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qtpy - for 2d corrected log cmap and other bugs
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Simon committed Oct 20, 2023
1 parent 6e4127f commit 0f7b795
Showing 1 changed file with 149 additions and 56 deletions.
205 changes: 149 additions & 56 deletions main/PyQtGUI/gui/GUI.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
import matplotlib.image as mpimg
import matplotlib.gridspec as gridspec
import matplotlib.colorbar as mcolorbar
import matplotlib.colors as colors
from matplotlib.backend_bases import *
from matplotlib.artist import Artist

Expand Down Expand Up @@ -836,18 +837,19 @@ def on_dblclick(self, event, idx):
n = canvasLayout[0]*canvasLayout[1]
self.currentPlot.h_setup = {k: True for k in range(n)}
self.currentPlot.selected_plot_index = None # this will allow to call drawGate and loop over all the gates
for index in range(n):
self.add(index)
self.currentPlot.h_setup[index] = False
ax = self.getSpectrumInfo("axis", index=index)
self.plotPlot(ax, index)
#reset the axis limits as it was before enlarge
#dont need to specify if log scale, it is checked inside setAxisScale, if 2D histo in log its z axis is set too.
dim = self.getSpectrumInfoREST("dim", index=index)
if dim == 1:
self.setAxisScale(ax, index, "x", "y")
elif dim == 2:
self.setAxisScale(ax, index, "x", "y", "z")
for index, name in self.getGeo().items():
if name is not None and name != "" and name != "empty":
self.add(index)
self.currentPlot.h_setup[index] = False
ax = self.getSpectrumInfo("axis", index=index)
self.plotPlot(ax, index)
#reset the axis limits as it was before enlarge
#dont need to specify if log scale, it is checked inside setAxisScale, if 2D histo in log its z axis is set too.
dim = self.getSpectrumInfoREST("dim", index=index)
if dim == 1:
self.setAxisScale(ax, index, "x", "y")
elif dim == 2:
self.setAxisScale(ax, index, "x", "y", "z")

#drawing back the dashed red rectangle on the unenlarged spectrum
self.removeRectangle()
Expand Down Expand Up @@ -940,9 +942,11 @@ def okCutoff(self):
if self.cutoffp.lineeditMax.text() != "" and self.cutoffp.lineeditMax.text().isdigit():
cutoffVal[1] = float(cutoffMax)
self.setSpectrumInfo(cutoff=cutoffVal, index=index)
else:
print("okCutoff - wrong min/max cutoff fomat, expect just a number per field")
return
#Order may be inverted
if cutoffVal[0] is not None and cutoffVal[1] is not None and cutoffVal[1] < cutoffVal[0]:
cutoffVal = [cutoffVal[1], cutoffVal[0]]
self.setSpectrumInfo(cutoff=cutoffVal, index=index)
print("okCutoff - Warning - cutoff values swapped because min > max")
self.updatePlot()
self.cutoffp.close()

Expand Down Expand Up @@ -1520,6 +1524,7 @@ def connectShMem(self):
print("before cpy.CPyConverter().Update")
s = cpy.CPyConverter().Update(bytes(hostname, encoding='utf-8'), bytes(port, encoding='utf-8'), bytes(mirror, encoding='utf-8'), bytes(user, encoding='utf-8'))


