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Refrainv.py
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Refrainv.py
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##Refrapy - Seismic Refraction Data Analysis
##Refrainv - Data inversion
##Author: Victor Guedes, MSc
##E-mail: vjs279@hotmail.com
from matplotlib import pyplot as plt
from matplotlib.path import Path
from matplotlib.patches import PathPatch
from mpl_toolkits.axes_grid1 import make_axes_locatable
from matplotlib.lines import Line2D
from matplotlib.colors import is_color_like
from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2Tk
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from tkinter import Tk, Toplevel, Frame, Button, Label, filedialog, messagebox, PhotoImage, simpledialog, Entry
from os import path, makedirs, getcwd, name
from obspy import read
from obspy.signal.filter import lowpass, highpass
from scipy.signal import resample
from scipy.interpolate import interp1d,griddata
from numpy import array, where, polyfit, linspace, meshgrid, column_stack, c_, savetxt, shape,reshape,concatenate, hstack, linalg, mean, sqrt, zeros, arange, linspace, square, sort, unique
from numpy import all as np_all
from Pmw import initialise, Balloon
import pygimli as pg
from pygimli.physics import TravelTimeManager
from tqdm import tqdm
import os
from datetime import datetime
import numpy as np
import pandas as pd
#own modules
from dtreader import dtreader
class Refrainv(Tk):
def __init__(self):
super().__init__()
self.geometry("1600x900")
self.title('Refrapy - Refrainv v2.0.0')
self.configure(bg = "#F0F0F0")
self.resizable(1,1)
#check if on windows with nt kernel:
if "nt" in name:
self.iconbitmap("%s/images/ico_refrapy.ico"%getcwd())
# if not, use unix formats
else:
self.iconbitmap("@"+getcwd()+"/images/ico_refrapy.xbm")
frame_toolbar = Frame(self)
frame_toolbar.grid(row=0,column=0,sticky="EW")
photo = PhotoImage(file="%s/images/ico_refrapy.gif"%getcwd())
labelPhoto = Label(frame_toolbar, image = photo, width = 151)
labelPhoto.image = photo
labelPhoto.grid(row=0, column =0, sticky="W")
self.statusLabel = Label(frame_toolbar, text = "Create or load a project to start", font=("Arial", 11))
self.statusLabel.grid(row = 0, column = 19, sticky = "W")
initialise(self)
self.ico_newProject = PhotoImage(file="%s/images/ico_newProject.gif"%getcwd())
self.ico_loadProject = PhotoImage(file="%s/images/ico_loadProject.gif"%getcwd())
self.ico_openPick = PhotoImage(file="%s/images/ico_loadPicks.gif"%getcwd())
self.ico_invTimeterms = PhotoImage(file="%s/images/vm.gif"%getcwd())
self.ico_invTomo = PhotoImage(file="%s/images/tomogram.gif"%getcwd())
self.ico_layerMode = PhotoImage(file="%s/images/camadas.gif"%getcwd())
self.ico_clearLayers = PhotoImage(file="%s/images/limpar.gif"%getcwd())
self.ico_layer1 = PhotoImage(file="%s/images/layer1.gif"%getcwd())
self.ico_layer2 = PhotoImage(file="%s/images/layer2.gif"%getcwd())
self.ico_layer3 = PhotoImage(file="%s/images/layer3.gif"%getcwd())
self.ico_reset = PhotoImage(file="%s/images/fechar.gif"%getcwd())
self.ico_plotOptions = PhotoImage(file="%s/images/ico_plotOptions.gif"%getcwd())
self.ico_save = PhotoImage(file="%s/images/salvar.gif"%getcwd())
self.ico_fit = PhotoImage(file="%s/images/ico_fit.gif"%getcwd())
self.ico_mergeResults = PhotoImage(file="%s/images/ico_mergeResults.gif"%getcwd())
self.ico_velmesh = PhotoImage(file="%s/images/ico_velmesh.gif"%getcwd())
self.ico_3d = PhotoImage(file="%s/images/ico_3d.gif"%getcwd())
self.ico_help = PhotoImage(file="%s/images/ico_help.gif"%getcwd())
bt = Button(frame_toolbar,image = self.ico_newProject,command = self.createProject,width=25)
bt.grid(row = 0, column = 1, sticky="W")
bl = Balloon(self)
bl.bind(bt,"Create new project path")
bt = Button(frame_toolbar,image = self.ico_loadProject,command = self.loadProject,width=25)
bt.grid(row = 0, column = 2, sticky="W")
