def imextents(self, im, buffer=1.):
"""
extents in pixel space - buffer in units of inner ap radius
"""
ca = self.imcoords(im, reg="ap")
c1 = self.imcoords(im, reg="bg1") # outer bg
if self.type == "circle":
dr = ca[2]
xra = c1[0] + (dr * buffer + c1[2]) * pl.array([-1, 1])
yra = c1[1] + (dr * buffer + c1[2]) * pl.array([-1, 1])
elif self.type == "polygon":
dx = minmax(ca[0, :])
dy = minmax(ca[1, :])
ctr = [mean(dx), mean(dy)]
dx = dx[1] - dx[0]
dy = dy[1] - dy[0]
dr = 0.5 * max(dx, dy)
xra = minmax(c1[0, :]) + dr * buffer * pl.array([-1, 1])
yra = minmax(c1[1, :]) + dr * buffer * pl.array([-1, 1])
xra[0] = pl.floor(xra[0]) + 1
yra[0] = pl.floor(yra[0]) + 1
xra[1] = pl.ceil(xra[1]) + 1
yra[1] = pl.ceil(yra[1]) + 1
if xra[0] < 0: xra[0] = 0
if yra[0] < 0: yra[0] = 0
s = im.shape - pl.array([1, 1]) # remember, transposed y,x
if xra[1] > s[1]: xra[1] = s[1]
if yra[1] > s[0]: yra[1] = s[0]
return int(xra[0]), int(yra[0]), int(xra[1]), int(yra[1])
def stack_vectors(data, win=1, hop=1, zero_pad=True):
"""
::
create an overlapping stacked vector sequence from a series of vectors
data - row-wise multidimensional data to stack
win - number of consecutive vectors to stack [1]
hop - number of vectors to advance per stack [1]
zero_pad - zero pad if incomplete stack at end
"""
data = pylab.atleast_2d(data)
nrows, dim = data.shape
hop = min(hop, nrows)
nvecs = nrows / int(hop) if not zero_pad else int(
pylab.ceil(nrows / float(hop)))
features = pylab.zeros((nvecs, win * dim))
i = 0
while i < nrows - win + 1:
features[i / hop, :] = data[i:i + win, :].reshape(1, -1)
i += hop
if i / hop < nvecs:
x = data[i::, :].reshape(1, -1)
features[i / hop, :] = pylab.c_[x,
pylab.zeros(
(1, win * dim - x.shape[1]))]
return features
def main(argv):
#if len(argv) < 4:
# print """Usage:
# """
# sys.exit(1)
#nlayers = int(argv[1])
# get number of layers
f = open(FLAGS.dir+"weights/nlayers.txt")
nlayers = int(f.readlines()[0])
f.close()
print str(nlayers) + " layer(s) detected."
pylab.figure(figsize=(32, 24), dpi=320, facecolor='w', edgecolor='k')
# Make a picture with the filters
[n_inputs, n_neurons, weights] = visualizing.weights_filename_to_array(FLAGS.dir+"weights/W0.txt")
image_side_length = int(pylab.sqrt(n_inputs))
nsubplot = pylab.ceil(pylab.sqrt(n_neurons))
for i in range(n_neurons):
filter = pylab.resize(weights[i], [image_side_length, image_side_length])
pylab.subplot(nsubplot, nsubplot, i+1)
pylab.imshow(filter, interpolation='nearest')
pylab.gray()
pylab.savefig(FLAGS.dir + "filters" + ".png")
pylab.clf()
# Make a picture with the all weights
nsubplot_vertical = nlayers+1
nsubplot_horizontal = 4
for i in range(nlayers):
# V
location = 1+(nlayers-i)*nsubplot_horizontal+0
filename = FLAGS.dir+"weights/V" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal, location,
filename, True, "V"+str(i))
# W
location = 1+(nlayers-i)*nsubplot_horizontal+1
filename = FLAGS.dir+"weights/W" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "W"+str(i))
# F
location = 1+(nlayers-i)*nsubplot_horizontal+2
filename = FLAGS.dir+"weights/F" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "F"+str(i))
# G
location = 1+(nlayers-i)*nsubplot_horizontal+3
filename = FLAGS.dir+"weights/G" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, True, "G"+str(i))
# Last layer
location = 1+1
filename = FLAGS.dir+"weights/W" + str(nlayers) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "W"+str(nlayers))
pylab.savefig(FLAGS.dir + "weights" + ".png")
# Make pictures with examples and representations
visualizing.visualize_representations(FLAGS.dir, nlayers)
def cons_vac(T):
"""
consentration is given by n(T)/N
(vacant parrticle-spaces divided
by total particle-spaces)
"""
k_b=8.617332478*1e-5;#[eV/K] boltzmanns constant
deltaeps=1; #[eV] infitisemial energy for each "particle-jump"
exponential = plt.exp( deltaeps/(T*k_b) ); #these values are way large.