# creates a dataframe for spectrum info
# use the spectrum name to merge both sources (REST and shared memory) of spectrum info
# info = {"id":[],"names":[],"dim":[],"binx":[],"minx":[],"maxx":[],"biny":[],"miny":[],"maxy":[],"data":[],"parameters":[],"type":[]}
Expand Down Expand Up @@ -1931,7 +1936,8 @@ def setAxisScale(self, ax, index, *scale):
if axisIsAutoScale:
#search in the current view
xmin, xmax = ax.get_xlim()
ymax = self.getMaxInRange(index, xmin=xmin, xmax=xmax)
#getMinMaxInRange returns only max for 1d
ymax = self.getMinMaxInRange(index, xmin=xmin, xmax=xmax)
if axisIsLog:
if ymin <= 0:
ymin = 0.001
Expand Down Expand Up @@ -1959,25 +1965,56 @@ def setAxisScale(self, ax, index, *scale):
zmin = self.getSpectrumInfo("minz", index=index)
zmax = self.getSpectrumInfo("maxz", index=index)
spectrum = self.getSpectrumInfo("spectrum", index=index)
if (not zmin or zmin is None or zmin == 0) and (not zmax or zmax is None or zmax == 0):
if (not zmin or zmin is None or zmin==0) and (not zmax or zmax is None or zmax==0):
zmin = self.minZ
zmax = self.maxZ
if axisIsAutoScale:
#search in the current view
xmin, xmax = ax.get_xlim()
ymin, ymax = ax.get_ylim()
zmax = self.getMaxInRange(index, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)
#getMinMaxInRange returns min and max for 2d
zmin, zmax = self.getMinMaxInRange(index, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)
self.setSpectrumInfo(maxz=zmax, index=index)
self.setSpectrumInfo(minz=zmin, index=index)
if axisIsLog:
if zmin and zmin <= 0 :
zmin = 0.001
zmin = math.log10(zmin)
zmax = math.log10(zmax)
spectrum.set_clim(vmin=zmin, vmax=zmax)
if axisIsLog:
self.setCmapNorm("log", index)
else :
#linearCentered not used so far but could be user choice
#while testing linearCentered notice that it is not well compatible with cutoff
#self.setCmapNorm("linearCentered", index)
self.setCmapNorm("linear", index)
self.setSpectrumInfo(spectrum=spectrum, index=index)
#Dont want to save z limits in spectrum info because in log: z_new = f(z_old)

def setCmapNorm(self, scale, index):
validScales = ["linear", "log", "linearCentered"]
if scale not in validScales or index is None:
return
spectrum = self.getSpectrumInfo("spectrum", index=index)
zmin, zmax = spectrum.get_clim()

if scale is validScales[0]:
spectrum.set_norm(colors.Normalize(vmin=zmin, vmax=zmax))
elif scale is validScales[1]:
if zmin and zmin <= 0 :
zmin = 0.001
print("setCmapNorm - warning - LogNorm with zmin<=0, may want to use CenteredNorm")
spectrum.set_norm(colors.LogNorm(vmin=zmin, vmax=zmax))
elif scale is validScales[2]:
palette = copy(plt.cm.jet)
palette.set_bad(color='white')
data = self.getSpectrumInfo("data", index=index)
spectrum.set_cmap(palette)
# set vcenter to variable set by user
spectrum.set_norm(centeredNorm(data,50000))
if self.getEnlargedSpectrum() is None:
ax = spectrum.axes
self.removeCb(ax)
divider = make_axes_locatable(ax)
cax = divider.append_axes('right', size='5%', pad=0.05)
self.currentPlot.figure.colorbar(spectrum, cax=cax, orientation='vertical')


def zoom(self, ax, index, flag):
if (DEBUG):
Expand Down Expand Up @@ -2063,9 +2100,9 @@ def autoScaleAxisBox(self):
else:
for index, name in self.getGeo().items():
if name:
ax = self.select_plot(index)
#ax = self.select_plot(index)
ax = self.getSpectrumInfo("axis", index=index)
dim = self.getSpectrumInfoREST("dim", index=index)

#Set y for 1D and z for 2D.
#dont need to specify if log scale, it is checked inside setAxisScale, if 2D histo in log its z axis is set too.
if dim == 1:
Expand All @@ -2079,10 +2116,10 @@ def autoScaleAxisBox(self):

# get data max within user defined range
# For 2D have to give two ranges (x,y), for 1D range x.
def getMaxInRange(self, index, **limits):
def getMinMaxInRange(self, index, **limits):
result = None
if not limits :
print("getMaxInRange - limits identifier not valid - expect xmin=val, xmax=val etc. for y with 2D")
print("getMinMaxInRange - limits identifier not valid - expect xmin=val, xmax=val etc. for y with 2D")
return
if "xmin" and "xmax" in limits:
xmin = limits["xmin"]
Expand Down Expand Up @@ -2112,10 +2149,47 @@ def getMaxInRange(self, index, **limits):
stepy = (float(maxy)-float(miny))/float(biny)
binminy = int((ymin-miny)/stepy)
binmaxy = int((ymax-miny)/stepy)
#Dont increase by 10% here...
result = data[binminy:binmaxy+1, binminx:binmaxx+1].max()
#Dont increase max by 10% here...
#truncData = data[binminy:binmaxy+1, binminx:binmaxx+1]
#Following two lines work for "small" array, replaced by custom function
#maximum = truncData.max()
#minimum = np.min(truncData[np.nonzero(truncData)])
minimum, maximum = self.customMinMax(data[binminy:binmaxy+1, binminx:binmaxx+1], binminy, binmaxy, binminx, binmaxx)
result = minimum, maximum
return result