b = Balloon(self)
b.bind(bt,"Load project path")
bt = Button(frame_toolbar, image = self.ico_openPick,command = self.loadPick)
bt.grid(row = 0, column = 3, sticky="W")
b = Balloon(self)
b.bind(bt,"Load pick file")
bt = Button(frame_toolbar, image = self.ico_layerMode,command = self.layersInterpretation)
bt.grid(row = 0, column = 4, sticky="W")
b = Balloon(self)
b.bind(bt,"Enable/disable layer assignmet mode (time-terms inversion)")
bt = Button(frame_toolbar, image = self.ico_layer1,command = self.assignLayer1)
bt.grid(row = 0, column = 5, sticky="W")
b = Balloon(self)
b.bind(bt,"Assign layer 1 (direct wave)")
bt = Button(frame_toolbar, image = self.ico_layer2,command = self.assignLayer2)
bt.grid(row = 0, column = 6, sticky="W")
b = Balloon(self)
b.bind(bt,"Assign layer 2 (refracted wave)")
bt = Button(frame_toolbar, image = self.ico_layer3,command = self.assignLayer3)
bt.grid(row = 0, column = 7, sticky="W")
b = Balloon(self)
b.bind(bt,"Assign layer 3 (refracted wave)")
bt = Button(frame_toolbar, image = self.ico_clearLayers,command = self.clearLayerAssignment)
bt.grid(row = 0, column = 8, sticky="W")
b = Balloon(self)
b.bind(bt,"Clear layer assignment")
bt = Button(frame_toolbar, image = self.ico_invTimeterms,command = self.runTimeTerms)
bt.grid(row = 0, column = 9, sticky="W")
b = Balloon(self)
b.bind(bt,"Run time-terms inversion")
bt = Button(frame_toolbar, image = self.ico_invTomo,command = self.runTomography)
bt.grid(row = 0, column = 10, sticky="W")
b = Balloon(self)
b.bind(bt,"Run tomography inversion")
bt = Button(frame_toolbar, image = self.ico_fit,command = self.showFit)
bt.grid(row = 0, column = 11, sticky="W")
b = Balloon(self)
b.bind(bt,"Show model response (fit)")
bt = Button(frame_toolbar, image = self.ico_velmesh,command = self.showPgResult)
bt.grid(row = 0, column = 12, sticky="W")
b = Balloon(self)
b.bind(bt,"Show tomography velocity model with mesh")
bt = Button(frame_toolbar, image = self.ico_3d,command = self.build3d)
bt.grid(row = 0, column = 13, sticky="W")
b = Balloon(self)
b.bind(bt,"3D view of velocity model")
bt = Button(frame_toolbar, image = self.ico_save,command = self.saveResults)
bt.grid(row = 0, column = 14, sticky="W")
b = Balloon(self)
b.bind(bt,"Save results")
bt = Button(frame_toolbar, image = self.ico_mergeResults,command = self.mergeResults)
bt.grid(row = 0, column = 15, sticky="W")
b = Balloon(self)
b.bind(bt,"View layers (time-terms) on tomography model")
bt = Button(frame_toolbar, image = self.ico_plotOptions,command = self.plotOptions)
bt.grid(row = 0, column = 16, sticky="W")
b = Balloon(self)
b.bind(bt,"Plot options")
bt = Button(frame_toolbar, image = self.ico_reset,command = self.reset)
bt.grid(row = 0, column = 17, sticky="W")
b = Balloon(self)
b.bind(bt,"Reset all")
bt = Button(frame_toolbar,image=self.ico_help,command = self.help)
bt.grid(row = 0, column = 18, sticky="W")
bl = Balloon(self)
bl.bind(bt,"Help")
self.protocol("WM_DELETE_WINDOW", self.kill)
self.initiateVariables()
def help(self):
helpWindow = Toplevel(self)
helpWindow.title('Refrapick - Help')
helpWindow.configure(bg = "#F0F0F0")
helpWindow.resizable(0,0)
#check if on windows with nt kernel:
if "nt" in name:
helpWindow.iconbitmap("%s/images/ico_refrapy.ico"%getcwd())
# if not, use unix formats
else:
helpWindow.iconbitmap("@"+getcwd()+"/images/ico_refrapy.xbm")
#helpWindow.iconbitmap("%s/images/ico_refrapy.ico"%getcwd())
Label(helpWindow, text = """Refrapy - Refrainv v2.0.0
Refrainv provides tools for seismic refraction data inversion.
If you use Refrapy in your work, please consider citing the following paper:
Guedes, V.J.C.B., Maciel, S.T.R., Rocha, M.P., 2022. Refrapy: A Python program for seismic refraction data analysis,
Computers and Geosciences. https://doi.org/10.1016/j.cageo.2021.105020.
To report a bug and for more information, please visit github.com/viictorjs/Refrapy.