return 1.0/(exponential);
try:
pot = int(sys.argv[1]);#power of number of particles
except:
pot = input("give the power of the temperature you want in your system")
tot_temp = 1*10**(pot); #total vacancies in system
plot_points = 1.0/float(tot_temp+1)
x = plt.linspace(0,int(tot_temp), plt.ceil(plot_points));
n_cons = cons_vac(x);
plt.plot(x,n_cons,"k-",label="n(T)/N");
plt.xlabel("temperature [K]");
plt.ylabel("consentration of vacancies");
plt.legend(numpoints=1, loc="lower right", borderpad=0.5);
plt.savefig("exercise_g_img"+str(self_int)+".png");
plt.show();
def main(argv):
#if len(argv) < 4:
# print """Usage:
# """
# sys.exit(1)
#nlayers = int(argv[1])
# get number of layers
f = open(FLAGS.dir + "weights/nlayers.txt")
nlayers = int(f.readlines()[0])
f.close()
print str(nlayers) + " layer(s) detected."
pylab.figure(figsize=(32, 24), dpi=320, facecolor='w', edgecolor='k')
# Make a picture with the filters
[n_inputs, n_neurons, weights
] = visualizing.weights_filename_to_array(FLAGS.dir + "weights/W0.txt")
image_side_length = int(pylab.sqrt(n_inputs))
nsubplot = pylab.ceil(pylab.sqrt(n_neurons))
for i in range(n_neurons):
filter = pylab.resize(weights[i],
[image_side_length, image_side_length])
pylab.subplot(nsubplot, nsubplot, i + 1)
pylab.imshow(filter, interpolation='nearest')
pylab.gray()
pylab.savefig(FLAGS.dir + "filters" + ".png")
pylab.clf()
# Make a picture with the all weights
nsubplot_vertical = nlayers + 1
nsubplot_horizontal = 4
for i in range(nlayers):
# V
location = 1 + (nlayers - i) * nsubplot_horizontal + 0
filename = FLAGS.dir + "weights/V" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, True, "V" + str(i))
# W
location = 1 + (nlayers - i) * nsubplot_horizontal + 1
filename = FLAGS.dir + "weights/W" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "W" + str(i))
# F
location = 1 + (nlayers - i) * nsubplot_horizontal + 2
filename = FLAGS.dir + "weights/F" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False, "F" + str(i))
# G
location = 1 + (nlayers - i) * nsubplot_horizontal + 3
filename = FLAGS.dir + "weights/G" + str(i) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, True, "G" + str(i))
# Last layer
location = 1 + 1
filename = FLAGS.dir + "weights/W" + str(nlayers) + ".txt"
visualizing.plot_weight_matrix(nsubplot_vertical, nsubplot_horizontal,
location, filename, False,
"W" + str(nlayers))
pylab.savefig(FLAGS.dir + "weights" + ".png")
# Make pictures with examples and representations
visualizing.visualize_representations(FLAGS.dir, nlayers)
def plotConn (include = ['all'], feature = 'strength', orderBy = 'gid', figSize = (10,10), groupBy = 'pop', groupByInterval = None, saveData = None, saveFig = None, showFig = True):
'''
Plot network connectivity
- include (['all',|'allCells','allNetStims',|,120,|,'E1'|,('L2', 56)|,('L5',[4,5,6])]): Cells to show (default: ['all'])
- feature ('weight'|'delay'|'numConns'|'probability'|'strength'|'convergence'|'divergence'): Feature to show in connectivity matrix;
the only features applicable to groupBy='cell' are 'weight', 'delay' and 'numConns'; 'strength' = weight * probability (default: 'strength')
- groupBy ('pop'|'cell'|'y'|: Show matrix for individual cells, populations, or by other numeric tag such as 'y' (default: 'pop')
- groupByInterval (int or float): Interval of groupBy feature to group cells by in conn matrix, e.g. 100 to group by cortical depth in steps of 100 um (default: None)
- orderBy ('gid'|'y'|'ynorm'|...): Unique numeric cell property to order x and y axes by, e.g. 'gid', 'ynorm', 'y' (requires groupBy='cells') (default: 'gid')
- figSize ((width, height)): Size of figure (default: (10,10))
- saveData (None|True|'fileName'): File name where to save the final data used to generate the figure;
if set to True uses filename from simConfig (default: None)
- saveFig (None|True|'fileName'): File name where to save the figure;
if set to True uses filename from simConfig (default: None)
- showFig (True|False): Whether to show the figure or not (default: True)
- Returns figure handles
'''
print('Plotting connectivity matrix...')
