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main_window.py
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#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import wx
import matplotlib.pyplot as plt
import numpy as np
import pyramid_sparse as pyr
import pyramid_process, distance
from os import path
import string
from gettext import install
from matplotlib.patches import Rectangle
from threading import *
from matplotlib.figure import Figure
from matplotlib.backends.backend_wxagg import \
FigureCanvasWxAgg as FigCanvas, \
NavigationToolbar2WxAgg as NavigationToolbar
import specter
import pylab
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.cm as cm
BLOCK = False
# Button definitions
ID_START = wx.NewId()
ID_STOP = wx.NewId()
# Define notification event for thread completion
EVT_RESULT_ID = wx.NewId()
def EVT_RESULT(win, func):
"""Define Result Event."""
win.Connect(-1, -1, EVT_RESULT_ID, func)
class ResultEvent(wx.PyEvent):
"""Simple event to carry arbitrary result data."""
def __init__(self, data):
"""Init Result Event."""
wx.PyEvent.__init__(self)
self.SetEventType(EVT_RESULT_ID)
self.data = data
# Thread class that executes processing
class WorkerThread(Thread):
"""Worker Thread Class."""
def __init__(self, notify_window, base_folder, size_pyramid, factor, filter_value):
"""Init Worker Thread Class."""
Thread.__init__(self)
self._notify_window = notify_window
self._want_abort = 0
self.base_folder = base_folder
self.size_pyramid = size_pyramid
self.factor = factor
self.filter = filter_value
# This starts the thread running on creation, but you could
# also make the GUI thread responsible for calling this
wx.CallAfter(self.start)
def run(self):
"""Run Worker Thread."""
# This is the code executing in the new thread. Simulation of
# a long process (well, 10s here) as a simple loop - you will
# need to structure your processing so that you periodically
# peek at the abort variable
if self.filter:
pyramid = pyr.build_and_filter(self.base_folder, self.size_pyramid, self.factor)
else:
pyramid = pyr.build(self.base_folder, self.size_pyramid, self.factor)
lev = pyr.level(pyramid, 2)
# Here's where the result would be returned (this is an
# example fixed result of the number 10, but it could be
# any Python object)
wx.PostEvent(self._notify_window, ResultEvent(pyramid))
def abort(self):
"""abort worker thread."""
# Method for use by main thread to signal an abort
self._want_abort = 1
class MainWindow(wx.Frame):
def __init__(self, *args, **kwds):
kwds["style"] = wx.CAPTION | wx.CLOSE_BOX | wx.MINIMIZE_BOX | wx.MAXIMIZE_BOX | wx.SYSTEM_MENU | wx.RESIZE_BORDER | wx.CLIP_CHILDREN
wx.Frame.__init__(self, *args, **kwds)
self.Bind(wx.EVT_CLOSE, lambda event: self.Destroy())
self.chromosomes = ["None"]
self.nb_levels = 0
self.panel = wx.Panel(self)
self.control_box = wx.StaticBox(self.panel)
self.button_loader = wx.Button(self.panel, wx.ID_ANY, ("Load Data"))
self.button_loader.Bind(wx.EVT_BUTTON, self.OnDir)
self.Status_dir = [wx.StaticText(self.panel, wx.ID_ANY, ("No data")), wx.StaticText(self.panel, wx.ID_ANY, ("No data"))]
self.button_viz = wx.Button(self.panel, wx.ID_ANY, ("Visualize"))
self.button_viz.Bind(wx.EVT_BUTTON, self.OnVisualize)
self.button_viz.Disable()
self.sync = wx.CheckBox(self.panel, wx.ID_ANY, label="Keep matrices in sync")
self.sync.SetValue(False)
self.sync.Bind(wx.EVT_CHECKBOX, self.OnSync)
self.auto_thresh = wx.CheckBox(self.panel, wx.ID_ANY, label="Auto-adjust threshold")
self.auto_thresh.SetValue(False)
self.browse_label = wx.StaticBox(self.panel, label="Matrix browsing")
self.browse_X_label = wx.StaticBox(self.panel, label="X")
self.browse_X_chr_label = wx.StaticBox(self.panel, label="Chromosome/Contig")
self.browse_X_chr = wx.Choice(self.panel, wx.ID_ANY, choices=self.chromosomes)
self.browse_X_chr.SetStringSelection("1")
self.browse_X_start = wx.TextCtrl(self.panel, wx.ID_ANY, "0")
self.browse_X_start_label = wx.StaticBox(self.panel, label="X start")
self.browse_X_end = wx.TextCtrl(self.panel, wx.ID_ANY, "0")
self.browse_X_end_label = wx.StaticBox(self.panel, label="X end")
self.browse_Y_label = wx.StaticBox(self.panel, label="Y")
self.browse_Y_chr_label = wx.StaticBox(self.panel, label="Chromosome/Contig")
self.browse_Y_chr = wx.Choice(self.panel, wx.ID_ANY, choices=self.chromosomes)
self.browse_X_chr.SetStringSelection("1")
self.browse_Y_start_label = wx.StaticBox(self.panel, label="Y start")
