class HistogramPlotHandler(HasTraits):
'''
Class for handling the histograms.
'''
# Index for the histogram plot
index = Array
# The selection handler object for the selected data
selection_handler = Instance(SelectionHandler)
# OVerlayPlotContainer for the histogram plot
container = Instance(OverlayPlotContainer)
# Number of bins of the histogram
nbins = Int(10)
# Whether the data is a pandas dataframe or a numpy array
AS_PANDAS_DATAFRAME = Bool
def __init__(self):
self.index = range(self.nbins)
self.selection_handler = SelectionHandler()
self.container = OverlayPlotContainer()
def draw_histogram(self):
'''
Default function called when drawing the histogram.
'''
for component in self.container.components:
self.container.remove(component)
self.selection_handler.create_selection()
if len(self.selection_handler.selected_indices) == 1:
tuple_list = self.selection_handler.selected_indices[0]
if self.AS_PANDAS_DATAFRAME:
column_name = self.data.columns[tuple_list[1]]
y = self.data[column_name]
self.index = np.arange(self.nbins)
hist = np.histogram(y, self.nbins)[0]
plotdata = ArrayPlotData(x=self.index, y=hist)
plot = Plot(plotdata)
plot.plot(("x", "y"), type='bar', bar_width=0.5)
self.container.add(plot)
else:
column = tuple_list[1]
y = self.data[:, column]
self.index = np.arange(self.nbins)
hist = np.histogram(y, self.nbins)[0]
plotdata = ArrayPlotData(x=self.index, y=hist)
plot = Plot(plotdata)
plot.plot(("x", "y"), type='bar', bar_width=0.5)
self.container.add(plot)
self.container.request_redraw()
self.selection_handler.flush()
class HistogramPlotHandler(HasTraits):
"""
Class for handling the histograms.
"""
# Index for the histogram plot
index = Array
# The selection handler object for the selected data
selection_handler = Instance(SelectionHandler)
# OVerlayPlotContainer for the histogram plot
container = Instance(OverlayPlotContainer)
# Number of bins of the histogram
nbins = Int(10)
# Whether the data is a pandas dataframe or a numpy array
AS_PANDAS_DATAFRAME = Bool
def __init__(self):
self.index = range(self.nbins)
self.selection_handler = SelectionHandler()
self.container = OverlayPlotContainer()
def draw_histogram(self):
"""
Default function called when drawing the histogram.
"""
for component in self.container.components:
self.container.remove(component)
self.selection_handler.create_selection()
if len(self.selection_handler.selected_indices) == 1:
tuple_list = self.selection_handler.selected_indices[0]
if self.AS_PANDAS_DATAFRAME:
column_name = self.data.columns[tuple_list[1]]
y = self.data[column_name]
self.index = np.arange(self.nbins)
hist = np.histogram(y, self.nbins)[0]
plotdata = ArrayPlotData(x=self.index, y=hist)
plot = Plot(plotdata)
plot.plot(("x", "y"), type="bar", bar_width=0.5)
self.container.add(plot)
else:
column = tuple_list[1]
y = self.data[:, column]
self.index = np.arange(self.nbins)
hist = np.histogram(y, self.nbins)[0]
plotdata = ArrayPlotData(x=self.index, y=hist)
plot = Plot(plotdata)
plot.plot(("x", "y"), type="bar", bar_width=0.5)
self.container.add(plot)
self.container.request_redraw()
self.selection_handler.flush()
class CellCropper(StackViewer):
template = Array
CC = Array
peaks = List
zero=Int(0)
tmp_size = Range(low=2, high=512, value=64, cols=4)
max_pos_x=Property(depends_on=['tmp_size'])
max_pos_y=Property(depends_on=['tmp_size'])
top = Range(low='zero',high='max_pos_y', value=20, cols=4)
left = Range(low='zero',high='max_pos_x', value=20, cols=4)
is_square = Bool
tmp_plot = Instance(Plot)
findpeaks = Button
peak_width = Range(low=2, high=200, value=10)
ShowCC = Bool
numpeaks_total = Int(0,cols=5)
numpeaks_img = Int(0,cols=5)
OK_custom=OK_custom_handler
thresh=Trait(None,None,List,Tuple,Array)
thresh_upper=Float(1.0)
thresh_lower=Float(-1.0)
tmp_img_idx=Int(0)
csr=Instance(BaseCursorTool)
traits_view = View(
Group(
Group(
Item("img_container",editor=ComponentEditor(), show_label=False),
HGroup(
Item("ShowCC", editor=BooleanEditor(), label="Show cross correlation image"),
Spring(),
Item("prev_img",editor=ButtonEditor(label="<"),show_label=False, enabled_when='numfiles > 1'),
Item("next_img",editor=ButtonEditor(label=">"),show_label=False, enabled_when='numfiles > 1'),
),
label="Original image", show_border=True, trait_modified="tab_selected",
orientation='vertical',),
VGroup(
Group(
HGroup(
Item("left", label="Left coordinate", style="custom"),
Spring(),
Item("top", label="Top coordinate", style="custom"),
),
Item("tmp_size", label="Template size", style="custom"),
Item("tmp_plot",editor=ComponentEditor(height=256, width=256), show_label=False, resizable=True),
label="Template", show_border=True),
Group(
HGroup(
Item("peak_width", label="Peak width", style="custom"),
Spring(),
Item("findpeaks",editor=ButtonEditor(label="Find Peaks"),show_label=False),
),
HGroup(
Item("thresh_lower",label="Threshold Lower Value", editor=TextEditor(evaluate=float,
format_str='%1.4f')),
Spring(),
Item("thresh_upper",label="Threshold Upper Value", editor=TextEditor(evaluate=float,
format_str='%1.4f')),
),
HGroup(
Item("numpeaks_img",label="Number of Cells selected (this image)",style='readonly'),
Spring(),
Item("numpeaks_total",label="Total",style='readonly'),
),
label="Peak parameters", show_border=True),
),
orientation='horizontal'),
buttons = [ Action(name='OK', enabled_when = 'numpeaks_total > 0' ),
CancelButton ],
title="Template Picker",
handler=OK_custom, kind='livemodal',
key_bindings = key_bindings,
width=940, height=530,resizable=True)
def __init__(self, controller, *args, **kw):
super(CellCropper, self).__init__(controller, *args, **kw)
try:
import cv
except:
try:
import cv2.cv as cv
except:
print "OpenCV unavailable. Can't do cross correlation without it. Aborting."
