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()
btn = HotButton(self,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
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, 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)
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')
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()
btn = HotButton(self, text=Message.LABEL_CREATE_PROJECT, font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
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, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
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 visualizeClasses(self, e=None):
classTemplate = "class_%03d"
averages = '%03d@' + self.protocol._getFileName('averages')
def getInfo2(level, classNo):
return classTemplate % classNo, averages % classNo
node = self.protocol.buildDendrogram()
g = Graph(root=node)
self.graph = g
self.win = Window("Select classes", self.formWindow, minsize=(1000, 600))
root = self.win.root
canvas = Canvas(root)
canvas.grid(row=0, column=0, sticky='nsew')
root.grid_columnconfigure(0, weight=1)
root.grid_rowconfigure(0, weight=1)
self.buttonframe = tk.Frame(root)
self.buttonframe.grid(row=2, column=0, columnspan=2)
self.win.createCloseButton(self.buttonframe).grid(row=0, column=0, sticky='n', padx=5, pady=5)
saveparticlesbtn = HotButton(self.buttonframe, "Particles", Icon.PLUS_CIRCLE, command=lambda: self.askCreateSubset('Particles', self.getSelectedNodesCount(2)))
saveparticlesbtn.grid(row=0, column=1, sticky='n', padx=5, pady=5)
btn = HotButton(self.buttonframe, "Classes", Icon.PLUS_CIRCLE, command=lambda: self.askCreateSubset('Classes', self.getSelectedNodesCount(1)))
btn.grid(row=0, column=2, sticky='n', padx=5, pady=5)
lt = LevelTree(g)
lt.DY = 135 # TODO: change in percent of the image size
lt.setCanvas(canvas)
lt.paint(self._createNode, maxLevel=self.maxLevel.get()-1)
canvas.updateScrollRegion()
return [self.win]
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 _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 _createControls(self, frame):
self._vars = {}
inputFrame = tk.Frame(frame)
inputFrame.grid(row=0, column=0)
for i, varName in enumerate(CUSTOMMASK_VARS):
self._createVarWidgets(inputFrame, varName, CUSTOMMASK_VARS[varName], i%2, i/2)
previewBtn = HotButton(frame, text='Preview', command=self._computeRightPreview)
previewBtn.grid(row=1, column=1, padx=5, pady=5)
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 __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 _createControls(self, frame):
self._vars = {}
inputFrame = tk.Frame(frame)
inputFrame.grid(row=0, column=0)
for i, varName in enumerate(CUSTOMMASK_VARS):
self._createVarWidgets(inputFrame, varName,
CUSTOMMASK_VARS[varName], i % 2, i // 2)
previewBtn = HotButton(frame,
text='Preview',
command=self._computeRightPreview)
previewBtn.grid(row=1, column=1, 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 __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 visualizeClasses(self, e=None):
classTemplate = "class_%03d"
averages = '%03d@' + self.protocol._getFileName('averages')
def getInfo2(level, classNo):
return classTemplate % classNo, averages % classNo
node = self.protocol.buildDendrogram(writeAverages=False)
g = Graph(root=node)
self.graph = g
self.win = Window("Select classes",
self.formWindow,
minsize=(1000, 600))
root = self.win.root
canvas = Canvas(root)
canvas.grid(row=0, column=0, sticky='nsew')
root.grid_columnconfigure(0, weight=1)
root.grid_rowconfigure(0, weight=1)
self.buttonframe = tk.Frame(root)
