def _plot_HiC(matrix_data, vmax, colors=['white', 'red']):
#vmax=thr
red_list = list()
green_list = list()
blue_list = list()
#colors=['white','red']
#colors=['darkblue','green','gold','darkred']
for color in colors:
col = Color(color).rgb
red_list.append(col[0])
green_list.append(col[1])
blue_list.append(col[2])
c = Colormap()
d = {'blue': blue_list, 'green': green_list, 'red': red_list}
mycmap = c.cmap(d)
fig, ax = plt.subplots(figsize=(8, 8))
#new_data=np.triu(matrix_data)
#new_data=np.transpose(new_data[:,::-1])
#mask = np.zeros_like(new_data)
#mask[np.tril_indices_from(mask,-1)] = True
#mask=np.transpose(mask[:,::-1])
#with sns.axes_style("white"):
#sns.heatmap(new_data,xticklabels=100,yticklabels=100,mask=mask,cmap=mycmap,cbar=False)
#ax.set_facecolor('w')
#fig.patch.set_facecolor('w')
ax.set_facecolor('w')
ax.grid(b=None)
sns.heatmap(matrix_data.T,
vmax=vmax,
xticklabels=100,
yticklabels=100,
cmap=mycmap,
cbar=False)
def get_html(self):
# We have 3 colors but sometimes you may have only one or 2.
# This may be an issue with canvasXpress. It seems essential
# to sort the color column so that names are sorted alphabetically
# and to include colors that are present in the sale order
"""try:
self.data.sort_values(by='color', inplace=True)
except:
self.data.sort("color", inplace=True)
"""
# Jinja related
from easydev import get_package_location
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools") + "/gdsctools/data/templates/")
template = env.get_template("scatter.html")
# We need to cireate 20 different colors
from colormap import Colormap
c = Colormap()
cmap = c.cmap_linear("red", "blue", "yellow", N=20)
colors = self.data[self._colname_color]
colors = ["red" for x in self.data[self._colname_color]]
jinja = {}
jinja["colors"] = ["rgba(205,0,0,0.5)"]
jinja["Group"] = colors
jinja['xlabel'] = '"%s"' % self.xlabel
jinja['ylabel'] = '"%s"' % self.ylabel
selection = [self._colname_x, self._colname_y]
text = []
for index in zip(self.data.index):
text.append("<pre>%s</pre>" %
self.data.ix[index][selection].to_string())
jinja['vars'] = text
#self.data.markersize /= (self.data.markersize.max()/3.)
self.data['markersize'] = 20
selection = [self._colname_x, self._colname_y, self._colname_size]
#First value is Y, second is X, following will be used in the
try: # introduced in pandas > 0.16.2
jinja['data'] = self.data[selection].round(3).values.tolist()
except: #for py3.3 on travis
jinja['data'] = np.around(self.data[selection]).values.tolist()
jinja[
'title'] = '"Regression coefficient vs Bayes factor for all drugs"'
jinja['minX'] = self.minX
jinja['minY'] = self.minY
jinja['maxX'] = self.maxX
jinja['maxY'] = self.maxY
self.html = template.render(jinja)
return self.html
def get_colors(self, sequencial):
c = Colormap()
if sequencial:
mycmap = c.cmap('YlGnBu')
else:
mycmap = c.cmap('tab10')
rgba = mycmap(np.linspace(0, 1, 256)) * 255
long = len(rgba)
return rgba, long
def get_html(self):
# We have 3 colors but sometimes you may have only one or 2.
# This may be an issue with canvasXpress. It seems essential
# to sort the color column so that names are sorted alphabetically
# and to include colors that are present in the sale order
"""try:
self.data.sort_values(by='color', inplace=True)
except:
self.data.sort("color", inplace=True)
"""
# Jinja related
from easydev import get_package_location
env = Environment()
env.loader = jinja2.FileSystemLoader(
get_package_location("gdsctools")
+ "/gdsctools/data/templates/")
template = env.get_template("scatter.html")
# We need to cireate 20 different colors
from colormap import Colormap
c = Colormap()
cmap = c.cmap_linear("red", "blue", "yellow", N=20)
colors = self.data[self._colname_color]
colors = ["red" for x in self.data[self._colname_color]]
jinja = {}
jinja["colors"] = ["rgba(205,0,0,0.5)"]
jinja["Group"] = colors
jinja['xlabel'] = '"%s"' % self.xlabel
jinja['ylabel'] = '"%s"' % self.ylabel
text = []
for index in zip(self.data.index):
text.append("<pre>%s</pre>" % self.data.ix[index].to_string())
jinja['vars'] = text
#self.data.markersize /= (self.data.markersize.max()/3.)
