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 _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 _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 _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 _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 _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 addActionsFrame(self):
""" Add the "toolbar" for actions like create project, import
project or filter"""
# Add the create project button
bg = "white"
btnFrame = tk.Frame(self, bg=bg)
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
# Add a filter box
# Add the Import project button
btn = tk.Label(btnFrame, bg=bg, text="Filter:", font=self.projNameFont)
btn.grid(row=0, column=2, sticky='nse', padx=10, pady=10)
self.filterBox = tk.Entry(btnFrame,
font=self.projNameFont,
textvariable=self.filter)
self.filterBox.grid(row=0, column=3, sticky='ne', padx=10, pady=12)
self.filterBox.bind('<Return>', self._onFilter)
self.filterBox.bind('<KP_Enter>', self._onFilter)
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.root = windows.root
self.vars = {}
self.checkvars = []
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
# Header section
headerFrame = tk.Frame(self, bg='white')
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Enter your desired values"
label = tk.Label(headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw',
bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Start demo",
font=self.bigFontBold,
command=self._onAction)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
gui.configureWeigths(frame)
buttonsFrame = tk.Frame(frame)
buttonsFrame.grid(row=0, column=0, sticky='ne')
closeButton = Button(buttonsFrame, 'Close', command=self.close,
imagePath='fa-times.png')
frame.grid(row=2, column=0, sticky='news', padx=5, pady=5)
def _fillButtonsFrame(self, frame):
subframe = tk.Frame(frame)
subframe.grid(row=0, column=0, sticky='nw')
frame.columnconfigure(1, weight=1)
ctfBtn = Button(subframe, "CTF Monitor", command=self._monitorCTF)
ctfBtn.grid(row=0, column=0, sticky='nw', padx=(0, 5))
sysBtn = Button(subframe,
"System Monitor",
command=self._monitorSystem)
sysBtn.grid(row=0, column=1, sticky='nw', padx=(0, 5))
htmlBtn = HotButton(subframe,
'Generate HTML Report',
command=self._generateHTML)
htmlBtn.grid(row=0, column=2, sticky='nw', padx=(0, 5))
closeBtn = self.createCloseButton(frame)
closeBtn.grid(row=0, column=1, sticky='ne')
def _createFigureBox(self, content):
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 _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 __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text=Message.LABEL_CREATE_PROJECT,
font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
text=Message.LABEL_IMPORT_PROJECT,
font=self.projNameFont,
command=self._onImportProject)
btn.grid(row=0, column=1, sticky='nw', padx=10, pady=10)
btnFrame.grid(row=0, column=0, sticky='nw')
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, columnspan=2, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def __init__(self, title, parent=None, weight=True, minsize=(400, 150),
icon="scipion_bn.xbm", **args):
"""
We assume the parent should be ProjectsView
"""
Window.__init__(self, title, parent.windows, weight=weight,
icon=icon, minsize=minsize, enableQueue=True)
self.root['background'] = 'white'
self.parent = parent
# Dirty hack, need to add a slash for the explorer to pick up the right default path.
self.projectsPath = getHomePath()+"/"
self.projLocation = tk.StringVar()
self.projLocation.set(self.projectsPath)
self.projName = tk.StringVar()
self.projName.set('')
self.searchLocation = tk.StringVar()
self.searchLocation.set('')
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.columnconfigure(1, weight=1)
content.config(bg='white')
content.grid(row=0, column=0, sticky='news',
padx=5, pady=5)
# Path explorer
labelProjectLocation = tk.Label(content, text="Project location", bg='white', bd=0)
labelProjectLocation.grid(row=0, column=0, sticky='nw', padx=5, pady=5)
self.entryBrowse = tk.Entry(content, bg=cfgEntryBgColor, width=40, textvariable=self.projLocation)
self.entryBrowse.grid(row=0, column=1, sticky='nw', padx=5, pady=5)
self.btnBrowse = IconButton(content, 'Browse', Icon.ACTION_BROWSE, highlightthickness=0,
command=self._browseProjectLocation)
self.btnBrowse.grid(row=0, column=2, sticky='e', padx=5, pady=5)
# Copy files check
labelCheck = tk.Label(content, text="Copy project", bg='white', borderwidth=0)
labelCheck.grid(row=1, column=0, sticky='nw', padx=5, pady=5)
self.tkCheckVar = tk.IntVar()
btnCheck = tk.Checkbutton(content, variable=self.tkCheckVar, highlightthickness=0, activebackground='white',
bg='white', bd=0)
btnCheck.grid(row=1, column=1, sticky='nw', padx=0, pady=5)
btnCopyHelp = IconButton(content, Message.LABEL_BUTTON_HELP, Icon.ACTION_HELP, highlightthickness=0,
command=lambda: self.showInfo('If checked, \"Project location\" will be copied. Otherwise a soft link to it will be created.'))