self.buttonframe.grid(row=2, column=0, columnspan=2)
self.win.createCloseButton(self.buttonframe).grid(row=0,
column=0,
sticky='n',
padx=5,
pady=5)
saveparticlesbtn = HotButton(self.buttonframe,
"Particles",
Icon.PLUS_CIRCLE,
command=self._askCreateParticles)
saveparticlesbtn.grid(row=0, column=1, sticky='n', padx=5, pady=5)
btn = HotButton(self.buttonframe,
"Classes",
Icon.PLUS_CIRCLE,
command=self._askCreateClasses)
btn.grid(row=0, column=2, sticky='n', padx=5, pady=5)
lt = LevelTree(g)
lt.DY = 135 # TODO: change in percent of the image size
lt.setCanvas(canvas)
lt.paint(self._createNode, maxLevel=self.maxLevel.get() - 1)
canvas.updateScrollRegion()
return [self.win]
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 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)
class PopulationWindow(gui.Window):
"""
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(620, 200), **kwargs)
self.population = kwargs.get('population')
self.callback = kwargs.get('callback', None)
self.plotter = None
self._variables = OrderedDict()
self._variablesDict = {}
self._loadVariables(self.population)
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
gui.configureWeigths(content)
def _loadVariables(self, population):
self.observations = population.getAllParameters()
mu, sigma, self.R, percentiles = population.getStats(self.observations)
for i, varName in enumerate(population.modelParameters):
v = PopulationVar(index=i,
varName=varName,
unitStr=PKPDUnit.codeToString(population.modelParameterUnits[i]),
mu=mu[i], sigma=sigma[i],
percentiles=[p[i] for p in percentiles])
self._variables[varName] = v
def _createContent(self, content):
# Create top frame with the variables list
self._createTopFrame(content)
# Create button frame with Plot button
self._createButtonsFrame(content)
# Create an info frame
self._createBottomFrame(content)
def _createTopFrame(self, content):
frame = tk.Frame(content)
lfSamples = tk.LabelFrame(frame, text='Plot')
gui.configureWeigths(frame)
lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
# Create tree for Population Variables
tp = PopulationVariablesTreeProvider(self._variables.values())
self.tree = BoundTree(frame, tp, height=10)
self.tree.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(frame)
frame.grid(row=0, column=0, sticky='news', padx=5, pady=(10, 5))
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
self.plotButton = HotButton(frame, ' Plot ', font=self.fontBold,
command=self._onPlotClick,
tooltip='Select one or two variables to plot ')
self.plotButton.grid(row=0, column=0, sticky='se', padx=5)
frame.grid(row=1, column=0, sticky='sew', padx=5, pady=5)
gui.configureWeigths(frame)
def _createBottomFrame(self, content):
frame = tk.Frame(content)
t = TaggedText(frame, height=10)
t.grid(row=0, column=0, sticky='news', padx=5, pady=5)
t.addLine("*Correlation Matrix*")
t.addText(np.array2string(self.R))
frame.grid(row=2, column=0, sticky='sew', padx=5, pady=5)
gui.configureWeigths(frame)
def _onPlotClick(self, e=None):
selection = self.tree.selection()
n = len(selection)
if n < 1 or n > 2:
self.showError("Select one or two variables to plot.")
else:
plotter = EmPlotter()
varX = self._variables[selection[0]]
xValues = self.observations[:, varX.index]
def _label(var):
return "%s [%s]" % (var.varName, var.unitStr)
if n == 1:
plotter.createSubPlot("Histogram", _label(varX), "Count")
plotter.plotHist(xValues, 50)
else: # n == 2
varY = self._variables[selection[1]]
yValues = self.observations[:, varY.index]
ax = plotter.createSubPlot("Scatter Plot",
_label(varX), _label(varY))
ax.plot(xValues, yValues, '.')
