class _ColumnLinkerPanel(wx.Panel):
def __init__(self, parent, table_a, table_b, col_a=None, col_b=None, allow_delete=True, **kwargs):
wx.Panel.__init__(self, parent, **kwargs)
self.table_a = table_a
self.table_b = table_b
self.aChoice = ComboBox(self, choices=db.GetColumnNames(table_a),
size=(100,-1), style=wx.CB_READONLY)
self.bChoice = ComboBox(self, choices=db.GetColumnNames(table_b),
size=(100,-1), style=wx.CB_READONLY)
if col_a in self.aChoice.Strings:
self.aChoice.Select(self.aChoice.Strings.index(col_a))
if col_b in self.bChoice.Strings:
self.bChoice.Select(self.bChoice.Strings.index(col_b))
if allow_delete:
self.x_btn = wx.Button(self, -1, 'x', size=(30,-1))
self.Sizer = wx.BoxSizer(wx.HORIZONTAL)
self.Sizer.Add(wx.StaticText(self, -1, table_a+'.'), 0, wx.TOP, 4)
self.Sizer.Add(self.aChoice, 1, wx.EXPAND)
self.Sizer.AddSpacer(10)
self.Sizer.Add(wx.StaticText(self, -1, '<=>'), 0, wx.TOP, 4)
self.Sizer.AddSpacer(10)
self.Sizer.Add(wx.StaticText(self, -1, table_b+'.'), 0, wx.TOP, 4)
self.Sizer.Add(self.bChoice, 1, wx.EXPAND)
if allow_delete:
self.Sizer.AddSpacer(10)
self.Sizer.Add(self.x_btn)
self.x_btn.Bind(wx.EVT_BUTTON, self.GrandParent.on_remove_panel)
def get_column_pair(self):
'''returns ((table_a, col_a), (table_b, col_b))
'''
return ((self.table_a, self.aChoice.Value),
(self.table_b, self.bChoice.Value))
class DataSourcePanel(wx.Panel):
'''
A panel with controls for selecting the source data for a boxplot
'''
def __init__(self, parent, figpanel, **kwargs):
wx.Panel.__init__(self, parent, **kwargs)
# the panel to draw charts on
self.SetBackgroundColour('white') # color for the background of panel
self.figpanel = figpanel
sizer = wx.BoxSizer(wx.VERTICAL)
self.x_columns = [] # column names to plot if selecting multiple columns
self.table_choice = ui.TableComboBox(self, -1, style=wx.CB_READONLY)
self.x_choice = ComboBox(self, -1, size=(200,-1), style=wx.CB_READONLY)
self.x_multiple = wx.Button(self, -1, 'select multiple')
self.group_choice = ComboBox(self, -1, choices=[NO_GROUP]+p._groups_ordered, style=wx.CB_READONLY)
self.group_choice.Select(0)
self.filter_choice = ui.FilterComboBox(self, style=wx.CB_READONLY)
self.filter_choice.Select(0)
self.update_chart_btn = wx.Button(self, -1, "Update Chart")
self.update_column_fields()
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "table:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.table_choice, 1, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(wx.StaticText(self, -1, "measurement:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.x_choice, 2, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(self.x_multiple, 0, wx.EXPAND|wx.TOP, 2)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 3, 0)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "group x-axis by:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.group_choice, 1, wx.EXPAND)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 3, 0)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "filter:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.filter_choice, 1, wx.EXPAND)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 3, 0)
sizer.Add(self.update_chart_btn)
self.x_multiple.Bind(wx.EVT_BUTTON, self.on_select_multiple)
self.table_choice.Bind(wx.EVT_COMBOBOX, self.on_table_selected)
self.x_choice.Bind(wx.EVT_COMBOBOX, self.on_column_selected)
self.update_chart_btn.Bind(wx.EVT_BUTTON, self.update_figpanel)
self.SetSizer(sizer)
self.Show(1)
def on_select_multiple(self, evt):
tablename = self.table_choice.GetString(self.table_choice.GetSelection())
column_names = self.get_numeric_columns_from_table(tablename)
dlg = wx.MultiChoiceDialog(self,
'Select the columns you would like to plot',
'Select Columns', column_names)
dlg.SetSelections([column_names.index(v) for v in self.x_columns])
if (dlg.ShowModal() == wx.ID_OK):
self.x_choice.SetValue(SELECT_MULTIPLE)
self.x_columns = [column_names[i] for i in dlg.GetSelections()]
self.group_choice.Disable()
self.group_choice.SetStringSelection(NO_GROUP)
def on_table_selected(self, evt):
table = self.table_choice.Value
if table == ui.TableComboBox.OTHER_TABLE:
t = ui.get_other_table_from_user(self)
if t is not None:
self.table_choice.Items = self.table_choice.Items[:-1] + [t] + self.table_choice.Items[-1:]
self.table_choice.Select(self.table_choice.Items.index(t))
else:
self.table_choice.Select(0)
return
self.group_choice.Enable()
self.x_columns = []
self.update_column_fields()
def on_column_selected(self, evt):
self.group_choice.Enable()
def update_column_fields(self):
tablename = self.table_choice.GetString(self.table_choice.GetSelection())
fieldnames = self.get_numeric_columns_from_table(tablename)
self.x_choice.Clear()
self.x_choice.AppendItems(fieldnames)
self.x_choice.Append(SELECT_MULTIPLE)
self.x_choice.SetSelection(0)
def get_numeric_columns_from_table(self, table):
''' Fetches names of numeric columns for the given table. '''
measurements = db.GetColumnNames(table)
types = db.GetColumnTypes(table)
return [m for m,t in zip(measurements, types) if t in (float, int)]
def update_figpanel(self, evt=None):
table = self.table_choice.Value
fltr = self.filter_choice.get_filter_or_none()
grouping = self.group_choice.Value
if self.x_choice.Value == SELECT_MULTIPLE:
points_dict = {}
for col in self.x_columns:
pts = self.loadpoints(table, col, fltr, NO_GROUP)
for k in list(pts.keys()): assert k not in points_dict
points_dict.update(pts)
else:
col = self.x_choice.Value
points_dict = self.loadpoints(table, col, fltr, grouping)
# Check if the user is creating a plethora of plots by accident
if 100 >= len(points_dict) > 25:
res = wx.MessageDialog(self, 'Are you sure you want to show %s box '
'plots on one axis?'%(len(points_dict)),
'Warning', style=wx.YES_NO|wx.NO_DEFAULT
).ShowModal()
if res != wx.ID_YES:
return
elif len(points_dict) > 100:
wx.MessageBox('Sorry, boxplot can not show more than 100 plots on\n'
'a single axis. Your current settings would plot %d.\n'
'Try using a filter to narrow your query.'