btnCopyHelp.grid(row=1, column=3, sticky='e', padx=2, pady=2)
# Project name
labelName = tk.Label(content, text='Project name (Optional)', bg='white', bd=0)
labelName.grid(row=2, column=0, sticky='nw', padx=5, pady=5)
entryName = tk.Entry(content, bg='white', width=20, textvariable=self.projName)
entryName.grid(row=2, column=1, sticky='nw', padx=5, pady=5)
# Path to search for raw data and restore broken links.
labelSearchLocation = tk.Label(content, text="Raw files location (Optional)", bg='white', bd=0)
labelSearchLocation.grid(row=3, column=0, sticky='nw', padx=5, pady=5)
self.entrySearchLocation = tk.Entry(content, bg='white', width=40, textvariable=self.searchLocation)
self.entrySearchLocation.grid(row=3, column=1, sticky='nw', padx=5, pady=5)
self.btnSearch = IconButton(content, 'Browse', Icon.ACTION_BROWSE, highlightthickness=0, command=self._browseSearchLocation)
self.btnSearch.grid(row=3, column=2, sticky='e', padx=5, pady=5)
btnSearchHelp = IconButton(content, Message.LABEL_BUTTON_HELP, Icon.ACTION_HELP, highlightthickness=0,
command=lambda: self.showInfo('Optional: Folder where raw files, binaries (movies, migcrographs,..) can be found. Used to repair broken links.'))
btnSearchHelp.grid(row=3, column=3, sticky='e', padx=2, pady=2)
self.initial_focus = entryName
btnCheck.select()
btnFrame = tk.Frame(content)
btnFrame.columnconfigure(0, weight=1)
btnFrame.grid(row=4, column=0, sticky='sew', padx=5, pady=(0, 5), columnspan=2)
btnFrame.config(bg='white')
# Create buttons
btnSelect = HotButton(btnFrame, 'Import', Icon.BUTTON_SELECT, command=self._select)
btnSelect.grid(row=0, column=0, sticky='e', padx=5, pady=5)
btnCancel = Button(btnFrame, 'Cancel', Icon.BUTTON_CANCEL, command=self.close)
btnCancel.grid(row=0, column=1, sticky='e', padx=5, pady=5)
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
self.vars = {}
self.checkvars = []
self.microscope = None
self.configDict = self.windows.config
# Regular expression to validate username and sample name
self.re = re.compile('\A[a-zA-Z0-9][a-zA-Z0-9_-]+[a-zA-Z0-9]\Z')
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = tkFont.Font(size=bigSize,
family=fontName,
weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize,
family=fontName,
weight='bold')
self.manager = Manager()
# Header section
headerFrame = tk.Frame(self, bg='white')
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Create New Session"
headerText += " %s" % pwutils.prettyTime(dateFormat='%Y-%m-%d')
label = tk.Label(headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw',
bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Create New Session",
activebackground="dark grey",
activeforeground='black',
font=self.bigFontBold,
command=self._onAction)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Cancel project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
def _fillContent(self, content):
frame = tk.Frame(content, bg='white')
frame.grid(row=0, column=0, sticky='news', padx=10, pady=15)
frame.columnconfigure(0, minsize=200)
self._lastRow = 0
def _createLabel(text, bold=False):
boldStr = 'bold' if bold else ''
return tk.Label(frame,
text=text,
font="helvetica 12 %s" % boldStr,
bg='white')
def __addLabeledWidget(text, widget=None, pady=5, bold=False):
label = _createLabel(text, bold)
label.grid(row=self._lastRow, column=0, sticky='ne', pady=pady)
if widget is not None:
widget.grid(row=self._lastRow,
column=1,
sticky='nw',
pady=pady,
padx=5)
self._lastRow += 1
return label