Author: Victor Guedes, MSc
E-mail: vjs279@hotmail.com
""",font=("Arial", 11)).pack()
helpWindow.tkraise()
def reset(self):
if messagebox.askyesno("Refrainv", "Clear all?"):
self.frame_plots.destroy()
self.frame_data.destroy()
self.frame_timeterms.destroy()
self.frame_tomography.destroy()
self.initiateVariables()
self.statusLabel.configure(text="Create or load a project to start",font=("Arial", 11))
messagebox.showinfo(title="Refrainv", message="All cleared successfully!")
def initiateVariables(self):
self.projReady = False
self.xdata = []
self.tdata = []
self.sources = []
self.dataArts = []
self.data_sourcesArts = []
self.data_pg = False
self.tomoPlot = False
self.timetermsPlot = False
self.timetermsInv = False
self.tomoMesh = False
self.showRayPath = False
self.rayPathColor = 'k'
self.colormap = "jet_r"
self.cmPlot = None
self.coords_3d = []
self.layerInterpretationMode = False
self.layer2interpretate = 1
self.layer1, self.layer2, self.layer3 = [],[],[]
self.velocity1,self.velocity2,self.velocity3 = 0,0,0
self.timeterms_response1_t, self.timeterms_response2_t, self.timeterms_response3_t = [],[],[]
self.layer1_color = "r"
self.layer2_color = "g"
self.layer3_color = "b"
self.showGrid = True
self.data_color = "k"
self.tomography_geohpones = False
self.tomography_sources = False
self.timeterms_geohpones = False
self.timeterms_sources = False
self.data_sources = True
self.showGeophones = False
self.geophonesPlot_timeterms = False
self.geophonesPlot_tomography = False
self.showSources = False
self.sourcesPlot_timeterms = False
self.sourcesPlot_tomography = False
self.sourcesPlot_data = False
self.dataLines = []
self.new_x_tomography, self.new_y_tomography = False, False
self.new_x_timeterms, self.new_y_timeterms = False, False
self.tomography_3d_ready = False
self.timeterms_3d_ready = False
self.showMerged = False
self.z2elev = False
self.__dict__.pop('tomostandards',None)
def kill(self):
out = messagebox.askyesno("Refrainv", "Do you want to close the software?")
if out: plt.close('all');self.destroy(); self.quit()
def assignLayer1(self):
if self.layerInterpretationMode:
self.layer2interpretate = 1
self.statusLabel.configure(text = 'Layer %d interpratation enabled!'%self.layer2interpretate)
def assignLayer2(self):
if self.layerInterpretationMode:
self.layer2interpretate = 2
self.statusLabel.configure(text = 'Layer %d interpratation enabled!'%self.layer2interpretate)
def assignLayer3(self):
if self.layerInterpretationMode:
self.layer2interpretate = 3
self.statusLabel.configure(text = 'Layer %d interpratation enabled!'%self.layer2interpretate)
def mergeResults(self):
if self.tomoPlot and self.timetermsPlot:
if self.showMerged == False:
if messagebox.askyesno("Refrainv", "Show layer(s) (from time-terms) over tomography model?"):
if self.layer2: self.merged_layer2, = self.ax_tomography.plot(self.gx_timeterms,self.z_layer2, c = "k")
if self.layer3: self.merged_layer3, = self.ax_tomography.plot(self.gx_timeterms,self.z_layer3, c = "k")
self.fig_tomography.canvas.draw()
self.showMerged = True
messagebox.showinfo(title="Refrainv", message="Layers displayed!")
else:
if messagebox.askyesno("Refrainv", "Remove layer(s) (from time-terms) over tomography model?"):
if self.layer2: self.merged_layer2.remove()
if self.layer3: self.merged_layer3.remove()
self.fig_tomography.canvas.draw()
self.showMerged = False
messagebox.showinfo(title="Refrainv", message="Layers removed!")
def clearLayerAssignment(self):
if messagebox.askyesno("Refrainv", "Clear layer interpretation?"):
del self.layer1[:]
del self.layer2[:]
del self.layer3[:]
for i in range(len(self.sources)):
for b in self.dataArts[i][self.sources[i]]:
b.set_color("white")
b.set_edgecolor("k")
self.fig_data.canvas.draw()
messagebox.showinfo(title="Refrainv", message="Layer assignment was cleared!")
