/
MPLTWidgetTest.py
executable file
·537 lines (488 loc) · 21 KB
/
MPLTWidgetTest.py
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import os
import sep
import argparse
from astropy.io import fits
from matplotlib.colors import LogNorm
from matplotlib.widgets import AxesWidget
import matplotlib
matplotlib.use('Qt4Agg')
from pylab import *
parser = argparse.ArgumentParser(description='Takes directory to run viewer on')
parser.add_argument('Cs', metavar='Folder', type=str, nargs=1, help='The Folder to scan threw')
parser.add_argument('-r', action='store_true', help='If true then the code will run recursivly in folders looking for all avalible targets, else the user must provide a path to a spesific target folder')
args = parser.parse_args()
recursive = args.r
dest_folder = args.Cs[0]
good_to_go = True
i = 0
start = os.path.abspath('.')
os.chdir('sdBs/' + dest_folder)
working_dir = os.path.abspath('.')
if recursive is True:
dirs = [x[0] for x in os.walk(working_dir)]
dirs.pop(0)
dirs = [x.split('/') for x in dirs]
dirs = [x[-1] for x in dirs]
xloc = 0
for x in dirs:
if x[0] == '.':
dirs.pop(xloc)
else:
xloc += 1
prev_message = ''
save_yes = False
while good_to_go is True:
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111)
folder = dirs[i]
changed = False
os.chdir(folder)
image_data = fits.getdata(folder + 'Count.fits')
mutable_image_data = fits.getdata(folder + 'Count.fits')
regionfile = open('region_' + folder + '.reg', 'rb')
regionread = regionfile.readlines()
regionread = [x.rstrip() for x in regionread]
size_info = regionread[4:7]
size_info = [x.replace('circle(', '') for x in size_info]
size_info = [x.replace(') # width=2', '') for x in size_info]
size_info = [x.replace(') # color=red width=2', '') for x in size_info]
size_info = [x.split(',') for x in size_info]
inc = 0
region_file = [0]*len(size_info)
for uvb in size_info:
region_file[inc] = float(uvb[-1][0:-2])
inc += 1
regionfile.close()
ax.set_aspect('equal')
im1 = ax.imshow(image_data, norm=LogNorm(), cmap='gray')
fig.colorbar(im1)
c1 = '#66ff66'
c2 = '#ff0000'
opts = dict(fc='none', ec=c1, lw=2)
opts2 = dict(fc='none', ec=c2, lw=2)
opts3 = dict(fc='none', ec=c2, lw=4)
axcolor = 'lightgoldenrodyellow'
# [ x, y, width, height]
axApp = axes([0.25, 0.01, 0.65, 0.01], axisbg=axcolor)
axInAn = axes([0.25, 0.03, 0.65, 0.01], axisbg=axcolor)
axOutAn = axes([0.25, 0.05, 0.65, 0.01], axisbg=axcolor)
axSave = axes([0.91, 0.40, 0.075, 0.075], axisbg=axcolor)
axNext = axes([0.91, 0.10, 0.075, 0.075], axisbg=axcolor)
axClose = axes([0.91, 0.55, 0.075, 0.075], axisbg=axcolor)
axPrevious = axes([0.91, 0.25, 0.075, 0.075], axisbg=axcolor)
axFit = axes([0.91, 0.70, 0.075, 0.075], axisbg=axcolor)
axReload = axes([0.91, 0.85, 0.075, 0.075], axisbg=axcolor)
axmin = fig.add_axes([0.4, 0.93, 0.5, 0.01], axisbg=axcolor)
axmax = fig.add_axes([0.4, 0.95, 0.5, 0.01], axisbg=axcolor)
smin = Slider(axmin, 'Min', 0.1, 50, valinit=2)
smax = Slider(axmax, 'Max', 0.1, 500, valinit=500)
ApInc = Slider(axApp, 'Aperture radius', 0, region_file[0] * 6 * 2, valinit=region_file[0])