self.browse_Y_start = wx.TextCtrl(self.panel, wx.ID_ANY, "0")
self.browse_Y_end_label = wx.StaticBox(self.panel, label="Y end")
self.browse_Y_end = wx.TextCtrl(self.panel, wx.ID_ANY, "0")
self.pixel_value_label = wx.StaticBox(self.panel, label="Pixel value:")
self.pixel_value = wx.StaticBox(self.panel, label="None")
self.pyramid_box = wx.StaticBox(self.panel, label="Pyramid settings")
self.pyramid_label = wx.StaticText(self.panel, wx.ID_ANY, ("Level"))
self.pyramid_level = wx.SpinCtrl(self.panel, wx.ID_ANY, "0",min=0,max=self.nb_levels)
self.pyramid_level.Disable()
self.matrix_mode_label = wx.StaticText(self.panel, wx.ID_ANY, ("Matrix mode"))
self.matrix_mode = wx.Choice(self.panel, wx.ID_ANY, choices=[_("Raw"), _("Normalized"), _("Correlation"), _("Convolution"), ("Correlation/Convolution")])
self.matrix_mode.SetStringSelection("Raw")
self.matrix_mode.Bind(wx.EVT_CHOICE, self.OnSelectMode)
self.matrix_mode.Disable()
self.vmax_label = wx.StaticText(self.panel, wx.ID_ANY, ("Saturation threshold"))
self.vmax = wx.TextCtrl(self.panel, wx.ID_ANY, "99%")
self.vmax.Disable()
self.marker_label = wx.StaticText(self.panel, wx.ID_ANY, ("Marker size"))
self.marker_size = wx.TextCtrl(self.panel, wx.ID_ANY, "0.0000000000000000005")
self.marker_size.Disable()
self.norm_box = wx.StaticBox(self.panel, label="Normalization settings")
self.norm_label = wx.StaticText(self.panel, wx.ID_ANY, ("Norm"))
self.norm = wx.Choice(self.panel, wx.ID_ANY, choices=[_("matrix-wise"),_("fragment-wise"), _("SCN"), _("mirnylib"), _("sparsity")])
self.norm.SetStringSelection("mirnylib")
self.norm.Bind(wx.EVT_CHOICE, self.OnSelectMode)
self.norm.Disable()
self.norm_iteration_label = wx.StaticText(self.panel, wx.ID_ANY, ("Norm iteration number"))
self.norm_iteration = wx.SpinCtrl(self.panel, wx.ID_ANY, "3",min=0,max=999)
self.norm_iteration.Disable()
self.norm_exposant_label = wx.StaticText(self.panel, wx.ID_ANY, ("Normalization power (or log)"))
self.norm_exposant = wx.TextCtrl(self.panel, wx.ID_ANY, "1")
self.norm_exposant.Disable()
self.norm_order_label = wx.StaticText(self.panel, wx.ID_ANY, ("Normalization order"))
self.norm_order = wx.TextCtrl(self.panel, wx.ID_ANY, "1")
self.norm_order.Disable()
self.convolution_box = wx.StaticBox(self.panel, label="Convolution settings")
self.convolution_label = wx.StaticText(self.panel, wx.ID_ANY, ("Convolution kernel sigma"))
self.convolution = wx.TextCtrl(self.panel, wx.ID_ANY, "1.5")
self.convolution.Disable()
self.convolution_gaussian_label = wx.StaticText(self.panel, wx.ID_ANY, ("Convolution iterations"))
self.convolution_gaussian = wx.SpinCtrl(self.panel, wx.ID_ANY, "1",min=0,max=999)
self.convolution_gaussian.Disable()
self.current_plot_id = 0
self.color_code_label = wx.StaticText(self.panel, wx.ID_ANY, ("Color code"))
self.color_code = wx.Choice(self.panel, wx.ID_ANY, choices=pyramid_process.cmaps)
self.color_code.SetStringSelection('jet')
self.color_code.Disable()
self.button_reset = wx.Button(self.panel, wx.ID_ANY, ("Reset"))
self.button_reset.Bind(wx.EVT_BUTTON, self.OnReset)
self.zoom = wx.Button(self.panel, wx.ID_ANY, ("Zoom"))
self.zoom.Bind(wx.EVT_BUTTON, self.OnZoom)
self.data_mode=["reads","reads"]
#main arrays - one for each canvas
self.data = [{'raw':None, 'processed':None, 'buffer':None},{'raw':None, 'processed':None, 'buffer':None}]
self.annotation = [{},{}]
self.zoom_coordinates = [[None,None],[None,None]]
#levels chosen
self.level = [None,None]
#canvas size
self.dpi = [110,110]
#these are used to bind matplotlib events
self.clickid = [0,0]
self.selectid = [0,0]
self.moveid = [0,0]
#figure and canvas stuff
self.fig = [Figure((3.0, 7.0), dpi=self.dpi[0],facecolor='1'),Figure((3.0, 7.0), dpi=self.dpi[1])]
self.canvas = [FigCanvas(self.panel, -1, self.fig[0]),FigCanvas(self.panel, -1, self.fig[1])]
for fig in self.fig:
fig.set_tight_layout(True)
#matplotlib event bindings - one for each canvas
self.clickid[0] = self.canvas[0].mpl_connect('button_press_event', lambda event: self.OnClickCanvas(event, 0))
self.selectid[0] = self.canvas[0].mpl_connect('button_release_event', lambda event: self.OnSelectCanvas(event, 0))
self.moveid[0] = self.canvas[0].mpl_connect('motion_notify_event', lambda event: self.OnMouseCanvas(event, 0))
self.moveid[0] = self.canvas[0].mpl_connect('axes_leave_event', lambda event: self.OnLeaveCanvas(event, 0))
self.clickid[1] = self.canvas[1].mpl_connect('button_press_event', lambda event: self.OnClickCanvas(event, 1))
