galaxy_ellipse.py
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# -*- coding: utf-8 -*-
title = "RingIntegration"
tip = "elliptic ring integration"
onein = -1
import copy as cp
import numpy as np
from nodmath import extract
from guiqwt import pyplot
from guidata.qt.QtGui import QMessageBox, QApplication, QCursor, QListView, QStandardItemModel, QStandardItem, QFont, QVBoxLayout
from guidata.dataset.datatypes import DataSet
from guidata.dataset.dataitems import (IntItem, StringItem, ChoiceItem, FloatItem, BoolItem)
from guidata.qt.QtCore import Qt
from guiqwt.events import setup_standard_tool_filter, KeyEventMatch
from guiqwt.tools import AnnotatedRectangle, RectangularShapeTool
from guiqwt.curve import PolygonMapItem
from guiqwt.styles import CurveParam
from guiqwt.config import _
def nint(x):
if x > 0: return int(x+0.5)
else: return int(x-0.5)
class NOD3_App:
def __init__(self, parent):
self.parent = parent
self.parent.activateWindow()
def Error(self, msg):
QMessageBox.critical(self.parent.parent(), title,
_(u"Error:")+"\n%s" % str(msg))
def compute_app(self, **args):
class FuncParam(DataSet):
posx = StringItem('Center x:', default="0:0:0")
posy = StringItem('Center y:', default="0:0:0")
major = FloatItem('Major axis:', default=0.0)
#minor = FloatItem('Minor axis:', default=0.0)
incl = FloatItem('Inclination [deg]:', default=0.0, min=0.0, max=89.0)
posang = FloatItem('Position angle:', default=0.0)
#naxis1 = IntItem('shape x')
#naxis2 = IntItem('shape y')
ringwidth = FloatItem('Ringwidth [arcsec]:')
ration = BoolItem("Ratio", default=False)
cursor = BoolItem("Cursor", default=True)
outfile = StringItem('Outfile:', default="ringint.out")
#inclination = FloatItem('Inclination [deg]:', default=0.0)
self.name = title.replace(" ", "")
if args == {}:
param = FuncParam(self.name, "Create the outer ring shape:\n\n(release cursor with the <space> key)")
else:
param = self.parent.ScriptParameter(name, args)
param = self.parent.read_defaults(param)
if not param.edit():
return
self.parent.write_defaults(param)
# if no parameter needed set param to None. activate next line
#param = None
self.parent.del_polygon("RingInt")
if param.cursor:
self.parent.get_box_positions(self.name,
lambda m, p, pos: self.function(m, p, pos),
param, nextbox=False, mshape="Ellipse")
else:
self.param = param
self.parent.compute_11(self.name, lambda m, p: self.function(m, p), None, onein)
def create_output_list(self):
# add source list box
self.sourcelist = QListView()
self.sourcelist.setWindowTitle('Galaxy ring integration results')
self.sourcelist.setMinimumSize(650, 200)
self.sourcelist.setFont(QFont('Monospace'))
self.model = QStandardItemModel(self.sourcelist)
self.sourcelist.setModel(self.model)
self.parent.LView = self.sourcelist
#self.model.appendRow(QStandardItem(header))
def PrintListBox(self, M, out):
if M == 1:
self.create_output_list()
text = " Ring Major Minor Points Beams Average Sigma Ring Flux Cumul. Flux"
self.model.appendRow(QStandardItem(text))
#text = " (arcsec) Not 0 Num (JY/BEAM ) (JY/BEAM ) (JY) (JY)"
text = " (arcsec) Not 0 Num (%s/BEAM ) (%s/BEAM ) (%s) (%s)" % (self.unit, self.unit, self.unit, self.unit)
self.model.appendRow(QStandardItem(text))
self.model.appendRow(QStandardItem(out))
#self.sourcelist.scrollToBottom()
self.sourcelist.show()
def print_out(self, filename, M, a, b, close=False):
if M == 1:
self.fout = open(filename, 'w')
out = "# Ring Major Minor Points Beams Average Sigma Ring Flux Cumul. Flux"
self.fout.write(out+"\n")
#out = "# (arcsec) Not 0 Num (JY/BEAM) (JY/BEAM) (JY) (JY)"
out = "# (arcsec) Not 0 Num (%s/BEAM) (%s/BEAM) (%s) (%s)" % (self.unit, self.unit, self.unit, self.unit)
self.fout.write(out+"\n")
beams = self.NUM * self.beam
out = str("%5d %6.1f %6.1f %5d %-9.4g %-9.4g %-9.4g %-9.4g %-9.4g" % (M, 2*a, 2*b, self.NUM, beams, self.mean, self.std, self.sum, self.cum))
#print out
self.fout.write(out+"\n")
self.PrintListBox(M, out)
if close:
self.fout.close()
def _integrate(self, data, r1, r2):
d = 1*data
mask1 = r1 <= 1.0
if type(r2) != type(None):
mask2 = r2 <= 1.0
mask = mask1 & ~mask2
else:
mask = mask1
self.cum = np.sum(d[mask1]) * self.beam
self.sum = np.sum(d[mask]) * self.beam
self.mean = np.mean(d[mask])
self.std = np.std(d[mask])
self.NUM = mask.ravel().tolist().count(True)
#print self.sum, self.mean
d[~mask] = np.nan
return d
def todeg(self, string):
d, m, s = string.split(":")
if string.find("-") == -1:
sign = 1
else:
sign = -1
ad = abs(float(d))
return sign*(ad + float(m)/60.0 + float(s)/3600.0)*self.parent.vu
def todms(self, degree):
degree = degree/self.parent.vu
sign = np.sign(degree)
ad = abs(degree)
d = int(ad)
md = (ad-d)*60
m = int(md)
s = (md-m)*60
if sign < 0:
return str("-%2.2d:%2.2d:%-5.2f" % (d, m, s))
else:
return str("%2.2d:%2.2d:%-5.2f" % (d, m, s))
def Ellipse(self, header, data, p, Pos):
rows, cols = data.shape
if type(Pos) == type(None):
x0 = self.todeg(p.posx)*15
y0 = self.todeg(p.posy)
a = p.major/2.0
#b = p.minor
b = a * np.cos(p.incl*np.pi/180.0)
phi = p.posang*np.pi/180.0
else:
x0, y0 = Pos[0][:2]
a = max(Pos[1][:2])/2
b = min(Pos[1][:2])/2
p.incl = np.arccos(b/a) * 180.0/np.pi
angle = Pos[2]
phi = angle * np.pi/180.0
if Pos[1][0] < Pos[1][1]:
phi = -(angle+90) * np.pi/180.0
else:
phi = -(angle+180) * np.pi/180.0
xpix0, ypix0 = self.parent.get_pixel_coordinates(x0, y0)
p.posx = self.todms(x0/15.)