cells, cellGids, netStimPops = getCellsInclude(include)
# Create plot
fig = figure(figsize=figSize)
fig.subplots_adjust(right=0.98) # Less space on right
fig.subplots_adjust(top=0.96) # Less space on top
fig.subplots_adjust(bottom=0.02) # Less space on bottom
h = axes()
# Calculate matrix if grouped by cell
if groupBy == 'cell':
if feature in ['weight', 'delay', 'numConns']:
connMatrix = zeros((len(cellGids), len(cellGids)))
countMatrix = zeros((len(cellGids), len(cellGids)))
else:
print 'Conn matrix with groupBy="cell" only supports features= "weight", "delay" or "numConns"'
return fig
cellInds = {cell['gid']: ind for ind,cell in enumerate(cells)}
# Order by
if len(cells) > 0:
if orderBy not in cells[0]['tags']: # if orderBy property doesn't exist or is not numeric, use gid
orderBy = 'gid'
elif not isinstance(cells[0]['tags'][orderBy], Number):
orderBy = 'gid'
if orderBy == 'gid':
yorder = [cell[orderBy] for cell in cells]
else:
yorder = [cell['tags'][orderBy] for cell in cells]
sortedGids = {gid:i for i,(y,gid) in enumerate(sorted(zip(yorder,cellGids)))}
cellInds = sortedGids
# Calculate conn matrix
for cell in cells: # for each postsyn cell
for conn in cell['conns']:
if conn['preGid'] != 'NetStim' and conn['preGid'] in cellInds:
if feature in ['weight', 'delay']:
if conn['preGid'] in cellInds:
connMatrix[cellInds[conn['preGid']], cellInds[cell['gid']]] += conn[feature]
countMatrix[cellInds[conn['preGid']], cellInds[cell['gid']]] += 1
if feature in ['weight', 'delay']: connMatrix = connMatrix / countMatrix
elif feature in ['numConns']: connMatrix = countMatrix
# Calculate matrix if grouped by pop
elif groupBy == 'pop':
# get list of pops
popsTemp = list(set([cell['tags']['popLabel'] for cell in cells]))
pops = [pop for pop in sim.net.allPops if pop in popsTemp]+netStimPops
popInds = {pop: ind for ind,pop in enumerate(pops)}
# initialize matrices
if feature in ['weight', 'strength']:
weightMatrix = zeros((len(pops), len(pops)))
elif feature == 'delay':
delayMatrix = zeros((len(pops), len(pops)))
countMatrix = zeros((len(pops), len(pops)))
# calculate max num conns per pre and post pair of pops
numCellsPop = {}
for pop in pops:
if pop in netStimPops:
numCellsPop[pop] = -1
else:
numCellsPop[pop] = len([cell for cell in cells if cell['tags']['popLabel']==pop])
maxConnMatrix = zeros((len(pops), len(pops)))
if feature == 'convergence': maxPostConnMatrix = zeros((len(pops), len(pops)))
if feature == 'divergence': maxPreConnMatrix = zeros((len(pops), len(pops)))
for prePop in pops:
for postPop in pops:
if numCellsPop[prePop] == -1: numCellsPop[prePop] = numCellsPop[postPop]
maxConnMatrix[popInds[prePop], popInds[postPop]] = numCellsPop[prePop]*numCellsPop[postPop]
if feature == 'convergence': maxPostConnMatrix[popInds[prePop], popInds[postPop]] = numCellsPop[postPop]
if feature == 'divergence': maxPreConnMatrix[popInds[prePop], popInds[postPop]] = numCellsPop[prePop]
# Calculate conn matrix
for cell in cells: # for each postsyn cell
for conn in cell['conns']:
if conn['preGid'] == 'NetStim':
prePopLabel = conn['preLabel']
else:
preCell = next((cell for cell in cells if cell['gid']==conn['preGid']), None)
prePopLabel = preCell['tags']['popLabel'] if preCell else None
if prePopLabel in popInds:
if feature in ['weight', 'strength']:
weightMatrix[popInds[prePopLabel], popInds[cell['tags']['popLabel']]] += conn['weight']
elif feature == 'delay':
delayMatrix[popInds[prePopLabel], popInds[cell['tags']['popLabel']]] += conn['delay']
countMatrix[popInds[prePopLabel], popInds[cell['tags']['popLabel']]] += 1
# Calculate matrix if grouped by numeric tag (eg. 'y')
elif groupBy in sim.net.allCells[0]['tags'] and isinstance(sim.net.allCells[0]['tags'][groupBy], Number):
if not isinstance(groupByInterval, Number):
print 'groupByInterval not specified'
return
# group cells by 'groupBy' feature (eg. 'y') in intervals of 'groupByInterval')
cellValues = [cell['tags'][groupBy] for cell in cells]
minValue = _roundFigures(groupByInterval * floor(min(cellValues) / groupByInterval), 3)
maxValue = _roundFigures(groupByInterval * ceil(max(cellValues) / groupByInterval), 3)
groups = arange(minValue, maxValue, groupByInterval)
groups = [_roundFigures(x,3) for x in groups]
print groups
if len(groups) < 2:
print 'groupBy %s with groupByInterval %s results in <2 groups'%(str(groupBy), str(groupByInterval))
return
groupInds = {group: ind for ind,group in enumerate(groups)}
# initialize matrices
if feature in ['weight', 'strength']:
weightMatrix = zeros((len(groups), len(groups)))
elif feature == 'delay':
delayMatrix = zeros((len(groups), len(groups)))
countMatrix = zeros((len(groups), len(groups)))
# calculate max num conns per pre and post pair of pops
numCellsGroup = {}
for group in groups:
numCellsGroup[group] = len([cell for cell in cells if group <= cell['tags'][groupBy] < (group+groupByInterval)])
maxConnMatrix = zeros((len(groups), len(groups)))
if feature == 'convergence': maxPostConnMatrix = zeros((len(groups), len(groups)))
if feature == 'divergence': maxPreConnMatrix = zeros((len(groups), len(groups)))
for preGroup in groups:
for postGroup in groups:
if numCellsGroup[preGroup] == -1: numCellsGroup[preGroup] = numCellsGroup[postGroup]
maxConnMatrix[groupInds[preGroup], groupInds[postGroup]] = numCellsGroup[preGroup]*numCellsGroup[postGroup]
if feature == 'convergence': maxPostConnMatrix[groupInds[prePop], groupInds[postGroup]] = numCellsPop[postGroup]
if feature == 'divergence': maxPreConnMatrix[groupInds[preGroup], groupInds[postGroup]] = numCellsPop[preGroup]
# Calculate conn matrix
for cell in cells: # for each postsyn cell
for conn in cell['conns']:
if conn['preGid'] == 'NetStim':
prePopLabel = -1 # maybe add in future
else:
preCell = next((cell for cell in cells if cell['gid']==conn['preGid']), None)
if preCell:
preGroup = _roundFigures(groupByInterval * floor(preCell['tags'][groupBy] / groupByInterval), 3)
else:
None
postGroup = _roundFigures(groupByInterval * floor(cell['tags'][groupBy] / groupByInterval), 3)
#print groupInds
if preGroup in groupInds:
if feature in ['weight', 'strength']:
weightMatrix[groupInds[preGroup], groupInds[postGroup]] += conn['weight']
elif feature == 'delay':
delayMatrix[groupInds[preGroup], groupInds[postGroup]] += conn['delay']
countMatrix[groupInds[preGroup], groupInds[postGroup]] += 1
# no valid groupBy
else:
print 'groupBy (%s) is not valid'%(str(groupBy))
return
if groupBy != 'cell':
if feature == 'weight':