return None
self.OK_custom=OK_custom_handler()
self.template = self.data[self.top:self.top+self.tmp_size,self.left:self.left+self.tmp_size]
tmp_plot_data=ArrayPlotData(imagedata=self.template)
tmp_plot=Plot(tmp_plot_data,default_origin="top left")
tmp_plot.img_plot("imagedata", colormap=jet)
tmp_plot.aspect_ratio=1.0
self.tmp_plot=tmp_plot
self.tmp_plotdata=tmp_plot_data
self.crop_sig=None
def render_image(self):
plot = super(CellCropper,self).render_image()
img=plot.img_plot("imagedata", colormap=gray)[0]
csr = CursorTool(img, drag_button='left', color='white',
line_width=2.0)
self.csr=csr
csr.current_position=self.left, self.top
img.overlays.append(csr)
self.img_plot=plot
return plot
# TODO: use base class render_scatter_overlay method
def render_scatplot(self):
peakdata=ArrayPlotData()
peakdata.set_data("index",self.peaks[self.img_idx][:,0])
peakdata.set_data("value",self.peaks[self.img_idx][:,1])
peakdata.set_data("color",self.peaks[self.img_idx][:,2])
scatplot=Plot(peakdata,aspect_ratio=self.img_plot.aspect_ratio,default_origin="top left")
scatplot.plot(("index", "value", "color"),
type="cmap_scatter",
name="my_plot",
color_mapper=jet(DataRange1D(low = 0.0,
high = 1.0)),
marker = "circle",
fill_alpha = 0.5,
marker_size = 6,
)
scatplot.x_grid.visible = False
scatplot.y_grid.visible = False
scatplot.range2d=self.img_plot.range2d
self.scatplot=scatplot
self.peakdata=peakdata
return scatplot
def _image_plot_container(self):
plot = self.render_image()
# Create a container to position the plot and the colorbar side-by-side
self.container=OverlayPlotContainer()
self.container.add(plot)
self.img_container = HPlotContainer(use_backbuffer = False)
self.img_container.add(self.container)
self.img_container.bgcolor = "white"
#ipdb.set_trace()
if self.numpeaks_img>0:
scatplot = self.render_scatplot()
self.container.add(scatplot)
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
return self.img_container
def draw_colorbar(self):
scatplot=self.scatplot
cmap_renderer = scatplot.plots["my_plot"][0]
selection = ColormappedSelectionOverlay(cmap_renderer, fade_alpha=0.35,
selection_type="range")
cmap_renderer.overlays.append(selection)
if self.thresh is not None:
cmap_renderer.color_data.metadata['selections']=self.thresh
cmap_renderer.color_data.metadata_changed={'selections':self.thresh}
# Create the colorbar, handing in the appropriate range and colormap
colormap=scatplot.color_mapper
colorbar = ColorBar(
index_mapper=LinearMapper(
range=DataRange1D(
low = -1.0,
high = 1.0)
),
orientation='v',
resizable='v',
width=30,
padding=20)
colorbar_selection=RangeSelection(component=colorbar)
colorbar.tools.append(colorbar_selection)
ovr=colorbar.overlays.append(
RangeSelectionOverlay(component=colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray",
metadata_name='selections'))
#ipshell('colorbar, colorbar_selection and ovr available:')
self.cbar_selection=colorbar_selection
self.cmap_renderer=cmap_renderer
colorbar.plot = cmap_renderer
colorbar.padding_top = scatplot.padding_top
colorbar.padding_bottom = scatplot.padding_bottom
self.colorbar=colorbar
return colorbar
@on_trait_change('ShowCC')
def toggle_cc_view(self):
if self.ShowCC:
self.update_CC()
grid_data_source = self.img_plot.range2d.sources[0]
grid_data_source.set_data(np.arange(self.CC.shape[1]),
np.arange(self.CC.shape[0]))
else:
self.img_plotdata.set_data("imagedata",self.data)
self.redraw_plots()
@on_trait_change("img_idx")
def update_img_depth(self):
"""
TODO: We look up the index in the model - first get a list of files, then get the name
of the file at the given index.
"""
super(CellCropper, self).update_img_depth()
if self.ShowCC:
self.update_CC()
self.redraw_plots()
def _get_max_pos_x(self):
max_pos_x=self.data.shape[-1]-self.tmp_size-1
if max_pos_x>0:
return max_pos_x
else:
return None
def _get_max_pos_y(self):
max_pos_y=self.data.shape[-2]-self.tmp_size-1
if max_pos_y>0:
return max_pos_y
else:
return None
@on_trait_change('left, top')
def update_csr_position(self):
if self.left>0:
self.csr.current_position=self.left,self.top
@on_trait_change('csr:current_position')
def update_top_left(self):
if self.csr.current_position[0]>0 or self.csr.current_position[1]>0:
if self.csr.current_position[0]>self.max_pos_x:
if self.csr.current_position[1]<self.max_pos_y:
self.top=self.csr.current_position[1]
else:
self.csr.current_position=self.max_pos_x, self.max_pos_y
elif self.csr.current_position[1]>self.max_pos_y:
self.left,self.top=self.csr.current_position[0],self.max_pos_y
else:
self.left,self.top=self.csr.current_position
@on_trait_change('left, top, tmp_size')
def update_tmp_plot(self):
self.template = self.data[self.top:self.top+self.tmp_size,self.left:self.left+self.tmp_size]
self.tmp_plotdata.set_data("imagedata", self.template)
grid_data_source = self.tmp_plot.range2d.sources[0]
grid_data_source.set_data(np.arange(self.tmp_size), np.arange(self.tmp_size))
self.tmp_img_idx=self.img_idx
if self.numpeaks_total>0:
print "clearing peaks"
self.peaks=[np.array([[0,0,-1]])]
self.update_CC()
return
def update_CC(self):
if self.ShowCC:
self.CC = cv_funcs.xcorr(self.template, self.data)
self.img_plotdata.set_data("imagedata",self.CC)
@on_trait_change('cbar_selection:selection')
def update_thresh(self):
try:
thresh=self.cbar_selection.selection
self.thresh=thresh
self.cmap_renderer.color_data.metadata['selections']=thresh
self.thresh_lower=thresh[0]
self.thresh_upper=thresh[1]
#cmap_renderer.color_data.metadata['selection_masks']=self.thresh
self.cmap_renderer.color_data.metadata_changed={'selections':thresh}
self.container.request_redraw()
self.img_container.request_redraw()
except:
pass
@on_trait_change('thresh_upper,thresh_lower')
def manual_thresh_update(self):
self.thresh=[self.thresh_lower,self.thresh_upper]
self.cmap_renderer.color_data.metadata['selections']=self.thresh
self.cmap_renderer.color_data.metadata_changed={'selections':self.thresh}
self.container.request_redraw()
self.img_container.request_redraw()
@on_trait_change('peaks,cbar_selection:selection,img_idx')
def calc_numpeaks(self):
try:
thresh=self.cbar_selection.selection
self.thresh=thresh
except:
thresh=[]
if thresh==[] or thresh==() or thresh==None:
thresh=(-1,1)
self.numpeaks_total=int(np.sum([np.sum(np.ma.masked_inside(self.peaks[i][:,2],thresh[0],thresh[1]).mask) for i in xrange(len(self.peaks))]))
try:
self.numpeaks_img=int(np.sum(np.ma.masked_inside(self.peaks[self.img_idx][:,2],thresh[0],thresh[1]).mask))
except:
self.numpeaks_img=0
@on_trait_change('findpeaks')
def locate_peaks(self):
peaks=[]
progress = ProgressDialog(title="Peak finder progress", message="Finding peaks on %s images"%self.numfiles, max=self.numfiles, show_time=True, can_cancel=False)
progress.open()
for idx in xrange(self.numfiles):
self.controller.set_active_index(idx)
self.data = self.controller.get_active_image()[:]
self.CC = cv_funcs.xcorr(self.template, self.data)
# peak finder needs peaks greater than 1. Multiply by 255 to scale them.
pks=pc.two_dim_findpeaks(self.CC*255, peak_width=self.peak_width, medfilt_radius=None)
pks[:,2]=pks[:,2]/255.
peaks.append(pks)
progress.update(idx+1)
#ipdb.set_trace()
self.peaks=peaks
self.redraw_plots()
def mask_peaks(self,idx):
thresh=self.cbar_selection.selection
if thresh==[]:
thresh=(-1,1)
mpeaks=np.ma.asarray(self.peaks[idx])
mpeaks[:,2]=np.ma.masked_outside(mpeaks[:,2],thresh[0],thresh[1])
return mpeaks
@on_trait_change("peaks")
def redraw_plots(self):
oldplot=self.img_plot
self.container.remove(oldplot)
newplot=self.render_image()
self.container.add(newplot)
self.img_plot=newplot
try:
# if these haven't been created before, this will fail. wrap in try to prevent that.
oldscat=self.scatplot
self.container.remove(oldscat)
oldcolorbar = self.colorbar
self.img_container.remove(oldcolorbar)
except:
pass
if self.numpeaks_img>0:
newscat=self.render_scatplot()
self.container.add(newscat)
self.scatplot=newscat
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
self.colorbar=colorbar
self.container.request_redraw()
self.img_container.request_redraw()
def crop_cells(self):
print "cropping cells..."
for idx in xrange(self.numfiles):
# filter the peaks that are outside the selected threshold
self.controller.set_active_index(idx)
self.data = self.controller.get_active_image()
self.name = self.controller.get_active_name()
peaks=np.ma.compress_rows(self.mask_peaks(idx))
tmp_sz=self.tmp_size
data=np.zeros((peaks.shape[0],tmp_sz,tmp_sz))
if data.shape[0] >0:
for i in xrange(peaks.shape[0]):
# crop the cells from the given locations
data[i,:,:]=self.data[peaks[i,1]:peaks[i,1]+tmp_sz,
peaks[i,0]:peaks[i,0]+tmp_sz]
# send the data to the controller for storage in the chest
self.controller.add_cells(name = self.name, data = data,
locations = peaks)
class KMeansPlotHandler(HasTraits):
"""
Class for plotting the k-means clusters.
