Established compatibility with the last pythonxy (matplotlib 1.4.3)

plus minor bug fixes and improved performance of marker drawing

Author: Malte

ebttools/core.py

@@ -43,13 +43,23 @@
 
 import codecs
 from collections import OrderedDict
-from configparser import ConfigParser
+
 import logging
 import numpy as np
 import os
 import scipy.ndimage
 from math import floor, ceil
 
+try:
+    from configparser import ConfigParser
+except ImportError as e:
+    #a compatibility hack for python2 if it does not have conifgparser
+    import sys
+    if sys.version_info[0] == 2:
+        from ConfigParser import ConfigParser
+    else:
+        raise e
+
 #define which array index corresponds to which color
 rgbMap = {"red":0,"green":1,"blue":2}
 
@@ -276,9 +286,9 @@ def rectangle_mask(self,x0, y0, width, height, angle=0.0):
         y0 : scalar
             y-value of rectangle center (in cm)
         width : scalar
-            width (x-dimension) of the rectangle
+            half-width (x-dimension) of the rectangle
         height : scalar
-            height (y-dimension) of the rectangle
+            half-height (y-dimension) of the rectangle
         angle : scalar, optional
             counter clockwise rotation angle of the rectangle
         test : bool, optional
@@ -287,7 +297,7 @@ def rectangle_mask(self,x0, y0, width, height, angle=0.0):
         Returns
         -------
         mask : ndarray
-            a mask to index the array an return a rectangular area
+            a mask to index the array and return a rectangular area
         """
 
         angle_rad = angle*np.pi/180.
@@ -298,7 +308,8 @@ def rectangle_mask(self,x0, y0, width, height, angle=0.0):
         #must be shifted by 0.5 pixels width.
         y, x = np.mgrid[-y0+0.5/self.DPC:(self.shape[0]+.5)/self.DPC-y0:1.0/self.DPC,
                         -x0+0.5/self.DPC:(self.shape[1]+.5)/self.DPC-x0:1.0/self.DPC]
-                
+        
+       
         #condition for a rectangle
         mask = np.logical_and(np.abs(x*np.cos(angle_rad)-y*np.sin(angle_rad)) <= width,
                               np.abs(x*np.sin(angle_rad)+y*np.cos(angle_rad)) <= height)
@@ -318,9 +329,9 @@ def rectangle_stats(self,x0, y0, width, height, angle=0.0, test=False):
         y0 : scalar
             y-value of rectangle center (in cm)
         width : scalar
-            width (x-dimension) of the rectangle
+            half-width (x-dimension) of the rectangle
         height : scalar
-            height (y-dimension) of the rectangle
+            half-height (y-dimension) of the rectangle
         angle : scalar, optional
             counter clockwise rotation angle of the rectangle
         test : bool, optional
@@ -459,7 +470,7 @@ def profile(self, x0, y0, x1, y1, interpolation="nearest",test=False):
 # for testing
 if __name__ == '__main__':
     #load some calibrations
-    calibs = load_calibrations(os.path.join(os.path.curdir,"Calibration"))
+    calibs = load_calibrations(os.path.join(os.path.abspath(os.path.curdir),"calibrations"))
     #create a simple scan (~4x4 cm)
     scan = np.zeros((470,470,3),dtype="uint8")
 
@@ -471,6 +482,8 @@ def profile(self, x0, y0, x1, y1, interpolation="nearest",test=False):
 
     doseDistribution = DoseArray(300.,calibs["example"],scan,255)
 
+    doseDistribution.rectangle_stats(1.0,1.0,0.5,0.5,0.,True)
+    
     mask = doseDistribution.rectangle_mask(0.4,0.5,0.2,0.1,0.0)
     print (doseDistribution[mask].shape)
 

ebttools/gui/dosewidget.py

@@ -82,14 +82,12 @@ def __call__(self, x, pos=None):
 def gauss(x, A, x0, sigma, offset):
     return A*np.exp(-np.square(x-x0)/(2*sigma**2))+offset
 
-#define possibilities for color maps and check their availability on 
-#the current installation
+#define possibilities for color maps and filter for their availability
+#on the current installation
 colorMapChoices = ["inferno","viridis","hot","gnuplot","spectral","jet",
                    "rainbow","gray","seismic"]
 
-for cmap in colorMapChoices:
-    if cmap not in colormaps():
-        colorMapChoices.remove(cmap)
+colorMapChoices = [cmap for cmap in colorMapChoices if cmap in colormaps()]
 
