IPKM/python3-damaris
Public Access
3
0 Fork 0
Code Issues 7 Pull Requests Actions Releases 8 Activity

added phasng for signal

Browse Source
This commit is contained in:
markusro committed 2026-10-22 00:17:01 +02:00
1 parent 12d7323851
commit 9d60eeabf6
4 files changed
+131 -24
Download Patch File Download Diff File Expand all files Collapse all files

No files matched your search

doc/manual.rst
+12
View File
@@ -107,6 +107,18 @@ There are now two possibilities to export the figure:
The plot can be navigated directly with the mouse: dragging with the left mouse button pans the view and the mouse wheel zooms in and out around the pointer position. Holding the right mouse button and dragging horizontally zooms only the x axis, dragging vertically zooms only the y axis (dragging right or up zooms in), just like the right button in the toolbar pan mode. This works on linear and logarithmic axes. The pan and zoom buttons in the toolbar below the plot are still available; while one of these toolbar modes is active, the direct mouse panning and right-button zooming are suspended so the toolbar behavior is unchanged. Note that with the autoscaling option enabled, the view is reset to the full data range whenever a new result arrives.
A horizontal slider (0-360°) with a "Phase:" label and a value read-out is available in the "Display" tab, located to the right of the "Source:" drop-down selector. This slider allows for a display-only interactive rotation of the displayed ADC_Result or Accumulation two-channel signal for visual phase correction. The rotation applies to all displayed scans and updates for the selected source.
This operation is display-only and is not written to HDF; it does not modify the result script data or affect CSV exports. The phase is reset to 0 when a new experiment or data pool is loaded. It is inert for data with a single channel or non-signal sources (e.g., TemperatureResult). Note that error bars and statistics are deliberately not rotated, so with the statistics option enabled and a non-zero phase, the error envelope will no longer bracket the rotated curve. For 90°, 180°, and 270° steps, the exact fast path in the phase calculation is used to avoid rounding noise.
The same rotation is available programmatically via the ``phase()`` method of the ``accu`` (Accumulation) and ``timesignal`` (ADC_Result) objects, which returns a rotated copy of the data without modifying the original object.
.. code-block:: python
:caption: Example of programmatic phase rotation
:linenos:
rotated = accu.phase(90) # returns a rotated copy, accu is unchanged
data["Rotated"] = rotated
Help Menu
=========
src/damaris/gui/DamarisGUI.py
+71 -23
View File
@@ -717,8 +717,6 @@ class DamarisGUI:
# cleanup
self.si = None
if self.monitor.overflow_job_ids:
logger.warning( "ADC overflow occurred in jobs: %s", ', '.join( [str( j ) for j in self.monitor.overflow_job_ids] ))
self.state = DamarisGUI.Edit_State
self.sw.enable_editing( )
self.toolbar_run_button.set_sensitive( True )
@@ -922,8 +920,6 @@ class DamarisGUI:
self.lockfile.del_experiment(self.id)
# now everything is stopped
if self.monitor.overflow_job_ids:
logger.warning( "ADC overflow occurred in jobs: %s", ', '.join( [str( j ) for j in self.monitor.overflow_job_ids] ))
self.state = DamarisGUI.Edit_State
self.sw.enable_editing( )
self.toolbar_run_button.set_sensitive( True )
@@ -2979,7 +2975,6 @@ class MonitorWidgets:
css.load_from_data( b".adc_ok { background-image: none; background-color: #4caf50; }"
b".adc_error { background-image: none; background-color: #e53935; }" )
gtk.StyleContext.add_provider_for_screen( gdk.Screen.get_default( ), css, gtk.STYLE_PROVIDER_PRIORITY_APPLICATION )
self.overflow_css = css
self.overflow_indicator_button = gtk.Button( label="ADC" )
self.overflow_indicator_button.set_tooltip_text( "ADC overflow indicator, red if an overflow occurred" )
self.overflow_job_ids = [ ]
@@ -3062,6 +3057,11 @@ class MonitorWidgets:
self.display_source_combobox.add_attribute( display_source_cell, 'text', 0 )
# GTK3 fix: Prevent blank space from child tree nodes in popup
self.display_source_combobox.set_wrap_width(1)
# interactive display phase rotation: display only, never stored in HDF
self.display_phase_scale = self.xml_gui.get_object( "display_phase_scale" )
self.display_phase_value_label = self.xml_gui.get_object( "display_phase_value_label" )
self.display_phase = 0
self.display_phase_scale.connect( "value-changed", self.display_phase_changed )
self.source_list_reset( )
self.display_source_path_label = self.xml_gui.get_object( "display_source_path_label" )
@@ -3095,6 +3095,7 @@ class MonitorWidgets:
self.source_list_cache = {}
def source_list_reset( self ):
self.display_phase_scale.set_value( 0 )
self.display_source_combobox.set_model(None)
try:
# OPTIMIZATION: Replacing the TreeStore is much faster than clear() for large trees
@@ -3463,6 +3464,25 @@ class MonitorWidgets:
event = DataPool.Event( DataPool.Event.updated_value, new_data_name )
glib.idle_add(self.datapool_idle_listener, event, priority=glib.PRIORITY_DEFAULT_IDLE )
def display_phase_changed( self, widget, data=None ):
"""
set the display phase in degrees (0-360) for the plotted signal
Example: monitor.display_phase_scale.set_value(90)
"""
self.display_phase = widget.get_value( )
self.display_phase_value_label.set_label( "%.0f°" % self.display_phase )
source = self.displayed_data[ 1 ]
if source is not None and isinstance( source, (Accumulation, ADC_Result) ) \
and source.get_number_of_channels( ) == 2:
# coalesce like the other display updates, dragging the slider
# emits one event per pointer motion
self.update_counter_lock.acquire( )
self.update_counter += 1
self.update_counter_lock.release( )
glib.idle_add( self.update_display_idle_event, self.displayed_data[ 0 ][ : ],
priority=glib.PRIORITY_DEFAULT_IDLE )
def display_autoscaling_toggled( self, widget, data=None ):
self.matplot_axes.set_autoscale_on( self.display_autoscaling_checkbutton.get_active( ) )
if self.displayed_data[ 0 ] is not None:
@@ -3737,7 +3757,7 @@ class MonitorWidgets:
Set the background color of the ADC indicator button: green if
clipped is False, red if clipped is True.