connMatrix = weightMatrix / countMatrix # avg weight per conn (fix to remove divide by zero warning)
elif feature == 'delay':
connMatrix = delayMatrix / countMatrix
elif feature == 'numConns':
connMatrix = countMatrix
elif feature in ['probability', 'strength']:
connMatrix = countMatrix / maxConnMatrix # probability
if feature == 'strength':
connMatrix = connMatrix * weightMatrix # strength
elif feature == 'convergence':
connMatrix = countMatrix / maxPostConnMatrix
elif feature == 'divergence':
connMatrix = countMatrix / maxPreConnMatrix
imshow(connMatrix, interpolation='nearest', cmap='jet', vmin=nanmin(connMatrix), vmax=nanmax(connMatrix)) #_bicolormap(gap=0)
# Plot grid lines
hold(True)
if groupBy == 'cell':
# Make pretty
step = int(len(cells)/10.0)
base = 100 if step>100 else 10
step = int(base * floor(float(step)/base))
h.set_xticks(arange(0,len(cells),step))
h.set_yticks(arange(0,len(cells),step))
h.set_xticklabels(arange(0,len(cells),step))
h.set_yticklabels(arange(0,len(cells),step))
h.xaxis.set_ticks_position('top')
xlim(-0.5,len(cells)-0.5)
ylim(len(cells)-0.5,-0.5)
clim(nanmin(connMatrix),nanmax(connMatrix))
elif groupBy == 'pop':
for ipop, pop in enumerate(pops):
plot(array([0,len(pops)])-0.5,array([ipop,ipop])-0.5,'-',c=(0.7,0.7,0.7))
plot(array([ipop,ipop])-0.5,array([0,len(pops)])-0.5,'-',c=(0.7,0.7,0.7))
# Make pretty
h.set_xticks(range(len(pops)))
h.set_yticks(range(len(pops)))
h.set_xticklabels(pops)
h.set_yticklabels(pops)
h.xaxis.set_ticks_position('top')
xlim(-0.5,len(pops)-0.5)
ylim(len(pops)-0.5,-0.5)
clim(nanmin(connMatrix),nanmax(connMatrix))
else:
for igroup, group in enumerate(groups):
plot(array([0,len(groups)])-0.5,array([igroup,igroup])-0.5,'-',c=(0.7,0.7,0.7))
plot(array([igroup,igroup])-0.5,array([0,len(groups)])-0.5,'-',c=(0.7,0.7,0.7))
# Make pretty
h.set_xticks([i-0.5 for i in range(len(groups))])
h.set_yticks([i-0.5 for i in range(len(groups))])
h.set_xticklabels([int(x) if x>1 else x for x in groups])
h.set_yticklabels([int(x) if x>1 else x for x in groups])
h.xaxis.set_ticks_position('top')
xlim(-0.5,len(groups)-0.5)
ylim(len(groups)-0.5,-0.5)
clim(nanmin(connMatrix),nanmax(connMatrix))
colorbar(label=feature, shrink=0.8) #.set_label(label='Fitness',size=20,weight='bold')
xlabel('post')
h.xaxis.set_label_coords(0.5, 1.06)
ylabel('pre')
title ('Connection '+feature+' matrix', y=1.08)
#save figure data
if saveData:
figData = {'connMatrix': connMatrix, 'feature': feature, 'groupBy': groupBy,
'include': include, 'saveData': saveData, 'saveFig': saveFig, 'showFig': showFig}
_saveFigData(figData, saveData, 'conn')
# save figure
if saveFig:
if isinstance(saveFig, str):
filename = saveFig
else:
filename = sim.cfg.filename+'_'+'conn.png'
savefig(filename)
# show fig
if showFig: _showFigure()
return fig
def setmask(self, im):
"""
input an image (for now an HDU) and set self.mask to
an array the size of the image with the phot region =1
and expanded background annulus =2
for now we also create a mask the size of the image, so I recommend
to extract a subimage and call this method with that input
this method well trim the polyon to fit in the image
"""
imshape = im.shape
mask = pl.zeros(imshape)
if self.type == "circle":
x, y, r = self.imcoords(im)
x0 = int(x)
y0 = int(y)