self.selectid[1] = self.canvas[1].mpl_connect('button_release_event', lambda event: self.OnSelectCanvas(event, 1))
self.moveid[1] = self.canvas[1].mpl_connect('motion_notify_event', lambda event: self.OnMouseCanvas(event, 1))
self.moveid[1] = self.canvas[1].mpl_connect('axes_leave_event', lambda event: self.OnLeaveCanvas(event, 1))
#adding plots to each canvas
self.axes = [self.fig[0].add_subplot(111),self.fig[1].add_subplot(111)]
self.plot_data = None
#whatever your mouse hovers
self.current_x_coordinate = 0
self.current_y_coordinate = 0
#when selecting a square, the place you clicked your mouse button - one for each canvas
self.first_x_coordinate = [0,0]
self.first_y_coordinate = [0,0]
#when selecting a square, the place you release your mouse button - one for each canvas
self.second_x_coordinate = [0,0]
self.second_y_coordinate = [0,0]
#if you're currently selecting
self.select_mode = False
#selection rectangles - one for each canvas
self.select_square = [Rectangle((0,0),0,0),Rectangle((0,0),0,0)]
#whatever chromosome or contig your mouse is hovering
self.current_chr = [None,None]
#plots for each canvas
self.base_axes = [self.fig[0].add_subplot(111),self.fig[1].add_subplot(111)]
#this is used to keep track of your original data after zooming
self.previous_axes = [None,None]
self.fasta_file = ""
self.statusbar = self.CreateStatusBar()
self.__set_properties()
self.__do_layout()
self.create_menu()
#each pyramid contains every level of binning
self.pyramid = [None,None]
def create_menu(self):
self.menubar = wx.MenuBar()
menu_file = wx.Menu()
m_load = menu_file.Append(-1,"&Load data\tL", "Load pyramid data")
self.Bind(wx.EVT_MENU, self.OnDir, m_load)
m_manual_load = menu_file.Append(-1, "&Load manually\tM", "Load a single matrix")
self.Bind(wx.EVT_MENU, self.OnManualLoad, m_manual_load)
m_pdb_load = menu_file.Append(-1, "&Load PDB\tP", "Load a PDB file")
self.Bind(wx.EVT_MENU, self.OnPDBLoad, m_pdb_load)
menu_file.AppendSeparator()
m_expt = menu_file.Append(-1, "&Save plot\tS", "Save plot to file")
self.Bind(wx.EVT_MENU, self.OnSavePlot, m_expt)
m_export = menu_file.Append(-1, "&Export matrix\tE", "Export matrix to txt")
self.Bind(wx.EVT_MENU, self.OnExport, m_export)
menu_file.AppendSeparator()
m_exit = menu_file.Append(-1, "E&xit\tCtrl-X", "Exit")
self.Bind(wx.EVT_MENU, lambda event: self.Destroy(), m_exit)
self.menubar.Append(menu_file, "&File")
menu_view = wx.Menu()
m_viz = menu_view.Append(-1, "&Visualize plot\tEnter", "Visualize plot")
self.Bind(wx.EVT_MENU, self.OnVisualize, m_viz)
m_newplot = menu_view.Append(-1, "&New plot\tCtrl-Enter", "New plot")
self.Bind(wx.EVT_MENU, self.OnNewPlot, m_newplot)
m_binkb = menu_view.Append(-1, "&Kb binning\tAlt-B", "Re-bin by base pairs")
self.Bind(wx.EVT_MENU, self.OnRebinKb, m_binkb)
m_zoom = menu_view.Append(-1, "&Zoom\tZ", "Zoom to coordinates")
self.Bind(wx.EVT_MENU, self.OnZoom, m_zoom)
self.menubar.Append(menu_view, "&View")
menu_plot = wx.Menu()
m_distance = menu_plot.Append(-1, "&Distance law\tCtrl-D", "Plot distance law")
self.Bind(wx.EVT_MENU, self.OnDistance, m_distance)
m_sparsity = menu_plot.Append(-1, "&Contact sparsity\tCtrl-G", "Plot genome sparsity")
self.Bind(wx.EVT_MENU, self.OnGenomicSparsity, m_sparsity)
self.menubar.Append(menu_plot, "&Plot")
menu_structure = wx.Menu()
m_shrec = menu_structure.Append(-1, "ShRec 3D\tCtrl-H", "3D Reconstruction")
self.Bind(wx.EVT_MENU, self.OnShrec, m_shrec)
m_pdb = menu_structure.Append(-1, "PDB\tAlt-P", "Export to PDB")
self.Bind(wx.EVT_MENU, self.OnPDB, m_pdb)
self.menubar.Append(menu_structure, "&Structure")
self.SetMenuBar(self.menubar)
def OnSavePlot(self, event):
file_choices = "PNG (*.png)|*.png"
id_canvas = self.current_plot_id
dlg = wx.FileDialog(
self,
message="Save plot as...",
defaultDir="~/",
defaultFile="plot.png",
wildcard=file_choices,
style=wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
self.canvas[id_canvas].print_figure(path, dpi=self.dpi[id_canvas]*2)
print("Saved to %s" % path)
def EraseSelection(self, id_canvas):
self.select_square[id_canvas].set_width(0)
self.select_square[id_canvas].set_height(0)
def OnZoom(self, event=None):
id_canvas = self.current_plot_id
sync = self.sync.GetValue()
if np.abs(self.select_square[id_canvas].get_width())>0.0 and np.abs(self.select_square[id_canvas].get_height())>0.0:
self.axes[id_canvas]=self.previous_axes[id_canvas]
self.canvas[id_canvas].draw()