>>> monitor.set_overflow_indicator(True) # button turns red
Example: monitor.set_overflow_indicator(True)
"""
style = self.overflow_indicator_button.get_style_context( )
style.remove_class( "adc_ok" )
@@ -3750,7 +3770,7 @@ class MonitorWidgets:
the list of job ids where an ADC overflow occurred, right click
opens a menu to reset the overflow state.
>>> monitor.overflow_indicator_button_press(button, event)
Example: monitor.overflow_indicator_button_press(button, event)
"""
if event.button == 1:
if self.overflow_job_ids:
@@ -3760,7 +3780,7 @@ class MonitorWidgets:
dialog = gtk.MessageDialog(parent=self.main_window,
type=gtk.MessageType.WARNING,
flags=gtk.DialogFlags.MODAL,
buttons=("_OK", gtk.ResponseType.OK))
buttons=gtk.ButtonsType.OK)
dialog.set_markup("ADC OVERFLOW in jobs:")
dialog.format_secondary_text( text )
dialog.run( )
@@ -3776,11 +3796,11 @@ class MonitorWidgets:
def clear_overflow_indicator( self, widget=None, event=None ):
"""
Reset handler for the ADC overflow warning: sets the circle back to
Reset handler for the ADC overflow warning: sets the indicator back to
green and clears the status bar warning, without starting a new
experiment.
>>> monitor.clear_overflow_indicator()
Example: monitor.clear_overflow_indicator()
"""
self.statusbar_overflow_label.set_text( "" )
self.set_overflow_indicator( False )
@@ -3885,11 +3905,41 @@ class MonitorWidgets:
return
if isinstance( in_result, Accumulation ) or isinstance( in_result, ADC_Result ) or isinstance( in_result, TemperatureResult ):
xmin = in_result.get_xmin( )
xmax = in_result.get_xmax( )
plot_result = in_result
if self.display_phase and isinstance( in_result, (Accumulation, ADC_Result) ) \
and in_result.get_number_of_channels( ) == 2:
# display only: plot a rotated copy, the pool object itself and
# any HDF storage keep the unrotated data. The rotation reads
# the raw channel arrays, so take the snapshot while holding the
# lock that the result scripts use to update them in place.
in_result.lock.acquire( )
try:
plot_result = in_result.phase( self.display_phase )
finally:
in_result.lock.release( )
if isinstance( plot_result, Accumulation ):
# the copy's y_square is not rotated, so its own error
# calculation would produce nonsense limits
plot_result.use_error = False
ymin = in_result.get_ymin( )
ymax = in_result.get_ymax( )
# error bars are read from the pool object, i.e. they are not
# phase rotated, and the rotated copy would derive them from
# mismatched y_square anyway
show_errors = (self.display_statistics_checkbutton.get_active( ) and
in_result.uses_statistics( ) and in_result.ready_for_drawing_error( ))
xmin = plot_result.get_xmin( )
xmax = plot_result.get_xmax( )
ymin = plot_result.get_ymin( )
ymax = plot_result.get_ymax( )
if plot_result is not in_result and show_errors:
# the plot draws the unrotated pool errors on the rotated data,
# so the axis limits must use that same combination
for i in range( plot_result.get_number_of_channels( ) ):
err = in_result.get_yerr( i )
ymin = min( ymin, (plot_result.get_ydata( i ) - err).min( ) )
ymax = max( ymax, (plot_result.get_ydata( i ) + err).max( ) )