def createPanels(self):
self.frame_plots = Frame(self, bg = "white")
self.frame_plots.grid(row = 1, column = 0, sticky = "NSWE")
self.frame_data = Frame(self.frame_plots)
self.frame_data.grid(row = 0, column = 0, sticky = "W", rowspan = 2)
self.fig_data = plt.figure(figsize = (6,8.1))
canvas_data = FigureCanvasTkAgg(self.fig_data, self.frame_data)
canvas_data.draw()
toolbar_data = NavigationToolbar2Tk(canvas_data, self.frame_data)
toolbar_data.update()
canvas_data._tkcanvas.pack()
self.ax_data = self.fig_data.add_subplot(111)
self.fig_data.patch.set_facecolor('#F0F0F0')
self.ax_data.set_title("Observed data")
self.ax_data.set_xlabel("POSITION [m]")
self.ax_data.set_ylabel("TIME [s]")
if self.showGrid: self.ax_data.grid(lw = .5, alpha = .5)
self.ax_data.spines['right'].set_visible(False)
self.ax_data.spines['top'].set_visible(False)
self.ax_data.yaxis.set_ticks_position('left')
self.ax_data.xaxis.set_ticks_position('bottom')
self.frame_timeterms = Frame(self.frame_plots)
self.frame_timeterms.grid(row = 0, column = 1, sticky = "NSWE")
self.fig_timeterms = plt.figure(figsize = (9.5,3.7))
canvas_timeterms = FigureCanvasTkAgg(self.fig_timeterms, self.frame_timeterms)
canvas_timeterms.draw()
toolbar_timeterms = NavigationToolbar2Tk(canvas_timeterms, self.frame_timeterms)
toolbar_timeterms.update()
canvas_timeterms._tkcanvas.pack()
self.ax_timeterms = self.fig_timeterms.add_subplot(111)
self.fig_timeterms.patch.set_facecolor('#F0F0F0')
self.ax_timeterms.set_title("Time-terms velocity model")
self.ax_timeterms.set_xlabel("POSITION [m]")
self.ax_timeterms.set_ylabel("DEPTH [m]")
if self.showGrid: self.ax_timeterms.grid(lw = .5, alpha = .5)
else: self.ax_timeterms.grid(False)
self.ax_timeterms.set_aspect("equal")
self.ax_timeterms.spines['right'].set_visible(False)
self.ax_timeterms.spines['top'].set_visible(False)
self.ax_timeterms.yaxis.set_ticks_position('left')
self.ax_timeterms.xaxis.set_ticks_position('bottom')
self.frame_tomography = Frame(self.frame_plots)
self.frame_tomography.grid(row = 1, column = 1, sticky = "NSWE")
self.fig_tomography = plt.figure(figsize = (9.5,3.7))
canvas_tomography = FigureCanvasTkAgg(self.fig_tomography, self.frame_tomography)
canvas_tomography.draw()
toolbar_tomography = NavigationToolbar2Tk(canvas_tomography, self.frame_tomography)
toolbar_tomography.update()
canvas_tomography._tkcanvas.pack()
self.ax_tomography = self.fig_tomography.add_subplot(111)
self.fig_tomography.patch.set_facecolor('#F0F0F0')
self.ax_tomography.set_title("Tomography velocity model")
self.ax_tomography.set_xlabel("POSITION [m]")
self.ax_tomography.set_ylabel("DEPTH [m]")
if self.showGrid: self.ax_tomography.grid(lw = .5, alpha = .5)
else: self.ax_tomography.grid(False)
self.ax_tomography.set_aspect("equal")
self.ax_tomography.spines['right'].set_visible(False)
self.ax_tomography.spines['top'].set_visible(False)
self.ax_tomography.yaxis.set_ticks_position('left')
self.ax_tomography.xaxis.set_ticks_position('bottom')
self.frame_plots.tkraise()
plt.close(self.fig_data)
plt.close(self.fig_tomography)
plt.close(self.fig_timeterms)
def createProject(self):
self.projPath = filedialog.askdirectory()
if self.projPath:
projName = simpledialog.askstring("Refrainv","Enter the name of the project to be created:")
if not path.exists(self.projPath+"/"+projName):
makedirs(self.projPath+"/"+projName)
local = self.projPath+"/"+projName+"/"
makedirs(local+"data")
self.p_data = local+"data/"
makedirs(local+"picks")
self.p_picks = local+"picks/"
makedirs(local+"models")
self.p_models = local+"models/"
makedirs(local+"gps")
self.p_gps = local+"gps/"
self.projPath = local
self.projReady = True
self.createPanels()
messagebox.showinfo(title="Refrainv", message="Successfully created the project!")
self.statusLabel.configure(text="Project path ready!",font=("Arial", 11))
else:
messagebox.showinfo(title="Refrainv", message="A project was detected, please choose another name or directory!")
def loadProject(self):
self.projPath = filedialog.askdirectory()
if self.projPath:
if path.exists(self.projPath+"/"+"data") and \
path.exists(self.projPath+"/"+"picks") and \
path.exists(self.projPath+"/"+"models") and \
path.exists(self.projPath+"/"+"gps"):
self.p_data = self.projPath+"/"+"data/"
self.p_picks = self.projPath+"/"+"picks/"
self.p_models = self.projPath+"/"+"models/"
self.p_gps = self.projPath+"/"+"gps/"
self.projReady = True
self.createPanels()
messagebox.showinfo(title="Refrainv", message="Successfully loaded the project path!")
self.statusLabel.configure(text="Project path ready!",font=("Arial", 11))
else: messagebox.showerror(title="Refrainv", message="Not all folders were detected!\nPlease, check the structure of the selected project.")
