IPKM/python3-damaris
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add FitResult fit overlays and close leaked HDF5 files after experiment stop
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FitResult is a new Drawable in damaris.data with x-values independent of
the measured points, so fits can be sampled on a dense grid. It is stored
as its own data pool entry (e.g. "measurement/fit"), written to and read
from the HDF5 data pool (damaris_type "FitResult", params as attributes),
and drawn by the GUI as overlay on its measurement, including a fit
parameter text box. Fits get no entry in the display tree, so measurement
rows stay directly selectable. Result scripts create them via
FitResult(x, y, title, source, params).

Additionally, HDF5 files that experiment or result scripts left open
(e.g. after a script failure) are closed when the experiment stops.
pytables keeps such handles registered process-wide, which blocked
reopening the dump file and the scripts' own files on the next run.

Generated by Mistral Vibe.
Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
This commit is contained in:
markusro committed 2026-10-18 17:11:05 +02:00
1 parent 947c4c7f8d
commit ab943c30ae
7 files changed
+296 -5
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src/damaris/gui/DamarisGUI.py
+117 -3
View File
@@ -90,7 +90,7 @@ from damaris.gui import ResultReader, ResultHandling
from damaris.gui import BackendDriver
#from damaris.gui.gtkcodebuffer import CodeBuffer, SyntaxLoader
#from damaris.data import Drawable # this is a base class, it should be used...
from damaris.data import DataPool, Accumulation, ADC_Result, MeasurementResult, TemperatureResult
from damaris.data import DataPool, Accumulation, ADC_Result, MeasurementResult, TemperatureResult, FitResult
# TemperatureMonitor imported lazily to avoid circular import issues
# default, can be set to true from start script
@@ -895,6 +895,11 @@ class DamarisGUI:
dump_size = os.stat( self.dump_filename ).st_size / 1e6
logger.info("Done (%.1f s, %.1f MB)", time.time( ) - self.dump_start_time, dump_size)
# close hdf5 files that the scripts left open (e.g. after a
# script failure), otherwise pytables keeps them registered
# as open and they block the next experiment run
self.close_left_open_hdf5_files( )
# keep data to display but throw away everything else
self.si = None
# delete lock file so that other experiment can start
@@ -1113,6 +1118,26 @@ class DamarisGUI:
return True
def close_left_open_hdf5_files( self ):
"""
close hdf5 files that experiment or result scripts left open,
e.g. after a script failure; pytables keeps such files registered
as open, so they cannot be reopened in the next experiment run
"""
open_files = getattr( tables.file, "_open_files", None )
if open_files is None:
return
if hasattr( open_files, "handlers" ):
filehandles = list( open_files.handlers )
else:
filehandles = list( open_files.values( ) )
for filehandle in filehandles:
try:
logger.warning( "Closing hdf5 file left open by script: %s", filehandle.filename )
filehandle.close( )
except Exception:
pass
def pause_experiment( self, widget, data=None ):
"""
pause experiment execution (that means delay backend and let others run)
@@ -3101,6 +3126,8 @@ class MonitorWidgets:
self.update_counter = 0
self.update_counter_lock = threading.Lock( )
self.description_text = None
self.fitresultlines = [ ]
self.fit_source_keys = set( )
self.clipping_marker = None
self.source_list_cache = {}
@@ -3260,6 +3287,7 @@ class MonitorWidgets:
self.source_list_reset( )
self.__rescale = True
self.displayed_data = [ None, None ]
self.fit_source_keys = set( )
self.display_source_path_label.set_label( "" )
self.clear_display( )
@@ -3389,9 +3417,18 @@ class MonitorWidgets:
self.renew_display( )
new_data_struct = None
elif event.what == DataPool.Event.new_key:
# update combo-box by inserting and rely on consistent information
self.source_list_add( event.subject )