plotter.show()
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)
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, **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)
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)
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 ClusteringWindow(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.dim = kwargs.get('dim')
self.data = kwargs.get('data')
self.callback = kwargs.get('callback', None)
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._createClusteringBox(content)
self._updateSelectionLabel()
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, '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 _createClusteringBox(self, content):
frame = tk.LabelFrame(content, text='Cluster')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1) #, minsize=30)
# Cluster line
self._addLabel(frame, 'Cluster name', 0, 0)
self.clusterVar = tk.StringVar()
clusterEntry = tk.Entry(frame,
textvariable=self.clusterVar,
width=30,
bg='white')
clusterEntry.grid(row=0, column=1, sticky='nw', pady=5)
buttonsFrame = tk.Frame(frame, bg='green')
buttonsFrame.grid(row=1, column=1, sticky='se', padx=5, pady=5)
buttonsFrame.columnconfigure(0, weight=1)
self.createBtn = HotButton(
buttonsFrame,
text='Create Cluster',
tooltip="Select some points to create the cluster",
imagePath='fa-plus-circle.png',
command=self._onCreateClick)
self.createBtn.grid(row=0, column=1)
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('')
for point in self.data:
point.setState(Point.NORMAL)
self._onUpdateClick()
def _onCreateClick(self, e=None):
if self.callback:
self.callback()
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.SELECTED)
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
else:
self.plotter.clear()
doShow = False
# Actually plot
baseList = [basename(n) for n in modeNameList]
self.data.XIND = modeList[0]
if dim == 1:
self.plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value",
"Number of images")
else:
self.data.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 = PointSelector(
ax, self.data, callback=self._updateSelectionLabel)
elif dim == 3:
del self.ps # Remove PointSelector
self.data.ZIND = modeList[2]
self.plotter.plotArray3D("%s %s %s" % tuple(baseList),
*baseList)
if doShow:
self.plotter.show()
else:
self.plotter.draw()
def _updateSelectionLabel(self):
selected = self.data.getSelectedSize()
self.selectionVar.set('%d / %d points' %
(selected, self.data.getSize()))
if selected:
self.createBtn.config(state=tk.NORMAL)
else:
self.createBtn.config(state=tk.DISABLED)
def getClusterName(self):
return self.clusterVar.get().strip()
def _onClosing(self):
if self.plotter:
self.plotter.close()
gui.Window._onClosing(self)
class PopulationWindow(gui.Window):
"""
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(620, 200), **kwargs)
self.population = kwargs.get('population')
self.callback = kwargs.get('callback', None)
self.plotter = None
self._variables = OrderedDict()
self._variablesDict = {}
self._loadVariables(self.population)
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
gui.configureWeigths(content)
def _loadVariables(self, population):
self.observations = population.getAllParameters()
mu, sigma, self.R, percentiles = population.getStats(self.observations)
for i, varName in enumerate(population.modelParameters):
v = PopulationVar(index=i,
varName=varName,
unitStr=PKPDUnit.codeToString(
population.modelParameterUnits[i]),
mu=mu[i],
sigma=sigma[i],
percentiles=[p[i] for p in percentiles])
self._variables[varName] = v
def _createContent(self, content):
# Create top frame with the variables list
self._createTopFrame(content)
# Create button frame with Plot button
self._createButtonsFrame(content)
# Create an info frame
self._createBottomFrame(content)
def _createTopFrame(self, content):
frame = tk.Frame(content)
lfSamples = tk.LabelFrame(frame, text='Plot')
gui.configureWeigths(frame)
lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
# Create tree for Population Variables
tp = PopulationVariablesTreeProvider(self._variables.values())
self.tree = BoundTree(frame, tp, height=10)
self.tree.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(frame)
frame.grid(row=0, column=0, sticky='news', padx=5, pady=(10, 5))
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
self.plotButton = HotButton(
frame,
' Plot ',
font=self.fontBold,
command=self._onPlotClick,
tooltip='Select one or two variables to plot ')
self.plotButton.grid(row=0, column=0, sticky='se', padx=5)
frame.grid(row=1, column=0, sticky='sew', padx=5, pady=5)
gui.configureWeigths(frame)
def _createBottomFrame(self, content):
frame = tk.Frame(content)
t = TaggedText(frame, height=10)
t.grid(row=0, column=0, sticky='news', padx=5, pady=5)
t.addLine("*Correlation Matrix*")
t.addText(np.array2string(self.R))
frame.grid(row=2, column=0, sticky='sew', padx=5, pady=5)
gui.configureWeigths(frame)
def _onPlotClick(self, e=None):
selection = self.tree.selection()
n = len(selection)
if n < 1 or n > 2:
self.showError("Select one or two variables to plot.")
else:
plotter = EmPlotter()
varX = self._variables[selection[0]]
xValues = self.observations[:, varX.index]
def _label(var):
return "%s [%s]" % (var.varName, var.unitStr)
if n == 1:
plotter.createSubPlot("Histogram", _label(varX), "Count")
plotter.plotHist(xValues, 50)
else: # n == 2
varY = self._variables[selection[1]]
yValues = self.observations[:, varY.index]
ax = plotter.createSubPlot("Scatter Plot", _label(varX),
_label(varY))
ax.plot(xValues, yValues, '.')
plotter.show()
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)
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)
class PreWhiteningDialog(dialog.Dialog):
def __init__(self, form, workingDir, **kwargs):
"""
Params:
parent: parent windows of the dialog.
provider: the TreeProvider to populate items tree.
