def get_upload_settings(self, general = True, file = None):
'''
'''
if file in self.fileSpecificSettings:
prevSettings = OrderedDict([(k,[v]) for k,v in self.fileSpecificUserSettings[file].items()])
else:
prevSettings = self.generalLoadSettings
dialog = simpleUserInputDialog(list(prevSettings.keys()),
[x[0] for x in prevSettings.values()],
list(self.generalLoadSettings.values()),
'Upload Settings',
'Settings have to be define for all files that should be uploaded.')
if len(dialog.selectionOutput) == len(comboBoxToGetInputFromUser):
if general:
self.loadSettings = self.adjust_setting_names(dialog.selectionOutput)
if len(self.fileSpecificSettings) != 0:
quest = tk.messagebox.askquestion('Overwrite?',
'File specific upload paramters were given. Do you want to discard them?',
parent=self.toplevel)
if quest == 'yes':
self.fileSpecificSettings = dict()
elif file is not None and general == False:
self.fileSpecificUserSettings[file] = dialog.selectionOutput.copy()
self.fileSpecificSettings[file] = self.adjust_setting_names(dialog.selectionOutput)
self.get_file_columns(self.dir,list(self.fileColumns.keys()))
def modify_legend(self,event = None, legendTitle = False): ''' Let's the user modify the legend. ''' if event is None: event = self.event ax = event.inaxes legend = self.check_for_legend(ax) if legend is not None: if legendTitle: textItems = [legend.get_title()] else: textItems = legend.get_texts() textStrings = [txt.get_text() for txt in textItems] optionList = [['None',textStrings[n]] for n in range(len(textStrings))] dialogWindow = simple_dialog.simpleUserInputDialog(textStrings,textStrings, optionList,'Change Legend Text','Modify legend text.') for txt in textItems: oldText = txt.get_text() if oldText in dialogWindow.selectionOutput: newText = dialogWindow.selectionOutput[oldText] txt.set_text(newText) self.redraw()
def change_limits(self, event = None):
'''
Allows the user to change axis limits.
'''
if event is None:
event = self.event
ax = event.inaxes
axisId = self.identify_id_of_axis(ax)
settingList = ['x min', 'x max', 'y min', 'y max']
textStrings = [self.axisItems[axisId]['xLimit'][0],
self.axisItems[axisId]['xLimit'][1],
self.axisItems[axisId]['yLimit'][0],
self.axisItems[axisId]['yLimit'][1]]
optionList = [[],[],[],[]]
dialogWindow = simple_dialog.simpleUserInputDialog(settingList,textStrings,
optionList,'Change axis limits','Change axis limits.')
if len(dialogWindow.selectionOutput) == 4:
try:
ax.set_xlim((float(dialogWindow.selectionOutput['x min']),
float(dialogWindow.selectionOutput['x max'])))
ax.set_ylim((float(dialogWindow.selectionOutput['y min']),
float(dialogWindow.selectionOutput['y max'])))
except:
tk.messagebox.showinfo('Error ..',
'Could not interpret input (examples: 2.3, 100, 34.0). Axis limits not changed.',
parent = self.toplevel)
def define_features(self, id):
dfString = self.blocks[id]['dataFrame'].get()
if dfString not in self.blockIdtoDfId:
tk.messagebox.showinfo('Error..',
'Please select a data frame.',
parent=self.toplevel)
return
dfID = self.blockIdtoDfId[dfString]
numColumns = self.dfClass.get_numeric_columns_by_id(dfID)
if self.blocks[id]['featureInCols'].instate(['selected']):
pass
else:
catColumns = self.dfClass.get_categorical_columns_by_id(dfID)
featureNamesDialog = simple_dialog.simpleUserInputDialog(
['Feature Names'], [catColumns[0]], catColumns,
'Select feature names column',
'Please select Column that holds feature names (Gene names, Lipid names)'
)
if len(featureNamesDialog.selectionOutput) == 0:
return
dialog = simple_dialog.simpleListboxSelection(
'Select feature columns.', numColumns, 'Feature Selection')
if len(dialog.selection) > 0:
featureColumns = dialog.selection
blockDF = self.dfClass.dfs[dfID][featureColumns]
if self.blocks[id]['featureInCols'].instate(['selected']):
self.blocks[id]['blockDF'] = blockDF
self.blocks[id][
'featureNames'] = blockDF.columns.values.tolist()
else:
self.blocks[id]['blockDF'] = blockDF.transpose().values
self.blocks[id][
'featureNames'] = featureNamesDialog.selectionOutput[
'Feature Names']
if self.blocks[id]['scaleData'].instate(['selected']):
self.blocks[id]['blockDF'] = StandardScaler().fit_transform(
self.blocks[id]['blockDF'])
self.blocks[id]['featureButton'].configure(text="\u221A")
def import_data(self):
'''
'''
importer = importDataFromDf(
self.dfClass,
title='Select data from preview as your x values.' +
' They must match either in row- or column-number the' +
' selected numeric columns: {}.'.format(self.n_cols),
requiredDataPoints=self.n_cols,
allowMultSelection=True)
## get selected data
selectionData = importer.get_data_selection()
## ensure that df Class has correct data selected (if user change it to select data)
#self.dfClass.set_current_data_by_id(self.dfID)
#print(selectionData)
if selectionData is None:
del importer
return
else:
shape = selectionData.shape
if shape[0] == self.n_cols and shape[1] == self.n_cols:
askAxis = simpleUserInputDialog(
['observations are in'], ['rows'], ['rows', 'columns'],
title='Select axis.',
infoText=
'Data selection shape matches in rows and columns. Please select where the observations are stored.'
