def __init__(self, title, masterWindow=None, weight=True, minsize=(900, 500),
icon=Icon.SCIPION_ICON, **kwargs):
Window.__init__(self, title, masterWindow, weight=weight,
icon=icon, minsize=minsize, enableQueue=True, **kwargs)
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.rowconfigure(1, weight=1)
content.grid(row=0, column=0, sticky='news')
self.content = content
if getattr(self, 'menuCfg', None):
Window.createMainMenu(self, self.menuCfg)
self.header = self.createHeaderFrame(content)
self.header.grid(row=0, column=0, sticky='new')
self.footer = tk.Frame(content, bg='white')
self.footer.grid(row=1, column=0, sticky='news')
self.view, self.viewWidget = None, None
self.viewFuncs = {VIEW_PROJECTS: ProjectsView,
VIEW_PROTOCOLS: ProtocolsView,
VIEW_DATA: ProjectDataView,
}
def __init__(self, title, masterWindow=None, weight=True, minsize=(900, 500),
icon="scipion_bn.xbm", **args):
Window.__init__(self, title, masterWindow, weight=weight,
icon=icon, minsize=minsize, enableQueue=True)
content = tk.Frame(self.root)
content.columnconfigure(0, weight=1)
content.rowconfigure(1, weight=1)
content.grid(row=0, column=0, sticky='news')
self.content = content
Window.createMainMenu(self, self.menuCfg)
self.header = self.createHeaderFrame(content)
self.header.grid(row=0, column=0, sticky='new')
self.footer = tk.Frame(content, bg='white')
self.footer.grid(row=1, column=0, sticky='news')
self.view, self.viewWidget = None, None
self.viewFuncs = {VIEW_PROJECTS: ProjectsView,
VIEW_PROTOCOLS: ProtocolsView,
VIEW_DATA: ProjectDataView,
}
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, 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()
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 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 __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, 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 SpiderViewerWard(SpiderViewerClassify):
_targets = [SpiderProtClassifyWard]
_label = "viewer ward"
def _defineParams(self, form):
SpiderViewerClassify._defineParams(self, form)
self.groupClass.addParam('maxLevel', IntParam, default=4,
label='Maximum level',
help='Maximum level of classes to show')
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 askCreateSubset(self, output, size):
headerLabel = 'Are you sure you want to create a new set of %s with %s %s?'%(output, size, 'element' if size == 1 else 'elements')
runname = askString('Question','Run name:', self.win.getRoot(), 30, defaultValue='ProtUserSubSet', headerLabel=headerLabel)
if runname:
createFunc = getattr(self, 'save' + output)
createFunc(runname)
def _createSubsetProtocol(self, createOutputFunc, label=None):
""" Create a subset of classes or particles. """
try:
project = self.getProject()
prot = project.newProtocol(ProtUserSubSet)
prot.setObjLabel(label)
prot.inputObject.set(self.protocol)
project._setupProtocol(prot)
prot.makePathsAndClean()
createOutputFunc(prot)
prot.setStatus(STATUS_FINISHED)
project._storeProtocol(prot)
#self.project.launchProtocol(prot, wait=True)
except Exception, ex:
import traceback
traceback.print_exc()
self.win.showError(str(ex))
class SpiderViewerWard(SpiderViewerClassify):
""" Visualization of Spider - classify Ward protocol results. """
_targets = [SpiderProtClassifyWard]
_label = "viewer ward"
def _defineParams(self, form):
SpiderViewerClassify._defineParams(self, form)
self.groupClass.addParam('maxLevel',
IntParam,
default=4,
label='Maximum level',
help='Maximum level of classes to show')
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 _askCreateParticles(self):
self._askCreateSubset('Particles', self.getSelectedNodesCount(2))
def _askCreateClasses(self):
self._askCreateSubset('Classes', self.getSelectedNodesCount(1))
def _askCreateSubset(self, output, size):
if self._selectionOverlap():
self.win.showError("Classes could not overlap in the tree.")
return
s = '' if size == 1 else 's'
headerLabel = 'Are you sure you want to create a new set of ' \
' %s with %s element%s?' % (output, size, s)
runname = askString('Question',
'Run name:',
self.win.getRoot(),
30,
defaultValue='ProtUserSubSet',
headerLabel=headerLabel)
if runname:
createFunc = getattr(self, 'save' + output)
createFunc(runname)
def _createSubsetProtocol(self, createOutputFunc, label=None):
""" Create a subset of classes or particles. """
try:
project = self.getProject()
prot = project.newProtocol(ProtUserSubSet)
prot.setObjLabel(label)
prot.inputObject.set(self.protocol)
project._setupProtocol(prot)
prot.makePathsAndClean()
createOutputFunc(prot)
prot.setStatus(STATUS_FINISHED)
project._storeProtocol(prot)
#self.project.launchProtocol(prot, wait=True)
except Exception, ex:
import traceback
traceback.print_exc()
self.win.showError(str(ex))