"""
# the data to cluster
data = Array
# the dataset created after preprocessing
dataset = Array
# the sklearn.cluster.KMeans object
kmeans = Instance(KMeans)
# Number of clusters
n_clusters = Int
# Maximum iterations for the clustering algorithm
max_iter = Int
# Container for the cluster plots
container = Instance(OverlayPlotContainer)
# the columns from the dataset to omit when performing clustering
to_omit = List
def __init__(self):
self.kmeans = KMeans()
self.container = OverlayPlotContainer()
def create_dataset(self):
"""
Creates a numpy array from the current selection to pass to the
sklearn.cluster.kmeans object.
"""
if self.to_omit:
if len(self.to_omit) > 0:
n_rows = self.data.shape[0]
n_cols = self.data.shape[1]
to_omit = []
for elem in self.to_omit:
if elem.isdigit():
to_omit.append(int(elem))
dataset = self.data[:, 0].reshape((n_rows, 1))
for elem in range(n_cols):
if elem not in to_omit:
if elem > 0:
dataset = np.hstack((dataset, self.data[:, elem].reshape((n_rows, 1))))
self.dataset = dataset
def plot_clusters(self):
"""
Plots the clusters after calling the .fit method of the sklearn kmeans
estimator.
"""
self.kmeans.n_clusters = self.n_clusters
self.kmeans.fit(self.dataset)
# Reducing dimensions of the dataset and the cluster centers for
# plottting
pca = PCA(n_components=2, whiten=True)
cluster_centers = pca.fit_transform(self.kmeans.cluster_centers_)
dataset_red = pca.fit_transform(self.dataset)
removed_components = []
for component in self.container.components:
removed_components.append(component)
for component in removed_components:
self.container.remove(component)
for i in range(self.n_clusters):
current_indices = find(self.kmeans.labels_ == i)
current_data = dataset_red[current_indices, :]
plotdata = ArrayPlotData(x=current_data[:, 0], y=current_data[:, 1])
plot = Plot(plotdata)
plot.plot(("x", "y"), type="scatter", color=tuple(COLOR_PALETTE[i]))
self.container.add(plot)
plotdata_cent = ArrayPlotData(x=cluster_centers[:, 0], y=cluster_centers[:, 1])
plot_cent = Plot(plotdata_cent)
plot_cent.plot(("x", "y"), type="scatter", marker="cross", marker_size=8)
self.container.add(plot_cent)
self.container.request_redraw()
class XYPlotHandler(HasTraits):
"""
Class for handling XY plots
"""
# Whether the data is a pandas dataframe
AS_PANDAS_DATAFRAME = Bool
# The container for all current plots. Gets updated everytime a plot is
# added.
container = OverlayPlotContainer
# This can be removed.
plotdata = ArrayPlotData
# The current Plot object.
plot = Plot
# ColorTrait, mainly required for the TraitsUIItem view.
color = ColorTrait("blue")
# Marker trait for the view
marker = marker_trait
# Marker size trait
marker_size = Int(4)
# An instance of SelectionHandler for adding plots from the current
# selection.
selection_handler = Instance(SelectionHandler)
# Bool traits for checking the type of the plot (discrete / continuous)
plot_type_disc = Bool
plot_type_cont = Bool
# The data from which to draw the plots, same as the table attribute of
# CsvModel
table = Array
# The pandas data frame if AS_PANDAS_DATAFRAME
data_frame = Instance(DataFrame)
# Contains the grid underlays of all the current plots
grid_underlays = List
# Used for viewing the list of the plots and the legend
plot_list_view = Dict
# TraitsUI view for plot properties, yet to find an enaml implementation
view = View(Item("color"), Item("marker"), Item("marker_size"))
# Trait that defines whether tools are present.
add_pan_tool = Bool
add_zoom_tool = Bool
add_dragzoom = Bool
# Whether grids and axes are visible
show_grid = Bool
def __init__(self):
self.selection_handler = SelectionHandler()
self.container = OverlayPlotContainer()
self.underlays = []
self.add_pan_tool = False
self.add_zoom_tool = False
self.add_dragzoom = False
self.show_grid = False
def add_xyplot_selection(self, plot_name):
"""
Called when the 'add plot from selection button is clicked.'
"""
self.selection_handler.create_selection()
if self.selection_handler.xyplot_check():
if self.AS_PANDAS_DATAFRAME:
x_column = self.data_frame.columns[self.selection_handler.selected_indices[0][1]]
y_column = self.data_frame.columns[self.selection_handler.selected_indices[1][1]]
x = np.array(self.data_frame[x_column])
y = np.array(self.data_frame[y_column])
self.plotdata = ArrayPlotData(x=x, y=y)
else:
first_column = self.selection_handler.selected_indices[0]
second_column = self.selection_handler.selected_indices[1]
self.plotdata = ArrayPlotData(x=self.table[:, first_column[1]], y=self.table[:, second_column[1]])
plot = Plot(self.plotdata)
if self.plot_type_disc:
plot_type = "scatter"
else:
plot_type = "line"
plot.plot(("x", "y"), type=plot_type, color=self.color, marker=self.marker, marker_size=self.marker_size)
self.plot = plot
for underlay in self.plot.underlays:
if isinstance(underlay, PlotGrid):
if underlay not in self.grid_underlays:
self.grid_underlays.append(underlay)
for underlay in self.grid_underlays:
if underlay in self.plot.underlays:
self.plot.underlays.remove(underlay)
if plot_name == "":
self.plot_list_view["plot" + str(len(self.plot_list_view))] = self.plot
else:
self.plot_list_view[plot_name] = self.plot
self.container.add(self.plot)
self.container.request_redraw()
self.selection_handler.flush()
def grid_toggle(self, checked):
"""
Called when the 'Show Grid' checkbox ins toggled
"""
if not checked:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay in plot.underlays:
plot.underlays.remove(underlay)
else:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay not in plot.underlays:
plot.underlays.append(underlay)
self.container.request_redraw()
def remove_selected_plots(self, selection):
"""
Called when the 'Remove Selected Plots' button is clicked
"""
remove_indices = []
for model_index in selection:
remove_indices.append(model_index[0].row)
remove_plots = []
for index in remove_indices:
remove_plots.append(self.plot_list_view.keys()[index])
removed_plots = []
for plot in remove_plots:
removed_plots.append(self.plot_list_view.pop(plot))
for plot in self.container.components:
self.container.remove(plot)
for plot in self.plot_list_view.keys():
self.container.add(self.plot_list_view[plot])
self.container.request_redraw()
def edit_selection(self, show_grid, plot_visible, plot_type_disc):
"""
Called to start editing the selected plot. Should accompany the 'Edit
Plot' dialog.
"""
# self.selection_handler.create_selection()
# index = self.selection_handler.selected_indices[0][0]
# plot_name = self.plot_list_view.keys()[index]
# plot = self.plot_list_view[plot_name]
self.container.remove(self.plot)
self.plot_type_disc = plot_type_disc
if self.plot_type_disc:
plot_type = "scatter"
else:
plot_type = "line"
plot = Plot(self.plot.data)
plot.plot(("x", "y"), color=self.color, type=plot_type, marker=self.marker, marker_size=self.marker_size)
self.plot = plot
self.plot.visible = plot_visible
grid_underlays = []
if not show_grid:
for underlay in self.plot.underlays:
if isinstance(underlay, PlotGrid):
grid_underlays.append(underlay)
for underlay in grid_underlays:
self.plot.underlays.remove(underlay)
self.container.add(self.plot)
self.container.request_redraw()
self.selection_handler.flush()
def _add_pan_tool_changed(self):
"""
Method called when the Pan Tool checkbox is checked or unchecked.
Adds the Pan Tool to the plot container if it isn't there and vice versa.