)
results = askAxis.selectionOutput
if len(results) == 0:
tk.messagebox.showinfo('Error..',
'No axis selected.',
parent=self)
elif results['observations are in'] == 'rows':
self.corr_data = selectionData
elif results['observations are in'] == 'columns':
self.corr_data = selectionData.transpose()
elif shape[1] == self.n_cols:
self.corr_data = selectionData.transpose()
elif shape[0] == self.n_cols:
self.corr_data = selectionData
self.correlationColumns = self.corr_data.columns.values.tolist()
self.corrButton.configure(state=tk.ACTIVE)
def add_image_to_axis(self, pathToFile = None, axisId = None):
'''
Add an image to a selected subplot.
'''
if self.check_if_axes_created() == False:
return
if pathToFile is None:
pathToFile = tf.askopenfilename(initialdir=path_file,
title="Choose File",parent = self.toplevel)
if pathToFile == '':
return
fileEnd = pathToFile.split('.')[-1]
if fileEnd != 'png':
tk.messagebox.showinfo('File error ..','At the moment only png files are supported.'+
' Your file path ends with: {}'.format(fileEnd),
parent = self.toplevel)
return
im = plt.imread(pathToFile)
if axisId is None:
axesInFigure = []
for id, props in self.figureProps.items():
axesInFigure.append('Subplot Id: {} - Label: {}'.format(id,props['axisLabel']))
## select axis
dialog = simple_dialog.simpleUserInputDialog(['Subplot: '],
[axesInFigure[0]],[axesInFigure],
title='Select subplot',infoText='Select subplot.')
axisId = int(float(dialog.selectionOutput['Subplot: '].split(' ')[2]))
ax = self.figureProps[axisId]['ax']
axOrigPosition = ax.get_position()
## show image
ax.imshow(im)
ax.axis('off')
self.infolabel.set('The original resolution is restored upon export.')
self.redraw()
self.align_image_in_axis(ax,axOrigPosition)
self.redraw()
self.mainFigureCollection.store_image_export(axisId,self.figureId,pathToFile)
def define_class(self, id):
'''
'''
dfString = self.blocks[id]['dataFrame'].get()
if dfString not in self.blockIdtoDfId:
tk.messagebox.showinfo('Error..',
'Please select a data frame.',
parent=self.toplevel)
return
dfID = self.blockIdtoDfId[dfString]
catColumns = self.dfClass.get_categorical_columns_by_id(dfID)
dialog = simple_dialog.simpleUserInputDialog(
['Class'], [catColumns[0]], catColumns, 'Select Class Columns',
'Please define column that holds information about the classes.')
self.blocks[id]['classNames'] = self.dfClass.dfs[dfID][
dialog.selectionOutput['Class']].values
self.blocks[id]['classButton'].configure(text="\u221A")
def rename_groups(self, event=None):
'''
'''
selection = self.get_selected_groups()
commonStart = self.find_longest_item_match(selection)
optionValues = [[commonStart[n], groupId]
for n, groupId in enumerate(selection)]
groupRenameDialog = simpleUserInputDialog(selection,
commonStart,
optionValues,
title='Rename groups',
infoText='')
renameOutput = groupRenameDialog.selectionOutput
if len(renameOutput) != 0:
for groupId, newName in renameOutput.items():
if newName == '':
continue
self.rename_group_in_tree(groupId, newName)