"""
self.form = form
self.workingDir = workingDir
buttons = [('Select', dialog.RESULT_YES),
('Cancel', dialog.RESULT_CANCEL)]
dialog.Dialog.__init__(self,
form.root,
"Pre-whitening",
buttons=buttons,
default='Select',
**kwargs)
def _runBeforePreWhitening(self):
prot = self.form.protocol
# Convert input volumes
ih = ImageHandler()
if prot.useSplitVolume:
ih.convert(prot.volumeHalf1.get(),
join(self.workingDir, 'volume1.map'))
ih.convert(prot.volumeHalf2.get(),
join(self.workingDir, 'volume2.map'))
else:
ih.convert(prot.inputVolume.get(),
join(self.workingDir, 'volume1.map'))
self.results = prot.runResmap(self.workingDir, wizardMode=True)
def _runPreWhitening(self, newElbowAngstrom, newRampWeight):
# Add resmap libraries to the path
results = self.results
self.figure.clear()
myCreatePrewhiteningFigure(results, self.figure, newElbowAngstrom,
newRampWeight)
def body(self, bodyFrame):
figFrame = FigureFrame(bodyFrame, figsize=(18, 9))
figFrame.grid(row=0, column=0, columnspan=5)
#self._runBeforePreWhitening(self.prot)
dialog.FlashMessage(self.form.root,
"Running Pre-Whitening tool...",
func=self._runBeforePreWhitening)
results = self.results
self.figure = figFrame.getFigure() #plt.figure(figsize=(18, 9))
self._runPreWhitening(results['newElbowAngstrom'],
results['newRampWeight'])
#bodyFrame.config()
bodyFrame.columnconfigure(0, weight=1)
bodyFrame.rowconfigure(0, weight=1)
controlsFrame = tk.Frame(bodyFrame)
controlsFrame.grid(row=1, column=0)
self.elbowSlider = LabelSlider(controlsFrame,
"Angstroms",
from_=2.1 * results['vxSize'],
to=100,
value=results['newElbowAngstrom'])
self.elbowSlider.grid(row=1, column=0, padx=5, pady=5)
self.rampSlider = LabelSlider(controlsFrame,
"Ramp weight",
from_=0.0,
to=1.,
value=results['newRampWeight'])
self.rampSlider.grid(row=1, column=1, padx=5, pady=5)
self.updateBtn = HotButton(
controlsFrame,
" Update ",
command=self._onUpdate,
tooltip="Update plots with new pre-whitening parameters.")
self.updateBtn.grid(row=1, column=2, padx=10, pady=5)
def getElbowValue(self):
return self.elbowSlider.get()
def getRampValue(self):
return self.rampSlider.get()
def _onUpdate(self, e=None):
self._runPreWhitening(self.getElbowValue(), self.getRampValue())
class ClusteringWindow(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.dim = kwargs.get('dim')
self.data = kwargs.get('data')
self.callback = kwargs.get('callback', None)
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._createClusteringBox(content)
self._updateSelectionLabel()
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, '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 _createClusteringBox(self, content):
frame = tk.LabelFrame(content, text='Cluster')
frame.columnconfigure(0, minsize=50)
frame.columnconfigure(1, weight=1)#, minsize=30)
# Cluster line
self._addLabel(frame, 'Cluster name', 0, 0)
self.clusterVar = tk.StringVar()
clusterEntry = tk.Entry(frame, textvariable=self.clusterVar,
width=30, bg='white')
clusterEntry.grid(row=0, column=1, sticky='nw', pady=5)
buttonsFrame = tk.Frame(frame, bg='green')
buttonsFrame.grid(row=1, column=1,
sticky='se', padx=5, pady=5)
buttonsFrame.columnconfigure(0, weight=1)
self.createBtn = HotButton(buttonsFrame, text='Create Cluster',
tooltip="Select some points to create the cluster",
imagePath='fa-plus-circle.png', command=self._onCreateClick)
self.createBtn.grid(row=0, column=1)
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('')
for point in self.data:
point.setState(Point.NORMAL)
self._onUpdateClick()
def _onCreateClick(self, e=None):
if self.callback:
self.callback()
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.SELECTED)
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
