def _createTrajectoriesBox(self, content):
frame = tk.LabelFrame(content, text='Trajectories')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Animation name
self._addLabel(frame, 'Name', 0, 0)
self.animationVar = tk.StringVar()
clusterEntry = tk.Entry(frame, textvariable=self.animationVar,
width=30, bg='white')
clusterEntry.grid(row=0, column=1, sticky='nw', pady=5)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=1, column=1,
sticky='se', padx=5, pady=5)
buttonsFrame.columnconfigure(0, weight=1)
self.generateBtn = HotButton(buttonsFrame, text='Generate Animation', state=tk.DISABLED,
tooltip='Select trajectory points to generate the animations',
imagePath='fa-plus-circle.png', command=self._onCreateClick)
self.generateBtn.grid(row=0, column=1, padx=5)
self.loadBtn = Button(buttonsFrame, text='Load', imagePath='fa-folder-open.png',
tooltip='Load a generated animation.',command=self._onLoadClick)
self.loadBtn.grid(row=0, column=2, padx=5)
self.closeBtn = Button(buttonsFrame, text='Close', imagePath=Icon.ACTION_CLOSE,
tooltip='Close window', command=self.close)
self.closeBtn.grid(row=0, column=3, padx=(5, 10))
frame.grid(row=1, column=0, sticky='new', padx=5, pady=(5, 10))
def _createTrajectoriesBox(self, content):
frame = tk.LabelFrame(content, text='Trajectories')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Animation name
self._addLabel(frame, 'Name', 0, 0)
self.animationVar = tk.StringVar()
clusterEntry = tk.Entry(frame, textvariable=self.animationVar,
width=30, bg='white')
clusterEntry.grid(row=0, column=1, sticky='nw', pady=5)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=1, column=1,
sticky='se', padx=5, pady=5)
buttonsFrame.columnconfigure(0, weight=1)
self.generateBtn = HotButton(buttonsFrame, text='Generate Animation', state=tk.DISABLED,
tooltip='Select trajectory points to generate the animations',
imagePath='fa-plus-circle.png', command=self._onCreateClick)
self.generateBtn.grid(row=0, column=1, padx=5)
self.loadBtn = Button(buttonsFrame, text='Load', imagePath='fa-folder-open.png',
tooltip='Load a generated animation.',command=self._onLoadClick)
self.loadBtn.grid(row=0, column=2, padx=5)
self.closeBtn = Button(buttonsFrame, text='Close', imagePath=Icon.ACTION_CLOSE,
tooltip='Close window', command=self.close)
self.closeBtn.grid(row=0, column=3, padx=(5, 10))
frame.grid(row=1, column=0, sticky='new', padx=5, pady=(5, 10))
def _createSamplesFrame(self, content):
frame = tk.Frame(content)
#frame = tk.LabelFrame(content, text='General')
lfSamples = tk.LabelFrame(frame, text='Samples')
gui.configureWeigths(frame)
lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
self.samplesTree = self._addBoundTree(lfSamples, SamplesTreeProvider,
10, fitting=self.fitting)
self.samplesTree.itemDoubleClick = self._onSampleDoubleClick
self.samplesTree.itemClick = self._onSampleClick
plotFrame = tk.Frame(lfSamples)
plotFrame.grid(row=1, column=0, sticky='ws', padx=5, pady=5)
# Add a combobox with the variable for time
timeVars = [v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_TIME]
timeVars += [v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_MEASUREMENT]
measureVars = [v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_MEASUREMENT]
def addVar(text, col, choices):
varFrame = tk.Frame(plotFrame)
varFrame.grid(row=0, column=col, sticky='new')
label = tk.Label(varFrame, text=text, font=self.fontBold)
label.grid(row=0, column=0, padx=5, pady=2, sticky='nw')
combo = ComboBox(varFrame, choices, width=10)
combo.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
radioVar = tk.IntVar()
radio = tk.Checkbutton(varFrame, text='Log10', variable=radioVar)
radio.grid(row=0, column=2, sticky='nw', padx=5, pady=5)
return combo, radio, radioVar
self.timeWidget = addVar('Time variable', 0, timeVars)
self.measureWidget = addVar('Measure variable', 1, measureVars)
self.measureWidget[2].set(True)
self.plotButton = Button(plotFrame, ' Plot ', font=self.fontBold,
command=self._onPlotClick,
tooltip='Select one or more samples to plot '
'their measures of the selected '
'variables (optionally in log).')
self.plotButton.grid(row=0, column=2, sticky='ne', padx=5)
self.plotSummaryButton = Button(plotFrame, ' Summary Plot ',
font=self.fontBold,
command=self._onPlotSummaryClick,
tooltip='Select several samples to plot'
' their statistics'
' (min, max, avg and std).')
self.plotSummaryButton.grid(row=1, column=2, sticky='ne',
padx=5, pady=5)
#frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
content.add(frame, sticky='news', padx=5, pady=5)
def _fillButtonsFrame(self, frame):
subframe = tk.Frame(frame)
subframe.grid(row=0, column=0, sticky='nw')
frame.columnconfigure(1, weight=1)
ctfBtn = Button(subframe, "CTF Monitor", command=self._monitorCTF)
ctfBtn.grid(row=0, column=0, sticky='nw', padx=(0, 5))
if self.protocol.createCtfMonitor() is None:
ctfBtn['state'] = 'disabled'
movieGainBtn = Button(subframe, "Movie Gain Monitor",
command=self._monitorMovieGain)
movieGainBtn.grid(row=0, column=1, sticky='nw', padx=(0, 5))
if self.protocol.createMovieGainMonitor() is None:
movieGainBtn['state'] = 'disabled'
sysBtn = Button(subframe, "System Monitor",
command=self._monitorSystem)
sysBtn.grid(row=0, column=2, sticky='nw', padx=(0, 5))
if self.protocol.createSystemMonitor() is None:
sysBtn['state'] = 'disabled'
htmlBtn = HotButton(subframe, 'Open HTML Report',
command=self._openHTML)
htmlBtn.grid(row=0, column=3, sticky='nw', padx=(0, 5))
closeBtn = self.createCloseButton(frame)
closeBtn.grid(row=0, column=1, sticky='ne')
def __init__(self, title, parent=None, weight=True, minsize=(400, 150),
icon="scipion_bn.xbm", **args):
"""
We assume the parent should be of ProjectsView
"""
Window.__init__(self, title, parent.windows, weight=weight,
icon=icon, minsize=minsize, enableQueue=True)
self.parent = parent
self.projectsPath = self.parent.manager.PROJECTS
self.projName = tk.StringVar()
self.projName.set('')
self.projLocation = tk.StringVar()
self.projLocation.set(self.projectsPath)
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.columnconfigure(1, weight=1)
content.config(bg='white')
content.grid(row=0, column=0, sticky='news',
padx=5, pady=5)
labelName = tk.Label(content, text=Message.LABEL_PROJECT, bg='white', bd=0)
labelName.grid(row=0, column=0, sticky='nw', padx=5, pady=5)
entryName = tk.Entry(content, bg=cfgEntryBgColor, width=20, textvariable=self.projName)
entryName.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
labelCheck = tk.Label(content, text="Use default location", bg='white', bd=0)
labelCheck.grid(row=1, column=0, sticky='nw', padx=5, pady=5)
self.tkCheckVar = tk.IntVar()
btnCheck = tk.Checkbutton(content, variable=self.tkCheckVar, bg='white', bd=0)
btnCheck.grid(row=1, column=1, sticky='nw', padx=5, pady=5)
self.browseFrame = tk.Frame(content, bg='white')
#self.browseFrame.columnconfigure(1, weight=1)
self.browseFrame.grid(row=2, column=0, padx=0, pady=0, columnspan=2, sticky='nw')
self.entryBrowse = tk.Entry(self.browseFrame, bg=cfgEntryBgColor, width=40, textvariable=self.projLocation)
self.entryBrowse.grid(row=0, column=0, sticky='nw', padx=5, pady=5)
self.btnBrowse = IconButton(self.browseFrame, 'Browse', Icon.ACTION_BROWSE, command=self._browsePath)
self.btnBrowse.grid(row=0, column=1, sticky='e', padx=5, pady=5)
self.initial_focus = entryName
self.tkCheckVar.trace('w', self._onVarChanged)
btnCheck.select()
btnFrame = tk.Frame(content)
btnFrame.columnconfigure(0, weight=1)
btnFrame.grid(row=3, column=0, sticky='sew', padx=5, pady=(0, 5), columnspan=2)
btnFrame.config(bg='white')
# Create buttons
btnSelect = HotButton(btnFrame, 'Create', Icon.BUTTON_SELECT, command=self._select)
btnSelect.grid(row=0, column=0, sticky='e', padx=5, pady=5)
btnCancel = Button(btnFrame, 'Cancel', Icon.BUTTON_CANCEL, command=self.close)
btnCancel.grid(row=0, column=1, sticky='e', padx=5, pady=5)
def _createFigureBox(self, content):
from pyworkflow.gui.matplotlib_image import FigureFrame
figFrame = FigureFrame(content, figsize=(6, 6))
figFrame.grid(row=0, column=0, padx=5, columnspan=2)
self.figure = figFrame.figure
applyBtn = HotButton(content, text='Apply B-factor',
command=self._onApplyBfactorClick)
applyBtn.grid(row=1, column=0, sticky='ne', padx=5, pady=5)
closeBtn = Button(content, text='Close', imagePath=Icon.ACTION_CLOSE,
command=self.close)
closeBtn.grid(row=1, column=1, sticky='ne', padx=5, pady=5)
def _createFigureBox(self, content):
from pyworkflow.gui.matplotlib_image import FigureFrame
figFrame = FigureFrame(content, figsize=(6, 6))
figFrame.grid(row=0, column=0, padx=5, columnspan=2)
self.figure = figFrame.figure
applyBtn = HotButton(content, text='Apply B-factor',
command=self._onApplyBfactorClick)
applyBtn.grid(row=1, column=0, sticky='ne', padx=5, pady=5)
closeBtn = Button(content, text='Close', imagePath=Icon.ACTION_CLOSE,
command=self.close)
closeBtn.grid(row=1, column=1, sticky='ne', padx=5, pady=5)
def _createFigureBox(self, content):
frame = tk.LabelFrame(content, text='Figure')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1) #, minsize=30)
# Create the 'Axes' label
self._addLabel(frame, 'Axes', 0, 0)
