Slicer3:Python - Revision history

Lasso: Revert changes (just realized the page is for Slicer3)

2019-09-07T05:06:14Z

Revert changes (just realized the page is for Slicer3)

2019-09-07T05:01:12Z

Interactive plot using wxWidgets GUI toolkit

2019-09-07T04:58:35Z

Non-interactive plot in Jupyter notebook

2019-09-07T04:58:09Z

Matplotlib plotting functionality

2019-09-07T04:53:42Z

Matplotlib plotting functionality

2012-05-11T16:31:09Z

2012-04-06T18:27:56Z

A few details on Python in Slicer

2011-04-13T00:54:56Z

Writing Slicer Modules in Python

2011-02-26T01:01:08Z

Writing Slicer Modules in Python

2011-02-18T16:21:09Z

Accessing Tensor Data

@@ Line 234: / Line 234: @@
 == Matplotlib plotting functionality ==
-Matplotlib may be used from within Slicer, but the default Tk backend locks up and crashes Slicer.  However, Matplotlib may still be used through other backends.  More details can be found on the [http://matplotlib.sourceforge.net/ MatPlotLib] pages.
+Matplotlib may be used from within Slicer, but currently (on the Mac) the Tk backend locks up and crashes Slicer.  However, Matplotlib may still be used through one of the non-GUI backends.  More details can be found on the [http://matplotlib.sourceforge.net/ MatPlotLib] pages.
-=== Non-interactive plot ===
+ import matplotlib
 [[Image:MatplotlibExample.png]]
 == Where to go from here ==

@@ Line 313: / Line 313: @@
 try:
    import matplotlib
-   import wxPython
+   import wx
 except ModuleNotFoundError:
    pip_install('matplotlib wxPython')
    import matplotlib
 # Get a volume from SampleData and compute its histogram

@@ Line 275: / Line 275: @@
 [[Image:MatplotlibExample.png]]
-=== Non-interactive plot in Jupyter notebook ===
+=== Plot in Jupyter notebook ===
 <pre>

@@ Line 238: / Line 238: @@
 === Non-interactive plot ===
 try:
    import matplotlib
@@ Line 270: / Line 271: @@
 imageWidget.setScaledContents(True)
 imageWidget.show()
 [[Image:MatplotlibExample.png]]
@@ Line 275: / Line 277: @@
 === Non-interactive plot in Jupyter notebook ===
 try:
    import matplotlib
@@ Line 301: / Line 304: @@
 savefig('MatplotlibExample.png')
 display(filename='MatplotlibExample.png', type="image/png", binary=True)
 [[Image:JupyterNotebookMatplotlibExample.png]]
@@ Line 306: / Line 310: @@
 === Interactive plot using wxWidgets GUI toolkit ===
 try:
    import matplotlib
@@ Line 324: / Line 329: @@
 matplotlib.use('WXAgg')
-# Show a plot using matplotlib
+# Show an interactive plot
 import matplotlib.pyplot as plt
 fig, ax = plt.subplots()
@@ Line 331: / Line 336: @@
 ax.set_ylim((0, 4e5))
 plt.show(block=False)
 == Where to go from here ==

@@ Line 234: / Line 234: @@
 == Matplotlib plotting functionality ==
-Matplotlib may be used from within Slicer, but currently (on the Mac) the Tk backend locks up and crashes Slicer.  However, Matplotlib may still be used through one of the non-GUI backends.  More details can be found on the [http://matplotlib.sourceforge.net/ MatPlotLib] pages.
+Matplotlib may be used from within Slicer, but the default Tk backend locks up and crashes Slicer.  However, Matplotlib may still be used through other backends.  More details can be found on the [http://matplotlib.sourceforge.net/ MatPlotLib] pages.
- import matplotlib
+=== Non-interactive plot ===
 [[Image:MatplotlibExample.png]]
 == Where to go from here ==

← Older revision		Revision as of 16:31, 11 May 2012
Line 1:		Line 1:
		+
		+	'''Note: this page describes the python interface in 3D Slicer version 3.x which is no longer the current release. For newer information, see the [[Slicer4:Python\| page describing the python interface to 3D Slicer 4.x]].'''
		+
	== Status of Python in Slicer ==		== Status of Python in Slicer ==
	As of Slicer 3.4, '''python''' and '''numpy''' are enabled by default.		As of Slicer 3.4, '''python''' and '''numpy''' are enabled by default.

@@ Line 92: / Line 92: @@
   numberOfPoints = surface.GetNumberOfPoints()
-the Python interpreter relies the call to the Tcl interpreter and returns the proper return value. Any object available to Tcl is the same object available to Python, and this allows for a great flexibility, as everything lives in a common space.
+the Python interpreter relays the call to the Tcl interpreter and returns the proper return value. Any object available to Tcl is the same object available to Python, and this allows for great flexibility, as everything lives in a common space.
-Writing modules (especially interactive modules) in Python can lead to quite a speed up in the development cycle, since the code is more concise, it requires less file shuffling and, more than anything, it doesn't need to be recompiled (in some cases you don't even need to exit Slicer).
+Writing modules (especially interactive modules) in Python can lead to quite a speed up in the development cycle, since the code is more concise, requires less file shuffling and more than anything, it doesn't need to be recompiled (in some cases you don't even need to exit Slicer).
 ==== NumPy tutorial ====

@@ Line 288: / Line 288: @@
 For full GUI module example: see Endoscopy module in Modules/Endoscopy (EndoscopyGUI.py)
-* See [[Slicer3:Python:ProcessMRMLEvents]] on how to observe MRML events in Python Scripted Modules
+* See [[Slicer3:Python:ScriptedModulesTipsNTricks]] for some Tips'n'Tricks in connection with writing Python Scripted Modules
 Painless Development in Slicer3 with Python, talk given by Demian Wassermann at the LMI, sept. 2008

← Older revision		Revision as of 01:01, 26 February 2011
Line 288:		Line 288:

	For full GUI module example: see Endoscopy module in Modules/Endoscopy (EndoscopyGUI.py)		For full GUI module example: see Endoscopy module in Modules/Endoscopy (EndoscopyGUI.py)
		+	* See [[Slicer3:Python:ProcessMRMLEvents]] on how to observe MRML events in Python Scripted Modules

	Painless Development in Slicer3 with Python, talk given by Demian Wassermann at the LMI, sept. 2008		Painless Development in Slicer3 with Python, talk given by Demian Wassermann at the LMI, sept. 2008

@@ Line 152: / Line 152: @@
 The default shape of this will be Nx9 where N is the total number of voxels in the volume.  You can convert these to tensors with something like:
-  d = Slicer.slicer.MRML['dti'].GetImageData().GetDimensions()
+  d = vNodes['dti'].GetImageData().GetDimensions()
   d.reverse()
   tensors = i.reshape(d+[3,3])