InAnInc = Slider(axInAn, 'Inner Annulus radius', 0, region_file[1] * 6 * 2, valinit=region_file[1])
OutAnInc = Slider(axOutAn, 'Outer Annulus radius', 1.5, region_file[2] * 2 * 2, valinit=region_file[2])
bSave = Button(axSave, 'Save')
bNext = Button(axNext, 'Next')
bClose = Button(axClose, 'Close')
bLast = Button(axPrevious, 'Back')
bAutoFit = Button(axFit, 'aFit')
bReload = Button(axReload, 'Reload')
center_y = image_data.shape[0] / 2.0
center_x = image_data.shape[1] / 2.0
AppR = ApInc.val
InR = InAnInc.val
OutR = OutAnInc.val
Aperture = Circle((center_x, center_y), AppR, **opts)
ax.add_patch(Aperture)
InnerAn = Circle((center_x, center_y), InR, **opts2)
ax.add_patch(InnerAn)
OuterAn = Circle((center_x, center_y), OutR, **opts3)
ax.add_patch(OuterAn)
ax.set_title(folder + ' | Target Number: ' + str(i+1) + ' (of ' + str(len(dirs)) + ')')
plt.figtext(.1, .975, 'previous message: ' + prev_message, style='italic', bbox={'facecolor': 'red', 'alpha': 0.5, 'pad': 5})
if save_yes is True:
bSave.color = 'green'
def updateAp(val):
global Aperture
global changed
changed = True
global ax
Aperture.remove()
Aperture = Circle((center_x, center_y), ApInc.val, **opts)
ax.add_patch(Aperture)
bSave.color = 'red'
def updateIn(val):
global InnerAn
global changed
changed = True
global ax
InnerAn.remove()
InnerAn = Circle((center_x, center_y), InAnInc.val, **opts2)
ax.add_patch(InnerAn)
bSave.color = 'red'
def updateOut(val):
global OuterAn
global changed
changed = True
global ax
OuterAn.remove()
OuterAn = Circle((center_x, center_y), OutAnInc.val, **opts3)
ax.add_patch(OuterAn)
bSave.color = 'red'
def Save(event):
global prev_message, save_yes
save_yes = True
regionfile = open('region_' + folder + '.reg', 'w')
# generates region files for use in ds9
regionfile.write('# Region file format: DS9 version 4.1\n'
'# Target Name: Test\n'
'global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 '
'dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1\n'
'fk5\n'
'circle(' + str(region_file[0]) + ', ' + str(region_file[1]) + ','
' ' + str(
ApInc.val * 6) + '") # width=2\n'
'circle(' + str(region_file[0]) + ', ' + str(region_file[0]) + ', '
' ' + str(
InAnInc.val * 6) + '") # color=red width=2\n'
'circle(' + str(region_file[0]) + ', ' + str(region_file[0]) + ', '
' ' + str(
OutAnInc.val * 2) + '") # color=red width=2\n')
regionfile.close()
prev_message = 'Saved ' + folder + ' region file'
plt.close()
os.chdir(working_dir)
def Next(event):
global changed
global i, dirs, prev_message, save_yes
save_yes = False
numdirs = len(dirs)
if numdirs - i > 1:
i += 1
if changed is True:
Save('None')
changed = False
else:
pass
plt.close()
os.chdir(working_dir)
else:
pass
def back(event):
global i, save_yes
save_yes = False
if i - 1 >= 0:
i -= 1
plt.close()
os.chdir(working_dir)
else:
pass
def close(event):
exit()
def auto_fit(image_data):
an_width = 3
temp_image_data = image_data
internal_image_data = temp_image_data.byteswap(True).newbyteorder()
bkg = sep.Background(internal_image_data)
thresh = 1.5 * bkg.globalback
objects = sep.extract(internal_image_data, thresh)
center_x = internal_image_data.shape[0]/2.0