%(len(points_dict)), 'Too many groups to plot')
return
self.figpanel.setpoints(points_dict)
if self.group_choice.Value != NO_GROUP:
self.figpanel.set_x_axis_label(grouping)
self.figpanel.set_y_axis_label(self.x_choice.Value)
self.figpanel.draw()
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()
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 save_settings(self):
'''
Called when saving a workspace to file.
returns a dictionary mapping setting names to values encoded as strings
'''
if self.x_choice.Value == SELECT_MULTIPLE:
cols = self.x_columns
else:
cols = [self.x_choice.GetString(self.x_choice.GetSelection())]
return {'table' : self.table_choice.Value,
'x-axis' : ','.join(cols),
'filter' : self.filter_choice.Value,
'x-lim' : self.figpanel.subplot.get_xlim(),
'y-lim' : self.figpanel.subplot.get_ylim(),
## 'grouping': self.group_choice.Value,
## 'version': '1',
}
def load_settings(self, settings):
'''load_settings is called when loading a workspace from file.
settings - a dictionary mapping setting names to values encoded as
strings.
'''
## if 'version' not in settings:
## settings['grouping'] = NO_GROUP
## settings['version'] = '1'
if 'table' in settings:
self.table_choice.SetStringSelection(settings['table'])
self.update_column_fields()
if 'x-axis' in settings:
cols = list(map(str.strip, settings['x-axis'].split(',')))
if len(cols) == 1:
self.x_choice.SetStringSelection(cols[0])
else:
self.x_choice.SetValue(SELECT_MULTIPLE)
self.x_columns = cols
if 'filter' in settings:
self.filter_choice.SetStringSelection(settings['filter'])
self.update_figpanel()
if 'x-lim' in settings:
self.figpanel.subplot.set_xlim(eval(settings['x-lim']))
if 'y-lim' in settings:
self.figpanel.subplot.set_ylim(eval(settings['y-lim']))
self.figpanel.draw()
class DataSourcePanel(wx.Panel):
'''
A panel with controls for selecting the source data for a histogramplot
'''
def __init__(self, parent, figpanel, **kwargs):
wx.Panel.__init__(self, parent, **kwargs)
# the panel to draw charts on
self.SetBackgroundColour('white') # color for the background of panel
self.figpanel = figpanel
sizer = wx.BoxSizer(wx.VERTICAL)
self.table_choice = ui.TableComboBox(self, -1, style=wx.CB_READONLY)
self.x_choice = ComboBox(self,
-1,
size=(200, -1),
choices=[''],
style=wx.CB_READONLY)
self.x_choice.Select(0)
self.bins_input = wx.SpinCtrl(self, -1, '100')
self.bins_input.SetRange(1, 400)
self.x_scale_choice = ComboBox(
self,
-1,
choices=[LINEAR_SCALE, LOG_SCALE, LOG2_SCALE],
style=wx.CB_READONLY)
self.x_scale_choice.Select(0)
self.y_scale_choice = ComboBox(self,
-1,
choices=[LINEAR_SCALE, LOG_SCALE],
style=wx.CB_READONLY)
self.y_scale_choice.Select(0)
self.filter_choice = ui.FilterComboBox(self, style=wx.CB_READONLY)
self.filter_choice.Select(0)
self.gate_choice = ui.GateComboBox(self, style=wx.CB_READONLY)
self.gate_choice.set_gatable_columns([self.x_column])
self.update_chart_btn = wx.Button(self, -1, "Update Chart")
self.update_column_fields()
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "x-axis:"), 0, wx.TOP, 4)
sz.AddSpacer(2)
sz.Add(self.table_choice, 1, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(self.x_choice, 2, wx.EXPAND)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 2, 0)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "x-scale:"), 0, wx.TOP, 4)
sz.AddSpacer(2)
sz.Add(self.x_scale_choice, 1, wx.EXPAND)
sz.AddSpacer(5)
sz.Add(wx.StaticText(self, -1, "y-scale:"), 0, wx.TOP, 4)
sz.AddSpacer(2)
sz.Add(self.y_scale_choice, 1, wx.EXPAND)
sz.AddSpacer(5)
sz.Add(wx.StaticText(self, -1, "bins:"), 0, wx.TOP, 4)
sz.AddSpacer(2)
sz.Add(self.bins_input)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 2, 0)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "filter:"), 0, wx.TOP, 4)
sz.AddSpacer(2)
sz.Add(self.filter_choice, 1, wx.EXPAND)
sz.AddSpacer(5)
sz.Add(wx.StaticText(self, -1, "gate:"), 0, wx.TOP, 4)
sz.AddSpacer(2)
sz.Add(self.gate_choice, 1, wx.EXPAND)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 2, 0)
sizer.Add(self.update_chart_btn)
self.table_choice.Bind(wx.EVT_COMBOBOX, self.on_table_selected)
self.update_chart_btn.Bind(wx.EVT_BUTTON, self.update_figpanel)
self.gate_choice.addobserver(self.on_gate_selected)
self.SetSizer(sizer)
self.Show(1)
@property
def x_column(self):
return sql.Column(
self.table_choice.GetString(self.table_choice.GetSelection()),
self.x_choice.GetString(self.x_choice.GetSelection()))
@property
def filter(self):
return self.filter_choice.get_filter_or_none()
def on_table_selected(self, evt):
table = self.table_choice.Value
if table == ui.TableComboBox.OTHER_TABLE:
t = ui.get_other_table_from_user(self)
if t is not None:
self.table_choice.Items = self.table_choice.Items[:-1] + [
t
] + self.table_choice.Items[-1:]
self.table_choice.Select(self.table_choice.Items.index(t))
else:
self.table_choice.Select(0)
return
self.update_column_fields()
def on_gate_selected(self, gate_name):
self.update_gate_helper()
def update_gate_helper(self):
gate_name = self.gate_choice.get_gatename_or_none()
if gate_name:
self.figpanel.gate_helper.set_displayed_gate(
p.gates[gate_name], self.x_column, None)
else:
self.figpanel.gate_helper.disable()
def update_column_fields(self):
tablename = self.table_choice.GetString(
self.table_choice.GetSelection())
fieldnames = self.get_numeric_columns_from_table(tablename)
self.x_choice.Clear()
self.x_choice.AppendItems(fieldnames)
self.x_choice.SetSelection(0)
def get_numeric_columns_from_table(self, table):
''' Fetches names of numeric columns for the given table. '''
measurements = db.GetColumnNames(table)
types = db.GetColumnTypes(table)
return [m for m, t in zip(measurements, types) if t in (float, int)]
def _plotting_per_object_data(self):
return (p.object_table and p.object_table
in [self.x_column.table, self.x_column.table]
or (self.x_column.table != p.image_table
and db.adjacent(p.object_table, self.x_column.table)))
def update_figpanel(self, evt=None):
self.gate_choice.set_gatable_columns([self.x_column])
points = self._load_points()
bins = int(self.bins_input.GetValue())
self.figpanel.set_x_label(self.x_column.col)
self.figpanel.set_x_scale(
self.x_scale_choice.GetString(self.x_scale_choice.GetSelection()))
self.figpanel.set_y_scale(
self.y_scale_choice.GetString(self.y_scale_choice.GetSelection()))
self.figpanel.setpoints(points, bins)
self.update_gate_helper()
self.figpanel.draw()
def _load_points(self):
q = sql.QueryBuilder()
select = [self.x_column]
q.set_select_clause(select)
if self.filter is not None:
q.add_filter(self.filter)
return np.array(db.execute(str(q))).T[0]
def save_settings(self):
'''save_settings is called when saving a workspace to file.
returns a dictionary mapping setting names to values encoded as strings
'''
d = {
'table':
self.table_choice.GetString(self.table_choice.GetSelection()),
'x-axis':
self.x_choice.GetString(self.x_choice.GetSelection()),
'bins':
self.bins_input.GetValue(),
'x-scale':
self.x_scale_choice.GetString(self.x_scale_choice.GetSelection()),
'y-scale':
self.y_scale_choice.GetString(self.y_scale_choice.GetSelection()),
'filter':
self.filter_choice.GetString(self.filter_choice.GetSelection()),
'x-lim':
self.figpanel.subplot.get_xlim(),
'y-lim':
self.figpanel.subplot.get_ylim(),
}
if self.gate_choice.get_gatename_or_none():
d['gate'] = self.gate_choice.GetString(
self.gate_choice.GetSelection())
return d
def load_settings(self, settings):
'''load_settings is called when loading a workspace from file.
settings - a dictionary mapping setting names to values encoded as
strings.