 _advSettings = EasyEditSettings([("area stat linecolor","red"),
                                  ("area stat linewidth",2.0),
@@ -732,7 +730,6 @@ def click_to_pos1(self, event):
     #catch if the focus leaves or enters a certain widget and connect matplotlib
     #button press callbacks accordingly
     def focus_change(self, old, new):
-        
         if (old == self.ui.xCenter or old == self.ui.yCenter or 
             old == self.ui.x0 or old == self.ui.y0 or 
             old == self.ui.x1 or old == self.ui.y1):

ebttools/gui/main.py

@@ -186,7 +186,7 @@ def create_mplframe(self):
     def load_settings(self):
         """load the setting of the GUI (called on startup)
         """
-        #create a QSettings object from ini file
+        #create a QSettings object to store the settings
         self.QtSettings=QtCore.QSettings("OncoRay","EBT Evaluation")
         #self.QtSettings=QtCore.QSettings("settings.ini",QtCore.QSettings.IniFormat)
 
@@ -397,7 +397,6 @@ def image_path_changed(self):
         except (IOError, OSError) as e:
             logging.error("failed to open file: "+str(e))
             return ()
- 
 
         #check the format of the loaded image and adjust the input field accordingly
         logging.debug("image mode: "+img.mode)
@@ -448,9 +447,52 @@ def image_path_changed(self):
 
 
 
+
+        
+        #check for dpi info
+        try:
+            dpi = img.info['dpi']
+            
+            #try string conversion and tuple first and then deal with type of number
+            if type(dpi) == str:
+                try:
+                    dpi = float(dpi)
+                except ValueError:
+                    logging.warning("Can not parse dpi info: "+dpi)
+                    dpi = 0
+            elif type(dpi) == tuple:
+                if len(dpi) == 1:
+                    dpi = dpi[0]
+                elif len(dpi) == 2:
+                    if dpi[0] == dpi[1]:
+                        dpi = dpi[0]
+                    else:
+                        logging.warning("different DPI for the two dimensions found " +
+                                        repr(dpi)+ " THIS IS NOT SUPPORTED")
+                        dpi = 0
+                else:
+                    logging.warning("dpi has more than 2 dimensions" +
+                                    repr(dpi)+ " DONT KNOW WHAT TO DO")
+                    dpi=0
+            
+            try:
+                dpi = float(dpi)
+                if not dpi.is_integer():
+                    logging.warning("non integer DPI of {:.4f} is not supported".format(dpi))
+            except TypeError: #unkown type of dpi
+                logging.warning("Can not parse dpi info: "+repr(dpi))
+                dpi = 0
+        except KeyError:
+            logging.debug("no dpi info")
+            dpi=0
+
         logging.debug("loaded image of dimensions: "+str(self.npImg.shape)+
-                      " and type: "+str(self.npImg.dtype))
-                      
+                      " and type: "+str(self.npImg.dtype)+
+                      ", with DPI: "+str(dpi))
+            
+        if dpi > 0:
+            self.ui.DPI.setValue(int(dpi))
+              
         #adjust UI elements to image properties
         self.ui.x0.setMaximum(self.npImg.shape[1])
         self.ui.x0.setValue(0)
@@ -522,20 +564,26 @@ def save_table_path_changed(self):
         self.saveTablePath = self.check_save_table_path(self.ui.saveTablePath.text())
 
     def selection_changed(self):
-        #try to remove old marker
+        #the point here is to redraw the marker as efficiently as possible, i.e.
+        #change as little of the existing plot as possible
+        
+        #try to update the old marker
         try:
-            self.selectionMarker.remove()
+            self.selectionMarker.set_bounds(self.ui.x0.value(),self.ui.y0.value(),
+                                            self.ui.x1.value()-self.ui.x0.value(),
+                                            self.ui.y1.value()-self.ui.y0.value())
+            self.subplot.draw_artist(self.selectionMarker)
         except AttributeError:
-            pass
-
-        #create a rectangle marker and draw it
-        rect = Rectangle((self.ui.x0.value(),self.ui.y0.value()),
-                         self.ui.x1.value()-self.ui.x0.value(),
-                         self.ui.y1.value()-self.ui.y0.value(),
-                         fill=False,color=self.settings["selection rectangle"],
-                         linewidth=2.0)
-        self.selectionMarker = self.subplot.add_artist(rect)
-        self.canvas.draw()        
+        #marker does not exist, create a new rectangle marker and draw it
+            rect = Rectangle((self.ui.x0.value(),self.ui.y0.value()),
+                             self.ui.x1.value()-self.ui.x0.value(),
+                             self.ui.y1.value()-self.ui.y0.value(),
+                             fill=False,color=self.settings["selection rectangle"],
+                             linewidth=2.0)
+            self.selectionMarker = self.subplot.add_artist(rect)
+
+        self.canvas.draw()
+        self.canvas.flush_events()        
 