# Create a listbox with x1, x2 ...
listbox = tk.Listbox(frame,
height=5,
selectmode=tk.MULTIPLE,
bg='white')
for x in range(1, self.dim + 1):
listbox.insert(tk.END, 'x%d' % x)
listbox.grid(row=0, column=1, padx=5, pady=5, sticky='nw')
self.listbox = listbox
# Selection controls
self._addLabel(frame, 'Selection', 1, 0)
# Selection label
self.selectionVar = tk.StringVar()
self.clusterLabel = tk.Label(frame, textvariable=self.selectionVar)
self.clusterLabel.grid(row=1,
column=1,
sticky='nw',
padx=5,
pady=(10, 5))
# --- Expression
expressionFrame = tk.Frame(frame)
expressionFrame.grid(row=2, column=1, sticky='news')
tk.Label(expressionFrame, text='Expression').grid(row=0,
column=0,
sticky='ne')
self.expressionVar = tk.StringVar()
expressionEntry = tk.Entry(expressionFrame,
textvariable=self.expressionVar,
width=30,
bg='white')
expressionEntry.grid(row=0, column=1, sticky='nw')
helpText = 'e.g. x1>0 and x1<100 or x3>20'
tk.Label(expressionFrame, text=helpText).grid(row=1,
column=1,
sticky='nw')
# Buttons
buttonFrame = tk.Frame(frame)
buttonFrame.grid(row=5, column=1, sticky='sew', pady=(10, 5))
buttonFrame.columnconfigure(0, weight=1)
resetBtn = Button(buttonFrame,
text='Reset',
command=self._onResetClick)
resetBtn.grid(row=0, column=0, sticky='ne', padx=(5, 0))
updateBtn = Button(buttonFrame,
text='Update Plot',
imagePath='fa-refresh.png',
command=self._onUpdateClick)
updateBtn.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=0, column=0, sticky='new', padx=5, pady=(10, 5))
def __init__(self, title, parent=None, weight=True, minsize=(400, 110),
icon="scipion_bn.xbm", **args):
"""
We assume the parent should be of ProjectsView
"""
Window.__init__(self, title, parent.windows, weight=weight,
icon=icon, minsize=minsize, enableQueue=True)
self.root['background'] = 'white'
self.parent = parent
self.projectsPath = self.parent.manager.PROJECTS
self.projName = tk.StringVar()
self.projName.set('')
self.projLocation = tk.StringVar()
self.projLocation.set(self.projectsPath)
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.columnconfigure(1, weight=3)
content.config(bg='white')
content.grid(row=0, column=0, sticky='news', padx=5, pady=5)
# Project name line
labelName = tk.Label(content, text=Message.LABEL_PROJECT + ' name', bg='white', bd=0)
labelName.grid(row=0, sticky=tk.W, padx=5, pady=5)
entryName = tk.Entry(content, bg=cfgEntryBgColor, width=20, textvariable=self.projName)
entryName.grid(row=0, column=1, columnspan=2, sticky=tk.W, padx=5, pady=5)
# Project location line
labelLocation = tk.Label(content, text=Message.LABEL_PROJECT + ' location', bg='white', bd=0)
labelLocation.grid(row=1, column=0, sticky='nw', padx=5, pady=5)
self.entryBrowse = tk.Entry(content, bg=cfgEntryBgColor, width=40, textvariable=self.projLocation)
self.entryBrowse.grid(row=1, column=1, sticky='nw', padx=5, pady=5)
self.btnBrowse = IconButton(content, 'Browse', Icon.ACTION_BROWSE, highlightthickness=0, command=self._browsePath)
self.btnBrowse.grid(row=1, column=2, sticky='e', padx=5, pady=5)
self.initial_focus = entryName
btnFrame = tk.Frame(content)
btnFrame.columnconfigure(0, weight=1)
btnFrame.grid(row=2, column=0, sticky='sew', padx=5, pady=(0, 5), columnspan=2)
btnFrame.config(bg='white')
# Create buttons
btnSelect = HotButton(btnFrame, 'Create', Icon.BUTTON_SELECT, command=self._select)
btnSelect.grid(row=0, column=0, sticky='e', padx=5, pady=5)
btnCancel = Button(btnFrame, 'Cancel', Icon.BUTTON_CANCEL, command=self.close)
btnCancel.grid(row=0, column=1, sticky='e', padx=5, pady=5)
def addActionsFrame(self):
""" Add the "toolbar" for actions like create project, import
project or filter"""
# Add the create project button
bg = "white"
btnFrame = tk.Frame(self, bg=bg)
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
# Add a filter box
# Add the Import project button
btn = tk.Label(btnFrame, bg=bg, text="Filter:", font=self.projNameFont)
btn.grid(row=0, column=2, sticky='nse', padx=10, pady=10)
self.filterBox = tk.Entry(btnFrame,
font=self.projNameFont,
textvariable=self.filter)
self.filterBox.grid(row=0, column=3, sticky='ne', padx=10, pady=12)
self.filterBox.bind('<Return>', self._onFilter)
self.filterBox.bind('<KP_Enter>', self._onFilter)
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.root = windows.root
self.vars = {}
self.checkvars = []
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
# Header section
headerFrame = tk.Frame(self, bg='white')
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Enter your desired values"
label = tk.Label(headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw',
bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Start demo",
font=self.bigFontBold,
command=self._onAction)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
gui.configureWeigths(frame)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=0, column=0, sticky='ne')
closeButton = Button(buttonsFrame, 'Close', command=self.close,
imagePath='fa-times.png')
closeButton.grid(row=0, column=0, sticky='ne', padx=5)
self.newButton = HotButton(buttonsFrame, ' New Experiment ',
command=self._onCreateClick,
tooltip='Create a new experiment with the '
'selected samples. You can also edit'
'title and comment.')
self.newButton.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
gui.configureWeigths(frame)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=0, column=0, sticky='ne')
closeButton = Button(buttonsFrame, 'Close', command=self.close,
imagePath='fa-times.png')
frame.grid(row=2, column=0, sticky='news', padx=5, pady=5)
def _createFittingButtonsFrame(self, content):
buttonsFrame = tk.Frame(content)
buttonsFrame.grid(row=0, column=0, sticky='ne')
plotValuesButton = Button(buttonsFrame, 'Plot Fit',
command=self._onPlotFitClick)
plotValuesButton.grid(row=0, column=0, sticky='sew', padx=5, pady=5)
openValuesButton = Button(buttonsFrame, 'Open Fit',
command=self._onOpenFitClick)
openValuesButton.grid(row=1, column=0, sticky='sew', padx=5, pady=5)
return buttonsFrame
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def _fillButtonsFrame(self, frame):
subframe = tk.Frame(frame)
subframe.grid(row=0, column=0, sticky='nw')
frame.columnconfigure(1, weight=1)
ctfBtn = Button(subframe, "CTF Monitor", command=self._monitorCTF)
ctfBtn.grid(row=0, column=0, sticky='nw', padx=(0, 5))
sysBtn = Button(subframe,
"System Monitor",
command=self._monitorSystem)
sysBtn.grid(row=0, column=1, sticky='nw', padx=(0, 5))
htmlBtn = HotButton(subframe,
'Generate HTML Report',
command=self._generateHTML)
htmlBtn.grid(row=0, column=2, sticky='nw', padx=(0, 5))
closeBtn = self.createCloseButton(frame)
closeBtn.grid(row=0, column=1, sticky='ne')
def _createFigureBox(self, content):
frame = tk.LabelFrame(content, text='Figure')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Create the 'Axes' label
self._addLabel(frame, 'Axes', 0, 0)
# Create a listbox with x1, x2 ...
listbox = tk.Listbox(frame, height=5,
selectmode=tk.MULTIPLE, bg='white')
for x in range(1, self.dim+1):
listbox.insert(tk.END, 'x%d' % x)
listbox.grid(row=0, column=1, padx=5, pady=5, sticky='nw')
self.listbox = listbox
# Selection controls
self._addLabel(frame, 'Rejection', 1, 0)
# Selection label
self.selectionVar = tk.StringVar()
self.clusterLabel = tk.Label(frame, textvariable=self.selectionVar)
self.clusterLabel.grid(row=1, column=1, sticky='nw', padx=5, pady=(10, 5))
self._updateSelectionLabel()
# --- Expression
expressionFrame = tk.Frame(frame)
expressionFrame.grid(row=2, column=1, sticky='news')
tk.Label(expressionFrame, text='Expression').grid(row=0, column=0, sticky='ne')
self.expressionVar = tk.StringVar()
expressionEntry = tk.Entry(expressionFrame, textvariable=self.expressionVar,
width=30, bg='white')
expressionEntry.grid(row=0, column=1, sticky='nw')
helpText = 'e.g. x1>0 and x1<100 or x3>20'
tk.Label(expressionFrame, text=helpText).grid(row=1, column=1, sticky='nw')
# Buttons
buttonFrame = tk.Frame(frame)
buttonFrame.grid(row=5, column=1, sticky='sew', pady=(10, 5))
buttonFrame.columnconfigure(0, weight=1)
resetBtn = Button(buttonFrame, text='Reset', command=self._onResetClick)
resetBtn.grid(row=0, column=0, sticky='ne', padx=(5, 0))
updateBtn = Button(buttonFrame, text='Update Plot', imagePath='fa-refresh.png',
command=self._onUpdateClick)
updateBtn.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=0, column=0, sticky='new', padx=5, pady=(10, 5))
def _createFigureBox(self, content):
frame = tk.LabelFrame(content, text="Figure")
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1) # , minsize=30)
# Create the 'Axes' label
self._addLabel(frame, "Axes", 0, 0)
# Create a listbox with x1, x2 ...
listbox = tk.Listbox(frame, height=5, selectmode=tk.MULTIPLE, bg="white")
for x in range(1, self.dim + 1):
listbox.insert(tk.END, "x%d" % x)
listbox.grid(row=0, column=1, padx=5, pady=5, sticky="nw")
self.listbox = listbox
# Selection controls
self._addLabel(frame, "Selection", 1, 0)
# Selection label
self.selectionVar = tk.StringVar()
self.clusterLabel = tk.Label(frame, textvariable=self.selectionVar)
self.clusterLabel.grid(row=1, column=1, sticky="nw", padx=5, pady=(10, 5))
# --- Expression
expressionFrame = tk.Frame(frame)
expressionFrame.grid(row=2, column=1, sticky="news")
tk.Label(expressionFrame, text="Expression").grid(row=0, column=0, sticky="ne")
self.expressionVar = tk.StringVar()
expressionEntry = tk.Entry(expressionFrame, textvariable=self.expressionVar, width=30, bg="white")
expressionEntry.grid(row=0, column=1, sticky="nw")
helpText = "e.g. x1>0 and x1<100 or x3>20"
tk.Label(expressionFrame, text=helpText).grid(row=1, column=1, sticky="nw")
# Buttons
buttonFrame = tk.Frame(frame)
buttonFrame.grid(row=5, column=1, sticky="sew", pady=(10, 5))
buttonFrame.columnconfigure(0, weight=1)
resetBtn = Button(buttonFrame, text="Reset", command=self._onResetClick)
resetBtn.grid(row=0, column=0, sticky="ne", padx=(5, 0))
updateBtn = Button(buttonFrame, text="Update Plot", imagePath="fa-refresh.png", command=self._onUpdateClick)
updateBtn.grid(row=0, column=1, sticky="ne", padx=5)
frame.grid(row=0, column=0, sticky="new", padx=5, pady=(10, 5))
class ExperimentWindow(gui.Window):
""" This class creates a Window that will display some Point's
contained in a Data object.