else:
self.plotter.clear()
doShow = False
# Actually plot
baseList = [basename(n) for n in modeNameList]
self.data.XIND = modeList[0]
if dim == 1:
self.plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.data.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 = PointSelector(ax, self.data, callback=self._updateSelectionLabel)
elif dim == 3:
del self.ps # Remove PointSelector
self.data.ZIND = modeList[2]
self.plotter.plotArray3D("%s %s %s" % tuple(baseList), *baseList)
if doShow:
self.plotter.show()
else:
self.plotter.draw()
def _updateSelectionLabel(self):
selected = self.data.getSelectedSize()
self.selectionVar.set('%d / %d points' % (selected, self.data.getSize()))
if selected:
self.createBtn.config(state=tk.NORMAL)
else:
self.createBtn.config(state=tk.DISABLED)
def getClusterName(self):
return self.clusterVar.get().strip()
def _onClosing(self):
if self.plotter:
self.plotter.close()
gui.Window._onClosing(self)
class PreWhiteningDialog(dialog.Dialog):
def __init__(self, form, workingDir, **kwargs):
"""
Params:
parent: parent windows of the dialog.
provider: the TreeProvider to populate items tree.
"""
self.form = form
self.workingDir = workingDir
buttons = [('Select', dialog.RESULT_YES), ('Cancel', dialog.RESULT_CANCEL)]
dialog.Dialog.__init__(self, form.root, "Pre-whitening", buttons=buttons, default='Select', **kwargs)
def _runBeforePreWhitening(self):
prot = self.form.protocol
# Convert input volumes
ih = ImageHandler()
if prot.useSplitVolume:
ih.convert(prot.volumeHalf1.get(), join(self.workingDir, 'volume1.map'))
ih.convert(prot.volumeHalf2.get(), join(self.workingDir, 'volume2.map'))
else:
ih.convert(prot.inputVolume.get(), join(self.workingDir, 'volume1.map'))
self.results = prot.runResmap(self.workingDir, wizardMode=True)
def _runPreWhitening(self, newElbowAngstrom, newRampWeight):
# Add resmap libraries to the path
results = self.results
self.figure.clear()
myCreatePrewhiteningFigure(results, self.figure, newElbowAngstrom, newRampWeight)
def body(self, bodyFrame):
figFrame = FigureFrame(bodyFrame, figsize=(18, 9))
figFrame.grid(row=0, column=0, columnspan=5)
#self._runBeforePreWhitening(self.prot)
dialog.FlashMessage(self.form.root, "Running Pre-Whitening tool...",
func=self._runBeforePreWhitening)
results = self.results
self.figure = figFrame.getFigure() #plt.figure(figsize=(18, 9))
self._runPreWhitening(results['newElbowAngstrom'],
results['newRampWeight'])
#bodyFrame.config()
bodyFrame.columnconfigure(0, weight=1)
bodyFrame.rowconfigure(0, weight=1)
controlsFrame = tk.Frame(bodyFrame)
controlsFrame.grid(row=1, column=0)
self.elbowSlider = LabelSlider(controlsFrame, "Angstroms", from_=2.1*results['vxSize'], to=100,
value=results['newElbowAngstrom'])
self.elbowSlider.grid(row=1, column=0, padx=5, pady=5)
self.rampSlider = LabelSlider(controlsFrame, "Ramp weight", from_=0.0, to=1.,
value=results['newRampWeight'])
self.rampSlider.grid(row=1, column=1, padx=5, pady=5)
self.updateBtn = HotButton(controlsFrame, " Update ",
command=self._onUpdate,
tooltip="Update plots with new pre-whitening parameters.")
self.updateBtn.grid(row=1, column=2, padx=10, pady=5)
def getElbowValue(self):
return self.elbowSlider.get()
def getRampValue(self):
return self.rampSlider.get()
def _onUpdate(self, e=None):
self._runPreWhitening(self.getElbowValue(), self.getRampValue())
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 __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
# 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')
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",
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 __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)