     def show_dose(self):
         logging.debug("calculating dose")

ebttools/gui/navtoolbar.py

@@ -27,7 +27,16 @@
 
 
 from matplotlib import rcParams as mplParams
-from matplotlib.backend_tools import Cursors
+from matplotlib import __version__ as mplVersion
+
+mplAbove1_5 = not ((int(mplVersion.split(".")[0]) < 2) and 
+                   (int(mplVersion.split(".")[1]) < 5))
+
+#in older matplotlib (<2 I believe) Cursors is in backend_bases, not it is in backend tools
+try:
+    from matplotlib.backend_tools import Cursors
+except:
+    from matplotlib.backend_bases import Cursors
 cursors = Cursors()
 
 class MyNavigationToolbar(NavigationToolbar2QT):
@@ -210,10 +219,14 @@ def selection_released(self, event):
         for selection_id in self._ids_selection:
             self.canvas.mpl_disconnect(selection_id)                                                              
         self.release(event)
-        self.draw()
+        if mplAbove1_5:
+            self.remove_rubberband()
+
         self._selectionStart = None
         self._button_pressed = None
         self._ids_selection = []
 
+        
+        
         #fire event
         self.canvas.callbacks.process("selection_changed")

run.py

@@ -1,15 +1,13 @@
 #! /bin/python
 # -*- coding: utf-8 -*-
 """
-Created on Sat Aug 12 21:02:24 2017
-
-@author: Malte
+Use this script to execute the EBT evaluation GUI
 """
 
 import os
 import sys
 
-sys.path.append(os.path.dirname(__file__))
+sys.path.insert(0,(os.path.dirname(__file__)))
 
 from ebttools.gui.main import run
 

setup.py

@@ -4,15 +4,23 @@
 setup script for ebttools
 """
 import os
-from setuptools import setup, find_packages
+from setuptools import setup, find_packages, __version__
+
+#check to have setuptools > v36.2
+version = __version__.split(".")
+if len(version) < 2:
+    raise ImportError("unkown version of setuptools, please update")
+if int(version[0]) < 36 or (int(version[0]) == 36 and int(version[1]) < 2):
+    raise ImportError("setuptools version "+ __version__ +" too low, needs at least 36.2")
+
 
 def read(fname):
     return open(os.path.join(os.path.dirname(__file__), fname)).read()
 
 
 setup(
     name='ebttools',
-    version='1.0.0',
+    version='1.1.0',
 
     packages=find_packages(exclude=("tests")), #automagically include all subfolders as packages, but don't install the tests
     package_data = {"":["*.png"],
@@ -25,10 +33,10 @@ def read(fname):
     author_email='[email protected]',
     url='https://github.com/mgotz/EBT_evalution',
 
-    install_requires=['matplotlib',
-                      'scipy',
-                      'numpy',
-                      'pillow',
+    install_requires=['matplotlib>=1.4.3',
+                      'scipy>=0.15.1',
+                      'numpy>=1.9.2',
+                      'pillow>=2.8.2',
                       'configparser;python_version<"3.2"',
                       'mg_dataprocessing>=1.0.0',
                       'mg_pyguitools>=1.1.1'],

tests/dosewidget_test.py

@@ -13,6 +13,8 @@
 import os
 import sys
 
+os.environ["QT_API"] = "pyqt5"
+
 #add base to path and load
 sys.path.append(os.path.join(sys.path[0],".."))
 from ebttools.gui.dosewidget import DoseWidget
@@ -45,8 +47,8 @@ def __init__(self):
         self.ui =  Ui_MainWindow()
         self.ui.setupUi(self) 
 
-        xDim = 4000 
-        yDim = 4000
+        xDim = 470 
+        yDim = 470
 
         #create a noise gaussian for test data
         x,y = np.meshgrid(np.linspace(0,xDim,yDim),np.linspace(0,xDim,yDim))