It will allow to launch 1D, 2D and 3D plots by selecting any
combination of the x1, x2...xn from the Point dimension.
Points can be selected by either Click and Drag in the Scatter plot or..
by creating an Expression.
Finally, there is a button 'Create Cluster' that will call a callback
fuction to take care of it.
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(420, 200), **kwargs)
self.experiment = kwargs.get('experiment')
self.fitting = kwargs.get('fitting', None)
self.callback = kwargs.get('callback', None)
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
content.columnconfigure(0, weight=1)
content.rowconfigure(0, weight=1)
self.plotter = None
def _createContent(self, content):
# Create and fill the frame containing the Experiment
# info, variables and doses
p = tk.PanedWindow(content, orient=tk.VERTICAL, bg='white')
p.grid(row=0, column=0, sticky='news', padx=5, pady=5)
self._createTopFrame(p)
# Create the middle frame containing the Samples Box
self._createSamplesFrame(p)
# Create the last frame with the buttons
self._createButtonsFrame(content)
#self._updateSelectionLabel()
def _createTopFrame(self, content):
frame = tk.Frame(content)
frame.columnconfigure(0, weight=1)
frame.rowconfigure(0, weight=1)
tab = ttk.Notebook(frame)
tab.grid(row=0, column=0, sticky='news', padx=5, pady=5)
def addTab(label):
lf = tk.Frame(tab)
tab.add(lf, text=label)
return lf
lfGeneral = addTab('General')
self._addLabel(lfGeneral, 'Title', 0, 0)
self._titleVar = tk.StringVar()
self._titleVar.set(self.experiment.general['title'])
titleEntry = tk.Entry(lfGeneral, width=26, textvariable=self._titleVar,
bg='white')
titleEntry.grid(row=0, column=1, sticky='nw', padx=5, pady=(5, 0))
self._addLabel(lfGeneral, 'Comment', 1, 0)
commentText = gui.text.Text(lfGeneral, width=30, height=3, bg='white')
commentText.setText(self.experiment.general['comment'])
commentText.grid(row=1, column=1, sticky='nw', padx=5, pady=(5, 0))
self._commentText = commentText
lfVars = addTab('Variables')
self.varsTree = self._addBoundTree(lfVars, VariablesTreeProvider, 5)
lfVias = addTab('Vias')
self.viasTree = self._addBoundTree(lfVias, ViasTreeProvider, 5)
lfDoses = addTab('Doses')
self.dosesTree = self._addBoundTree(lfDoses, DosesTreeProvider, 5)
lfGroups = addTab('Groups')
self.groupsTree = self._addBoundTree(lfGroups, GroupsTreeProvider, 5)
# Fitting tab
if self.fitting:
tabFitting = addTab('Fitting')
t = TaggedText(tabFitting, width=80, height=10, bg='white')
t.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
t.setText('Select one of the samples to see more information.')
t.setReadOnly(True)
self.fittingText = t
# Buttons for fitting
buttonsFrame = self._createFittingButtonsFrame(tabFitting)
buttonsFrame.grid(row=0, column=1, sticky='news', padx=5, pady=5)
#frame.grid(row=0, column=0, sticky='news', padx=5, pady=(10, 5))
content.add(frame, sticky='news', padx=5, pady=5)
def _createSamplesFrame(self, content):
frame = tk.Frame(content)
#frame = tk.LabelFrame(content, text='General')
lfSamples = tk.LabelFrame(frame, text='Samples')
gui.configureWeigths(frame)
lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
self.samplesTree = self._addBoundTree(lfSamples, SamplesTreeProvider,
10, fitting=self.fitting)
self.samplesTree.itemDoubleClick = self._onSampleDoubleClick
self.samplesTree.itemClick = self._onSampleClick
plotFrame = tk.Frame(lfSamples)
plotFrame.grid(row=1, column=0, sticky='ws', padx=5, pady=5)
# Add a combobox with the variable for time
timeVars = [v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_TIME]
timeVars += [v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_MEASUREMENT]
measureVars = [v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_MEASUREMENT]
def addVar(text, col, choices):
varFrame = tk.Frame(plotFrame)
varFrame.grid(row=0, column=col, sticky='new')
label = tk.Label(varFrame, text=text, font=self.fontBold)
label.grid(row=0, column=0, padx=5, pady=2, sticky='nw')
combo = ComboBox(varFrame, choices, width=10)
combo.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
radioVar = tk.IntVar()
radio = tk.Checkbutton(varFrame, text='Log10', variable=radioVar)
radio.grid(row=0, column=2, sticky='nw', padx=5, pady=5)
return combo, radio, radioVar
self.timeWidget = addVar('Time variable', 0, timeVars)
self.measureWidget = addVar('Measure variable', 1, measureVars)
self.measureWidget[2].set(True)
self.plotButton = Button(plotFrame, ' Plot ', font=self.fontBold,
command=self._onPlotClick,
tooltip='Select one or more samples to plot '
'their measures of the selected '
'variables (optionally in log).')
self.plotButton.grid(row=0, column=2, sticky='ne', padx=5)
self.plotSummaryButton = Button(plotFrame, ' Summary Plot ',
font=self.fontBold,
command=self._onPlotSummaryClick,
tooltip='Select several samples to plot'
' their statistics'
' (min, max, avg and std).')
self.plotSummaryButton.grid(row=1, column=2, sticky='ne',
padx=5, pady=5)
#frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
content.add(frame, sticky='news', padx=5, pady=5)
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
gui.configureWeigths(frame)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=0, column=0, sticky='ne')
closeButton = Button(buttonsFrame, 'Close', command=self.close,
imagePath='fa-times.png')
closeButton.grid(row=0, column=0, sticky='ne', padx=5)
self.newButton = HotButton(buttonsFrame, ' New Experiment ',
command=self._onCreateClick,
tooltip='Create a new experiment with the '
'selected samples. You can also edit'
'title and comment.')
self.newButton.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
def _createFittingButtonsFrame(self, content):
buttonsFrame = tk.Frame(content)
buttonsFrame.grid(row=0, column=0, sticky='ne')
plotValuesButton = Button(buttonsFrame, 'Plot Fit',
command=self._onPlotFitClick)
plotValuesButton.grid(row=0, column=0, sticky='sew', padx=5, pady=5)
openValuesButton = Button(buttonsFrame, 'Open Fit',
command=self._onOpenFitClick)
openValuesButton.grid(row=1, column=0, sticky='sew', padx=5, pady=5)
return buttonsFrame
def _addLabel(self, parent, text, r, c):
label = tk.Label(parent, text=text, font=self.fontBold)
label.grid(row=r, column=c, padx=5, pady=5, sticky='ne')
return label
def _addBoundTree(self, parent, ProviderClass, height, **kwargs):
bt = BoundTree(parent, ProviderClass(self.experiment, **kwargs),
height=height)
bt.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(parent)
return bt
def getUnits(self, varName):
return self.experiment.variables[varName].getUnitsString()
def getLabel(self, varName, useLog):
varLabel = '%s [%s]' % (varName, self.getUnits(varName))
if useLog:
varLabel = "log10(%s)" % varLabel
return varLabel
def getTimeVarName(self):
return self.timeWidget[0].getText()
def useTimeLog(self):
return self.timeWidget[2].get()
def getTimeLabel(self):
return self.getLabel(self.getTimeVarName(), self.useTimeLog())
def getMeasureVarName(self):
return self.measureWidget[0].getText()
def useMeasureLog(self):
return self.measureWidget[2].get()
def getMeasureLabel(self):
return self.getLabel(self.getMeasureVarName(), self.useMeasureLog())
def getPlotValues(self, sample):
xValues, yValues = sample.getXYValues(self.getTimeVarName(),
self.getMeasureVarName())
xValues=xValues[0] # From [array(...)] to array(...)
yValues=yValues[0]
useMeasureLog = self.useMeasureLog()
useTimeLog = self.useTimeLog()
if not (useMeasureLog or useTimeLog):
return xValues, yValues
# If log will be used either for time or measure var
# we need to filter elements larger than 0
newXValues = []
newYValues = []
def _value(v, useLog):
if useLog:
return math.log10(v) if v > 0 else None
return v
for x, y in izip(xValues, yValues):
x = _value(x, useTimeLog)
y = _value(y, useMeasureLog)
if x is not None and y is not None:
newXValues.append(x)
newYValues.append(y)
return newXValues, newYValues
def _onPlotClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
if self.plotter is None or self.plotter.isClosed():
self.plotter = EmPlotter()
doShow = True
ax = self.plotter.createSubPlot("Plot", self.getTimeLabel(),
self.getMeasureLabel())
self.plotDict = {}
else:
doShow = False
ax = self.plotter.getLastSubPlot()
samples = [self.experiment.samples[k] for k in sampleKeys]
for s in samples:
if not s.sampleName in self.plotDict:
x, y = self.getPlotValues(s)
ax.plot(x, y, label=s.sampleName)
self.plotDict[s.sampleName] = True
leg = ax.legend()
if leg:
leg.draggable()
if doShow:
self.plotter.show()
else:
self.plotter.draw()
else:
self.showInfo("Please select some sample(s) to plot.")
def _onPlotSummaryClick(self, e=None):
sampleKeys = self.samplesTree.selection()
n = len(sampleKeys)
if n == 1:
self.showInfo("Please select several samples to plot.")
else:
if n > 1:
samples = [self.experiment.samples[k] for k in sampleKeys]
else:
samples = self.experiment.samples.values()
dataDict = {} # key will be time values
for s in samples:
xValues, yValues = self.getPlotValues(s)
for x, y in izip(xValues, yValues):
if x in dataDict:
dataDict[x].append(y)
else:
dataDict[x] = [y]
sortedTime = sorted(dataDict.keys())
# We will store five values (min, 25%, 50%, 75%, max)
# for each of the time entries computed
percentileList = [0, 25, 50, 75, 100]
Y = np.zeros((len(sortedTime), 5))
for i, t in enumerate(sortedTime):
Y[i,:] = np.percentile(dataDict[t], percentileList)
plotter = EmPlotter()
ax = plotter.createSubPlot("Summary Plot", self.getTimeLabel(),
self.getMeasureLabel())
ax.plot(sortedTime, Y[:, 0], 'r--', label="Minimum")
ax.plot(sortedTime, Y[:, 1], 'b--', label="25%")
ax.plot(sortedTime, Y[:, 2], 'g', label="50% (Median)")
ax.plot(sortedTime, Y[:, 3], 'b--', label="75%")
ax.plot(sortedTime, Y[:, 4], 'r--', label="Maximum")
ax.legend()
plotter.show()
def _onCreateClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys and self.callback:
self.callback()
else:
self.showInfo("Please select some sample(s) to create a new experiment.")