"""
broadcaster = BroadcasterTool()
for plot in self.container.components:
if self.add_pan_tool:
pan = PanTool(plot)
broadcaster.tools.append(pan)
self.container.tools.append(broadcaster)
else:
for tool in self.container.tools:
if isinstance(tool, BroadcasterTool):
self.container.tools.remove(tool)
def _add_zoom_tool_changed(self):
"""
Method called when the Zoom Tool checkbox is checked or unchecked.
Adds the Zoom Tool to the plot container if it isn't there and vice versa.
"""
broadcaster = BroadcasterTool()
for plot in self.container.components:
if self.add_zoom_tool:
pan = ZoomTool(plot)
broadcaster.tools.append(pan)
self.container.tools.append(broadcaster)
else:
for tool in self.container.tools:
if isinstance(tool, BroadcasterTool):
self.container.tools.remove(tool)
def _add_dragzoom_changed(self):
"""
Method called when the Pan Tool checkbox is checked or unchecked.
Adds the Pan Tool to the plot container if it isn't there and vice versa.
"""
broadcaster = BroadcasterTool()
for plot in self.container.components:
if self.add_dragzoom:
pan = BetterSelectingZoom(
plot,
always_on=True,
tool_mode="box",
drag_button="left",
color="lightskyblue",
alpha=0.4,
border_color="dodgerblue",
)
broadcaster.tools.append(pan)
self.container.tools.append(broadcaster)
else:
for tool in self.container.tools:
if isinstance(tool, BroadcasterTool):
self.container.tools.remove(tool)
def _show_grid_changed(self):
"""
Called when the Show grid checkbox is checked or unchecked. Adds a grid
if one is not present and removes if present.
"""
if not self.show_grid:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay in plot.underlays:
plot.underlays.remove(underlay)
else:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay not in plot.underlays:
plot.underlays.append(underlay)
self.container.request_redraw()
def reassign_current_plot(self):
"""
Reassigns the currently selected plot.
"""
self.selection_handler.create_selection()
plot_index = self.selection_handler.selected_indices[0][0]
plot_name = self.plot_list_view.keys()[plot_index]
self.plot = self.plot_list_view[plot_name]
self.selection_handler.flush()
class StackedPlot(ChacoPlot):
offset = Range(0.0, 1.0, 0.015)
value_range = Range(0.01, 1.05, 1.00)
flip_order = Bool(False)
def _get_traits_group(self):
return VGroup(
HGroup(Item("flip_order"), Item("offset"), Item("value_range")),
UItem("component", editor=ComponentEditor()),
)
def __init__(self):
super(StackedPlot, self).__init__()
self.container = OverlayPlotContainer(
bgcolor="white", use_backbuffer=True, border_visible=True, padding=50, padding_left=110, fill_padding=True
)
self.data = ArrayPlotData()
self.chaco_plot = None
self.value_mapper = None
self.index_mapper = None
self.x_axis = PlotAxis(
component=self.container,
orientation="bottom",
title=u"Angle (2\u0398)",
title_font=settings.axis_title_font,
tick_label_font=settings.tick_font,
)
y_axis_title = "Normalized intensity (%s)" % get_value_scale_label("linear")
self.y_axis = PlotAxis(
component=self.container,
orientation="left",
title=y_axis_title,
title_font=settings.axis_title_font,
tick_label_font=settings.tick_font,
)
self.container.overlays.extend([self.x_axis, self.y_axis])
self.container.tools.append(TraitsTool(self.container, classes=[LinePlot, PlotAxis]))
self.colors = []
self.last_flip_order = self.flip_order
@on_trait_change("offset, value_range, flip_order")
def _replot_data(self):
self._plot(self.data_x, None, self.data_z, self.scale)
self.container.request_redraw()
def _prepare_data(self, datasets):
interpolate = True
stack = stack_datasets(datasets)
if interpolate:
(x, z) = interpolate_datasets(stack, points=4800)
x = array([x] * len(datasets))
else:
x, z = map(np.transpose, np.transpose(stack))
return x, None, z
def _plot(self, x, y, z, scale):
self.data_x, self.data_z, self.scale = x, z, scale
if self.container.components:
self.colors = map(lambda plot: plot.color, self.container.components)
if self.last_flip_order != self.flip_order:
self.colors.reverse()
self.container.remove(*self.container.components)
# Use a custom renderer so plot lines are clickable
self.chaco_plot = Plot(self.data, renderer_map={"line": ClickableLinePlot})
self.chaco_plot.bgcolor = "white"
self.value_mapper = None
self.index_mapper = None
if len(self.data_x) == len(self.colors):
colors = self.colors[:]
else:
colors = ["black"] * len(self.data_x)
if self.flip_order:
z = z[::-1]
spacing = (z.max(axis=1) - z.min(axis=1)).min() * self.value_range
offset = spacing * self.offset
for i, (x_row, z_row) in enumerate(zip(x, z)):
self.data.set_data("data_x_" + str(i), x_row)
self.data.set_data("data_y_offset_" + str(i), z_row * self.value_range + offset * i)
plots = self.chaco_plot.plot(("data_x_" + str(i), "data_y_offset_" + str(i)), color=colors[i], type="line")
plot = plots[0]
self.container.add(plot)
# Required for double-clicking plots
plot.index.sort_order = "ascending"
plot.value.sort_order = "ascending"
if self.value_mapper is None:
self.index_mapper = plot.index_mapper
self.value_mapper = plot.value_mapper
else:
plot.value_mapper = self.value_mapper
self.value_mapper.range.add(plot.value)
plot.index_mapper = self.index_mapper
self.index_mapper.range.add(plot.index)
range = self.value_mapper.range
range.high = (range.high - range.low) * self.value_range + range.low
self.x_axis.mapper = self.index_mapper
self.y_axis.mapper = self.value_mapper
self.y_axis.title = "Normalized intensity (%s)" % get_value_scale_label(scale)
self.zoom_tool = ClickUndoZoomTool(
plot,
tool_mode="box",
always_on=True,
pointer="cross",
drag_button=settings.zoom_button,
undo_button=settings.undo_button,
)
plot.overlays.append(self.zoom_tool)
self.last_flip_order = self.flip_order
return self.container
def _reset_view(self):
self.zoom_tool.revert_history_all()
class KMeansPlotHandler(HasTraits):
'''
Class for plotting the k-means clusters.
'''
# the data to cluster
data = Array
# the dataset created after preprocessing
dataset = Array
# the sklearn.cluster.KMeans object
kmeans = Instance(KMeans)
# Number of clusters
n_clusters = Int
# Maximum iterations for the clustering algorithm
max_iter = Int
# Container for the cluster plots
container = Instance(OverlayPlotContainer)
# the columns from the dataset to omit when performing clustering
to_omit = List
def __init__(self):
self.kmeans = KMeans()
self.container = OverlayPlotContainer()
def create_dataset(self):
'''
Creates a numpy array from the current selection to pass to the
sklearn.cluster.kmeans object.
'''
if self.to_omit:
if len(self.to_omit) > 0:
n_rows = self.data.shape[0]
n_cols = self.data.shape[1]
to_omit = []
for elem in self.to_omit:
if elem.isdigit():
to_omit.append(int(elem))
dataset = self.data[:, 0].reshape((n_rows, 1))
for elem in range(n_cols):
if elem not in to_omit:
if elem > 0:
dataset = np.hstack(
(dataset, self.data[:, elem].reshape(
(n_rows, 1))))
self.dataset = dataset
def plot_clusters(self):
'''
Plots the clusters after calling the .fit method of the sklearn kmeans
estimator.
