Merge pull request #31 from gpilab/develop

Minor updates and Matplotlib 3 compatibility

Author: borupdaniel

EXTRA_PKGS.md

@@ -0,0 +1,4 @@
+## This file is a collection of extra packages that are either being used in the development of new core nodes, or are of potential general interest to MRI researchers.
+
+- [pyqtgraph]: a graphics library with some advantages over `matplotlib`. Currently being used in development of an image analysis node.
+- [BioSPPy](https://github.com/PIA-Group/BioSPPy): A toolbox for biosignal processing written in Python. Useful for processing physiology data. Only available from `pip`, not `conda`, making it difficult to use within GPI itself.

display/GPI/CrossSection_GPI.py

@@ -41,9 +41,8 @@
 
 import numpy as np
 from matplotlib.figure import Figure
-from matplotlib.backends.backend_qt4agg import (
-    FigureCanvasQTAgg as FigureCanvas,
-    NavigationToolbar2QT as NavigationToolbar)
+from matplotlib.backends.backend_qt5agg import (
+    FigureCanvas, NavigationToolbar2QT as NavigationToolbar)
 
 from scipy import ndimage
 
@@ -54,7 +53,6 @@ class MatplotDisplay2(gpi.GenericWidgetGroup):
     def __init__(self, title, parent=None):
         super().__init__(title, parent)
 
-        #self.data = self.get_data2()
         self._data = None
         self.create_main_frame()
         self.on_draw()
@@ -91,9 +89,6 @@ def create_main_frame(self):
         vbox.addWidget(self.mpl_toolbar)
         self.setLayout(vbox)
 
-    def get_data2(self):
-        return np.arange(20).reshape([4, 5]).copy()
-
     def on_draw(self):
         self.fig.clear()
         self.axes = self.fig.add_subplot(111)
@@ -104,8 +99,6 @@ def on_draw(self):
         if self._data is None:
             return
 
-        self.fig.hold(True)
-
         # plot each set
         # print "--------------------plot the data"
         for data in self._data:

display/GPI/Matplotlib_GPI.py

@@ -38,19 +38,17 @@
 import os
 import matplotlib
 
-import matplotlib as mpl
-print('matplotlib version: ', mpl.__version__)
+print('matplotlib version: ', matplotlib.__version__)
 
 import gpi
 from gpi import QtCore, QtGui, QtWidgets
 
 import numpy as np
 from matplotlib.figure import Figure
 #from matplotlib.backend_bases import key_press_handler
-from matplotlib.backends.backend_qt4agg import (
-    FigureCanvasQTAgg as FigureCanvas,
-    NavigationToolbar2QT as NavigationToolbar)
-from matplotlib.backends.backend_qt4 import SubplotToolQt
+from matplotlib.backends.backend_qt5agg import (
+    FigureCanvas, NavigationToolbar2QT as NavigationToolbar)
+from matplotlib.backends.backend_qt5 import SubplotToolQt
 
 class MainWin_close(QtWidgets.QMainWindow):
     window_closed = gpi.Signal()
@@ -104,8 +102,6 @@ def _init_toolbar(self):
                 if tooltip_text is not None:
                     a.setToolTip(tooltip_text)
 
-        self.buttons = {}
-
         # Add the x,y location widget at the right side of the toolbar
         # The stretch factor is 1 which means any resizing of the toolbar
         # will resize this label instead of the buttons.
@@ -119,9 +115,6 @@ def _init_toolbar(self):
             labelAction = self.addWidget(self.locLabel)
             labelAction.setVisible(True)
 
-        # reference holder for subplots_adjust window
-        self.adj_window = None
-
 ###############################################################################
 # -*- coding: utf-8 -*-
 #
@@ -135,19 +128,14 @@ def _init_toolbar(self):
 import os.path as osp
 
 try:
-    import matplotlib.backends.qt4_editor.formlayout as formlayout
+    import matplotlib.backends.qt_editor.formlayout as formlayout
 except:
-    try:
-        import matplotlib.backends.qt_editor.formlayout as formlayout
-    except:
-        formlayout = None
-        print("formlayout can't be found, line options will be disabled")
+    formlayout = None
+    print("formlayout can't be found, line options will be disabled")
 
-#from matplotlib.backends.qt4_compat import QtGui
 from matplotlib import markers
 
 def get_icon(name):
-    import matplotlib
     basedir = osp.join(matplotlib.rcParams['datapath'], 'images')
     return QtGui.QIcon(osp.join(basedir, name))
 
@@ -268,7 +256,6 @@ def apply_callback(data):
         figure = axes.get_figure()
         figure.canvas.draw()
 
-    # formlayout disappears in matplotlib 1.4.0
     if formlayout is not None:
         data = formlayout.fedit(datalist, title="Figure options", parent=parent, icon=get_icon('qt4_editor_options.svg'), apply=apply_callback)
 
@@ -996,8 +983,10 @@ def on_key_press(self, event):
 
 class ExternalNode(gpi.NodeAPI):
 
-    """A Qt embedded plot window using the code from:
+    """A Qt embedded plot window originally using the code from:
     http://matplotlib.org/examples/user_interfaces/embedding_in_qt4_wtoolbar.html
+    Updated by DDB in Feb. 2020 using the qt5 code from:
+    https://matplotlib.org/examples/user_interfaces/embedding_in_qt5.html
     keyboard shortcuts can be found here:
     http://matplotlib.org/users/navigation_toolbar.html#navigation-keyboard-shortcuts