# Have seen malloc error if data array too large
# Divide data array in sub-arrays with sub-(min, max) and then find the global-(min, max)
def customMinMax(self, data, binminy, binmaxy, binminx, binmaxx):
diffX = binmaxx - binminx
diffY = binmaxy - binminy
if diffX < 200 and diffY < 200:
maximum = data.max()
minimum = np.min(data[np.nonzero(data)])
return minimum, maximum
else :
stepX = diffX if diffX < 200 else 200
stepY = diffY if diffY < 200 else 200
rangeX = list(range(binminx, binmaxx, stepX))
rangeY = list(range(binminy, binmaxy, stepY))
subMax = []
subMin = []
yprev = binmaxy+1
xprev = binmaxx+1
for x in rangeX[::-1]:
for y in rangeY[::-1]:
subData = data[y:yprev,x:xprev]
nonZeroIndices = np.where(subData != 0)
filteredSubData = subData[nonZeroIndices]
if filteredSubData is not None and filteredSubData.size > 0:
subMax.append(filteredSubData.max())
subMin.append(filteredSubData.min())
yprev = y
xprev = x
minimum = min(subMin)
maximum = max(subMax)
return minimum, maximum


def getAxisProperties(self, index):
if (DEBUG):
Expand Down Expand Up @@ -2151,17 +2225,20 @@ def customHomeButtonCallback(self, index=None):
ax.set_xlim(xmin, xmax)
if dim == 1:
#Similar to autoscale, in principle ymin and ymax are not defined in ReST for 1D so set to ymin=0 and autoscale for ymax
ymax = self.getMaxInRange(idx, xmin=xmin, xmax=xmax)
#getMinMaxInRange gives only min for 1d
ymax = self.getMinMaxInRange(idx, xmin=xmin, xmax=xmax)
ax.set_ylim(ymin, ymax)
if self.getSpectrumInfo("log", index=idx) :
ax.set_yscale("linear")
# y limits should be known at this point for both cases 1D/2D
if dim == 2:
ax.set_ylim(ymin, ymax)
zmax = self.getMaxInRange(idx, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)
spectrum.set_clim(vmin=self.minZ, vmax=zmax)
#getMinMaxInRange gives min and max for 2d
zmin, zmax = self.getMinMaxInRange(idx, xmin=xmin, xmax=xmax, ymin=ymin, ymax=ymax)
spectrum.set_clim(vmin=zmin, vmax=zmax)
self.setCmapNorm("linear", idx)
self.setSpectrumInfo(maxz=zmax, index=idx)
self.setSpectrumInfo(minz=self.minZ, index=idx)
self.setSpectrumInfo(minz=zmin, index=idx)

self.setSpectrumInfo(log=None, index=idx)
self.setSpectrumInfo(minx=xmin, index=idx)
Expand Down Expand Up @@ -2315,7 +2392,7 @@ def check_index(self):
def select_plot(self, index):
for i, axis in enumerate(self.currentPlot.figure.axes):
# retrieve the subplot from the click
if (i == index):
if (i == index and axis is not None):
return axis


Expand Down Expand Up @@ -2381,7 +2458,7 @@ def setupPlot(self, axis, index):
w = np.ma.masked_where(w < maxCutoff, w)
if dim == 2:
w = np.ma.masked_where(w < maxCutoff, w)
#used in getMaxInRange to take into account also the cutoff if there is one
#used in getMinMaxInRange to take into account also the cutoff if there is one
self.setSpectrumInfo(data=w, index=index)

# update axis
Expand All @@ -2406,15 +2483,21 @@ def setupPlot(self, axis, index):
# empty data for initialization
if w is None:
w = np.zeros((int(binx), int(biny)))

# setup up palette
if (self.wConf.button2D_option.currentText() == 'Dark'):
#self.palette = 'plasma'
self.palette = 'plasma_r'
else:
self.palette = copy(plt.cm.plasma)
w = np.ma.masked_where(w < 0.1, w)
self.palette.set_bad(color='white')
# for later ...
# if (self.wConf.button2D_option.currentText() == 'Dark'):
# #self.palette = 'plasma'
# self.palette = 'plasma_r'
# else:
# self.palette = copy(plt.cm.plasma)
# w = np.ma.masked_where(w < 0.1, w)
# self.palette.set_bad(color='white')

self.palette = copy(plt.cm.plasma)
w = np.ma.masked_where(w == 0, w)
self.palette.set_bad(color='white')

