def loadpoints(self, tablename, col, fltr=None, grouping=NO_GROUP):
'''
Returns a dict mapping x label values to lists of values from col
'''
q = sql.QueryBuilder()
select = [sql.Column(tablename, col)]
if grouping != NO_GROUP:
dm = datamodel.DataModel.getInstance()
group_cols = dm.GetGroupColumnNames(grouping, include_table_name=True)
select += [sql.Column(*col.split('.')) for col in group_cols]
q.set_select_clause(select)
if fltr is not None:
q.add_filter(fltr)
res = db.execute(str(q))
res = np.array(res, dtype=object)
# replaces Nones with NaNs
for row in res:
if row[0] is None:
row[0] = np.nan
points_dict = {}
if self.group_choice.Value != NO_GROUP:
for row in res:
groupkey = tuple(row[1:])
points_dict[groupkey] = points_dict.get(groupkey, []) + [row[0]]
else:
points_dict = {col : [r[0] for r in res]}
return points_dict
def get_filter(self):
table = self.tableChoice.Value
column = self.colChoice.Value
comparator = self.comparatorChoice.GetValue()
value = self.valueField.GetValue()
if self._get_col_type() in [int, float, long]:
# Don't quote numbers
return sql.Filter(sql.Column(table, column), comparator, '%s'%(value))
if comparator.upper() in ['IS', 'IS NOT'] and value.upper() == 'NULL':
# Don't quote comparisons to NULL
return sql.Filter(sql.Column(table, column), comparator, '%s'%(value))
return sql.Filter(sql.Column(table, column), comparator, '"%s"'%(value))
def UpdatePlateMaps(self):
self.measurement = self.measurementsChoice.Value
measurement = self.measurement
table = self.sourceChoice.Value
self.aggMethod = self.aggregationMethodsChoice.Value
categorical = measurement not in get_numeric_columns_from_table(table)
fltr = self.filterChoice.Value
self.colorBar.ClearNotifyWindows()
q = sql.QueryBuilder()
well_key_cols = [sql.Column(p.image_table, col) for col in well_key_columns()]
select = list(well_key_cols)
if not categorical:
if self.aggMethod=='mean':
select += [sql.Column(table, measurement, 'AVG')]
elif self.aggMethod=='stdev':
select += [sql.Column(table, measurement, 'STDDEV')]
elif self.aggMethod=='cv%':
# stddev(col) / avg(col) * 100
select += [sql.Expression(
sql.Column(table, measurement, 'STDDEV'), ' / ',
sql.Column(table, measurement, 'AVG'), ' * 100')]
elif self.aggMethod=='sum':
select += [sql.Column(table, measurement, 'SUM')]
elif self.aggMethod=='min':
select += [sql.Column(table, measurement, 'MIN')]
elif self.aggMethod=='max':
select += [sql.Column(table, measurement, 'MAX')]
elif self.aggMethod=='median':
select += [sql.Column(table, measurement, 'MEDIAN')]
elif self.aggMethod=='none':
select += [sql.Column(table, measurement)]
else:
select += [sql.Column(table, measurement)]
q.set_select_clause(select)
q.set_group_columns(well_key_cols)
if fltr not in (FilterComboBox.NO_FILTER, FilterComboBox.NEW_FILTER, ''):
if fltr in p._filters:
q.add_filter(p._filters[fltr])
elif fltr in p.gates:
q.add_filter(p.gates[fltr].as_filter())
else:
raise Exception('Could not find filter "%s" in gates or filters'%(fltr))
wellkeys_and_values = db.execute(str(q))
wellkeys_and_values = np.array(wellkeys_and_values, dtype=object)
# Replace measurement None's with nan
for row in wellkeys_and_values:
if row[-1] is None:
row[-1] = np.nan
data = []
key_lists = []
dmax = -np.inf
dmin = np.inf
if p.plate_id:
for plateChoice, plateMap in zip(self.plateMapChoices, self.plateMaps):
plate = plateChoice.Value
plateMap.SetPlate(plate)
self.colorBar.AddNotifyWindow(plateMap)
self.keys_and_vals = [v for v in wellkeys_and_values if str(v[0])==plate]
platedata, wellkeys, ignore = FormatPlateMapData(self.keys_and_vals, categorical)
data += [platedata]
key_lists += [wellkeys]
if not categorical:
dmin = np.nanmin([float(kv[-1]) for kv in self.keys_and_vals]+[dmin])
dmax = np.nanmax([float(kv[-1]) for kv in self.keys_and_vals]+[dmax])
else:
self.colorBar.AddNotifyWindow(self.plateMaps[0])
platedata, wellkeys, ignore = FormatPlateMapData(wellkeys_and_values, categorical)
data += [platedata]
key_lists += [wellkeys]
if not categorical:
dmin = np.nanmin([float(kv[-1]) for kv in wellkeys_and_values])
dmax = np.nanmax([float(kv[-1]) for kv in wellkeys_and_values])
if not categorical:
if len(wellkeys_and_values) > 0:
# Compute the global extents if there is any data whatsoever
gmin = np.nanmin([float(vals[-1]) for vals in wellkeys_and_values])
gmax = np.nanmax([float(vals[-1]) for vals in wellkeys_and_values])
if np.isinf(dmin) or np.isinf(dmax):
gmin = gmax = dmin = dmax = 1.