self.data['markersize'] = 20
selection = [self._colname_x, self._colname_y, self._colname_size]
#First value is Y, second is X, following will be used in the
try: # introduced in pandas > 0.16.2
jinja['data'] = self.data[selection].round(3).values.tolist()
except: #for py3.3 on travis
jinja['data'] = np.around(self.data[selection]).values.tolist()
jinja['title'] = '"Regression coefficient/ttest/bayes factor for all drugs"'
jinja['minX'] = 0
jinja['minY'] = 0
jinja['maxX'] = 1
jinja['maxY'] = self.data[self._colname_y].max() * 1.1
self.html = template.render(jinja)
return self.html
def cmap_builder(name, name2=None, name3=None):
"""return a colormap object compatible with matplotlib
If only parameter **name** is provided, it should be a known matplotlib
colormap name (e.g., jet). If **name2** is provided, then a new colormap
is created going from the color **name** to the color **name2** with a
linear scale. Finally, if **name3** is provided, a linear scaled colormap
is built from color **name** to color **name3** with the intermediate color
being the **name2**
Matplotlib colormap map names
"""
c = Colormap()
# an R colormap
if name and name2 and name3:
return c.cmap_linear(name, name2, name3)
elif name and name2:
return c.cmap_bicolor(name, name2)
elif name == 'heat':
return c.get_cmap_heat()
elif name == 'heat_r':
return c.get_cmap_heat_r()
# matplotlic colormaps
elif name in c.colormaps:
return c.cmap(name)
# some custom diverging colormaps with black in the middle.
elif name in c.diverging_black:
return c.cmap(name)
else:
#valid = c.colormaps + c.diverging_black
txt = "name provided {0} is not recognised. ".format(name)
txt += "\n valid name can be found in colormap.colormap_names"
raise ValueError(txt)
def getColormapViews(self):
"""
Return a list of the colormap views defined by the layout.
If there is more than one colormap view in the current
application layout, each one can be accessed via its own element
in the list. For example, if there are 3 colormap views in the
GUI, the following sequence of commands can be used to load a
different colormap in each one:
c = v.getColormapViews()
c[0].setColormap('coolwarm')
c[1].setColormap('spring')
c[2].setColormap('cubehelix')
Returns
-------
list
A list of Colormap objects.
"""
commandStr = "getColormapViews"
colormapViewsList = self.con.cmdTagList(commandStr)
colormapViews = []
if (colormapViewsList[0] != ""):
for cmv in colormapViewsList:
colormapView = Colormap(cmv, self.con)
colormapViews.append(colormapView)
return colormapViews
def _show_chic_clusterresult3(Results,
matrix_data,
colors=['white', 'green', 'blue', 'red']):
if np.max(matrix_data.shape) < 3000:
thr = np.percentile(matrix_data, 99.5)
else:
thr = np.percentile(matrix_data, 99.9)
matrix_data[matrix_data > thr] = thr
print(thr)
red_list = list()
green_list = list()
blue_list = list()
#['darkblue','seagreen','yellow','gold','coral','hotpink','red']
for color in colors:
col = Color(color).rgb
red_list.append(col[0])
green_list.append(col[1])
blue_list.append(col[2])
c = Colormap()
d = {'blue': blue_list, 'green': green_list, 'red': red_list}
mycmap = c.cmap(d)
#plt.subplots(figsize=(8,8))
#sns.heatmap(np.transpose(matrix_data[:,::-1]),cmap=mycmap)
#sns.heatmap(np.transpose(matrix_data[:,::-1]),xticklabels=100,yticklabels=500,cmap=mycmap)
plt.subplots(figsize=(8, 8))
#sns.heatmap(np.transpose(matrix_data[:,::-1]),cmap=mycmap)
#sns.heatmap(np.transpose(matrix_data[:,::-1]),xticklabels=100,yticklabels=500,cmap=mycmap,cbar=False)
sns.heatmap(matrix_data.T,
xticklabels=100,
yticklabels=1000,
cmap=mycmap,
cbar=False)
for i in Results.index:
upper = Results.ix[i, 'upper']
bottom = Results.ix[i, 'bottom']
left = Results.ix[i, 'left']
right = Results.ix[i, 'right']
x_loc = [upper, upper, bottom, bottom, upper]
y_loc = [left, right, right, left, left]
plt.plot(x_loc, y_loc, '-', color='k', lw=2.5)
plt.grid(b=None)
plt.show()
def test_soften():
c = Colormap(10)
c.flat(0, 10, (0, 0, 0))
c.flat(3, 6, (255, 128, 64))
c.soften()
assert np.array_equal(
c.cmap, [[0, 0, 0], [0, 0, 0], [63, 32, 16], [191, 96, 48],
[255, 128, 64], [191, 96, 48], [63, 32, 16], [0, 0, 0],
[0, 0, 0], [0, 0, 0]]), "Array didn't soften properly"
def get_colormap(self, choice):
imcategory, imtype = choice
if imcategory == 'Common':
if imtype in self.fileclass.channels[
'ir'] or imtype in self.fileclass.channels['wv']:
return 'gray_r'
return 'gray'
cmap = Colormap.get_colormap(imtype)
if cmap == 0:
print(imtype.upper() + '色阶存在问题。将使用灰度色阶。')
return 'gray_r'
return cmap
def test_rotate():
c = Colormap(130)
c.flat(0, 130, (0, 0, 0))
c.flat(0, 1, (1, 1, 1))
v1 = sum(c.cmap[0])
c.rotate(1)
assert np.array_equal(c.cmap[0], [0, 0, 0]), \
"Array 0th element didn't shift out (%s)" % str(c.cmap[0])
assert np.array_equal(c.cmap[1], [1, 1, 1]), \
"Array 1st element didn't shift in (%s)" % str(c.cmap[1])
v2 = sum(c.cmap[0])
c.rotate(-1)
v3 = sum(c.cmap[0])
# when we rotate out and rotate back, there should be net zero change to
# the value of the first element. But the interim first element shoud be
# different
assert v1 == v3, "Array didn't rotate back (0)"
assert v2 != v3, "Array didn't rotate back (1)"
def test_rotate():
c = Colormap(130)
c.flat(0, 130, (0, 0, 0))
c.flat(0, 1, (1, 1, 1))
v1 = sum(c.cmap[0])
c.rotate(1)
assert np.array_equal(c.cmap[0], [0, 0, 0]), \
"Array 0th element didn't shift out (%s)" % str(c.cmap[0])
assert np.array_equal(c.cmap[1], [1, 1, 1]), \
"Array 1st element didn't shift in (%s)" % str(c.cmap[1])
v2 = sum(c.cmap[0])
c.rotate(-1)
v3 = sum(c.cmap[0])
# when we rotate out and rotate back, there should be net zero change to
# the value of the first element. But the interim first element shoud be
# different
assert v1 == v3, "Array didn't rotate back (0)"
assert v2 != v3, "Array didn't rotate back (1)"
def getLinkedColormaps(self):
"""
Get the colormaps that are linked to this image view.