'''
if 'table' in settings:
self.table_choice.SetStringSelection(settings['table'])
self.update_column_fields()
if 'x-axis' in settings:
self.x_choice.SetStringSelection(settings['x-axis'])
if 'bins' in settings:
self.bins_input.SetValue(int(settings['bins']))
if 'x-scale' in settings:
self.x_scale_choice.SetStringSelection(settings['x-scale'])
if 'y-scale' in settings:
self.y_scale_choice.SetStringSelection(settings['y-scale'])
if 'filter' in settings:
self.filter_choice.SetStringSelection(settings['filter'])
self.update_figpanel()
if 'x-lim' in settings:
self.figpanel.subplot.set_xlim(eval(settings['x-lim']))
if 'y-lim' in settings:
self.figpanel.subplot.set_ylim(eval(settings['y-lim']))
if 'gate' in settings:
self.gate_choice.SetStringSelection(settings['gate'])
self.figpanel.gate_helper.set_displayed_gate(
p.gates[settings['gate']], self.x_column, None)
self.figpanel.draw()
class ColumnFilterPanel(wx.Panel):
'''
Creates a UI that allows the user to create WHERE clauses by selecting
1) a DB column name, 2) a comparator, and 3) a value
'''
def __init__(self,
parent,
tables,
allow_delete=True,
expression=None,
**kwargs):
wx.Panel.__init__(self, parent, **kwargs)
self.fieldSets = []
self.tables = tables
self.types = {}
self.types[p.image_table] = db.GetColumnTypes(p.image_table)
self.tableChoice = ComboBox(self,
choices=self.tables,
size=(150, -1),
style=wx.CB_READONLY)
self.tableChoice.Select(0)
self.colChoice = ComboBox(self,
choices=db.GetColumnNames(p.image_table),
size=(150, -1),
style=wx.CB_READONLY)
self.colChoice.Select(0)
self.comparatorChoice = ComboBox(self,
size=(80, -1),
style=wx.CB_READONLY)
self.update_comparator_choice()
self.valueField = wx.ComboBox(self, -1, value='')
if allow_delete:
self.x_btn = wx.Button(self, -1, 'x', size=(30, -1))
## if expression is not None:
## self.set_expression(expression)
colSizer = wx.BoxSizer(wx.HORIZONTAL)
colSizer.Add(self.tableChoice, 1, wx.EXPAND)
colSizer.AddSpacer(5)
colSizer.Add(self.colChoice, 1, wx.EXPAND)
colSizer.AddSpacer(5)
colSizer.Add(self.comparatorChoice, 0.5, wx.EXPAND)
colSizer.AddSpacer(5)
colSizer.Add(self.valueField, 1, wx.EXPAND)
if allow_delete:
colSizer.AddSpacer(5)
colSizer.Add(self.x_btn, 0, wx.EXPAND)
self.SetSizer(colSizer)
self.tableChoice.Bind(wx.EVT_COMBOBOX, self.on_select_table)
self.colChoice.Bind(wx.EVT_COMBOBOX, self.on_select_col)
if allow_delete:
self.x_btn.Bind(wx.EVT_BUTTON, self.on_remove)
self.Fit()
def on_remove(self, evt):
self.GrandParent.remove(self)
def on_select_col(self, evt):
self.update_comparator_choice()
self.update_value_choice()
def on_select_table(self, evt):
self.update_col_choice()
self.update_comparator_choice()
self.update_value_choice()
def update_col_choice(self):
table = self.tableChoice.Value
self.colChoice.SetItems(db.GetColumnNames(table))
self.colChoice.Select(0)
def _get_col_type(self):
table = self.tableChoice.Value
colidx = self.colChoice.GetSelection()
return db.GetColumnTypes(table)[colidx]
def update_comparator_choice(self):
coltype = self._get_col_type()
comparators = []
if coltype == str:
comparators = ['=', '!=', 'REGEXP', 'IS', 'IS NOT']
if coltype in (int, float):
comparators = ['=', '!=', '<', '>', '<=', '>=', 'IS', 'IS NOT']
self.comparatorChoice.SetItems(comparators)
self.comparatorChoice.Select(0)
def update_value_choice(self):
table = self.tableChoice.Value
column = self.colChoice.Value
colidx = self.colChoice.GetSelection()
coltype = db.GetColumnTypes(table)[colidx]
vals = []
# if coltype == str:# or coltype == int or coltype == long:
# res = db.execute('SELECT DISTINCT %s FROM %s ORDER BY %s'%(column, table, column))
# vals = [str(row[0]) for row in res]
self.valueField.SetItems(vals)
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):
# 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))
class PlotControl(wx.Panel):
'''
Control panel for the dimensionality reduction analysis
'''
def __init__(self, parent, fig_sco, fig_load, **kwargs):
wx.Panel.__init__(self, parent, **kwargs)
self.fig_sco = fig_sco
self.fig_load = fig_load
sizer = wx.BoxSizer(wx.VERTICAL)
self.method_choice = ComboBox(self,
-1,
choices=[SVD, TSNE],
style=wx.CB_READONLY)
self.method_choice.Select(0)
self.update_chart_btn = wx.Button(self, -1, "Show plot")
self.help_btn = wx.Button(self, -1, "About")
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "Method:"))
sz.AddSpacer(5)
sz.Add(self.method_choice, 1, wx.EXPAND)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 5, 0)
sz2 = wx.BoxSizer(wx.HORIZONTAL)
sz2.Add(self.help_btn, wx.LEFT)
sz2.AddSpacer(400)
sz2.Add(self.update_chart_btn, wx.RIGHT)
sizer.Add(sz2, 1, wx.EXPAND)
sizer.Add(-1, 5, 0)
wx.EVT_BUTTON(self.update_chart_btn, -1, self.on_show_pressed)
wx.EVT_BUTTON(self.help_btn, -1, self.on_show_about)
self.SetSizer(sizer)
self.Show(1)
def on_show_about(self, evt):
'''
Shows a message box with the version number etc.