x1,y1,x2,y2 = tuple([coord for element in self.zoom_coordinates[id_canvas] for coord in element])
x1,x2 = min(x1,x2),max(x1,x2)
y1,y2 = min(y1,y2),max(y1,y2)
self.axes[id_canvas].set_xlim(x1,x2)
self.axes[id_canvas].set_ylim(y2,y1)
print "I zoom to the square of coordinates "+str((x1,y1))+" and "+str((x2,y2))
self.EraseSelection(id_canvas)
self.canvas[id_canvas].draw()
if sync: #yeah this is ugly there's certainly a nicer way to do it
self.axes[not id_canvas]=self.previous_axes[not id_canvas]
self.canvas[not id_canvas].draw()
self.axes[not id_canvas].set_xlim(x1,x2)
self.axes[not id_canvas].set_ylim(y1,y2)
self.EraseSelection(not id_canvas)
self.canvas[not id_canvas].draw()
else:
self.zoom_frame = ZoomWindow(None, wx.ID_ANY, "'")
self.zoom_frame.main_window = self
app.SetTopWindow(self.zoom_frame)
self.zoom_frame.Show()
def OnSync(self, event):
if not (self.data[0] is None) and (not self.data[1] is None):
if self.sync.GetValue():
self.OnSelectCanvas(None, 0)
else:
self.data_part[0]=self.data[0]
self.data_part[1]=self.data[1]
def OnRebinKb(self, event):
id_canvas = self.current_plot_id
x1,y1,x2,y2 = tuple([coord for element in self.zoom_coordinates[id_canvas] for coord in element])
x1,x2 = min(x1,x2),max(x1,x2)
y1,y2 = min(y1,y2),max(y1,y2)
M = pyramid_process.square(self.data[id_canvas]['buffer'][x1:x2,y1:y2])
N = pyramid_process.rebin_kb(M,self.level[id_canvas].S_o_A_frags)
self.data[id_canvas]['buffer'] = N
self.display(N)
def OnGenomicSparsity(self, event):
id_canvas = self.current_plot_id
s = self.data[id_canvas]['buffer']
s_total = np.sqrt(np.sum(s))
sum_sparsity = [np.sum(R) for R in s]/s_total
try:
sparsity = self.level[id_canvas].sparsity
print sparsity
except AttributeError:
"warning: no pyramid data"
try:
plt.plot(sum_sparsity)
plt.plot(sparsity)
except:
print "Data in left plot is corrupted or absent, skipping"
plt.show()
def OnShrec(self, event, pdb=False):
id_canvas = self.current_plot_id
x1,y1,x2,y2 = tuple([coord for element in self.zoom_coordinates[id_canvas] for coord in element])
x1,x2 = min(x1,x2),max(x1,x2)
y1,y2 = min(y1,y2),max(y1,y2)
M = pyramid_process.square(self.data[id_canvas]['buffer'][x1:x2,y1:y2])
N = pyramid_process.trim_for_sparsity(M)
N = specter.remove_disconnected_matrix(N)
s = specter.contact_to_coordinates(N,n=3)
X,Y,Z = specter.coordinates_to_pdb(s)
if self.data_mode[id_canvas]=="reads":
contigs = np.array(self.level[id_canvas].S_o_A_frags['id_c']).astype(int)
print contigs.shape
m = min(M.shape)
n = len(self.chromosomes)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
index = []
md = np.diag(M)
nd = np.diag(N)
print md,nd
for j in range(min(nd.shape)):
k = 0
while md[j+k] != nd[j] and k<2*m:
k+=1
index.append(k+j)
indices = np.array(index)
colors = plt.get_cmap(self.color_code.GetStringSelection())(np.linspace(0, 1, n))
for i in range(1,n+1):
ax.scatter(X[contigs[indices]==i],Y[contigs[indices]==i],Z[contigs[indices]==i], color=colors[i-1])
plt.show()
else:
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(X,Y,Z)
plt.show(block=BLOCK)
if pdb:
n = min(len(X),len(Y),len(Z))
if self.data_mode[id_canvas] == "reads":
letters = (string.ascii_uppercase+string.ascii_lowercase+string.digits+string.punctuation)*int(n/94 +1)
length = np.abs(self.level[id_canvas].S_o_A_frags['len_bp'][index])
print length
length = np.sqrt(length)
print length
lmax = np.max(length)
length *= 10.0/lmax
print length
length[length<0.1] = 0.1
print length
length = np.around(length,2)
print length
else:
letters = "A"*(n+1)
length = [0.00]*(n+1)
filename = self.Status_dir[id_canvas].GetLabel()+".pdb"
with open(filename, 'w') as f:
for i in range(1,n):
line = "ATOM" #1-4 "ATOM"
line += " " #5-6 unused
line += str(i).rjust(5) #7-11 atom serial number
line += " " #12 unused
line += "OW".rjust(4) #13-16 atom name
line += " " #17 alternate location indicator
line += "SOL" #18-20 residue name
line += " " #21 unused
line += letters[contigs[i]-1] #22 chain identifier
line += str(i).rjust(4) #23-26 residue sequence number
line += " " #27 code for insertion of residues
line += " " #28-30 unused
line += str(X[i]).rjust(8) #31-38 X orthogonal Å coordinate
line += str(Y[i]).rjust(8) #39-46 Y orthogonal Å coordinate
line += str(Z[i]).rjust(8) #47-54 Z orthogonal Å coordinate
line += "1.00".rjust(6) #55-60 Occupancy
line += str(length[i-1]).rjust(6) #61-66 Temperature factor
line += " " #67-72 unused
line += " " #73-76 segment identifier
line += "O".rjust(2) #77-78 element symbol