dx = x - x0
dy = y - y0
# grr pixel centers again - is this right?
# dx=dx-0.5; dy=dy-0.5
bg0_r = self.imcoords(im, reg="bg0")[2] #-0.2 # fudge
bg1_r = self.imcoords(im, reg="bg1")[2] #+0.2 # fudge
bg1_r0 = int(pl.ceil(bg1_r))
r2 = r**2
bg0_r2 = bg0_r**2
bg1_r2 = bg1_r**2
for i in pl.array(range(2 * bg1_r0 + 1)) - bg1_r0:
for j in pl.array(range(2 * bg1_r0 + 1)) - bg1_r0:
if y0 + j >= 0 and x0 + i >= 0 and y0 + j < (
imshape[0] - 1) and x0 + i < (imshape[1] - 1):
d2 = (1. * i - dx)**2 + (1. * j - dy)**2
# d2 = (i-x)**2 + (j-y)**2 -> (i-x0-(x-x0))**2 + ...
if d2 <= r2:
mask[y0 + j,
x0 + i] = 1 # remember indices inverted
if d2 >= bg0_r2 and d2 <= bg1_r2:
mask[y0 + j,
x0 + i] = 2 # remember indices inverted
# if x0+i==6:
# print i,j,x0+i,y0+j,dx,dy,d2,bg0_r2,bg1_r2
elif self.type == "polygon":
# turn annulus back into mask, will trim at edges of image
from matplotlib.path import Path
from matplotlib import __version__ as mpver
v = mpver.split('.')
if v[0] < 1:
raise Exception(
"need matplotlib >=1.3.1, or tell remy to add fallback nxutils option for Path.contains_points"
)
elif v[1] < 3:
raise Exception(
"need matplotlib >=1.3.1, or tell remy to add fallback nxutils option for Path.contains_points"
)
elif v[2] < 1:
raise Exception(
"need matplotlib >=1.3.1, or tell remy to add fallback nxutils option for Path.contains_points"
)
# Create vertex coordinates for each grid cell
x, y = pl.meshgrid(pl.arange(imshape[1]), pl.arange(imshape[0]))
x, y = x.flatten(), y.flatten()
points = pl.vstack((x, y)).T
mask1 = Path(self.imcoords(im, reg="bg1")).contains_points(points)
mask1 = mask1.reshape((imshape[0], imshape[1]))
mask0 = Path(self.imcoords(im, reg="bg0")).contains_points(points)
#,radius=1)
mask0 = mask0.reshape((imshape[0], imshape[1]))
mask = Path(self.imcoords(im, reg="ap")).contains_points(points)
mask = mask.reshape((imshape[0], imshape[1]))
mask = mask + (1 * mask1 - 1 * mask0) * 2
else:
raise Exception("unknown region type %s" % self.type)
self.mask = mask
return mask
self_int = int(self_name[7])
except:
print "error in integer: exg_att#.py"
def cons_vac(T):
"""
consentration is given by n(T)/N
(vacant parrticle-spaces divided
by total particle-spaces)
"""
k_b=8.617332478*1e-5;#[eV/K] boltzmanns constant
deltaeps=1; #[eV] infitisemial energy for each "particle-jump"
exponential = plt.exp( deltaeps/(T*k_b) ); #these values are way large.