'''
message = (
'Dimensionality Reduction Plot was developed at the Intelligent Systems Dept., '
'Radboud Universiteit Nijmegen as part of the CellProfiler project and is'
' distributed under the GNU General Public License version 2.\n'
'\n'
'For more information about the dimensionality reduction algorithms check:\n'
'\n'
'*Singular Value Decomposition: http://www.snl.salk.edu/~shlens/pca.pdf\n'
'\n'
'*t-SNE: http://homepage.tudelft.nl/19j49/t-SNE.html\n')
dlg = wx.MessageDialog(self,
message,
'CellProfiler Analyst 2.0',
style=wx.OK | wx.ICON_INFORMATION)
dlg.ShowModal()
def on_show_pressed(self, evt):
'''
Show the selected dimensionality reduction plot on the canvas
'''
selected_method = self.method_choice.GetStringSelection()
if selected_method == SVD:
self.fig_sco.plot_pca()
self.fig_load.plot_pca()
elif selected_method == TSNE:
self.fig_sco.plot_tsne()
self.fig_load.clean_canvas()
class PlateViewer(wx.Frame, CPATool):
def __init__(self, parent, size=(800, -1), **kwargs):
wx.Frame.__init__(self,
parent,
-1,
size=size,
title='Plate Viewer',
**kwargs)
CPATool.__init__(self)
self.SetName(self.tool_name)
self.SetBackgroundColour("white") # Fixing the color
# Check for required properties fields.
fail = False
for field in required_fields:
if not p.field_defined(field):
fail = True
raise Exception(
'Properties field "%s" is required for PlateViewer.' %
(field))
if fail:
self.Destroy()
return
self.chMap = p.image_channel_colors[:]
self.menuBar = wx.MenuBar()
self.SetMenuBar(self.menuBar)
self.fileMenu = wx.Menu()
self.exitMenuItem = self.fileMenu.Append(
id=wx.ID_EXIT,
item='Exit\tCtrl+Q',
helpString='Close Plate Viewer')
self.GetMenuBar().Append(self.fileMenu, 'File')
self.menuBar.Append(
cpa.helpmenu.make_help_menu(
self, manual_url="https://cellprofiler.org/viii-plate-viewer"),
'Help')
save_csv_menu_item = self.fileMenu.Append(-1,
'Save table to CSV\tCtrl+S')
self.Bind(wx.EVT_MENU, self.on_save_csv, save_csv_menu_item)
self.Bind(wx.EVT_MENU, lambda _: self.Close(), id=wx.ID_EXIT)
dataSourceSizer = wx.StaticBoxSizer(
wx.StaticBox(self, label='Source:'), wx.VERTICAL)
dataSourceSizer.Add(wx.StaticText(self, label='Data source:'))
self.sourceChoice = TableComboBox(self, -1, size=fixed_width)
dataSourceSizer.Add(self.sourceChoice)
dataSourceSizer.Add(-1, 3, 0)
dataSourceSizer.Add(wx.StaticText(self, label='Measurement:'))
measurements = get_non_blob_types_from_table(p.image_table)
self.measurementsChoice = ComboBox(self,
choices=measurements,
size=fixed_width,
style=wx.CB_READONLY)
self.measurementsChoice.Select(0)
dataSourceSizer.Add(self.measurementsChoice)
dataSourceSizer.Add(wx.StaticText(self, label='Filter:'))
self.filterChoice = FilterComboBox(self,
size=fixed_width,
style=wx.CB_READONLY)
dataSourceSizer.Add(self.filterChoice)
groupingSizer = wx.StaticBoxSizer(
wx.StaticBox(self, label='Data aggregation:'), wx.VERTICAL)
groupingSizer.Add(wx.StaticText(self, label='Aggregation method:'))
aggregation = ['mean', 'sum', 'median', 'stdev', 'cv%', 'min', 'max']
self.aggregationMethodsChoice = ComboBox(self,
choices=aggregation,
size=fixed_width)
self.aggregationMethodsChoice.Select(0)
groupingSizer.Add(self.aggregationMethodsChoice)
viewSizer = wx.StaticBoxSizer(
wx.StaticBox(self, label='View options:'), wx.VERTICAL)
viewSizer.Add(wx.StaticText(self, label='Color map:'))
maps = [
m for m in list(matplotlib.cm.datad.keys()) if not m.endswith("_r")
]
maps.sort()
self.colorMapsChoice = ComboBox(self, choices=maps, size=fixed_width)
self.colorMapsChoice.SetSelection(maps.index('jet'))
viewSizer.Add(self.colorMapsChoice)
viewSizer.Add(-1, 3, 0)
viewSizer.Add(wx.StaticText(self, label='Well display:'))
if p.image_thumbnail_cols:
choices = pmp.all_well_shapes
else:
choices = list(pmp.all_well_shapes)
choices.remove(pmp.THUMBNAIL)
self.wellDisplayChoice = ComboBox(self,
choices=choices,
size=fixed_width)
self.wellDisplayChoice.Select(0)
viewSizer.Add(self.wellDisplayChoice)
viewSizer.Add(-1, 3, 0)
viewSizer.Add(wx.StaticText(self, label='Number of plates:'))
self.numberOfPlatesTE = wx.TextCtrl(self,
-1,
'1',
style=wx.TE_PROCESS_ENTER)
viewSizer.Add(self.numberOfPlatesTE)
if not p.plate_id:
self.numberOfPlatesTE.Disable()
annotationSizer = wx.StaticBoxSizer(
wx.StaticBox(self, label='Annotation:'), wx.VERTICAL)
annotationSizer.Add(wx.StaticText(self, label='Annotation column:'))
annotationColSizer = wx.BoxSizer(wx.HORIZONTAL)
self.annotation_cols = dict([
(col, db.GetColumnType(p.image_table, col))
for col in db.GetUserColumnNames(p.image_table)
])
self.annotationCol = ComboBox(self,
choices=list(
self.annotation_cols.keys()),
size=(120, -1))
if len(self.annotation_cols) > 0:
self.annotationCol.SetSelection(0)
annotationColSizer.Add(self.annotationCol,
flag=wx.ALIGN_CENTER_VERTICAL)
annotationColSizer.AddSpacer(3)
self.addAnnotationColBtn = wx.Button(self, -1, 'Add', size=(44, -1))
annotationColSizer.Add(self.addAnnotationColBtn,
flag=wx.ALIGN_CENTER_VERTICAL)
annotationSizer.Add(annotationColSizer)
annotationSizer.Add(-1, 3, 0)
annotationSizer.Add(wx.StaticText(self, label='Label:'))
self.annotationLabel = wx.TextCtrl(
self, -1, 'Select wells') #, style=wx.TE_PROCESS_ENTER)
self.annotationLabel.Disable()
self.annotationLabel.SetForegroundColour(wx.Colour(80, 80, 80))
self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY)
annotationSizer.Add(self.annotationLabel)
annotationSizer.Add(-1, 3, 0)
self.outlineMarked = wx.CheckBox(self,
-1,
label='Outline annotated wells')
annotationSizer.Add(self.outlineMarked)
annotationSizer.Add(-1, 3, 0)
self.annotationShowVals = wx.CheckBox(self,
-1,
label='Show values on plate')
annotationSizer.Add(self.annotationShowVals)
if len(db.GetUserColumnNames(p.image_table)) == 0:
self.outlineMarked.Disable()
self.annotationShowVals.Disable()
controlSizer = wx.BoxSizer(wx.VERTICAL)
controlSizer.Add(dataSourceSizer, 0, wx.EXPAND)
controlSizer.Add(-1, 3, 0)
controlSizer.Add(groupingSizer, 0, wx.EXPAND)
controlSizer.Add(-1, 3, 0)
controlSizer.Add(viewSizer, 0, wx.EXPAND)
controlSizer.Add(-1, 3, 0)
controlSizer.Add(annotationSizer, 0, wx.EXPAND)
self.plateMapSizer = wx.GridSizer(1, 1, 5, 5)
self.plateMaps = []
self.plateMapChoices = []
self.rightSizer = wx.BoxSizer(wx.VERTICAL)
self.rightSizer.Add(self.plateMapSizer, 1, wx.EXPAND | wx.BOTTOM, 10)