'''
self.kmeans.n_clusters = self.n_clusters
self.kmeans.fit(self.dataset)
# Reducing dimensions of the dataset and the cluster centers for
# plottting
pca = PCA(n_components=2, whiten=True)
cluster_centers = pca.fit_transform(self.kmeans.cluster_centers_)
dataset_red = pca.fit_transform(self.dataset)
removed_components = []
for component in self.container.components:
removed_components.append(component)
for component in removed_components:
self.container.remove(component)
for i in range(self.n_clusters):
current_indices = find(self.kmeans.labels_ == i)
current_data = dataset_red[current_indices, :]
plotdata = ArrayPlotData(x=current_data[:, 0],
y=current_data[:, 1])
plot = Plot(plotdata)
plot.plot(("x", "y"),
type='scatter',
color=tuple(COLOR_PALETTE[i]))
self.container.add(plot)
plotdata_cent = ArrayPlotData(x=cluster_centers[:, 0],
y=cluster_centers[:, 1])
plot_cent = Plot(plotdata_cent)
plot_cent.plot(("x", "y"),
type='scatter',
marker='cross',
marker_size=8)
self.container.add(plot_cent)
self.container.request_redraw()
class XYPlotHandler(HasTraits):
'''
Class for handling XY plots
'''
# Whether the data is a pandas dataframe
AS_PANDAS_DATAFRAME = Bool
# The container for all current plots. Gets updated everytime a plot is
# added.
container = OverlayPlotContainer
# This can be removed.
plotdata = ArrayPlotData
# The current Plot object.
plot = Plot
# ColorTrait, mainly required for the TraitsUIItem view.
color = ColorTrait("blue")
# Marker trait for the view
marker = marker_trait
# Marker size trait
marker_size = Int(4)
# An instance of SelectionHandler for adding plots from the current
# selection.
selection_handler = Instance(SelectionHandler)
# Bool traits for checking the type of the plot (discrete / continuous)
plot_type_disc = Bool
plot_type_cont = Bool
# The data from which to draw the plots, same as the table attribute of
# CsvModel
table = Array
# The pandas data frame if AS_PANDAS_DATAFRAME
data_frame = Instance(DataFrame)
# Contains the grid underlays of all the current plots
grid_underlays = List
# Used for viewing the list of the plots and the legend
plot_list_view = Dict
# TraitsUI view for plot properties, yet to find an enaml implementation
view = View(Item('color'), Item('marker'), Item('marker_size'))
# Trait that defines whether tools are present.
add_pan_tool = Bool
add_zoom_tool = Bool
add_dragzoom = Bool
# Whether grids and axes are visible
show_grid = Bool
def __init__(self):
self.selection_handler = SelectionHandler()
self.container = OverlayPlotContainer()
self.underlays = []
self.add_pan_tool = False
self.add_zoom_tool = False
self.add_dragzoom = False
self.show_grid = False
def add_xyplot_selection(self, plot_name):
'''
Called when the 'add plot from selection button is clicked.'
'''
self.selection_handler.create_selection()
if self.selection_handler.xyplot_check():
if self.AS_PANDAS_DATAFRAME:
x_column = self.data_frame.columns[
self.selection_handler.selected_indices[0][1]]
y_column = self.data_frame.columns[
self.selection_handler.selected_indices[1][1]]
x = np.array(self.data_frame[x_column])
y = np.array(self.data_frame[y_column])
self.plotdata = ArrayPlotData(x=x, y=y)
else:
first_column = self.selection_handler.selected_indices[0]
second_column = self.selection_handler.selected_indices[1]
self.plotdata = ArrayPlotData(x=self.table[:, first_column[1]],
y=self.table[:,
second_column[1]])
plot = Plot(self.plotdata)
if self.plot_type_disc:
plot_type = 'scatter'
else:
plot_type = 'line'
plot.plot(("x", "y"),
type=plot_type,
color=self.color,
marker=self.marker,
marker_size=self.marker_size)
self.plot = plot
for underlay in self.plot.underlays:
if isinstance(underlay, PlotGrid):
if underlay not in self.grid_underlays:
self.grid_underlays.append(underlay)
for underlay in self.grid_underlays:
if underlay in self.plot.underlays:
self.plot.underlays.remove(underlay)
if plot_name == '':
self.plot_list_view['plot' +
str(len(self.plot_list_view))] = self.plot
else:
self.plot_list_view[plot_name] = self.plot
self.container.add(self.plot)
self.container.request_redraw()
self.selection_handler.flush()
def grid_toggle(self, checked):
'''
Called when the 'Show Grid' checkbox ins toggled
'''
if not checked:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay in plot.underlays:
plot.underlays.remove(underlay)
else:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay not in plot.underlays:
plot.underlays.append(underlay)
self.container.request_redraw()
def remove_selected_plots(self, selection):
'''
Called when the 'Remove Selected Plots' button is clicked
'''
remove_indices = []
for model_index in selection:
remove_indices.append(model_index[0].row)
remove_plots = []
for index in remove_indices:
remove_plots.append(self.plot_list_view.keys()[index])
removed_plots = []
for plot in remove_plots:
removed_plots.append(self.plot_list_view.pop(plot))
for plot in self.container.components:
self.container.remove(plot)
for plot in self.plot_list_view.keys():
self.container.add(self.plot_list_view[plot])
self.container.request_redraw()
def edit_selection(self, show_grid, plot_visible, plot_type_disc):
'''
Called to start editing the selected plot. Should accompany the 'Edit
Plot' dialog.
'''
#self.selection_handler.create_selection()
#index = self.selection_handler.selected_indices[0][0]
#plot_name = self.plot_list_view.keys()[index]
#plot = self.plot_list_view[plot_name]
self.container.remove(self.plot)
self.plot_type_disc = plot_type_disc
if self.plot_type_disc:
plot_type = 'scatter'
else:
plot_type = 'line'
plot = Plot(self.plot.data)
plot.plot(("x", "y"),
color=self.color,
type=plot_type,
marker=self.marker,
marker_size=self.marker_size)
self.plot = plot
self.plot.visible = plot_visible
grid_underlays = []
if not show_grid:
for underlay in self.plot.underlays:
if isinstance(underlay, PlotGrid):
grid_underlays.append(underlay)
for underlay in grid_underlays:
self.plot.underlays.remove(underlay)
self.container.add(self.plot)
self.container.request_redraw()
self.selection_handler.flush()
def _add_pan_tool_changed(self):
'''
Method called when the Pan Tool checkbox is checked or unchecked.
Adds the Pan Tool to the plot container if it isn't there and vice versa.
'''
broadcaster = BroadcasterTool()
for plot in self.container.components:
if self.add_pan_tool:
pan = PanTool(plot)
broadcaster.tools.append(pan)
self.container.tools.append(broadcaster)
else:
for tool in self.container.tools:
if isinstance(tool, BroadcasterTool):
self.container.tools.remove(tool)
def _add_zoom_tool_changed(self):
'''
Method called when the Zoom Tool checkbox is checked or unchecked.
Adds the Zoom Tool to the plot container if it isn't there and vice versa.
'''
broadcaster = BroadcasterTool()
for plot in self.container.components:
if self.add_zoom_tool:
pan = ZoomTool(plot)
broadcaster.tools.append(pan)
self.container.tools.append(broadcaster)
else:
for tool in self.container.tools:
if isinstance(tool, BroadcasterTool):
self.container.tools.remove(tool)
def _add_dragzoom_changed(self):
'''
Method called when the Pan Tool checkbox is checked or unchecked.
Adds the Pan Tool to the plot container if it isn't there and vice versa.
'''
broadcaster = BroadcasterTool()
for plot in self.container.components:
if self.add_dragzoom:
pan = BetterSelectingZoom(plot,
always_on=True,
tool_mode='box',
drag_button='left',
color='lightskyblue',
alpha=0.4,
border_color='dodgerblue')
broadcaster.tools.append(pan)
self.container.tools.append(broadcaster)
else:
for tool in self.container.tools:
if isinstance(tool, BroadcasterTool):
self.container.tools.remove(tool)
def _show_grid_changed(self):
'''
Called when the Show grid checkbox is checked or unchecked. Adds a grid
if one is not present and removes if present.
'''
if not self.show_grid:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay in plot.underlays:
plot.underlays.remove(underlay)
else:
for plot in self.container.components:
for underlay in self.grid_underlays:
if underlay not in plot.underlays:
plot.underlays.append(underlay)
self.container.request_redraw()
def reassign_current_plot(self):
'''
Reassigns the currently selected plot.