line += "\n"
f.write(line)
def OnPDB(self, event):
self.OnShrec(event,pdb=True)
def OnDistance(self, event):
id_canvas = self.current_plot_id
plt.xscale("log")
plt.yscale("log")
x1,y1,x2,y2 = tuple([coord for element in self.zoom_coordinates[id_canvas] for coord in element])
x1,x2 = min(x1,x2),max(x1,x2)
y1,y2 = min(y1,y2),max(y1,y2)
try:
plt.plot(distance.distance_diagonal_law((self.data[0]['buffer'][x1:x2,y1:y2])))
except:
print "Data in left plot is corrupted or absent, skipping"
try:
plt.plot(distance.distance_diagonal_law((self.data[1]['buffer'][x1:x2,y1:y2])))
except:
print "Data in right plot is corrupted or absent, skipping"
plt.show()
def OnExport(self, event):
id_canvas = self.current_plot_id
file_choices = "txt (*.txt)|*.txt| gz (*.gz)|*.gz"
x1,y1,x2,y2 = tuple([coord for element in self.zoom_coordinates[id_canvas] for coord in element])
x1,x2 = min(x1,x2),max(x1,x2)
y1,y2 = min(y1,y2),max(y1,y2)
s = self.data[id_canvas]['buffer'][x1:x2,y1:y2]
if np.any(s):
dlg = wx.FileDialog(
self,
message="Save matrix as...",
defaultDir="~/",
defaultFile="matrix.txt",
wildcard=file_choices,
style=wx.SAVE)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
np.savetxt(path, s)
print("Saved to %s" % path)
else:
wx.MessageBox("Loaded data is corrupt or absent", "Pyramid data error", wx.OK|wx.ICON_ERROR)
def acquire_level(self, id_canvas=None):
if id_canvas is None:
id_canvas = self.current_plot_id
pyramid_level = self.pyramid_level.GetValue()
if self.data_mode[id_canvas] == "reads":
print "Loading reads."
#acquiring data
if self.pyramid[id_canvas] is None:
wx.MessageBox("Loaded data is corrupt or absent", "Pyramid data error", wx.OK|wx.ICON_ERROR)
return False
else:
self.level[id_canvas] = self.pyramid[id_canvas].get_level(pyramid_level)
print "Loaded level "+str(pyramid_level)
self.chromosomes = tuple([str(i) for i in set(self.level[id_canvas].S_o_A_frags['id_c'])])
self.browse_X_chr.SetItems(self.chromosomes)
self.browse_Y_chr.SetItems(self.chromosomes)
s = self.level[id_canvas].sparse_mat_csr
s = np.array(s.todense(),dtype=np.float64)
s_temp = s.astype(float)
diag = np.diag(s.diagonal())
transpose = s.T
s = s_temp + transpose - diag
self.data[id_canvas]['raw'] = np.copy(s)
print "Converted to full matrix"
elif self.data_mode[id_canvas] == "manual":
print "j'ai chargé la pyramide manuellement"
if pyramid_level <= len(self.pyramid[id_canvas])-1:
s = self.pyramid[id_canvas][pyramid_level]
else:
s = np.copy(self.pyramid[id_canvas][len(self.pyramid[id_canvas])-1])
for i in range(pyramid_level-len(self.pyramid[id_canvas])+1):
s = pyramid_process.manual_bin(s)
self.pyramid[id_canvas].append(s)
self.data[id_canvas]['raw'] = s
elif self.data_mode[id_canvas] == "model":
print "j'ai chargé une matrice modèle"
else:
pass
self.data[id_canvas]['buffer'] = self.data[id_canvas]['processed'] = self.data[id_canvas]['raw']
shape = self.data[id_canvas]['buffer'].shape
self.zoom_coordinates[id_canvas] = [[0,0],list(shape)]
return True
def display(self, M, id_canvas=None):
if id_canvas is None:
id_canvas = self.current_plot_id
colormap = self.color_code.GetStringSelection()
if self.auto_thresh.GetValue():
m = np.mean(M)
std = np.std(M)
self.vmax.SetValue(str(m+std))
threshold = self.vmax.GetValue()
if threshold[-1] == "%":
threshold = np.percentile(M,np.float64(threshold[:-1]))
markersize = float(self.marker_size.GetValue())
if id_canvas >= 0:
print self.zoom_coordinates
print id_canvas
x1,y1,x2,y2 = tuple([coord for element in self.zoom_coordinates[id_canvas] for coord in element])
x1,x2 = min(x1,x2),max(x1,x2)
y1,y2 = min(y1,y2),max(y1,y2)
print (x1,y1,x2,y2)
s = M[x1:x2,y1:y2]
print "j'affiche la matrice "+str(id_canvas)
self.axes[id_canvas].clear()
self.axes[id_canvas].spy(s, precision=0, markersize=markersize)
self.base_axes[id_canvas].spy(s, precision=0, markersize=markersize, markeredgewidth=0)
canvas_image = self.axes[id_canvas].imshow(s,vmin=0,vmax=threshold,interpolation='nearest')
canvas_image.set_cmap(colormap)
self.canvas[id_canvas].draw()
else:
plt.figure()
plt.spy(M, precision=0, markersize=float(self.marker_size.GetValue()))
try:
plot_image = plt.imshow(M, vmin=0,vmax=threshold,interpolation='nearest')
plot_image.set_cmap(colormap)
except MemoryError:
print "Warning: memory overload"
except TypeError:
print "Type Error, skipping imshow"
plt.show(block=BLOCK)
def process(self, s):
if s is None:
print "Can't process empty data!"