center_y = internal_image_data.shape[1]/2.0
center = [center_x, center_y]
smallest_dFoc = 1000000000
radii = 21
count = 0
for i, j in zip(objects['x'], objects['y']):
pos = [i, j]
dFoc = math.sqrt(((pos[0]-center[0])**2) + ((pos[1]-center[1])**2))
if abs(dFoc) < smallest_dFoc:
smallest_dFoc = dFoc
minx = objects['xmin'][count]
miny = objects['ymin'][count]
maxx = objects['xmax'][count]
maxy = objects['ymax'][count]
radii = abs(math.sqrt(((maxx-minx)**2)+((maxy-miny)**2)))
else:
pass
count += 1
i = 0
while i < 25:
theta = 0
area = 0
while theta <= 2*pi:
area += (((i+.1)**2)/2) - ((i**2)/2)
theta += .001
flux, fluxerr, flag = sep.sum_circann(internal_image_data, internal_image_data.shape[0]/2, internal_image_data.shape[1]/2, i, i+an_width)
metric = ((flux/area) - bkg.globalback)/bkg.globalrms
if i > 1:
if metric < smallest_metric:
smallest_metric = metric
annulus = [i, i+an_width]
else:
smallest_metric = metric
annulus = [i, i+an_width]
i += 1
i = 1
an = [math.ceil(x*6) for x in annulus]
if radii > an[0]:
radii = an[0] - 0.5
if radii > 30:
radii = 30
else:
pass
return {'Ap': radii, 'InAn': an[0], 'OutAn': an[1]}
def aFit(event):
global mutable_image_data, Aperture, InnerAn, OuterAn, changed
new_size = auto_fit(mutable_image_data)
changed = True
OuterAn.remove()
Aperture.remove()
InnerAn.remove()
InnerAn = Circle((center_x, center_y), new_size['InAn']*6, **opts2)
OuterAn = Circle((center_x, center_y), new_size['OutAn']*6, **opts3)
Aperture = Circle((center_x, center_y), new_size['Ap']*2, **opts)
ax.add_patch(Aperture)
ax.add_patch(InnerAn)
ax.add_patch(OuterAn)
InAnInc.set_val(new_size['InAn']*6)
OutAnInc.set_val(new_size['OutAn']*6)
ApInc.set_val(new_size['Ap']*2)
def mpl_load(event):
os.chdir(start)
python = sys.executable
os.execl(python, python, * sys.argv)
def update(val):
global image_data
im1.set_clim([smin.val,smax.val])
fig.canvas.draw()
smin.on_changed(update)
smax.on_changed(update)
bReload.on_clicked(mpl_load)
bAutoFit.on_clicked(aFit)
bLast.on_clicked(back)
bClose.on_clicked(close)
bSave.on_clicked(Save)
bNext.on_clicked(Next)
ApInc.on_changed(updateAp)
InAnInc.on_changed(updateIn)
OutAnInc.on_changed(updateOut)
get_current_fig_manager().window.raise_()
plt.show()
else:
while good_to_go is True:
current_path = os.path.abspath('.')
current_path = current_path.split('/')
folder = current_path[-1]
fig = plt.figure(figsize=(10, 10))
ax = fig.add_subplot(111)
changed = False
image_data = fits.getdata(folder + 'Count.fits')
mutable_image_data = fits.getdata(folder + 'Count.fits')
regionfile = open('region_' + folder + '.reg', 'rb')
regionread = regionfile.readlines()
regionread = [x.rstrip() for x in regionread]
size_info = regionread[4:7]
size_info = [x.replace('circle(', '') for x in size_info]
size_info = [x.replace(') # width=2', '') for x in size_info]
size_info = [x.replace(') # color=red width=2', '') for x in size_info]
size_info = [x.split(',') for x in size_info]
inc = 0
region_file = [0]*len(size_info)
for uvb in size_info:
region_file[inc] = float(uvb[-1][0:-2])
inc += 1
regionfile.close()
ax.set_aspect('equal')
im1 = ax.imshow(image_data, norm=LogNorm(), cmap='gray')
