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Workaround for bug in fontspin control when resizing GUI when changin…
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…g font size by implementing QDoubleSpinBox.mouseReleaseEvent() as a signal rather than using buggy valueChanged().

Bug fix for scaling radii properly according to data values
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@Oeffner
Oeffner committed Jul 30, 2022
1 parent b906a8c commit ea59614
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Showing 4 changed files with 55 additions and 26 deletions.
28 changes: 20 additions & 8 deletions crys3d/hklviewer/HKLviewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@
except Exception as e: # if invoked by a generic python that doesn't know cctbx modules
from . import hklviewer_gui
from .helpers import ( MillerArrayTableView, MillerArrayTableForm, MyhorizontalHeader,
MillerArrayTableModel, MPLColourSchemes, MillerTableColumnHeaderDialog )
MillerArrayTableModel, MPLColourSchemes, MillerTableColumnHeaderDialog, MyQDoubleSpinBox )


class MakeNewDataForm(QDialog):
Expand Down Expand Up @@ -78,22 +78,27 @@ def __init__(self, parent=None):
self.aboutlabel.setWordWrap(True)
self.aboutlabel.setTextInteractionFlags(Qt.TextBrowserInteraction);
self.aboutlabel.setOpenExternalLinks(True);
self.aboutlabel.setMaximumSize(QSize(16777215, 16777215))
self.writeAboutstr("")
self.copyrightstxt = QTextEdit()
self.copyrightstxt.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOn)
self.copyrightstxt.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOn)
self.copyrightstxt.setReadOnly(True)
self.copyrightstxt.setLineWrapMode(QTextEdit.LineWrapMode.NoWrap)
self.copyrightstxt.setMinimumSize(QSize(400, 100))
self.copyrightstxt.setMaximumSize(QSize(16777215, 16777215))
sp = QSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred)
self.copyrightstxt.setMinimumSize(QSize(350, 150))
self.copyrightstxt.setSizePolicy(sp)
self.aboutlabel.setSizePolicy(sp)
self.OKbtn = QPushButton()
self.OKbtn.setText("OK")
self.OKbtn.clicked.connect(self.onOK)
mainLayout.addWidget(self.aboutlabel, 0, 0, 1, 3)
mainLayout.addWidget(self.copyrightstxt, 1, 0, 1, 3)
mainLayout.addWidget(self.OKbtn, 2, 1, 1, 1)
self.setLayout(mainLayout)
self.setMinimumSize(QSize(350, 200))
self.setMinimumSize(QSize(400, 300))
self.setSizePolicy(sp)
self.setFixedSize( self.sizeHint() )
def writeAboutstr(self, versionstr):
aboutstr = """<html><head/><body><p>
Expand Down Expand Up @@ -318,13 +323,17 @@ def __init__(self, thisapp, isembedded=False): #, cctbxpython=None):
self.mousesensitxtbox = QLineEdit('')
self.mousesensitxtbox.setReadOnly(True)

self.fontspinBox = QDoubleSpinBox()
self.fontspinBox = MyQDoubleSpinBox()
self.fontspinBox.setSingleStep(1)
self.fontspinBox.setRange(4, 50)
self.font = QFont()
self.font.setFamily(self.font.defaultFamily())
self.fontspinBox.setValue(self.font.pointSize())
self.fontspinBox.valueChanged.connect(self.onFontsizeChanged)
self.fontspinBox.editingFinished.connect(self.onFontsizeChanged)
# valueChanged signal is buggy and gets triggered twice when onFontsizeChanged takes too long
# This may cause font step=2 rather than step=1
# Workaround is to use onMouseRelease invoked by MyQDoubleSpinBox.mouseReleaseEvent
self.fontspinBox.onMouseRelease = self.onFontsizeChanged
self.Fontsize_labeltxt = QLabel()
self.Fontsize_labeltxt.setText("Font size:")

Expand Down Expand Up @@ -678,7 +687,7 @@ def onSaveReflectionFile(self):
def SettingsDialog(self):
self.settingsform.show()
# don't know why valueChanged.connect() method only takes effect from here on
self.fontspinBox.valueChanged.connect(self.onFontsizeChanged)
#self.fontspinBox.valueChanged.connect(self.onFontsizeChanged)
self.settingsform.activateWindow()