def loadPick(self):
if self.projReady:
if self.data_pg:
if messagebox.askyesno("Refrainv", "Load new data? (all current analysis have to be cleared)"): self.reset();
if self.data_pg == False:
pickFile = filedialog.askopenfilename(title='Open', initialdir = self.projPath+"/picks/", filetypes=[('Pick file', '*.sgt'),('Protomo Tools','*.#dt')])
self.lineName = path.basename(pickFile)[:-4]
if path.basename(pickFile)[-4:]=='.#dt':
dtreader( pickFile,self.lineName)
pickFile=pickFile[:-4]+'.sgt'
if pickFile:
self.data_pg = pg.DataContainer(pickFile, 's g')
with open(pickFile, "r") as file:
lines = file.readlines()
npoints = int(lines[0].split()[0])
sgx = [float(i.split()[0]) for i in lines[2:2+npoints]]
sgz = [float(i.split()[1]) for i in lines[2:2+npoints]]
sgtindx = lines.index("#s g t\n")
s = [int(i.split()[0]) for i in lines[sgtindx+1:]]
g = [int(i.split()[1]) for i in lines[sgtindx+1:]]
t = [float(i.split()[2]) for i in lines[sgtindx+1:]]
sx = [sgx[i-1] for i in s]
gx = [sgx[i-1] for i in g]
gz = [sgz[i-1] for i in g]
self.gx = gx
self.gz = gz
self.sgx = sgx
self.sgz = sgz
#self.dx = self.gx[1]-self.gx[0]
self.dx=np.median(np.abs(np.diff(self.gx)))
self.sx, self.sz = [], []
for i in list(set(s)):
self.sx.append(sgx[i-1])
self.sz.append(sgz[i-1])
print("what")
if any(z > 0 for z in gz):
self.z2elev = True
if self.z2elev:
self.ax_timeterms.set_ylabel("ELEVATION [m]")
self.ax_tomography.set_ylabel("ELEVATION [m]")
self.fig_timeterms.canvas.draw()
self.fig_tomography.canvas.draw()
#saving computing time by setting sme apras outside of loop:
#seize=self.dx*4
seize=self.dx
#taking out some appends from below as append is slow
self.sources=list(set(sx))
for i,src in enumerate(tqdm(list(set(sx)))):
# self.sources.append(src)
self.xdata.append({src:[]})
self.tdata.append({src:[]})
self.dataArts.append({src:[]})
if self.data_sources:
if self.showSources:
#plots the source points
sourcePlot = self.ax_data.scatter(src,0,c="y",edgecolor="k",s=100,marker="*",zorder=99)
self.data_sourcesArts.append(sourcePlot)
for j,x in enumerate(gx):
if sx[j] == src:
self.xdata[i][src].append(x)
self.tdata[i][src].append(t[j])
#dataPlot = self.ax_data.scatter(x,t[j],facecolors='w',s=seize,edgecolor=self.data_color,picker=self.dx,zorder=99)
#self.dataArts[i][src].append(dataPlot)
#replace that awful loop:
sxarray=np.array(sx)
gxarray=np.array(gx)
tarray=np.array(t)
all_src_occurence_indexes=np.where(sxarray==src)[0]
all_x_occurences=gxarray[ all_src_occurence_indexes]
all_t_occurences=tarray[ all_src_occurence_indexes]
dataPlot=self.ax_data.scatter(all_x_occurences,all_t_occurences,facecolors='w',s=seize,edgecolor=self.data_color,picker=self.dx,zorder=99)
self.dataArts[i][src].append(dataPlot)
dataLine, = self.ax_data.plot(self.xdata[i][src], self.tdata[i][src], c = self.data_color)
self.dataLines.append(dataLine)
self.fig_data.canvas.draw()
messagebox.showinfo(title="Refrainv", message="Traveltimes data have been loaded successfully!")
def runTimeTerms(self):
if self.layer1 and self.layer2 or self.layer1 and self.layer3:
self.clearTimeTermsPlot()
regw = simpledialog.askfloat("Refrainv", "Enter the regularization weight to be used for data inversion or cancel for default (lambda = 0.1)")
if regw == None: regw = 0.1
gx = list(set(self.gx))
self.gx_timeterms = gx
gz = self.gz[:len(gx)]
self.gz_timeterms = gz
def solve(layer, G, d, w):
rMs = zeros((int(len(layer)), int(len(self.sources)+len(gx)+1)))
r = 0
for i in range(len(gx)):
for j in range(len(self.sources)):
if self.sources[j] > min(gx) and self.sources[j] < max(gx): #se for fonte intermediaria
if gx[i]+self.dx >= self.sources[j] and gx[i]-self.dx <= self.sources[j]:
rMs[r][j] = w
rMs[r][len(self.sources)+i] = -w
r += 1
elif self.sources[j] <= min(gx):
if gx[i]-self.dx <= self.sources[j]:
rMs[r][j] = w
rMs[r][len(self.sources)+i] = -w
r += 1
elif self.sources[j] >= max(gx):
if gx[i]+self.dx >= self.sources[j]:
rMs[r][j] = w
rMs[r][len(self.sources)+i] = -w
r += 1
rMs = rMs[~np_all(rMs == 0, axis=1)] #regularization matrix of time-terms from sources
rMg = zeros((int(len(layer)), int(len(self.sources)+len(gx)+1)))
for i,j in zip(range(shape(rMg)[0]), range(shape(rMg)[1])):
try:
rMg[i][len(self.sources)+j] = w
rMg[i][len(self.sources)+j+1] = -w