self.colorBar = ColorBarPanel(self, 'jet', size=(-1, 25))
self.rightSizer.Add(self.colorBar, 0, wx.EXPAND)
mainSizer = wx.BoxSizer(wx.HORIZONTAL)
mainSizer.Add(controlSizer, 0, wx.LEFT | wx.TOP | wx.BOTTOM, 10)
mainSizer.Add(self.rightSizer, 1, wx.EXPAND | wx.ALL, 10)
self.SetSizer(mainSizer)
self.SetClientSize((self.Size[0], self.Sizer.CalcMin()[1]))
self.sourceChoice.Bind(wx.EVT_COMBOBOX, self.UpdateMeasurementChoice)
self.measurementsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectMeasurement)
self.measurementsChoice.Select(0)
self.aggregationMethodsChoice.Bind(wx.EVT_COMBOBOX,
self.OnSelectAggregationMethod)
self.colorMapsChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectColorMap)
self.numberOfPlatesTE.Bind(wx.EVT_TEXT_ENTER,
self.OnEnterNumberOfPlates)
self.wellDisplayChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectWellDisplay)
self.annotationCol.Bind(wx.EVT_COMBOBOX, self.OnSelectAnnotationCol)
self.addAnnotationColBtn.Bind(wx.EVT_BUTTON, self.OnAddAnnotationCol)
self.annotationLabel.Bind(wx.EVT_KEY_UP, self.OnEnterAnnotation)
self.outlineMarked.Bind(wx.EVT_CHECKBOX, self.OnOutlineMarked)
self.annotationShowVals.Bind(wx.EVT_CHECKBOX,
self.OnShowAnnotationValues)
self.filterChoice.Bind(wx.EVT_COMBOBOX, self.OnSelectFilter)
self.AddPlateMap()
self.OnSelectMeasurement()
def AddPlateMap(self, plateIndex=0):
'''
Adds a new blank plateMap to the PlateMapSizer.
'''
data = np.ones(p.plate_shape)
# Try to get explicit labels for all wells.
res = db.execute(
'SELECT DISTINCT %s FROM %s WHERE %s != "" and %s IS NOT NULL' %
(dbconnect.UniqueWellClause(), p.image_table, p.well_id,
p.well_id))
if p.plate_id:
self.plateMapChoices += [
ComboBox(self, choices=db.GetPlateNames(), size=(400, -1))
]
self.plateMapChoices[-1].Select(plateIndex)
self.plateMapChoices[-1].Bind(wx.EVT_COMBOBOX, self.OnSelectPlate)
#plate_col_type = db.GetColumnType(p.image_table, p.plate_id)
#plate_id = plate_col_type(self.plateMapChoices[-1].GetString(plateIndex))
plateMapChoiceSizer = wx.BoxSizer(wx.HORIZONTAL)
plateMapChoiceSizer.Add(wx.StaticText(self, label='Plate:'),
flag=wx.ALIGN_CENTER_VERTICAL)
plateMapChoiceSizer.Add(self.plateMapChoices[-1],
flag=wx.ALIGN_CENTER_VERTICAL)
well_keys = res
platemap = pmp.PlateMapPanel(self,
data,
well_keys,
p.plate_shape,
colormap=self.colorMapsChoice.Value,
well_disp=self.wellDisplayChoice.Value)
platemap.add_well_selection_handler(self.OnSelectWell)
self.plateMaps += [platemap]
singlePlateMapSizer = wx.BoxSizer(wx.VERTICAL)
if p.plate_id:
singlePlateMapSizer.Add(plateMapChoiceSizer, 0, wx.ALIGN_CENTER)
singlePlateMapSizer.Add(platemap, 1, wx.EXPAND)
self.plateMapSizer.Add(singlePlateMapSizer, 1, wx.EXPAND)
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 UpdateMeasurementChoice(self, evt=None):
'''
Handles the selection of a source table (per-image or per-object) from
a choice box. The measurement choice box is populated with the names
of numeric columns from the selected table.
'''
table = self.sourceChoice.Value
if table == TableComboBox.OTHER_TABLE:
t = get_other_table_from_user(self)
if t is not None:
self.sourceChoice.Items = self.sourceChoice.Items[:-1] + [
t
] + self.sourceChoice.Items[-1:]
self.sourceChoice.Select(self.sourceChoice.Items.index(t))
table = t
else:
self.sourceChoice.Select(0)
return
self.measurementsChoice.SetItems(get_non_blob_types_from_table(table))
self.measurementsChoice.Select(0)
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def on_save_csv(self, evt):
defaultFileName = 'my_plate_table.csv'
saveDialog = wx.FileDialog(self,
message="Save as:",
defaultDir=os.getcwd(),
defaultFile=defaultFileName,
wildcard='csv|*',
style=(wx.FD_SAVE | wx.FD_OVERWRITE_PROMPT
| wx.FD_CHANGE_DIR))
if saveDialog.ShowModal() == wx.ID_OK:
filename = saveDialog.GetPath()
self.save_to_csv(filename)
self.Title = filename
saveDialog.Destroy()
def save_to_csv(self, filename):
with open(filename, 'w', newline="") as f:
w = csv.writer(f)
w.writerow(
['Plate', 'Well', self.measurement + ' ' + self.aggMethod])
w.writerows(self.keys_and_vals)
logging.info('Table saved to %s' % filename)
def OnSelectPlate(self, evt):
''' Handles the selection of a plate from the plate choice box. '''
self.UpdatePlateMaps()
def OnSelectMeasurement(self, evt=None):
''' Handles the selection of a measurement to plot from a choice box. '''
selected_measurement = self.measurementsChoice.Value
table = self.sourceChoice.Value
numeric_measurements = get_numeric_columns_from_table(table)
if (selected_measurement in numeric_measurements):
self.aggregationMethodsChoice.Enable()
self.colorMapsChoice.Enable()
else:
self.aggregationMethodsChoice.Disable()
self.colorMapsChoice.Disable()
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectAggregationMethod(self, evt=None):
''' Handles the selection of an aggregation method from the choice box. '''
self.colorBar.ResetInterval()
self.UpdatePlateMaps()
def OnSelectColorMap(self, evt=None):
''' Handles the selection of a color map from a choice box. '''
map = self.colorMapsChoice.Value
cm = matplotlib.cm.get_cmap(map)
self.colorBar.SetMap(map)
for plateMap in self.plateMaps:
plateMap.SetColorMap(map)
def OnSelectWellDisplay(self, evt=None):
''' Handles the selection of a well display choice from a choice box. '''
sel = self.wellDisplayChoice.Value
if sel.lower() == 'image':
dlg = wx.MessageDialog(
self,
'This mode will render each well as a shrunken image loaded '
'from that well. This feature is currently VERY SLOW since it '
'requires loading hundreds of full sized images. Are you sure '
'you want to continue?', 'Load all images?',
wx.OK | wx.CANCEL | wx.ICON_QUESTION)
if dlg.ShowModal() != wx.ID_OK:
self.wellDisplayChoice.SetSelection(0)
return
if sel.lower() in ['image', 'thumbnail']:
self.colorBar.Hide()
else:
self.colorBar.Show()
for platemap in self.plateMaps:
platemap.SetWellDisplay(sel)
def OnEnterNumberOfPlates(self, evt=None):
''' Handles the entry of a plates to view from a choice box. '''
try:
nPlates = int(self.numberOfPlatesTE.GetValue())
except:
logging.warn(
'Invalid # of plates! Please enter a number between 1 and 100')
return
if nPlates > 100:
logging.warn(
'Too many plates! Please enter a number between 1 and 100')
return
if nPlates < 1:
logging.warn('You must display at least 1 plate.')