#check if enlarged mode, dont want to modify spectrum dict in enlarged mode
self.setSpectrumInfo(spectrum=axis.imshow(w,
interpolation='none',
Expand All @@ -2440,7 +2523,7 @@ def setupPlot(self, axis, index):


# geometrically add plots to the right place and calls plotting
# should be called only by addPlot and on_dblclick when entering enlarged mode
# should be called only by addPlot and on_dblclick when entering/exiting enlarged mode
def add(self, index):
a = None
#cannot use getSpectrumAxes here because the underlying list is built in setupPlot
Expand Down Expand Up @@ -2518,6 +2601,10 @@ def addPlot(self):
self.currentPlot.h_limits[index] = {}
self.currentPlot.h_setup[index] = True
self.add(index)
#When add with button "add" the default state is unlog
self.currentPlot.logButton.setDown(False)
#Reset log
self.setSpectrumInfo(log=False, index=index)
# if gate in gateList:
self.drawAllGates()
#draw dashed red rectangle to indicate where the next plot would be added, based on next_plot_index, selected_plot_index is unchanged.
Expand Down Expand Up @@ -2546,7 +2633,7 @@ def create_range(self, bins, vmin, vmax):
# fill spectrum with new data
# called in addPlot and updatePlot
# dont actually draw the plot in this function
def plotPlot(self, axis, index, threshold=0.1):
def plotPlot(self, axis, index):
currentPlot = self.currentPlot
if (DEBUG):
print("Inside plotPlot")
Expand Down Expand Up @@ -2578,7 +2665,7 @@ def plotPlot(self, axis, index, threshold=0.1):
w = np.ma.masked_where(w > maxCutoff, w)
if w is None or len(w) <= 0:
return
#used in getMaxInRange to take into account also the cutoff if there is one
#used in getMinMaxInRange to take into account also the cutoff if there is one
self.setSpectrumInfo(data=w, index=index)

if dim == 1:
Expand All @@ -2589,8 +2676,9 @@ def plotPlot(self, axis, index, threshold=0.1):
else:
if (DEBUG):
print("2d case..")
if (self.wConf.button2D_option.currentText() == 'Light'):
w = np.ma.masked_where(w < threshold, w)
# color modes for later...
# if (self.wConf.button2D_option.currentText() == 'Light'):
w = np.ma.masked_where(w == 0, w)
spectrum.set_data(w)
self.setSpectrumInfo(spectrum=spectrum, index=index)
self.currentPlot = currentPlot
Expand Down Expand Up @@ -3630,15 +3718,15 @@ def applyCopy(self):
# set minZ/maxZ
if dim == 2 and (flags[3] or flags[4]):
#unlog the zlim_src because setAxisScale in updatePlot will apply log() to the limits (twice if dont unlog first...)
if scale_src_bool:
#setAxisScale dont save zlim in the dictionnary...
zmin = 10**(zlim_src[0])
zmax = 10**(zlim_src[1])
self.setSpectrumInfo(minz=zmin, index=index)
self.setSpectrumInfo(maxz=zmax, index=index)
else:
self.setSpectrumInfo(minz=zlim_src[0], index=index)
self.setSpectrumInfo(maxz=zlim_src[1], index=index)
# if scale_src_bool:
# #setAxisScale dont save zlim in the dictionnary...
# zmin = 10**(zlim_src[0])
# zmax = 10**(zlim_src[1])
# self.setSpectrumInfo(minz=zmin, index=index)
# self.setSpectrumInfo(maxz=zmax, index=index)
# else:
self.setSpectrumInfo(minz=zlim_src[0], index=index)
self.setSpectrumInfo(maxz=zlim_src[1], index=index)
self.updatePlot()
except:
pass
Expand Down Expand Up @@ -4319,3 +4407,8 @@ def __init__(self, parent=None):
mainLayout.addLayout(buttonsLayout, 2, 0, 1, 0)
self.setLayout(mainLayout)

class centeredNorm(colors.Normalize):
def __init__(self, data, vcenter=0, halfrange=None, clip=False):
if halfrange is None:
halfrange = np.max(np.abs(data - vcenter))
super().__init__(vmin=vcenter - halfrange, vmax=vcenter + halfrange, clip=clip)

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