def _onSampleClick(self, obj):
# In fitting mode we need to display some information for
# the given sample fit
if self.fitting:
selection = self.samplesTree.selection()
if selection:
sampleKey = selection[0]
sampleFit = self.fitting.getSampleFit(sampleKey)
textMsg = sampleFit.getBasicInfo()
else:
textMsg = 'Select one of the samples to see more information.'
self.fittingText.setReadOnly(False)
self.fittingText.setText(textMsg)
self.fittingText.setReadOnly(True)
if not (self.plotter is None or self.plotter.isClosed()):
self._onPlotClick()
def _onSampleDoubleClick(self, obj):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
MeasureWindow(masterWindow=self,
sample=self.experiment.samples[sampleKeys[0]]).show()
def _onPlotFitClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
def _value(v, useLog):
if useLog:
return math.log10(v) if v > 0 else None
return v
def _values(values, useLog=self.useMeasureLog()):
return [_value(float(x), useLog) for x in values]
def _plot(varLabelX, varLabelY, x, y, yp):
plotter = EmPlotter()
ax = plotter.createSubPlot("Plot", varLabelX, varLabelY)
xValues = _values(x, useLog=self.useTimeLog())
ax.plot(xValues, _values(y), 'x', label="Observations")
idx = np.argsort(xValues)
ypValues = _values(yp)
ax.plot(np.asarray(xValues)[idx], np.asarray(ypValues)[idx], 'g', label="Fit")
leg = ax.legend()
if leg:
leg.draggable()
plotter.show()
# Get first selected element
fit = self.fitting.getSampleFit(sampleKeys[0])
if fit==None:
return
varLabelX = self.getLabel(self.fitting.predictor.varName,
self.useTimeLog())
if type(self.fitting.predicted)==list:
i=0
for v in self.fitting.predicted:
varLabelY = self.getLabel(v.varName, self.useMeasureLog())
_plot(varLabelX, varLabelY, fit.x[i], fit.y[i], fit.yp[i])
i+=1
else:
varLabelY = self.getLabel(self.fitting.predicted.varName,
self.useMeasureLog())
_plot(varLabelX, varLabelY, fit.x[0], fit.y[0], fit.yp[0])
else:
self.showInfo("Please select some sample(s) to plot.")
def _onOpenFitClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
# Get first selected element
fit = self.fitting.getSampleFit(sampleKeys[0])
FitWindow(masterWindow=self,
fitting=self.fitting, sampleFit=fit).show()
else:
self.showInfo("Please select some sample(s) to plot.")
def _onClosing(self):
if self.plotter:
self.plotter.close()
gui.Window._onClosing(self)
class ExperimentWindow(gui.Window):
""" This class creates a Window that will display some Point's
contained in a Data object.
It will allow to launch 1D, 2D and 3D plots by selecting any
combination of the x1, x2...xn from the Point dimension.
Points can be selected by either Click and Drag in the Scatter plot or..
by creating an Expression.
Finally, there is a button 'Create Cluster' that will call a callback
fuction to take care of it.
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(420, 200), **kwargs)
self.experiment = kwargs.get('experiment')
self.fitting = kwargs.get('fitting', None)
self.callback = kwargs.get('callback', None)
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
content.columnconfigure(0, weight=1)
content.rowconfigure(0, weight=1)
self.plotter = None
def _createContent(self, content):
# Create and fill the frame containing the Experiment
# info, variables and doses
p = tk.PanedWindow(content, orient=tk.VERTICAL, bg='white')
p.grid(row=0, column=0, sticky='news', padx=5, pady=5)
self._createTopFrame(p)
# Create the middle frame containing the Samples Box
self._createSamplesFrame(p)
# Create the last frame with the buttons
self._createButtonsFrame(content)
#self._updateSelectionLabel()
def _createTopFrame(self, content):
frame = tk.Frame(content)
frame.columnconfigure(0, weight=1)
frame.rowconfigure(0, weight=1)
tab = ttk.Notebook(frame)
tab.grid(row=0, column=0, sticky='news', padx=5, pady=5)
def addTab(label):
lf = tk.Frame(tab)
tab.add(lf, text=label)
return lf
lfGeneral = addTab('General')
self._addLabel(lfGeneral, 'Title', 0, 0)
self._titleVar = tk.StringVar()
if 'title' in self.experiment.general:
self._titleVar.set(self.experiment.general['title'])
else:
self._titleVar.set("")
titleEntry = tk.Entry(lfGeneral,
width=26,
textvariable=self._titleVar,
bg='white')
titleEntry.grid(row=0, column=1, sticky='nw', padx=5, pady=(5, 0))
self._addLabel(lfGeneral, 'Comment', 1, 0)
commentText = gui.text.Text(lfGeneral, width=30, height=3, bg='white')
if 'comment' in self.experiment.general:
commentText.setText(self.experiment.general['comment'])
else:
commentText.setText("")
commentText.grid(row=1, column=1, sticky='nw', padx=5, pady=(5, 0))
self._commentText = commentText
lfVars = addTab('Variables')
self.varsTree = self._addBoundTree(lfVars, VariablesTreeProvider, 5)
lfVias = addTab('Vias')
self.viasTree = self._addBoundTree(lfVias, ViasTreeProvider, 5)
lfDoses = addTab('Doses')
self.dosesTree = self._addBoundTree(lfDoses, DosesTreeProvider, 5)
lfGroups = addTab('Groups')
self.groupsTree = self._addBoundTree(lfGroups, GroupsTreeProvider, 5)
# Fitting tab
if self.fitting:
tabFitting = addTab('Fitting')
t = TaggedText(tabFitting, width=80, height=10, bg='white')
t.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
t.setText('Select one of the samples to see more information.')
t.setReadOnly(True)
self.fittingText = t
# Buttons for fitting
buttonsFrame = self._createFittingButtonsFrame(tabFitting)
buttonsFrame.grid(row=0, column=1, sticky='news', padx=5, pady=5)
#frame.grid(row=0, column=0, sticky='news', padx=5, pady=(10, 5))
content.add(frame, sticky='news', padx=5, pady=5)
def _createSamplesFrame(self, content):
frame = tk.Frame(content)
#frame = tk.LabelFrame(content, text='General')
lfSamples = tk.LabelFrame(frame, text='Samples')
gui.configureWeigths(frame)
lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
self.samplesTree = self._addBoundTree(lfSamples,
SamplesTreeProvider,
10,
fitting=self.fitting)
self.samplesTree.itemDoubleClick = self._onSampleDoubleClick
self.samplesTree.itemClick = self._onSampleClick
plotFrame = tk.Frame(lfSamples)
plotFrame.grid(row=1, column=0, sticky='ws', padx=5, pady=5)
# Add a combobox with the variable for time
timeVars = [
v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_TIME
]
timeVars += [
v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_MEASUREMENT
]
measureVars = [
v.varName for v in self.experiment.variables.values()
if v.role == v.ROLE_MEASUREMENT
]
def addVar(text, col, choices):
varFrame = tk.Frame(plotFrame)
varFrame.grid(row=0, column=col, sticky='new')
label = tk.Label(varFrame, text=text, font=self.fontBold)
label.grid(row=0, column=0, padx=5, pady=2, sticky='nw')
if len(choices) == 0:
choices = ['']
combo = ComboBox(varFrame, choices, width=10)
combo.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
radioVar = tk.IntVar()
radio = tk.Checkbutton(varFrame, text='Log10', variable=radioVar)
radio.grid(row=0, column=2, sticky='nw', padx=5, pady=5)
return combo, radio, radioVar
self.timeWidget = addVar('Time variable', 0, timeVars)
self.measureWidget = addVar('Measure variable', 1,
list(set(measureVars + timeVars)))
self.measureWidget[2].set(True)
self.plotButton = Button(plotFrame,
' Plot ',
font=self.fontBold,
command=self._onPlotClick,
tooltip='Select one or more samples to plot '
'their measures of the selected '
'variables (optionally in log).')
self.plotButton.grid(row=0, column=2, sticky='ne', padx=5)
self.useCurrentPlotVar = tk.IntVar()
self.useCurrentPlot = tk.Checkbutton(plotFrame,
text='Use current plot',
variable=self.useCurrentPlotVar)
self.useCurrentPlot.grid(row=1, column=0, sticky='nw', padx=5, pady=5)
self.plotSummaryButton = Button(
plotFrame,
' Summary Plot ',
font=self.fontBold,
command=self._onPlotSummaryClick,
tooltip='Select several samples to plot'
' their statistics'
' (min, max, avg and std).')
self.plotSummaryButton.grid(row=1,
column=2,
sticky='ne',
padx=5,
pady=5)
#frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
content.add(frame, sticky='news', padx=5, pady=5)
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
gui.configureWeigths(frame)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=0, column=0, sticky='ne')
closeButton = Button(buttonsFrame,
'Close',
command=self.close,
imagePath='fa-times.png')
closeButton.grid(row=0, column=0, sticky='ne', padx=5)
self.newButton = HotButton(buttonsFrame,
' New Experiment ',
command=self._onCreateClick,
tooltip='Create a new experiment with the '
'selected samples. You can also edit'
'title and comment.')
self.newButton.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=1, column=0, sticky='news', padx=5, pady=5)
def _createFittingButtonsFrame(self, content):
buttonsFrame = tk.Frame(content)
buttonsFrame.grid(row=0, column=0, sticky='ne')
plotValuesButton = Button(buttonsFrame,
'Plot Fit',
command=self._onPlotFitClick)
plotValuesButton.grid(row=0, column=0, sticky='sew', padx=5, pady=5)
openValuesButton = Button(buttonsFrame,
'Open Fit',
command=self._onOpenFitClick)
openValuesButton.grid(row=1, column=0, sticky='sew', padx=5, pady=5)
return buttonsFrame
def _addLabel(self, parent, text, r, c):
label = tk.Label(parent, text=text, font=self.fontBold)
label.grid(row=r, column=c, padx=5, pady=5, sticky='ne')
return label
def _addBoundTree(self, parent, ProviderClass, height, **kwargs):
bt = BoundTree(parent,
ProviderClass(self.experiment, **kwargs),
height=height)
bt.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(parent)
return bt
def getUnits(self, varName):
return self.experiment.variables[varName].getUnitsString()
def getLabel(self, varName, useLog):
varLabel = '%s [%s]' % (varName, self.getUnits(varName))
if useLog:
varLabel = "log10(%s)" % varLabel
return varLabel
def getTimeVarName(self):
return self.timeWidget[0].getText()
def useTimeLog(self):
return self.timeWidget[2].get()
def getTimeLabel(self):
return self.getLabel(self.getTimeVarName(), self.useTimeLog())
def getMeasureVarName(self):
return self.measureWidget[0].getText()
def useMeasureLog(self):
return self.measureWidget[2].get()
def getMeasureLabel(self):
return self.getLabel(self.getMeasureVarName(), self.useMeasureLog())
def getPlotValues(self, sample):
xValues, yValues = sample.getXYValues(self.getTimeVarName(),
self.getMeasureVarName())
xValues = xValues[0] # From [array(...)] to array(...)
