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SNR_GUI_003.py
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SNR_GUI_003.py
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#########################################
#
# A test UI for SNR plot
# Simple plot for stack images, error images, SNR image and pure spectra
# Version: 0.01 created on 04-Nov-2019, first created by Anika Beer & Joseph, modified by Man I
#
#
# Required Packages:
# Pyqtgraph
# astropy
# sys
# numpy
# argparse
# os
# re
# copy
#
# Change list:
# V0.02 12-Dec-2019
# - Added time consuming caculator
# - Added functions to load one or two cubes
# - Replaced SNR maps to be second flux map if two cubes are selected
# - Locked SNR to IMAGE1 & IMAGE 2
# - Changed the execution method of v0.02
# - How to call the script?
# - cube1 & cube2 have to be the same size
# - cube1: shall be blue (shorter wavelength)
# - cube2: shall be red (longer wavelength)
# - cube2 - cube1 == -1
# -- python SNR_GUI_002.py FILE_DIRECTORY FILENAME(cube1, no .fit suffix) NUMBER_OF_FILES (only accepted 1 or 2)
#
#
# V0.03 20-Dec-2019
# - Added buttons to scale image fluxes in log-scale or linear-scale
# - Made two scale bars to be the same size (Bar1 & Bar2)
# - Fixed the error cube when only one cube is loaded-in
# - Used deep.copy to copy data cube
#
# To-Do List:
# Add Raise ERROR messages
# Try to make it prettier
# Fix a warning in np.log10..
# Vary the image scale bars
#
##########################################
# interface packages
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
import pyqtgraph as pg
# calulation packages
import numpy as np
import argparse
import sys
import os
from astropy.io import fits
import re
import copy
class SNR_GUI(QWidget):
# load definition
def __init__(self):
super().__init__()
# Definition of the arguments, call interface function
parser = argparse.ArgumentParser()
parser.add_argument('Directory', help = 'Location of files')
parser.add_argument('FileName', help = 'Name of the galaxy as in file to be used, no path is required')
parser.add_argument('Num', help = 'Number of file(s) to be used')
args = parser.parse_args()
self.path = args.Directory
self.pre = args.FileName
self.number = args.Num
self.initUI()
def initUI(self):
# The major plot function, this tells you how the interface structure.
pg.setConfigOption( 'background', 'w')
pg.setConfigOption( 'foreground', 'k')
app = pg.mkQApp()
# Enable antialiasing
pg.setConfigOptions(antialias=True)
# set windows
self.window = pg.GraphicsWindow(title='TEST Data SNR Interface')
self.window.resize(1250,1000)
#Load paradise data, variables
self.paradise_data()
# set first image
self.p1 = self.window.addPlot(title='IMAGE 1')
self.image1 = pg.ImageItem()
self.image1.setImage(image = self.stackflux())
self.p1.addItem(self.image1, row=1, col=0)
self.p1.setMenuEnabled(enableMenu=False)
# set first image control bar
self.hist1 = pg.HistogramLUTItem(fillHistogram=False)
self.hist1.setImageItem(self.image1)
self.hist1.setLevels(-1,8)
self.hist1.setHistogramRange(-1,8)
self.window.addItem(self.hist1)
# set second image
self.p2 = self.window.addPlot(title='IMAGE 2')
self.image2 = pg.ImageItem()
if self.number == 1:
self.image2.setImage(image = self.SNR_data())
else:
self.SNR_data_red()
self.stackflux_red()
self.SNR_data()
self.image2.setImage(image = self.stackflux_red())
self.p2.addItem(self.image2, row=1, col=2)
self.p2.setMenuEnabled(enableMenu=False)
# set second control bar
hist2 = pg.HistogramLUTItem(fillHistogram=False)
hist2.setImageItem(self.image2)
hist2.setLevels(-1,8)
hist2.setHistogramRange(-1,8)
self.window.addItem(hist2)
# set third plot
self.p3 = self.window.addPlot(title='Input', row=2, col=0, colspan=4)
self.p3.plot(self.cube._wave, self.cube._data[:, self.y_mid, self.x_mid], pen=(0,0,0), name='Input')
if self.number == str(2):
self.p3.plot(self.cube2._wave, self.cube2._data[:,self.y_mid, self.x_mid], pen=(0,153,153))
self.p3.setXRange(min(self.cube._wave), max(self.cube._wave))