Returns
-------
list
A list of Colormap objects.
"""
resultList = self.con.cmdTagList("getLinkedColormaps",
imageView=self.getId())
linkedColormapViews = []
if (resultList[0] != ""):
for colormap in resultList:
linkedColormapView = Colormap(colormap, self.con)
linkedColormapViews.append(linkedColormapView)
return linkedColormapViews
def diff_reflect():
diff_reflect_cdict = {
'red':
((0.000, 0.000, 0.000), (0.333, 1.000, 1.000), (0.417, 0.000, 0.000),
(0.500, 0.000, 0.000), (0.583, 1.000, 1.000), (0.750, 1.000, 1.000),
(0.833, 1.000, 1.000), (1.000, 1.000, 1.000)),
'green':
((0.000, 0.000, 0.000), (0.333, 1.000, 1.000), (0.417, 0.000, 0.000),
(0.500, 1.000, 1.000), (0.583, 1.000, 1.000), (0.750, 0.000, 0.000),
(0.833, 0.000, 0.000), (1.000, 1.000, 1.000)),
'blue':
((0.000, 0.000, 0.000), (0.333, 1.000, 1.000), (0.417, 1.000, 1.000),
(0.500, 1.000, 1.000), (0.583, 0.000, 0.000), (0.750, 0.000, 0.000),
(0.833, 1.000, 1.000), (1.000, 1.000, 1.000))
}
diff_reflect_coltbl = Colormap(
'DIFF_REFLECT_COLTBL',
diff_reflect_cdict) #You will need to import this
return diff_reflect_coltbl
def get_options(self):
wv_colormaps, ir_colormaps = Colormap.get_colormap_list()
for imtype in self.channel_flag.keys():
if self.channel_flag[imtype]:
self.common_imoptions['Common'].append(imtype)
for imtype in self.fileclass.composite.keys():
composite_flag = [
self.channel_flag[channel_require]
for channel_require in self.fileclass.composite[imtype]
]
if all(composite_flag):
self.common_imoptions['Composite'].append(imtype)
for wv in self.fileclass.channels['wv']:
if self.channel_flag[wv]:
self.spec_imoptions['WV强化']['channels'].append(wv)
self.spec_imoptions['WV强化']['colormaps'] = wv_colormaps
for ir in self.fileclass.channels['ir']:
if self.channel_flag[ir]:
self.spec_imoptions['IR强化']['channels'].append(ir)
self.spec_imoptions['IR强化']['colormaps'] = ir_colormaps
def test_soften():
c = Colormap(10)
c.flat(0, 10, (0, 0, 0))
c.flat(3, 6, (255, 128, 64))
c.soften()
assert np.array_equal(c.cmap, [
[0, 0, 0],
[0, 0, 0],
[63, 32, 16],
[191, 96, 48],
[255, 128, 64],
[191, 96, 48],
[63, 32, 16],
[0, 0, 0],
[0, 0, 0],
[0, 0, 0]
]), "Array didn't soften properly"
def cmap_builder(name, name2=None, name3=None):
"""return a colormap object compatible with matplotlib
If only parameter **name** is provided, it should be a known matplotlib
colormap name (e.g., jet). If **name2** is provided, then a new colormap
is created going from the color **name** to the color **name2** with a
linear scale. Finally, if **name3** is provided, a linear scaled colormap
is built from color **name** to color **name3** with the intermediate color
being the **name2**
Matplotlib colormap map names
"""
c = Colormap()
# an R colormap
if name and name2 and name3:
return c.cmap_linear(name, name2, name3)
elif name and name2:
return c.cmap_bicolor(name, name2)
elif name == 'heat':
return c.get_cmap_heat()
elif name == 'heat_r':
return c.get_cmap_heat_r()
# matplotlic colormaps
elif name in c.colormaps:
return c.cmap(name)
# some custom diverging colormaps with black in the middle.
elif name in c.diverging_black:
return c.cmap(name)
elif name.count("_") == 2:
name1, name2, name3 = name.split("_")
return c.cmap_linear(name1, name2, name3)
else:
#valid = c.colormaps + c.diverging_black
txt = "name provided {0} is not recognised. ".format(name)
txt += "\n valid name can be found in colormap.colormap_names"
raise ValueError(txt)
def alignmultiple(niifiles,
subjectid,
outputprefix,
mcmask='brainmask',
skips=(5, 5, 5),
rots=(0, 0, 0)):
'''
alignmultiple(niifiles, subjectid, outputprefix, mcmask,skips,rots)
<niifiles> is a list of NIFTI filenames
<subjectid> is like 'C0001'
<outputprefix> is like 'T1average'
<mcmask>: can be
'brainmask', a str, indicates that we use a skullstripped brain mask returned by
afni utility and then use this mask to align multiple files
[mn, sd], a list, with the mn and sd outputs of defineellipse3d.m.