yValues = yValues[0]
useMeasureLog = self.useMeasureLog()
useTimeLog = self.useTimeLog()
if not (useMeasureLog or useTimeLog):
return xValues, yValues
# If log will be used either for time or measure var
# we need to filter elements larger than 0
newXValues = []
newYValues = []
def _value(v, useLog):
if useLog:
return math.log10(v) if v > 0 else None
return v
for x, y in izip(xValues, yValues):
x = _value(x, useTimeLog)
y = _value(y, useMeasureLog)
if x is not None and y is not None:
newXValues.append(x)
newYValues.append(y)
return newXValues, newYValues
def reuseFigure(self):
return None if not self.useCurrentPlotVar.get() else 'active'
def _onPlotClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
if self.plotter is None or self.plotter.isClosed():
self.plotter = EmPlotter(style='seaborn-whitegrid',
figure=self.reuseFigure())
doShow = True
ax = self.plotter.createSubPlot("Plot", self.getTimeLabel(),
self.getMeasureLabel())
self.plotDict = {}
else:
doShow = False
ax = self.plotter.getLastSubPlot()
samples = [self.experiment.samples[k] for k in sampleKeys]
for s in samples:
if not s.sampleName in self.plotDict or not doShow:
x, y = self.getPlotValues(s)
label = s.sampleName
if not doShow:
label += " " + self.getTimeVarName(
) + " vs " + self.getMeasureVarName()
ax.plot(x, y, label=label)
self.plotDict[s.sampleName] = True
leg = ax.legend()
if leg:
leg.set_draggable(True)
if doShow:
self.plotter.show()
else:
self.plotter.draw()
else:
self.showInfo("Please select some sample(s) to plot.")
def _onPlotSummaryClick(self, e=None):
sampleKeys = self.samplesTree.selection()
n = len(sampleKeys)
if n == 1:
self.showInfo("Please select several samples to plot.")
else:
if n > 1:
samples = [self.experiment.samples[k] for k in sampleKeys]
else:
samples = list(self.experiment.samples.values())
xmin = 1e38
xmax = -1e38
for s in samples:
xValues, _ = self.getPlotValues(s)
xmin = min(xmin, min(xValues))
xmax = max(xmax, max(xValues))
dataDict = {} # key will be time values
xrange = np.arange(xmin, xmax, (xmax - xmin) / 300.0)
for s in samples:
xValues, yValues = self.getPlotValues(s)
xValuesUnique, yValuesUnique = uniqueFloatValues(
xValues, yValues)
B = InterpolatedUnivariateSpline(xValuesUnique,
yValuesUnique,
k=1)
yrange = B(xrange)
for x, y in izip(xrange, yrange):
if x in dataDict:
dataDict[x].append(y)
else:
dataDict[x] = [y]
sortedTime = sorted(dataDict.keys())
# We will store five values (min, 25%, 50%, 75%, max)
# for each of the time entries computed
percentileList = [0, 25, 50, 75, 100]
Y = np.zeros((len(sortedTime), 5))
for i, t in enumerate(sortedTime):
Y[i, :] = np.percentile(dataDict[t], percentileList)
plotter = EmPlotter(style='seaborn-whitegrid',
figure=self.reuseFigure())
# *** Pending
ax = plotter.createSubPlot("Summary Plot", self.getTimeLabel(),
self.getMeasureLabel())
ax.plot(sortedTime, Y[:, 0], 'r--', label="Minimum")
ax.plot(sortedTime, Y[:, 1], 'b--', label="25%")
ax.plot(sortedTime, Y[:, 2], 'g', label="50% (Median)")
ax.plot(sortedTime, Y[:, 3], 'b--', label="75%")
ax.plot(sortedTime, Y[:, 4], 'r--', label="Maximum")
ax.grid(True)
ax.legend()
plotter.show()
def _onCreateClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys and self.callback:
self.callback()
else:
self.showInfo(
"Please select some sample(s) to create a new experiment.")
def _onSampleClick(self, obj):
# In fitting mode we need to display some information for
# the given sample fit
if self.fitting:
selection = self.samplesTree.selection()
if selection:
sampleKey = selection[0]
sampleFit = self.fitting.getSampleFit(sampleKey)
textMsg = sampleFit.getBasicInfo()
else:
textMsg = 'Select one of the samples to see more information.'
self.fittingText.setReadOnly(False)
self.fittingText.setText(textMsg)
self.fittingText.setReadOnly(True)
if not (self.plotter is None or self.plotter.isClosed()):
self._onPlotClick()
def _onSampleDoubleClick(self, obj):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
MeasureWindow(
masterWindow=self,
sample=self.experiment.samples[sampleKeys[0]]).show()
def _onPlotFitClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
def _value(v, useLog):
if useLog:
return math.log10(v) if v > 0 else None
return v
def _values(values, useLog=self.useMeasureLog()):
return [_value(float(x), useLog) for x in values]
def _plot(varLabelX, varLabelY, x, y, yp):
plotter = EmPlotter(style='seaborn-whitegrid',
figure=self.reuseFigure())
ax = plotter.createSubPlot("Plot", varLabelX, varLabelY)
xValues = _values(x, useLog=self.useTimeLog())
ax.plot(xValues, _values(y), 'x', label="Observations")
idx = np.argsort(xValues)
ypValues = _values(yp)
ax.plot(np.asarray(xValues)[idx],
np.asarray(ypValues)[idx],
'g',
label="Fit")
leg = ax.legend()
if leg:
leg.set_draggable(True)
plotter.show()
# Get first selected element
fit = self.fitting.getSampleFit(sampleKeys[0])
if fit == None:
return
varLabelX = self.getLabel(self.fitting.predictor.varName,
self.useTimeLog())
if type(self.fitting.predicted) == list:
i = 0
for v in self.fitting.predicted:
varLabelY = self.getLabel(v.varName, self.useMeasureLog())
_plot(varLabelX, varLabelY, fit.x[i], fit.y[i], fit.yp[i])
i += 1
else:
varLabelY = self.getLabel(self.fitting.predicted.varName,
self.useMeasureLog())
_plot(varLabelX, varLabelY, fit.x[0], fit.y[0], fit.yp[0])
else:
self.showInfo("Please select some sample(s) to plot.")
def _onOpenFitClick(self, e=None):
sampleKeys = self.samplesTree.selection()
if sampleKeys:
# Get first selected element
fit = self.fitting.getSampleFit(sampleKeys[0])
FitWindow(masterWindow=self, fitting=self.fitting,
sampleFit=fit).show()
else:
self.showInfo("Please select some sample(s) to plot.")
def _onClosing(self):
if self.plotter:
self.plotter.close()
gui.Window._onClosing(self)
def __init__(self, title, parent=None, weight=True, minsize=(400, 150),
icon="scipion_bn.xbm", **args):
"""
We assume the parent should be ProjectsView
"""
Window.__init__(self, title, parent.windows, weight=weight,
icon=icon, minsize=minsize, enableQueue=True)
self.root['background'] = 'white'
self.parent = parent
# Dirty hack, need to add a slash for the explorer to pick up the right default path.
self.projectsPath = getHomePath()+"/"
self.projLocation = tk.StringVar()
self.projLocation.set(self.projectsPath)
self.projName = tk.StringVar()
self.projName.set('')
self.searchLocation = tk.StringVar()
self.searchLocation.set('')
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.columnconfigure(1, weight=1)
content.config(bg='white')
content.grid(row=0, column=0, sticky='news',
padx=5, pady=5)
# Path explorer
labelProjectLocation = tk.Label(content, text="Project location", bg='white', bd=0)
labelProjectLocation.grid(row=0, column=0, sticky='nw', padx=5, pady=5)
self.entryBrowse = tk.Entry(content, bg=cfgEntryBgColor, width=40, textvariable=self.projLocation)
self.entryBrowse.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
self.btnBrowse = IconButton(content, 'Browse', Icon.ACTION_BROWSE, highlightthickness=0,
command=self._browseProjectLocation)
self.btnBrowse.grid(row=0, column=2, sticky='e', padx=5, pady=5)
# Copy files check
labelCheck = tk.Label(content, text="Copy project", bg='white', borderwidth=0)
labelCheck.grid(row=1, column=0, sticky='nw', padx=5, pady=5)
self.tkCheckVar = tk.IntVar()
btnCheck = tk.Checkbutton(content, variable=self.tkCheckVar, highlightthickness=0, activebackground='white',
bg='white', bd=0)
btnCheck.grid(row=1, column=1, sticky='nw', padx=0, pady=5)
btnCopyHelp = IconButton(content, Message.LABEL_BUTTON_HELP, Icon.ACTION_HELP, highlightthickness=0,
command=lambda: self.showInfo('If checked, \"Project location\" will be copied. Otherwise a soft link to it will be created.'))
btnCopyHelp.grid(row=1, column=3, sticky='e', padx=2, pady=2)
# Project name
labelName = tk.Label(content, text='Project name (Optional)', bg='white', bd=0)
labelName.grid(row=2, column=0, sticky='nw', padx=5, pady=5)
entryName = tk.Entry(content, bg='white', width=20, textvariable=self.projName)
entryName.grid(row=2, column=1, sticky='nw', padx=5, pady=5)
# Path to search for raw data and restore broken links.
labelSearchLocation = tk.Label(content, text="Raw files location (Optional)", bg='white', bd=0)
labelSearchLocation.grid(row=3, column=0, sticky='nw', padx=5, pady=5)
self.entrySearchLocation = tk.Entry(content, bg='white', width=40, textvariable=self.searchLocation)
self.entrySearchLocation.grid(row=3, column=1, sticky='nw', padx=5, pady=5)
self.btnSearch = IconButton(content, 'Browse', Icon.ACTION_BROWSE, highlightthickness=0, command=self._browseSearchLocation)
self.btnSearch.grid(row=3, column=2, sticky='e', padx=5, pady=5)
btnSearchHelp = IconButton(content, Message.LABEL_BUTTON_HELP, Icon.ACTION_HELP, highlightthickness=0,
command=lambda: self.showInfo('Optional: Folder where raw files, binaries (movies, migcrographs,..) can be found. Used to repair broken links.'))