self.p3.setYRange(np.amin(self.cube._data[:, self.y_mid, self.x_mid]), np.amax(self.cube._data[:, self.y_mid, self.x_mid]))
self.textposx = 0
self.textposy = 0
#cross hair and text
self.text = pg.TextItem(anchor=(0,1),color=(255,153,51))
self.p1.addItem(self.text)
self.vLine = pg.InfiniteLine(angle=90, movable=False, pen=(255,153,51))
self.hLine = pg.InfiniteLine(angle=0, movable=False, pen=(255,153,51))
self.p1.addItem(self.vLine, ignoreBounds=True)
self.p1.addItem(self.hLine, ignoreBounds=True)
self.vb = self.p1.vb
self.text2 = pg.TextItem(anchor=(0,1),color=(255,153,51))
self.p2.addItem(self.text2)
self.vLine2 = pg.InfiniteLine(angle=90, movable=False, pen=(255,153,51))
self.hLine2 = pg.InfiniteLine(angle=0, movable=False, pen=(255,153,51))
self.p2.addItem(self.vLine2, ignoreBounds=True)
self.p2.addItem(self.hLine2, ignoreBounds=True)
self.vb2 = self.p2.vb
# executions
self.proxy = pg.SignalProxy(self.p1.scene().sigMouseMoved, rateLimit=120, slot=self.mouseMoved)
self.image1.mouseClickEvent = self.mouseClickImg
self.proxy2 = pg.SignalProxy(self.p2.scene().sigMouseMoved, rateLimit=120, slot=self.mouseMoved)
self.image2.mouseClickEvent = self.mouseClickImg
# Add button widget
self.button = pg.LayoutWidget()
self.button1 = QPushButton('IMAGE 1 - log scale')
self.button2 = QPushButton('IMAGE 1 - linear scale')
self.button3 = QPushButton('IMAGE2 - log scale')
self.button4 = QPushButton('IMAGE2 - linear scale')
self.button.addWidget(self.button1, row=0,col=0)
self.button.addWidget(self.button2, row=0,col=1)
self.button.addWidget(self.button3, row=0,col=2)
self.button.addWidget(self.button4, row=0,col=3)
self.button.setParent(self.window)
self.button.show()
#click bottom
self.button1.clicked.connect(self.Button1Clicked)
self.button2.clicked.connect(self.Button2Clicked)
self.button3.clicked.connect(self.Button3Clicked)
self.button4.clicked.connect(self.Button4Clicked)
def paradise_data(self):
# load spectra
# Now it only fit for PyParadise readable data format.
if self.number == str(1) or self.number == str(2):
self.cube = fits.open(self.path + self.pre + '.fit')
self.cube._data = np.array(list(map(lambda x: x[0] * x[1], zip(self.cube[1].data, self.cube[5].data))))
self.cube._wave = self.cube[1].header['CRVAL3'] + np.arange(self.cube[1].header['NAXIS3']) * self.cube[1].header['CD3_3']
(self.z,self.y,self.x) = np.array(self.cube._data).shape
self.x_mid = self.x//2
self.y_mid = self.y//2
if self.number == str(2):
num_fil = re.sub("\D", "", self.pre)
self.pre2 = "stackcube_" + str(int(num_fil) - 1)
self.cube2 = fits.open(self.path + self.pre2 + '.fit')
self.cube2._data = np.array(list(map(lambda x: x[0] * x[1], zip(self.cube2[1].data, self.cube2[5].data))))
self.cube2._wave = self.cube2[1].header['CRVAL3'] + np.arange(self.cube2[1].header['NAXIS3']) * self.cube2[1].header['CD3_3']
(self.z2,self.y2,self.x2) = np.array(self.cube2._data).shape
self.cube._wave = np.concatenate((self.cube._wave, self.cube2._wave), axis=0)
self.cube._data = np.concatenate((self.cube._data, self.cube2._data), axis=0)
def stackflux(self):
# Stack Image for cube 1
# Get the collapse flux from WEAVE data
self.map= self.cube[6].data
self.imagesum = np.transpose(self.map)/1e5
print(max(self.imagesum.flatten()))
return self.imagesum
def stackflux_red(self):
# Stack Image for cube2
# Get the collapse flux
if self.number == str(2):
self.map2= self.cube2[6].data
self.imagesum2 = np.transpose(self.map2)/1e5
else:
self.imagesum2 = np.transpose(self.cube[7].data)
return self.imagesum2
def SNR_data(self):
# SNR calculation for cube1, initally it only used one number. It will be used PyAstronomy package as its final method.
self.snr=[]
for xvar in range(self.x):
for yvar in range(self.y):
if self.cube._data[300, yvar, xvar] != 0:
snrEsti = np.median(self.cube._data[1500:2000,yvar,xvar])/np.std(self.cube._data[1500:2000,yvar,xvar])
self.snr.append(snrEsti)
else:
self.snr.append(0)
self.imageData = np.array(self.snr).reshape(self.x,self.y)
return self.imageData
def SNR_data_red(self):
