)
c.setup_callable_system(self.system)
getattr(self, cname).setup_callable_system(self.system)
if not self.traits_inited():
super().__init__(**traits)
self.name_changed_event = True
self.setup()
def setup_callables(self):
"""
Setup Callable attributes that belong to this object.
"""
defaults = self.get_default_callables()
for key, value in list(defaults.items()):
self._postponed_callables.setdefault(key, value)
for key in self.callables:
value = self._postponed_callables.pop(key)
value.setup_callable_system(self.system, init=True)
setattr(self, key, value)
def cleanup(self):
"""
Write here whatever cleanup actions are needed when object is no longer used.
"""
def __str__(self):
return self.name
def __repr__(self):
return u"'%s'" % self.name