def __createCombobox(options, readOnly=True, callback=None, width=38):
var = tk.StringVar()
s = ttk.Style()
state = 'readonly' if readOnly else 'edit'
combo = ttk.Combobox(frame,
textvariable=var,
state=state,
width=width)
combo['values'] = options
combo.var = var
if callback:
combo.bind('<<ComboboxSelected>>', callback)
return combo
def _getSessionAction():
micIndex = self._micChooser.getSelectedIndex()
if micIndex is None:
return "Select Microscope"
camIndex = self._switchCam.widgets[micIndex].getSelectedIndex()
if camIndex is None:
return "Select Camera"
resourceId = self._micChooser.getSelectedIndex() + 1
if resourceId in self._bookings:
b = self._bookings[resourceId]
values = {
'CEM': b['application_code'],
'Owner': b['owner']['name'],
'Creator': b['creator']['name']
}
else:
values = {}
b = None
for k, v in self._textVars.items():
v.set(values.get(k, '-'))
self._current_booking = b
if b is None:
return ("There is no booking for this microscope. "
"Check the booking system. ")
return None
def _checkSessionAction():
action = _getSessionAction()
if action is None:
msg = self._createSession().getId()
else:
msg = action
self._sessionLabel.config(fg='red' if action else 'green')
self._sessionVar.set(msg)
self._createStatus = 'disabled' if action else 'normal'
btn = getattr(self, '_newSessionBtn', None)
if btn is not None:
btn.config(state=self._createStatus)
class Switcher(tk.Frame):
def __init__(self, *args, **kwargs):
tk.Frame.__init__(self, *args, **kwargs)
self._index = -1
self.widgets = []
def add(self, widget):
self.widgets.append(widget)
def set(self, i):
if i < 0 or i >= len(self.widgets):
raise Exception("Invalid index")
if self._index >= 0:
self.widgets[self._index].grid_forget()
self.widgets[i].grid(row=0, column=0, sticky='news')
self._index = i
def _showCameraOptions(chooser):
""" Show the correct camera options depending on the
selected microscope. """
i = chooser.getSelectedIndex()
self._switchCam.set(i)
_checkSessionAction()
def _onChange(*args):
if hasattr(self, '_sessionLabel'):
_checkSessionAction()
def _onChangePreprocessing(*args):
""" Called when the selection is changed. """
i = self._prepChooser.getSelectedIndex()
self._switchPre.set(i)
EXTRA_PAD = 30
f1 = OptionChooser(frame, bg='white', optionWidth=200)
f1.onSelectionChanged(_showCameraOptions)
f1.addOption('Krios α', self.data.getResourceFile("titan_small.gif"))
f1.addOption('Krios β', self.data.getResourceFile("titan_small.gif"))
f1.addOption('Talos', self.data.getResourceFile("talos_small.gif"))
__addLabeledWidget("Microscope", f1, bold=True)
self._micOrder = {TITAN_A: 0, TITAN_B: 1, TALOS: 2}
self._micChooser = f1
self._switchCam = Switcher(frame)
def _addCamChooser(*options):
oc = OptionChooser(self._switchCam, bg='white', optionWidth=200)
for o in options:
oc.addOption(o)
self._switchCam.add(oc)
oc.selectIndex(0)
oc.onSelectionChanged(_onChange)
for mic in MICROSCOPES:
_addCamChooser(*MIC_CAMERAS[mic])
#camChoosers = [_createChooser(*MIC_CAMERAS[mic]) for mic in MICROSCOPES]
# f2 = camChoosers[0]
# self._camRow = self._lastRow
__addLabeledWidget("Camera", self._switchCam)
# --------- Load some data ---------------
from emhub.client import DataClient
from emhub.utils import datetime_to_isoformat
apiJsonFile = getDataFile('api.json')
with open(apiJsonFile) as f:
apiJson = json.load(f)
dc = DataClient(apiJson['emhub']['url'])
dc.login(apiJson['emhub']['user'], apiJson['emhub']['password'])
start = datetime_to_isoformat(self.data.date.replace(hour=0))