# Warn if there was no data for this plate (and no filter was used)
if fltr == FilterComboBox.NO_FILTER:
wx.MessageBox('No numeric data was found in "%s.%s" for plate "%s"'
%(table, measurement, plate), 'Warning')
else:
gmin = gmax = 1.
if fltr == FilterComboBox.NO_FILTER:
wx.MessageBox('No numeric data was found in %s.%s'
%(table, measurement), 'Warning')
if categorical:
self.colorBar.Hide()
else:
self.colorBar.Show()
self.colorBar.SetLocalExtents([dmin,dmax])
self.colorBar.SetGlobalExtents([gmin,gmax])
self.rightSizer.Layout()
for keys, d, plateMap in zip(key_lists, data, self.plateMaps):
plateMap.SetWellKeys(keys)
if categorical:
plateMap.SetData(np.ones(d.shape) * np.nan)
plateMap.SetTextData(d)
else:
plateMap.SetData(d, data_range=self.colorBar.GetLocalExtents(),
clip_interval=self.colorBar.GetLocalInterval(),
clip_mode=self.colorBar.GetClipMode())
for keys, d, plateMap in zip(key_lists, data, self.plateMaps):
plateMap.SetWellKeys(keys)
if categorical:
plateMap.SetData(np.ones(d.shape) * np.nan)
plateMap.SetTextData(d)
else:
plateMap.SetData(d, data_range=self.colorBar.GetLocalExtents(),
clip_interval=self.colorBar.GetLocalInterval(),
clip_mode=self.colorBar.GetClipMode())
def y_column(self):
return sql.Column(self.y_table_choice.GetStringSelection(),
self.y_choice.GetStringSelection())
## self.reset()
## logging.error('Can not load old filter')
## self.Refresh()
if __name__ == "__main__":
import sys
import logging
logging.basicConfig(level=logging.DEBUG)
app = wx.PySimpleApp()
# Load a properties file if passed in args
if len(sys.argv) > 1:
propsFile = sys.argv[1]
p.LoadFile(propsFile)
else:
p.LoadFile('/Users/afraser/cpa_example/example.properties')
p._filters['test'] = sql.Filter(
('per_image', 'gene'), 'REGEXP', 'MAP*', 'OR',
sql.Column('per_image', 'gene'), 'IS', 'NULL')
p._filters_ordered += ['test']
p._filters['test2'] = sql.Filter(('per_image', 'well'), '!=', 'A01')
p._filters_ordered += ['test2']
cff = ColumnFilterDialog(None, tables=[p.image_table])
if cff.ShowModal() == wx.OK:
print cff.get_filter()
cff.Destroy()
app.MainLoop()
def x_column(self):
return sql.Column(
self.table_choice.GetString(self.table_choice.GetSelection()),
self.x_choice.GetString(self.x_choice.GetSelection()))
def y_column(self):
y_table_choice_id = self.y_table_choice.GetSelection()
y_choice_id = self.y_choice.GetSelection()
return sql.Column(self.y_table_choice.GetString(y_table_choice_id),
self.y_choice.GetString(y_choice_id))
def x_column(self):
x_table_choice_id = self.x_table_choice.GetSelection()
x_choice_id = self.x_choice.GetSelection()
return sql.Column(self.x_table_choice.GetString(x_table_choice_id),
self.x_choice.GetString(x_choice_id))