<skips> is number of slices to skip in each of the 3 dimensions.
Default: (5, 5, 5).
<rots> is a 3-vector with number of CCW rotations to apply for each slicing.
Default: (0, 0, 0).
The purpose of this function is to align and average all of the NIFTI files
and write out a new NIFTI file.
We pause for the user to manually define an binary 3D ellipse on the
first NIFTI in order to restrict the alignment procedure to those voxels.
Consider, for example, restricting the ellipse to cortex and maybe a little bit
of surrounding space.
We loop over NIFTIs after the first one to align each with the first using
a rigid-body transformation and a correlation metric. Slices are extracted
using cubic interpolation to derive volumes that match the first.
Our final volume is the mean of all of the volumes (first volume plus the
resliced versions of the remaining volumes).
We write out a NIFTI file to <anatomicals>/<outputprefix>.nii.gz using the first NIFTI as a template.
Inspections of results are written to a directory <ppresults>/<outputprefix>figures.
history:
2016/09/02 - change where files are written; fix the gzipping
2016/07/12 - switch to _untouch_
2016/06/10 - force non-finite values in resliced volumes to be 0 (flirt fails otherwise)
2016/05/29 - added visualization of residuals
#========================
below is by RZ:
#========================
Note:
We differ from XXX
To do:
- implement the ellipse, and alignment
- implement the brain extraction and alignment using afni or fsl
history:
20180714 accept the pathlib object for niftitiles
20180620 RZ created this file based on cvnalignmultiple.m
'''
from RZutilpy.cvnpy import cvnpath
from RZutilpy.system import unix_wrapper
from RZutilpy.imageprocess import makeimagestack3dfiles
from RZutilpy.mri import savenifti
import nibabel as nib
from numpy import isnan, isfinite, percentile, abs, all, stack
from os.path import dirname, join
from colormap import Colormap
from pathlib import Path
# calc
dir0 = cvnpath('anatomicals') / subjectid
pp0 = cvnpath('ppresults') / subjectid
# match files
if all([isinstance(p, Path) for p in niifiles]):
niifiles = [str(p) for p in niifiles]
niifiles = matchfiles(
niifiles) # after matchfiles niifiles become pathlib objects
# load the first volume
vol1 = nib.load(str(niifiles[0]))
vol1data = vol1.get_data().astype('f4') # 32 bit floating point
vol1data[isnan(vol1data)] = 0
# ===============================================
# use afni to align all volumnes
# ===============================================
# here is different from KK' cvnalignmultiple.m, we use afni linear align utility
# to align multiple volumes
# let's create a brainmask using afni utility
datadir = niifiles.parent
brainmaskfile = datadir / 'T1alignbrainmask.nii.gz'
# skullstrip to create the mask
result = unix_wrapper('3dSkullStrip -input {} -prefix {} -mask_vol'.format(
str(niifiles[0]), str(brainmaskfile)))
# on stone 3DSkullStrip cannot specify the output directory... afni bug??
# we manually move the mask file
result = unix_wrapper('mv T1alignbrainmask.nii.gz %s/'.format(
str(datadir)))
# read the mask vol file
brainmask = nib.load(str(brainmaskfile)).get_data()
# inspect first volume and brainmask
makeimagestack3dfiles(vol1data,
join(str(pp0), '{}figures'.format(outputprefix),
'vol{:03d}'.format(0)),
skips,
rots,
wantnorm=1,
addborder=1)
makeimagestack3dfiles(brainmask,
join(str(pp0), '%sfigures'.format(outputprefix),
'brainmask'),
skips,
rots,
wantnorm=1,
addborder=1)
# ===============================================
# # manually define ellipse on the first volume for use in the auto alignment
# if isempty(mcmask)
# [f,mn,sd] = defineellipse3d(vol1data)
# mcmask = {mn sd}
# fprintf('mcmask = %s\n',cell2str(mcmask))
# else
# mn = mcmask{1}
# sd = mcmask{2}
# loop over volumes
outputfiles = [p[:-7] + '_aligned.nii.gz' for p in niifiles]
vols = [] # note that this list does not contain the 1st volume
for p in range(1, len(niifiles)):
# issue the cmd as list. This is the input for unix_wrapper
cmd = ['3dAllineate',\
'-base', niifiles[0], '-source', niifiles[p], '-prefix', outputfiles[p],\
'-weight', brainmaskfile, '-1Dparam_save', niifiles[p][:-7],\
'-interp', 'cubic', '-cost', 'crM', '-final', 'wsinc5']
# do it
unix_wrapper(cmd)
## start the alignment
#alignvolumedata(vol2data,vol2size,vol1data,vol1size) # NOTICE THAT FIRST VOLUME IS THE TARGET!