p.posy = self.todms(y0)
p.major = round(2*a, 4)
p.minor = round(2*b, 4)
p.posang = round(phi*180./np.pi, 4)
p.cursor = False
self.parent.write_defaults(p)
t = np.pi/180.0 * np.arange(360.0)
pos = []
off = []
col = []
M = 0
f = self.parent.vu / 3600.0
if p.ration:
f1 = f * a/b
else:
f1 = f
theta = np.pi/2.0 - phi
rot = np.array([[np.cos(theta), -np.sin(theta)], [np.sin(theta), np.cos(theta)]])
yy, xx = np.ogrid[:rows, :cols]
xr, yr = np.dot(rot, np.array([xx-xpix0, yy-ypix0]))
xplt = []
yplt = []
first = True
if 'BUNIT' in header:
self.unit = header['BUNIT']
else:
self.unit = "?"
while b > f*p.ringwidth/4.0 or first:
first = False
x = x0 + a*np.cos(theta)*np.cos(t) - b*np.sin(theta)*np.sin(t)
y = y0 + a*np.sin(theta)*np.cos(t) + b*np.cos(theta)*np.sin(t)
l = len(x)
ap = a / self.parent.vu / abs(header['CDELT1'])
bp = b / self.parent.vu / abs(header['CDELT2'])
r = (xr/ap)**2 + (yr/bp)**2
if M > 0:
d = self._integrate(data, r1, r)
self.print_out(p.outfile, M, A, B)
xplt.append(a)
yplt.append(self.mean)
#if M == 3: return d
A = np.round(1*a, decimals=1)
B = np.round(1*b, decimals=1)
r1 = 1*r
pos.append(np.array([x, y]).T)
off.append([M, M*l])
col.append([0xffffffff, 0x00000000])
#col.append([0xff000000, 0x00000000])
M += 1
b -= f*p.ringwidth
a -= f1*p.ringwidth
d = self._integrate(data, r1, None)
self.plot(xplt, yplt)
self.print_out(p.outfile, M, A, B, close=True)
positions = cp.copy(pos)
pos = np.concatenate(pos)
off = np.array(off)
curveparam = CurveParam(title="PolygonMap", icon="ellipse.png")
curveparam.label = "RingInt"
crv = PolygonMapItem(curveparam=curveparam)
crv.set_data(pos, off, col)
crv.setTitle(curveparam.label)
crv.Name = "Polygons"
#crv.Positions = self.projection(positions)
crv.Positions = positions
crv.Color = 'white'
crv.Linewidth = 1.0
crv.Pixel = False
crv.Factor = self.parent.vu
crv.update_params()
self.parent.plot.add_item(crv)
self.parent.plot.replot()
QApplication.restoreOverrideCursor()
def projection(self, pos):
i, j, k = np.shape(pos)
for m in range(i):
for n in range(j):
l, b = pos[m][n]
x, y = self.parent.get_pixel_coordinates(l, b)
l1, b1 = self.parent.get_plot_coordinates(x, y)
pos[m][n] = (l1*self.parent.vu, b1*self.parent.vu)
return pos
def plot(self, x, y):
if self.parent.vu == 3600.0: unit="arcsec"
elif self.parent.vu == 60.0: unit="arcmin"
else: unit="degree"
self.parent.fig = pyplot.figure("Ring Integration")
pyplot.plot(x, y, "B.")
pyplot.plot(x, y, "r-")
#pyplot.legend(pos="TR")
pyplot.xlabel("Radius [%s]" % unit)
pyplot.ylabel("Intensity")
pyplot.zlabel("Ring Integration")
pyplot.show(mainloop=False)
def function(self, m, p, pos=None):
if hasattr(self, "param"): p = self.param
if not 'BMAJ' in m.header or not 'BMIN' in m.header:
self.Error("BMAJ and BMIN not found in header, please define the FWHM")
return [], p
self.parent.del_polygon("RingInt")
self.parent.poly_visible = True
self.parent.delete_item('MapEllipse')
self.beam = abs(m.header['CDELT1'] * m.header['CDELT2']) / (m.header['BMAJ'] * m.header['BMIN'])
m.data = self.Ellipse(m.header, m.data, p, pos)
return [], p