Fixing the log plot options (Fixes #7)

src/data/Drawable.py

@@ -2,6 +2,9 @@
 
 import threading
 
+import numpy as np
+
+
 #############################################################################
 #                                                                           #
 # Name: Class Drawable                                                      #
@@ -136,6 +139,11 @@ class Drawable:
         "Returns minimun of x"
         return self.x.min()
 
+    def get_xminpos(self):
+        "Returns smallest positive value of x"
+        mask = self.x > 0
+        return self.x[mask].min()
+
     def set_xmin(self, xmin):
         "Sets minimum of x"
         self.xmin = xmin
@@ -155,6 +163,19 @@ class Drawable:
         else:
             return self.y.min()
 
+    def get_yminpos(self):
+        "Returns smallest positive value of y"
+        if type(self.y) == type([]):
+            ymins = []
+            for ys in self.y:
+                mask = ys > 0
+                ymins.append(ys[mask].min())
+            ymin = min(ymins)
+        else:
+            mask = self.y > 0
+            ymin = y[mask].min()
+        return ymin
+
     def set_ymin(self, ymin):
         "Sets minimum of y"
         self.ymin = ymin

src/gui/DamarisGUI.py

@@ -5,11 +5,9 @@ import math
 import sys
 import platform
 import io
-import codecs
 import os.path
 import traceback
 import tables
-import types
 import xml.parsers.expat
 import threading
 import webbrowser
@@ -23,7 +21,8 @@ gi.require_version('GtkSource', '3.0')
 # import 3rd party modules
 # gui graphics
 from gi.repository import GObject as gobject
-import sqlite3,uuid
+import sqlite3
+import uuid
 
 from gi.repository import Gtk as gtk
 
@@ -37,7 +36,6 @@ from gi.repository import GtkSource as gtksourceview2
 gobject.type_register(gtksourceview2.View)
 
 from gi.repository import Pango as pango
-import cairo
 
 # array math
 import numpy
@@ -756,7 +754,7 @@ class DamarisGUI:
             # create new dump file name
             try:
                 self.dump_filename = actual_config.get( "data_pool_name" ) % extensions_dict
-            except ValueError as e:
+            except ValueError:
                 print("invalid formating character in '" + actual_config.get( "data_pool_name" ) + "'")
                 self.dump_filename = "DAMARIS_data_pool.h5"
                 print("reseting dumpfile to " + self.dump_filename)
@@ -1352,7 +1350,7 @@ get_job_id get_description set_description get_xdata get_ydata set_xdate set_yda
             return 0
 
         current_page = self.main_notebook.get_current_page( )
-        if not current_page in [ 0, 1 ]:
+        if current_page not in [ 0, 1 ]:
             return 0
         script = self.get_scripts( )[ current_page ]
         try:
@@ -2441,7 +2439,7 @@ class MonitorWidgets:
         register a listener and save reference to data
         assume to be in gtk/gdk lock
         """
-        if not self.data_pool is None:
+        if self.data_pool is not None:
             # maybe some extra cleanup needed
             print("ToDo: cleanup widgets")
             if self.displayed_data[ 1 ] is not None and hasattr( self.displayed_data[ 1 ], "unregister_listener" ):
@@ -2588,7 +2586,7 @@ class MonitorWidgets:
         elif event.what == DataPool.Event.deleted_key:
             # update combo-box by removing and rely on consistent information
             gdk.threads_enter( )
-            if (not self.displayed_data[ 0 ] is None and
+            if (self.displayed_data[ 0 ] is not None and
                         self.displayed_data[ 0 ] == event.subject):
                 self.displayed_data = [ None, None ]
                 none_iter = self.source_list_find( [ 'None' ] )
@@ -2875,13 +2873,20 @@ class MonitorWidgets:
         self.display_y_scaling_combobox.set_sensitive( True )
         x_scale = self.display_x_scaling_combobox.get_active_text()
         y_scale = self.display_y_scaling_combobox.get_active_text()
+
         if x_scale == "lin":
             self.matplot_axes.set_xscale("linear")
         elif x_scale == "log10":
-            self.matplot_axes.set_xscale("log", basex=10, nonposx="mask")
+            self.matplot_axes.set_xscale("log", base=10, nonpositive="mask")
         elif x_scale == "ppm":
             self.matplot_axes.set_xscale("linear")
             self.matplot_axes.invert_xaxis()
+
+        if y_scale == "lin":
+            self.matplot_axes.set_yscale("linear")
+        elif y_scale == "log10":
+            self.matplot_axes.set_yscale("log", base=10, nonpositive="mask")
+
         if not hasattr( self, "__rescale" ):
             self.__rescale = True
 
@@ -2930,8 +2935,11 @@ class MonitorWidgets:
         if isinstance( in_result, Accumulation ) or isinstance( in_result, ADC_Result ):
 
             xmin = in_result.get_xmin( )
+            xminpos = in_result.get_xminpos( )
             xmax = in_result.get_xmax( )
+
             ymin = in_result.get_ymin( )
+            yminpos = in_result.get_yminpos()
             ymax = in_result.get_ymax( )
 
             # # Check for log-scale
@@ -2955,20 +2963,21 @@ class MonitorWidgets:
                     self.matplot_axes.set_xscale( "linear" )
                     self.matplot_axes.set_xlim(xmin, xmax)
                 elif x_scale == "log10":
-                    self.matplot_axes.set_xscale("log", basex=10, nonposx="mask")
-                    self.matplot_axes.set_xlim(xmin, xmax)
+                    self.matplot_axes.set_xscale("log", base=10, nonpositive="mask")
+                    self.matplot_axes.set_xlim(xminpos, xmax)
                 elif x_scale == "ppm":
                     self.matplot_axes.set_xscale("linear")
                     self.matplot_axes.set_xlabel("PPM")
                     #self.display_autoscaling_checkbutton.set_active(True) #partial fix T141
                     self.matplot_axes.set_xlim(xmax, xmin)
                     #self.matplot_axes.invert_xaxis()
+
                 if  y_scale == "lin":
                     self.matplot_axes.set_yscale( "linear" )
+                    self.matplot_axes.set_ylim(ymin, ymax)
                 elif y_scale == "log10":
-                    self.matplot_axes.set_yscale("log", basex=10, nonposy="mask")
-                #self.matplot_axes.set_xlim( xmin, xmax )
-                self.matplot_axes.set_ylim( ymin, ymax )
+                    self.matplot_axes.set_yscale("log", base=10, nonpositive="mask")
+                    self.matplot_axes.set_ylim( yminpos, ymax )
                 self.__rescale = False
 
             # Autoscaling activated?