# auto-align (rigid-body, correlation)
#alignvolumedata_auto(mn,sd,[1 1 1 1 1 1 0 0 0 0 0 0],[4 4 4])
#alignvolumedata_auto(mn,sd,[1 1 1 1 1 1 0 0 0 0 0 0],[2 2 2])
#alignvolumedata_auto(mn,sd,[1 1 1 1 1 1 0 0 0 0 0 0],[1 1 1])
# get the transformation
#tr = alignvolumedata_exporttransformation
# get slices from vol2 to match vol1
#matchvol = extractslices(vol2data,vol2size,vol1data,vol1size,tr)
# read the aligned volume
matchvol = nib.load(outputfiles[p]).get_data()
assert all(matchvol.shape == vol1data.shape
), 'This # %d volume have a different size!' % p
# REALLY IMPORTANT: ENSURE FINITE (e.g. flirt blows up otherwise)
matchvol[~isfinite(matchvol)] = 0
# inspect it
makeimagestack3dfiles(matchvol,
join(pp0, '%sfigures' % outputprefix,
'vol%03d' % p),
skips,
rots,
wantnorm=1,
addborder=1)
# record it into the list
vols.append(matchvol)
# average all vols
meanvol = sum(vols) / len(vols)
# inspect it
makeimagestack3dfiles(meanvol,
join(pp0, '%sfigures' % outputprefix, 'volavg'),
skips,
rots,
wantnorm=1,
addborder=1)
# finally, write out residual images
# prepare colormap
if len(vols) != 1:
mx = percentile(stack([abs(vol - meanvol) for vol in vols], axis=-1),
99)
[makeimagestack3dfiles(vol-meanvol, join(pp0, '%sfigures' % outputprefix, 'resid%03d' % p),\
skips,rots, cmap=Colormap().cmap_linear('blue','black','red'), wantnorm=(-mx, mx), \
addborder=1) for p, vol in enumerate(vols)]
# save the mean vol NIFTI file as output
savenifti(meanvol, join(dir0, '%s.nii.gz' % outputprefix), niftiobj=vol1)
samplenum = "None"
imnum = 1
vidnum = 1
exposure = float(10000.0) # value in microseconds
avg = 0
t0 = time.time()
t, avg1, avg2, avg3, oldt, oldavg1, oldavg2, oldavg3, oldert, olderavg1, olderavg2, olderavg3 = [], [], [], [], [], [], [], [], [], [], [], []
x1, y1, x2, y2 = 0, 0, 640, 480
a1, b1, a2, b2 = 0, 0, 640, 480
c1, d1, c2, d2 = 0, 0, 640, 480
i = 1
red, green, blue = True, False, False
path = 'C:/Users/Palmstrom Lab/Desktop/FRHEED/'
filename = 'default'
#### Define colormap ####
cmp = Colormap()
FRHEEDcmap = cmp.cmap_linear('black', 'green', 'white')
cm.register_cmap(name='RHEEDgreen', cmap=FRHEEDcmap)
cmap = cm.gray
#cmp.test_colormap(FRHEEDcmap)
#### Loading UI file from qt designer ####
form_class = uic.loadUiType("FRHEED backup.ui")[0]
#### Define "shortcut" for queue ####
q = queue.Queue()
#### Define video recording codec ####
fourcc = cv2.VideoWriter_fourcc(*'MP4V')
#### Set default appearance of plots ####
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 0.0)
#### Connect to RHEED camera ####
system = PySpin.System.GetInstance()
def main(cli_D=2.03,
new_gx=0e-8,
anion_flux=False,
default_xz=-0.85,
jkccup=1e-12,
nrcomps=2,
dz=1e-7,
textra=100,
say='',
stretch=False):
"""
cli_D # um2/s
:return: sim, gui: it is useful to return these objects for access after simulation
"""
print("main")
sim = Simulator().get_instance()
gui = sim.gui()
dt = 0.001 # s
length = 10e-5
comp = Compartment("reference",
z=-0.85,
cli=0.0052,
ki=0.0123,
nai=0.014,
length=length,
radius=default_radius_short,
stretch_w=stretch)
# copies left
compl = comp.copy("dendrite left")
# copies right
compr = []
compr.append(comp.copy("dendrite right " + str(1)))
for i in range(nrcomps):
compr.append(comp.copy("dendrite right " + str(i + 2)))
# find steady-state values of ions
sim.run(stop=100,
dt=0.001,
plot_update_interval=50,
data_collect_interval=5,
block_after=False)
# set diffusion value
cli_D *= 1e-7 # cm2 to dm2 (D in dm2/s)
ki_D = 1.96
ki_D *= 1e-7 # cm2 to dm2 (D in dm2/s)
nai_D = 1.33
nai_D *= 1e-7
diffusion_object = []
# connect with Diffusion
diffusion_object.append(
Diffusion(compl, comp, ions={
'cli': cli_D,
'ki': ki_D,
'nai': nai_D
}))
diffusion_object.append(
Diffusion(comp,
compr[0],
ions={
'cli': cli_D,
'ki': ki_D,
'nai': nai_D
}))
for i in range(nrcomps):
diffusion_object.append(
Diffusion(compr[i],
compr[i + 1],
ions={
'cli': cli_D,
'ki': ki_D,
'nai': nai_D
}))
# heatmap incorporating compartment heights
sc = 1e7
htplot = Colormap("cmap", 0, compr)
totalht, initvals = htplot.heatmap(compl,
comp,