# SNR calculation for cube2, initally it only used one number. It will be used PyAstronomy package as its final method.
if self.number == str(2):
self.snr2=[]
for xvar in range(self.x):
for yvar in range(self.y):
if self.cube2._data[300, yvar, xvar] != 0:
snrEsti = np.median(self.cube2._data[1500:2000,yvar,xvar])/np.std(self.cube2._data[1500:2000,yvar,xvar])
self.snr2.append(snrEsti)
else:
self.snr2.append(0)
else:
self.snr2 = self.SNR_data()
self.imageData2 = np.array(self.snr2).reshape(self.x,self.y)
return self.imageData2
def Button1Clicked(self):
imagesum_log_0 = copy.deepcopy(self.imagesum)
imagesum_log_0[np.isnan(imagesum_log_0)] = 0
imagesum_log_0[np.isinf(imagesum_log_0)] = 0
imagesum_log_1 = imagesum_log_0.flatten()
imagesum_log_2 = np.where(imagesum_log_1 > 0, np.log10(imagesum_log_1), imagesum_log_1)
self.imagesum_log = imagesum_log_2.reshape(self.x, self.y)
self.image1.setImage(image = self.imagesum_log)
self.p1.addItem(self.image1, row=0, col=0)
self.p1.setMenuEnabled(enableMenu=False)
def Button2Clicked(self):
self.imagebutton = self.stackflux()
self.image1.setImage(image = self.imagebutton)
self.p1.addItem(self.image1, row=0, col=0)
self.p1.setMenuEnabled(enableMenu=False)
self.hist1 = pg.HistogramLUTItem(fillHistogram=False)
self.hist1.setImageItem(self.image1)
self.hist1.setLevels(-1,8)
self.hist1.setHistogramRange(-1,8)
def Button3Clicked(self):
imagesum2_log_0 = copy.deepcopy(self.imagesum2)
imagesum2_log_0[np.isnan(imagesum2_log_0)] = 0
imagesum2_log_0[np.isinf(imagesum2_log_0)] = 0
imagesum2_log_1 = imagesum2_log_0.flatten()
imagesum2_log_2 = np.where(imagesum2_log_1 > 0, np.log10(imagesum2_log_1), imagesum2_log_1)
self.imagesum2_log = imagesum2_log_2.reshape(self.x, self.y)
self.image2.setImage(image = self.imagesum2_log)
self.p2.addItem(self.image2, row=3, col=0)
self.p2.setMenuEnabled(enableMenu=False)
def Button4Clicked(self):
self.imagebutton4 = self.stackflux_red()
self.image2.setImage(image = self.imagebutton4)
self.p2.addItem(self.image2, row=0, col=0)
self.p2.setMenuEnabled(enableMenu=False)
self.hist2 = pg.HistogramLUTItem(fillHistogram=False)
self.hist2.setImageItem(self.image2)
self.hist2.setLevels(-1,8)
self.hist2.setHistogramRange(-1,8)
def mouseMoved(self, evt):
# Set mouse movement
pos = evt[0] ## using signal proxy turns original arguments into a tuple
if self.p1.sceneBoundingRect().contains(pos):
mousePoint = self.p1.vb.mapSceneToView(pos)
self.indexx = int(np.floor(mousePoint.x()))
self.indexy = int(np.floor(mousePoint.y()))
if (self.indexx >= 0 and self.indexx < self.x) and (self.indexy >= 0 and self.indexy < self.y):
self.text.setText("x=%1.0f, y=%1.0f, SNR=%0.01f" % (self.indexx,self.indexy,self.imageData[self.indexx,self.indexy]))
self.text2.setText("x=%1.0f, y=%1.0f, SNR=%0.01f" % (self.indexx,self.indexy,self.imageData2[self.indexx,self.indexy]))
self.textposx = mousePoint.x()
self.textposy = mousePoint.y()
if (self.indexx > self.x_mid): #and indexx < (len(imageData)+len(imageData)*0.3)):
self.textposx = mousePoint.x() - int(self.x * 0.4)
if (self.indexy > self.y - self.y * .1):
self.textposy = mousePoint.y()-int(self.y * 0.1)
self.text.setPos(self.textposx,self.textposy)
self.vLine.setPos(mousePoint.x())
self.hLine.setPos(mousePoint.y())
self.text2.setPos(self.textposx,self.textposy)
self.vLine2.setPos(mousePoint.x())
self.hLine2.setPos(mousePoint.y())
def mouseClickImg(self, event):
# Set mouse clicked
pos_add = event.pos() # position of the mouse
self.pixelx = int(np.floor(pos_add[int(0)]))
self.pixely = int(np.floor(pos_add[int(1)]))
self.p3.clear()
#Add new data
self.p3.setYRange(np.amin(self.cube._data[:, self.pixely, self.pixelx]), np.amax(self.cube._data[:, self.pixely, self.pixelx]))
self.p3.plot(self.cube._wave, self.cube._data[:, self.pixely, self.pixelx], pen=(0,0,0), name="Input")
if self.number == str(2):
self.p3.plot(self.cube2._wave, self.cube2._data[:,self.pixely, self.pixelx], pen=(0,153,153))
# Start Qt event loop unless running in interactive mode or using pyside
if __name__ == '__main__':
import time
start_time = time.time()
#Select instance of QApplication
if not QApplication.instance():
app = QApplication(sys.argv)
else:
app = QApplication.instance()
#Run the GUI if being run in interactive mode
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
ex = SNR_GUI()
print("--- %s seconds ---" % (time.time() - start_time))
sys.exit(app.exec_())