btnSearchHelp.grid(row=3, column=3, sticky='e', padx=2, pady=2)
self.initial_focus = entryName
btnCheck.select()
btnFrame = tk.Frame(content)
btnFrame.columnconfigure(0, weight=1)
btnFrame.grid(row=4, column=0, sticky='sew', padx=5, pady=(0, 5), columnspan=2)
btnFrame.config(bg='white')
# Create buttons
btnSelect = HotButton(btnFrame, 'Import', Icon.BUTTON_SELECT, command=self._select)
btnSelect.grid(row=0, column=0, sticky='e', padx=5, pady=5)
btnCancel = Button(btnFrame, 'Cancel', Icon.BUTTON_CANCEL, command=self.close)
btnCancel.grid(row=0, column=1, sticky='e', padx=5, pady=5)
def _fillContent(self, content):
frame = tk.Frame(content, bg='white')
frame.grid(row=0, column=0, sticky='news', padx=10, pady=15)
frame.columnconfigure(0, minsize=200)
self._lastRow = 0
def _createLabel(text, bold=False):
boldStr = 'bold' if bold else ''
return tk.Label(frame,
text=text,
font="helvetica 12 %s" % boldStr,
bg='white')
def __addLabeledWidget(text, widget=None, pady=5, bold=False):
label = _createLabel(text, bold)
label.grid(row=self._lastRow, column=0, sticky='ne', pady=pady)
if widget is not None:
widget.grid(row=self._lastRow,
column=1,
sticky='nw',
pady=pady,
padx=5)
self._lastRow += 1
return label
def __createCombobox(options, readOnly=True, callback=None, width=38):
var = tk.StringVar()
s = ttk.Style()
state = 'readonly' if readOnly else 'edit'
combo = ttk.Combobox(frame,
textvariable=var,
state=state,
width=width)
combo['values'] = options
combo.var = var
if callback:
combo.bind('<<ComboboxSelected>>', callback)
return combo
def _getSessionAction():
micIndex = self._micChooser.getSelectedIndex()
if micIndex is None:
return "Select Microscope"
camIndex = self._switchCam.widgets[micIndex].getSelectedIndex()
if camIndex is None:
return "Select Camera"
resourceId = self._micChooser.getSelectedIndex() + 1
if resourceId in self._bookings:
b = self._bookings[resourceId]
values = {
'CEM': b['application_code'],
'Owner': b['owner']['name'],
'Creator': b['creator']['name']
}
else:
values = {}
b = None
for k, v in self._textVars.items():
v.set(values.get(k, '-'))
self._current_booking = b
if b is None:
return ("There is no booking for this microscope. "
"Check the booking system. ")
return None
def _checkSessionAction():
action = _getSessionAction()
if action is None:
msg = self._createSession().getId()
else:
msg = action
self._sessionLabel.config(fg='red' if action else 'green')
self._sessionVar.set(msg)
self._createStatus = 'disabled' if action else 'normal'
btn = getattr(self, '_newSessionBtn', None)
if btn is not None:
btn.config(state=self._createStatus)
class Switcher(tk.Frame):
def __init__(self, *args, **kwargs):
tk.Frame.__init__(self, *args, **kwargs)
self._index = -1
self.widgets = []
def add(self, widget):
self.widgets.append(widget)
def set(self, i):
if i < 0 or i >= len(self.widgets):
raise Exception("Invalid index")
if self._index >= 0:
self.widgets[self._index].grid_forget()
self.widgets[i].grid(row=0, column=0, sticky='news')
self._index = i
def _showCameraOptions(chooser):
""" Show the correct camera options depending on the
selected microscope. """
i = chooser.getSelectedIndex()
self._switchCam.set(i)
_checkSessionAction()
def _onChange(*args):
if hasattr(self, '_sessionLabel'):
_checkSessionAction()
def _onChangePreprocessing(*args):
""" Called when the selection is changed. """
i = self._prepChooser.getSelectedIndex()
self._switchPre.set(i)
EXTRA_PAD = 30
f1 = OptionChooser(frame, bg='white', optionWidth=200)
f1.onSelectionChanged(_showCameraOptions)
f1.addOption('Krios α', self.data.getResourceFile("titan_small.gif"))
f1.addOption('Krios β', self.data.getResourceFile("titan_small.gif"))
f1.addOption('Talos', self.data.getResourceFile("talos_small.gif"))
__addLabeledWidget("Microscope", f1, bold=True)
self._micOrder = {TITAN_A: 0, TITAN_B: 1, TALOS: 2}
self._micChooser = f1
self._switchCam = Switcher(frame)
def _addCamChooser(*options):
oc = OptionChooser(self._switchCam, bg='white', optionWidth=200)
for o in options:
oc.addOption(o)
self._switchCam.add(oc)
oc.selectIndex(0)
oc.onSelectionChanged(_onChange)
for mic in MICROSCOPES:
_addCamChooser(*MIC_CAMERAS[mic])
#camChoosers = [_createChooser(*MIC_CAMERAS[mic]) for mic in MICROSCOPES]
# f2 = camChoosers[0]
# self._camRow = self._lastRow
__addLabeledWidget("Camera", self._switchCam)
# --------- Load some data ---------------
from emhub.client import DataClient
from emhub.utils import datetime_to_isoformat
apiJsonFile = getDataFile('api.json')
with open(apiJsonFile) as f:
apiJson = json.load(f)
dc = DataClient(apiJson['emhub']['url'])
dc.login(apiJson['emhub']['user'], apiJson['emhub']['password'])
start = datetime_to_isoformat(self.data.date.replace(hour=0))
end = datetime_to_isoformat(self.data.date.replace(hour=23, minute=59))
r = dc.request('get_bookings_range',
jsonData={
'start': start,
'end': end
})
self._bookings = {
b['resource']['id']: b
for b in r.json() if b['type'] == 'booking'
}
users = {}
def get_user(user_id):
if user_id not in users:
r = dc.request('get_users',
jsonData={'condition': 'id=%s' % user_id})
users[user_id] = r.json()[0]
return users[user_id]
def get_application_code(b):
# Take only the first part of the application label
# (because it can contains the alias in parenthesis)
m = re.search("\([^,]+(,([^,]*))\)", b['title'])
return 'fac' if m is None else m.group(2).upper().strip()
for b in self._bookings.values():
b['owner'] = get_user(b['owner']['id'])
b['creator'] = get_user(b['creator']['id'])
b['application_code'] = get_application_code(b)
dc.logout()
self._textVars = {}
def _addLabeledText(label, text):
var = tk.StringVar()
var.set(text)
labelWidget = _createLabel(text)
labelWidget.config(textvariable=var)
self._textVars[label] = var
__addLabeledWidget(label, labelWidget, bold=True)
_addLabeledText("CEM", '')
_addLabeledText("Owner", '')
_addLabeledText("Creator", '')
# --------- Session block ----------------
self._sessionVar = tk.StringVar()
self._sessionLabel = tk.Label(frame,
textvariable=self._sessionVar,
bg='white',
fg='red')
__addLabeledWidget("Session ID",
self._sessionLabel,
pady=(EXTRA_PAD, 0),
bold=True)
# --------- Preprocessing block ----------------
f4 = OptionChooser(frame, bg='white', optionWidth=200)
f4.addOption('Scipion', self.data.getResourceFile("scipion_logo.gif"))
f4.addOption('Scipion (custom)',
self.data.getResourceFile("scipion_logo.gif"))
f4.addOption(LABEL_NONE, self.data.getResourceFile("none.gif"))
f4.onSelectionChanged(_onChangePreprocessing)
self._prepChooser = f4
__addLabeledWidget("Pre-processing",
f4,
pady=(EXTRA_PAD, 0),
bold=True)
self._switchPre = Switcher(frame, bg='white')
def _addFrame():
preFrame = tk.Frame(self._switchPre, bg='white')
self._switchPre.add(preFrame)
return preFrame
preFrame1 = _addFrame()
preOptions = [("Motion correction",
['relion - motioncor', 'motioncor2']),
("CTF estimation", ['ctffind4', 'gctf'])]
self._preDict = {}
for row, (text, options) in enumerate(preOptions):
label = tk.Label(preFrame1,
text=text,
font="helvetica 12",
bg='white')
label.grid(row=row, column=0, sticky='ne')
v = tk.StringVar()
for i, o in enumerate(options):
rb = tk.Radiobutton(preFrame1,
text=o,
variable=v,
value=o,
bg='white')
rb.grid(row=row, column=i + 1, sticky='nw')
v.set(options[0])
self._preDict[text] = v
preFrame2 = _addFrame()
self._workflowVar = tk.StringVar()
entry = ttk.Entry(preFrame2, width=50, textvariable=self._workflowVar)
entry.grid(column=0, row=0)
def _onChoose(fileInfo):
self._workflowVar.set(fileInfo.getPath())
def _chooseWorkflow():
browser = FileBrowserWindow(
"Select the one of the predefined MTF files",
self.windows,
getDataFile('workflows'),
onSelect=_onChoose)
browser.show()
button = Button(preFrame2, text="Browse", command=_chooseWorkflow)
button.grid(column=1, row=0)
preFrame3 = _addFrame()
__addLabeledWidget('', self._switchPre)
f4.selectIndex(0)
f1.selectIndex(self._micOrder[self.data.microscope])
# Select Scipion as default for pre-processing
_checkSessionAction()
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
self.vars = {}
self.checkvars = []
self.microscope = None
self.configDict = self.windows.config
# Regular expression to validate username and sample name
self.re = re.compile('\A[a-zA-Z0-9][a-zA-Z0-9_-]+[a-zA-Z0-9]\Z')
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Header section
headerFrame = tk.Frame(self, bg='white')
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Create New Session"
headerText += " %s" % pwutils.prettyTime(dateFormat='%Y-%m-%d')
label = tk.Label(headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw',
bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Create New Session",
activebackground="dark grey",
activeforeground='black',
font=self.bigFontBold,
command=self._onAction)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Cancel project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
def _fillButtonsFrame(self, frame):
subframe = tk.Frame(frame)
subframe.grid(row=0, column=0, sticky='nw')
frame.columnconfigure(1, weight=1)
ctfBtn = Button(subframe, "CTF Monitor", command=self._monitorCTF)
ctfBtn.grid(row=0, column=0, sticky='nw', padx=(0, 5))
if self.protocol.createCtfMonitor() is None:
ctfBtn['state'] = 'disabled'
movieGainBtn = Button(subframe,
"Movie Gain Monitor",
command=self._monitorMovieGain)
movieGainBtn.grid(row=0, column=1, sticky='nw', padx=(0, 5))
if self.protocol.createMovieGainMonitor() is None:
movieGainBtn['state'] = 'disabled'
sysBtn = Button(subframe,
"System Monitor",
command=self._monitorSystem)
sysBtn.grid(row=0, column=2, sticky='nw', padx=(0, 5))
if self.protocol.createSystemMonitor() is None:
sysBtn['state'] = 'disabled'
htmlBtn = HotButton(subframe,
'Open HTML Report',
command=self._openHTML)
htmlBtn.grid(row=0, column=3, sticky='nw', padx=(0, 5))
closeBtn = self.createCloseButton(frame)
closeBtn.grid(row=0, column=1, sticky='ne')
class TrajectoriesWindow(gui.Window):
""" This class creates a Window that will display some Point's
contained in a Data object.