'''
self.selection_handler.create_selection()
plot_index = self.selection_handler.selected_indices[0][0]
plot_name = self.plot_list_view.keys()[plot_index]
self.plot = self.plot_list_view[plot_name]
self.selection_handler.flush()
class StackedPlot(ChacoPlot):
offset = Range(0.0, 1.0, 0.015)
value_range = Range(0.01, 1.05, 1.00)
flip_order = Bool(False)
def _get_traits_group(self):
return VGroup(
HGroup(
Item('flip_order'),
Item('offset'),
Item('value_range'),
),
UItem('component', editor=ComponentEditor()),
)
def __init__(self):
super(StackedPlot, self).__init__()
self.container = OverlayPlotContainer(bgcolor='white',
use_backbuffer=True,
border_visible=True,
padding=50,
padding_left=110,
fill_padding=True
)
self.data = ArrayPlotData()
self.chaco_plot = None
self.value_mapper = None
self.index_mapper = None
self.x_axis = MyPlotAxis(component=self.container,
orientation='bottom',
title=u'Angle (2\u0398)',
title_font=settings.axis_title_font,
tick_label_font=settings.tick_font)
y_axis_title = 'Normalized intensity (%s)' % get_value_scale_label('linear')
self.y_axis = MyPlotAxis(component=self.container,
orientation='left',
title=y_axis_title,
title_font=settings.axis_title_font,
tick_label_font=settings.tick_font)
self.container.overlays.extend([self.x_axis, self.y_axis])
self.container.tools.append(
TraitsTool(self.container, classes=[LinePlot,MyPlotAxis]))
self.colors = []
self.last_flip_order = self.flip_order
@on_trait_change('offset, value_range, flip_order')
def _replot_data(self):
self._plot(self.data_x, None, self.data_z, self.scale)
self.container.request_redraw()
# def _prepare_data(self, datasets):
def _prepare_data(self, stack):
# stack = stack_datasets(datasets)
x = stack[:,:,0]
z = stack[:,:,2]
return x, None, z
def _plot(self, x, y, z, scale):
self.data_x, self.data_z, self.scale = x, z, scale
if self.container.components:
self.colors = map(lambda plot: plot.color, self.container.components)
if self.last_flip_order != self.flip_order:
self.colors.reverse()
self.container.remove(*self.container.components)
# Use a custom renderer so plot lines are clickable
self.chaco_plot = Plot(self.data,
renderer_map={ 'line': ClickableLinePlot })
self.chaco_plot.bgcolor = 'white'
self.value_mapper = None
self.index_mapper = None
if len(self.data_x) == len(self.colors):
colors = self.colors[:]
else:
colors = ['black'] * len(self.data_x)
if self.flip_order:
z = z[::-1]
spacing = (z.max(axis=1) - z.min(axis=1)).min() * self.value_range
offset = spacing * self.offset
for i, (x_row, z_row) in enumerate(zip(x, z)):
self.data.set_data('data_x_' + str(i), x_row)
self.data.set_data('data_y_offset_' + str(i), z_row * self.value_range + offset * i)
plots = self.chaco_plot.plot(('data_x_' + str(i), 'data_y_offset_' + str(i)), color=colors[i], type='line')
plot = plots[0]
self.container.add(plot)
# Required for double-clicking plots
plot.index.sort_order = 'ascending'
plot.value.sort_order = 'ascending'
if self.value_mapper is None:
self.index_mapper = plot.index_mapper
self.value_mapper = plot.value_mapper
else:
plot.value_mapper = self.value_mapper
self.value_mapper.range.add(plot.value)
plot.index_mapper = self.index_mapper
self.index_mapper.range.add(plot.index)
range = self.value_mapper.range
range.high = (range.high - range.low) * self.value_range + range.low
self.x_axis.mapper = self.index_mapper
self.y_axis.mapper = self.value_mapper
self.y_axis.title = 'Normalized intensity (%s)' % \
get_value_scale_label(scale)
self.zoom_tool = ClickUndoZoomTool(
plot, tool_mode="box", always_on=True, pointer="cross",
drag_button=settings.zoom_button,
undo_button=settings.undo_button,
)
plot.overlays.append(self.zoom_tool)
self.last_flip_order = self.flip_order
return self.container
def _reset_view(self):
self.zoom_tool.revert_history_all()
class TemplatePicker(HasTraits):
template = Array
CC = Array
peaks = List
zero=Int(0)
tmp_size = Range(low=2, high=512, value=64, cols=4)
max_pos_x=Property(depends_on=['tmp_size'])
max_pos_y=Property(depends_on=['tmp_size'])
top = Range(low='zero',high='max_pos_y', value=20, cols=4)
left = Range(low='zero',high='max_pos_x', value=20, cols=4)
is_square = Bool
img_plot = Instance(Plot)
tmp_plot = Instance(Plot)
findpeaks = Button
next_img = Button
prev_img = Button
peak_width = Range(low=2, high=200, value=10)
tab_selected = Event
ShowCC = Bool
img_container = Instance(Component)
container = Instance(Component)
colorbar= Instance(Component)
numpeaks_total = Int(0,cols=5)
numpeaks_img = Int(0,cols=5)
OK_custom=OK_custom_handler
cbar_selection = Instance(RangeSelection)
cbar_selected = Event
thresh=Trait(None,None,List,Tuple,Array)
thresh_upper=Float(1.0)
thresh_lower=Float(0.0)
numfiles=Int(1)
img_idx=Int(0)
tmp_img_idx=Int(0)
csr=Instance(BaseCursorTool)
traits_view = View(
Group(
Group(
Item("img_container",editor=ComponentEditor(), show_label=False),
HGroup(
Item("ShowCC", editor=BooleanEditor(), label="Show cross correlation image"),
Spring(),
Item("prev_img",editor=ButtonEditor(label="<"),show_label=False, enabled_when='numfiles > 1'),
Item("next_img",editor=ButtonEditor(label=">"),show_label=False, enabled_when='numfiles > 1'),
),
label="Original image", show_border=True, trait_modified="tab_selected",
orientation='vertical',),
VGroup(
Group(
HGroup(
Item("left", label="Left coordinate", style="custom"),
Spring(),
Item("top", label="Top coordinate", style="custom"),
),
Item("tmp_size", label="Template size", style="custom"),
Item("tmp_plot",editor=ComponentEditor(height=256, width=256), show_label=False, resizable=True),
label="Template", show_border=True),
Group(
HGroup(
Item("peak_width", label="Peak width", style="custom"),
Spring(),
Item("findpeaks",editor=ButtonEditor(label="Find Peaks"),show_label=False),
),
HGroup(
Item("thresh_lower",label="Threshold Lower Value", editor=TextEditor(evaluate=float,
format_str='%1.4f')),
Spring(),
Item("thresh_upper",label="Threshold Upper Value", editor=TextEditor(evaluate=float,
format_str='%1.4f')),
),
HGroup(
Item("numpeaks_img",label="Number of Cells selected (this image)",style='readonly'),
Spring(),
Item("numpeaks_total",label="Total",style='readonly'),
),
label="Peak parameters", show_border=True),
),
orientation='horizontal'),
buttons = [ Action(name='OK', enabled_when = 'numpeaks_total > 0' ),
CancelButton ],
title="Template Picker",
handler=OK_custom, kind='livemodal',
key_bindings = key_bindings,
width=940, height=530,resizable=True)
def __init__(self, signal_instance):
super(TemplatePicker, self).__init__()
try:
import cv
except:
try:
import cv2.cv as cv
except:
print "OpenCV unavailable. Can't do cross correlation without it. Aborting."