Expand Down Expand Up @@ -1297,7 +1306,8 @@ def onShowTooltips(self, val):
self.ttip_click_invoke = "hover"


def onFontsizeChanged(self, val):
def onFontsizeChanged(self):
val = self.fontspinBox.value()
font = self.app.font()
font.setPointSize(val);
self.fontsize = val
Expand All @@ -1311,6 +1321,7 @@ def onFontsizeChanged(self, val):
self.textAlerts.setFont(font)
self.SpaceGrpUCellText.setFont(font)


def onBrowserFontsizeChanged(self, val):
self.browserfontsize = val
self.send_message("NGL.fontsize = %d" %val)
Expand Down Expand Up @@ -2436,8 +2447,9 @@ def UsePersistedQsettings(self):
self.onTextbufferSizeChanged(int(self.textinfosize))
self.bufsizespinBox.setValue(int(self.textinfosize))
if self.fontsize is not None:
self.onFontsizeChanged(int(self.fontsize))
#self.onFontsizeChanged(int(self.fontsize))
self.fontspinBox.setValue(int(self.fontsize))
self.onFontsizeChanged()
if self.browserfontsize is not None:
self.onBrowserFontsizeChanged(int(self.browserfontsize))
self.browserfontspinBox.setValue(int(self.browserfontsize))
Expand Down
33 changes: 18 additions & 15 deletions crys3d/hklviewer/display2.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ def generate_systematic_absences(array,
return absence_array


def nth_power_scale(dataarray, nth_power):
def nth_power_scale(dataarray, nth_power, is_sigmas=False):
"""
set nth_power to a number for dampening or enhancing the
difference between the smallest and the largest values.
Expand All @@ -65,14 +65,18 @@ def nth_power_scale(dataarray, nth_power):
If nth_power=NaN then an automatic value is computed that maps the smallest
values to 0.1 of the largest values
"""
absdat = flex.abs(dataarray).as_double()
absdat2 = graphics_utils.NoNansArray(absdat) # much faster than flex.double([e for e in absdat if not math.isnan(e)])
maxdat = flex.max(absdat2)
mindat = max(1e-10*maxdat, flex.min(absdat2) )
maxdat = flex.max(dataarray)
mindat = flex.min(dataarray)
offset = mindat - 0.001 # avoid log(0)
offsetmin = mindat - offset
offsetmax = maxdat - offset
offsetarr = dataarray - offset
# only autoscale for sensible values of maxdat and mindat
if math.isnan(nth_power) and maxdat > mindat : # amounts to automatic scale
nth_power = math.log(0.2)/(math.log(mindat) - math.log(maxdat))
datascaled = flex.pow(absdat, nth_power)
nth_power = math.log(10)/(math.log(offsetmax) - math.log(offsetmin))
if is_sigmas:
nth_power *= -1.0 # want small sigmas to have larger radii and large sigmas to have smaller radii
datascaled = flex.pow(offsetarr, nth_power)
return datascaled, nth_power


Expand Down Expand Up @@ -352,25 +356,26 @@ def generate_view_data(self):
# assuming last part of the labels indicates the phase label as in ["FCALC","PHICALC"]
self.colourlabel = "Phase of " + self.miller_array.info().label_string()
elif (settings.sigma_color_radius) and sigmas is not None:
data_for_colors = sigmas.as_double()
data_for_colors = 1.0/sigmas.as_double()
self.colourlabel = "Sigma of " + self.miller_array.info().label_string()
else :
data_for_colors = flex.abs(data.deep_copy())

uc = self.work_array.unit_cell()
self.min_dist = min(uc.reciprocal_space_vector((1,1,1))) * self.renderscale
min_radius = 0.05 * self.min_dist
max_radius = 0.5 * self.min_dist
if (settings.sigma_color_radius) and sigmas is not None:
data_for_radii, self.nth_power_scale_radii = nth_power_scale(flex.abs(sigmas.as_double().deep_copy()),
settings.nth_power_scale_radii)
data_for_radii, self.nth_power_scale_radii = nth_power_scale(sigmas.as_double().deep_copy(),
settings.nth_power_scale_radii, True)
else :
data_for_radii, self.nth_power_scale_radii = nth_power_scale(flex.abs(data.deep_copy()),
data_for_radii, self.nth_power_scale_radii = nth_power_scale(data.deep_copy(),
settings.nth_power_scale_radii)
if (settings.slice_mode):
data = data.select(self.slice_selection)
# Computing rgb colours of each reflection is slow so make a small array
# of precomputed colours to use as a lookup table for each reflection
if isinstance(data, flex.complex_double):
if isinstance(data, flex.complex_double): # map coefficients are coloured by phase values
COL = MplColorHelper(settings.color_scheme, 0, 360)
rgbcolarray = [ COL.get_rgb(d)[0:3] for d in range(360) ]
if self.isUsingFOMs():
Expand Down Expand Up @@ -409,8 +414,7 @@ def generate_view_data(self):
colors = colors.select(self.slice_selection)
data_for_radii = data_for_radii.select(self.slice_selection)
if len(data_for_radii):
#dat2 = flex.abs(flex.double([e for e in data_for_radii if not math.isnan(e)]))
dat2 = flex.abs(flex.double( graphics_utils.NoNansArray( data_for_radii, 0.1 ) ))
dat2 = flex.double( graphics_utils.NoNansArray( data_for_radii, 0.1 ) )
# don't divide by 0 if dealing with selection of Rfree array where all values happen to be zero
scale = max_radius/(flex.max(dat2) + 0.001)
radii = data_for_radii * (self.settings.scale * scale)
Expand All @@ -424,7 +428,6 @@ def generate_view_data(self):
self.colors = colors
if isinstance(data, flex.complex_double):
self.foms = foms_for_colours
#print(min_dist, min_radius, max_radius, flex.min(data_for_radii), flex.max(data_for_radii), scale)