fig.colorbar(im1)
c1 = '#66ff66'
c2 = '#ff0000'
opts = dict(fc='none', ec=c1, lw=2)
opts2 = dict(fc='none', ec=c2, lw=2)
opts3 = dict(fc='none', ec=c2, lw=4)
axcolor = 'lightgoldenrodyellow'
# [ x, y, width, height]
axApp = axes([0.25, 0.01, 0.65, 0.01], axisbg=axcolor)
axInAn = axes([0.25, 0.03, 0.65, 0.01], axisbg=axcolor)
axOutAn = axes([0.25, 0.05, 0.65, 0.01], axisbg=axcolor)
axSave = axes([0.91, 0.40, 0.075, 0.075], axisbg=axcolor)
axNext = axes([0.91, 0.10, 0.075, 0.075], axisbg=axcolor)
axClose = axes([0.91, 0.55, 0.075, 0.075], axisbg=axcolor)
axPrevious = axes([0.91, 0.25, 0.075, 0.075], axisbg=axcolor)
axFit = axes([0.91, 0.70, 0.075, 0.075], axisbg=axcolor)
axReload = axes([0.91, 0.85, 0.075, 0.075], axisbg=axcolor)
axmin = fig.add_axes([0.4, 0.93, 0.5, 0.01], axisbg=axcolor)
axmax = fig.add_axes([0.4, 0.95, 0.5, 0.01], axisbg=axcolor)
smin = Slider(axmin, 'Min', 0.1, 50, valinit=2)
smax = Slider(axmax, 'Max', 0.1, 500, valinit=500)
ApInc = Slider(axApp, 'Aperture radius', 0, region_file[0] * 6 * 2, valinit=region_file[0])
InAnInc = Slider(axInAn, 'Inner Annulus radius', 0, region_file[1] * 6 * 2, valinit=region_file[1])
OutAnInc = Slider(axOutAn, 'Outer Annulus radius', 1.5, region_file[2] * 2 * 2, valinit=region_file[2])
bSave = Button(axSave, 'Save')
bNext = Button(axNext, 'Next')
bClose = Button(axClose, 'Close')
bLast = Button(axPrevious, 'Back')
bAutoFit = Button(axFit, 'aFit')
bReload = Button(axReload, 'Reload')
center_y = image_data.shape[0] / 2.0
center_x = image_data.shape[1] / 2.0
AppR = ApInc.val
InR = InAnInc.val
OutR = OutAnInc.val
Aperture = Circle((center_x, center_y), AppR, **opts)
ax.add_patch(Aperture)
InnerAn = Circle((center_x, center_y), InR, **opts2)
ax.add_patch(InnerAn)
OuterAn = Circle((center_x, center_y), OutR, **opts3)
ax.add_patch(OuterAn)
ax.set_title(folder + ' | Target Number: ' + str(i+1) + ' (of ' + str(len(dirs)) + ')')
plt.figtext(.1, .975, 'previous message: ' + prev_message, style='italic', bbox={'facecolor': 'red', 'alpha': 0.5, 'pad': 5})
bNext.color = 'red'
bLast.color = 'red'
if save_yes is True:
bSave.color = 'green'
def updateAp(val):
global Aperture
global changed
changed = True
global ax
Aperture.remove()
Aperture = Circle((center_x, center_y), ApInc.val, **opts)
ax.add_patch(Aperture)
bSave.color = 'red'
def updateIn(val):
global InnerAn
global changed
changed = True
global ax
InnerAn.remove()
InnerAn = Circle((center_x, center_y), InAnInc.val, **opts2)
ax.add_patch(InnerAn)
bSave.color = 'red'
def updateOut(val):
global OuterAn
global changed
changed = True
global ax
OuterAn.remove()
OuterAn = Circle((center_x, center_y), OutAnInc.val, **opts3)
ax.add_patch(OuterAn)
bSave.color = 'red'
def Save(event):
global prev_message, save_yes
save_yes = True
regionfile = open('region_' + folder + '.reg', 'w')
# generates region files for use in ds9
regionfile.write('# Region file format: DS9 version 4.1\n'
'# Target Name: Test\n'
'global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 '
'dash=0 fixed=0 edit=1 move=1 delete=1 include=1 source=1\n'
'fk5\n'