return
print "Matrix size: "+str(s.shape)
matrix_name = self.matrix_mode.GetStringSelection().lower()
normalization = self.norm.GetStringSelection()
iterations = self.norm_iteration.GetValue()
norm_exposant=float(self.norm_exposant.GetValue())
convolution_gaussian_number = self.convolution_gaussian.GetValue()
convolution_sigma = float(self.convolution.GetValue())
order = self.norm_order.GetValue()
M = pyramid_process.process(s,matrix_name,normalization,order,iterations,norm_exposant,convolution_gaussian_number,convolution_sigma)
print "Processing "+matrix_name.lower()+" matrix"
return M
def OnVisualize(self, event, id_canvas=None):
if id_canvas is None:
id_canvas = self.current_plot_id
self.visualize(id_canvas)
if self.sync.GetValue():
self.visualize(id_canvas=not id_canvas)
def visualize(self,id_canvas=None):
if id_canvas is None:
id_canvas = self.current_plot_id
self.acquire_level(id_canvas=id_canvas)
M = self.data[id_canvas]['raw']
P = self.process(M)
if P is None:
print "Can't visualize empty data!"
return
self.data[id_canvas]['processed'] = np.copy(P)
self.data[id_canvas]['buffer'] = P
self.display(P, id_canvas=id_canvas)
def OnNewPlot(self, event):
id_canvas = self.current_plot_id
self.acquire_level(id_canvas=id_canvas)
M = self.data[id_canvas]['raw']
P = self.process(M)
self.display(P, id_canvas=-1)
def OnReset(self, event, id_canvas=None):
if id_canvas is None:
id_canvas = self.current_plot_id
self.reset(id_canvas)
if self.sync.GetValue():
self.reset(id_canvas=not id_canvas)
def reset(self, id_canvas=None):
if id_canvas is None:
id_canvas = self.current_plot_id
P = self.data[id_canvas]['buffer']
original_shape = self.data[id_canvas]['buffer'].shape
self.zoom_coordinates[id_canvas] = [[0,0],list(original_shape)]
self.display(P,id_canvas=id_canvas)
def OnDir(self, event):
# Args below are: parent, question, dialog title, default answer
dd = wx.DirDialog(None, "Select directory to open", bank_path, 0, (10, 10), wx.Size(400, 300))
# This function returns the button pressed to close the dialog
ret = dd.ShowModal()
self.data_directory = ""
if ret == wx.ID_OK:
dd.Destroy()
self.data_directory = dd.GetPath()
print('You selected: %s\n' % self.data_directory)
self.frame_2 = LoaderWindow(None, wx.ID_ANY, "'")
self.frame_2.data_directory = self.data_directory
self.frame_2.main_window = self
app.SetTopWindow(self.frame_2)
self.frame_2.Show()
else:
print('You clicked cancel')
dd.Destroy()
def OnManualLoad(self, event):
dd = wx.FileDialog(None, "Select matrix file to open", bank_path)
# This function returns the button pressed to close the dialog
ret = dd.ShowModal()
self.data_path = ""
if ret == wx.ID_OK:
self.data_path = dd.GetPath()
print('You selected: %s\n' % self.data_path)
else:
print('You clicked cancel')
dd.Destroy()
if self.data_path:
print "Loading "+self.data_path
id_canvas = self.current_plot_id
matrix = np.loadtxt(self.data_path)
self.pyramid[id_canvas] = []
self.pyramid[id_canvas].append(matrix)
self.data[id_canvas]['raw'] = matrix
self.data[id_canvas]['trated'] = matrix
self.data[id_canvas]['buffer'] = matrix
n = np.min(self.data[id_canvas]['buffer'].shape)
ideal_size = 800
folder = self.data_path.split('/')[-1][:15]
self.Status_dir[id_canvas].SetLabel(folder)
self.Status_dir[id_canvas].SetForegroundColour((0,130,0))
font = wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD)
self.Status_dir[id_canvas].SetFont(font)
self.button_viz.Enable()
self.pyramid_level.Enable()
self.pyramid_level.SetRange(0,int(n/3))
self.pyramid_level.SetValue(int(n/ideal_size))
self.vmax.Enable()
self.marker_size.Enable()
self.matrix_mode.Enable()
self.color_code.Enable()
self.data_mode[id_canvas] = "manual"
def OnPDBLoad(self, event):
dd = wx.FileDialog(None, "Select PDB file to open", bank_path)
# This function returns the button pressed to close the dialog
ret = dd.ShowModal()
self.data_path = ""
if ret == wx.ID_OK:
self.data_path = dd.GetPath()
print('You selected: %s\n' % self.data_path)
else:
print('You clicked cancel')
dd.Destroy()
if self.data_path:
print "Loading "+self.data_path
id_canvas = self.current_plot_id
matrix = specter.pdb_to_contact(self.data_path)
self.pyramid[id_canvas] = matrix
self.data[id_canvas]['raw'] = matrix
self.data[id_canvas]['trated'] = matrix
self.data[id_canvas]['buffer'] = matrix
print matrix.shape
n = np.min(self.data[id_canvas]['buffer'].shape)
ideal_size = 800
folder = self.data_path.split('/')[-1][:15]
self.Status_dir[id_canvas].SetLabel(folder)