compr,
sc,
0,
all=1,
init_vals=None)
htplot.heatmap(compl, comp, compr, sc, totalht, all=1, init_vals=initvals)
voltage_reversal_graph_comp = gui.add_graph() \
.add_ion_conc(comp, "ecl", line_style='g', y_units_scale=1000, y_plot_units='mV') \
.add_ion_conc(comp, "ek", line_style='b', y_units_scale=1000, y_plot_units='mV') \
.add_voltage(comp, line_style='k', y_units_scale=1000, y_plot_units='mV')
voltage_reversal_graph_compr = gui.add_graph() \
.add_ion_conc(compr[-1], "ecl", line_style='g', y_units_scale=1000, y_plot_units='mV') \
.add_ion_conc(compr[-1], "ek", line_style='b', y_units_scale=1000, y_plot_units='mV') \
.add_voltage(compr[-1], line_style='k', y_units_scale=1000, y_plot_units='mV')
voltage_reversal_graph_compl = gui.add_graph() \
.add_ion_conc(compl, "ecl", line_style='g', y_units_scale=1000, y_plot_units='mV') \
.add_ion_conc(compl, "ek", line_style='b', y_units_scale=1000, y_plot_units='mV') \
.add_voltage(compl, line_style='k', y_units_scale=1000, y_plot_units='mV')
voltage_reversal_graph_compr1 = gui.add_graph() \
.add_ion_conc(compr[0], "ecl", line_style='g', y_units_scale=1000, y_plot_units='mV') \
.add_ion_conc(compr[0], "ek", line_style='b', y_units_scale=1000, y_plot_units='mV') \
.add_voltage(compr[0], line_style='k', y_units_scale=1000, y_plot_units='mV')
# run simulation with diffusion
sim.run(continuefor=10,
dt=dt,
plot_update_interval=5,
data_collect_interval=1)
print(datetime.datetime.now())
print_concentrations(
[comp, compl, compr[-1]],
title="Ion concentrations given diffusion between compartments")
htplot.heatmap(compl, comp, compr, sc, totalht, all=1, init_vals=initvals)
# (optionally) change anion conductance
prev_comp_gx = comp.gx
comp.gx = new_gx
comp.dz = dz
voltage_reversal_graph_comp.save(say + 'reference.eps')
if dz != 0:
z_graph = gui.add_graph() \
.add_ion_conc(comp, "z", line_style='m')
if comp.gx > 0:
x_graph = gui.add_graph() \
.add_ion_conc(comp, "absox", line_style='m') \
.add_ion_conc(compl, "absox", line_style=':m') \
.add_ion_conc(compr[0], "absox", line_style='m--')
# (optionally) change anion flux
if anion_flux:
comp.xz = default_xz
comp.xmz = (comp.z * comp.xi - comp.xz * comp.xi_temp) / comp.xm
print('Anion flux with fixed anions having net charge', comp.xmz,
'while a proportion of', (1 - comp.ratio),
'of all impermeants are temporarily mobile anions of charge',
comp.xz)
z_graph = gui.add_graph() \
.add_ion_conc(comp, "z", line_style='m')
# (optionally) change kcc2
prev_comp_pkcc2 = comp.pkcc2
if jkccup is not None:
comp.jkccup = jkccup
g_graph = gui.add_graph() \
.add_ion_conc(comp, "pkcc2", line_style='k')
vol_graph = gui.add_graph() \
.add_ion_conc(comp, "w", line_style='b') \
.add_ion_conc(compl, "w", line_style=':b') \
.add_ion_conc(compr[0], "w", line_style='b--')
sim.run(continuefor=textra,
dt=dt * 0.001,
plot_update_interval=textra / 32,
data_collect_interval=textra / 32)
print(datetime.datetime.now())
print_concentrations(
[comp, compl, compr[-1]],
title="Ion concentrations during event from the dendritic compartment")
# heatmap incorporating compartment heights
htplot.heatmap(compl,
comp,
compr,
sc,
totalht,
all=1,
init_vals=initvals,
title=[
say + 'all_halfway_df.eps', say + 'all_halfway_ecl.eps',
say + 'all_halfway_vm.eps'
])
voltage_reversal_graph_comp.save(say + 'reference.eps')
sim.run(continuefor=textra,
dt=dt * 0.001,
plot_update_interval=textra / 2,
data_collect_interval=textra / 16)
print(datetime.datetime.now())
print_concentrations(
[comp, compl, compr[-1]],
title=
"Ion concentrations immediately after event from the dendritic compartment"
)
# heatmap incorporating compartment heights
htplot.heatmap(compl, comp, compr, sc, totalht, all=1, init_vals=initvals)
comp.gx = prev_comp_gx
comp.jkccup = 0
comp.dz = 0
voltage_reversal_graph_comp.save(say + 'reference.eps')
sim.run(continuefor=textra * 1,
dt=dt * 0.001,
plot_update_interval=textra / 2,
data_collect_interval=textra / 4)
print(datetime.datetime.now())
print_concentrations([comp, compl, compr[-1]],
title="Ion concentrations at almost steady state")