self.numberOfPlatesTE.SetValue('1')
nPlates = 1
# Record the indices of the plates currently selected.
# Pad the list with sequential plate indices then crop to the new number of plates.
currentPlates = [
plateChoice.GetSelection() for plateChoice in self.plateMapChoices
]
currentPlates = (currentPlates +
[(currentPlates[-1] + 1 + p) % len(db.GetPlateNames())
for p in range(nPlates)])[:nPlates]
# Remove all plateMaps
self.plateMapSizer.Clear(delete_windows=True)
self.plateMaps = []
self.plateMapChoices = []
# Restructure the plateMapSizer appropriately
rows = cols = np.ceil(np.sqrt(nPlates))
self.plateMapSizer.SetRows(rows)
self.plateMapSizer.SetCols(cols)
# Add the plate maps
for plateIndex in currentPlates:
self.AddPlateMap(plateIndex)
self.UpdatePlateMaps()
self.plateMapSizer.Layout()
# Update outlines
self.OnOutlineMarked()
def OnSelectWell(self):
'''When wells are selected: display their annotation in the annotation
label control. If multiple annotations are found then make sure the
user knows.
'''
wellkeys = []
for pm in self.plateMaps:
wellkeys += pm.get_selected_well_keys()
if len(wellkeys) > 0 and self.annotationCol.Value != '':
self.annotationLabel.Enable()
self.annotationLabel.SetForegroundColour(wx.BLACK)
self.annotationLabel.SetBackgroundColour(wx.WHITE)
annotations = db.execute('SELECT %s FROM %s WHERE %s' %
(self.annotationCol.Value, p.image_table,
GetWhereClauseForWells(wellkeys)))
annotations = list(set([a[0] for a in annotations]))
if len(annotations) == 1:
if annotations[0] == None:
self.annotationLabel.SetValue('')
else:
self.annotationLabel.SetValue(str(annotations[0]))
else:
self.annotationLabel.SetValue(','.join(
[str(a) for a in annotations if a is not None]))
else:
self.annotationLabel.Disable()
self.annotationLabel.SetForegroundColour(wx.Colour(80, 80, 80))
self.annotationLabel.SetBackgroundColour(wx.LIGHT_GREY)
self.annotationLabel.SetValue('Select wells')
def OnAddAnnotationCol(self, evt):
'''Add a new user annotation column to the database.
'''
dlg = wx.TextEntryDialog(self, 'New annotation column name: User_',
'Add Annotation Column')
if dlg.ShowModal() != wx.ID_OK:
return
new_column = 'User_' + dlg.GetValue()
# user-type ==> (sql-type, python-type)
coltypes = {'Text': ('VARCHAR(255)', str), 'Number': ('FLOAT', float)}
dlg = wx.SingleChoiceDialog(
self,
'What type of annotation column would you like to add?\nThis can not be changed.',
'Add Annotation Column', list(coltypes.keys()), wx.CHOICEDLG_STYLE)
if dlg.ShowModal() != wx.ID_OK:
return
usertype = dlg.GetStringSelection()
db.AppendColumn(p.image_table, new_column, coltypes[usertype][0])
self.annotation_cols[new_column] = coltypes[usertype][1]
self.annotationCol.Items += [new_column]
self.annotationCol.SetSelection(len(self.annotation_cols) - 1)
current_selection = self.measurementsChoice.GetSelection()
self.measurementsChoice.SetItems(self.measurementsChoice.Strings +
[new_column])
if self.annotationShowVals.IsChecked():
column = self.annotationCol.Value
self.sourceChoice.SetStringSelection(p.image_table)
self.measurementsChoice.SetStringSelection(column)
self.UpdatePlateMaps()
else:
self.measurementsChoice.SetSelection(current_selection)
self.annotationShowVals.Enable()
self.outlineMarked.Enable()
self.OnSelectWell()
def OnSelectAnnotationCol(self, evt=None):
'''Handles selection of an annotation column.
'''
col = self.annotationCol.Value
if col == '':
return
coltype = self.annotation_cols[col]
self.OnSelectWell()
self.OnOutlineMarked()
if self.annotationShowVals.IsChecked():
if coltype != str:
self.colorMapsChoice.Enable()
else:
self.colorMapsChoice.Disable()
self.measurementsChoice.SetStringSelection(col)
self.UpdatePlateMaps()
def OnEnterAnnotation(self, evt=None):
'''Store the annotation value in the annotation column of the db.
'''
if evt.KeyCode < 32 or evt.KeyCode > 127:
return
column = self.annotationCol.Value
value = self.annotationLabel.Value
wellkeys = []
for pm in self.plateMaps:
wellkeys += pm.get_selected_well_keys()
if value == '':
value = None
elif self.annotation_cols[column] == float:
try:
value = float(value)
self.annotationLabel.SetForegroundColour(wx.BLACK)
except:
self.annotationLabel.SetForegroundColour(wx.Color(255, 0, 0))
return
db.UpdateWells(p.image_table, column, value, wellkeys)
if self.outlineMarked.IsChecked():
for pm in self.plateMaps:
if value is None:
pm.UnOutlineWells(wellkeys)
else:
pm.OutlineWells(wellkeys)
if (self.sourceChoice.Value == p.image_table
and self.measurementsChoice.Value == column):
self.UpdatePlateMaps()
def OnOutlineMarked(self, evt=None):
'''Outlines all non-NULL values of the current annotation
'''
# Disable filters when outlining marked wells
#if self.outlineMarked.IsChecked():
#self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER)
#self.filterChoice.Disable()
#else:
#if not self.annotationShowVals.IsChecked():
#self.filterChoice.Enable()
# Update outlined wells in PlateMapPanels
for pm in self.plateMaps:
if self.outlineMarked.IsChecked():
column = self.annotationCol.Value
if p.plate_id:
res = db.execute('SELECT %s, %s FROM %s WHERE %s="%s"' %
(dbconnect.UniqueWellClause(), column,
p.image_table, p.plate_id, pm.plate))
else:
# if there's no plate_id, we assume there is only 1 plate
# and fetch all the data
res = db.execute(
'SELECT %s, %s FROM %s' %
(dbconnect.UniqueWellClause(), column, p.image_table))
keys = [tuple(r[:-1]) for r in res if r[-1] is not None]
pm.SetOutlinedWells(keys)
else:
pm.SetOutlinedWells([])
self.UpdatePlateMaps()
def OnShowAnnotationValues(self, evt=None):
'''Handler for the show values checkbox.
