def on_save_table_to_db(self, evt):
valid = False
while not valid:
dlg = wx.TextEntryDialog(self,
'What do you want to name your table?',
'Save table to database', self.Title)
if dlg.ShowModal() != wx.ID_OK:
return
tablename = dlg.GetValue()
if not re.match('^[A-Za-z]\w*$', tablename):
wx.MessageDialog(
self, 'Table name must begin with a letter and may'
'only contain letters, digits and "_"',
'Invalid table name',
wx.OK | wx.ICON_INFORMATION).ShowModal()
elif db.table_exists(tablename):
dlg = wx.MessageDialog(
self,
'The table "%s" already exists in the database. Overwrite it?'
% (tablename), 'Table already exists',
wx.YES_NO | wx.NO_DEFAULT | wx.ICON_WARNING)
if dlg.ShowModal() == wx.ID_YES:
valid = True
else:
valid = True
dlg = wx.SingleChoiceDialog(
self, 'Do you want to be able to access\n'
'this table after you close CPA?', 'Save table to database',
['Store for this session only.', 'Store permanently.'],
wx.CHOICEDLG_STYLE)
if dlg.ShowModal() != wx.ID_OK:
return
temporary = (dlg.GetSelection() == 0)
colnames = [
self.grid.Table.GetColLabelValueWithoutDecoration(col)
for col in range(self.grid.Table.GetNumberCols())
]
data = [[
self.grid.Table.GetValue(row, col)
for col in range(self.grid.Table.GetNumberCols())
] for row in range(self.grid.Table.GetNumberRows())]
db.CreateTableFromData(data,
dbconnect.clean_up_colnames(colnames),
tablename,
temporary=temporary)
self.Title = tablename
try:
wx.GetApp().user_tables += [tablename]
for plot in wx.GetApp().get_plots():
if plot.tool_name == 'PlateViewer':
plot.AddTableChoice(tablename)
except AttributeError:
# running without main UI
user_tables = wx.GetApp().user_tables = []
def OnWriteTempTableToDB(self, evt):
from classifier import Classifier
db.CreateTempTableFromData(self.grid.GetTable().data,
dbconnect.clean_up_colnames(self.grid.GetTable().col_labels),
'__Classifier_output')
try:
if self.GetParent().pmb:
self.GetParent().pmb.AddTableChoice('__Classifier_output')
except:
pass
def on_save_table_to_db(self, evt):
valid = False
while not valid:
dlg = wx.TextEntryDialog(self, 'What do you want to name your table?',
'Save table to database', self.Title)
if dlg.ShowModal() != wx.ID_OK:
return
tablename = dlg.GetValue()
if not re.match('^[A-Za-z]\w*$', tablename):
wx.MessageDialog(self, 'Table name must begin with a letter and may'
'only contain letters, digits and "_"',
'Invalid table name', wx.OK|wx.ICON_INFORMATION).ShowModal()
elif db.table_exists(tablename):
dlg = wx.MessageDialog(self,
'The table "%s" already exists in the database. Overwrite it?'%(tablename),
'Table already exists', wx.YES_NO|wx.NO_DEFAULT|wx.ICON_WARNING)
if dlg.ShowModal() == wx.ID_YES:
valid = True
else:
valid = True
dlg = wx.SingleChoiceDialog(self, 'Do you want to be able to access\n'
'this table after you close CPA?', 'Save table to database',
['Store for this session only.', 'Store permanently.'],
wx.CHOICEDLG_STYLE)
if dlg.ShowModal() != wx.ID_OK:
return
temporary = (dlg.GetSelection() == 0)
colnames = [self.grid.Table.GetColLabelValueWithoutDecoration(col)
for col in range(self.grid.Table.GetNumberCols())]
data = [[self.grid.Table.GetValue(row, col)
for col in range(self.grid.Table.GetNumberCols())]
for row in range(self.grid.Table.GetNumberRows())]
db.CreateTableFromData(data, dbconnect.clean_up_colnames(colnames),
tablename, temporary=temporary)
self.Title = tablename
try:
wx.GetApp().user_tables += [tablename]
for plot in wx.GetApp().get_plots():
if plot.tool_name == 'PlateViewer':
plot.AddTableChoice(tablename)
except AttributeError:
# running without main UI
user_tables = wx.GetApp().user_tables = []
def create_per_object_table(well_result_files):
'''doc -- measurements_index DOM document object
'''
def get_column_names(well_res_file):
'''parses reported column names out of the given well_results_file'''
ob_col_dict = {}
doc = dom.parse(os.path.join(results_dir, well_res_file))
for ref in doc.getElementsByTagName('ParameterAnnotations'):
for param in ref.getElementsByTagName('Parameter'):
ob_col_dict[param.getAttribute('id')] = dict(
param.attributes.items())
params_node = doc.getElementsByTagName(
'ResultTable')[0].getElementsByTagName('Parameters')[0]
measurement_ids = [
p.getAttribute('parID')
for p in params_node.getElementsByTagName('Parameter')
]