htplot.heatmap(compl,
comp,
compr,
sc,
totalht,
all=1,
init_vals=initvals,
title=[
say + 'all_end_df.eps', say + 'all_end_ecl.eps',
say + 'all_end_vm.eps'
])
voltage_reversal_graph_comp.save(say + 'reference.eps')
sim.run(continuefor=textra * 1,
dt=dt * 0.001,
plot_update_interval=textra / 2,
data_collect_interval=textra / 4)
print(datetime.datetime.now())
print_concentrations([comp, compl, compr[-1]],
title="Ion concentrations at steady state")
# heatmap incorporating compartment heights
htplot.heatmap(compl,
comp,
compr,
sc,
totalht,
all=1,
init_vals=initvals,
title=[
say + 'all_end_df.eps', say + 'all_end_ecl.eps',
say + 'all_end_vm.eps'
])
voltage_reversal_graph_comp.save(say + 'reference.eps')
sim.run(continuefor=textra * 2,
dt=dt * 0.001,
plot_update_interval=textra / 2,
data_collect_interval=textra / 4)
print(datetime.datetime.now())
print_concentrations([comp, compl, compr[-1]],
title="Ion concentrations at steady state")
# heatmap incorporating compartment heights
htplot.heatmap(compl,
comp,
compr,
sc,
totalht,
all=1,
init_vals=initvals,
title=[
say + 'all_end_df.eps', say + 'all_end_ecl.eps',
say + 'all_end_vm.eps'
])
voltage_reversal_graph_comp.save(say + 'reference.eps')
sim.run(continuefor=textra * 2,
dt=dt * 0.001,
plot_update_interval=textra / 2,
data_collect_interval=textra / 4)
print(datetime.datetime.now())
print_concentrations([comp, compl, compr[-1]],
title="Ion concentrations at steady state")
# heatmap incorporating compartment heights
htplot.heatmap(compl,
comp,
compr,
sc,
totalht,
all=1,
init_vals=initvals,
title=[
say + 'all_end_df.eps', say + 'all_end_ecl.eps',
say + 'all_end_vm.eps'
])
voltage_reversal_graph_comp.save(say + 'reference.eps')
sim.run(continuefor=textra * 2,
dt=dt * 0.001,
plot_update_interval=textra / 2,
data_collect_interval=textra / 4)
print(datetime.datetime.now())
print_concentrations([comp, compl, compr[-1]],
title="Ion concentrations at steady state")
# heatmap incorporating compartment heights
htplot.heatmap(compl,
comp,
compr,
sc,
totalht,
all=1,
init_vals=initvals,
title=[
say + 'all_end_df.eps', say + 'all_end_ecl.eps',
say + 'all_end_vm.eps'
])
voltage_reversal_graph_comp.save(say + 'reference.eps')
return sim, gui
def grow(nr=3, textra=10):
print("growing via anions")
sim = Simulator().get_instance()
gui = sim.gui()
dt = 0.001 # s
comp = []
comp.append(
Compartment("initial growth cone",
z=-0.85,
cli=0.00433925284075134,
ki=0.1109567493822927,
nai=0.0255226350779378,
length=5e-5,
radius=default_radius_short))
# steady state
sim.run(stop=100,
dt=0.001,
plot_update_interval=500,
data_collect_interval=5,
block_after=False)
# set diffusion value
cli_D = 2.03
cli_D *= 1e-7 # cm2 to dm2 (D in dm2/s)
ki_D = 1.96
ki_D *= 1e-7 # cm2 to dm2 (D in dm2/s)
nai_D = 1.33
nai_D *= 1e-7
#another compartment
comp.append(comp[0].copy("compartment 1"))
comp[1].L = 10e-5
comp[1].w = np.pi * comp[1].r**2 * comp[1].L
diffusion_object = [
Diffusion(comp[0],
comp[1],
ions={
'cli': cli_D,
'ki': ki_D,
'nai': nai_D
})
]
# heatmap incorporating compartment heights
sc = 1e5
htplot = Colormap("dendrite", comp[0].w + comp[1].w, comp)
totalht, init_vals = htplot.smallheatmap(comp,
sc,
int(htplot.totalh * sc),
all=0,
init_val=None)
# plot
voltage_reversal_graph_comp = gui.add_graph() \
.add_ion_conc(comp[0], "ecl", line_style='g', y_units_scale=1000, y_plot_units='mV') \
.add_ion_conc(comp[0], "ek", line_style='b', y_units_scale=1000, y_plot_units='mV') \
.add_voltage(comp[0], line_style='k', y_units_scale=1000, y_plot_units='mV')
volume_graph = gui.add_graph()
volume_graph.add_var(volume_graph.time,
"time",
htplot,
"comp0w",
line_style='k')
volume_graph.add_var(volume_graph.time,
"time",
htplot,
"totalh",
line_style='b')
sim.run(continuefor=1,
dt=dt * 0.001,
plot_update_interval=0.5,
data_collect_interval=textra / 16)
# growth
for i in range(nr):
htplot.smallheatmap(comp,
sc,
totalht,
all=0,
init_val=init_vals,
name='graphs/grow_done' + str(i) + '.eps')
comp[0].gx = 1
# stop at certain length
while comp[0].L < 15e-5:
print("Fluxing compartment's length: " + str(comp[0].L))