self.Status_dir[id_canvas].SetForegroundColour((0,130,0))
font = wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD)
self.Status_dir[id_canvas].SetFont(font)
self.button_viz.Enable()
self.pyramid_level.Enable()
self.pyramid_level.SetRange(0,int(n/3))
self.pyramid_level.SetValue(int(n/ideal_size))
self.vmax.Enable()
self.marker_size.Enable()
self.matrix_mode.Enable()
self.color_code.Enable()
self.data_mode[id_canvas] = "manual"
def OnSelectMode(self, event):
matrix_name = self.matrix_mode.GetStringSelection().lower()
norm_name = self.norm.GetStringSelection().lower()
print "Selecting "+norm_name
if "norm" in matrix_name or "corr" in matrix_name or "conv" in matrix_name:
self.norm_exposant.Enable()
self.norm.Enable()
self.norm_iteration.Enable()
if not norm_name in ["scn", "mirnylib"]:
self.norm_iteration.Disable()
else:
self.norm_iteration.Enable()
if not "wise" in norm_name:
self.norm_order.Disable()
else:
self.norm_order.Enable()
if "convolution" in matrix_name:
self.convolution.Enable()
self.convolution_gaussian.Enable()
else:
self.convolution.Disable()
self.convolution_gaussian.Disable()
else:
self.convolution.Disable()
self.convolution_gaussian.Disable()
self.norm_exposant.Disable()
self.norm.Disable()
self.norm_iteration.Disable()
def OnClickCanvas(self, event, id_canvas):
if event.xdata and event.ydata:
self.first_x_coordinate[id_canvas] = event.xdata
self.first_y_coordinate[id_canvas] = event.ydata
self.current_plot_id = id_canvas
self.fig[id_canvas].set_facecolor('1')
self.EraseSelection(id_canvas)
self.canvas[id_canvas].draw()
self.fig[not id_canvas].set_facecolor('0.75')
self.canvas[not id_canvas].draw()
self.previous_axes = self.axes
font = wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.BOLD)
default_font = wx.Font(9, wx.DEFAULT, wx.NORMAL, wx.NORMAL)
self.Status_dir[id_canvas].SetFont(font)
self.Status_dir[not id_canvas].SetFont(default_font)
if self.first_x_coordinate[id_canvas] and self.first_y_coordinate[id_canvas]:
self.select_mode=True
def OnSelectCanvas(self, event, id_canvas):
if not event.xdata is None:
self.second_x_coordinate[id_canvas] = event.xdata
if not event.ydata is None:
self.second_y_coordinate[id_canvas] = event.ydata
self.select_mode = False
if self.second_x_coordinate[id_canvas] != self.first_x_coordinate[id_canvas] and self.first_y_coordinate[id_canvas] != self.second_y_coordinate[id_canvas]:
coordinates_status = "Display "+str(id_canvas+1)+", x1 = "+str(self.first_x_coordinate[id_canvas])+", y1 = "+str(self.first_y_coordinate[id_canvas])+\
"x2 = "+str(self.second_x_coordinate[id_canvas])+", y2 = "+str(self.second_y_coordinate[id_canvas])
self.statusbar.SetStatusText(coordinates_status)
first_x_ordered, second_x_ordered = int(min(self.first_x_coordinate[id_canvas],self.second_x_coordinate[id_canvas])),\
int(max(self.first_x_coordinate[id_canvas],self.second_x_coordinate[id_canvas]))
second_y_ordered, first_y_ordered = int(min(self.first_y_coordinate[id_canvas],self.second_y_coordinate[id_canvas])),\
int(max(self.first_y_coordinate[id_canvas],self.second_y_coordinate[id_canvas]))
self.zoom_coordinates[id_canvas] = [[first_x_ordered,first_y_ordered],[second_x_ordered,second_y_ordered]]
if self.sync.GetValue():
self.zoom_coordinates[not id_canvas] = [[first_x_ordered,first_y_ordered],[second_x_ordered,second_y_ordered]]
def OnMouseCanvas(self, event, id_canvas):
#pixel coords
if not event.xdata is None:
self.current_x_coordinate = event.xdata
if not event.ydata is None:
self.current_y_coordinate = event.ydata
coordinates_status = "Display "+str(id_canvas+1)+", x = "+str(self.current_x_coordinate)+", y = "+str(self.current_y_coordinate)
self.statusbar.SetStatusText(coordinates_status)
#genome coords
if (not self.data[id_canvas]['buffer'] is None) and self.current_x_coordinate and self.current_y_coordinate:
self.pixel_value.SetLabel(str(float(self.data[id_canvas]['buffer'][self.current_x_coordinate,self.current_y_coordinate])))
if self.data_mode[id_canvas] == "reads":
self.browse_X_chr.SetStringSelection(str(self.level[id_canvas].S_o_A_frags['id_c'][int(self.current_x_coordinate)]))
self.browse_Y_chr.SetStringSelection(str(self.level[id_canvas].S_o_A_frags['id_c'][int(self.current_y_coordinate)]))
self.browse_X_start.SetValue(str(self.level[id_canvas].S_o_A_frags['start_bp'][int(self.current_x_coordinate)]))
self.browse_Y_start.SetValue(str(self.level[id_canvas].S_o_A_frags['start_bp'][int(self.current_y_coordinate)]))
self.browse_X_end.SetValue(str(self.level[id_canvas].S_o_A_frags['start_bp'][int(self.current_x_coordinate)]\