return 1.0/(1 + exponential);
pot = 5;#power of number of particles
tot_vac = 1*10**(pot); #total vacancies in system
jumps = plt.ceil(tot_vac/float(1e+3)); #frequency of points on x-axis
x = plt.array(range(1,int(tot_vac),int(jumps)));
n_cons = cons_vac(x);
plt.plot(x,n_cons,"k-",label="n(T)/N");
plt.xlabel("temperature [K]");
plt.ylabel("consentration of vacancies");
plt.legend(numpoints=1, loc="upper right", borderpad=0.5);
plt.savefig("exercise_g_img"+str(self_int)+".png");
plt.show();
def plotcalng(caltable='',
xaxis='',
yaxis='',
poln='',
field='',
antenna='',
spw='',
timerange='',
plotncolumns=2,
subplot='',
overwrite=False,
clearpanel='Auto',
iteration='',
plotrange=[],
showflags=False,
plotsymbol='.',
plotcolor='blue',
markersize=5.0,
fontsize=10.0,
showgui=False,
figfile=''):
if subplot != "":
print("Warning, the subplot parameter is ignored")
selection = __parse_input(caltable, xaxis, yaxis, field, spw, antenna,
poln, timerange)
data = __get_data(caltable, selection['xaxis'], selection['yaxis'],
iteration, selection['poln'], selection['field'],
selection['antenna'], selection['spw'],
selection['timerange'])
# Create grid of subplots
nplots = max(1, len(data))
ncolumns = min(nplots, plotncolumns)
nrows = int(pl.ceil(nplots / ncolumns))
# Unfortunately, matplot doesn't properly scale fig size with nrows / ncolumns
if nplots == 1:
figsize = (4, 3)
else:
figsize = (8, 3 * nrows)
fig, axs = pl.subplots(nrows,
ncolumns,
figsize=figsize,
constrained_layout=True)
if not isinstance(axs, pl.ndarray):
axs = pl.array([[axs]])
elif len(axs.shape) == 1:
axs = axs.reshape([1, axs.shape[0]])
nremove = nrows * ncolumns - nplots
for i in range(0, nremove):
axs[-1][ncolumns - i - 1].set_visible(False)
ticklocator = dates.AutoDateLocator()
tickformatter = dates.AutoDateFormatter(ticklocator)
#print(data.keys())
#print('nplots = {}, ncolumns = {}, nrows = {}, nremove = {}'.format(nplots, ncolumns, nrows, nremove))
#print(len(axs), len(axs[-1]))
for i, key in enumerate(data):
row = i // ncolumns
column = i % ncolumns
ax = axs[row][column]
f = data[key]
for plotkey in f:
if (plotkey == "label"):
ax.set_title(f[plotkey])
continue
xy = f[plotkey]
axislabels = []
for j, axistype in enumerate(
(selection['xaxis'], selection['yaxis'])):
if axistype == "TIME":
ax.xaxis.set_major_locator(ticklocator)
ax.xaxis.set_major_formatter(tickformatter)
xy[j] = dates.date2num(xy[j])
axislabels.append('Time')
elif axistype == "CHAN":
axislabels.append("Channel")
elif axistype == "ANTENNA":
axislabels.append("Antenna")
elif axistype == "FREQ":
maxval = max(xy[j])
if maxval >= 1e10:
xy[j] /= 1e9
unit = "GHz"
elif maxval > 1e7:
xy[j] /= 1e6
unit = "MHz"
elif maxval > 1e4:
xy[j] /= 1000
unit = "KHz"
else:
unit = "Hz"
axislabels.append("Frequency [{}]".format(unit))
elif axistype == "DELAY":
axislabels.append("Delay [ns]")
elif axistype == "RATE":
xy[j] *= 1e12
axislabels.append("Delay rate [ps / s]")
elif axistype == "DISP":
# TEC conversion parameter from Mevius LOFAR school notes
xy /= 1.334537
axislabels.append("Dispersive delay [miliTEC]")
elif axistype == "AMP":
axislabels.append("Gain Amplitude")
elif axistype == "PHASE":
axislabels.append("Gain Phase [degrees]")
elif axistype == "TSYS":
axislabels.append("TSYS [K]")
else:
print("Unknown axis type:", axistype)
raise ValueError()
ax.plot(xy[0], xy[1], plotsymbol, label=xy[2])
ax.set_xlabel(axislabels[0])
ax.set_ylabel(axislabels[1])
if plotrange != []:
# CASA convention: if min==max in plotrange for axis then autoscale that axis
if plotrange[0] != plotrange[1]:
ax.set_xlim(plotrange[0], plotrange[1])
if plotrange[2] != plotrange[3]:
ax.set_ylim(plotrange[2], plotrange[3])
if xaxis.upper() == "TIME":
fig.autofmt_xdate()
if figfile != "":
fig.savefig(figfile)