def isUsingFOMs(self):
Expand Down
13 changes: 10 additions & 3 deletions crys3d/hklviewer/helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from .qt import QCursor, QKeySequence
from .qt import ( QAbstractItemView, QCheckBox, QTableWidget, QAction, QDoubleSpinBox,
QMenu, QTableView, QDialog, QSpinBox, QLabel, QComboBox, QGridLayout, QGroupBox,
QScrollArea, QVBoxLayout, QHeaderView, QTableWidgetItem
QScrollArea, QVBoxLayout, QHeaderView, QTableWidgetItem, QSizePolicy
)
import math, csv
from io import StringIO
Expand All @@ -24,10 +24,16 @@ def stepBy(self, steps):
QDoubleSpinBox.stepBy(self, steps)
if hasattr(self, "onStepBy"):
self.onStepBy()
def mouseReleaseEvent(self, event):
# used by NGL_HKLViewer.fontspinBox since changing fonts and resizing windows is slow and
# valueChanged() will then mistakenly be fired twice when clicking once on the spin control
QDoubleSpinBox.mouseReleaseEvent(self, event)
if hasattr(self, "onMouseRelease"):
self.onMouseRelease()


class MyhorizontalHeader(QHeaderView):
# Assigned to HeaderDataTableWidget (HKLViewer.NGL_HKLViewer.millertable) but in
# Assigned to HeaderDataTableWidget (NGL_HKLViewer.millertable) but in
# NGL_HKLViewer.createFileInfoBox() as to avoid a very long chain of parents when
# accessing select_millertable_column_dlg()
# Display the labels of the columns in the millertable
Expand Down Expand Up @@ -295,14 +301,15 @@ def __init__(self, parent=None, width=5, height=4, dpi=dpi):
# total size of canvas
self.fig.set_size_inches(7,40) # total size of canvas
super(MplCanvas, self).__init__(self.fig)
cid = self.fig.canvas.mpl_connect('button_press_event', self.on_press)
self.cid1 = self.fig.canvas.mpl_connect('button_press_event', self.on_press)

def on_press(self, event):
if event.inaxes is not None:
self.parent.selcolmap = cmaps[event.inaxes.get_subplotspec().rowspan.start]
self.parent.updatelabel()
self.parent.EnactColourMapSelection()


# TODO work out scaling of canvas to match QApplication.setAttribute(Qt.AA_EnableHighDpiScaling)
# and
class MPLColourSchemes(QtWidgets.QDialog):
Expand Down
7 changes: 7 additions & 0 deletions crys3d/hklviewer/jsview_3d.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -342,9 +342,11 @@ def update_settings(self, diff_phil, curphilparam) :

if has_phil_path(diff_phil, "color_scheme"):
self.add_colour_scheme_to_dict()
self.sceneisdirty = True

if has_phil_path(diff_phil, "color_powscale"):
self.add_colour_powscale_to_dict()
self.sceneisdirty = True

if has_phil_path(diff_phil, "nth_power_scale_radii"):
self.add_nth_power_scale_radii_to_dict()
Expand Down Expand Up @@ -1363,6 +1365,11 @@ def getprecision(v1,v2):
self.calc_rotation_axes()
nvaluelabels = int(ln/self.params.viewer.ncolourlabels )
colourgradstrs = []
if self.params.hkls.sigma_color_radius:
lst = list(colourscalararray)
lst.reverse() # flip labels on chart when showing sigmas
colourscalararray = flex.double(lst )

# if displaying phases from map coefficients together with fom values then
for g,colourgradarray in enumerate(colourgradarrays):
self.colourgradientvalues = []
Expand Down

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