if isinstance( self.data_pool.get( event.subject ), FitResult ):
# fits are shown as overlay on their measurement only,
# they do not get their own entry in the display tree
self.fit_source_keys.add( event.subject )
else:
# update combo-box by inserting and rely on consistent information
self.source_list_add( event.subject )
elif event.what == DataPool.Event.deleted_key:
if event.subject in self.fit_source_keys:
# fit entries are not in the display tree
self.fit_source_keys.discard( event.subject )
return
# update combo-box by removing and rely on consistent information
if (self.displayed_data[ 0 ] is not None and
self.displayed_data[ 0 ] == event.subject):
@@ -3724,6 +3761,15 @@ class MonitorWidgets:
self.measurementresultgraph = None
self.matplot_axes.clear( )
self.matplot_axes.grid( True )
if not hasattr( self, "fitresultlines" ):
self.fitresultlines = [ ]
elif self.fitresultlines:
for line in self.fitresultlines:
try:
line.remove( )
except:
pass
self.fitresultlines = [ ]
if not hasattr( self, "graphen" ):
self.graphen = [ ]
elif self.graphen:
@@ -3966,10 +4012,36 @@ class MonitorWidgets:
self.matplot_axes.lines.remove( self.measurementresultline[ 0 ] )
self.measurementresultline = None
# remove fit overlay lines
for line in self.fitresultlines:
try:
line.remove( )
except:
pass
self.fitresultlines = [ ]
# collect fits belonging to this measurement:
# either by source attribute or by nested data pool key
displayed_key = self.displayed_data[ 0 ]
fit_results = [ ]
for key in self.data_pool.keys( ):
if key == displayed_key:
continue
fit = self.data_pool.get( key )
if isinstance( fit, FitResult ) and \
(fit.source == displayed_key or key.startswith( displayed_key + "/" )):
fit_results.append( (key, fit) )
fit_results.sort( key=lambda key_fit: key_fit[ 0 ] )
fit_xydata = [ fit.get_lineplotdata( ) for key, fit in fit_results ]
[ k, v, e ] = in_result.get_errorplotdata( )
if k.shape[ 0 ] != 0:
xmin = k.min( )
ymin = (v - e).min( )
for fx, fy in fit_xydata:
if fx.shape[ 0 ] != 0:
xmin = min( xmin, fx.min( ) )
ymin = min( ymin, fy.min( ) )
if xmin > 0:
self.display_x_scaling_combobox.set_sensitive( True )
@@ -3997,6 +4069,10 @@ class MonitorWidgets:
if self.__rescale: # or self.display_autoscaling_checkbutton.get_active():
xmax = k.max( )
ymax = (v + e).max( )
for fx, fy in fit_xydata:
if fx.shape[ 0 ] != 0:
xmax = max( xmax, fx.max( ) )
ymax = max( ymax, fy.max( ) )
# is there a range problem?
if xmin == xmax or ymin == ymax:
# fix range and scaling problems
@@ -4038,6 +4114,44 @@ class MonitorWidgets:
if k.shape[ 0 ] != 0 and v.shape == k.shape:
self.measurementresultline = self.matplot_axes.plot( k, v, 'r-' )
# draw the fits as overlay lines
fit_colors = [ "green", "purple", "darkorange" ]
for i, (fx, fy) in enumerate( fit_xydata ):
if fx.shape[ 0 ] != 0 and fy.shape == fx.shape:
self.fitresultlines.extend(
self.matplot_axes.plot( fx, fy, "-",
color=fit_colors[ i % len( fit_colors ) ],
linewidth=1.5 ) )
# show fit parameters
description_lines = [ ]
for fit_key, fit in fit_results:
if fit.params:
if len( fit_results ) > 1:
description_lines.append( str( fit.get_title( ) or fit_key ) )
for param_key in fit.params:
param_value = fit.params[ param_key ]
if isinstance( param_value, float ):
description_lines.append( "%s = %.4g" % (param_key, param_value) )
else:
description_lines.append( "%s = %s" % (param_key, param_value) )
if description_lines:
description_string = "\n".join( description_lines )
if self.description_text is None:
self.description_text = self.matplot_axes.text(0.98, 0.95, description_string,
size=10,
transform=self.matplot_axes.transAxes,
va='top', ha='right', ma='left',
bbox=dict(facecolor='lightgray', alpha=0.5, boxstyle='round,pad=0.2'))
else:
self.description_text.set_text( description_string )
elif self.description_text is not None:
try:
self.description_text.remove()
except:
pass
self.description_text = None
# Any title to be set?
title = in_result.get_title( ) + ""