def _loadAnimationData(self, obj):
prot = self.protocol
animationName = obj.getFileName() # assumes that obj.getFileName is the folder of animation
animationPath = prot._getExtraPath(animationName)
#animationName = animationPath.split('animation_')[-1]
animationRoot = join(animationPath, animationName)
animationSuffixes = ['.vmd', '.pdb', 'trajectory.txt']
for s in animationSuffixes:
f = animationRoot + s
if not exists(f):
self.errorMessage('Animation file "%s" not found. ' % f)
return
# Load animation trajectory points
trajectoryPoints = np.loadtxt(animationRoot + 'trajectory.txt')
data = PathData(dim=trajectoryPoints.shape[1])
for i, row in enumerate(trajectoryPoints):
data.addPoint(Point(pointId=i+1, data=list(row), weight=1))
self.trajectoriesWindow.setPathData(data)
self.trajectoriesWindow.setAnimationName(animationName)
self.trajectoriesWindow._onUpdateClick()
def _showVmd():
vmdFn = animationRoot + '.vmd'
VmdView(' -e %s' % vmdFn).show()
self.getTkRoot().after(500, _showVmd)
def _loadAnimationData(self, obj):
prot = self.protocol
animationName = obj.getFileName(
) # assumes that obj.getFileName is the folder of animation
animationPath = prot._getExtraPath(animationName)
#animationName = animationPath.split('animation_')[-1]
animationRoot = join(animationPath, animationName)
animationSuffixes = ['.vmd', '.pdb', 'trajectory.txt']
for s in animationSuffixes:
f = animationRoot + s
if not exists(f):
self.errorMessage('Animation file "%s" not found. ' % f)
return
# Load animation trajectory points
trajectoryPoints = np.loadtxt(animationRoot + 'trajectory.txt')
data = PathData(dim=trajectoryPoints.shape[1])
for i, row in enumerate(trajectoryPoints):
data.addPoint(Point(pointId=i + 1, data=list(row), weight=1))
self.trajectoriesWindow.setPathData(data)
self.trajectoriesWindow.setAnimationName(animationName)
self.trajectoriesWindow._onUpdateClick()
def _showVmd():
vmdFn = animationRoot + '.vmd'
VmdView(' -e %s' % vmdFn).show()
self.getTkRoot().after(500, _showVmd)
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)
def _loadData(self):
from pyworkflow.em.packages.xmipp3.nma.data import PathData
data = PathData(dim=2)
bfactorFile = self.protocol._getPath('bfactor.txt')
if os.path.exists(bfactorFile):
f = open(bfactorFile)
values = map(float, f.readline().split())
f.close()
p1 = data.createEmptyPoint()
p1.setX(values[0])
p1.setY(values[1])
data.addPoint(p1)
p2 = data.createEmptyPoint()
p2.setX(values[2])
p2.setY(values[3])
data.addPoint(p2)
data.bfactor = values[4]
else:
data.bfactor = 0
return data
def _loadData(self):
from pyworkflow.em.packages.xmipp3.nma.data import PathData
data = PathData(dim=2)
bfactorFile = self.protocol._getPath('bfactor.txt')
if os.path.exists(bfactorFile):
f = open(bfactorFile)
values = map(float, f.readline().split())
f.close()
p1 = data.createEmptyPoint()
p1.setX(values[0])
p1.setY(values[1])
data.addPoint(p1)
p2 = data.createEmptyPoint()
p2.setX(values[2])
p2.setY(values[3])
data.addPoint(p2)
data.bfactor = values[4]
else:
data.bfactor = 0
return data
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)
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 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)