return None
self.OK_custom=OK_custom_handler()
self.sig=signal_instance
if not hasattr(self.sig.mapped_parameters,"original_files"):
self.titles=[os.path.splitext(self.sig.mapped_parameters.title)[0]]
else:
self.numfiles=len(self.sig.mapped_parameters.original_files.keys())
self.titles=self.sig.mapped_parameters.original_files.keys()
tmp_plot_data=ArrayPlotData(imagedata=self.sig.data[self.img_idx,self.top:self.top+self.tmp_size,self.left:self.left+self.tmp_size])
tmp_plot=Plot(tmp_plot_data,default_origin="top left")
tmp_plot.img_plot("imagedata", colormap=jet)
tmp_plot.aspect_ratio=1.0
self.tmp_plot=tmp_plot
self.tmp_plotdata=tmp_plot_data
self.img_plotdata=ArrayPlotData(imagedata=self.sig.data[self.img_idx,:,:])
self.img_container=self._image_plot_container()
self.crop_sig=None
def render_image(self):
plot = Plot(self.img_plotdata,default_origin="top left")
img=plot.img_plot("imagedata", colormap=gray)[0]
plot.title="%s of %s: "%(self.img_idx+1,self.numfiles)+self.titles[self.img_idx]
plot.aspect_ratio=float(self.sig.data.shape[2])/float(self.sig.data.shape[1])
csr = CursorTool(img, drag_button='left', color='white',
line_width=2.0)
self.csr=csr
csr.current_position=self.left, self.top
img.overlays.append(csr)
# attach the rectangle tool
plot.tools.append(PanTool(plot,drag_button="right"))
zoom = ZoomTool(plot, tool_mode="box", always_on=False, aspect_ratio=plot.aspect_ratio)
plot.overlays.append(zoom)
self.img_plot=plot
return plot
def render_scatplot(self):
peakdata=ArrayPlotData()
peakdata.set_data("index",self.peaks[self.img_idx][:,0])
peakdata.set_data("value",self.peaks[self.img_idx][:,1])
peakdata.set_data("color",self.peaks[self.img_idx][:,2])
scatplot=Plot(peakdata,aspect_ratio=self.img_plot.aspect_ratio,default_origin="top left")
scatplot.plot(("index", "value", "color"),
type="cmap_scatter",
name="my_plot",
color_mapper=jet(DataRange1D(low = 0.0,
high = 1.0)),
marker = "circle",
fill_alpha = 0.5,
marker_size = 6,
)
scatplot.x_grid.visible = False
scatplot.y_grid.visible = False
scatplot.range2d=self.img_plot.range2d
self.scatplot=scatplot
self.peakdata=peakdata
return scatplot
def _image_plot_container(self):
plot = self.render_image()
# Create a container to position the plot and the colorbar side-by-side
self.container=OverlayPlotContainer()
self.container.add(plot)
self.img_container = HPlotContainer(use_backbuffer = False)
self.img_container.add(self.container)
self.img_container.bgcolor = "white"
if self.numpeaks_img>0:
scatplot = self.render_scatplot()
self.container.add(scatplot)
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
return self.img_container
def draw_colorbar(self):
scatplot=self.scatplot
cmap_renderer = scatplot.plots["my_plot"][0]
selection = ColormappedSelectionOverlay(cmap_renderer, fade_alpha=0.35,
selection_type="range")
cmap_renderer.overlays.append(selection)
if self.thresh is not None:
cmap_renderer.color_data.metadata['selections']=self.thresh
cmap_renderer.color_data.metadata_changed={'selections':self.thresh}
# Create the colorbar, handing in the appropriate range and colormap
colormap=scatplot.color_mapper
colorbar = ColorBar(index_mapper=LinearMapper(range=DataRange1D(low = 0.0,
high = 1.0)),
orientation='v',
resizable='v',
width=30,
padding=20)
colorbar_selection=RangeSelection(component=colorbar)
colorbar.tools.append(colorbar_selection)
ovr=colorbar.overlays.append(RangeSelectionOverlay(component=colorbar,
border_color="white",
alpha=0.8,
fill_color="lightgray",
metadata_name='selections'))
#ipshell('colorbar, colorbar_selection and ovr available:')
self.cbar_selection=colorbar_selection
self.cmap_renderer=cmap_renderer
colorbar.plot = cmap_renderer
colorbar.padding_top = scatplot.padding_top
colorbar.padding_bottom = scatplot.padding_bottom
self.colorbar=colorbar
return colorbar
@on_trait_change('ShowCC')
def toggle_cc_view(self):
if self.ShowCC:
self.update_CC()
grid_data_source = self.img_plot.range2d.sources[0]
grid_data_source.set_data(np.arange(self.CC.shape[1]),
np.arange(self.CC.shape[0]))
else:
self.img_plotdata.set_data("imagedata",self.sig.data[self.img_idx,:,:])
self.redraw_plots()
@on_trait_change("img_idx")
def update_img_depth(self):
if self.ShowCC:
self.update_CC()
else:
self.img_plotdata.set_data("imagedata",self.sig.data[self.img_idx,:,:])
self.img_plot.title="%s of %s: "%(self.img_idx+1,self.numfiles)+self.titles[self.img_idx]
self.redraw_plots()
def _get_max_pos_x(self):
max_pos_x=self.sig.data.shape[-1]-self.tmp_size-1
if max_pos_x>0:
return max_pos_x
else:
return None
def _get_max_pos_y(self):
max_pos_y=self.sig.data.shape[-2]-self.tmp_size-1
if max_pos_y>0:
return max_pos_y
else:
return None
@on_trait_change('next_img')
def increase_img_idx(self,info):
if self.img_idx==(self.numfiles-1):
self.img_idx=0
else:
self.img_idx+=1
@on_trait_change('prev_img')
def decrease_img_idx(self,info):
if self.img_idx==0:
self.img_idx=self.numfiles-1
else:
self.img_idx-=1
@on_trait_change('left, top')
def update_csr_position(self):
if self.left>0:
self.csr.current_position=self.left,self.top
@on_trait_change('csr:current_position')
def update_top_left(self):
if self.csr.current_position[0]>0 or self.csr.current_position[1]>0:
if self.csr.current_position[0]>self.max_pos_x:
if self.csr.current_position[1]<self.max_pos_y:
self.top=self.csr.current_position[1]
else:
self.csr.current_position=self.max_pos_x, self.max_pos_y
elif self.csr.current_position[1]>self.max_pos_y:
self.left,self.top=self.csr.current_position[0],self.max_pos_y
else:
self.left,self.top=self.csr.current_position
@on_trait_change('left, top, tmp_size')
def update_tmp_plot(self):
self.tmp_plotdata.set_data("imagedata",
self.sig.data[self.img_idx,self.top:self.top+self.tmp_size,self.left:self.left+self.tmp_size])
grid_data_source = self.tmp_plot.range2d.sources[0]
grid_data_source.set_data(np.arange(self.tmp_size), np.arange(self.tmp_size))
self.tmp_img_idx=self.img_idx
if self.numpeaks_total>0:
print "clearing peaks"
self.peaks=[np.array([[0,0,-1]])]
return
@on_trait_change('left, top, tmp_size')
def update_CC(self):
if self.ShowCC:
self.CC = cv_funcs.xcorr(self.sig.data[self.tmp_img_idx,self.top:self.top+self.tmp_size,
self.left:self.left+self.tmp_size],
self.sig.data[self.img_idx,:,:])
self.img_plotdata.set_data("imagedata",self.CC)
@on_trait_change('cbar_selection:selection')
def update_thresh(self):
try:
thresh=self.cbar_selection.selection
self.thresh=thresh
self.cmap_renderer.color_data.metadata['selections']=thresh
self.thresh_lower=thresh[0]
self.thresh_upper=thresh[1]
#cmap_renderer.color_data.metadata['selection_masks']=self.thresh
self.cmap_renderer.color_data.metadata_changed={'selections':thresh}
self.container.request_redraw()
self.img_container.request_redraw()
except:
pass
@on_trait_change('thresh_upper,thresh_lower')
def manual_thresh_update(self):
self.thresh=[self.thresh_lower,self.thresh_upper]
self.cmap_renderer.color_data.metadata['selections']=self.thresh
self.cmap_renderer.color_data.metadata_changed={'selections':self.thresh}
self.container.request_redraw()
self.img_container.request_redraw()
@on_trait_change('peaks,cbar_selection:selection,img_idx')
def calc_numpeaks(self):
try:
thresh=self.cbar_selection.selection
self.thresh=thresh
except:
thresh=[]
if thresh==[] or thresh==() or thresh==None:
thresh=(0,1)
self.numpeaks_total=int(np.sum([np.sum(np.ma.masked_inside(self.peaks[i][:,2],thresh[0],thresh[1]).mask) for i in xrange(len(self.peaks))]))
try:
self.numpeaks_img=int(np.sum(np.ma.masked_inside(self.peaks[self.img_idx][:,2],thresh[0],thresh[1]).mask))
except:
self.numpeaks_img=0
@on_trait_change('findpeaks')
def locate_peaks(self):
from hyperspy import peak_char as pc
peaks=[]
"""from hyperspy.misc.progressbar import ProgressBar, \
Percentage, RotatingMarker, ETA, Bar
widgets = ['Locating peaks: ', Percentage(), ' ', Bar(marker=RotatingMarker()),
' ', ETA()]
pbar = ProgressBar(widgets=widgets, maxval=100).start()"""
progress = ProgressDialog(title="Peak finder progress", message="Finding peaks on %s images"%self.numfiles, max=self.numfiles, show_time=True, can_cancel=False)
progress.open()
for idx in xrange(self.numfiles):
#pbar.update(float(idx)/self.numfiles*100)
self.CC = cv_funcs.xcorr(self.sig.data[self.tmp_img_idx,
self.top:self.top+self.tmp_size,
self.left:self.left+self.tmp_size],
self.sig.data[idx,:,:])