return [ob_col_dict[id]['name'] for id in measurement_ids]
# Get per-object column names
default_columns = ['ImageNumber', 'ObjectNumber', 'Well', 'X', 'Y']
param_columns = get_column_names(well_result_files[0])
colnames = default_columns + param_columns
coltypes = ['INTEGER', 'INTEGER', 'VARCHAR(3)', 'REAL', 'REAL']
coltypes += ['REAL'] * len(param_columns)
colnames = dbconnect.clean_up_colnames(colnames)
db.create_empty_table('per_object', colnames, coltypes)
db.create_default_indexes_on_table('per_object')
# create object measurement matrix
for well_res_file in well_result_files:
#
# TODO: Object number should change for every image, not every well
#
object_number = 1
doc = dom.parse(os.path.join(results_dir, well_res_file))
platename = doc.getElementsByTagName('PlateName')[0].firstChild.data
r = doc.getElementsByTagName('ResultTable')[0].getAttribute('Row')
c = doc.getElementsByTagName('ResultTable')[0].getAttribute('Col')
pid = doc.getElementsByTagName('ResultTable')[0].getAttribute(
'PlaneID')
tid = doc.getElementsByTagName('ResultTable')[0].getAttribute(
'TimepointID')
wellname = convert_rowcol_to_wellid(r, c)
rows = []
for tr in doc.getElementsByTagName(
'ResultTable')[0].getElementsByTagName('tr'):
fid = tr.getAttribute('FieldID')
query = 'SELECT ImageNumber FROM per_image WHERE Plate="%s" AND ' \
'Well="%s" AND FieldID="%s" AND PlaneID="%s" AND ' \
'TimepointID="%s"'%(platename, wellname, fid, pid, tid)
image_number = db.execute(query)[0][0]
row = [
image_number, object_number, wellname,
float(tr.getAttribute('x')),
float(tr.getAttribute('y'))
]
row += [
float(col.firstChild.data) for col in tr.childNodes
if col.firstChild
]
rows += [row]
object_number += 1
# Insert rows from this well result file
db.insert_rows_into_table('per_object', colnames, coltypes, rows)
db.Commit()
def create_per_object_table(well_result_files):
'''doc -- measurements_index DOM document object
'''
def get_column_names(well_res_file):
'''parses reported column names out of the given well_results_file'''
ob_col_dict = {}
doc = dom.parse(os.path.join(results_dir, well_res_file))
for ref in doc.getElementsByTagName('ParameterAnnotations'):
for param in ref.getElementsByTagName('Parameter'):
ob_col_dict[param.getAttribute('id')] = dict(param.attributes.items())
params_node = doc.getElementsByTagName('ResultTable')[0].getElementsByTagName('Parameters')[0]
measurement_ids = [p.getAttribute('parID')
for p in params_node.getElementsByTagName('Parameter')]
return [ob_col_dict[id]['name'] for id in measurement_ids]
# Get per-object column names
default_columns = ['ImageNumber', 'ObjectNumber', 'Well', 'X', 'Y']
param_columns = get_column_names(well_result_files[0])
colnames = default_columns + param_columns
coltypes = ['INTEGER', 'INTEGER', 'VARCHAR(3)', 'REAL', 'REAL']
coltypes += ['REAL'] * len(param_columns)
colnames = dbconnect.clean_up_colnames(colnames)
db.create_empty_table('per_object', colnames, coltypes)
db.create_default_indexes_on_table('per_object')
# create object measurement matrix
for well_res_file in well_result_files:
#
# TODO: Object number should change for every image, not every well
#
object_number = 1
doc = dom.parse(os.path.join(results_dir, well_res_file))
platename = doc.getElementsByTagName('PlateName')[0].firstChild.data
r = doc.getElementsByTagName('ResultTable')[0].getAttribute('Row')
c = doc.getElementsByTagName('ResultTable')[0].getAttribute('Col')
pid = doc.getElementsByTagName('ResultTable')[0].getAttribute('PlaneID')
tid = doc.getElementsByTagName('ResultTable')[0].getAttribute('TimepointID')
wellname = convert_rowcol_to_wellid(r, c)
rows = []
for tr in doc.getElementsByTagName('ResultTable')[0].getElementsByTagName('tr'):
fid = tr.getAttribute('FieldID')
query = 'SELECT ImageNumber FROM per_image WHERE Plate="%s" AND ' \
'Well="%s" AND FieldID="%s" AND PlaneID="%s" AND ' \
'TimepointID="%s"'%(platename, wellname, fid, pid, tid)
image_number = db.execute(query)[0][0]
row = [image_number,
object_number,
wellname,
float(tr.getAttribute('x')),
float(tr.getAttribute('y'))]
row += [float(col.firstChild.data)
for col in tr.childNodes if col.firstChild]
rows += [row]
object_number += 1
# Insert rows from this well result file
db.insert_rows_into_table('per_object', colnames, coltypes, rows)
db.Commit()