except: pass
rMg = rMg[~np_all(rMg == 0, axis=1)][:-2] #regularization matrix of time-terms from geophones
rM = concatenate((rMs, rMg))
rd = hstack((d, [i*0 for i in range(shape(rM)[0])]))
rG = concatenate((G, rM))
sol, sse, rank, sv = linalg.lstsq(rG, rd)
return sol
if self.layer1:
d1 = array([self.layer1[i][1] for i in range(len(self.layer1))])
G1 = array([self.layer1[i][3] for i in range(len(self.layer1))])
G1 = reshape(G1, (len(G1),1))
slowness = []
for time,delta in zip(d1,G1):
if delta == 0: pass
else: slowness.append(time/delta)
mean_slowness = mean(slowness)
v1 = 1/mean_slowness
self.velocity1 = v1
list_ot1, list_pt1 = [],[]
self.timeterms_response1_x = []
self.timeterms_response1_t = []
for p in self.layer1:
x = p[-3]
geop = p[0]
ot = p[1] #observed traveltime
pt = x/v1 #predicted traveltime
list_ot1.append(ot)
list_pt1.append(pt)
self.timeterms_response1_x.append(geop)
self.timeterms_response1_t.append(pt)
self.timeterms_respLayer1 = list_pt1
self.timeterms_response = list_pt1
timeterms_observed = list_ot1
if self.layer2:
d2 = array([self.layer2[i][1] for i in range(len(self.layer2))])
G2 = zeros((int(len(self.layer2)),
int(len(self.sources)+len(gx)+1)))
for i in range(len(self.layer2)):
G2[i][self.layer2[i][-2]] = 1
G2[i][self.layer2[i][-1]+len(self.sources)] = 1
G2[i][-1] = self.layer2[i][-3]
sol_layer2 = solve(self.layer2, G2, d2, regw)
v2 = 1/sol_layer2[-1]
self.velocity2 = v2
dtg2 = array([i for i in sol_layer2[len(self.sources):-1]]) #delay-time of all geophones
dts2 = array([i for i in sol_layer2[:len(self.sources)]]) #delay-time of all sources
z_layer2 = gz-((dtg2*v1*v2)/(sqrt((v2**2)-(v1**2))))
self.z_layer2 = z_layer2
list_ot2, list_pt2 = [],[]
self.timeterms_response2_x = []
self.timeterms_response2_t = []
for p in self.layer2:
s = p[-2]
g = p[-1]
x = p[-3]
ot = p[1] #observed traveltime
geop = p[0]
pt = dts2[s]+dtg2[g]+sol_layer2[-1]*x #predicted traveltime
list_ot2.append(ot)
list_pt2.append(pt)
self.timeterms_response2_x.append(geop)
self.timeterms_response2_t.append(pt)
self.timeterms_respLayer2 = list_pt2
self.timeterms_response += list_pt2
timeterms_observed += list_ot2
if self.layer3:
d3 = array([self.layer3[i][1] for i in range(len(self.layer3))])
G3 = zeros((int(len(self.layer3)),
int(len(self.sources)+len(gx)+1)))
for i in range(len(self.layer3)):
G3[i][self.layer3[i][-2]] = 1
G3[i][self.layer3[i][-1]+len(self.sources)] = 1
G3[i][-1] = self.layer3[i][-3]
sol_layer3 = solve(self.layer3, G3, d3, regw)
v3 = 1/sol_layer3[-1] #m/s
self.velocity3 = v3
dtg3 = array([i for i in sol_layer3[len(self.sources):-1]]) #delay-time of all geophones3
dts3 = array([i for i in sol_layer3[:len(self.sources)]]) #delay-time of all sources3
if self.velocity2: upvmed = (v1+v2)/2
else: upvmed = v1
z_layer3 = gz-((dtg3*upvmed*v3)/(sqrt((v3**2)-(upvmed**2))))
self.z_layer3 = z_layer3
list_ot3, list_pt3 = [],[]
self.timeterms_response3_x = []
self.timeterms_response3_t = []
for p in self.layer3:
s = p[-2]
g = p[-1]
geop = p[0]
x = p[-3]
ot = p[1] #observed traveltime
pt = dts3[s]+dtg3[g]+sol_layer3[-1]*x #predicted traveltime
list_ot3.append(ot)
list_pt3.append(pt)
self.timeterms_response3_x.append(geop)
self.timeterms_response3_t.append(pt)
self.timeterms_respLayer3 = list_pt3
self.timeterms_response += list_pt3
timeterms_observed += list_ot3
if self.layer1 and self.layer2 and not self.layer3:
self.fill_layer1 = self.ax_timeterms.fill_between(gx, z_layer2, gz, color = self.layer1_color, alpha = 1,edgecolor = "k", label = "%d m/s"%v1)
self.fill_layer2 = self.ax_timeterms.fill_between(gx, z_layer2, min(z_layer2)*1.5, color = self.layer2_color,alpha = 1,edgecolor = "k", label = "%d m/s"%v2)
elif self.layer1 and self.layer2 and self.layer3:
self.fill_layer1 = self.ax_timeterms.fill_between(gx, z_layer2, gz, color = self.layer1_color,alpha = 1,edgecolor = "k", label = "%d m/s"%v1)
self.fill_layer2 = self.ax_timeterms.fill_between(gx,z_layer2, z_layer3,color = self.layer2_color, alpha = 1,edgecolor = "k", label = "%d m/s"%v2)
self.fill_layer3 = self.ax_timeterms.fill_between(gx,z_layer3, min(z_layer3)*0.99, color = self.layer3_color,alpha = 1,edgecolor = "k", label = "%d m/s"%v3)
if self.layer1 and self.layer3 and not self.layer2:
self.fill_layer1 = self.ax_timeterms.fill_between(gx, z_layer3, gz, color = self.layer1_color,alpha = 1,edgecolor = "k", label = "%d m/s"%v1)
self.fill_layer3 = self.ax_timeterms.fill_between(gx, z_layer3, min(z_layer3)*0.99, color = self.layer3_color,alpha = 1,edgecolor = "k",label = "%d m/s"%v3)
self.ax_timeterms.legend(loc="best")
self.timetermsPlot = True
self.fig_timeterms.canvas.draw()
self.timeterms_rmse = sqrt(mean((array(self.timeterms_response)-array(timeterms_observed))**2))
self.timeterms_relrmse = (sqrt(mean(square((array(timeterms_observed) - array(self.timeterms_response)) / array(timeterms_observed))))) * 100
#messagebox.showinfo('Refrainv','Absolute RMSE = %.2f ms\nRelative RMSE = %.2f%%'%(rmse*1000,relrmse))
self.showFit()
def layersInterpretation(self):
if self.data_pg:
if self.layerInterpretationMode == False:
self.layerInterpretationMode = True
self.statusLabel.configure(text = 'Layer %d interpratation enabled!'%self.layer2interpretate)
def onpick(event):
art = event.artist
artx = art.get_offsets()[0][0]
artt = art.get_offsets()[0][1]
for i in range(len(self.sources)):
if art in self.dataArts[i][self.sources[i]]:
arts = self.sources[i]
iS = i
if artx >= arts:
for b in self.dataArts[iS][arts]:
bx = b.get_offsets()[0][0]
iG = where(array(self.dataArts[iS][arts]) == b)[0][0]
if arts <= bx <= artx:
bt = b.get_offsets()[0][1]
if self.layer2interpretate == 1 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer1:
b.set_color(self.layer1_color)
self.layer1.append((bx,bt,arts,abs(arts-bx),iS, iG))#geophone_position , arrival_time , source_poisition , offset , index_source , index_geophone
if (bx,bt,arts,abs(arts-bx),iS, iG) in self.layer2:
self.layer2.remove((bx,bt,arts,abs(arts-bx),iS, iG))
elif self.layer2interpretate == 2 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer1 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer2:
b.set_color(self.layer2_color)
self.layer2.append((bx,bt,arts,abs(arts-bx),iS, iG))
if (bx,bt,arts,abs(arts-bx),iS, iG) in self.layer3:
self.layer3.remove((bx,bt,arts,abs(arts-bx),iS, iG))
elif self.layer2interpretate == 3 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer2 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer1 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer3:
b.set_color(self.layer3_color)
self.layer3.append((bx,bt,arts,abs(arts-bx),iS, iG))
elif artx <= arts:
for b in self.dataArts[iS][arts]:
bx = b.get_offsets()[0][0]
iG = where(array(self.dataArts[iS][arts]) == b)[0][0]
if arts >= bx >= artx:
bt = b.get_offsets()[0][1]
if self.layer2interpretate == 1 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer1:
b.set_color(self.layer1_color)
self.layer1.append((bx,bt,arts,abs(arts-bx),iS, iG))
if (bx,bt,arts,abs(arts-bx),iS, iG) in self.layer2:
self.layer2.remove((bx,bt,arts,abs(arts-bx),iS, iG))
elif self.layer2interpretate == 2 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer1 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer2:
b.set_color(self.layer2_color)
self.layer2.append((bx,bt,arts,abs(arts-bx),iS, iG))
if (bx,bt,arts,abs(arts-bx),iS, iG) in self.layer3:
self.layer3.remove((bx,bt,arts,abs(arts-bx),iS, iG))
elif self.layer2interpretate == 3 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer2 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer1 and (bx,bt,arts,abs(arts-bx),iS, iG) not in self.layer3:
b.set_color(self.layer3_color)
self.layer3.append((bx,bt,arts,abs(arts-bx),iS, iG))
self.fig_data.canvas.draw()
def onkey(event):
if event.key == "1": self.layer2interpretate = 1
elif event.key == "2": self.layer2interpretate = 2
elif event.key == "3": self.layer2interpretate = 3
self.statusLabel.configure(text = 'Layer %d interpratation enabled!'%self.layer2interpretate)
if event.key == "C" or event.key == "c":
if messagebox.askyesno("Refrainv", "Clear layer interpretation?"):
del self.layer1[:]
del self.layer2[:]
del self.layer3[:]
for i in range(len(self.sources)):
for b in self.dataArts[i][self.sources[i]]:
b.set_color("white")
b.set_edgecolor("k")
self.fig_data.canvas.draw()
self.timeterms_pickEvent = self.fig_data.canvas.mpl_connect('pick_event', onpick)
self.timeterms_keyEvent = self.fig_data.canvas.mpl_connect('key_press_event', onkey)
messagebox.showinfo('Refrapy','Layer interpretation enabled!')