'circle(' + str(region_file[0]) + ', ' + str(region_file[1]) + ','
' ' + str(
ApInc.val * 6) + '") # width=2\n'
'circle(' + str(region_file[0]) + ', ' + str(region_file[0]) + ', '
' ' + str(
InAnInc.val * 6) + '") # color=red width=2\n'
'circle(' + str(region_file[0]) + ', ' + str(region_file[0]) + ', '
' ' + str(
OutAnInc.val * 2) + '") # color=red width=2\n')
regionfile.close()
prev_message = 'Saved ' + folder + ' region file'
plt.close()
def Next(event):
global prev_message
prev_message = 'No Where to go'
def back(event):
global prev_message
prev_message = 'No Where to go'
def close(event):
exit()
def auto_fit(image_data):
an_width = 3
temp_image_data = image_data
internal_image_data = temp_image_data.byteswap(True).newbyteorder()
bkg = sep.Background(internal_image_data)
thresh = 1.5 * bkg.globalback
objects = sep.extract(internal_image_data, thresh)
center_x = internal_image_data.shape[0]/2.0
center_y = internal_image_data.shape[1]/2.0
center = [center_x, center_y]
smallest_dFoc = 1000000000
radii = 21
count = 0
for i, j in zip(objects['x'], objects['y']):
pos = [i, j]
dFoc = math.sqrt(((pos[0]-center[0])**2) + ((pos[1]-center[1])**2))
if abs(dFoc) < smallest_dFoc:
smallest_dFoc = dFoc
minx = objects['xmin'][count]
miny = objects['ymin'][count]
maxx = objects['xmax'][count]
maxy = objects['ymax'][count]
radii = abs(math.sqrt(((maxx-minx)**2)+((maxy-miny)**2)))
else:
pass
count += 1
i = 0
while i < 25:
theta = 0
area = 0
while theta <= 2*pi:
area += (((i+.1)**2)/2) - ((i**2)/2)
theta += .001
flux, fluxerr, flag = sep.sum_circann(internal_image_data, internal_image_data.shape[0]/2, internal_image_data.shape[1]/2, i, i+an_width)
metric = (flux - bkg.globalback)/bkg.globalrms
metric /= area
if i > 1:
if metric < smallest_metric:
smallest_metric = metric
annulus = [i, i+an_width]
else:
smallest_metric = metric
annulus = [i, i+an_width]
i += 1
i = 1
an = [math.ceil(x*6) for x in annulus]
if radii > an[0]:
radii = an[0] - 0.5
if radii > 30:
radii = 30
else:
pass
return {'Ap': radii, 'InAn': an[0], 'OutAn': an[1]}
def aFit(event):
global mutable_image_data, Aperture, InnerAn, OuterAn, changed
new_size = auto_fit(mutable_image_data)
changed = True
OuterAn.remove()
Aperture.remove()
InnerAn.remove()
InnerAn = Circle((center_x, center_y), new_size['InAn']*6, **opts2)
OuterAn = Circle((center_x, center_y), new_size['OutAn']*6, **opts3)
Aperture = Circle((center_x, center_y), new_size['Ap']*2, **opts)
ax.add_patch(Aperture)
ax.add_patch(InnerAn)
ax.add_patch(OuterAn)
InAnInc.set_val(new_size['InAn']*6)
OutAnInc.set_val(new_size['OutAn']*6)
ApInc.set_val(new_size['Ap']*2)
def mpl_load(event):
os.chdir(start)
python = sys.executable
os.execl(python, python, * sys.argv)
def update(val):
global image_data
im1.set_clim([smin.val,smax.val])
fig.canvas.draw()
smin.on_changed(update)
smax.on_changed(update)
bReload.on_clicked(mpl_load)
bAutoFit.on_clicked(aFit)
bLast.on_clicked(back)
bClose.on_clicked(close)
bSave.on_clicked(Save)
bNext.on_clicked(Next)
ApInc.on_changed(updateAp)
InAnInc.on_changed(updateIn)
OutAnInc.on_changed(updateOut)
get_current_fig_manager().window.raise_()
plt.show()