end = datetime_to_isoformat(self.data.date.replace(hour=23, minute=59))
r = dc.request('get_bookings_range',
jsonData={
'start': start,
'end': end
})
self._bookings = {
b['resource']['id']: b
for b in r.json() if b['type'] == 'booking'
}
users = {}
def get_user(user_id):
if user_id not in users:
r = dc.request('get_users',
jsonData={'condition': 'id=%s' % user_id})
users[user_id] = r.json()[0]
return users[user_id]
def get_application_code(b):
# Take only the first part of the application label
# (because it can contains the alias in parenthesis)
m = re.search("\([^,]+(,([^,]*))\)", b['title'])
return 'fac' if m is None else m.group(2).upper().strip()
for b in self._bookings.values():
b['owner'] = get_user(b['owner']['id'])
b['creator'] = get_user(b['creator']['id'])
b['application_code'] = get_application_code(b)
dc.logout()
self._textVars = {}
def _addLabeledText(label, text):
var = tk.StringVar()
var.set(text)
labelWidget = _createLabel(text)
labelWidget.config(textvariable=var)
self._textVars[label] = var
__addLabeledWidget(label, labelWidget, bold=True)
_addLabeledText("CEM", '')
_addLabeledText("Owner", '')
_addLabeledText("Creator", '')
# --------- Session block ----------------
self._sessionVar = tk.StringVar()
self._sessionLabel = tk.Label(frame,
textvariable=self._sessionVar,
bg='white',
fg='red')
__addLabeledWidget("Session ID",
self._sessionLabel,
pady=(EXTRA_PAD, 0),
bold=True)
# --------- Preprocessing block ----------------
f4 = OptionChooser(frame, bg='white', optionWidth=200)
f4.addOption('Scipion', self.data.getResourceFile("scipion_logo.gif"))
f4.addOption('Scipion (custom)',
self.data.getResourceFile("scipion_logo.gif"))
f4.addOption(LABEL_NONE, self.data.getResourceFile("none.gif"))
f4.onSelectionChanged(_onChangePreprocessing)
self._prepChooser = f4
__addLabeledWidget("Pre-processing",
f4,
pady=(EXTRA_PAD, 0),
bold=True)
self._switchPre = Switcher(frame, bg='white')
def _addFrame():
preFrame = tk.Frame(self._switchPre, bg='white')
self._switchPre.add(preFrame)
return preFrame
preFrame1 = _addFrame()
preOptions = [("Motion correction",
['relion - motioncor', 'motioncor2']),
("CTF estimation", ['ctffind4', 'gctf'])]
self._preDict = {}
for row, (text, options) in enumerate(preOptions):
label = tk.Label(preFrame1,
text=text,
font="helvetica 12",
bg='white')
label.grid(row=row, column=0, sticky='ne')
v = tk.StringVar()
for i, o in enumerate(options):
rb = tk.Radiobutton(preFrame1,
text=o,
variable=v,
value=o,
bg='white')
rb.grid(row=row, column=i + 1, sticky='nw')
v.set(options[0])
self._preDict[text] = v
preFrame2 = _addFrame()
self._workflowVar = tk.StringVar()
entry = ttk.Entry(preFrame2, width=50, textvariable=self._workflowVar)
entry.grid(column=0, row=0)
def _onChoose(fileInfo):
self._workflowVar.set(fileInfo.getPath())
def _chooseWorkflow():
browser = FileBrowserWindow(
"Select the one of the predefined MTF files",
self.windows,
getDataFile('workflows'),
onSelect=_onChoose)
browser.show()
button = Button(preFrame2, text="Browse", command=_chooseWorkflow)
button.grid(column=1, row=0)
preFrame3 = _addFrame()
__addLabeledWidget('', self._switchPre)
f4.selectIndex(0)
f1.selectIndex(self._micOrder[self.data.microscope])
# Select Scipion as default for pre-processing
_checkSessionAction()
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, **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 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,
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)