# Initial rescaling needed?
if self.__rescale:
@@ -3900,7 +3950,7 @@ class MonitorWidgets:
self.matplot_axes.set_xscale( "linear" )
self.matplot_axes.set_xlim(xmin, xmax)
elif x_scale == "log10":
xminpos = in_result.get_xminpos( )
xminpos = plot_result.get_xminpos( )
self.matplot_axes.set_xscale("log", base=10, nonpositive="mask")
self.matplot_axes.set_xlim(xminpos, xmax)
elif x_scale == "ppm":
@@ -3914,7 +3964,7 @@ class MonitorWidgets:
self.matplot_axes.set_yscale( "linear" )
self.matplot_axes.set_ylim(ymin, ymax)
elif y_scale == "log10":
yminpos = in_result.get_yminpos()
yminpos = plot_result.get_yminpos()
self.matplot_axes.set_yscale("log", base=10, nonpositive="mask")
self.matplot_axes.set_ylim( yminpos, ymax )
self.__rescale = False
@@ -3954,14 +4004,14 @@ class MonitorWidgets:
ylim_max > ymax + 0.2 * ydiff or ylim_min < ymin - 0.2 * ydiff):
self.matplot_axes.set_ylim(ymin, ymax)
xdata = in_result.get_xdata( )
chans = in_result.get_number_of_channels( )
xdata = plot_result.get_xdata( )
chans = plot_result.get_number_of_channels( )
data = [ ]
colors = [ (0, 0, 0.8, 1), (0.7, 0, 0, 1), (0, 0.7, 0, 1), (0.7, 0.5, 0, 1),
(0, 0, 0, 1) ] # rgba tuples: blue, red, green, yellow
for i in range( chans ):
data.append( in_result.get_ydata( i ) )
data.append( plot_result.get_ydata( i ) )
moving_average = data_slice = None
if max_points_to_display > 0 and len( xdata ) > max_points_to_display:
@@ -3990,8 +4040,7 @@ class MonitorWidgets:
self.graphen[ i ].set_data( xdata, data[ i ] )
# Statistics activated?
if (self.display_statistics_checkbutton.get_active( ) and
in_result.uses_statistics( ) and in_result.ready_for_drawing_error( )):
if show_errors:
for i in range( chans ):
err = in_result.get_yerr( i )
if moving_average is not None:
@@ -4067,11 +4116,10 @@ class MonitorWidgets:
# the warning is only justified for results with a valid job_id;
# results without job id (e.g. backend errors) only get the plot marker
if getattr(in_result, "job_id", None) is not None:
if self.statusbar_overflow_label.get_text() == "":
self.statusbar_overflow_label.set_markup('<span foreground="red" weight="bold">ADC OVERFLOW</span>')
self.set_overflow_indicator( True )
if in_result.job_id not in self.overflow_job_ids:
self.overflow_job_ids.append( in_result.job_id )
self.statusbar_overflow_label.set_markup( '<span foreground="red" weight="bold">ADC OVERFLOW</span>' )
logger.warning( "ADC overflow detected in job %s", in_result.job_id )
elif self.clipping_marker is not None:
try:
src/damaris/gui/damaris3.glade
+47
View File
@@ -37,6 +37,12 @@
<property name="step-increment">1</property>
<property name="page-increment">1</property>
</object>
<object class="GtkAdjustment" id="display_phase_adjustment">
<property name="upper">360</property>
<property name="value">0</property>
<property name="step-increment">1</property>
<property name="page-increment">10</property>
</object>
<object class="GtkMenu" id="documentation_menu">
<property name="visible">True</property>
<property name="can-focus">False</property>
@@ -1096,6 +1102,47 @@ Public License instead of this License.
<property name="position">1</property>
</packing>
</child>
<child>
<object class="GtkLabel" id="display_phase_label">
<property name="visible">True</property>
<property name="can-focus">False</property>
<property name="label" translatable="yes"> Phase:</property>
</object>
<packing>
<property name="expand">False</property>
<property name="fill">False</property>
<property name="position">2</property>
</packing>
</child>
<child>
<object class="GtkScale" id="display_phase_scale">
<property name="visible">True</property>
<property name="can-focus">True</property>
<property name="width-request">150</property>
<property name="draw-value">False</property>
<property name="digits">0</property>
<property name="round-digits">0</property>
<property name="adjustment">display_phase_adjustment</property>
</object>
<packing>
<property name="expand">False</property>
<property name="fill">False</property>
<property name="position">3</property>
</packing>
</child>
<child>
<object class="GtkLabel" id="display_phase_value_label">
<property name="visible">True</property>
<property name="can-focus">False</property>
<property name="label" translatable="yes">0°</property>
<property name="width-chars">4</property>
</object>
<packing>
<property name="expand">False</property>
<property name="fill">False</property>
<property name="position">4</property>
</packing>
</child>
</object>
<packing>
<property name="y-options"/>
tests/res_test.py
+1 -1
View File
@@ -11,7 +11,6 @@ def result():
accu = Accumulation(error=False)
for num,ts in enumerate(results):
data["accu"] = accu
data["data/ts %i"%num] = ts+0
ts.write_to_hdf(h5, "/", f"adc_{num}", f"adc_{num}")
data["fft"] = (ts+0).fft()
@@ -32,6 +31,7 @@ def result():
data["test/fit"] = fit
data["test"] = r
accu+=ts
data["accu"] = accu+0
print(accu)
data["accu_fft"] = accu.fft().autophase()
accu.write_to_hdf(h5, "/", "name", "title")