It will allow to draw and adjust trajectories along 2D axes.
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(420, 200), **kwargs)
self.dim = kwargs.get('dim')
self.data = kwargs.get('data')
self.pathData = PathData(dim=self.dim)
self.callback = kwargs.get('callback', None)
self.loadCallback = kwargs.get('loadCallback', None)
self.numberOfPoints = kwargs.get('numberOfPoints', 10)
self.plotter = None
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
content.columnconfigure(0, weight=1)
#content.rowconfigure(1, weight=1)
def _createContent(self, content):
self._createFigureBox(content)
self._createTrajectoriesBox(content)
def _addLabel(self, parent, text, r, c):
label = tk.Label(parent, text=text, font=self.fontBold)
label.grid(row=r, column=c, padx=5, pady=5, sticky='ne')
return label
def _createFigureBox(self, content):
frame = tk.LabelFrame(content, text='Figure')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Create the 'Axes' label
self._addLabel(frame, 'Axes', 0, 0)
# Create a listbox with x1, x2 ...
listbox = tk.Listbox(frame, height=5,
selectmode=tk.MULTIPLE, bg='white')
for x in range(1, self.dim+1):
listbox.insert(tk.END, 'x%d' % x)
listbox.grid(row=0, column=1, padx=5, pady=5, sticky='nw')
self.listbox = listbox
# Selection controls
self._addLabel(frame, 'Rejection', 1, 0)
# Selection label
self.selectionVar = tk.StringVar()
self.clusterLabel = tk.Label(frame, textvariable=self.selectionVar)
self.clusterLabel.grid(row=1, column=1, sticky='nw', padx=5, pady=(10, 5))
self._updateSelectionLabel()
# --- Expression
expressionFrame = tk.Frame(frame)
expressionFrame.grid(row=2, column=1, sticky='news')
tk.Label(expressionFrame, text='Expression').grid(row=0, column=0, sticky='ne')
self.expressionVar = tk.StringVar()
expressionEntry = tk.Entry(expressionFrame, textvariable=self.expressionVar,
width=30, bg='white')
expressionEntry.grid(row=0, column=1, sticky='nw')
helpText = 'e.g. x1>0 and x1<100 or x3>20'
tk.Label(expressionFrame, text=helpText).grid(row=1, column=1, sticky='nw')
# Buttons
buttonFrame = tk.Frame(frame)
buttonFrame.grid(row=5, column=1, sticky='sew', pady=(10, 5))
buttonFrame.columnconfigure(0, weight=1)
resetBtn = Button(buttonFrame, text='Reset', command=self._onResetClick)
resetBtn.grid(row=0, column=0, sticky='ne', padx=(5, 0))
updateBtn = Button(buttonFrame, text='Update Plot', imagePath='fa-refresh.png',
command=self._onUpdateClick)
updateBtn.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=0, column=0, sticky='new', padx=5, pady=(10, 5))
def _createTrajectoriesBox(self, content):
frame = tk.LabelFrame(content, text='Trajectories')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Animation name
self._addLabel(frame, 'Name', 0, 0)
self.animationVar = tk.StringVar()
clusterEntry = tk.Entry(frame, textvariable=self.animationVar,
width=30, bg='white')
clusterEntry.grid(row=0, column=1, sticky='nw', pady=5)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=1, column=1,
sticky='se', padx=5, pady=5)
buttonsFrame.columnconfigure(0, weight=1)
self.generateBtn = HotButton(buttonsFrame, text='Generate Animation', state=tk.DISABLED,
tooltip='Select trajectory points to generate the animations',
imagePath='fa-plus-circle.png', command=self._onCreateClick)
self.generateBtn.grid(row=0, column=1, padx=5)
self.loadBtn = Button(buttonsFrame, text='Load', imagePath='fa-folder-open.png',
tooltip='Load a generated animation.',command=self._onLoadClick)
self.loadBtn.grid(row=0, column=2, padx=5)
self.closeBtn = Button(buttonsFrame, text='Close', imagePath=Icon.ACTION_CLOSE,
tooltip='Close window', command=self.close)
self.closeBtn.grid(row=0, column=3, padx=(5, 10))
frame.grid(row=1, column=0, sticky='new', padx=5, pady=(5, 10))
def _onResetClick(self, e=None):
""" Clean the expression and the current selection. """
self.expressionVar.set('')
self.pathData.clear()
for point in self.data.iterAll():
point.setState(Point.NORMAL)
self._onUpdateClick()
self.generateBtn.config(state=tk.DISABLED)
def _onCreateClick(self, e=None):
if self.callback:
self.callback()
def _onLoadClick(self, e=None):
if self.loadCallback:
self.loadCallback()
def setPathData(self, data):
self.pathData = data
def _evalExpression(self):
""" Evaluate the input expression and add
matching points to the selection.
"""
value = self.expressionVar.get().strip()
if value:
for point in self.data:
if point.eval(value):
point.setState(Point.DISCARDED)
def setDataIndex(self, indexName, value):
""" Set which point data index will be used as X, Y or Z. """
setattr(self.data, indexName, value)
setattr(self.pathData, indexName, value)
def _onUpdateClick(self, e=None):
components = self.listbox.curselection()
dim = len(components)
if not dim:
self.showWarning("Please select some Axis before update plots.")
else:
modeList = components
modeNameList = ['x%d' % (m+1) for m in components]
missingList = []
if missingList:
return [self.errorMessage("Invalid mode(s) *%s*\n." % (', '.join(missingList)),
title="Invalid input")]
if self.plotter is None or self.plotter.isClosed():
self.plotter = XmippNmaPlotter(data=self.data)
doShow = True
#self.plotter.useLastPlot = True
else:
self.plotter.clear()
doShow = False
# Actually plot
baseList = [basename(n) for n in modeNameList]
self.setDataIndex('XIND', modeList[0])
self.ps = None
if dim == 1:
self.plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.setDataIndex('YIND', modeList[1])
if dim == 2:
self._evalExpression()
self._updateSelectionLabel()
ax = self.plotter.createSubPlot("Click and drag to add points to the Cluster",
*baseList)
self.ps = PointPath(ax, self.data, self.pathData,
callback=self._checkNumberOfPoints)
elif dim == 3:
#del self.ps # Remove PointSelector
self.setDataIndex('ZIND', modeList[2])
self.plotter.plotArray3D("%s %s %s" % tuple(baseList), *baseList)
if doShow:
self.plotter.show()
else:
self.plotter.draw()
def _updateSelectionLabel(self):
self.selectionVar.set('%d / %d points' % (self.data.getDiscardedSize(),
self.data.getSize()))
def _checkNumberOfPoints(self):
""" Check that if the number of points was selected
and add new ones if needed.
"""
while (self.pathData.getSize() < self.numberOfPoints):
self.pathData.splitLongestSegment()
self._onUpdateClick()
self.generateBtn.config(state=tk.NORMAL)
def getAnimationName(self):
return self.animationVar.get().strip()
def setAnimationName(self, value):
self.animationVar.set(value)
def _onClosing(self):
if self.plotter:
self.plotter.close()
gui.Window._onClosing(self)
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, **kwargs)
self.windows = windows
self.manager = windows.manager
self.data = windows.data
self.root = windows.root
self.vars = {}
self.checkvars = []
self._createStatus = 'disabled'
# Regular expression to validate username and sample name
self.re = re.compile('\A[a-zA-Z][a-zA-Z0-9_-]+\Z')
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
bigfont = tkFont.Font(family="Helvetica", size=12)
#self.option_add("*TCombobox*Listbox*Font", bigfont)
self.option_add("*Font", bigfont)
self.manager = Manager()
# Header section
headerFrame = tk.Frame(self)
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Create New Session"
headerText += " %s" % pwutils.prettyTime(dateFormat='%Y-%m-%d')
label = tk.Label(
headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw', #bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
versionText = 'version: %s' % VERSION
label2 = tk.Label(
headerFrame,
text=versionText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw', # bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
headerFrame.columnconfigure(1, weight=1)
label2.grid(row=0, column=1, sticky='ne', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Create New Session",
font=self.bigFontBold,
command=self._onAction,
state=self._createStatus)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
self._newSessionBtn = btn
# Add the Import project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
class TrajectoriesWindow(gui.Window):
""" This class creates a Window that will display some Point's
contained in a Data object.
It will allow to draw and adjust trajectories along 2D axes.