'''
if self.annotationShowVals.IsChecked():
column = self.annotationCol.Value
self.sourceChoice.SetStringSelection(p.image_table)
self.measurementsChoice.SetItems(
get_non_blob_types_from_table(p.image_table))
self.measurementsChoice.SetStringSelection(column)
self.filterChoice.SetStringSelection(FilterComboBox.NO_FILTER)
self.sourceChoice.Disable()
self.measurementsChoice.Disable()
self.filterChoice.Disable()
self.aggregationMethodsChoice.Disable()
self.aggregationMethodsChoice.SetValue('none')
else:
self.sourceChoice.Enable()
self.measurementsChoice.Enable()
if not self.outlineMarked.IsChecked():
self.filterChoice.Enable()
if db.GetColumnType(self.sourceChoice.Value,
self.measurementsChoice.Value) != str:
self.aggregationMethodsChoice.Enable()
self.aggregationMethodsChoice.SetSelection(0)
self.UpdatePlateMaps()
def OnSelectFilter(self, evt):
self.filterChoice.on_select(evt)
self.UpdatePlateMaps()
self.colorBar.ResetInterval()
def save_settings(self):
'''save_settings is called when saving a workspace to file.
returns a dictionary mapping setting names to values encoded as strings
'''
settings = {
'table': self.sourceChoice.Value,
'measurement': self.measurementsChoice.Value,
'aggregation': self.aggregationMethodsChoice.Value,
'colormap': self.colorMapsChoice.Value,
'well display': self.wellDisplayChoice.Value,
'number of plates': self.numberOfPlatesTE.GetValue(),
}
for i, choice in enumerate(self.plateMapChoices):
settings['plate %d' % (i + 1)] = choice.Value
return settings
def load_settings(self, settings):
'''load_settings is called when loading a workspace from file.
settings - a dictionary mapping setting names to values encoded as
strings.
'''
if 'table' in settings:
self.sourceChoice.SetStringSelection(settings['table'])
self.UpdateMeasurementChoice()
if 'measurement' in settings:
self.measurementsChoice.SetStringSelection(settings['measurement'])
self.OnSelectMeasurement()
if 'aggregation' in settings:
self.aggregationMethodsChoice.SetStringSelection(
settings['aggregation'])
self.OnSelectAggregationMethod()
if 'colormap' in settings:
self.colorMapsChoice.SetStringSelection(settings['colormap'])
self.OnSelectColorMap()
if 'number of plates' in settings:
self.numberOfPlatesTE.SetValue(settings['number of plates'])
self.OnEnterNumberOfPlates()
for s, v in list(settings.items()):
if s.startswith('plate '):
self.plateMapChoices[int(s.strip('plate ')) - 1].SetValue(v)
# set well display last since each step currently causes a redraw and
# this could take a long time if they are displaying images
if 'well display' in settings:
self.wellDisplayChoice.SetStringSelection(settings['well display'])
self.OnSelectWellDisplay()
class ScatterControlPanel(wx.Panel):
'''
A panel with controls for selecting the source data for a scatterplot
'''
def __init__(self, parent, figpanel, **kwargs):
wx.Panel.__init__(self, parent, **kwargs)
# the panel to draw charts on
self.figpanel = figpanel
self.SetBackgroundColour('white') # color for the background of panel
sizer = wx.BoxSizer(wx.VERTICAL)
self.x_table_choice = ui.TableComboBox(self, -1, style=wx.CB_READONLY)
self.y_table_choice = ui.TableComboBox(self, -1, style=wx.CB_READONLY)
self.x_choice = ComboBox(self, -1, choices=[''], size=(200,-1), style=wx.CB_READONLY)
self.x_choice.Select(0)
self.y_choice = ComboBox(self, -1, choices=[''], size=(200,-1), style=wx.CB_READONLY)
self.y_choice.Select(0)
self.x_scale_choice = ComboBox(self, -1, choices=[LINEAR_SCALE, LOG_SCALE], size=(90,-1), style=wx.CB_READONLY)
self.x_scale_choice.Select(0)
self.y_scale_choice = ComboBox(self, -1, choices=[LINEAR_SCALE, LOG_SCALE], size=(90,-1), style=wx.CB_READONLY)
self.y_scale_choice.Select(0)
self.filter_choice = ui.FilterComboBox(self, style=wx.CB_READONLY)
self.filter_choice.Select(0)
self.gate_choice = ui.GateComboBox(self, style=wx.CB_READONLY)
self.gate_choice.set_gatable_columns([self.x_column, self.y_column])
self.update_chart_btn = wx.Button(self, -1, "Update Chart")
self.update_x_choices()
self.update_y_choices()
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "x-axis:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.x_table_choice, 1, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(self.x_choice, 2, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(wx.StaticText(self, -1, "scale:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.x_scale_choice)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 2, 0)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "y-axis:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.y_table_choice, 1, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(self.y_choice, 2, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(wx.StaticText(self, -1, "scale:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.y_scale_choice)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 2, 0)
sz = wx.BoxSizer(wx.HORIZONTAL)
sz.Add(wx.StaticText(self, -1, "filter:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.filter_choice, 1, wx.EXPAND)
sz.AddSpacer(3)
sz.Add(wx.StaticText(self, -1, "gate:"), 0, wx.TOP, 4)
sz.AddSpacer(3)
sz.Add(self.gate_choice, 1, wx.EXPAND)
sizer.Add(sz, 1, wx.EXPAND)
sizer.Add(-1, 2, 0)
sizer.Add(self.update_chart_btn)
self.x_table_choice.Bind(wx.EVT_COMBOBOX, self.on_x_table_selected)
self.y_table_choice.Bind(wx.EVT_COMBOBOX, self.on_y_table_selected)
self.gate_choice.addobserver(self.on_gate_selected)
self.update_chart_btn.Bind(wx.EVT_BUTTON, self.update_figpanel)
self.SetSizer(sizer)
self.Show(1)
@property
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))
@property
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))
@property
def filter(self):
return self.filter_choice.get_filter_or_none()
def on_x_table_selected(self, evt):
table = self.x_table_choice.Value
if table == ui.TableComboBox.OTHER_TABLE:
t = ui.get_other_table_from_user(self)
if t is not None:
self.x_table_choice.Items = self.x_table_choice.Items[:-1] + [t] + self.x_table_choice.Items[-1:]
self.x_table_choice.Select(self.x_table_choice.Items.index(t))
sel = self.y_table_choice.GetSelection()