+self.level[id_canvas].S_o_A_frags['len_bp'][int(self.current_x_coordinate)]))
self.browse_Y_end.SetValue(str(self.level[id_canvas].S_o_A_frags['start_bp'][int(self.current_y_coordinate)]\
+self.level[id_canvas].S_o_A_frags['len_bp'][int(self.current_y_coordinate)]))
if self.select_mode and self.previous_axes and id_canvas == self.current_plot_id:
self.select_square[id_canvas].set_width(self.current_x_coordinate - self.first_x_coordinate[id_canvas])
self.select_square[id_canvas].set_height(self.current_y_coordinate - self.first_y_coordinate[id_canvas])
self.select_square[id_canvas].set_xy((self.first_x_coordinate[id_canvas], self.first_y_coordinate[id_canvas]))
self.select_square[id_canvas].set_linestyle('dashed')
self.axes[id_canvas] = self.previous_axes[id_canvas]
self.axes[id_canvas].add_patch(self.select_square[id_canvas])
self.canvas[id_canvas].draw()
def OnLeaveCanvas(self, event, id_canvas):
self.select_mode = False
def __set_properties(self):
self.SetTitle(_("Pyramid Toolbox"))
self.SetSize((350, 120))
self.button_loader.SetMinSize((150, 27))
self.Status_dir[0].SetMinSize((149, 17))
self.Status_dir[1].SetMinSize((149, 17))
self.button_viz.SetMinSize((149, 27))
def __do_layout(self):
flag_local = wx.ALIGN_CENTER_VERTICAL
flag_sizer = wx.VERTICAL
global_sizer = wx.GridBagSizer(5,5)
button_sizer = wx.GridBagSizer(5,5)
control_sizer = wx.StaticBoxSizer(self.control_box, flag_sizer)
local_control_sizer = wx.GridBagSizer(5,5)
local_control_sizer.Add(self.button_loader, (0,0), flag = flag_local)
local_control_sizer.Add(self.Status_dir[0], (2,0), flag = flag_local)
local_control_sizer.Add(self.Status_dir[1], (2,1), flag = flag_local)
local_control_sizer.Add(self.button_viz, (0,1), flag = flag_local)
local_control_sizer.Add(self.button_reset, (3,1), flag = flag_local)
local_control_sizer.Add(self.zoom, (3,0), flag=flag_local)
local_control_sizer.Add(self.sync, (4,0), flag = flag_local)
local_control_sizer.Add(self.auto_thresh, (4,1), flag = flag_local)
control_sizer.Add(local_control_sizer, flag=wx.LEFT|wx.TOP, border=5)
# local_view_sizer = wx.GridBagSizer(5,5)
# local_view_sizer.Add(self.set_selection_mode,(1,0), (1,3), flag = flag_local)
button_sizer.Add(control_sizer,(0,0))
# button_sizer.Add(local_view_sizer,(1,0))
browse_sizer = wx.StaticBoxSizer(self.browse_label, flag_sizer)
local_browse_sizer = wx.GridBagSizer(5,10)
browse_X_sizer = wx.StaticBoxSizer(self.browse_X_label, flag_sizer)
local_browse_X_sizer = wx.GridBagSizer(5,10)
local_browse_X_sizer.Add(self.browse_X_chr_label,(0,0),flag=flag_local)
local_browse_X_sizer.Add(self.browse_X_chr,(0,1),flag=flag_local)
local_browse_X_sizer.Add(self.browse_X_start_label,(1,0),flag=flag_local)
local_browse_X_sizer.Add(self.browse_X_start,(1,1),flag=flag_local)
local_browse_X_sizer.Add(self.browse_X_end_label,(2,0),flag=flag_local)
local_browse_X_sizer.Add(self.browse_X_end,(2,1),flag=flag_local)
browse_X_sizer.Add(local_browse_X_sizer,flag=wx.LEFT|wx.TOP, border=5)
browse_Y_sizer = wx.StaticBoxSizer(self.browse_Y_label, flag_sizer)
local_browse_Y_sizer = wx.GridBagSizer(5,10)
local_browse_Y_sizer.Add(self.browse_Y_chr_label,(0,0),flag=flag_local)
local_browse_Y_sizer.Add(self.browse_Y_chr,(0,1),flag=flag_local)
local_browse_Y_sizer.Add(self.browse_Y_start_label,(1,0),flag=flag_local)
local_browse_Y_sizer.Add(self.browse_Y_start,(1,1),flag=flag_local)
local_browse_Y_sizer.Add(self.browse_Y_end_label,(2,0),flag=flag_local)
local_browse_Y_sizer.Add(self.browse_Y_end,(2,1),flag=flag_local)
browse_Y_sizer.Add(local_browse_Y_sizer,flag=wx.LEFT|wx.TOP, border=5)
local_pixel_sizer = wx.GridBagSizer(5,10)
local_pixel_sizer.Add(self.pixel_value_label,(0,0),flag=flag_local)
local_pixel_sizer.Add(self.pixel_value,(0,1),flag=flag_local)
local_browse_sizer.Add(browse_X_sizer,(0,0))
local_browse_sizer.Add(browse_Y_sizer,(0,1))
local_browse_sizer.Add(local_pixel_sizer,(1,0))
browse_sizer.Add(local_browse_sizer,flag=wx.LEFT|wx.TOP, border=5)
button_sizer.Add(browse_sizer,(0,1))
pyramid_sizer = wx.StaticBoxSizer(self.pyramid_box, flag_sizer)
local_pyramid_sizer = wx.GridBagSizer(2,5)
local_pyramid_sizer.Add(self.pyramid_label, (0,0), flag = flag_local)
local_pyramid_sizer.Add(self.pyramid_level, (0,1), flag = flag_local)
local_pyramid_sizer.Add(self.vmax_label, (1,0), flag = flag_local)
local_pyramid_sizer.Add(self.vmax, (1,1), flag = flag_local)
local_pyramid_sizer.Add(self.marker_label, (2,0), flag = flag_local)