else:
self.fig_data.canvas.mpl_disconnect(self.timeterms_pickEvent)
self.fig_data.canvas.mpl_disconnect(self.timeterms_keyEvent)
self.statusLabel.configure(text = 'Layer interpratation disabled')
messagebox.showinfo('Refrainv','Layer interpretation disabled!')
self.layerInterpretationMode = False
def clearTomoPlot(self):
self.fig_tomography.clf()
self.ax_tomography = self.fig_tomography.add_subplot(111)
self.fig_tomography.patch.set_facecolor('#F0F0F0')
self.ax_tomography.set_title("Tomography velocity model")
self.ax_tomography.set_xlabel("POSITION [m]")
if self.z2elev: self.ax_tomography.set_ylabel("ELEVATION [m]")
else: self.ax_tomography.set_ylabel("DEPTH [m]")
if self.showGrid: self.ax_tomography.grid(lw = .5, alpha = .5)
else: self.ax_tomography.grid(False)
if self.showMerged:
if self.layer2: self.merged_layer2.remove()
if self.layer3: self.merged_layer3.remove()
self.showMerged = False
self.ax_tomography.set_aspect("equal")
self.ax_tomography.spines['right'].set_visible(False)
self.ax_tomography.spines['top'].set_visible(False)
self.ax_tomography.yaxis.set_ticks_position('left')
self.ax_tomography.xaxis.set_ticks_position('bottom')
self.tomoPlot = False
self.fig_tomography.canvas.draw()
def clearTimeTermsPlot(self):
self.fig_timeterms.clf()
self.ax_timeterms = self.fig_timeterms.add_subplot(111)
self.fig_timeterms.patch.set_facecolor('#F0F0F0')
self.ax_timeterms.set_title("Time-terms velocity model")
self.ax_timeterms.set_xlabel("POSITION [m]")
if self.z2elev: self.ax_timeterms.set_ylabel("ELEVATION [m]")
else: self.ax_timeterms.set_ylabel("DEPTH [m]")
if self.showGrid: self.ax_timeterms.grid(lw = .5, alpha = .5)
else: self.ax_timeterms.grid(False)
if self.showMerged:
if self.layer2: self.merged_layer2.remove()
if self.layer3: self.merged_layer3.remove()
self.showMerged = False
self.ax_timeterms.set_aspect("equal")
self.ax_timeterms.spines['right'].set_visible(False)
self.ax_timeterms.spines['top'].set_visible(False)
self.ax_timeterms.yaxis.set_ticks_position('left')
self.ax_timeterms.xaxis.set_ticks_position('bottom')
self.timetermsPlot = False
self.fig_timeterms.canvas.draw()
def runTomography(self):
if self.data_pg:
self.mgr = TravelTimeManager()
tomoWindow = Toplevel(self)
tomoWindow.title('Refrainv - Tomography')
tomoWindow.configure(bg = "#F0F0F0")
tomoWindow.geometry("300x680")
tomoWindow.resizable(0,True)
#check if on windows with nt kernel:
if "nt" in name:
tomoWindow.iconbitmap("%s/images/ico_refrapy.ico"%getcwd())
# if not, use unix formats
else:
tomoWindow.iconbitmap("@"+getcwd()+"/images/ico_refrapy.xbm")
#tomoWindow.iconbitmap("%s/images/ico_refrapy.ico"%getcwd())
def viewMesh():
maxDepth = float(maxDepth_entry.get())
paraDX = float(paraDX_entry.get())
paraMaxCellSize = float(paraMaxCellSize_entry.get())
paraQuality =float(paraQuality_entry.get())
self.tomoMesh = self.mgr.createMesh(data=self.data_pg,paraDepth=maxDepth,paraDX=paraDX,paraMaxCellSize=paraMaxCellSize,quality=paraQuality)
meshWindow = Toplevel(self)
meshWindow.title('Refrainv - Mesh')
meshWindow.configure(bg = "#F0F0F0")