self.y_table_choice.Items = self.y_table_choice.Items[:-1] + [t] + self.y_table_choice.Items[-1:]
self.y_table_choice.SetSelection(sel)
else:
self.x_table_choice.Select(0)
return
self.update_x_choices()
def on_y_table_selected(self, evt):
table = self.y_table_choice.Value
if table == ui.TableComboBox.OTHER_TABLE:
t = ui.get_other_table_from_user(self)
if t is not None:
self.y_table_choice.Items = self.y_table_choice.Items[:-1] + [t] + self.y_table_choice.Items[-1:]
self.y_table_choice.Select(self.y_table_choice.Items.index(t))
sel = self.x_table_choice.GetSelection()
self.x_table_choice.Items = self.x_table_choice.Items[:-1] + [t] + self.x_table_choice.Items[-1:]
self.x_table_choice.SetSelection(sel)
else:
self.y_table_choice.Select(0)
return
self.update_y_choices()
def on_gate_selected(self, gate_name):
self.update_gate_helper()
def update_gate_helper(self):
gate_name = self.gate_choice.get_gatename_or_none()
if gate_name:
# Deactivate the lasso tool
self.figpanel.get_toolbar().toggle_user_tool('lasso', False)
self.figpanel.gate_helper.set_displayed_gate(p.gates[gate_name], self.x_column, self.y_column)
else:
self.figpanel.gate_helper.disable()
def update_x_choices(self):
tablename = self.x_table_choice.Value
fieldnames = db.GetColumnNames(tablename)
self.x_choice.Clear()
self.x_choice.AppendItems(fieldnames)
self.x_choice.SetSelection(0)
def update_y_choices(self):
tablename = self.y_table_choice.Value
fieldnames = db.GetColumnNames(tablename)
self.y_choice.Clear()
self.y_choice.AppendItems(fieldnames)
self.y_choice.SetSelection(0)
def _plotting_per_object_data(self):
return (p.object_table is not None and
p.object_table in [self.x_column.table, self.y_column.table]
or (self.x_column.table != p.image_table and db.adjacent(p.object_table, self.x_column.table))
or (self.y_column.table != p.image_table and db.adjacent(p.object_table, self.y_column.table))
)
def update_figpanel(self, evt=None):
self.gate_choice.set_gatable_columns([self.x_column, self.y_column])
self.gate_choice.update_info()
keys_and_points = self._load_points()
col_types = self.get_selected_column_types()
# Convert keys and points into a np array
# NOTE: We must set dtype "object" on creation or values like 0.34567e-9
# may be truncated to 0.34567e (error) or 0.345 (no error) when
# the array contains strings.
kps = np.array(keys_and_points, dtype='object')
# Strip out keys
if self._plotting_per_object_data():
key_indices = list(range(len(object_key_columns())))
else:
key_indices = list(range(len(image_key_columns())))
keys = kps[:,key_indices].astype(int)
# Strip out x coords
if col_types[0] in (float, int):
xpoints = kps[:,-2].astype('float32')
else:
xpoints = kps[:,-2]
# Strip out y coords
if col_types[1] in (float, int):
ypoints = kps[:,-1].astype('float32')
else:
ypoints = kps[:,-1]
# plot the points
self.figpanel.set_points(xpoints, ypoints)
self.figpanel.set_keys(keys)
self.figpanel.set_x_scale(self.x_scale_choice.Value)
self.figpanel.set_y_scale(self.y_scale_choice.Value)
self.figpanel.set_x_label(self.x_column.col)
self.figpanel.set_y_label(self.y_column.col)
self.update_gate_helper()
self.figpanel.redraw()
self.figpanel.draw()
def _load_points(self):
q = sql.QueryBuilder()
select = []
#
# If there's an object table fetch object keys. Else fetch image keys.
#
# TODO: linking per-well data doesn't work if we fetch keys this way
#
if self._plotting_per_object_data():
select += [sql.Column(p.object_table, col) for col in object_key_columns()]
else:
select += [sql.Column(p.image_table, col) for col in image_key_columns()]
select += [self.x_column, self.y_column]
q.set_select_clause(select)
if self.filter != None:
q.add_filter(self.filter)
q.add_where(sql.Expression(self.x_column, 'IS NOT NULL'))
q.add_where(sql.Expression(self.y_column, 'IS NOT NULL'))
return db.execute(str(q))
def get_selected_column_types(self):
''' Returns a tuple containing the x and y column types. '''
return (db.GetColumnType(self.x_table_choice.Value, self.x_choice.Value),
db.GetColumnType(self.y_table_choice.Value, self.y_choice.Value))
def save_settings(self):
'''save_settings is called when saving a workspace to file.
returns a dictionary mapping setting names to values encoded as strings
'''
d = {'x-table' : self.x_table_choice.Value,
'y-table' : self.y_table_choice.Value,
'x-axis' : self.x_choice.Value,
'y-axis' : self.y_choice.Value,
'x-scale' : self.x_scale_choice.Value,
'y-scale' : self.y_scale_choice.Value,
'filter' : self.filter_choice.Value,
'x-lim' : self.figpanel.subplot.get_xlim(),
'y-lim' : self.figpanel.subplot.get_ylim(),
'version' : '1',
}
if self.gate_choice.get_gatename_or_none():
gate_choice_id = self.gate_choice.GetSelection()
d['gate'] = self.gate_choice.GetString(gate_choice_id)
return d
def load_settings(self, settings):
'''load_settings is called when loading a workspace from file.
settings - a dictionary mapping setting names to values encoded as
strings.
'''
if 'version' not in settings:
if 'table' in settings:
settings['x-table'] = settings['table']
settings['y-table'] = settings['table']
settings['version'] = '1'
if 'x-table' in settings:
self.x_table_choice.SetStringSelection(settings['x-table'])
self.update_x_choices()
if 'y-table' in settings:
self.y_table_choice.SetStringSelection(settings['y-table'])
self.update_y_choices()
if 'x-axis' in settings:
self.x_choice.SetStringSelection(settings['x-axis'])
if 'y-axis' in settings:
self.y_choice.SetStringSelection(settings['y-axis'])
if 'x-scale' in settings:
self.x_scale_choice.SetStringSelection(settings['x-scale'])
if 'y-scale' in settings:
self.y_scale_choice.SetStringSelection(settings['y-scale'])
if 'filter' in settings:
self.filter_choice.SetStringSelection(settings['filter'])
self.update_figpanel()
if 'x-lim' in settings:
self.figpanel.subplot.set_xlim(eval(settings['x-lim']))
if 'y-lim' in settings:
self.figpanel.subplot.set_ylim(eval(settings['y-lim']))
if 'gate' in settings:
self.gate_choice.SetStringSelection(settings['gate'])
self.figpanel.gate_helper.set_displayed_gate(
p.gates[settings['gate']], self.x_column, self.y_column)
self.figpanel.draw()