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(420, 200), **kwargs)
self.dim = kwargs.get('dim')
self.data = kwargs.get('data')
self.pathData = PathData(dim=self.dim)
self.callback = kwargs.get('callback', None)
self.loadCallback = kwargs.get('loadCallback', None)
self.numberOfPoints = kwargs.get('numberOfPoints', 10)
self.plotter = None
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
content.columnconfigure(0, weight=1)
#content.rowconfigure(1, weight=1)
def _createContent(self, content):
self._createFigureBox(content)
self._createTrajectoriesBox(content)
def _addLabel(self, parent, text, r, c):
label = tk.Label(parent, text=text, font=self.fontBold)
label.grid(row=r, column=c, padx=5, pady=5, sticky='ne')
return label
def _createFigureBox(self, content):
frame = tk.LabelFrame(content, text='Figure')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Create the 'Axes' label
self._addLabel(frame, 'Axes', 0, 0)
# Create a listbox with x1, x2 ...
listbox = tk.Listbox(frame, height=5,
selectmode=tk.MULTIPLE, bg='white')
for x in range(1, self.dim+1):
listbox.insert(tk.END, 'x%d' % x)
listbox.grid(row=0, column=1, padx=5, pady=5, sticky='nw')
self.listbox = listbox
# Selection controls
self._addLabel(frame, 'Rejection', 1, 0)
# Selection label
self.selectionVar = tk.StringVar()
self.clusterLabel = tk.Label(frame, textvariable=self.selectionVar)
self.clusterLabel.grid(row=1, column=1, sticky='nw', padx=5, pady=(10, 5))
self._updateSelectionLabel()
# --- Expression
expressionFrame = tk.Frame(frame)
expressionFrame.grid(row=2, column=1, sticky='news')
tk.Label(expressionFrame, text='Expression').grid(row=0, column=0, sticky='ne')
self.expressionVar = tk.StringVar()
expressionEntry = tk.Entry(expressionFrame, textvariable=self.expressionVar,
width=30, bg='white')
expressionEntry.grid(row=0, column=1, sticky='nw')
helpText = 'e.g. x1>0 and x1<100 or x3>20'
tk.Label(expressionFrame, text=helpText).grid(row=1, column=1, sticky='nw')
# Buttons
buttonFrame = tk.Frame(frame)
buttonFrame.grid(row=5, column=1, sticky='sew', pady=(10, 5))
buttonFrame.columnconfigure(0, weight=1)
resetBtn = Button(buttonFrame, text='Reset', command=self._onResetClick)
resetBtn.grid(row=0, column=0, sticky='ne', padx=(5, 0))
updateBtn = Button(buttonFrame, text='Update Plot', imagePath='fa-refresh.png',
command=self._onUpdateClick)
updateBtn.grid(row=0, column=1, sticky='ne', padx=5)
frame.grid(row=0, column=0, sticky='new', padx=5, pady=(10, 5))
def _createTrajectoriesBox(self, content):
frame = tk.LabelFrame(content, text='Trajectories')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Animation name
self._addLabel(frame, 'Name', 0, 0)
self.animationVar = tk.StringVar()
clusterEntry = tk.Entry(frame, textvariable=self.animationVar,
width=30, bg='white')
clusterEntry.grid(row=0, column=1, sticky='nw', pady=5)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=1, column=1,
sticky='se', padx=5, pady=5)
buttonsFrame.columnconfigure(0, weight=1)
self.generateBtn = HotButton(buttonsFrame, text='Generate Animation', state=tk.DISABLED,
tooltip='Select trajectory points to generate the animations',
imagePath='fa-plus-circle.png', command=self._onCreateClick)
self.generateBtn.grid(row=0, column=1, padx=5)
self.loadBtn = Button(buttonsFrame, text='Load', imagePath='fa-folder-open.png',
tooltip='Load a generated animation.',command=self._onLoadClick)
self.loadBtn.grid(row=0, column=2, padx=5)
self.closeBtn = Button(buttonsFrame, text='Close', imagePath=Icon.ACTION_CLOSE,
tooltip='Close window', command=self.close)
self.closeBtn.grid(row=0, column=3, padx=(5, 10))
frame.grid(row=1, column=0, sticky='new', padx=5, pady=(5, 10))
def _onResetClick(self, e=None):
""" Clean the expression and the current selection. """
self.expressionVar.set('')
self.pathData.clear()
for point in self.data.iterAll():
point.setState(Point.NORMAL)
self._onUpdateClick()
self.generateBtn.config(state=tk.DISABLED)
def _onCreateClick(self, e=None):
if self.callback:
self.callback()
def _onLoadClick(self, e=None):
if self.loadCallback:
self.loadCallback()
def setPathData(self, data):
self.pathData = data
def _evalExpression(self):
""" Evaluate the input expression and add
matching points to the selection.
"""
value = self.expressionVar.get().strip()
if value:
for point in self.data:
if point.eval(value):
point.setState(Point.DISCARDED)
def setDataIndex(self, indexName, value):
""" Set which point data index will be used as X, Y or Z. """
setattr(self.data, indexName, value)
setattr(self.pathData, indexName, value)
def _onUpdateClick(self, e=None):
components = self.listbox.curselection()
dim = len(components)
if not dim:
self.showWarning("Please select some Axis before update plots.")
else:
modeList = components
modeNameList = ['x%d' % (m+1) for m in components]
missingList = []
if missingList:
return [self.errorMessage("Invalid mode(s) *%s*\n." % (', '.join(missingList)),
title="Invalid input")]
if self.plotter is None or self.plotter.isClosed():
self.plotter = FlexNmaPlotter(data=self.data)
doShow = True
#self.plotter.useLastPlot = True
else:
self.plotter.clear()
doShow = False
# Actually plot
baseList = [basename(n) for n in modeNameList]
self.setDataIndex('XIND', modeList[0])
self.ps = None
if dim == 1:
self.plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.setDataIndex('YIND', modeList[1])
if dim == 2:
self._evalExpression()
self._updateSelectionLabel()
ax = self.plotter.createSubPlot("Click and drag to add points to the Cluster",
*baseList)
self.ps = PointPath(ax, self.data, self.pathData,
callback=self._checkNumberOfPoints)
elif dim == 3:
#del self.ps # Remove PointSelector
self.setDataIndex('ZIND', modeList[2])
self.plotter.plotArray3D("%s %s %s" % tuple(baseList), *baseList)
if doShow:
self.plotter.show()
else:
self.plotter.draw()
def _updateSelectionLabel(self):
self.selectionVar.set('%d / %d points' % (self.data.getDiscardedSize(),
self.data.getSize()))
def _checkNumberOfPoints(self):
""" Check that if the number of points was selected
and add new ones if needed.
"""
while (self.pathData.getSize() < self.numberOfPoints):
self.pathData.splitLongestSegment()
self._onUpdateClick()
self.generateBtn.config(state=tk.NORMAL)
def getAnimationName(self):
return self.animationVar.get().strip()
def setAnimationName(self, value):
self.animationVar.set(value)
def _onClosing(self):
if self.plotter:
self.plotter.close()
gui.Window._onClosing(self)
def __init__(self,
parent,
windows,
template=None,
argsList=[],
showScheduleOption=True,
schedule=True,
showProjectOption=True,
showProject=True,
showProjectName=True,
**kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.root = windows.root
self.vars = {}
self.checkvars = []
self.template = template
self.argsList = argsList
self.showScheduleOption = showScheduleOption
self.schedule = schedule
self.showProjectOption = showProjectOption
self.showProject = showProject
self.showProjectName = showProjectName
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.columnconfigure(0, minsize=120)
bodyFrame.columnconfigure(1, minsize=120, weight=1)
bodyFrame.grid(row=0, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text=ACCEPT_BUTTON,
font=self.bigFontBold,
command=self._onReadDataFromTemplateForm)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
font=self.bigFontBold,
command=self._closeCallback)
btn.grid(row=0, column=0, sticky='ne', pady=10)
btnFrame.columnconfigure(0, weight=1)
btnFrame.grid(row=1, column=0, sticky='news')
self.columnconfigure(0, weight=1)
def __init__(self,
title,
parent=None,
weight=True,
minsize=(400, 150),
icon="scipion_bn.xbm",
**args):
"""
We assume the parent should be of ProjectsView
"""
Window.__init__(self,
title,
parent.windows,
weight=weight,
icon=icon,
minsize=minsize,
enableQueue=True)
self.parent = parent
self.projectsPath = self.parent.manager.PROJECTS
self.projName = tk.StringVar()
self.projName.set('')
self.projLocation = tk.StringVar()
self.projLocation.set(self.projectsPath)
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.columnconfigure(1, weight=1)
content.config(bg='white')
content.grid(row=0, column=0, sticky='news', padx=5, pady=5)
labelName = tk.Label(content,
text=Message.LABEL_PROJECT,
bg='white',
bd=0)
labelName.grid(row=0, column=0, sticky='nw', padx=5, pady=5)
entryName = tk.Entry(content,
bg=cfgEntryBgColor,
width=20,
textvariable=self.projName)
entryName.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
labelCheck = tk.Label(content,
text="Use default location",
bg='white',
bd=0)
labelCheck.grid(row=1, column=0, sticky='nw', padx=5, pady=5)
self.tkCheckVar = tk.IntVar()
btnCheck = tk.Checkbutton(content,
variable=self.tkCheckVar,
bg='white',
bd=0)
btnCheck.grid(row=1, column=1, sticky='nw', padx=5, pady=5)
self.browseFrame = tk.Frame(content, bg='white')
#self.browseFrame.columnconfigure(1, weight=1)
self.browseFrame.grid(row=2,
column=0,
padx=0,
pady=0,
columnspan=2,
sticky='nw')
self.entryBrowse = tk.Entry(self.browseFrame,
bg=cfgEntryBgColor,
width=40,
textvariable=self.projLocation)
self.entryBrowse.grid(row=0, column=0, sticky='nw', padx=5, pady=5)
self.btnBrowse = IconButton(self.browseFrame,
'Browse',
Icon.ACTION_BROWSE,
command=self._browsePath)
self.btnBrowse.grid(row=0, column=1, sticky='e', padx=5, pady=5)
self.initial_focus = entryName
self.tkCheckVar.trace('w', self._onVarChanged)
btnCheck.select()
btnFrame = tk.Frame(content)
btnFrame.columnconfigure(0, weight=1)
btnFrame.grid(row=3,
column=0,
sticky='sew',
padx=5,
pady=(0, 5),
columnspan=2)
btnFrame.config(bg='white')
# Create buttons
btnSelect = HotButton(btnFrame,
'Create',
Icon.BUTTON_SELECT,
command=self._select)
btnSelect.grid(row=0, column=0, sticky='e', padx=5, pady=5)
btnCancel = Button(btnFrame,
'Cancel',
Icon.BUTTON_CANCEL,
command=self.close)
btnCancel.grid(row=0, column=1, sticky='e', padx=5, pady=5)
def _fillButtonsFrame(self, frame):
subframe = tk.Frame(frame)
subframe.grid(row=0, column=0, sticky='nw')
frame.columnconfigure(1, weight=1)
imgPlainBtn = Button(subframe,
"View plain images",
command=self._viewPlainImages)
imgPlainBtn.grid(row=0, column=0, sticky='nw', padx=(0, 5))
if self._getModel() is None:
imgPlainBtn['state'] = 'disabled'
imgOverlaidBtn = Button(subframe,
"View images with spots",
command=self._viewOverlaidImages)
imgOverlaidBtn.grid(row=0, column=1, sticky='nw', padx=(0, 5))
if None in {self._getModel(), self._getRefls()}:
imgOverlaidBtn['state'] = 'disabled'
reciprocalBtn = Button(subframe,
"View reciprocal lattice",
command=self._viewReciprocal)
reciprocalBtn.grid(row=0, column=2, sticky='nw', padx=(0, 5))
if None in {self._getModel(), self._getRefls()}:
reciprocalBtn['state'] = 'disabled'
htmlBtn = HotButton(subframe,
'Open HTML Report',
command=self._openHTML)
htmlBtn.grid(row=0, column=3, sticky='nw', padx=(0, 5))
if self._getHtml() is None:
htmlBtn['state'] = 'disabled'
closeBtn = self.createCloseButton(frame)
closeBtn.grid(row=0, column=1, sticky='ne')