sim.run(continuefor=0.5,
dt=dt * 0.001,
plot_update_interval=0.25,
data_collect_interval=textra / 16)
if 9.9e-5 < comp[0].L < 10.3e-5:
htplot.smallheatmap(comp,
sc,
totalht,
all=0,
init_val=init_vals,
name='graphs/grow_interim' + str(i) +
'.eps')
comp[0].gx = 0
print_concentrations(comp, str(i))
# split compartments
comp.insert(0, comp[0].copy("compartment " + str(i)))
comp[1].L -= 5e-5
comp[0].L = 5e-5
comp[0].w = np.pi * comp[0].r**2 * comp[0].L
comp[1].w = np.pi * comp[1].r**2 * comp[1].L
print_concentrations(comp, str(i))
# update total height
htplot.comp = comp
# update diffusion
diffusion_object.append(
Diffusion(comp[0],
comp[1],
ions={
'cli': cli_D,
'ki': ki_D,
'nai': nai_D
}))
for a in comp:
print(a.name)
for j in diffusion_object:
print(j.name)
sim.run(continuefor=10,
dt=dt * 0.001,
plot_update_interval=5,
data_collect_interval=textra / 16)
htplot.smallheatmap(comp,
sc,
totalht,
all=1,
init_val=init_vals,
name='graphs/grow_end.eps')
sim.run(continuefor=4,
dt=dt * 0.001,
plot_update_interval=2,
data_collect_interval=0.5)
htplot.smallheatmap(comp,
sc,
totalht,
all=1,
init_val=init_vals,
name='graphs/grow_end.eps')
return sim, gui
def make_u_plot(u_fname,
make_single,
make_with_metric,
label_p,
u_zonal=None,
u_zonal_NH=None,
Method=None,
Method_NH=None,
lat_elem_SH=None,
lat_elem_NH=None,
STJ_lat=None,
method_choice=None,
time=None,
file_out_syntax=None):
open_data = False
if open_data:
#open jet data from file
filename = '{0}/STJ_data_{1}.nc'.format(data_out_dir, file_out_syntax)
assert os.path.isfile(
filename
), 'File ' + filename + ' does not exist. Need jet latitude for plotting.'
var_jet = openNetCDF4_get_data(filename)
jet_NH = var_jet['STJ_lat'][:, 0]
jet_SH = var_jet['STJ_lat'][:, 1]
else:
#use data just calculated
jet_NH = STJ_lat[0]
jet_SH = STJ_lat[1]
#open u wind data - on pressure levels
assert os.path.isfile(u_fname), 'File ' + u_fname + ' does not exist.'
var = openNetCDF4_get_data(u_fname)
# check that input pressure is in pascal
if var[label_p].max() < 90000.0:
var[label_p] = var[label_p] * 100.0
lev250 = FindClosestElem(25000, var[label_p], 0)[0]
if 'var131' in var:
uwnd = var['var131'][time, lev250, :, :]
else:
uwnd = var['u'][time, lev250, :, :]
if make_single:
fname_out = '{}/uwind_{}_with_wind_{}.eps'.format(
plot_dir, t_elem[t], file_out_syntax)
fig = plt.figure(figsize=(10, 5))
# wind plot
ax1 = plt.subplot2grid((10, 20), (0, 0), colspan=16, rowspan=9)
# zonal mean
ax2 = plt.subplot2grid((10, 20), (0, 16), colspan=5, rowspan=9)
# colour bar
ax_cb = plt.subplot2grid((10, 20), (9, 0), colspan=20)
save_plot = True
plot_u(plt,
ax1,
ax2,
ax_cb,
jet_NH,
jet_SH,
uwnd,
var,
t,
t_elem,
fname_out,
save_plot,
make_single=make_single)
if make_with_metric:
fname_out = '{}/validation_uwind_{}_{}.eps'.format(
plot_dir, time, file_out_syntax)
fig = plt.figure(figsize=(10, 12))
#SH
ax1 = plt.subplot2grid(
(37, 26), (0, 0), rowspan=22,
colspan=12) #half across/gap/half accross. 18 deep
#NH
ax2 = plt.subplot2grid((37, 26), (0, 12), rowspan=22, colspan=12)
# wind plot
ax3 = plt.subplot2grid((37, 26), (22, 0), rowspan=13, colspan=20)
# zonal mean
ax4 = plt.subplot2grid((37, 26), (22, 20), rowspan=13, colspan=5)
# colour bar
ax_cb = plt.subplot2grid((37, 26), (35, 0), rowspan=2, colspan=37)
bounds = np.arange(-50, 60, 5.0)
cm = Colormap()
cmap = cm.cmap_linear('#0033ff', '#FFFFFF', '#990000') #blue/red
#cmap = pylab.cm.get_cmap('RdBu_r')
PlottingObject = Plotting(Method, 'cby')
plot_cbar = False
#u_zonal = MeanOverDim(data=uwnd, dim=1)
PlottingObject.poly_2PV_line('SH',
u_zonal,
lat_elem_SH,
time,
fig,
ax1,
plot_cbar,
ax_cb,
bounds,
cmap,
plot_type='subplot_all',
pause=False,
click=False,
save_plot=False)
# NH
PlottingObject2 = Plotting(Method_NH, method_choice)
PlottingObject2.poly_2PV_line('NH',
u_zonal_NH,
lat_elem_NH,
time,
fig,
ax2,
plot_cbar,
None,
bounds,
cmap,
plot_type='subplot_all',
pause=False,
click=False,
save_plot=False)
save_plot = True
plot_u(plt,
ax3,
ax4,
ax_cb,
jet_NH,
jet_SH,
uwnd,
var,
bounds,
cmap,
time,
fname_out,
save_plot,
make_single=False)