# peak finder needs peaks greater than 1. Multiply by 255 to scale them.
pks=pc.two_dim_findpeaks(self.CC*255, peak_width=self.peak_width, medfilt_radius=None)
pks[:,2]=pks[:,2]/255.
peaks.append(pks)
progress.update(idx+1)
#pbar.finish()
self.peaks=peaks
def mask_peaks(self,idx):
thresh=self.cbar_selection.selection
if thresh==[]:
thresh=(0,1)
mpeaks=np.ma.asarray(self.peaks[idx])
mpeaks[:,2]=np.ma.masked_outside(mpeaks[:,2],thresh[0],thresh[1])
return mpeaks
@on_trait_change("peaks")
def redraw_plots(self):
oldplot=self.img_plot
self.container.remove(oldplot)
newplot=self.render_image()
self.container.add(newplot)
self.img_plot=newplot
try:
# if these haven't been created before, this will fail. wrap in try to prevent that.
oldscat=self.scatplot
self.container.remove(oldscat)
oldcolorbar = self.colorbar
self.img_container.remove(oldcolorbar)
except:
pass
if self.numpeaks_img>0:
newscat=self.render_scatplot()
self.container.add(newscat)
self.scatplot=newscat
colorbar = self.draw_colorbar()
self.img_container.add(colorbar)
self.colorbar=colorbar
self.container.request_redraw()
self.img_container.request_redraw()
def crop_cells_stack(self):
from hyperspy.signals.aggregate import AggregateCells
if self.numfiles==1:
self.crop_sig=self.crop_cells()
return
else:
crop_agg=[]
for idx in xrange(self.numfiles):
peaks=np.ma.compress_rows(self.mask_peaks(idx))
if peaks.any():
crop_agg.append(self.crop_cells(idx))
self.crop_sig=AggregateCells(*crop_agg)
return
def crop_cells(self,idx=0):
print "cropping cells..."
from hyperspy.signals.image import Image
# filter the peaks that are outside the selected threshold
peaks=np.ma.compress_rows(self.mask_peaks(idx))
tmp_sz=self.tmp_size
data=np.zeros((peaks.shape[0],tmp_sz,tmp_sz))
if not hasattr(self.sig.mapped_parameters,"original_files"):
parent=self.sig
else:
parent=self.sig.mapped_parameters.original_files[self.titles[idx]]
pmp=parent.mapped_parameters
positions=np.zeros((peaks.shape[0],1),dtype=[('filename','a256'),('id','i4'),('position','f4',(1,2))])
for i in xrange(peaks.shape[0]):
# crop the cells from the given locations
data[i,:,:]=self.sig.data[idx,peaks[i,1]:peaks[i,1]+tmp_sz,peaks[i,0]:peaks[i,0]+tmp_sz]
positions[i]=(self.titles[idx],i,peaks[i,:2])
crop_sig=Image({'data':data,
'mapped_parameters':{
'title':'Cropped cells from %s'%self.titles[idx],
'record_by':'image',
'locations':positions,
'original_files':{pmp.title:parent},
}
})
return crop_sig
class StackedPlot(ChacoPlot):
offset = Range(0.0, 1.0, 0.015)
value_range = Range(0.01, 1.05, 1.00)
flip_order = Bool(False)
def _get_traits_group(self):
return VGroup(
HGroup(
Item('flip_order'),
Item('offset'),
Item('value_range'),
),
UItem('component', editor=ComponentEditor()),
)
def __init__(self):
super(StackedPlot, self).__init__()
self.container = OverlayPlotContainer(bgcolor='white',
use_backbuffer=True,
border_visible=True,
padding=50,
padding_left=110,
fill_padding=True
)
self.data = ArrayPlotData()
self.chaco_plot = None
self.value_mapper = None
self.index_mapper = None
self.x_axis = PlotAxis(component=self.container,
orientation='bottom',
title=u'Angle (2\u0398)',
title_font=settings.axis_title_font,
tick_label_font=settings.tick_font)
y_axis_title = 'Normalized intensity (%s)' % get_value_scale_label('linear')
self.y_axis = PlotAxis(component=self.container,
orientation='left',
title=y_axis_title,
title_font=settings.axis_title_font,
tick_label_font=settings.tick_font)
self.container.overlays.extend([self.x_axis, self.y_axis])
self.container.tools.append(
TraitsTool(self.container, classes=[LinePlot,PlotAxis]))
self.colors = []
self.last_flip_order = self.flip_order
@on_trait_change('offset, value_range, flip_order')
def _replot_data(self):
self._plot(self.data_x, None, self.data_z, self.scale)
self.container.request_redraw()
def _prepare_data(self, datasets):
interpolate = True
stack = stack_datasets(datasets)
if interpolate:
(x, z) = interpolate_datasets(stack, points=4800)
x = array([x] * len(datasets))
else:
x, z = map(np.transpose, np.transpose(stack))
return x, None, z
def _plot(self, x, y, z, scale):
self.data_x, self.data_z, self.scale = x, z, scale
if self.container.components:
self.colors = map(lambda plot: plot.color, self.container.components)
if self.last_flip_order != self.flip_order:
self.colors.reverse()
self.container.remove(*self.container.components)
# Use a custom renderer so plot lines are clickable
self.chaco_plot = Plot(self.data,
renderer_map={ 'line': ClickableLinePlot })
self.chaco_plot.bgcolor = 'white'
self.value_mapper = None
self.index_mapper = None
if len(self.data_x) == len(self.colors):
colors = self.colors[:]
else:
colors = ['black'] * len(self.data_x)
if self.flip_order:
z = z[::-1]
spacing = (z.max(axis=1) - z.min(axis=1)).min() * self.value_range
offset = spacing * self.offset
for i, (x_row, z_row) in enumerate(zip(x, z)):
self.data.set_data('data_x_' + str(i), x_row)
self.data.set_data('data_y_offset_' + str(i), z_row * self.value_range + offset * i)
plots = self.chaco_plot.plot(('data_x_' + str(i), 'data_y_offset_' + str(i)), color=colors[i], type='line')
plot = plots[0]
self.container.add(plot)
# Required for double-clicking plots
plot.index.sort_order = 'ascending'
plot.value.sort_order = 'ascending'
if self.value_mapper is None:
self.index_mapper = plot.index_mapper
self.value_mapper = plot.value_mapper
else:
plot.value_mapper = self.value_mapper
self.value_mapper.range.add(plot.value)
plot.index_mapper = self.index_mapper
self.index_mapper.range.add(plot.index)
range = self.value_mapper.range
range.high = (range.high - range.low) * self.value_range + range.low
self.x_axis.mapper = self.index_mapper
self.y_axis.mapper = self.value_mapper
self.y_axis.title = 'Normalized intensity (%s)' % \
get_value_scale_label(scale)
self.zoom_tool = ClickUndoZoomTool(
plot, tool_mode="box", always_on=True, pointer="cross",
drag_button=settings.zoom_button,
undo_button=settings.undo_button,
)
plot.overlays.append(self.zoom_tool)
self.last_flip_order = self.flip_order
return self.container
def _reset_view(self):
self.zoom_tool.revert_history_all()
